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Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals

Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic d...

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Autores principales: Yuri, Tamaki, Kimball, Rebecca T., Harshman, John, Bowie, Rauri C. K., Braun, Michael J., Chojnowski, Jena L., Han, Kin-Lan, Hackett, Shannon J., Huddleston, Christopher J., Moore, William S., Reddy, Sushma, Sheldon, Frederick H., Steadman, David W., Witt, Christopher C., Braun, Edward L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009869/
https://www.ncbi.nlm.nih.gov/pubmed/24832669
http://dx.doi.org/10.3390/biology2010419
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author Yuri, Tamaki
Kimball, Rebecca T.
Harshman, John
Bowie, Rauri C. K.
Braun, Michael J.
Chojnowski, Jena L.
Han, Kin-Lan
Hackett, Shannon J.
Huddleston, Christopher J.
Moore, William S.
Reddy, Sushma
Sheldon, Frederick H.
Steadman, David W.
Witt, Christopher C.
Braun, Edward L.
author_facet Yuri, Tamaki
Kimball, Rebecca T.
Harshman, John
Bowie, Rauri C. K.
Braun, Michael J.
Chojnowski, Jena L.
Han, Kin-Lan
Hackett, Shannon J.
Huddleston, Christopher J.
Moore, William S.
Reddy, Sushma
Sheldon, Frederick H.
Steadman, David W.
Witt, Christopher C.
Braun, Edward L.
author_sort Yuri, Tamaki
collection PubMed
description Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions.
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spelling pubmed-40098692014-05-07 Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals Yuri, Tamaki Kimball, Rebecca T. Harshman, John Bowie, Rauri C. K. Braun, Michael J. Chojnowski, Jena L. Han, Kin-Lan Hackett, Shannon J. Huddleston, Christopher J. Moore, William S. Reddy, Sushma Sheldon, Frederick H. Steadman, David W. Witt, Christopher C. Braun, Edward L. Biology (Basel) Article Insertion/deletion (indel) mutations, which are represented by gaps in multiple sequence alignments, have been used to examine phylogenetic hypotheses for some time. However, most analyses combine gap data with the nucleotide sequences in which they are embedded, probably because most phylogenetic datasets include few gap characters. Here, we report analyses of 12,030 gap characters from an alignment of avian nuclear genes using maximum parsimony (MP) and a simple maximum likelihood (ML) framework. Both trees were similar, and they exhibited almost all of the strongly supported relationships in the nucleotide tree, although neither gap tree supported many relationships that have proven difficult to recover in previous studies. Moreover, independent lines of evidence typically corroborated the nucleotide topology instead of the gap topology when they disagreed, although the number of conflicting nodes with high bootstrap support was limited. Filtering to remove short indels did not substantially reduce homoplasy or reduce conflict. Combined analyses of nucleotides and gaps resulted in the nucleotide topology, but with increased support, suggesting that gap data may prove most useful when analyzed in combination with nucleotide substitutions. MDPI 2013-03-13 /pmc/articles/PMC4009869/ /pubmed/24832669 http://dx.doi.org/10.3390/biology2010419 Text en © 2013 by the authors; licensee MDPI, Basel, Switzerland. http://creativecommons.org/licenses/by/3.0/ This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
spellingShingle Article
Yuri, Tamaki
Kimball, Rebecca T.
Harshman, John
Bowie, Rauri C. K.
Braun, Michael J.
Chojnowski, Jena L.
Han, Kin-Lan
Hackett, Shannon J.
Huddleston, Christopher J.
Moore, William S.
Reddy, Sushma
Sheldon, Frederick H.
Steadman, David W.
Witt, Christopher C.
Braun, Edward L.
Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
title Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
title_full Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
title_fullStr Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
title_full_unstemmed Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
title_short Parsimony and Model-Based Analyses of Indels in Avian Nuclear Genes Reveal Congruent and Incongruent Phylogenetic Signals
title_sort parsimony and model-based analyses of indels in avian nuclear genes reveal congruent and incongruent phylogenetic signals
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4009869/
https://www.ncbi.nlm.nih.gov/pubmed/24832669
http://dx.doi.org/10.3390/biology2010419
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