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Phylogenetic Signal of Indels and the Neoavian Radiation

A Phylogenomic Supertree of Birds

Department of Biology, University of Florida, Gainesville, FL 32607, USA
Department of Biological Sciences, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA
Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA
Department of Vertebrate Zoology, MRC 163, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
Behavior, Ecology, Evolution and Systematics Program, University of Maryland, College Park, MD 20742, USA
Department of Ecology, Evolution and Behavior; and, Bell Museum of Natural History, St. Paul, MN 55108, USA
Department of Earth Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EQ, UK
Bruce Museum, Greenwich, CT 06830, USA
U.S. Geological Survey, Patuxent Wildlife Research Center, 12100 Beech Forest Rd., Laurel, MD 20708, USA
Division of Birds, National Museum of Natural History, Smithsonian Institution, Washington, DC 20013, USA
Department of Ecology and Evolutionary Biology and Biodiversity Institute, University of Kansas, Lawrence, KS 66045, USA
Museum of Natural Science, Louisiana State University, 119 Foster Hall, Baton Rouge, LA 70803, USA
Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024, USA
Author to whom correspondence should be addressed.
Diversity 2019, 11(7), 109;
Received: 31 May 2019 / Revised: 5 July 2019 / Accepted: 7 July 2019 / Published: 10 July 2019
(This article belongs to the Special Issue Genomic Analyses of Avian Evolution)
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. View Full-Text
Keywords: supertree; phylogeny; avian; genome; molecular clock; fossil calibrations; timetree; bootstrap support; phylogenomics supertree; phylogeny; avian; genome; molecular clock; fossil calibrations; timetree; bootstrap support; phylogenomics
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MDPI and ACS Style

Kimball, R.T.; Oliveros, C.H.; Wang, N.; White, N.D.; Barker, F.K.; Field, D.J.; Ksepka, D.T.; Chesser, R.T.; Moyle, R.G.; Braun, M.J.; Brumfield, R.T.; Faircloth, B.C.; Smith, B.T.; Braun, E.L. A Phylogenomic Supertree of Birds. Diversity 2019, 11, 109.

AMA Style

Kimball RT, Oliveros CH, Wang N, White ND, Barker FK, Field DJ, Ksepka DT, Chesser RT, Moyle RG, Braun MJ, Brumfield RT, Faircloth BC, Smith BT, Braun EL. A Phylogenomic Supertree of Birds. Diversity. 2019; 11(7):109.

Chicago/Turabian Style

Kimball, Rebecca T., Carl H. Oliveros, Ning Wang, Noor D. White, F. K. Barker, Daniel J. Field, Daniel T. Ksepka, R. T. Chesser, Robert G. Moyle, Michael J. Braun, Robb T. Brumfield, Brant C. Faircloth, Brian T. Smith, and Edward L. Braun. 2019. "A Phylogenomic Supertree of Birds" Diversity 11, no. 7: 109.

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