Genomics and ornithology

Edwards, Scott V.

doi:10.1007/s10336-007-0238-x

Cited by 3 publications

(4 citation statements)

References 28 publications

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“…One of the strategies suggested to change this picture is to survey variation in a large number of immune candidate genes; for example, in mosquitoes (Waterhouse et al 2007), salmon (Tonteri et al 2010), and Drosophila (Obbard et al 2009). However, multicandidate gene studies have been unrealistic in birds due to the lack of comparative genomic information (Edwards 2007); until recently the domestic chicken ( Gallus gallus ) was the only bird with a characterized genome (International Chicken Genome Sequencing Consortium 2004). Recently, the second bird genome, that of the zebra finch ( Taeniopygia guttata ), was released (Warren et al 2010), opening up this field for avian research (Ellegren 2007; Clayton et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

Ekblom

French

Slate

et al. 2010

Genome Biology and Evolution

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Genes of the immune system are generally considered to evolve rapidly due to host–parasite coevolution. They are therefore of great interest in evolutionary biology and molecular ecology. In this study, we manually annotated 144 avian immune genes from the zebra finch (Taeniopygia guttata) genome and conducted evolutionary analyses of these by comparing them with their orthologs in the chicken (Gallus gallus). Genes classified as immune receptors showed elevated dN/dS ratios compared with other classes of immune genes. Immune genes in general also appear to be evolving more rapidly than other genes, as inferred from a higher dN/dS ratio compared with the rest of the genome. Furthermore, ten genes (of 27) for which sequence data were available from at least three bird species showed evidence of positive selection acting on specific codons. From transcriptome data of eight different tissues, we found evidence for expression of 106 of the studied immune genes, with primary expression of most of these in bursa, blood, and spleen. These immune-related genes showed a more tissue-specific expression pattern than other genes in the zebra finch genome. Several of the avian immune genes investigated here provide strong candidates for in-depth studies of molecular adaptation in birds.

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Section: Introductionmentioning

confidence: 99%

Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

Ekblom

French

Slate

et al. 2010

Genome Biology and Evolution

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“…). Considering the complex history of Zosterops generally (Clegg et al ., ; Moyle et al ., ), we suggest that more detailed analyses featuring the entire radiation and the use of multilocus or genomic datasets are necessary to clarify the history of this group (Edwards, Jennings & Shedlock, ; Edwards, ; Lerner & Fleischer, ).…”

Section: Discussionmentioning

confidence: 99%

Comparative phylogeography of Australo-Papuan mangrove-restricted and mangrove-associated avifaunas

Nyári

Joseph

2013

Biol J Linn Soc Lond

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The world's richest mangrove‐restricted avifauna is in Australia and New Guinea. The history of differentiation of the species involved and their patterns of intraspecific genetic variation remain poorly known. Here, we use sequence data derived from two mitochondrial protein‐coding genes to study the evolutionary history of eight co‐distributed mangrove‐restricted and mangrove‐associated birds from the Australian part of this region. Utilizing a comparative phylogeographical framework, we observed that the study species present concordantly located phylogeographical breaks across their shared geographical distribution, a plausible signature of common mechanisms of vicariance underlying this pattern. Barriers such as the Canning Gap, Bonaparte Gap, and the Carpentarian Gaps all had important but varying degrees of impact on the studied species. The Burdekin Gap along Australia's eastern seaboard probably had only a minor influence as a barrier to gene flow in mangrove birds. Statistical phylogeographical simulations were able to discriminate among alternative scenarios involving six different geographical and temporal population separations. Species exhibiting recent colonizations into mangroves include Rhipidura phasiana, Myiagra ruficollis, and Myzomela erythrocephala. By contrast, Peneoenanthe pulverulenta, Pachycephala melanura, Pachycephala lanioides, Zosterops luteus, and Colluricincla megarhyncha all had deeper histories, reflected as more marked phylogeographical divisions separating populations on the eastern seaboard/Cape York Peninsula from more western regions such as the Arnhem Land, the Pilbara, and the Kimberley. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109, 574–598.

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“…In contrast, the costs associated with genome-wide data collection have precluded broad applications of genomics studies for a while. If we take the publication of the chicken genome (Hillier et al 2004) as a milestone in avian genomics, we have since seen merely reviews and opinion papers in specific bird journals (Balakrishnan et al 2010;Edwards 2007;Piertney 2006). The reasons are twofold: the financial and analytical burden remains a challenge that is hard to overcome, and avian genomics projects are at the forefront of inter-and cross-disciplinary research and, therefore, are rarely published in specific ornithology journals, which we also observe in most examples presented in this review.…”

Section: Discussionmentioning

confidence: 99%

“…So far, genomic studies of birds have not become as widespread as genetics did in the early 1990s, despite the availability of genomic technology for some years (Edwards 2007). The first genomic studies on birds were clearly motivated by agricultural interests.…”

Section: Ornithology In the Age Of Genomicsmentioning

confidence: 99%

Avian genomics: fledging into the wild!

Kraus

Wink

2015

J Ornithol

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Next generation sequencing (NGS) technologies provide great resources to study bird evolution and avian functional genomics. They also allow for the identification of suitable high-resolution markers for detailed analyses of the phylogeography of a species or the connectivity of migrating birds between breeding and wintering populations. This review discusses the application of DNA markers for the study of systematics and phylogeny, but also population genetics and phylogeography. Emphasis in this review is on the new methodology of NGS and its use to study avian genomics. The recent publication of the first phylogenomic tree of birds based on genome data of 48 bird taxa from 34 orders is presented in more detail.

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Genomics and ornithology

Cited by 3 publications

References 28 publications

Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

Evolutionary Analysis and Expression Profiling of Zebra Finch Immune Genes

Comparative phylogeography of Australo-Papuan mangrove-restricted and mangrove-associated avifaunas

Avian genomics: fledging into the wild!

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