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Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix

The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured...

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Autores principales: Kimball, Rebecca T., Braun, Edward L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006227/
https://www.ncbi.nlm.nih.gov/pubmed/24795852
http://dx.doi.org/10.7717/peerj.361
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author Kimball, Rebecca T.
Braun, Edward L.
author_facet Kimball, Rebecca T.
Braun, Edward L.
author_sort Kimball, Rebecca T.
collection PubMed
description The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets that are independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. The inclusion or exclusion of mitochondrial data had a limited impact upon analyses upon analyses using either concatenated data or multispecies coalescent methods. Some of the key phylogenetic findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order.
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spelling pubmed-40062272014-05-02 Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix Kimball, Rebecca T. Braun, Edward L. PeerJ Evolutionary Studies The resolution of rapid evolutionary radiations or “bushes” in the tree of life has been one of the most difficult and interesting problems in phylogenetics. The avian order Galliformes appears to have undergone several rapid radiations that have limited the resolution of prior studies and obscured the position of taxa important both agriculturally and as model systems (chicken, turkey, Japanese quail). Here we present analyses of a multi-locus data matrix comprising over 15,000 sites, primarily from nuclear introns but also including three mitochondrial regions, from 46 galliform taxa with all gene regions sampled for all taxa. The increased sampling of unlinked nuclear genes provided strong bootstrap support for all but a small number of relationships. Coalescent-based methods to combine individual gene trees and analyses of datasets that are independent of published data indicated that this well-supported topology is likely to reflect the galliform species tree. The inclusion or exclusion of mitochondrial data had a limited impact upon analyses upon analyses using either concatenated data or multispecies coalescent methods. Some of the key phylogenetic findings include support for a second major clade within the core phasianids that includes the chicken and Japanese quail and clarification of the phylogenetic relationships of turkey. Jackknifed datasets suggested that there is an advantage to sampling many independent regions across the genome rather than obtaining long sequences for a small number of loci, possibly reflecting the differences among gene trees that differ due to incomplete lineage sorting. Despite the novel insights we obtained using this increased sampling of gene regions, some nodes remain unresolved, likely due to periods of rapid diversification. Resolving these remaining groups will likely require sequencing a very large number of gene regions, but our analyses now appear to support a robust backbone for this order. PeerJ Inc. 2014-04-22 /pmc/articles/PMC4006227/ /pubmed/24795852 http://dx.doi.org/10.7717/peerj.361 Text en © 2014 Kimball and Braun http://creativecommons.org/licenses/by/3.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Evolutionary Studies
Kimball, Rebecca T.
Braun, Edward L.
Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
title Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
title_full Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
title_fullStr Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
title_full_unstemmed Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
title_short Does more sequence data improve estimates of galliform phylogeny? Analyses of a rapid radiation using a complete data matrix
title_sort does more sequence data improve estimates of galliform phylogeny? analyses of a rapid radiation using a complete data matrix
topic Evolutionary Studies
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006227/
https://www.ncbi.nlm.nih.gov/pubmed/24795852
http://dx.doi.org/10.7717/peerj.361
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