A Phylogenomic Supertree of Birds

Kimball, Rebecca T. and Oliveros, Carl H. and Wang, Ning and White, Noor D. and Barker, F. Keith and Field, Daniel J. and Ksepka, Daniel T. and Chesser, R. Terry and Moyle, Robert G. and Braun, Michael J. and Brumfield, Robb T. and Faircloth, Brant C. and Smith, Brian Tilston and Braun, Edward L. (2019) A Phylogenomic Supertree of Birds. Diversity, 11 (7). p. 109. ISSN 1424-2818 DOI https://doi.org/10.3390/d11070109

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Abstract

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.

Item Type: Article
Uncontrolled Keywords: 2019AREP; IA75
Subjects: 04 - Palaeobiology
Divisions: 04 - Palaeobiology
07 - Gold Open Access
Journal or Publication Title: Diversity
Volume: 11
Page Range: p. 109
Identification Number: https://doi.org/10.3390/d11070109
Depositing User: Sarah Humbert
Date Deposited: 15 Nov 2019 13:22
Last Modified: 15 Nov 2019 13:27
URI: http://eprints.esc.cam.ac.uk/id/eprint/4534

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