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Chloroplast Phylogenomic Inference of Green Algae Relationships

The green algal phylum Chlorophyta has six diverse classes, but the phylogenetic relationship of the classes within Chlorophyta remains uncertain. In order to better understand the ancient Chlorophyta evolution, we have applied a site pattern sorting method to study compositional heterogeneity and t...

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Autores principales: Sun, Linhua, Fang, Ling, Zhang, Zhenhua, Chang, Xin, Penny, David, Zhong, Bojian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742797/
https://www.ncbi.nlm.nih.gov/pubmed/26846729
http://dx.doi.org/10.1038/srep20528
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author Sun, Linhua
Fang, Ling
Zhang, Zhenhua
Chang, Xin
Penny, David
Zhong, Bojian
author_facet Sun, Linhua
Fang, Ling
Zhang, Zhenhua
Chang, Xin
Penny, David
Zhong, Bojian
author_sort Sun, Linhua
collection PubMed
description The green algal phylum Chlorophyta has six diverse classes, but the phylogenetic relationship of the classes within Chlorophyta remains uncertain. In order to better understand the ancient Chlorophyta evolution, we have applied a site pattern sorting method to study compositional heterogeneity and the model fit in the green algal chloroplast genomic data. We show that the fastest-evolving sites are significantly correlated with among-site compositional heterogeneity, and these sites have a much poorer fit to the evolutionary model. Our phylogenomic analyses suggest that the class Chlorophyceae is a monophyletic group, and the classes Ulvophyceae, Trebouxiophyceae and Prasinophyceae are non-monophyletic groups. Our proposed phylogenetic tree of Chlorophyta will offer new insights to investigate ancient green algae evolution, and our analytical framework will provide a useful approach for evaluating and mitigating the potential errors of phylogenomic inferences.
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spelling pubmed-47427972016-02-09 Chloroplast Phylogenomic Inference of Green Algae Relationships Sun, Linhua Fang, Ling Zhang, Zhenhua Chang, Xin Penny, David Zhong, Bojian Sci Rep Article The green algal phylum Chlorophyta has six diverse classes, but the phylogenetic relationship of the classes within Chlorophyta remains uncertain. In order to better understand the ancient Chlorophyta evolution, we have applied a site pattern sorting method to study compositional heterogeneity and the model fit in the green algal chloroplast genomic data. We show that the fastest-evolving sites are significantly correlated with among-site compositional heterogeneity, and these sites have a much poorer fit to the evolutionary model. Our phylogenomic analyses suggest that the class Chlorophyceae is a monophyletic group, and the classes Ulvophyceae, Trebouxiophyceae and Prasinophyceae are non-monophyletic groups. Our proposed phylogenetic tree of Chlorophyta will offer new insights to investigate ancient green algae evolution, and our analytical framework will provide a useful approach for evaluating and mitigating the potential errors of phylogenomic inferences. Nature Publishing Group 2016-02-05 /pmc/articles/PMC4742797/ /pubmed/26846729 http://dx.doi.org/10.1038/srep20528 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/
spellingShingle Article
Sun, Linhua
Fang, Ling
Zhang, Zhenhua
Chang, Xin
Penny, David
Zhong, Bojian
Chloroplast Phylogenomic Inference of Green Algae Relationships
title Chloroplast Phylogenomic Inference of Green Algae Relationships
title_full Chloroplast Phylogenomic Inference of Green Algae Relationships
title_fullStr Chloroplast Phylogenomic Inference of Green Algae Relationships
title_full_unstemmed Chloroplast Phylogenomic Inference of Green Algae Relationships
title_short Chloroplast Phylogenomic Inference of Green Algae Relationships
title_sort chloroplast phylogenomic inference of green algae relationships
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742797/
https://www.ncbi.nlm.nih.gov/pubmed/26846729
http://dx.doi.org/10.1038/srep20528
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