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dc.contributor.authorHime, Paul M.
dc.contributor.authorLemmon, Alan R.
dc.contributor.authorLemmon, Emily C. 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.contributor.authorKortyna, Michelle L.
dc.contributor.authorKeogh, J. Scott
dc.contributor.authorDonnellan, Stephen C.
dc.contributor.authorMueller, Rachel Lockridge
dc.contributor.authorRaxworthy, Christopher J.
dc.contributor.authorKunte, Krushnamegh
dc.contributor.authorRon, Santiago R.
dc.contributor.authorDas, Sandeep
dc.contributor.authorGaitonde, Nikhil
dc.contributor.authorGreen, David M.
dc.contributor.authorLabisko, Jim
dc.contributor.authorChe, Jing
dc.contributor.authorWeisrock, David W.
dc.date.accessioned2022-01-10T21:59:07Z
dc.date.available2022-01-10T21:59:07Z
dc.date.issued2020-06-20
dc.identifier.citationHime, P. M., Lemmon, A. R., Lemmon, E., Prendini, E., Brown, J. M., Thomson, R. C., Kratovil, J. D., Noonan, B. P., Pyron, R. A., Peloso, P., Kortyna, M. L., Keogh, J. S., Donnellan, S. C., Mueller, R. L., Raxworthy, C. J., Kunte, K., Ron, S. R., Das, S., Gaitonde, N., Green, D. M., … Weisrock, D. W. (2021). Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life. Systematic biology, 70(1), 49–66. https://doi.org/10.1093/sysbio/syaa034en_US
dc.identifier.urihttp://hdl.handle.net/1808/32387
dc.description.abstractMolecular 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.en_US
dc.publisherOxford University Pressen_US
dc.rights© The Author(s) 2020. Published by Oxford University Press on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.en_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_US
dc.subjectAICen_US
dc.subjectAmphibiaen_US
dc.subjectBatrachiaen_US
dc.subjectPhylogenyen_US
dc.subjectGene tree–species tree discordanceen_US
dc.subjectGenomicsen_US
dc.subjectInformation theoryen_US
dc.titlePhylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Lifeen_US
dc.typeArticleen_US
kusw.kuauthorHime, Paul M.
kusw.kudepartmentBiodiversity Instituteen_US
dc.identifier.doi10.1093/sysbio/syaa034en_US
kusw.oaversionScholarly/refereed, publisher versionen_US
kusw.oapolicyThis item meets KU Open Access policy criteria.en_US
dc.identifier.pmidPMC7823230en_US
dc.rights.accessrightsopenAccessen_US


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© The Author(s) 2020. Published by Oxford University Press on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.
Except where otherwise noted, this item's license is described as: © The Author(s) 2020. Published by Oxford University Press on behalf of the Society of Systematic Biologists. This is an Open Access article distributed under the terms of the Creative Commons Attribution License.