A Phylogenomic Supertree of Birds

Rebecca T. Kimball, Carl H. Oliveros, Ning Wang, Noor D. White, F. Keith Barker, Daniel J. Field, Daniel T. Ksepka, R. Terry Chesser, Robert G. Moyle, Michael J. Braun, Robb T. Brumfield, Brant C. Faircloth, Brian Tilston Smith, Edward L. Braun

Research output: Contribution to journalArticlepeer-review

83 Scopus citations

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.

Original languageEnglish (US)
Article number109
JournalDiversity
Volume11
Issue number7
DOIs
StatePublished - Jul 2019

Bibliographical note

Funding Information:
This research was funded by the US National Science Foundation, grant numbers DEB-1655683 (to R.T.K. and E.L.B), DEB-1655624 (to B.C.F. and R.T.B.), DEB-1655559 (to F.K.B.), DEB-1655736 to (B.T.S; subcontracts to D.T.K. and R.T.C.). M.J.B., N.D.W., R.T.B., E.L.B., and B.C.F. were supported by grants from the Smithsonian Grand Challenges Consortia. Acknowledgments

Publisher Copyright:
© 2019 by the authors.

Keywords

  • avian
  • bootstrap support
  • fossil calibrations
  • genome
  • molecular clock
  • phylogenomics
  • phylogeny
  • supertree
  • timetree

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