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A Phylogenomic Supertree of Birds
Open AccessReview

Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies

1,* and 1,2,3,4,*
Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
China National GeneBank, BGI–Shenzhen, Shenzhen 518083, China
Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
Authors to whom correspondence should be addressed.
Diversity 2019, 11(7), 115;
Received: 8 June 2019 / Revised: 7 July 2019 / Accepted: 15 July 2019 / Published: 18 July 2019
(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)
PDF [2527 KB, uploaded 18 July 2019]


Birds are a group with immense availability of genomic resources, and hundreds of forthcoming genomes at the doorstep. We review recent developments in whole genome sequencing, phylogenomics, and comparative genomics of birds. Short read based genome assemblies are common, largely due to efforts of the Bird 10K genome project (B10K). Chromosome-level assemblies are expected to increase due to improved long-read sequencing. The available genomic data has enabled the reconstruction of the bird tree of life with increasing confidence and resolution, but challenges remain in the early splits of Neoaves due to their explosive diversification after the Cretaceous-Paleogene (K-Pg) event. Continued genomic sampling of the bird tree of life will not just better reflect their evolutionary history but also shine new light onto the organization of phylogenetic signal and conflict across the genome. The comparatively simple architecture of avian genomes makes them a powerful system to study the molecular foundation of bird specific traits. Birds are on the verge of becoming an extremely resourceful system to study biodiversity from the nucleotide up. View Full-Text
Keywords: whole genome sequencing; phylogenomics; comparative genomics; incongruence; birds; Neoaves whole genome sequencing; phylogenomics; comparative genomics; incongruence; birds; Neoaves

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Stiller, J.; Zhang, G. Comparative Phylogenomics, a Stepping Stone for Bird Biodiversity Studies. Diversity 2019, 11, 115.

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