Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life

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dc.contributor.authorHIME, PAUL M.
dc.contributor.authorLemmon, Alan R.
dc.contributor.authorLemmon, Emily Moriarty
dc.contributor.authorPRENDINI, ELIZABETH
dc.contributor.authorBrown, Jeremy M.
dc.contributor.authorTHOMSON, ROBERT C.
dc.contributor.authorKRATOVIL, JUSTIN D.
dc.contributor.authorNoonan, Brice P.
dc.contributor.authorPyron, R. Alexander
dc.contributor.authorPELOSO, PEDRO L. V.
dc.date.accessioned2022-10-19T21:29:06Z
dc.date.available2022-10-19T21:29:06Z
dc.date.issued2021
dc.date.updated2021-11-28T07:24:09Z
dc.description.abstractThe Author(s) 2020. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. Molecular phylogenies have yielded strong support for many parts of the amphibian Tree of Life, but poor support for the resolution of deeper nodes, including relationships among families and orders. To clarify these relationships, we provide a phylogenomic perspective on amphibian relationships by developing a taxon-specific Anchored Hybrid Enrichment protocol targeting hundreds of conserved exons which are effective across the class. After obtaining data from 220 loci for 286 species (representing 94% of the families and 44% of the genera), we estimate a phylogeny for extant amphibians and identify gene tree-species tree conflict across the deepest branches of the amphibian phylogeny. We perform locus-by-locus genealogical interrogation of alternative topological hypotheses for amphibian monophyly, focusing on interordinal relationships. We find that phylogenetic signal deep in the amphibian phylogeny varies greatly across loci in a manner that is consistent with incomplete lineage sorting in the ancestral lineage of extant amphibians. Our results overwhelmingly support amphibian monophyly and a sister relationship between frogs and salamanders, consistent with the Batrachia hypothesis. Species tree analyses converge on a small set of topological hypotheses for the relationships among extant amphibian families. These results clarify several contentious portions of the amphibian Tree of Life, which in conjunction with a set of vetted fossil calibrations, support a surprisingly younger timescale for crown and ordinal amphibian diversification than previously reported. More broadly, our study provides insight into the sources, magnitudes, and heterogeneity of support across loci in phylogenomic data sets.[AIC; Amphibia; Batrachia; Phylogeny; gene tree-species tree discordance; genomics; information theory.].en_AU
dc.description.sponsorshipThis work was supported by grants from a graduate student research award from the Society of Systematic Biologists and the University of Kentucky G.F. Ribble Endowment (to P.M.H.), by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES/BEX 2806/09-6 to P.L.V.P.), and by the National Science Foundation (DEB-0949532 and DEB-1355000 to D.W.W., DEB-1120516 to E.M.L., IIP-1313554 to A.R.L. and E.M.L, DEB-1355071 to J.M.B., DEB-1441719 to R.A.P., DEB-1311442 to P.L.V.P., DEB-1354506 to R.C.T., DEB-1021247 to E.P. and C.J.R., DEB-1021299 to K.M. Kjer, and DEB-1257610, DEB-0641023, DEB-0423286, and DEB-9984496 to C.J.R.), and the Australian Research Council (DP120104146 to J.S.K. and S.C.D.). S.R.R. thanks SENESCYT (Arca de Noé Initiative; SRR and O. Torres-Carvajal principal investigators) for funding for tissue collection. J.L. was supported by the Systematics Association and the Linnean Society Systematics Research Fund. This material is based upon work supported by the National Science Foundation Graduate Research Fellowship Program (DGE-3048109801 to P.M.H.) and by the National Science Foundation-supported National Center for Supercomputing Applications Blue Waters Graduate Research Fellowship Program (under Grant No. 0725070, subaward 15836, to P.M.H.). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.en_AU
dc.format.mimetypeapplication/pdfen_AU
dc.identifier.issn1063-5157en_AU
dc.identifier.urihttp://hdl.handle.net/1885/275650
dc.language.isoen_AUen_AU
dc.provenanceThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, providedthe original work is properly cited.en_AU
dc.publisherTaylor & Francis Groupen_AU
dc.relationhttp://purl.org/au-research/grants/arc/DP120104146en_AU
dc.rights© 2020 The authorsen_AU
dc.rights.licenseCreative Commons Attribution licenceen_AU
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_AU
dc.sourceSystematic Biologyen_AU
dc.titlePhylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Lifeen_AU
dc.typeJournal articleen_AU
dcterms.accessRightsOpen Accessen_AU
local.bibliographicCitation.issue1en_AU
local.bibliographicCitation.lastpage66en_AU
local.bibliographicCitation.startpage49en_AU
local.contributor.affiliationHIME, PAUL M., Biodiversity Institute, University of Kansasen_AU
local.contributor.affiliationLemmon, Alan R., Florida State Universityen_AU
local.contributor.affiliationLemmon, Emily Moriarty, Florida State Universityen_AU
local.contributor.affiliationPRENDINI, ELIZABETH, 5Division of Vertebrate Zoology: Herpetology, American Museum of Natural Historyen_AU
local.contributor.affiliationBrown, Jeremy M., Louisiana State Universityen_AU
local.contributor.affiliationTHOMSON, ROBERT C., School of Life Sciences, University of Hawai’ien_AU
local.contributor.affiliationKRATOVIL, JUSTIN D., Department of Biology, University of Kentuckyen_AU
local.contributor.affiliationNoonan, Brice P., University of Mississippien_AU
local.contributor.affiliationPyron, R. Alexander, The George Washington Universityen_AU
local.contributor.affiliationPELOSO, PEDRO L. V., Division of Vertebrate Zoology: Herpetology, American Museum of Natural Historyen_AU
local.contributor.affiliationKeogh, Scott, College of Science, ANUen_AU
local.contributor.authoremailu9807405@anu.edu.auen_AU
local.contributor.authoruidKeogh, Scott, u9807405en_AU
local.description.notesImported from ARIESen_AU
local.identifier.absfor310400 - Evolutionary biologyen_AU
local.identifier.absseo280102 - Expanding knowledge in the biological sciencesen_AU
local.identifier.ariespublicationa383154xPUB17437en_AU
local.identifier.citationvolume70en_AU
local.identifier.doi10.1093/sysbio/syaa034en_AU
local.identifier.scopusID2-s2.0-85098675124
local.identifier.uidSubmittedBya383154en_AU
local.publisher.urlhttps://academic.oup.com/en_AU
local.type.statusPublished Versionen_AU

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