Analyzing and synthesizing phylogenies using tree alignment graphs.

Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as we...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Stephen A Smith, Joseph W Brown, Cody E Hinchliff
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/36eb0530398c445693823a0322a91ac3
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:36eb0530398c445693823a0322a91ac3
record_format	dspace
spelling	oai:doaj.org-article:36eb0530398c445693823a0322a91ac32021-11-18T05:53:33ZAnalyzing and synthesizing phylogenies using tree alignment graphs.1553-734X1553-735810.1371/journal.pcbi.1003223https://doaj.org/article/36eb0530398c445693823a0322a91ac32013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24086118/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.Stephen A SmithJoseph W BrownCody E HinchliffPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 9, Iss 9, p e1003223 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Stephen A Smith Joseph W Brown Cody E Hinchliff Analyzing and synthesizing phylogenies using tree alignment graphs.
description	Phylogenetic trees are used to analyze and visualize evolution. However, trees can be imperfect datatypes when summarizing multiple trees. This is especially problematic when accommodating for biological phenomena such as horizontal gene transfer, incomplete lineage sorting, and hybridization, as well as topological conflict between datasets. Additionally, researchers may want to combine information from sets of trees that have partially overlapping taxon sets. To address the problem of analyzing sets of trees with conflicting relationships and partially overlapping taxon sets, we introduce methods for aligning, synthesizing and analyzing rooted phylogenetic trees within a graph, called a tree alignment graph (TAG). The TAG can be queried and analyzed to explore uncertainty and conflict. It can also be synthesized to construct trees, presenting an alternative to supertrees approaches. We demonstrate these methods with two empirical datasets. In order to explore uncertainty, we constructed a TAG of the bootstrap trees from the Angiosperm Tree of Life project. Analysis of the resulting graph demonstrates that areas of the dataset that are unresolved in majority-rule consensus tree analyses can be understood in more detail within the context of a graph structure, using measures incorporating node degree and adjacency support. As an exercise in synthesis (i.e., summarization of a TAG constructed from the alignment trees), we also construct a TAG consisting of the taxonomy and source trees from a recent comprehensive bird study. We synthesized this graph into a tree that can be reconstructed in a repeatable fashion and where the underlying source information can be updated. The methods presented here are tractable for large scale analyses and serve as a basis for an alternative to consensus tree and supertree methods. Furthermore, the exploration of these graphs can expose structures and patterns within the dataset that are otherwise difficult to observe.
format	article
author	Stephen A Smith Joseph W Brown Cody E Hinchliff
author_facet	Stephen A Smith Joseph W Brown Cody E Hinchliff
author_sort	Stephen A Smith
title	Analyzing and synthesizing phylogenies using tree alignment graphs.
title_short	Analyzing and synthesizing phylogenies using tree alignment graphs.
title_full	Analyzing and synthesizing phylogenies using tree alignment graphs.
title_fullStr	Analyzing and synthesizing phylogenies using tree alignment graphs.
title_full_unstemmed	Analyzing and synthesizing phylogenies using tree alignment graphs.
title_sort	analyzing and synthesizing phylogenies using tree alignment graphs.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/36eb0530398c445693823a0322a91ac3
work_keys_str_mv	AT stephenasmith analyzingandsynthesizingphylogeniesusingtreealignmentgraphs AT josephwbrown analyzingandsynthesizingphylogeniesusingtreealignmentgraphs AT codyehinchliff analyzingandsynthesizingphylogeniesusingtreealignmentgraphs
_version_	1718424659098075136

Analyzing and synthesizing phylogenies using tree alignment graphs.

Ejemplares similares