Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.

The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we eva...

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Autores principales:	Bin Lu, Weizhao Yang, Qiang Dai, Jinzhong Fu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/12d98cb032804d3babc46ee55196c84b
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spelling	oai:doaj.org-article:12d98cb032804d3babc46ee55196c84b2021-11-18T08:45:19ZUsing genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.1932-620310.1371/journal.pone.0079348https://doaj.org/article/12d98cb032804d3babc46ee55196c84b2013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24278129/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a "genes as characters" approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters provides a convenient method for examining gene and genome evolution.Bin LuWeizhao YangQiang DaiJinzhong FuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 11, p e79348 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bin Lu Weizhao Yang Qiang Dai Jinzhong Fu Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.
description	The phylogenetic position of turtles within the vertebrate tree of life remains controversial. Conflicting conclusions from different studies are likely a consequence of systematic error in the tree construction process, rather than random error from small amounts of data. Using genomic data, we evaluate the phylogenetic position of turtles with both conventional concatenated data analysis and a "genes as characters" approach. Two datasets were constructed, one with seven species (human, opossum, zebra finch, chicken, green anole, Chinese pond turtle, and western clawed frog) and 4584 orthologous genes, and the second with four additional species (soft-shelled turtle, Nile crocodile, royal python, and tuatara) but only 1638 genes. Our concatenated data analysis strongly supported turtle as the sister-group to archosaurs (the archosaur hypothesis), similar to several recent genomic data based studies using similar methods. When using genes as characters and gene trees as character-state trees with equal weighting for each gene, however, our parsimony analysis suggested that turtles are possibly sister-group to diapsids, archosaurs, or lepidosaurs. None of these resolutions were strongly supported by bootstraps. Furthermore, our incongruence analysis clearly demonstrated that there is a large amount of inconsistency among genes and most of the conflict relates to the placement of turtles. We conclude that the uncertain placement of turtles is a reflection of the true state of nature. Concatenated data analysis of large and heterogeneous datasets likely suffers from systematic error and over-estimates of confidence as a consequence of a large number of characters. Using genes as characters offers an alternative for phylogenomic analysis. It has potential to reduce systematic error, such as data heterogeneity and long-branch attraction, and it can also avoid problems associated with computation time and model selection. Finally, treating genes as characters provides a convenient method for examining gene and genome evolution.
format	article
author	Bin Lu Weizhao Yang Qiang Dai Jinzhong Fu
author_facet	Bin Lu Weizhao Yang Qiang Dai Jinzhong Fu
author_sort	Bin Lu
title	Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.
title_short	Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.
title_full	Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.
title_fullStr	Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.
title_full_unstemmed	Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.
title_sort	using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/12d98cb032804d3babc46ee55196c84b
work_keys_str_mv	AT binlu usinggenesascharactersandaparsimonyanalysistoexplorethephylogeneticpositionofturtles AT weizhaoyang usinggenesascharactersandaparsimonyanalysistoexplorethephylogeneticpositionofturtles AT qiangdai usinggenesascharactersandaparsimonyanalysistoexplorethephylogeneticpositionofturtles AT jinzhongfu usinggenesascharactersandaparsimonyanalysistoexplorethephylogeneticpositionofturtles
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Using genes as characters and a parsimony analysis to explore the phylogenetic position of turtles.

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