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

Abstract 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 relation... Full description

Journal Title: Systematic biology 2021, Vol.70 (1), p.49-66
Main Author: Hime, Paul M
Other Authors: 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
Format: Electronic Article Electronic Article
Language: English
Subjects:
Publisher: England: Oxford University Press
ID: ISSN: 1063-5157
Link: https://www.ncbi.nlm.nih.gov/pubmed/32359157
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recordid: cdi_oup_primary_10_1093_sysbio_syaa034
title: Phylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
format: Article
creator:
  • 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
subjects:
  • AcademicSubjects
  • Regular
  • SCI01130
ispartof: Systematic biology, 2021, Vol.70 (1), p.49-66
description: Abstract 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.]
language: eng
source:
identifier: ISSN: 1063-5157
fulltext: no_fulltext
issn:
  • 1063-5157
  • 1076-836X
url: Link


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titlePhylogenomics Reveals Ancient Gene Tree Discordance in the Amphibian Tree of Life
creatorHime, 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
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creatorcontribHime, 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 ; Leaché, Adam
descriptionAbstract 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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16Ron, Santiago R
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20Labisko, Jim
21Che, Jing
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descriptionAbstract 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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authorHime, 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
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notesPaul M. Hime and Alan R. Lemmon contributed equally to this article.
abstractAbstract 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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