What Have We Learned from the First 500 Avian Genomes?

  title={What Have We Learned from the First 500 Avian Genomes?},
  author={Gustavo A. Bravo and C. Jonathan Schmitt and Scott V. Edwards},
  journal={Annual Review of Ecology, Evolution, and Systematics},
The increased capacity of DNA sequencing has significantly advanced our understanding of the phylogeny of birds and the proximate and ultimate mechanisms molding their genomic diversity. In less than a decade, the number of available avian reference genomes has increased to over 500—approximately 5% of bird diversity—placing birds in a privileged position to advance the fields of phylogenomics and comparative, functional, and population genomics. Whole-genome sequence data, as well as indels… 
Genomic architecture drives population structuring in Amazonian birds
It is shown that the effects of intrinsic genomic characteristics and selection can be disentangled from the neutral processes to elucidate how speciation hypotheses and biogeographic patterns are sensitive to genomic architecture.
Protein Structure, Models of Sequence Evolution, and Data Type Effects in Phylogenetic Analyses of Mitochondrial Data: A Case Study in Birds
It is believed that incorporating protein structure into analyses of mitochondrially-encoded proteins improved model fit and will improve analyses of mitogenomic data, both in birds and in other taxa.
Genome Assembly and Evolutionary Analysis of the Mandarin Duck Aix galericulata Reveal Strong Genome Conservation among Ducks
This new reference genome will improve the understanding of the morphological and physiological characteristics of ducks and provide a valuable resource for functional genomics studies to investigate the feather traits of the mandarin duck.
Comparative Population Genomics of Cryptic Speciation and Adaptive Divergence in Bicknell’s and Gray-Cheeked Thrushes (Aves: Catharus bicknelli and Catharus minimus)
Evidence of rapid evolution of the Z-chromosome and elevated divergence consistent with natural selection on genomic regions near genes involved with neuronal processes in C. bicknelli is found.
Divergence time estimation of Galliformes based on the best gene shopping scheme of ultraconserved elements
A robust galliform backbone time tree that can be combined with more fossil records to further facilitate the understanding of the evolution of Galliformes and can be used as a resource for comparative and biogeographic studies in this group.
Avian Introgression Patterns are Consistent With Haldane’s Rule
Genomic data provide exciting opportunities to obtain a more fine-grained picture of introgression rates across the genome, which can consequently be linked to ecological and behavioral observations, potentially leading to novel insights into the genetic mechanisms underpinning Haldane's Rule.
Olfactory receptor subgenome and expression in a highly olfactory procellariiform seabird.
A high-quality genome and nasal epithelium transcriptome is assembled of the Leach's storm-petrel to extensively characterize their olfactory receptor (OR) repertoire and provide valuable insight into the expression, development, and macroevolution of olfaction in seabirds.
Establishment of the Primary Avian Gonadal Somatic Cell Lines for Cytogenetic Studies
It was found that the ovary-derived cell cultures of the great tit were composed of fibroblasts mainly, but also contained interstitial and granulosa cells, and could be used for the generation of high quality material for various cytogenetic and genomic studies.
De Novo Whole-Genome Sequencing and Assembly of the Yellow-Throated Bunting (Emberiza elegans) Provides Insights into Its Evolutionary Adaptation
This newly generated de novo genome of the yellow-throated bunting using long reads provide the research community with a valuable resource for further studies of population genetic diversity and genome evolution in this species.
Museum Genomics.
Museum genomics collections are poised to address challenges and, with increasingly sensitive genomics approaches, will catalyze a future era of reproducibility, innovation, and insight made possible through integrating museum and genome sciences.