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Tackling Rapid Radiations With Targeted Sequencing

In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogeneti...

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Autores principales: Larridon, Isabel, Villaverde, Tamara, Zuntini, Alexandre R., Pokorny, Lisa, Brewer, Grace E., Epitawalage, Niroshini, Fairlie, Isabel, Hahn, Marlene, Kim, Jan, Maguilla, Enrique, Maurin, Olivier, Xanthos, Martin, Hipp, Andrew L., Forest, Félix, Baker, William J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962237/
https://www.ncbi.nlm.nih.gov/pubmed/31998342
http://dx.doi.org/10.3389/fpls.2019.01655
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author Larridon, Isabel
Villaverde, Tamara
Zuntini, Alexandre R.
Pokorny, Lisa
Brewer, Grace E.
Epitawalage, Niroshini
Fairlie, Isabel
Hahn, Marlene
Kim, Jan
Maguilla, Enrique
Maurin, Olivier
Xanthos, Martin
Hipp, Andrew L.
Forest, Félix
Baker, William J.
author_facet Larridon, Isabel
Villaverde, Tamara
Zuntini, Alexandre R.
Pokorny, Lisa
Brewer, Grace E.
Epitawalage, Niroshini
Fairlie, Isabel
Hahn, Marlene
Kim, Jan
Maguilla, Enrique
Maurin, Olivier
Xanthos, Martin
Hipp, Andrew L.
Forest, Félix
Baker, William J.
author_sort Larridon, Isabel
collection PubMed
description In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. Despite ample taxon sampling, relationships in many genera remain poorly understood, hampered by diversification rates that outpace mutation rates in the loci used. The C4 Cyperus clade of the genus Cyperus has been particularly difficult to resolve. Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. The power to resolve shallow-level relationships was tested using a summary species tree method and a concatenated maximum likelihood approach. High resolution and support are obtained using both approaches, but high levels of missing data disproportionately impact the latter. Targeted sequencing provides new insights into the evolution of morphology in the C4 Cyperus clade, demonstrating for example that the former segregate genus Alinula is polyphyletic despite its seeming morphological integrity. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex comprises a clade separate from and sister to the core C4 Cyperus clade. Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations.
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spelling pubmed-69622372020-01-29 Tackling Rapid Radiations With Targeted Sequencing Larridon, Isabel Villaverde, Tamara Zuntini, Alexandre R. Pokorny, Lisa Brewer, Grace E. Epitawalage, Niroshini Fairlie, Isabel Hahn, Marlene Kim, Jan Maguilla, Enrique Maurin, Olivier Xanthos, Martin Hipp, Andrew L. Forest, Félix Baker, William J. Front Plant Sci Plant Science In phylogenetic studies across angiosperms, at various taxonomic levels, polytomies have persisted despite efforts to resolve them by increasing sampling of taxa and loci. The large amount of genomic data now available and statistical tools to analyze them provide unprecedented power for phylogenetic inference. Targeted sequencing has emerged as a strong tool for estimating species trees in the face of rapid radiations, lineage sorting, and introgression. Evolutionary relationships in Cyperaceae have been studied mostly using Sanger sequencing until recently. Despite ample taxon sampling, relationships in many genera remain poorly understood, hampered by diversification rates that outpace mutation rates in the loci used. The C4 Cyperus clade of the genus Cyperus has been particularly difficult to resolve. Previous studies based on a limited set of markers resolved relationships among Cyperus species using the C3 photosynthetic pathway, but not among C4 Cyperus clade taxa. We test the ability of two targeted sequencing kits to resolve relationships in the C4 Cyperus clade, the universal Angiosperms-353 kit and a Cyperaceae-specific kit. Sequences of the targeted loci were recovered from data generated with both kits and used to investigate overlap in data between kits and relative efficiency of the general and custom approaches. The power to resolve shallow-level relationships was tested using a summary species tree method and a concatenated maximum likelihood approach. High resolution and support are obtained using both approaches, but high levels of missing data disproportionately impact the latter. Targeted sequencing provides new insights into the evolution of morphology in the C4 Cyperus clade, demonstrating for example that the former segregate genus Alinula is polyphyletic despite its seeming morphological integrity. An unexpected result is that the Cyperus margaritaceus-Cyperus niveus complex comprises a clade separate from and sister to the core C4 Cyperus clade. Our results demonstrate that data generated with a family-specific kit do not necessarily have more power than those obtained with a universal kit, but that data generated with different targeted sequencing kits can often be merged for downstream analyses. Moreover, our study contributes to the growing consensus that targeted sequencing data are a powerful tool in resolving rapid radiations. Frontiers Media S.A. 2020-01-09 /pmc/articles/PMC6962237/ /pubmed/31998342 http://dx.doi.org/10.3389/fpls.2019.01655 Text en Copyright © 2020 Larridon, Villaverde, Zuntini, Pokorny, Brewer, Epitawalage, Fairlie, Hahn, Kim, Maguilla, Maurin, Xanthos, Hipp, Forest and Baker http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Larridon, Isabel
Villaverde, Tamara
Zuntini, Alexandre R.
Pokorny, Lisa
Brewer, Grace E.
Epitawalage, Niroshini
Fairlie, Isabel
Hahn, Marlene
Kim, Jan
Maguilla, Enrique
Maurin, Olivier
Xanthos, Martin
Hipp, Andrew L.
Forest, Félix
Baker, William J.
Tackling Rapid Radiations With Targeted Sequencing
title Tackling Rapid Radiations With Targeted Sequencing
title_full Tackling Rapid Radiations With Targeted Sequencing
title_fullStr Tackling Rapid Radiations With Targeted Sequencing
title_full_unstemmed Tackling Rapid Radiations With Targeted Sequencing
title_short Tackling Rapid Radiations With Targeted Sequencing
title_sort tackling rapid radiations with targeted sequencing
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6962237/
https://www.ncbi.nlm.nih.gov/pubmed/31998342
http://dx.doi.org/10.3389/fpls.2019.01655
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