<?xml version="1.0" encoding="UTF-8"?><xml><records><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Bernardi, G</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome organization and species formation in vertebrates.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of molecular evolution</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Mol. Evol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">1993</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1993 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">37</style></volume><pages><style face="normal" font="default" size="100%">331-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Some years ago Wilson and co-workers proposed that the higher rates of karyotypic change and species formation of mammals compared to cold-blooded vertebrates are due to the formation of small demes, as favored by the social structuring and brain development of the former. Here, evidence is reviewed which indicates that mammals are more prone to karyotypic change and species formation than cold-blooded vertebrates because of their different genome organization. Similar evidence has also recently become available for birds. While this different organization appears to be a necessary and, in all likelihood, a sufficient condition for the increased rates of karyotypic change and species formation found in mammals, it is still possible that social structuring and brain development may have played an additional accelerating role.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/8308903?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Peterson, D G</style></author><author><style face="normal" font="default" size="100%">Stack, S M</style></author><author><style face="normal" font="default" size="100%">Healy, J L</style></author><author><style face="normal" font="default" size="100%">Donohoe, B S</style></author><author><style face="normal" font="default" size="100%">Anderson, L K</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The relationship between synaptonemal complex length and genome size in four vertebrate classes (Osteicthyes, Reptilia, Aves, Mammalia).</style></title><secondary-title><style face="normal" font="default" size="100%">Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Chromosome Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">1994</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1994 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2</style></volume><pages><style face="normal" font="default" size="100%">153-62</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We investigated the relationship between synaptonemal complex (SC) length and genome size in 18 species of vertebrates from the classes Osteicthyes (bony fish), Reptilia (reptiles), Aves (birds), and Mammalia (mammals). When total SC length was plotted against genome size for all 18 vertebrate species, there did not appear to be a correlation between the two variables. However, when birds were excluded from the data and a linear regression analysis was performed, variation in genome size accounted for approximately 50% of the variation in total SC length (r2 = 0.47). Dividing the average total SC length for a species by its 4C DNA amount yields the species' SC/DNA ratio. SC/DNA ratios of birds were approximately twice as high as the SC/DNA ratios of reptiles and mammals. Bony fish showed intraclass divergence in SC/DNA ratios. The sunfish (Centrarchidae) had SC/DNA ratios almost as high as those of birds, while the remaining fish in the study had SC/DNA ratios similar to those of reptiles and mammals. These observations indicate that inter and intraclass divergence in the relationship between total SC length and genome size has occurred in the vertebrates. Coupled with evidence from the literature, our results also suggest that SC/DNA ratios are positively correlated with crossover frequency.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/8032674?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Richardson, M K</style></author><author><style face="normal" font="default" size="100%">Hanken, J</style></author><author><style face="normal" font="default" size="100%">Gooneratne, M L</style></author><author><style face="normal" font="default" size="100%">Pieau, C</style></author><author><style face="normal" font="default" size="100%">Raynaud, A</style></author><author><style face="normal" font="default" size="100%">Selwood, L</style></author><author><style face="normal" font="default" size="100%">Wright, G M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development.</style></title><secondary-title><style face="normal" font="default" size="100%">Anatomy and embryology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Anat. Embryol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">1997</style></year><pub-dates><date><style  face="normal" font="default" size="100%">1997 Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">196</style></volume><pages><style face="normal" font="default" size="100%">91-106</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Embryos of different species of vertebrate share a common organisation and often look similar. Adult differences among species become more apparent through divergence at later stages. Some authors have suggested that members of most or all vertebrate clades pass through a virtually identical, conserved stage. This idea was promoted by Haeckel, and has recently been revived in the context of claims regarding the universality of developmental mechanisms. Thus embryonic resemblance at the tailbud stage has been linked with a conserved pattern of developmental gene expression - the zootype. Haeckel's drawings of the external morphology of various vertebrates remain the most comprehensive comparative data purporting to show a conserved stage. However, their accuracy has been questioned and only a narrow range of species was illustrated. In view of the current widespread interest in evolutionary developmental biology, and especially in the conservation of developmental mechanisms, re-examination of the extent of variation in vertebrate embryos is long overdue. We present here the first review of the external morphology of tailbud embryos, illustrated with original specimens from a wide range of vertebrate groups. We find that embryos at the tailbud stage - thought to correspond to a conserved stage - show variations in form due to allometry, heterochrony, and differences in body plan and somite number. These variations foreshadow important differences in adult body form. Contrary to recent claims that all vertebrate embryos pass through a stage when they are the same size, we find a greater than 10-fold variation in greatest length at the tailbud stage. Our survey seriously undermines the credibility of Haeckel's drawings, which depict not a conserved stage for vertebrates, but a stylised amniote embryo. In fact, the taxonomic level of greatest resemblance among vertebrate embryos is below the subphylum. The wide variation in morphology among vertebrate embryos is difficult to reconcile with the idea of a phyogenetically-conserved tailbud stage, and suggests that at least some developmental mechanisms are not highly constrained by the zootype. Our study also highlights the dangers of drawing general conclusions about vertebrate development from studies of gene expression in a small number of laboratory species.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/9278154?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Pollock, D D</style></author><author><style face="normal" font="default" size="100%">Eisen, J A</style></author><author><style face="normal" font="default" size="100%">Doggett, N A</style></author><author><style face="normal" font="default" size="100%">Cummings, M P</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A case for evolutionary genomics and the comprehensive examination of sequence biodiversity.</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular biology and evolution</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Mol. Biol. Evol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2000</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2000 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">1776-88</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Comparative analysis is one of the most powerful methods available for understanding the diverse and complex systems found in biology, but it is often limited by a lack of comprehensive taxonomic sampling. Despite the recent development of powerful genome technologies capable of producing sequence data in large quantities (witness the recently completed first draft of the human genome), there has been relatively little change in how evolutionary studies are conducted. The application of genomic methods to evolutionary biology is a challenge, in part because gene segments from different organisms are manipulated separately, requiring individual purification, cloning, and sequencing. We suggest that a feasible approach to collecting genome-scale data sets for evolutionary biology (i.e., evolutionary genomics) may consist of combination of DNA samples prior to cloning and sequencing, followed by computational reconstruction of the original sequences. This approach will allow the full benefit of automated protocols developed by genome projects to be realized; taxon sampling levels can easily increase to thousands for targeted genomes and genomic regions. Sequence diversity at this level will dramatically improve the quality and accuracy of phylogenetic inference, as well as the accuracy and resolution of comparative evolutionary studies. In particular, it will be possible to make accurate estimates of normal evolution in the context of constant structural and functional constraints (i.e., site-specific substitution probabilities), along with accurate estimates of changes in evolutionary patterns, including pairwise coevolution between sites, adaptive bursts, and changes in selective constraints. These estimates can then be used to understand and predict the effects of protein structure and function on sequence evolution and to predict unknown details of protein structure, function, and functional divergence. In order to demonstrate the practicality of these ideas and the potential benefit for functional genomic analysis, we describe a pilot project we are conducting to simultaneously sequence large numbers of vertebrate mitochondrial genomes.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11110893?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Thomas, James W</style></author><author><style face="normal" font="default" size="100%">Touchman, Jeffrey W</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Vertebrate genome sequencing: building a backbone for comparative genomics.</style></title><secondary-title><style face="normal" font="default" size="100%">Trends in genetics : TIG</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Trends Genet.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">18</style></volume><pages><style face="normal" font="default" size="100%">104-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The human genome sequence provides a reference point from which we can compare ourselves with other organisms. Interspecies comparison is a powerful tool for inferring function from genomic sequence and could ultimately lead to the discovery of what makes humans unique. To date, most comparative sequencing has focused on pair-wise comparisons between human and a limited number of other vertebrates, such as mouse. Targeted approaches now exist for mapping and sequencing vertebrate bacterial artificial chromosomes (BACs) from numerous species, allowing rapid and detailed molecular and phylogenetic investigation of multi-megabase loci. Such targeted sequencing is complementary to current whole-genome sequencing projects, and would benefit greatly from the creation of BAC libraries from a diverse range of vertebrates.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/11818143?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Burns, Kevin J</style></author><author><style face="normal" font="default" size="100%">Hackett, Shannon J</style></author><author><style face="normal" font="default" size="100%">Klein, Nedra K</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenetic relationships and morphological diversity in Darwin's finches and their relatives.</style></title><secondary-title><style face="normal" font="default" size="100%">Evolution; international journal of organic evolution</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Evolution</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">56</style></volume><pages><style face="normal" font="default" size="100%">1240-52</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Despite the importance of Darwin's finches to the development of evolutionary theory, the origin of the group has only recently been examined using a rigorous, phylogenetic methodology that includes many potential outgroups. Knowing the evolutionary relationships of Darwin's finches to other birds is important for understanding the context from which this adaptive radiation arose. Here we show that analysis of mitochondrial DNA sequence data from the cytochrome b gene confirm that Darwin's finches are monophyletic. In addition, many taxa previously proposed as the sister taxon to Darwin's finches can be excluded as their closest living relative. Darwin's finches are part of a well-supported monophyletic group of species, all of which build a domed nest. All but two of the non-Darwin's finches included in this clade occur on Caribbean islands and most are Caribbean endemics. These close relatives of Darwin's finches show a diversity of bill types and feeding behaviors similar to that observed among Darwin's finches themselves. Recent studies have shown that adaptive evolution in Darwin's finches occurred relatively quickly. Our data show that among the relatives of Darwin's finches, the evolution of bill diversity was also rapid and extensive.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12144023?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Gregory, T Ryan</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome size and developmental parameters in the homeothermic vertebrates.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome / National Research Council Canada = Génome / Conseil national de recherches Canada</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2002</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2002 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">45</style></volume><pages><style face="normal" font="default" size="100%">833-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Although unrelated to any intuitive notions of organismal complexity, haploid genome sizes (C values) are correlated with a variety of cellular and organismal parameters in different taxa. In some cases, these relationships are universal--notably, genome size correlates positively with cell size in each of the vertebrate classes. Other relationships are apparently relevant only in particular groups. For example, although genome size is inversely correlated with metabolic rate in both mammals and birds, no such relationship is found in amphibians. More recently, it has been suggested that developmental rate and (or) longevity are related to genome size in birds. In the present study, a large dataset was used to examine possible relationships between genome size and various developmental parameters in both birds and mammals. In neither group does development appear to be of relevance to genome size evolution (except perhaps indirectly in birds through the intermediation of body size and (or) within the rodents), a situation very different from that found in amphibians. These findings make it clear that genome size evolution cannot be understood without reference to the particular biology of the organisms under study.</style></abstract><issue><style face="normal" font="default" size="100%">5</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/12416615?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Horton, Amy C</style></author><author><style face="normal" font="default" size="100%">Mahadevan, Navin R</style></author><author><style face="normal" font="default" size="100%">Ruvinsky, Ilya</style></author><author><style face="normal" font="default" size="100%">Gibson-Brown, Jeremy J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of experimental zoology. Part B, Molecular and developmental evolution</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Exp. Zool. B Mol. Dev. Evol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Oct 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">299</style></volume><pages><style face="normal" font="default" size="100%">41-53</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The widely accepted notion that two whole-genome duplications occurred during early vertebrate evolution (the 2R hypothesis) stems from the fact that vertebrates often possess several genes corresponding to a single invertebrate homolog. However the number of genes predicted by the Human Genome Project is less than twice as many as in the Drosophila melanogaster or Caenorhabditis elegans genomes. This ratio could be explained by two rounds of genome duplication followed by extensive gene loss, by a single genome duplication, by sequential local duplications, or by a combination of any of the above. The traditional method used to distinguish between these possibilities is to reconstruct the phylogenetic relationships of vertebrate genes to their invertebrate orthologs; ratios of invertebrate-to-vertebrate counterparts are then used to infer the number of gene duplication events. The lancelet, amphioxus, is the closest living invertebrate relative of the vertebrates, and unlike protostomes such as flies or nematodes, is therefore the most appropriate outgroup for understanding the genomic composition of the last common ancestor of all vertebrates. We analyzed the relationships of all available amphioxus genes to their vertebrate homologs. In most cases, one to three vertebrate genes are orthologous to each amphioxus gene (median number=2). Clearly this result, and those of previous studies using this approach, cannot distinguish between alternative scenarios of chordate genome expansion. We conclude that phylogenetic analyses alone will never be sufficient to determine whether genome duplication(s) occurred during early chordate evolution, and argue that a &quot;phylogenomic&quot; approach, which compares paralogous clusters of linked genes from complete amphioxus and human genome sequences, will be required if the pattern and process of early chordate genome evolution is ever to be reconstructed.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/14508816?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Makeeva, N V</style></author><author><style face="normal" font="default" size="100%">Pestova, A A</style></author><author><style face="normal" font="default" size="100%">Borodina, T A</style></author><author><style face="normal" font="default" size="100%">Madera, D A</style></author><author><style face="normal" font="default" size="100%">Ivanov, D V</style></author><author><style face="normal" font="default" size="100%">Stepanova, E V</style></author><author><style face="normal" font="default" size="100%">Baranova, A V</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">[Fundamental and applied aspects of comparative genomics of vertebrates]</style></title><secondary-title><style face="normal" font="default" size="100%">Genetika</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genetika</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2003</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2003 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">39</style></volume><pages><style face="normal" font="default" size="100%">1157-71</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Human Genome Project stimulated the development of efficient strategies and relevant hardware for complete genome sequencing. The comparative genomic approach extends the possibilities of using the sequencing data to identify new genes or conserved regulatory regions by means of nucleotide sequence alignment of the particular regions of the mouse and human genomes, or to trace the evolutionary events resulting in the genome structure of modern mammals. The review focuses on the use of new molecular cytogenetic methods along with computer-aided analysis of the genomes in vertebrates. Several factors hindering data analysis are considered. The currently available information on gene evolution rate inferred from comparative genomic data is presented. The origin and evolution of the genomes of several species are discussed.</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/14582384?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Vinogradov, Alexander E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome size and extinction risk in vertebrates.</style></title><secondary-title><style face="normal" font="default" size="100%">Proceedings. Biological sciences / The Royal Society</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Biol. Sci.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Aug 22</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">271</style></volume><pages><style face="normal" font="default" size="100%">1701-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The hypothesis of 'selfish DNA' is tested for the case of animals using the relation between genome size and conservation status of a given species. In contrast to plants, where the larger genome was previously shown to increase the likelihood of extinction, the picture is more complicated in animals. At the within-families and within-orders levels, the larger genome increases the risk of extinction only in reptiles and birds (which have the smallest genomes among tetrapods). In fishes and amphibians, the effect is caused by the higher taxonomic levels (above order). In several phylogenetic lineages of anamniotes, there is a correlation between a higher fraction of threatened species and a lower number of extant species in a lineage with the larger genome. In mammals, no effect was observed at any taxonomic level. The obtained data support the concept of hierarchical selection. It is also shown that, in plants and reptiles, the probability of being threatened increases from less than 10% to more than 80% with the increase in genome size, which can help in establishing conservation priorities.</style></abstract><issue><style face="normal" font="default" size="100%">1549</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15306290?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Franck, Erik</style></author><author><style face="normal" font="default" size="100%">Madsen, Ole</style></author><author><style face="normal" font="default" size="100%">van Rheede, Teun</style></author><author><style face="normal" font="default" size="100%">Ricard, Guénola</style></author><author><style face="normal" font="default" size="100%">Huynen, Martijn A</style></author><author><style face="normal" font="default" size="100%">de Jong, Wilfried W</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evolutionary diversity of vertebrate small heat shock proteins.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of molecular evolution</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Mol. Evol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">59</style></volume><pages><style face="normal" font="default" size="100%">792-805</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">All vertebrates express multiple small heat shock proteins (sHsps), which are important components of the cellular chaperoning machinery and display a spectacular diversity of functions. This ranges from remodeling the cytoskeleton and inhibiting apoptosis to serving as structural proteins in eye lens and sperm tail. Most information is available for the 10 known mammalian sHsps, formally named HspB1-B10. Only three of them (Hsp27/B1, alphaA-crystallin/B4, alphaB-crystallin/B5) have been reported from nonmammalian vertebrates, while an apparent paralog, Hsp30/B11, is found in frogs and teleost fish. To reconstruct the evolutionary diversification of the sHsps in vertebrates, we searched for additional sHsps in genome, protein, and EST databases and sequenced some avian and amphibian sHsps (HspB2, Hsp30/B11). The urochordate Ciona intestinalis was included in the search, as the outgroup of vertebrates. Orthologs of seven mammalian sHsps were now found in other vertebrate classes. Two novel sHsps, named HspB11 and HspB12, were recognized in birds, and four novel sHsps, named HspB12-B15, in teleost fish. Secondary structure predictions of orthologous sHsps from different vertebrate classes indicate conservation of the beta-sandwich structure of the functionally important C-terminal &quot;alpha-crystallin domain,&quot; while the N-terminal domains generally have alpha-helical structures, despite their pronounced sequence variation. The constructed chordate sHsp tree is supported by shared introns, indels, and diagnostic sequences. The tree distinguishes putative orthologous and paralogous relationships, which will facilitate the functional and structural comparison of the various vertebrate sHsps. The 15 recognized paralogous vertebrate sHsps reflect the period of extensive gene duplications early in vertebrate evolution. Eleven of these sHsps are grouped in a clade that might be specific for chordates. It is inferred that at least 13 intron insertions have occurred during the evolution of chordate sHsp genes, while a single ancient intron is maintained in some lineages, in line with the general trend of massive intron gain before or during early vertebrate radiation. Interesting is the occurrence of several head-to-head located pairs of chordate sHsp genes.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15599511?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><translated-authors><author><style face="normal" font="default" size="100%">International Chicken Genome Sequencing Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nature</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Dec 9</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">432</style></volume><pages><style face="normal" font="default" size="100%">695-716</style></pages><abstract><style face="normal" font="default" size="100%">We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.</style></abstract><issue><style face="normal" font="default" size="100%">7018</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15592404?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Reiner, Anton</style></author><author><style face="normal" font="default" size="100%">Perkel, David J</style></author><author><style face="normal" font="default" size="100%">Mello, Claudio V</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Songbirds and the revised avian brain nomenclature.</style></title><secondary-title><style face="normal" font="default" size="100%">Annals of the New York Academy of Sciences</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Ann. N. Y. Acad. Sci.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">1016</style></volume><pages><style face="normal" font="default" size="100%">77-108</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">It has become increasingly clear that the standard nomenclature for many telencephalic and related brainstem structures of the avian brain is based on flawed once-held assumptions of homology to mammalian brain structures, greatly hindering functional comparisons between avian and mammalian brains. This has become especially problematic for those researchers studying the neurobiology of birdsong, the largest single group within the avian neuroscience community. To deal with the many communication problems this has caused among researchers specializing in different vertebrate classes, the Avian Brain Nomenclature Forum, held at Duke University from July 18-20, 2002, set out to develop a new terminology for the avian telencephalon and some allied brainstem cell groups. In one major step, the erroneous conception that the avian telencephalon consists mainly of a hypertrophied basal ganglia has been purged from the telencephalic terminology, and the actual parts of the basal ganglia and its brainstem afferent cell groups have been given new names to reflect their now-evident homologies. The telencephalic regions that were incorrectly named to reflect presumed homology to mammalian basal ganglia have been renamed as parts of the pallium. The prefixes used for the new names for the pallial subdivisions have retained most established abbreviations, in an effort to maintain continuity with the pre-existing nomenclature. Here we present a brief synopsis of the inaccuracies in the old nomenclature, a summary of the nomenclature changes, and details of changes for specific songbird vocal and auditory nuclei. We believe this new terminology will promote more accurate understanding of the broader neurobiological implications of song control mechanisms and facilitate the productive exchange of information between researchers studying avian and mammalian systems.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15313771?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><translated-authors><author><style face="normal" font="default" size="100%">International Human Genome Sequencing Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">Finishing the euchromatic sequence of the human genome.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nature</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2004</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2004 Oct 21</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">431</style></volume><pages><style face="normal" font="default" size="100%">931-45</style></pages><abstract><style face="normal" font="default" size="100%">The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers approximately 99% of the euchromatic genome and is accurate to an error rate of approximately 1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human genome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead.</style></abstract><issue><style face="normal" font="default" size="100%">7011</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15496913?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Stone, Eric A</style></author><author><style face="normal" font="default" size="100%">Cooper, Gregory M</style></author><author><style face="normal" font="default" size="100%">Sidow, Arend</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Trade-offs in detecting evolutionarily constrained sequence by comparative genomics.</style></title><secondary-title><style face="normal" font="default" size="100%">Annual review of genomics and human genetics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Annu Rev Genomics Hum Genet</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">143-64</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">As whole-genome sequencing efforts extend beyond more traditional model organisms to include a deep diversity of species, comparative genomic analyses will be further empowered to reveal insights into the human genome and its evolution. The discovery and annotation of functional genomic elements is a necessary step toward a detailed understanding of our biology, and sequence comparisons have proven to be an integral tool for that task. This review is structured to broadly reflect the statistical challenges in discriminating these functional elements from the bulk of the genome that has evolved neutrally. Specifically, we review the comparative genomics literature in terms of specificity, sensitivity, and phylogenetic scope, as well as the trade-offs that relate these factors in standard analyses. We consider the impact of an expanding diversity of orthologous sequences on our ability to resolve functional elements. This impact is assessed through both recent comparative analyses of deep alignments and mathematical modeling.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16124857?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author><author><style face="normal" font="default" size="100%">Güntürkün, Onur</style></author><author><style face="normal" font="default" size="100%">Bruce, Laura</style></author><author><style face="normal" font="default" size="100%">Csillag, András</style></author><author><style face="normal" font="default" size="100%">Karten, Harvey</style></author><author><style face="normal" font="default" size="100%">Kuenzel, Wayne</style></author><author><style face="normal" font="default" size="100%">Medina, Loreta</style></author><author><style face="normal" font="default" size="100%">Paxinos, George</style></author><author><style face="normal" font="default" size="100%">Perkel, David J</style></author><author><style face="normal" font="default" size="100%">Shimizu, Toru</style></author><author><style face="normal" font="default" size="100%">Striedter, Georg</style></author><author><style face="normal" font="default" size="100%">Wild, J Martin</style></author><author><style face="normal" font="default" size="100%">Ball, Gregory F</style></author><author><style face="normal" font="default" size="100%">Dugas-Ford, Jennifer</style></author><author><style face="normal" font="default" size="100%">Durand, Sarah E</style></author><author><style face="normal" font="default" size="100%">Hough, Gerald E</style></author><author><style face="normal" font="default" size="100%">Husband, Scott</style></author><author><style face="normal" font="default" size="100%">Kubikova, Lubica</style></author><author><style face="normal" font="default" size="100%">Lee, Diane W</style></author><author><style face="normal" font="default" size="100%">Mello, Claudio V</style></author><author><style face="normal" font="default" size="100%">Powers, Alice</style></author><author><style face="normal" font="default" size="100%">Siang, Connie</style></author><author><style face="normal" font="default" size="100%">Smulders, Tom V</style></author><author><style face="normal" font="default" size="100%">Wada, Kazuhiro</style></author><author><style face="normal" font="default" size="100%">White, Stephanie A</style></author><author><style face="normal" font="default" size="100%">Yamamoto, Keiko</style></author><author><style face="normal" font="default" size="100%">Yu, Jing</style></author><author><style face="normal" font="default" size="100%">Reiner, Anton</style></author><author><style face="normal" font="default" size="100%">Butler, Ann B</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">Avian Brain Nomenclature Consortium</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">Avian brains and a new understanding of vertebrate brain evolution.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature reviews. Neuroscience</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Rev. Neurosci.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">151-9</style></pages><abstract><style face="normal" font="default" size="100%">We believe that names have a powerful influence on the experiments we do and the way in which we think. For this reason, and in the light of new evidence about the function and evolution of the vertebrate brain, an international consortium of neuroscientists has reconsidered the traditional, 100-year-old terminology that is used to describe the avian cerebrum. Our current understanding of the avian brain - in particular the neocortex-like cognitive functions of the avian pallium - requires a new terminology that better reflects these functions and the homologies between avian and mammalian brains.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15685220?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ashurst, J L</style></author><author><style face="normal" font="default" size="100%">Chen, C-K</style></author><author><style face="normal" font="default" size="100%">Gilbert, J G R</style></author><author><style face="normal" font="default" size="100%">Jekosch, K</style></author><author><style face="normal" font="default" size="100%">Keenan, S</style></author><author><style face="normal" font="default" size="100%">Meidl, P</style></author><author><style face="normal" font="default" size="100%">Searle, S M</style></author><author><style face="normal" font="default" size="100%">Stalker, J</style></author><author><style face="normal" font="default" size="100%">Storey, R</style></author><author><style face="normal" font="default" size="100%">Trevanion, S</style></author><author><style face="normal" font="default" size="100%">Wilming, L</style></author><author><style face="normal" font="default" size="100%">Hubbard, T</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Vertebrate Genome Annotation (Vega) database.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic acids research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Jan 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">33</style></volume><pages><style face="normal" font="default" size="100%">D459-65</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Vertebrate Genome Annotation (Vega) database (http://vega.sanger.ac.uk) has been designed to be a community resource for browsing manual annotation of finished sequences from a variety of vertebrate genomes. Its core database is based on an Ensembl-style schema, extended to incorporate curation-specific metadata. In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality annotation of the published human chromosome sequences. In addition, it is also possible to view various finished regions from other vertebrates, including mouse and zebrafish. Vega displays only manually annotated gene structures built using transcriptional evidence, which can be examined in the browser. Attempts have been made to standardize the annotation procedure across each vertebrate genome, which should aid comparative analysis of orthologues across the different finished regions.</style></abstract><issue><style face="normal" font="default" size="100%">Database issue</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15608237?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Loveland, Jane</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">VEGA, the genome browser with a difference.</style></title><secondary-title><style face="normal" font="default" size="100%">Briefings in bioinformatics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Brief. Bioinformatics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">189-93</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The Vertebrate Genome Annotation (Vega) database is a community resource for browsing manual annotation from a variety of vertebrate genomes of finished sequence (http://vega.sanger.ac.uk). Vega is different from other genome browsers as it has a standardised classification of genes which encompasses pseudogenes and non-coding transcripts. The data is manually curated, which is more accurate at identifying splice variants, pseudogenes poly(A) features, non-coding and complex gene structures and arrangements than current automated methods. The database also contains annotation from regions, not just whole genomes, and displays multiple species annotation (human, mouse, dog and zebrafish) for comparative analysis. Vega encourages community feedback that results in annotation updates and manual annotation of finished vertebrate sequence.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15975227?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Edwards, Scott V</style></author><author><style face="normal" font="default" size="100%">Bryan Jennings, W</style></author><author><style face="normal" font="default" size="100%">Shedlock, Andrew M</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenetics of modern birds in the era of genomics.</style></title><secondary-title><style face="normal" font="default" size="100%">Proceedings. Biological sciences / The Royal Society</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Biol. Sci.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 May 22</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">272</style></volume><pages><style face="normal" font="default" size="100%">979-92</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In the 14 years since the first higher-level bird phylogenies based on DNA sequence data, avian phylogenetics has witnessed the advent and maturation of the genomics era, the completion of the chicken genome and a suite of technologies that promise to add considerably to the agenda of avian phylogenetics. In this review, we summarize current approaches and data characteristics of recent higher-level bird studies and suggest a number of as yet untested molecular and analytical approaches for the unfolding tree of life for birds. A variety of comparative genomics strategies, including adoption of objective quality scores for sequence data, analysis of contiguous DNA sequences provided by large-insert genomic libraries, and the systematic use of retroposon insertions and other rare genomic changes all promise an integrated phylogenetics that is solidly grounded in genome evolution. The avian genome is an excellent testing ground for such approaches because of the more balanced representation of single-copy and repetitive DNA regions than in mammals. Although comparative genomics has a number of obvious uses in avian phylogenetics, its application to large numbers of taxa poses a number of methodological and infrastructural challenges, and can be greatly facilitated by a 'community genomics' approach in which the modest sequencing throughputs of single PI laboratories are pooled to produce larger, complementary datasets. Although the polymerase chain reaction era of avian phylogenetics is far from complete, the comparative genomics era-with its ability to vastly increase the number and type of molecular characters and to provide a genomic context for these characters-will usher in a host of new perspectives and opportunities for integrating genome evolution and avian phylogenetics.</style></abstract><issue><style face="normal" font="default" size="100%">1567</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16024355?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">McAuliffe, Jon D</style></author><author><style face="normal" font="default" size="100%">Jordan, Michael I</style></author><author><style face="normal" font="default" size="100%">Pachter, Lior</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Subtree power analysis and species selection for comparative genomics.</style></title><secondary-title><style face="normal" font="default" size="100%">Proceedings of the National Academy of Sciences of the United States of America</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Natl. Acad. Sci. U.S.A.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 May 31</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">102</style></volume><pages><style face="normal" font="default" size="100%">7900-5</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations: the lineal scope encompassing the biological phenomena of interest, and the optimal species within that scope for detecting functional elements. We introduce a statistical framework for optimal species subset selection, based on maximizing power to detect conserved sites. Analysis of a phylogenetic star topology shows theoretically that the optimal species subset is not in general the most evolutionarily diverged subset. We then demonstrate this finding empirically in a study of vertebrate species. Our results suggest that marsupials are prime sequencing candidates.</style></abstract><issue><style face="normal" font="default" size="100%">22</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/15911755?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Burmeister, Sabrina S</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author><author><style face="normal" font="default" size="100%">Fernald, Russell D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Rapid behavioral and genomic responses to social opportunity.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS biology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Nov</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">e363</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">From primates to bees, social status regulates reproduction. In the cichlid fish Astatotilapia (Haplochromis) burtoni, subordinate males have reduced fertility and must become dominant to reproduce. This increase in sexual capacity is orchestrated by neurons in the preoptic area, which enlarge in response to dominance and increase expression of gonadotropin-releasing hormone 1 (GnRH1), a peptide critical for reproduction. Using a novel behavioral paradigm, we show for the first time that subordinate males can become dominant within minutes of an opportunity to do so, displaying dramatic changes in body coloration and behavior. We also found that social opportunity induced expression of the immediate-early gene egr-1 in the anterior preoptic area, peaking in regions with high densities of GnRH1 neurons, and not in brain regions that express the related peptides GnRH2 and GnRH3. This genomic response did not occur in stable subordinate or stable dominant males even though stable dominants, like ascending males, displayed dominance behaviors. Moreover, egr-1 in the optic tectum and the cerebellum was similarly induced in all experimental groups, showing that egr-1 induction in the anterior preoptic area of ascending males was specific to this brain region. Because egr-1 codes for a transcription factor important in neural plasticity, induction of egr-1 in the anterior preoptic area by social opportunity could be an early trigger in the molecular cascade that culminates in enhanced fertility and other long-term physiological changes associated with dominance.</style></abstract><issue><style face="normal" font="default" size="100%">11</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16216088?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Prakash, Amol</style></author><author><style face="normal" font="default" size="100%">Tompa, Martin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Discovery of regulatory elements in vertebrates through comparative genomics.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature biotechnology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Biotechnol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2005</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2005 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">23</style></volume><pages><style face="normal" font="default" size="100%">1249-56</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We have analyzed issues of reliability in studies in which comparative genomic approaches have been applied to the discovery of regulatory elements at a genome-wide level in vertebrates. We point out some potential problems with such studies, including difficulties in accurately identifying orthologous promoter regions. Many of these subtle analytical problems have become apparent only when studying the more complex vertebrate genomes. By determining motif reliability, we compared existing tools when applied to the discovery of vertebrate regulatory elements. We then used a statistical clustering method to produce a computational catalog of high quality putative regulatory elements from vertebrates, some of which are widely conserved among vertebrates and many of which are novel regulatory elements. The results provide a glimpse into the wealth of information that comparative genomics can yield and suggest the need for further improvement of genome-wide comparative computational techniques.</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16211068?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Carter, David</style></author><author><style face="normal" font="default" size="100%">Durbin, Richard</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Vertebrate gene finding from multiple-species alignments using a two-level strategy.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome biology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">7 Suppl 1</style></volume><pages><style face="normal" font="default" size="100%">S6.1-12</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: One way in which the accuracy of gene structure prediction in vertebrate DNA sequences can be improved is by analyzing alignments with multiple related species, since functional regions of genes tend to be more conserved. RESULTS: We describe DOGFISH, a vertebrate gene finder consisting of a cleanly separated site classifier and structure predictor. The classifier scores potential splice sites and other features, using sequence alignments between multiple vertebrate species, while the structure predictor hypothesizes coding transcripts by combining these scores using a simple model of gene structure. This also identifies and assigns confidence scores to possible additional exons. Performance is assessed on the ENCODE regions. We predict transcripts and exons across the whole human genome, and identify over 10,000 high confidence new coding exons not in the Ensembl gene set. CONCLUSION: We present a practical multiple species gene prediction method. Accuracy improves as additional species, up to at least eight, are introduced. The novel predictions of the whole-genome scan should support efficient experimental verification.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16925840?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Margulies, Elliott H</style></author><author><style face="normal" font="default" size="100%">Chen, Christina W</style></author><author><style face="normal" font="default" size="100%">Green, Eric D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Differences between pair-wise and multi-sequence alignment methods affect vertebrate genome comparisons.</style></title><secondary-title><style face="normal" font="default" size="100%">Trends in genetics : TIG</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Trends Genet.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">22</style></volume><pages><style face="normal" font="default" size="100%">187-93</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Producing complete and accurate alignments of multiple genomic sequences is complex and prone to errors, especially with sequences generated from highly diverged species. In this article, we show that multi-sequence (as opposed to pair-wise) alignment methods are substantially better at aligning (or 'capturing') all of the available orthologous sequence from phylogenetically diverse vertebrates (i.e. those separated by relatively long branch lengths). Maximum gains are obtained only when sequences from many species are aligned. Such multi-sequence alignments contain significant amounts of exonic and highly conserved non-exonic sequences that are not captured in pair-wise alignments, thus illustrating the importance of the alignment method used for performing comparative genome analyses.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16499991?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Smith, V Anne</style></author><author><style face="normal" font="default" size="100%">Yu, Jing</style></author><author><style face="normal" font="default" size="100%">Smulders, Tom V</style></author><author><style face="normal" font="default" size="100%">Hartemink, Alexander J</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Computational inference of neural information flow networks.</style></title><secondary-title><style face="normal" font="default" size="100%">PLoS computational biology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS Comput. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Nov 24</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">2</style></volume><pages><style face="normal" font="default" size="100%">e161</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Determining how information flows along anatomical brain pathways is a fundamental requirement for understanding how animals perceive their environments, learn, and behave. Attempts to reveal such neural information flow have been made using linear computational methods, but neural interactions are known to be nonlinear. Here, we demonstrate that a dynamic Bayesian network (DBN) inference algorithm we originally developed to infer nonlinear transcriptional regulatory networks from gene expression data collected with microarrays is also successful at inferring nonlinear neural information flow networks from electrophysiology data collected with microelectrode arrays. The inferred networks we recover from the songbird auditory pathway are correctly restricted to a subset of known anatomical paths, are consistent with timing of the system, and reveal both the importance of reciprocal feedback in auditory processing and greater information flow to higher-order auditory areas when birds hear natural as opposed to synthetic sounds. A linear method applied to the same data incorrectly produces networks with information flow to non-neural tissue and over paths known not to exist. To our knowledge, this study represents the first biologically validated demonstration of an algorithm to successfully infer neural information flow networks.</style></abstract><issue><style face="normal" font="default" size="100%">11</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17121460?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Ferreira, Adriana R J</style></author><author><style face="normal" font="default" size="100%">Smulders, Tom V</style></author><author><style face="normal" font="default" size="100%">Sameshima, Koichi</style></author><author><style face="normal" font="default" size="100%">Mello, Claudio V</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">VOCALIZATIONS AND ASSOCIATED BEHAVIORS OF THE SOMBRE HUMMINGBIRD (APHANTOCHROA CIRRHOCHLORIS) AND THE RUFOUS-BREASTED HERMIT (GLAUCIS HIRSUTUS).</style></title><secondary-title><style face="normal" font="default" size="100%">The Auk</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Auk</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Oct</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">123</style></volume><pages><style face="normal" font="default" size="100%">1129-1148</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Vocal behavior in tropical hummingbirds is a new area of study. Here, we present findings on the vocalizations and associated behaviors of two species: Sombre Hummingbird (Aphantochroa cirrhochloris) and Rufous-breasted Hermit (Glaucis hirsutus). These are the only hummingbirds in which the brain areas activated by singing have been demonstrated. They are also among the basal species of their respective subfamilies, Trochilinae and Phaethornithinae and, thus, represent early stages in the evolution of hummingbird vocal communication. We found that the two species exhibit distinctive vocalizations and behaviors. Sombre Hummingbird calls had more modulation and were often used during agonistic interactions, whereas Rufous-breasted Hermit calls had higher pitch and purer tones and were produced in less aggressive interactions. Sombre Hummingbird song was highly stereotyped in syllable structure and syntax, whereas Rufous-breasted Hermit song was highly variable. Comparative analysis points to consistent similarities in use of vocalizations by the Sombre Hummingbird and other trochilines, and by the Rufous-breasted Hermit and other phaethornithines. We hypothesize that differences in vocal behavior between hummingbird lineages arise as adaptations to their foraging strategies.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18802498?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Wada, Kazuhiro</style></author><author><style face="normal" font="default" size="100%">Howard, Jason T</style></author><author><style face="normal" font="default" size="100%">McConnell, Patrick</style></author><author><style face="normal" font="default" size="100%">Whitney, Osceola</style></author><author><style face="normal" font="default" size="100%">Lints, Thierry</style></author><author><style face="normal" font="default" size="100%">Rivas, Miriam V</style></author><author><style face="normal" font="default" size="100%">Horita, Haruhito</style></author><author><style face="normal" font="default" size="100%">Patterson, Michael A</style></author><author><style face="normal" font="default" size="100%">White, Stephanie A</style></author><author><style face="normal" font="default" size="100%">Scharff, Constance</style></author><author><style face="normal" font="default" size="100%">Haesler, Sebastian</style></author><author><style face="normal" font="default" size="100%">Zhao, Shengli</style></author><author><style face="normal" font="default" size="100%">Sakaguchi, Hironobu</style></author><author><style face="normal" font="default" size="100%">Hagiwara, Masatoshi</style></author><author><style face="normal" font="default" size="100%">Shiraki, Toshiyuki</style></author><author><style face="normal" font="default" size="100%">Hirozane-Kishikawa, Tomoko</style></author><author><style face="normal" font="default" size="100%">Skene, Pate</style></author><author><style face="normal" font="default" size="100%">Hayashizaki, Yoshihide</style></author><author><style face="normal" font="default" size="100%">Carninci, Piero</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes.</style></title><secondary-title><style face="normal" font="default" size="100%">Proceedings of the National Academy of Sciences of the United States of America</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Natl. Acad. Sci. U.S.A.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Oct 10</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">103</style></volume><pages><style face="normal" font="default" size="100%">15212-7</style></pages><abstract><style face="normal" font="default" size="100%">Songbirds have one of the most accessible neural systems for the study of brain mechanisms of behavior. However, neuroethological studies in songbirds have been limited by the lack of high-throughput molecular resources and gene-manipulation tools. To overcome these limitations, we constructed 21 regular, normalized, and subtracted full-length cDNA libraries from brains of zebra finches in 57 developmental and behavioral conditions in an attempt to clone as much of the brain transcriptome as possible. From these libraries, approximately 14,000 transcripts were isolated, representing an estimated 4,738 genes. With the cDNAs, we created a hierarchically organized transcriptome database and a large-scale songbird brain cDNA microarray. We used the arrays to reveal a set of 33 genes that are regulated in forebrain vocal nuclei by singing behavior. These genes clustered into four anatomical and six temporal expression patterns. Their functions spanned a large range of cellular and molecular categories, from signal transduction, trafficking, and structural, to synaptically released molecules. With the full-length cDNAs and a lentiviral vector system, we were able to overexpress, in vocal nuclei, proteins of representative singing-regulated genes in the absence of singing. This publicly accessible resource http://songbirdtranscriptome.net can now be used to study molecular neuroethological mechanisms of behavior.</style></abstract><issue><style face="normal" font="default" size="100%">41</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17018643?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Amemiya, Chris T</style></author><author><style face="normal" font="default" size="100%">Gomez-Chiarri, Marta</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparative genomics in vertebrate evolution and development.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of experimental zoology. Part A, Comparative experimental biology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Exp. Zoolog. Part A Comp. Exp. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2006</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2006 Sep 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">305</style></volume><pages><style face="normal" font="default" size="100%">672-82</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The vast quantities of publicly available DNA sequencing data and genome resources are enabling biologists to investigate age-old problems in biology that were not addressable previously. In this review, we discuss how comparative genomics is practiced and how the data can be used to make biological inferences with respect to vertebrate evolution and development. Examples are taken from the well-known HOX clusters, which are always a high-priority target for genomic analyses due to their inferred role in the evolution of metazoans. In addition, we briefly discuss the application of genomic approaches to problems in comparative endocrinology.</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/16902957?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Retelska, Dorota</style></author><author><style face="normal" font="default" size="100%">Beaudoing, Emmanuel</style></author><author><style face="normal" font="default" size="100%">Notredame, Cédric</style></author><author><style face="normal" font="default" size="100%">Jongeneel, C Victor</style></author><author><style face="normal" font="default" size="100%">Bucher, Philipp</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">398</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: The comparison of complete genomes has revealed surprisingly large numbers of conserved non-protein-coding (CNC) DNA regions. However, the biological function of CNC remains elusive. CNC differ in two aspects from conserved protein-coding regions. They are not conserved across phylum boundaries, and they do not contain readily detectable sub-domains. Here we characterize the persistence length and time of CNC and conserved protein-coding regions in the vertebrate and insect lineages. RESULTS: The persistence length is the length of a genome region over which a certain level of sequence identity is consistently maintained. The persistence time is the evolutionary period during which a conserved region evolves under the same selective constraints. Our main findings are: (i) Insect genomes contain 1.60 times less conserved information than vertebrates; (ii) Vertebrate CNC have a higher persistence length than conserved coding regions or insect CNC; (iii) CNC have shorter persistence times as compared to conserved coding regions in both lineages. CONCLUSION: Higher persistence length of vertebrate CNC indicates that the conserved information in vertebrates and insects is organized in functional elements of different lengths. These findings might be related to the higher morphological complexity of vertebrates and give clues about the structure of active CNC elements. Shorter persistence time might explain the previously puzzling observations of highly conserved CNC within each phylum, and of a lack of conservation between phyla. It suggests that CNC divergence might be a key factor in vertebrate evolution. Further evolutionary studies will help to relate individual CNC to specific developmental processes.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17973996?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Itoh, Yuichiro</style></author><author><style face="normal" font="default" size="100%">Melamed, Esther</style></author><author><style face="normal" font="default" size="100%">Yang, Xia</style></author><author><style face="normal" font="default" size="100%">Kampf, Kathy</style></author><author><style face="normal" font="default" size="100%">Wang, Susanna</style></author><author><style face="normal" font="default" size="100%">Yehya, Nadir</style></author><author><style face="normal" font="default" size="100%">Van Nas, Atila</style></author><author><style face="normal" font="default" size="100%">Replogle, Kirstin</style></author><author><style face="normal" font="default" size="100%">Band, Mark R</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author><author><style face="normal" font="default" size="100%">Schadt, Eric E</style></author><author><style face="normal" font="default" size="100%">Lusis, Aldons J</style></author><author><style face="normal" font="default" size="100%">Arnold, Arthur P</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Dosage compensation is less effective in birds than in mammals.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of biology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">2</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: In animals with heteromorphic sex chromosomes, dosage compensation of sex-chromosome genes is thought to be critical for species survival. Diverse molecular mechanisms have evolved to effectively balance the expressed dose of X-linked genes between XX and XY animals, and to balance expression of X and autosomal genes. Dosage compensation is not understood in birds, in which females (ZW) and males (ZZ) differ in the number of Z chromosomes. RESULTS: Using microarray analysis, we compared the male:female ratio of expression of sets of Z-linked and autosomal genes in two bird species, zebra finch and chicken, and in two mammalian species, mouse and human. Male:female ratios of expression were significantly higher for Z genes than for autosomal genes in several finch and chicken tissues. In contrast, in mouse and human the male:female ratio of expression of X-linked genes is quite similar to that of autosomal genes, indicating effective dosage compensation even in humans, in which a significant percentage of genes escape X-inactivation. CONCLUSION: Birds represent an unprecedented case in which genes on one sex chromosome are expressed on average at constitutively higher levels in one sex compared with the other. Sex-chromosome dosage compensation is surprisingly ineffective in birds, suggesting that some genomes can do without effective sex-specific sex-chromosome dosage compensation mechanisms.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17352797?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Li, Xiaoching</style></author><author><style face="normal" font="default" size="100%">Wang, Xiu-Jie</style></author><author><style face="normal" font="default" size="100%">Tannenhauser, Jonathan</style></author><author><style face="normal" font="default" size="100%">Podell, Sheila</style></author><author><style face="normal" font="default" size="100%">Mukherjee, Piali</style></author><author><style face="normal" font="default" size="100%">Hertel, Moritz</style></author><author><style face="normal" font="default" size="100%">Biane, Jeremy</style></author><author><style face="normal" font="default" size="100%">Masuda, Shoko</style></author><author><style face="normal" font="default" size="100%">Nottebohm, Fernando</style></author><author><style face="normal" font="default" size="100%">Gaasterland, Terry</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genomic resources for songbird research and their use in characterizing gene expression during brain development.</style></title><secondary-title><style face="normal" font="default" size="100%">Proceedings of the National Academy of Sciences of the United States of America</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Natl. Acad. Sci. U.S.A.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Apr 17</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">104</style></volume><pages><style face="normal" font="default" size="100%">6834-9</style></pages><abstract><style face="normal" font="default" size="100%">Vocal learning and neuronal replacement have been studied extensively in songbirds, but until recently, few molecular and genomic tools for songbird research existed. Here we describe new molecular/genomic resources developed in our laboratory. We made cDNA libraries from zebra finch (Taeniopygia guttata) brains at different developmental stages. A total of 11,000 cDNA clones from these libraries, representing 5,866 unique gene transcripts, were randomly picked and sequenced from the 3' ends. A web-based database was established for clone tracking, sequence analysis, and functional annotations. Our cDNA libraries were not normalized. Sequencing ESTs without normalization produced many developmental stage-specific sequences, yielding insights into patterns of gene expression at different stages of brain development. In particular, the cDNA library made from brains at posthatching day 30-50, corresponding to the period of rapid song system development and song learning, has the most diverse and richest set of genes expressed. We also identified five microRNAs whose sequences are highly conserved between zebra finch and other species. We printed cDNA microarrays and profiled gene expression in the high vocal center of both adult male zebra finches and canaries (Serinus canaria). Genes differentially expressed in the high vocal center were identified from the microarray hybridization results. Selected genes were validated by in situ hybridization. Networks among the regulated genes were also identified. These resources provide songbird biologists with tools for genome annotation, comparative genomics, and microarray gene expression analysis.</style></abstract><issue><style face="normal" font="default" size="100%">16</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17426146?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Neural systems for vocal learning in birds and humans: a synopsis.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of ornithology / DO-G</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Ornithol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Dec 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">148</style></volume><pages><style face="normal" font="default" size="100%">35-44</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">I present here a synopsis on a hypothesis that I derived on the similarities and differences of vocal learning systems in vocal learning birds for learned song and in humans for spoken language. This hypothesis states that vocal learning birds-songbirds, parrots, and hummingbirds-and humans have comparable specialized forebrain regions that are not found in their close vocal non-learning relatives. In vocal learning birds, these forebrain regions appear to be divided into two sub-pathways, a vocal motor pathway mainly used to produce learned vocalizations and a pallial-basal-ganglia-thalamic loop mainly used to learn and modify the vocalizations. I propose that humans have analogous forebrain pathways within and adjacent to the motor and pre-motor cortices, respectively, used to produce and learn speech. Recent advances have supported the existence of the seven cerebral vocal nuclei in the vocal learning birds and the proposed brain regions in humans. The results in birds suggest that the reason why the forebrain regions are similar across distantly related vocal learners is that the vocal pathways may have evolved out of a pre-existing motor pathway that predates the ancient split from the common ancestor of birds and mammals. Although this hypothesis will require the development of novel technologies to be fully tested, the existing evidence suggest that there are strong genetic constraints on how vocal learning neural systems can evolve.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19684872?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Danchin, Etienne G J</style></author><author><style face="normal" font="default" size="100%">Levasseur, Anthony</style></author><author><style face="normal" font="default" size="100%">Rascol, Virginie Lopez</style></author><author><style face="normal" font="default" size="100%">Gouret, Philippe</style></author><author><style face="normal" font="default" size="100%">Pontarotti, Pierre</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The use of evolutionary biology concepts for genome annotation.</style></title><secondary-title><style face="normal" font="default" size="100%">Journal of experimental zoology. Part B, Molecular and developmental evolution</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Exp. Zool. B Mol. Dev. Evol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Jan 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">308</style></volume><pages><style face="normal" font="default" size="100%">26-36</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The past decade has seen the completion of numerous whole-genome sequencing projects, began with bacterial genomes and continued with eukaryotic species from different phyla: fungi, plants and animals. Besides, more biological information are produced and are shared thanks to information exchange systems, and more biological concepts, as well as more bioinformatics tools, are available. In this article, we will describe how the evolutionary biology concepts, as well as computer science, are useful for a better understanding of biology in general and genome annotation in particular. The genome annotation process consists of taking the raw DNA produced, for example, by the genome sequencing projects, adding the layers of analysis and interpretation necessary to extract its biological significance and placing it in the context of our understanding of biological processes. Genome annotation is a multistep process falling into two broad categories: structural and functional annotation.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17016828?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Zhu, Wei</style></author><author><style face="normal" font="default" size="100%">Buell, C Robin</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Improvement of whole-genome annotation of cereals through comparative analyses.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">299-310</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Rice is an important model species for the Poaceae and other monocotyledonous plants. With the availability of a near-complete, finished, and annotated rice genome, we performed genome level comparisons between rice and all plant species in which large genomic or transcriptomic data sets are available to determine the utility of cross-species sequence for structural and functional annotation of the rice genome. Through comparative analyses with four plant genome sequence data sets and transcript assemblies from 185 plant species, we were able to confirm and improve the structural annotation of the rice genome. Support for 38,109 (89.3%) of the total 42,653 nontransposable element-related genes in the rice genome in the form of a rice expressed sequence tag, full-length cDNA, or plant homolog from our comparative analyses could be found. Although the majority of the putative homologs were obtained from Poaceae species, putative homologs were identified in dicotyledonous angiosperms, gymnosperms, and other plants such as algae, moss, and fern. A set of rice genes (7669) lacking a putative homolog was identified which may be lineage-specific genes that evolved after speciation and have a role in species diversity. Improvements to the current rice gene structural annotation could be identified from our comparative alignments and we were able to identify 487 genes which were mostly likely missed in the current rice genome annotation and another 500 genes for structural annotation review. We were able to demonstrate the utility of cross-species comparative alignments in the identification of noncoding sequences and in confirmation of gene nesting in rice.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17284677?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Organ, Chris L</style></author><author><style face="normal" font="default" size="100%">Shedlock, Andrew M</style></author><author><style face="normal" font="default" size="100%">Meade, Andrew</style></author><author><style face="normal" font="default" size="100%">Pagel, Mark</style></author><author><style face="normal" font="default" size="100%">Edwards, Scott V</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Origin of avian genome size and structure in non-avian dinosaurs.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nature</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Mar 8</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">446</style></volume><pages><style face="normal" font="default" size="100%">180-4</style></pages><abstract><style face="normal" font="default" size="100%">Avian genomes are small and streamlined compared with those of other amniotes by virtue of having fewer repetitive elements and less non-coding DNA. This condition has been suggested to represent a key adaptation for flight in birds, by reducing the metabolic costs associated with having large genome and cell sizes. However, the evolution of genome architecture in birds, or any other lineage, is difficult to study because genomic information is often absent for long-extinct relatives. Here we use a novel bayesian comparative method to show that bone-cell size correlates well with genome size in extant vertebrates, and hence use this relationship to estimate the genome sizes of 31 species of extinct dinosaur, including several species of extinct birds. Our results indicate that the small genomes typically associated with avian flight evolved in the saurischian dinosaur lineage between 230 and 250 million years ago, long before this lineage gave rise to the first birds. By comparison, ornithischian dinosaurs are inferred to have had much larger genomes, which were probably typical for ancestral Dinosauria. Using comparative genomic data, we estimate that genome-wide interspersed mobile elements, a class of repetitive DNA, comprised 5-12% of the total genome size in the saurischian dinosaur lineage, but was 7-19% of total genome size in ornithischian dinosaurs, suggesting that repetitive elements became less active in the saurischian lineage. These genomic characteristics should be added to the list of attributes previously considered avian but now thought to have arisen in non-avian dinosaurs, such as feathers, pulmonary innovations, and parental care and nesting.</style></abstract><issue><style face="normal" font="default" size="100%">7132</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17344851?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Nakatani, Yoichiro</style></author><author><style face="normal" font="default" size="100%">Takeda, Hiroyuki</style></author><author><style face="normal" font="default" size="100%">Kohara, Yuji</style></author><author><style face="normal" font="default" size="100%">Morishita, Shinichi</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2007</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2007 Sep</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">1254-65</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Although several vertebrate genomes have been sequenced, little is known about the genome evolution of early vertebrates and how large-scale genomic changes such as the two rounds of whole-genome duplications (2R WGD) affected evolutionary complexity and novelty in vertebrates. Reconstructing the ancestral vertebrate genome is highly nontrivial because of the difficulty in identifying traces originating from the 2R WGD. To resolve this problem, we developed a novel method capable of pinning down remains of the 2R WGD in the human and medaka fish genomes using invertebrate tunicate and sea urchin genes to define ohnologs, i.e., paralogs produced by the 2R WGD. We validated the reconstruction using the chicken genome, which was not considered in the reconstruction step, and observed that many ancestral proto-chromosomes were retained in the chicken genome and had one-to-one correspondence to chicken microchromosomes, thereby confirming the reconstructed ancestral genomes. Our reconstruction revealed a contrast between the slow karyotype evolution after the second WGD and the rapid, lineage-specific genome reorganizations that occurred in the ancestral lineages of major taxonomic groups such as teleost fishes, amphibians, reptiles, and marsupials.</style></abstract><issue><style face="normal" font="default" size="100%">9</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/17652425?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Replogle, Kirstin</style></author><author><style face="normal" font="default" size="100%">Arnold, Arthur P</style></author><author><style face="normal" font="default" size="100%">Ball, Gregory F</style></author><author><style face="normal" font="default" size="100%">Band, Mark</style></author><author><style face="normal" font="default" size="100%">Bensch, Staffan</style></author><author><style face="normal" font="default" size="100%">Brenowitz, Eliot A</style></author><author><style face="normal" font="default" size="100%">Dong, Shu</style></author><author><style face="normal" font="default" size="100%">Drnevich, Jenny</style></author><author><style face="normal" font="default" size="100%">Ferris, Margaret</style></author><author><style face="normal" font="default" size="100%">George, Julia M</style></author><author><style face="normal" font="default" size="100%">Gong, George</style></author><author><style face="normal" font="default" size="100%">Hasselquist, Dennis</style></author><author><style face="normal" font="default" size="100%">Hernandez, Alvaro G</style></author><author><style face="normal" font="default" size="100%">Kim, Ryan</style></author><author><style face="normal" font="default" size="100%">Lewin, Harris A</style></author><author><style face="normal" font="default" size="100%">Liu, Lei</style></author><author><style face="normal" font="default" size="100%">Lovell, Peter V</style></author><author><style face="normal" font="default" size="100%">Mello, Claudio V</style></author><author><style face="normal" font="default" size="100%">Naurin, Sara</style></author><author><style face="normal" font="default" size="100%">Rodriguez-Zas, Sandra</style></author><author><style face="normal" font="default" size="100%">Thimmapuram, Jyothi</style></author><author><style face="normal" font="default" size="100%">Wade, Juli</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The Songbird Neurogenomics (SoNG) Initiative: community-based tools and strategies for study of brain gene function and evolution.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">131</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: Songbirds hold great promise for biomedical, environmental and evolutionary research. A complete draft sequence of the zebra finch genome is imminent, yet a need remains for application of genomic resources within a research community traditionally focused on ethology and neurobiological methods. In response, we developed a core set of genomic tools and a novel collaborative strategy to probe gene expression in diverse songbird species and natural contexts. RESULTS: We end-sequenced cDNAs from zebra finch brain and incorporated additional sequences from community sources into a database of 86,784 high quality reads. These assembled into 31,658 non-redundant contigs and singletons, which we annotated via BLAST search of chicken and human databases. The results are publicly available in the ESTIMA:Songbird database. We produced a spotted cDNA microarray with 20,160 addresses representing 17,214 non-redundant products of an estimated 11,500-15,000 genes, validating it by analysis of immediate-early gene (zenk) gene activation following song exposure and by demonstrating effective cross hybridization to genomic DNAs of other songbird species in the Passerida Parvorder. Our assembly was also used in the design of the &quot;Lund-zfa&quot; Affymetrix array representing approximately 22,000 non-redundant sequences. When the two arrays were hybridized to cDNAs from the same set of male and female zebra finch brain samples, both arrays detected a common set of regulated transcripts with a Pearson correlation coefficient of 0.895. To stimulate use of these resources by the songbird research community and to maintain consistent technical standards, we devised a &quot;Community Collaboration&quot; mechanism whereby individual birdsong researchers develop experiments and provide tissues, but a single individual in the community is responsible for all RNA extractions, labelling and microarray hybridizations. CONCLUSION: Immediately, these results set the foundation for a coordinated set of 25 planned experiments by 16 research groups probing fundamental links between genome, brain, evolution and behavior in songbirds. Energetic application of genomic resources to research using songbirds should help illuminate how complex neural and behavioral traits emerge and evolve.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18366674?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Rosenbloom, Kate</style></author><author><style face="normal" font="default" size="100%">Taylor, James</style></author><author><style face="normal" font="default" size="100%">Schaeffer, Stephen</style></author><author><style face="normal" font="default" size="100%">Kent, Jim</style></author><author><style face="normal" font="default" size="100%">Haussler, David</style></author><author><style face="normal" font="default" size="100%">Webb Miller</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenomic resources at the UCSC Genome Browser.</style></title><secondary-title><style face="normal" font="default" size="100%">Methods in molecular biology (Clifton, N.J.)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Methods Mol. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">422</style></volume><pages><style face="normal" font="default" size="100%">133-44</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The UC Santa Cruz Genome Browser provides a number of resources that can be used for phylogenomic studies, including (1) whole-genome sequence data from a number of vertebrate species, (2) pairwise alignments of the human genome sequence to a number of other vertebrate genome, (3) a simultaneous alignment of 17 vertebrate genomes (most of them incompletely sequenced) that covers all of the human sequence, (4) several independent sets of multiple alignments covering 1% of the human genome (ENCODE regions), (5) extensive sequence annotation for interpreting those sequences and alignments, and (6) sequence, alignments, and annotations from certain other species, including an alignment of nine insect genomes. We illustrate the use of these resources in the context of assigning rare genomic changes to the branch of the phylogenetic tree where they appear to have occurred, or of looking for evidence supporting a particular possible tree topology. Sample source code for performing such studies is available.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18629665?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Feenders, Gesa</style></author><author><style face="normal" font="default" size="100%">Liedvogel, Miriam</style></author><author><style face="normal" font="default" size="100%">Rivas, Miriam</style></author><author><style face="normal" font="default" size="100%">Zapka, Manuela</style></author><author><style face="normal" font="default" size="100%">Horita, Haruhito</style></author><author><style face="normal" font="default" size="100%">Hara, Erina</style></author><author><style face="normal" font="default" size="100%">Wada, Kazuhiro</style></author><author><style face="normal" font="default" size="100%">Mouritsen, Henrik</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Molecular mapping of movement-associated areas in the avian brain: a motor theory for vocal learning origin.</style></title><secondary-title><style face="normal" font="default" size="100%">PloS one</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS ONE</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">e1768</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Vocal learning is a critical behavioral substrate for spoken human language. It is a rare trait found in three distantly related groups of birds-songbirds, hummingbirds, and parrots. These avian groups have remarkably similar systems of cerebral vocal nuclei for the control of learned vocalizations that are not found in their more closely related vocal non-learning relatives. These findings led to the hypothesis that brain pathways for vocal learning in different groups evolved independently from a common ancestor but under pre-existing constraints. Here, we suggest one constraint, a pre-existing system for movement control. Using behavioral molecular mapping, we discovered that in songbirds, parrots, and hummingbirds, all cerebral vocal learning nuclei are adjacent to discrete brain areas active during limb and body movements. Similar to the relationships between vocal nuclei activation and singing, activation in the adjacent areas correlated with the amount of movement performed and was independent of auditory and visual input. These same movement-associated brain areas were also present in female songbirds that do not learn vocalizations and have atrophied cerebral vocal nuclei, and in ring doves that are vocal non-learners and do not have cerebral vocal nuclei. A compilation of previous neural tracing experiments in songbirds suggests that the movement-associated areas are connected in a network that is in parallel with the adjacent vocal learning system. This study is the first global mapping that we are aware for movement-associated areas of the avian cerebrum and it indicates that brain systems that control vocal learning in distantly related birds are directly adjacent to brain systems involved in movement control. Based upon these findings, we propose a motor theory for the origin of vocal learning, this being that the brain areas specialized for vocal learning in vocal learners evolved as a specialization of a pre-existing motor pathway that controls movement.</style></abstract><issue><style face="normal" font="default" size="100%">3</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18335043?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Lovell, Peter V</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author><author><style face="normal" font="default" size="100%">Replogle, Kirstin L</style></author><author><style face="normal" font="default" size="100%">Mello, Claudio V</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Birdsong &quot;transcriptomics&quot;: neurochemical specializations of the oscine song system.</style></title><secondary-title><style face="normal" font="default" size="100%">PloS one</style></secondary-title><alt-title><style face="normal" font="default" size="100%">PLoS ONE</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">3</style></volume><pages><style face="normal" font="default" size="100%">e3440</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Vocal learning is a rare and complex behavioral trait that serves as a basis for the acquisition of human spoken language. In songbirds, vocal learning and production depend on a set of specialized brain nuclei known as the song system. METHODOLOGY/PRINCIPAL FINDINGS: Using high-throughput functional genomics we have identified approximately 200 novel molecular markers of adult zebra finch HVC, a key node of the song system. These markers clearly differentiate HVC from the general pallial region to which HVC belongs, and thus represent molecular specializations of this song nucleus. Bioinformatics analysis reveals that several major neuronal cell functions and specific biochemical pathways are the targets of transcriptional regulation in HVC, including: 1) cell-cell and cell-substrate interactions (e.g., cadherin/catenin-mediated adherens junctions, collagen-mediated focal adhesions, and semaphorin-neuropilin/plexin axon guidance pathways); 2) cell excitability (e.g., potassium channel subfamilies, cholinergic and serotonergic receptors, neuropeptides and neuropeptide receptors); 3) signal transduction (e.g., calcium regulatory proteins, regulators of G-protein-related signaling); 4) cell proliferation/death, migration and differentiation (e.g., TGF-beta/BMP and p53 pathways); and 5) regulation of gene expression (candidate retinoid and steroid targets, modulators of chromatin/nucleolar organization). The overall direction of regulation suggest that processes related to cell stability are enhanced, whereas proliferation, growth and plasticity are largely suppressed in adult HVC, consistent with the observation that song in this songbird species is mostly stable in adulthood. CONCLUSIONS/SIGNIFICANCE: Our study represents one of the most comprehensive molecular genetic characterizations of a brain nucleus involved in a complex learned behavior in a vertebrate. The data indicate numerous targets for pharmacological and genetic manipulations of the song system, and provide novel insights into mechanisms that might play a role in the regulation of song behavior and/or vocal learning.</style></abstract><issue><style face="normal" font="default" size="100%">10</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18941504?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Margulies, Elliott H</style></author><author><style face="normal" font="default" size="100%">Ewan Birney</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Approaches to comparative sequence analysis: towards a functional view of vertebrate genomes.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature reviews. Genetics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nat. Rev. Genet.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">9</style></volume><pages><style face="normal" font="default" size="100%">303-13</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The comparison of genomic sequences is now a common approach to identifying and characterizing functional regions in vertebrate genomes. However, for theoretical reasons and because of practical issues, the generation of these data sets is non-trivial and can have many pitfalls. We are currently seeing an explosion of comparative sequence data, the benefits and limitations of which need to be disseminated to the scientific community. This Review provides a critical overview of the different types of sequence data that are available for analysis and of contemporary comparative sequence analysis methods, highlighting both their strengths and limitations. Approaches to determining the biological significance of constrained sequence are also explored.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18347593?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Horita, Haruhito</style></author><author><style face="normal" font="default" size="100%">Wada, Kazuhiro</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Early onset of deafening-induced song deterioration and differential requirements of the pallial-basal ganglia vocal pathway.</style></title><secondary-title><style face="normal" font="default" size="100%">The European journal of neuroscience</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Eur. J. Neurosci.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">28</style></volume><pages><style face="normal" font="default" size="100%">2519-32</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Similar to humans, songbirds rely on auditory feedback to maintain the acoustic and sequence structure of adult learned vocalizations. When songbirds are deafened, the learned features of song, such as syllable structure and sequencing, eventually deteriorate. However, the time-course and initial phases of song deterioration have not been well studied, particularly in the most commonly studied songbird, the zebra finch. Here, we observed previously uncharacterized subtle but significant changes to learned song within a few days following deafening. Syllable structure became detectably noisier and silent intervals between song motifs increased. Although song motif sequences remained stable at 2 weeks, as previously reported, pronounced changes occurred in longer stretches of song bout sequences. These included deletions of syllables between song motifs, changes in the frequency at which specific chunks of song were produced and stuttering for birds that had some repetitions of syllables before deafening. Changes in syllable structure and song bout sequence occurred at different rates, indicating different mechanisms for their deterioration. The changes in syllable structure required an intact lateral part but not the medial part of the pallial-basal ganglia vocal pathway, whereas changes in the song bout sequence did not require lateral or medial portions of the pathway. These findings indicate that deafening-induced song changes in zebra finches can be detected rapidly after deafening, that acoustic and sequence changes can occur independently, and that, within this time period, the pallial-basal ganglia vocal pathway controls the acoustic structure changes but not the song bout sequence changes.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19087177?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Muffato, Matthieu</style></author><author><style face="normal" font="default" size="100%">Roest Crollius, Hugues</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Paleogenomics in vertebrates, or the recovery of lost genomes from the mist of time.</style></title><secondary-title><style face="normal" font="default" size="100%">BioEssays : news and reviews in molecular, cellular and developmental biology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Bioessays</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Feb</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">30</style></volume><pages><style face="normal" font="default" size="100%">122-34</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Knowledge of the structure of ancestral genomes provides the basis of a new framework to better represent and interpret results from genomic and evolutionary studies. Because these ancestors lived tens of hundreds of million years ago, this knowledge will inevitably take the form of abstract representations, reconstructed on the basis both of experimental evidence collected on extant genomes and of our understanding of evolutionary processes. This is the field of Paleogenomics, a young discipline that is providing an increasingly precise picture of our ancestral vertebrate genomes based on cytogenetic data, genome sequences and new algorithmic developments. Many recent studies have focused on the ancestral placental mammal and teleost fish genomes, although the outlines of even more distant pre-vertebrate ancestors are being reported.</style></abstract><issue><style face="normal" font="default" size="100%">2</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18200550?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Karolchik, D</style></author><author><style face="normal" font="default" size="100%">Kuhn, R M</style></author><author><style face="normal" font="default" size="100%">Baertsch, R</style></author><author><style face="normal" font="default" size="100%">Barber, G P</style></author><author><style face="normal" font="default" size="100%">Clawson, H</style></author><author><style face="normal" font="default" size="100%">Diekhans, M</style></author><author><style face="normal" font="default" size="100%">Giardine, B</style></author><author><style face="normal" font="default" size="100%">Harte, R A</style></author><author><style face="normal" font="default" size="100%">Hinrichs, A S</style></author><author><style face="normal" font="default" size="100%">Hsu, F</style></author><author><style face="normal" font="default" size="100%">Kober, K M</style></author><author><style face="normal" font="default" size="100%">Miller, W</style></author><author><style face="normal" font="default" size="100%">Pedersen, J S</style></author><author><style face="normal" font="default" size="100%">Pohl, A</style></author><author><style face="normal" font="default" size="100%">Raney, B J</style></author><author><style face="normal" font="default" size="100%">Rhead, B</style></author><author><style face="normal" font="default" size="100%">Rosenbloom, K R</style></author><author><style face="normal" font="default" size="100%">Smith, K E</style></author><author><style face="normal" font="default" size="100%">Stanke, M</style></author><author><style face="normal" font="default" size="100%">Thakkapallayil, A</style></author><author><style face="normal" font="default" size="100%">Trumbower, H</style></author><author><style face="normal" font="default" size="100%">Wang, T</style></author><author><style face="normal" font="default" size="100%">Zweig, A S</style></author><author><style face="normal" font="default" size="100%">Haussler, D</style></author><author><style face="normal" font="default" size="100%">Kent, W J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The UCSC Genome Browser Database: 2008 update.</style></title><secondary-title><style face="normal" font="default" size="100%">Nucleic acids research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nucleic Acids Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jan</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">36</style></volume><pages><style face="normal" font="default" size="100%">D773-9</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.</style></abstract><issue><style face="normal" font="default" size="100%">Database issue</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18086701?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Axelsson, Erik</style></author><author><style face="normal" font="default" size="100%">Hultin-Rosenberg, Lina</style></author><author><style face="normal" font="default" size="100%">Brandström, Mikael</style></author><author><style face="normal" font="default" size="100%">Zwahlén, Martin</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author><author><style face="normal" font="default" size="100%">Ellegren, Hans</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Natural selection in avian protein-coding genes expressed in brain.</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular ecology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Mol. Ecol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">17</style></volume><pages><style face="normal" font="default" size="100%">3008-17</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The evolution of birds from theropod dinosaurs took place approximately 150 million years ago, and was associated with a number of specific adaptations that are still evident among extant birds, including feathers, song and extravagant secondary sexual characteristics. Knowledge about the molecular evolutionary background to such adaptations is lacking. Here, we analyse the evolution of &gt; 5000 protein-coding gene sequences expressed in zebra finch brain by comparison to orthologous sequences in chicken. Mean d(N)/d(S) is 0.085 and genes with their maximal expression in the eye and central nervous system have the lowest mean d(N)/d(S) value, while those expressed in digestive and reproductive tissues exhibit the highest. We find that fast-evolving genes (those which have higher than expected rate of nonsynonymous substitution, indicative of adaptive evolution) are enriched for biological functions such as fertilization, muscle contraction, defence response, response to stress, wounding and endogenous stimulus, and cell death. After alignment to mammalian orthologues, we identify a catalogue of 228 genes that show a significantly higher rate of protein evolution in the two bird lineages than in mammals. These accelerated bird genes, representing candidates for avian-specific adaptations, include genes implicated in vocal learning and other cognitive processes. Moreover, colouration genes evolve faster in birds than in mammals, which may have been driven by sexual selection for extravagant plumage characteristics.</style></abstract><issue><style face="normal" font="default" size="100%">12</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18482257?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hackett, Shannon J</style></author><author><style face="normal" font="default" size="100%">Kimball, Rebecca T</style></author><author><style face="normal" font="default" size="100%">Reddy, Sushma</style></author><author><style face="normal" font="default" size="100%">Bowie, Rauri C K</style></author><author><style face="normal" font="default" size="100%">Braun, Edward L</style></author><author><style face="normal" font="default" size="100%">Braun, Michael J</style></author><author><style face="normal" font="default" size="100%">Chojnowski, Jena L</style></author><author><style face="normal" font="default" size="100%">Cox, W Andrew</style></author><author><style face="normal" font="default" size="100%">Han, Kin-Lan</style></author><author><style face="normal" font="default" size="100%">Harshman, John</style></author><author><style face="normal" font="default" size="100%">Huddleston, Christopher J</style></author><author><style face="normal" font="default" size="100%">Marks, Ben D</style></author><author><style face="normal" font="default" size="100%">Miglia, Kathleen J</style></author><author><style face="normal" font="default" size="100%">Moore, William S</style></author><author><style face="normal" font="default" size="100%">Sheldon, Frederick H</style></author><author><style face="normal" font="default" size="100%">Steadman, David W</style></author><author><style face="normal" font="default" size="100%">Witt, Christopher C</style></author><author><style face="normal" font="default" size="100%">Yuri, Tamaki</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A phylogenomic study of birds reveals their evolutionary history.</style></title><secondary-title><style face="normal" font="default" size="100%">Science (New York, N.Y.)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Science</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Jun 27</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">320</style></volume><pages><style face="normal" font="default" size="100%">1763-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Deep avian evolutionary relationships have been difficult to resolve as a result of a putative explosive radiation. Our study examined approximately 32 kilobases of aligned nuclear DNA sequences from 19 independent loci for 169 species, representing all major extant groups, and recovered a robust phylogeny from a genome-wide signal supported by multiple analytical methods. We documented well-supported, previously unrecognized interordinal relationships (such as a sister relationship between passerines and parrots) and corroborated previously contentious groupings (such as flamingos and grebes). Our conclusions challenge current classifications and alter our understanding of trait evolution; for example, some diurnal birds evolved from nocturnal ancestors. Our results provide a valuable resource for phylogenetic and comparative studies in birds.</style></abstract><issue><style face="normal" font="default" size="100%">5884</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18583609?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Pinaud, Raphael</style></author><author><style face="normal" font="default" size="100%">Osorio, Cristina</style></author><author><style face="normal" font="default" size="100%">Alzate, Oscar</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Profiling of experience-regulated proteins in the songbird auditory forebrain using quantitative proteomics.</style></title><secondary-title><style face="normal" font="default" size="100%">The European journal of neuroscience</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Eur. J. Neurosci.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">27</style></volume><pages><style face="normal" font="default" size="100%">1409-22</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Auditory and perceptual processing of songs are required for a number of behaviors in songbirds such as vocal learning, territorial defense, mate selection and individual recognition. These neural processes are accompanied by increased expression of a few transcription factors, particularly in the caudomedial nidopallium (NCM), an auditory forebrain area believed to play a key role in auditory learning and song discrimination. However, these molecular changes are presumably part of a larger, yet uncharacterized, protein regulatory network. In order to gain further insight into this network, we performed two-dimensional differential in-gel expression (2D-DIGE) experiments, extensive protein quantification analyses, and tandem mass spectrometry in the NCM of adult songbirds hearing novel songs. A subset of proteins was selected for immunocytochemistry in NCM sections to confirm the 2D-DIGE findings and to provide additional quantitative and anatomical information. Using these methodologies, we found that stimulation of freely behaving birds with conspecific songs did not significantly impact the NCM proteome 5 min after stimulus onset. However, following 1 and 3 h of stimulation, a significant number of proteins were consistently regulated in NCM. These proteins spanned a range of functional categories that included metabolic enzymes, cytoskeletal molecules, and proteins involved in neurotransmitter secretion and calcium binding. Our findings suggest that auditory processing of vocal communication signals in freely behaving songbirds triggers a cascade of protein regulatory events that are dynamically regulated through activity-dependent changes in calcium levels.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18364021?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Stapley, J</style></author><author><style face="normal" font="default" size="100%">Birkhead, T R</style></author><author><style face="normal" font="default" size="100%">Burke, T</style></author><author><style face="normal" font="default" size="100%">Slate, J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution.</style></title><secondary-title><style face="normal" font="default" size="100%">Genetics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genetics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 May</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">179</style></volume><pages><style face="normal" font="default" size="100%">651-67</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Passeriformes are the largest order of birds and one of the most widely studied groups in evolutionary biology and ecology. Until recently genomic tools in passerines relied on chicken genomic resources. Here we report the construction and analysis of a whole-genome linkage map for the zebra finch (Taeniopygia guttata) using a 354-bird pedigree. The map contains 876 SNPs dispersed across 45 linkage groups and we found only a few instances of interchromosomal rearrangement between the zebra finch and the chicken genomes. Interestingly, there was a greater than expected degree of intrachromosomal rearrangements compared to the chicken, suggesting that gene order is not conserved within avian chromosomes. At 1068 cM the map is approximately only one quarter the length of the chicken linkage map, providing further evidence that the chicken has an unusually high recombination rate. Male and female linkage-map lengths were similar, suggesting no heterochiasmy in the zebra finch. This whole-genome map is the first for any passerine and a valuable tool for the zebra finch genome sequence project and for studies of quantitative trait loci.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18493078?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Robinson, Gene E</style></author><author><style face="normal" font="default" size="100%">Fernald, Russell D</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genes and social behavior.</style></title><secondary-title><style face="normal" font="default" size="100%">Science (New York, N.Y.)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Science</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Nov 7</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">322</style></volume><pages><style face="normal" font="default" size="100%">896-900</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">What genes and regulatory sequences contribute to the organization and functioning of neural circuits and molecular pathways in the brain that support social behavior? How does social experience interact with information in the genome to modulate brain activity? Here, we address these questions by highlighting progress that has been made in identifying and understanding two key &quot;vectors of influence&quot; that link genes, the brain, and social behavior: (i) Social information alters gene expression in the brain to influence behavior, and (ii) genetic variation influences brain function and social behavior. We also discuss how evolutionary changes in genomic elements influence social behavior and outline prospects for a systems biology of social behavior.</style></abstract><issue><style face="normal" font="default" size="100%">5903</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18988841?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Harshman, John</style></author><author><style face="normal" font="default" size="100%">Braun, Edward L</style></author><author><style face="normal" font="default" size="100%">Braun, Michael J</style></author><author><style face="normal" font="default" size="100%">Huddleston, Christopher J</style></author><author><style face="normal" font="default" size="100%">Bowie, Rauri C K</style></author><author><style face="normal" font="default" size="100%">Chojnowski, Jena L</style></author><author><style face="normal" font="default" size="100%">Hackett, Shannon J</style></author><author><style face="normal" font="default" size="100%">Han, Kin-Lan</style></author><author><style face="normal" font="default" size="100%">Kimball, Rebecca T</style></author><author><style face="normal" font="default" size="100%">Marks, Ben D</style></author><author><style face="normal" font="default" size="100%">Miglia, Kathleen J</style></author><author><style face="normal" font="default" size="100%">Moore, William S</style></author><author><style face="normal" font="default" size="100%">Reddy, Sushma</style></author><author><style face="normal" font="default" size="100%">Sheldon, Frederick H</style></author><author><style face="normal" font="default" size="100%">Steadman, David W</style></author><author><style face="normal" font="default" size="100%">Steppan, Scott J</style></author><author><style face="normal" font="default" size="100%">Witt, Christopher C</style></author><author><style face="normal" font="default" size="100%">Yuri, Tamaki</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Phylogenomic evidence for multiple losses of flight in ratite birds.</style></title><secondary-title><style face="normal" font="default" size="100%">Proceedings of the National Academy of Sciences of the United States of America</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Natl. Acad. Sci. U.S.A.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2008</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2008 Sep 9</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">105</style></volume><pages><style face="normal" font="default" size="100%">13462-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Ratites (ostriches, emus, rheas, cassowaries, and kiwis) are large, flightless birds that have long fascinated biologists. Their current distribution on isolated southern land masses is believed to reflect the breakup of the paleocontinent of Gondwana. The prevailing view is that ratites are monophyletic, with the flighted tinamous as their sister group, suggesting a single loss of flight in the common ancestry of ratites. However, phylogenetic analyses of 20 unlinked nuclear genes reveal a genome-wide signal that unequivocally places tinamous within ratites, making ratites polyphyletic and suggesting multiple losses of flight. Phenomena that can mislead phylogenetic analyses, including long branch attraction, base compositional bias, discordance between gene trees and species trees, and sequence alignment errors, have been eliminated as explanations for this result. The most plausible hypothesis requires at least three losses of flight and explains the many morphological and behavioral similarities among ratites by parallel or convergent evolution. Finally, this phylogeny demands fundamental reconsideration of proposals that relate ratite evolution to continental drift.</style></abstract><issue><style face="normal" font="default" size="100%">36</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/18765814?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Costantini, Maria</style></author><author><style face="normal" font="default" size="100%">Cammarano, Rosalia</style></author><author><style face="normal" font="default" size="100%">Bernardi, Giorgio</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The evolution of isochore patterns in vertebrate genomes.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">146</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Previous work from our laboratory showed that (i) vertebrate genomes are mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous in base composition; (ii) isochores belong to a small number of families (five in the human genome) characterized by different GC levels; (iii) isochore family patterns are different in fishes/amphibians and mammals/birds, the latter showing GC-rich isochore families that are absent or very scarce in the former; (iv) there are two modes of genome evolution, a conservative one in which isochore patterns basically do not change (e.g., among mammalian orders), and a transitional one, in which they do change (e.g., between amphibians and mammals); and (v) isochores are tightly linked to a number of basic biological properties, such as gene density, gene expression, replication timing and recombination. RESULTS: The present availability of a number of fully sequenced genomes ranging from fishes to mammals allowed us to carry out investigations that (i) more precisely quantified our previous conclusions; (ii) showed that the different isochore families of vertebrate genomes are largely conserved in GC levels and dinucleotide frequencies, as well as in isochore size; and (iii) isochore family patterns can be either conserved or change within both warm- and cold-blooded vertebrates. CONCLUSION: On the basis of the results presented, we propose that (i) the large conservation of GC levels and dinucleotide frequencies may reflect the conservation of chromatin structures; (ii) the conservation of isochore size may be linked to the role played by isochores in chromosome structure and replication; (iii) the formation, the maintainance and the changes of isochore patterns are due to natural selection.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19344507?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Fox, Samuel</style></author><author><style face="normal" font="default" size="100%">Filichkin, Sergei</style></author><author><style face="normal" font="default" size="100%">Mockler, Todd C</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Applications of ultra-high-throughput sequencing.</style></title><secondary-title><style face="normal" font="default" size="100%">Methods in molecular biology (Clifton, N.J.)</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Methods Mol. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">553</style></volume><pages><style face="normal" font="default" size="100%">79-108</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The genomics era has enabled scientists to more readily pose truly global questions regarding mutation, evolution, gene and genome structure, function, and regulation. Just as Sanger sequencing ushered in a paradigm shift that enabled the molecular basis of biological questions to be directly addressed, to an even greater degree, ultra-high-throughput DNA sequencing is poised to dramatically change the nature of biological research. New sequencing technologies have opened the door for novel questions to be addressed at the level of the entire genome in the areas of comparative genomics, systems biology, metagenomics, and genome biology. These new sequencing technologies provide a tremendous amount of DNA sequence data to be collected at an astounding pace, with reduced costs, effort, and time as compared to Sanger sequencing. Applications of ultra-high-throughput sequencing (UHTS) are essentially limited only by the imaginations of researchers, and include genome sequencing/resequencing, small RNA discovery, deep SNP discovery, chromatin immunoprecipitation (ChIP) and RNA immunoprecipitation (RIP) coupled with sequence identification, transcriptome analysis including empirical annotation, discovery and characterization of alternative splicing, and gene expression profiling. This technology will have a profound impact on plant breeding, biotechnology, and our fundamental understanding of plant evolution, development, and environmental responses. In this chapter, we provide an overview of UHTS approaches and their applications. We also describe a protocol we have developed for deep sequencing of plant transcriptomes using the Illumina/Solexa sequencing platform.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19588102?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Tomaszycki, Michelle L</style></author><author><style face="normal" font="default" size="100%">Peabody, Camilla</style></author><author><style face="normal" font="default" size="100%">Replogle, Kirstin</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author><author><style face="normal" font="default" size="100%">Tempelman, Robert J</style></author><author><style face="normal" font="default" size="100%">Wade, Juli</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Sexual differentiation of the zebra finch song system: potential roles for sex chromosome genes.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC neuroscience</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Neurosci</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">24</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Recent evidence suggests that some sex differences in brain and behavior might result from direct genetic effects, and not solely the result of the organizational effects of steroid hormones. The present study examined the potential role for sex-biased gene expression during development of sexually dimorphic singing behavior and associated song nuclei in juvenile zebra finches. RESULTS: A microarray screen revealed more than 2400 putative genes (with a false discovery rate less than 0.05) exhibiting sex differences in the telencephalon of developing zebra finches. Increased expression in males was confirmed in 12 of 20 by qPCR using cDNA from the whole telencephalon; all of these appeared to be located on the Z sex chromosome. Six of the genes also showed increased expression in one or more of the song control nuclei of males at post-hatching day 25. Although the function of half of the genes is presently unknown, we have identified three as: 17-beta-hydroxysteroid dehydrogenase type IV, methylcrotonyl-CoA carboxylase, and sorting nexin 2. CONCLUSION: The data suggest potential influences of these genes in song learning and/or masculinization of song system morphology, both of which are occurring at this developmental stage.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19309515?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Southey, Bruce R</style></author><author><style face="normal" font="default" size="100%">Rodriguez-Zas, Sandra L</style></author><author><style face="normal" font="default" size="100%">Sweedler, Jonathan V</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">228</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: Neuropeptides are cell to cell signalling molecules that regulate many critical biological processes including development, growth and reproduction. These peptides result from the complex processing of prohormone proteins, making their characterization both challenging and resource demanding. In fact, only 42 neuropeptide genes have been empirically confirmed in cattle. Neuropeptide research using high-throughput technologies such as microarray and mass spectrometry require accurate annotation of prohormone genes and products. However, the annotation and associated prediction efforts, when based solely on sequence homology to species with known neuropeptides, can be problematic. RESULTS: Complementary bioinformatic resources were integrated in the first survey of the cattle neuropeptide complement. Functional neuropeptide characterization was based on gene expression profiles from microarray experiments. Once a gene is identified, knowledge of the enzymatic processing allows determination of the final products. Prohormone cleavage sites were predicted using several complementary cleavage prediction models and validated against known cleavage sites in cattle and other species. Our bioinformatics approach identified 92 cattle prohormone genes, with 84 of these supported by expressed sequence tags. Notable findings included an absence of evidence for a cattle relaxin 1 gene and evidence for a cattle galanin-like peptide pseudogene. The prohormone processing predictions are likely accurate as the mammalian proprotein convertase enzymes, except for proprotein convertase subtilisin/kexin type 9, were also identified. Microarray analysis revealed the differential expression of 21 prohormone genes in the liver associated with nutritional status and 8 prohormone genes in the placentome of embryos generated using different reproductive techniques. The neuropeptide cleavage prediction models had an exceptional performance, correctly predicting cleavage in more than 86% of the prohormone sequence positions. CONCLUSION: A substantial increase in the number of cattle prohormone genes identified and insights into the expression profiles of neuropeptide genes were obtained from the integration of bioinformatics tools and database resources and gene expression information. Approximately 20 prohormones with no empirical evidence were detected and the prohormone cleavage sites were predicted with high accuracy. Most prohormones were supported by expressed sequence tag data and many were differentially expressed across nutritional and reproductive conditions. The complete set of cattle prohormone sequences identified and the cleavage prediction approaches are available at http://neuroproteomics.scs.uiuc.edu/neuropred.html.</style></abstract><accession-num><style face="normal" font="default" size="100%">19445702</style></accession-num><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19445702?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kassahn, Karin S</style></author><author><style face="normal" font="default" size="100%">Dang, Vinh T</style></author><author><style face="normal" font="default" size="100%">Wilkins, Simon J</style></author><author><style face="normal" font="default" size="100%">Perkins, Andrew C</style></author><author><style face="normal" font="default" size="100%">Ragan, Mark A</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Aug</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">19</style></volume><pages><style face="normal" font="default" size="100%">1404-18</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The significance of whole-genome duplications (WGD) for vertebrate evolution remains controversial, in part because the mechanisms by which WGD contributed to functional evolution or speciation are still incompletely characterized. Fish genomes provide an ideal context in which to examine the consequences of WGD, because the teleost lineage experienced an additional WGD soon after divergence from tetrapods and because five teleost genomes are available for comparative analysis. Here we present an integrated approach to characterize these post-duplication genomes based on genome-scale synteny, phylogenetic, temporal, and spatial gene expression and on protein sequence data. A minimum of 3%-4% of protein-coding loci have been retained in two copies in each of the five fish genomes, and many of these duplicates are key developmental genes that function as transcription factors or signaling molecules. Almost all duplicate gene pairs we examined have diverged in spatial and/or temporal expression during embryogenesis. A quarter of duplicate pairs have diverged in function via the acquisition of novel protein domains or via changes in the subcellular localization of their encoded proteins. We compared the spatial expression and protein domain architecture of zebrafish WGD-duplicates to those of their single mouse ortholog and found many examples supporting a model of neofunctionalization. WGD-duplicates have acquired novel protein domains more often than have single-copy genes. Post-WGD changes at the gene regulatory level were more common than changes at the protein level. We conclude that the most significant consequence of WGD for vertebrate evolution has been to enable more-specialized regulatory control of development via the acquisition of novel spatiotemporal expression domains. We find limited evidence that reciprocal gene loss led to reproductive isolation and speciation in this lineage.</style></abstract><issue><style face="normal" font="default" size="100%">8</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19439512?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Navratilova, Pavla</style></author><author><style face="normal" font="default" size="100%">Becker, Thomas S</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genomic regulatory blocks in vertebrates and implications in human disease.</style></title><secondary-title><style face="normal" font="default" size="100%">Briefings in functional genomics &amp; proteomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Brief Funct Genomic Proteomic</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Jul</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">333-42</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Despite a recent explosion in the production of vertebrate genome sequence data and large-scale efforts to completely annotate the human genome, we still have scant knowledge of the principles that built vertebrate genomes in evolution, and of genome architecture and its functional significance. We review approaches using bioinformatics, zebrafish transgenesis, and recent findings in the molecular basis of gene regulation and tie these in with mechanisms for the maintenance of long-range conserved synteny across all vertebrate genomes. Specifically, we discuss the recently discovered genomic regulatory blocks which we argue are principal units of vertebrate genome evolution and serve as the foundations onto which evolutionary innovations are built through sequence evolution and insertion of new cis-regulatory elements. We subsequently discuss how these arrangements relate to common human heritable diseases and their significance in disease causality.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19561171?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Smith, Jeramiah J</style></author><author><style face="normal" font="default" size="100%">Antonacci, Francesca</style></author><author><style face="normal" font="default" size="100%">Eichler, Evan E</style></author><author><style face="normal" font="default" size="100%">Amemiya, Chris T</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Programmed loss of millions of base pairs from a vertebrate genome.</style></title><secondary-title><style face="normal" font="default" size="100%">Proceedings of the National Academy of Sciences of the United States of America</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Proc. Natl. Acad. Sci. U.S.A.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Jul 7</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">106</style></volume><pages><style face="normal" font="default" size="100%">11212-7</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">In general, the strict preservation of broad-scale structure is thought to be critical for maintaining the precisely tuned functionality of vertebrate genomes, although nearly all vertebrate species undergo a small number of programmed local rearrangements during development (e.g., remodeling of adaptive immune receptor loci). However, a limited number of metazoan species undergo much more extensive reorganizations as a normal feature of their development. Here, we show that the sea lamprey (Petromyzon marinus), a jawless vertebrate, undergoes a dramatic remodeling of its genome, resulting in the elimination of hundreds of millions of base pairs (and at least one transcribed locus) from many somatic cell lineages during embryonic development. These studies reveal the highly dynamic nature of the lamprey genome and provide the first example of broad-scale programmed rearrangement of a definitively vertebrate genome. Understanding the mechanisms by which this vertebrate species regulates such extensive remodeling of its genome will provide invaluable insight into factors that can promote stability and change in vertebrate genomes.</style></abstract><issue><style face="normal" font="default" size="100%">27</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19561299?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Turner, Daniel J</style></author><author><style face="normal" font="default" size="100%">Keane, Thomas M</style></author><author><style face="normal" font="default" size="100%">Sudbery, Ian</style></author><author><style face="normal" font="default" size="100%">Adams, David J</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Next-generation sequencing of vertebrate experimental organisms.</style></title><secondary-title><style face="normal" font="default" size="100%">Mammalian genome : official journal of the International Mammalian Genome Society</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Mamm. Genome</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20</style></volume><pages><style face="normal" font="default" size="100%">327-38</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Next-generation sequencing technologies are revolutionizing biology by allowing for genome-wide transcription factor binding-site profiling, transcriptome sequencing, and more recently, whole-genome resequencing. While it is currently not possible to generate complete de novo assemblies of higher-vertebrate genomes using next-generation sequencing, improvements in sequence read lengths and throughput, coupled with new assembly algorithms for large data sets, will soon make this a reality. These developments will in turn spawn a revolution in how genomic data are used to understand genetics and how model organisms are used for disease gene discovery. This review provides an overview of the current next-generation sequencing platforms and the newest computational tools for the analysis of next-generation sequencing data. We also describe how next-generation sequencing may be applied in the context of vertebrate model organism genetics.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19452216?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">London, Sarah E</style></author><author><style face="normal" font="default" size="100%">Dong, Shu</style></author><author><style face="normal" font="default" size="100%">Replogle, Kirstin</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Developmental shifts in gene expression in the auditory forebrain during the sensitive period for song learning.</style></title><secondary-title><style face="normal" font="default" size="100%">Developmental neurobiology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Dev Neurobiol</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Jun</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">69</style></volume><pages><style face="normal" font="default" size="100%">437-50</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">A male zebra finch begins to learn to sing by memorizing a tutor's song during a sensitive period in juvenile development. Tutor song memorization requires molecular signaling within the auditory forebrain. Using microarray and in situ hybridizations, we tested whether the auditory forebrain at an age just before tutoring expresses a different set of genes compared with later life after song learning has ceased. Microarray analysis revealed differences in expression of thousands of genes in the male auditory forebrain at posthatch day 20 (P20) compared with adulthood. Furthermore, song playbacks had essentially no impact on gene expression in P20 auditory forebrain, but altered expression of hundreds of genes in adults. Most genes that were song-responsive in adults were expressed at constitutively high levels at P20. Using in situ hybridization with a representative sample of 44 probes, we confirmed these effects and found that birds at P20 and P45 were similar in their gene expression patterns. Additionally, eight of the probes showed male-female differences in expression. We conclude that the developing auditory forebrain is in a very different molecular state from the adult, despite its relatively mature gross morphology and electrophysiological responsiveness to song stimuli. Developmental gene expression changes may contribute to fine-tuning of cellular and molecular properties necessary for song learning.</style></abstract><issue><style face="normal" font="default" size="100%">7</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19360720?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><translated-authors><author><style face="normal" font="default" size="100%">Genome 10K Community of Scientists</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species.</style></title><secondary-title><style face="normal" font="default" size="100%">The Journal of heredity</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Hered.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Nov-Dec</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">100</style></volume><pages><style face="normal" font="default" size="100%">659-74</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The human genome project has been recently complemented by whole-genome assessment sequence of 32 mammals and 24 nonmammalian vertebrate species suitable for comparative genomic analyses. Here we anticipate a precipitous drop in costs and increase in sequencing efficiency, with concomitant development of improved annotation technology and, therefore, propose to create a collection of tissue and DNA specimens for 10,000 vertebrate species specifically designated for whole-genome sequencing in the very near future. For this purpose, we, the Genome 10K Community of Scientists (G10KCOS), will assemble and allocate a biospecimen collection of some 16,203 representative vertebrate species spanning evolutionary diversity across living mammals, birds, nonavian reptiles, amphibians, and fishes (ca. 60,000 living species). In this proposal, we present precise counts for these 16,203 individual species with specimens presently tagged and stipulated for DNA sequencing by the G10KCOS. DNA sequencing has ushered in a new era of investigation in the biological sciences, allowing us to embark for the first time on a truly comprehensive study of vertebrate evolution, the results of which will touch nearly every aspect of vertebrate biological enquiry.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19892720?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Clayton, David F</style></author><author><style face="normal" font="default" size="100%">Balakrishnan, Christopher N</style></author><author><style face="normal" font="default" size="100%">London, Sarah E</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Integrating genomes, brain and behavior in the study of songbirds.</style></title><secondary-title><style face="normal" font="default" size="100%">Current biology : CB</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Curr. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2009</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2009 Sep 29</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">19</style></volume><pages><style face="normal" font="default" size="100%">R865-73</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Songbirds share some essential traits but are extraordinarily diverse, allowing comparative analyses aimed at identifying specific genotype-phenotype associations. This diversity encompasses traits like vocal communication and complex social behaviors that are of great interest to humans, but that are not well represented in other accessible research organisms. Many songbirds are readily observable in nature and thus afford unique insight into the links between environment and organism. The distinctive organization of the songbird brain will facilitate analysis of genomic links to brain and behavior. Access to the zebra finch genome sequence will, therefore, prompt new questions and provide the ability to answer those questions.</style></abstract><issue><style face="normal" font="default" size="100%">18</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/19788884?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Blakesley, Robert W</style></author><author><style face="normal" font="default" size="100%">Hansen, Nancy F</style></author><author><style face="normal" font="default" size="100%">Gupta, Jyoti</style></author><author><style face="normal" font="default" size="100%">McDowell, Jennifer C</style></author><author><style face="normal" font="default" size="100%">Maskeri, Baishali</style></author><author><style face="normal" font="default" size="100%">Barnabas, Beatrice B</style></author><author><style face="normal" font="default" size="100%">Brooks, Shelise Y</style></author><author><style face="normal" font="default" size="100%">Coleman, Holly</style></author><author><style face="normal" font="default" size="100%">Haghighi, Payam</style></author><author><style face="normal" font="default" size="100%">Ho, Shi-Ling</style></author><author><style face="normal" font="default" size="100%">Schandler, Karen</style></author><author><style face="normal" font="default" size="100%">Stantripop, Sirintorn</style></author><author><style face="normal" font="default" size="100%">Vogt, Jennifer L</style></author><author><style face="normal" font="default" size="100%">Thomas, Pamela J</style></author><author><style face="normal" font="default" size="100%">Bouffard, Gerard G</style></author><author><style face="normal" font="default" size="100%">Green, Eric D</style></author></authors><translated-authors><author><style face="normal" font="default" size="100%">NISC Comparative Sequencing Program</style></author></translated-authors></contributors><titles><title><style face="normal" font="default" size="100%">Effort required to finish shotgun-generated genome sequences differs significantly among vertebrates.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC genomics</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Genomics</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">21</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">BACKGROUND: The approaches for shotgun-based sequencing of vertebrate genomes are now well-established, and have resulted in the generation of numerous draft whole-genome sequence assemblies. In contrast, the process of refining those assemblies to improve contiguity and increase accuracy (known as 'sequence finishing') remains tedious, labor-intensive, and expensive. As a result, the vast majority of vertebrate genome sequences generated to date remain at a draft stage. RESULTS: To date, our genome sequencing efforts have focused on comparative studies of targeted genomic regions, requiring sequence finishing of large blocks of orthologous sequence (average size 0.5-2 Mb) from various subsets of 75 vertebrates. This experience has provided a unique opportunity to compare the relative effort required to finish shotgun-generated genome sequence assemblies from different species, which we report here. Importantly, we found that the sequence assemblies generated for the same orthologous regions from various vertebrates show substantial variation with respect to misassemblies and, in particular, the frequency and characteristics of sequence gaps. As a consequence, the work required to finish different species' sequences varied greatly. Application of the same standardized methods for finishing provided a novel opportunity to &quot;assay&quot; characteristics of genome sequences among many vertebrate species. It is important to note that many of the problems we have encountered during sequence finishing reflect unique architectural features of a particular vertebrate's genome, which in some cases may have important functional and/or evolutionary implications. Finally, based on our analyses, we have been able to improve our procedures to overcome some of these problems and to increase the overall efficiency of the sequence-finishing process, although significant challenges still remain. CONCLUSION: Our findings have important implications for the eventual finishing of the draft whole-genome sequences that have now been generated for a large number of vertebrates.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20064230?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Greenwold, Matthew J</style></author><author><style face="normal" font="default" size="100%">Sawyer, Roger H</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genomic organization and molecular phylogenies of the beta (beta) keratin multigene family in the chicken (Gallus gallus) and zebra finch (Taeniopygia guttata): implications for feather evolution.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC evolutionary biology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">BMC Evol. Biol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">10</style></volume><pages><style face="normal" font="default" size="100%">148</style></pages><abstract><style face="normal" font="default" size="100%">BACKGROUND: The epidermal appendages of reptiles and birds are constructed of beta (beta) keratins. The molecular phylogeny of these keratins is important to understanding the evolutionary origin of these appendages, especially feathers. Knowing that the crocodilian beta-keratin genes are closely related to those of birds, the published genomes of the chicken and zebra finch provide an opportunity not only to compare the genomic organization of their beta-keratins, but to study their molecular evolution in archosaurians. RESULTS: The subfamilies (claw, feather, feather-like, and scale) of beta-keratin genes are clustered in the same 5' to 3' order on microchromosome 25 in chicken and zebra finch, although the number of claw and feather genes differs between the species. Molecular phylogenies show that the monophyletic scale genes are the basal group within birds and that the monophyletic avian claw genes form the basal group to all feather and feather-like genes. Both species have a number of feather clades on microchromosome 27 that form monophyletic groups. An additional monophyletic cluster of feather genes exist on macrochromosome 2 for each species. Expression sequence tag analysis for the chicken demonstrates that all feather beta-keratin clades are expressed. CONCLUSIONS: Similarity in the overall genomic organization of beta-keratins in Galliformes and Passeriformes suggests similar organization in all Neognathae birds, and perhaps in the ancestral lineages leading to modern birds, such as the paravian Anchiornis huxleyi. Phylogenetic analyses demonstrate that evolution of archosaurian epidermal appendages in the lineage leading to birds was accompanied by duplication and divergence of an ancestral beta-keratin gene cluster. As morphological diversification of epidermal appendages occurred and the beta-keratin multigene family expanded, novel beta-keratin genes were selected for novel functions within appendages such as feathers.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20482795?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Völker, Martin</style></author><author><style face="normal" font="default" size="100%">Backström, Niclas</style></author><author><style face="normal" font="default" size="100%">Skinner, Benjamin M</style></author><author><style face="normal" font="default" size="100%">Langley, Elizabeth J</style></author><author><style face="normal" font="default" size="100%">Bunzey, Sydney K</style></author><author><style face="normal" font="default" size="100%">Ellegren, Hans</style></author><author><style face="normal" font="default" size="100%">Griffin, Darren K</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20</style></volume><pages><style face="normal" font="default" size="100%">503-11</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the zebra finch, provides, for the first time, an ideal opportunity to analyze the relationship between structural genomic variation (chromosomal and CNV) and recombination on a genome-wide level. The aims of this study were therefore threefold: (1) to combine bioinformatics, physical mapping to produce comprehensive comparative maps of the genomes of chicken and zebra finch. In so doing, this allowed the identification of evolutionary chromosomal rearrangements distinguishing them. The previously reported interchromosomal conservation of synteny was confirmed, but a larger than expected number of intrachromosomal rearrangements were reported; (2) to hybridize zebra finch genomic DNA to a chicken tiling path microarray and identify CNVs in the zebra finch genome relative to chicken; 32 interspecific CNVs were identified; and (3) to test the hypothesis that there is an association between CNV, chromosomal rearrangements, and recombination by correlating data from (1) and (2) with recombination rate data from a high-resolution genetic linkage map of the zebra finch. We found a highly significant association of both chromosomal rearrangements and CNVs with elevated recombination rates. The results thus provide support for the notion of recombination-based processes playing a major role in avian genome evolution.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20357050?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Stapley, Jessica</style></author><author><style face="normal" font="default" size="100%">Birkhead, Tim R</style></author><author><style face="normal" font="default" size="100%">Burke, Terry</style></author><author><style face="normal" font="default" size="100%">Slate, Jon</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20</style></volume><pages><style face="normal" font="default" size="100%">496-502</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">The extent of nonrandom association of alleles at two or more loci, termed linkage disequilibrium (LD), can reveal much about population demography, selection, and recombination rate, and is a key consideration when designing association mapping studies. Here, we describe a genome-wide analysis of LD in the zebra finch (Taeniopygia guttata) using 838 single nucleotide polymorphisms and present LD maps for all assembled chromosomes. We found that LD declined with physical distance approximately five times faster on the microchromosomes compared to macrochromosomes. The distribution of LD across individual macrochromosomes also varied in a distinct pattern. In the center of the macrochromosomes there were large blocks of markers, sometimes spanning tens of mega bases, in strong LD whereas on the ends of macrochromosomes LD declined more rapidly. Regions of high LD were not simply the result of suppressed recombination around the centromere and this pattern has not been observed previously in other taxa. We also found evidence that this pattern of LD has remained stable across many generations. The variability in LD between and within chromosomes has important implications for genome wide association studies in birds and for our understanding of the distribution of recombination events and the processes that govern them.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20357051?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Backström, Niclas</style></author><author><style face="normal" font="default" size="100%">Forstmeier, Wolfgang</style></author><author><style face="normal" font="default" size="100%">Schielzeth, Holger</style></author><author><style face="normal" font="default" size="100%">Mellenius, Harriet</style></author><author><style face="normal" font="default" size="100%">Nam, Kiwoong</style></author><author><style face="normal" font="default" size="100%">Bolund, Elisabeth</style></author><author><style face="normal" font="default" size="100%">Webster, Matthew T</style></author><author><style face="normal" font="default" size="100%">Ost, Torbjörn</style></author><author><style face="normal" font="default" size="100%">Schneider, Melanie</style></author><author><style face="normal" font="default" size="100%">Kempenaers, Bart</style></author><author><style face="normal" font="default" size="100%">Ellegren, Hans</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The recombination landscape of the zebra finch Taeniopygia guttata genome.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20</style></volume><pages><style face="normal" font="default" size="100%">485-95</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single nucleotide polymorphisms in a multigeneration pedigree of more than 1000 zebra finches (Taeniopygia guttata) to develop a genetic linkage map, and then we used these map data together with the recently available draft genome sequence of the zebra finch to estimate recombination rates in 1 Mb intervals across the genome. The average zebra finch recombination rate (1.5 cM/Mb) is higher than in humans, but significantly lower than in chicken. The local rates of recombination in chicken and zebra finch were only weakly correlated, demonstrating evolutionary turnover of the recombination landscape in birds. The distribution of recombination events was heavily biased toward ends of chromosomes, with a stronger telomere effect than so far seen in any organism. In fact, the recombination rate was as low as 0.1 cM/Mb in intervals up to 100 Mb long in the middle of the larger chromosomes. We found a positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs. Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20357052?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Itoh, Yuichiro</style></author><author><style face="normal" font="default" size="100%">Replogle, Kirstin</style></author><author><style face="normal" font="default" size="100%">Kim, Yong-Hwan</style></author><author><style face="normal" font="default" size="100%">Wade, Juli</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author><author><style face="normal" font="default" size="100%">Arnold, Arthur P</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Sex bias and dosage compensation in the zebra finch versus chicken genomes: general and specialized patterns among birds.</style></title><secondary-title><style face="normal" font="default" size="100%">Genome research</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Genome Res.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">20</style></volume><pages><style face="normal" font="default" size="100%">512-8</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">We compared global patterns of gene expression between two bird species, the chicken and zebra finch, with regard to sex bias of autosomal versus Z chromosome genes, dosage compensation, and evolution of sex bias. Both species appear to lack a Z chromosome-wide mechanism of dosage compensation, because both have a similar pattern of significantly higher expression of Z genes in males relative to females. Unlike the chicken Z chromosome, which has female-specific expression of the noncoding RNA MHM (male hypermethylated) and acetylation of histone 4 lysine 16 (H4K16) near MHM, the zebra finch Z chromosome appears to lack the MHM sequence and acetylation of H4K16. The zebra finch also does not show the reduced male-to-female (M:F) ratio of gene expression near MHM similar to that found in the chicken. Although the M:F ratios of Z chromosome gene expression are similar across tissues and ages within each species, they differ between the two species. Z genes showing the greatest species difference in M:F ratio were concentrated near the MHM region of the chicken Z chromosome. This study shows that the zebra finch differs from the chicken because it lacks a specialized region of greater dosage compensation along the Z chromosome, and shows other differences in sex bias. These patterns suggest that different avian taxa may have evolved specific compensatory mechanisms.</style></abstract><issue><style face="normal" font="default" size="100%">4</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20357053?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Warren, Wesley C</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author><author><style face="normal" font="default" size="100%">Ellegren, Hans</style></author><author><style face="normal" font="default" size="100%">Arnold, Arthur P</style></author><author><style face="normal" font="default" size="100%">LaDeana W. Hillier</style></author><author><style face="normal" font="default" size="100%">Künstner, Axel</style></author><author><style face="normal" font="default" size="100%">Searle, Steve</style></author><author><style face="normal" font="default" size="100%">White, Simon</style></author><author><style face="normal" font="default" size="100%">Vilella, Albert J</style></author><author><style face="normal" font="default" size="100%">Fairley, Susan</style></author><author><style face="normal" font="default" size="100%">Heger, Andreas</style></author><author><style face="normal" font="default" size="100%">Kong, Lesheng</style></author><author><style face="normal" font="default" size="100%">Chris P. Ponting</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author><author><style face="normal" font="default" size="100%">Mello, Claudio V</style></author><author><style face="normal" font="default" size="100%">Minx, Pat</style></author><author><style face="normal" font="default" size="100%">Lovell, Peter</style></author><author><style face="normal" font="default" size="100%">Velho, Tarciso A F</style></author><author><style face="normal" font="default" size="100%">Ferris, Margaret</style></author><author><style face="normal" font="default" size="100%">Balakrishnan, Christopher N</style></author><author><style face="normal" font="default" size="100%">Sinha, Saurabh</style></author><author><style face="normal" font="default" size="100%">Blatti, Charles</style></author><author><style face="normal" font="default" size="100%">London, Sarah E</style></author><author><style face="normal" font="default" size="100%">Li, Yun</style></author><author><style face="normal" font="default" size="100%">Lin, Ya-Chi</style></author><author><style face="normal" font="default" size="100%">George, Julia</style></author><author><style face="normal" font="default" size="100%">Sweedler, Jonathan</style></author><author><style face="normal" font="default" size="100%">Southey, Bruce</style></author><author><style face="normal" font="default" size="100%">Gunaratne, Preethi</style></author><author><style face="normal" font="default" size="100%">Watson, Michael</style></author><author><style face="normal" font="default" size="100%">Nam, Kiwoong</style></author><author><style face="normal" font="default" size="100%">Backström, Niclas</style></author><author><style face="normal" font="default" size="100%">Smeds, Linnea</style></author><author><style face="normal" font="default" size="100%">Nabholz, Benoit</style></author><author><style face="normal" font="default" size="100%">Itoh, Yuichiro</style></author><author><style face="normal" font="default" size="100%">Whitney, Osceola</style></author><author><style face="normal" font="default" size="100%">Pfenning, Andreas R</style></author><author><style face="normal" font="default" size="100%">Howard, Jason</style></author><author><style face="normal" font="default" size="100%">Völker, Martin</style></author><author><style face="normal" font="default" size="100%">Skinner, Bejamin M</style></author><author><style face="normal" font="default" size="100%">Griffin, Darren K</style></author><author><style face="normal" font="default" size="100%">Ye, Liang</style></author><author><style face="normal" font="default" size="100%">McLaren, William M</style></author><author><style face="normal" font="default" size="100%">Flicek, Paul</style></author><author><style face="normal" font="default" size="100%">Quesada, Victor</style></author><author><style face="normal" font="default" size="100%">Velasco, Gloria</style></author><author><style face="normal" font="default" size="100%">Lopez-Otin, Carlos</style></author><author><style face="normal" font="default" size="100%">Puente, Xose S</style></author><author><style face="normal" font="default" size="100%">Olender, Tsviya</style></author><author><style face="normal" font="default" size="100%">Lancet, Doron</style></author><author><style face="normal" font="default" size="100%">Smit, Arian F A</style></author><author><style face="normal" font="default" size="100%">Hubley, Robert</style></author><author><style face="normal" font="default" size="100%">Konkel, Miriam K</style></author><author><style face="normal" font="default" size="100%">Walker, Jerilyn A</style></author><author><style face="normal" font="default" size="100%">Batzer, Mark A</style></author><author><style face="normal" font="default" size="100%">Gu, Wanjun</style></author><author><style face="normal" font="default" size="100%">Pollock, David D</style></author><author><style face="normal" font="default" size="100%">Chen, Lin</style></author><author><style face="normal" font="default" size="100%">Cheng, Ze</style></author><author><style face="normal" font="default" size="100%">Eichler, Evan E</style></author><author><style face="normal" font="default" size="100%">Stapley, Jessica</style></author><author><style face="normal" font="default" size="100%">Slate, Jon</style></author><author><style face="normal" font="default" size="100%">Ekblom, Robert</style></author><author><style face="normal" font="default" size="100%">Birkhead, Tim</style></author><author><style face="normal" font="default" size="100%">Burke, Terry</style></author><author><style face="normal" font="default" size="100%">Burt, David</style></author><author><style face="normal" font="default" size="100%">Scharff, Constance</style></author><author><style face="normal" font="default" size="100%">Adam, Iris</style></author><author><style face="normal" font="default" size="100%">Richard, Hugues</style></author><author><style face="normal" font="default" size="100%">Sultan, Marc</style></author><author><style face="normal" font="default" size="100%">Soldatov, Alexey</style></author><author><style face="normal" font="default" size="100%">Lehrach, Hans</style></author><author><style face="normal" font="default" size="100%">Edwards, Scott V</style></author><author><style face="normal" font="default" size="100%">Yang, Shiaw-Pyng</style></author><author><style face="normal" font="default" size="100%">Li, Xiaoching</style></author><author><style face="normal" font="default" size="100%">Graves, Tina</style></author><author><style face="normal" font="default" size="100%">Fulton, Lucinda</style></author><author><style face="normal" font="default" size="100%">Nelson, Joanne</style></author><author><style face="normal" font="default" size="100%">Chinwalla, Asif</style></author><author><style face="normal" font="default" size="100%">Hou, Shunfeng</style></author><author><style face="normal" font="default" size="100%">Mardis, Elaine R</style></author><author><style face="normal" font="default" size="100%">Wilson, Richard K</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The genome of a songbird.</style></title><secondary-title><style face="normal" font="default" size="100%">Nature</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Nature</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">genome</style></keyword><keyword><style  face="normal" font="default" size="100%">songbird</style></keyword><keyword><style  face="normal" font="default" size="100%">zebra finch</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr 1</style></date></pub-dates></dates><urls><web-urls><url><style face="normal" font="default" size="100%">http://www.nature.com/nature/journal/v464/n7289/full/nature08819.html</style></url></web-urls></urls><volume><style face="normal" font="default" size="100%">464</style></volume><pages><style face="normal" font="default" size="100%">757-62</style></pages><abstract><style face="normal" font="default" size="100%">The zebra finch is an important model organism in several fields with unique relevance to human neuroscience. Like other songbirds, the zebra finch communicates through learned vocalizations, an ability otherwise documented only in humans and a few other animals and lacking in the chicken-the only bird with a sequenced genome until now. Here we present a structural, functional and comparative analysis of the genome sequence of the zebra finch (Taeniopygia guttata), which is a songbird belonging to the large avian order Passeriformes. We find that the overall structures of the genomes are similar in zebra finch and chicken, but they differ in many intrachromosomal rearrangements, lineage-specific gene family expansions, the number of long-terminal-repeat-based retrotransposons, and mechanisms of sex chromosome dosage compensation. We show that song behaviour engages gene regulatory networks in the zebra finch brain, altering the expression of long non-coding RNAs, microRNAs, transcription factors and their targets. We also show evidence for rapid molecular evolution in the songbird lineage of genes that are regulated during song experience. These results indicate an active involvement of the genome in neural processes underlying vocal communication and identify potential genetic substrates for the evolution and regulation of this behaviour.</style></abstract><issue><style face="normal" font="default" size="100%">7289</style></issue><accession-num><style face="normal" font="default" size="100%">20360741</style></accession-num><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20360741?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Balakrishnan, Christopher N</style></author><author><style face="normal" font="default" size="100%">Ekblom, Robert</style></author><author><style face="normal" font="default" size="100%">Volker, Martin</style></author><author><style face="normal" font="default" size="100%">Westerdahl, Helena</style></author><author><style face="normal" font="default" size="100%">Godinez, Ricardo</style></author><author><style face="normal" font="default" size="100%">Kotkiewicz, Holly</style></author><author><style face="normal" font="default" size="100%">David W. Burt</style></author><author><style face="normal" font="default" size="100%">Graves, Tina</style></author><author><style face="normal" font="default" size="100%">Griffin, Darren K</style></author><author><style face="normal" font="default" size="100%">Warren, Wesley C</style></author><author><style face="normal" font="default" size="100%">Edwards, Scott V</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Gene duplication and fragmentation in the zebra finch major histocompatibility complex.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC biology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">29</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">ABSTRACT: BACKGROUND: Due to its high polymorphism and importance for disease resistance, the major histocompatibility complex (MHC) has been an important focus of many vertebrate genome projects. Avian MHC organization is of particular interest because the chicken Gallus gallus, the avian species with the best characterized MHC, possesses a highly streamlined minimal essential MHC, which is linked to resistance against specific pathogens. It remains unclear the extent to which this organization describes the situation in other birds and whether it represents a derived or ancestral condition. The sequencing of the zebra finch Taeniopygia guttata genome, in combination with targeted bacterial artificial chromosome (BAC) sequencing, has allowed us to characterize an MHC from a highly divergent and diverse avian lineage, the passerines. RESULTS: The zebra finch MHC exhibits a complex structure and history involving gene duplication and fragmentation. The zebra finch MHC includes multiple Class I and Class II genes, some of which appear to be pseudogenes, and spans a much more extensive genomic region than the chicken MHC, as evidenced by the presence of MHC genes on each of seven BACs spanning 739 kb. Cytogenetic (FISH) evidence and the genome assembly itself place core MHC genes on as many as four chromosomes with TAP and Class I genes mapping to different chromosomes. MHC Class II regions are further characterized by high endogenous retroviral content. Lastly, we find strong evidence of selection acting on sites within passerine MHC Class I and Class II genes. CONCLUSION: The zebra finch MHC differs markedly from that of the chicken, the only other bird species with a complete genome sequence. The apparent lack of synteny between TAP and the expressed MHC Class I locus is in fact reminiscent of a pattern seen in some mammalian lineages and may represent convergent evolution. Our analyses of the zebra finch MHC suggest a complex history involving chromosomal fission, gene duplication and translocation in the history of the MHC in birds, and highlight striking differences in MHC structure and organization among avian lineages.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20359332?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">London, Sarah E</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Genomic and neural analysis of the estradiol-synthetic pathway in the zebra finch.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC neuroscience</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">46</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">ABSTRACT: BACKGROUND: Steroids are small molecule hormones derived from cholesterol. Steroids affect many tissues, including the brain. In the zebra finch, estrogenic steroids are particularly interesting because they masculinize the neural circuit that controls singing and their synthesis in the brain is modulated by experience. Here, we analyzed the zebra finch genome assembly to assess the content, conservation, and organization of genes that code for components of the estrogen-synthetic pathway and steroid nuclear receptors. Based on these analyses, we also investigated neural expression of a cholesterol transport protein gene in the context of song neurobiology. RESULTS: We present sequence-based analysis of twenty steroid-related genes using the genome assembly and other resources. Generally, zebra finch genes showed high homology to genes in other species. The diversity of steroidogenic enzymes and receptors may be lower in songbirds than in mammals; we were unable to identify all known mammalian isoforms of the 3beta-hydroxysteroid dehydrogenase and 17beta-hydroxysteroid dehydrogenase families in the zebra finch genome assembly, and not all splice sites described in mammals were identified in the corresponding zebra finch genes. We did identify two factors, Nobox and NR1H2-RXR, that may be important for coordinated transcription of multiple steroid-related genes. We found very little qualitative overlap in predicted transcription factor binding sites in the genes for two cholesterol transport proteins, the 18 kDa cholesterol transport protein (TSPO) and steroidogenic acute regulatory protein (StAR). We therefore performed in situ hybridization for TSPO and found that its mRNA was not always detected in brain regions where StAR and steroidogenic enzymes were previously shown to be expressed. Also, transcription of TSPO, but not StAR, may be regulated by the experience of hearing song. CONCLUSIONS: The genes required for estradiol synthesis and action are represented in the zebra finch genome assembly, though the complement of steroidogenic genes may be smaller in birds than in mammals. Coordinated transcription of multiple steroidogenic genes is possible, but results were inconsistent with the hypothesis that StAR and TSPO mRNAs are co-regulated. Integration of genomic and neuroanatomical analyses will continue to provide insights into the evolution and function of steroidogenesis in the songbird brain.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20359328?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Quesada, Victor</style></author><author><style face="normal" font="default" size="100%">Velasco, Gloria</style></author><author><style face="normal" font="default" size="100%">Puente, Xose S</style></author><author><style face="normal" font="default" size="100%">Warren, Wesley C</style></author><author><style face="normal" font="default" size="100%">Lopez-Otin, Carlos</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparative genomic analysis of the zebra finch degradome provides new insights into evolution of proteases in birds and mammals.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC genomics</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">11</style></volume><pages><style face="normal" font="default" size="100%">220</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">ABSTRACT: BACKGROUND: The degradome -the complete repertoire of proteases in an organism- is involved in multiple key biological and pathological processes. Previous studies in several organisms have yielded sets of curated protease sequences which may be used to characterize the degradome in a novel genome by similarity. Differences between degradomes can then be related to physiological traits of the species under study. Therefore, the sequencing of the zebra finch genome allows the comparison between the degradomes of mammals and birds and may help to understand the biological peculiarities of the zebra finch. RESULTS: A set of curated protease sequences from humans and chicken was used to predict the sequences of 460 protease and protease-like genes in the zebra finch genome. This analysis revealed important differences in the evolution of mammalian and bird degradomes, including genomic expansions and deletions of caspases, cytotoxic proteases, kallikreins, matrix metalloproteases, and trypsin-like proteases. Furthermore, we found several zebra finch-specific features, such as duplications in CASP3 and BACE, and a large genomic expansion of acrosin. CONCLUSIONS: We have compared the degradomes of zebra finch, chicken and several mammalian species, with the finding of multiple differences which illustrate the evolution of the protease complement of these organisms. Detailed analysis of these changes in zebra finch proteases has shown that they are mainly related to immunological, developmental, reproductive and neural functions.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20359326?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Hellgren, Olof</style></author><author><style face="normal" font="default" size="100%">Ekblom, Robert</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Evolution of a cluster of innate immune genes (beta-defensins) along the ancestral lines of chicken and zebra finch.</style></title><secondary-title><style face="normal" font="default" size="100%">Immunome research</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">6</style></volume><pages><style face="normal" font="default" size="100%">3</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">ABSTRACT: BACKGROUND: Avian beta-defensins (AvBDs) represent a group of innate immune genes with broad antimicrobial activity. Within the chicken genome, previous work identified 14 AvBDs in a cluster on chromosome three. The release of a second bird genome, the zebra finch, allows us to study the comparative evolutionary history of these gene clusters between from two species that shared a common ancestor about 100 million years ago. RESULTS: A phylogenetic analysis of the beta-defensin gene clusters in the chicken and the zebra finch identified several cases of gene duplication and gene loss along their ancestral lines. In the zebra finch genome a cluster of 22 AvBD genes were identified, all located within 125Kbp on chromosome three. Ten of the 22 genes were found to be highly conserved with orthologous genes in the chicken genome. The remaining 12 genes were all located within a cluster of 58 Kbp and are suggested to be a result of recent gene duplication events that occurred after the galliformes- passeriformes split (G-P split) and where no duplications have happened along the chicken line. Within the chicken genome, AvBD6 was found to be a duplication of AvBD7, whereas the gene AvDB14 seems to have been lost along the ancestral line of the zebra finch. The duplicated beta-defensin genes have had a significantly higher accumulation of non-synonymous over synonymous substitutions compared to the genes that have not undergone duplication since the G-P split. The expression patterns of avian beta-defensin genes seem to be well conserved between chicken and zebra finch. CONCLUSION: The genomic comparisons of the beta-defensins gene clusters of the chicken and zebra finch illuminate the evolutionary history of this gene complex. Along their ancestral lines, several gene duplication events have occurred in the passerine line after the galliformes-passeriformes split giving rise to 12 novel genes compared to a single duplication event in the galliformes line. After the duplication events, the duplicated genes have been subject to a relaxed selection pressure compared to the non-duplicated genes, thus supporting models of evolution by gene duplication.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20359324?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Xie, Fang</style></author><author><style face="normal" font="default" size="100%">London, Sarah E</style></author><author><style face="normal" font="default" size="100%">Southey, Bruce R</style></author><author><style face="normal" font="default" size="100%">Annangudi, Suresh P</style></author><author><style face="normal" font="default" size="100%">Amare, Andinet</style></author><author><style face="normal" font="default" size="100%">Rodriguez-Zas, Sandra L</style></author><author><style face="normal" font="default" size="100%">Clayton, David F</style></author><author><style face="normal" font="default" size="100%">Sweedler, Jonathan V</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">The zebra finch neuropeptidome: prediction, detection and expression.</style></title><secondary-title><style face="normal" font="default" size="100%">BMC biology</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Apr 1</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">8</style></volume><pages><style face="normal" font="default" size="100%">28</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">ABSTRACT: BACKGROUND: Among songbirds, the zebra finch (Taeniopygia guttata) is an excellent model system for investigating the neural mechanisms underlying complex behaviours such as vocal communication, learning and social interactions. Neuropeptides and peptide hormones are cell-to-cell signalling molecules known to mediate similar behaviours in other animals. However, in the zebra finch, this information is limited. With the newly-released zebra finch genome as a foundation, we combined bioinformatics, mass-spectrometry (MS)-enabled peptidomics and molecular techniques to identify the complete suite of neuropeptide prohormones and final peptide products and their distributions. RESULTS: Complementary bioinformatic resources were integrated to survey the zebra finch genome, identifying 70 putative prohormones. Ninety peptides derived from 24 predicted prohormones were characterized using several MS platforms; tandem MS confirmed a majority of the sequences. Most of the peptides described here were not known in the zebra finch or other avian species, although homologous prohormones exist in the chicken genome. Among the zebra finch peptides discovered were several unique vasoactive intestinal and adenylate cyclase activating polypeptide 1 peptides created by cleavage at sites previously unreported in mammalian prohormones. MS-based profiling of brain areas required for singing detected 13 peptides within one brain nucleus, HVC; in situ hybridization detected 13 of the 15 prohormone genes examined within at least one major song control nucleus. Expression mapping also identified prohormone messenger RNAs in areas associated with spatial learning and social behaviours. Based on the whole-genome analysis, 40 prohormone probes were found on a commonly used zebra finch brain microarray. Analysis of these newly annotated transcripts revealed that six prohormone probes showed altered expression after birds heard song playbacks in a paradigm of song recognition learning; we partially verify this result experimentally. CONCLUSIONS: The zebra finch peptidome and prohormone complement is now characterized. Based on previous microarray results on zebra finch vocal learning and synaptic plasticity, a number of these prohormones show significant changes during learning. Interestingly, most mammalian prohormones have counterparts in the zebra finch, demonstrating that this songbird uses similar biochemical pathways for neurotransmission and hormonal regulation. These findings enhance investigation into neuropeptide-mediated mechanisms of brain function, learning and behaviour in this model.</style></abstract><issue><style face="normal" font="default" size="100%">1</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20359331?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Künstner, Axel</style></author><author><style face="normal" font="default" size="100%">Wolf, Jochen B W</style></author><author><style face="normal" font="default" size="100%">Backström, Niclas</style></author><author><style face="normal" font="default" size="100%">Whitney, Osceola</style></author><author><style face="normal" font="default" size="100%">Balakrishnan, Christopher N</style></author><author><style face="normal" font="default" size="100%">Day, Lainy</style></author><author><style face="normal" font="default" size="100%">Edwards, Scott V</style></author><author><style face="normal" font="default" size="100%">Janes, Daniel E</style></author><author><style face="normal" font="default" size="100%">Schlinger, Barney A</style></author><author><style face="normal" font="default" size="100%">Wilson, Richard K</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author><author><style face="normal" font="default" size="100%">Warren, Wesley C</style></author><author><style face="normal" font="default" size="100%">Ellegren, Hans</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.</style></title><secondary-title><style face="normal" font="default" size="100%">Molecular ecology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">Mol. Ecol.</style></alt-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Mar</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">19 Suppl 1</style></volume><pages><style face="normal" font="default" size="100%">266-76</style></pages><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with approximately 1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (d(S)) and chromosome size. Analyses of the mean d(N)/d(S) ratio (omega) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with omega as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20331785?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kubikova, Lubica</style></author><author><style face="normal" font="default" size="100%">Wada, Kazuhiro</style></author><author><style face="normal" font="default" size="100%">Jarvis, Erich D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Dopamine receptors in a songbird brain.</style></title><secondary-title><style face="normal" font="default" size="100%">The Journal of comparative neurology</style></secondary-title><alt-title><style face="normal" font="default" size="100%">J. Comp. Neurol.</style></alt-title></titles><keywords><keyword><style  face="normal" font="default" size="100%">catecholamine</style></keyword><keyword><style  face="normal" font="default" size="100%">chicken</style></keyword><keyword><style  face="normal" font="default" size="100%">D1</style></keyword><keyword><style  face="normal" font="default" size="100%">D2</style></keyword><keyword><style  face="normal" font="default" size="100%">egr1</style></keyword><keyword><style  face="normal" font="default" size="100%">song nuclei</style></keyword><keyword><style  face="normal" font="default" size="100%">zebra finch</style></keyword><keyword><style  face="normal" font="default" size="100%">ZENK</style></keyword></keywords><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Mar 15</style></date></pub-dates></dates><volume><style face="normal" font="default" size="100%">518</style></volume><pages><style face="normal" font="default" size="100%">741-69</style></pages><abstract><style face="normal" font="default" size="100%">Dopamine is a key neuromodulatory transmitter in the brain. It acts through dopamine receptors to affect changes in neural activity, gene expression, and behavior. In songbirds, dopamine is released into the striatal song nucleus Area X, and the levels depend on social contexts of undirected and directed singing. This differential release is associated with differential expression of activity-dependent genes, such as egr1 (avian zenk), which in mammalian brain are modulated by dopamine receptors. Here we cloned from zebra finch brain cDNAs of all avian dopamine receptors: the D1 (D1A, D1B, D1D) and D2 (D2, D3, D4) families. Comparative sequence analyses of predicted proteins revealed expected phylogenetic relationships, in which the D1 family exists as single exon and the D2 family exists as spliced exon genes. In both zebra finch and chicken, the D1A, D1B, and D2 receptors were highly expressed in the striatum, the D1D and D3 throughout the pallium and within the mesopallium, respectively, and the D4 mainly in the cerebellum. Furthermore, within the zebra finch, all receptors, except for D4, showed differential expression in song nuclei relative to the surrounding regions and developmentally regulated expression that decreased for most receptors during the sensory acquisition and sensorimotor phases of song learning. Within Area X, half of the cells expressed both D1A and D2 receptors, and a higher proportion of the D1A-only-containing neurons expressed egr1 during undirected but not during directed singing. Our findings are consistent with hypotheses that dopamine receptors may be involved in song development and social context-dependent behaviors.</style></abstract><issue><style face="normal" font="default" size="100%">6</style></issue><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20058221?dopt=Abstract</style></custom1></record><record><source-app name="Biblio" version="6.x">Drupal-Biblio</source-app><ref-type>17</ref-type><contributors><authors><author><style face="normal" font="default" size="100%">Kordis, D</style></author></authors></contributors><titles><title><style face="normal" font="default" size="100%">Transposable Elements in Reptilian and Avian (Sauropsida) Genomes.</style></title><secondary-title><style face="normal" font="default" size="100%">Cytogenetic and genome research</style></secondary-title></titles><dates><year><style  face="normal" font="default" size="100%">2010</style></year><pub-dates><date><style  face="normal" font="default" size="100%">2010 Mar 6</style></date></pub-dates></dates><language><style face="normal" font="default" size="100%">eng</style></language><abstract><style face="normal" font="default" size="100%">Transposable elements (TEs) have profound effects on the structure, function and evolution of their host genomes. Our knowledge about these agents of genomic change in sauropsids, a sister group of mammals that includes all extant reptiles and birds, is still very limited. Invaluable information concerning the diversity, activity and repetitive landscapes in sauropsids has recently emerged from analyses of the draft genomes of chicken and Anolis and other preliminary reptilian genome sequencing projects. Avian and reptilian genomes differ significantly in the classes of TEs present, their fractional representation in the genome and by the level of TE activity. While lepidosaurian genomes contain many young, active TE families, the extant avian genomes have very few active TE lineages. Most reptilian genomes possess quite rich TE repertoires that differ considerably from those of birds and mammals, being more similar in diversity to that of lower vertebrates. The large amount of recently accumulated genome-wide data on TEs in diverse lineages of sauropsids has provided a remarkable opportunity to review current knowledge about TEs of sauropsids in their genomic context.</style></abstract><custom1><style face="normal" font="default" size="100%">http://www.ncbi.nlm.nih.gov/pubmed/20215725?dopt=Abstract</style></custom1></record></records></xml>
