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

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...

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Autores principales: Hime, Paul M, Lemmon, Alan R, Lemmon, Emily C Moriarty, Prendini, Elizabeth, Brown, Jeremy M, Thomson, Robert C, Kratovil, Justin D, Noonan, Brice P, Pyron, R Alexander, Peloso, Pedro L V, Kortyna, Michelle L, Keogh, J Scott, Donnellan, Stephen C, Mueller, Rachel Lockridge, Raxworthy, Christopher J, Kunte, Krushnamegh, Ron, Santiago R, Das, Sandeep, Gaitonde, Nikhil, Green, David M, Labisko, Jim, Che, Jing, Weisrock, David W
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823230/
https://www.ncbi.nlm.nih.gov/pubmed/32359157
http://dx.doi.org/10.1093/sysbio/syaa034
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author Hime, Paul M
Lemmon, Alan R
Lemmon, Emily C Moriarty
Prendini, Elizabeth
Brown, Jeremy M
Thomson, Robert C
Kratovil, Justin D
Noonan, Brice P
Pyron, R Alexander
Peloso, Pedro L V
Kortyna, Michelle L
Keogh, J Scott
Donnellan, Stephen C
Mueller, Rachel Lockridge
Raxworthy, Christopher J
Kunte, Krushnamegh
Ron, Santiago R
Das, Sandeep
Gaitonde, Nikhil
Green, David M
Labisko, Jim
Che, Jing
Weisrock, David W
author_facet Hime, Paul M
Lemmon, Alan R
Lemmon, Emily C Moriarty
Prendini, Elizabeth
Brown, Jeremy M
Thomson, Robert C
Kratovil, Justin D
Noonan, Brice P
Pyron, R Alexander
Peloso, Pedro L V
Kortyna, Michelle L
Keogh, J Scott
Donnellan, Stephen C
Mueller, Rachel Lockridge
Raxworthy, Christopher J
Kunte, Krushnamegh
Ron, Santiago R
Das, Sandeep
Gaitonde, Nikhil
Green, David M
Labisko, Jim
Che, Jing
Weisrock, David W
author_sort Hime, Paul M
collection PubMed
description 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.]
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spelling pubmed-78232302021-01-27 Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life Hime, Paul M Lemmon, Alan R Lemmon, Emily C Moriarty Prendini, Elizabeth Brown, Jeremy M Thomson, Robert C Kratovil, Justin D Noonan, Brice P Pyron, R Alexander Peloso, Pedro L V Kortyna, Michelle L Keogh, J Scott Donnellan, Stephen C Mueller, Rachel Lockridge Raxworthy, Christopher J Kunte, Krushnamegh Ron, Santiago R Das, Sandeep Gaitonde, Nikhil Green, David M Labisko, Jim Che, Jing Weisrock, David W Syst Biol Regular Articles 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.] Oxford University Press 2020-06-30 /pmc/articles/PMC7823230/ /pubmed/32359157 http://dx.doi.org/10.1093/sysbio/syaa034 Text en © The Author(s) 2020. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Regular Articles
Hime, Paul M
Lemmon, Alan R
Lemmon, Emily C Moriarty
Prendini, Elizabeth
Brown, Jeremy M
Thomson, Robert C
Kratovil, Justin D
Noonan, Brice P
Pyron, R Alexander
Peloso, Pedro L V
Kortyna, Michelle L
Keogh, J Scott
Donnellan, Stephen C
Mueller, Rachel Lockridge
Raxworthy, Christopher J
Kunte, Krushnamegh
Ron, Santiago R
Das, Sandeep
Gaitonde, Nikhil
Green, David M
Labisko, Jim
Che, Jing
Weisrock, David W
Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
title Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
title_full Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
title_fullStr Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
title_full_unstemmed Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
title_short Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
title_sort phylogenomics reveals ancient gene tree discordance in the amphibian tree of life
topic Regular Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7823230/
https://www.ncbi.nlm.nih.gov/pubmed/32359157
http://dx.doi.org/10.1093/sysbio/syaa034
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