Coalescent-based genome analyses resolve the early branches of the euarchontoglires.

Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermopt...

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Autores principales:	Vikas Kumar, Björn M Hallström, Axel Janke
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/202ac81d6040461dbcde0e07340ca463
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spelling	oai:doaj.org-article:202ac81d6040461dbcde0e07340ca4632021-11-18T07:51:14ZCoalescent-based genome analyses resolve the early branches of the euarchontoglires.1932-620310.1371/journal.pone.0060019https://doaj.org/article/202ac81d6040461dbcde0e07340ca4632013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23560065/?tool=EBIhttps://doaj.org/toc/1932-6203Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.Vikas KumarBjörn M HallströmAxel JankePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 4, p e60019 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Vikas Kumar Björn M Hallström Axel Janke Coalescent-based genome analyses resolve the early branches of the euarchontoglires.
description	Despite numerous large-scale phylogenomic studies, certain parts of the mammalian tree are extraordinarily difficult to resolve. We used the coding regions from 19 completely sequenced genomes to study the relationships within the super-clade Euarchontoglires (Primates, Rodentia, Lagomorpha, Dermoptera and Scandentia) because the placement of Scandentia within this clade is controversial. The difficulty in resolving this issue is due to the short time spans between the early divergences of Euarchontoglires, which may cause incongruent gene trees. The conflict in the data can be depicted by network analyses and the contentious relationships are best reconstructed by coalescent-based analyses. This method is expected to be superior to analyses of concatenated data in reconstructing a species tree from numerous gene trees. The total concatenated dataset used to study the relationships in this group comprises 5,875 protein-coding genes (9,799,170 nucleotides) from all orders except Dermoptera (flying lemurs). Reconstruction of the species tree from 1,006 gene trees using coalescent models placed Scandentia as sister group to the primates, which is in agreement with maximum likelihood analyses of concatenated nucleotide sequence data. Additionally, both analytical approaches favoured the Tarsier to be sister taxon to Anthropoidea, thus belonging to the Haplorrhine clade. When divergence times are short such as in radiations over periods of a few million years, even genome scale analyses struggle to resolve phylogenetic relationships. On these short branches processes such as incomplete lineage sorting and possibly hybridization occur and make it preferable to base phylogenomic analyses on coalescent methods.
format	article
author	Vikas Kumar Björn M Hallström Axel Janke
author_facet	Vikas Kumar Björn M Hallström Axel Janke
author_sort	Vikas Kumar
title	Coalescent-based genome analyses resolve the early branches of the euarchontoglires.
title_short	Coalescent-based genome analyses resolve the early branches of the euarchontoglires.
title_full	Coalescent-based genome analyses resolve the early branches of the euarchontoglires.
title_fullStr	Coalescent-based genome analyses resolve the early branches of the euarchontoglires.
title_full_unstemmed	Coalescent-based genome analyses resolve the early branches of the euarchontoglires.
title_sort	coalescent-based genome analyses resolve the early branches of the euarchontoglires.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/202ac81d6040461dbcde0e07340ca463
work_keys_str_mv	AT vikaskumar coalescentbasedgenomeanalysesresolvetheearlybranchesoftheeuarchontoglires AT bjornmhallstrom coalescentbasedgenomeanalysesresolvetheearlybranchesoftheeuarchontoglires AT axeljanke coalescentbasedgenomeanalysesresolvetheearlybranchesoftheeuarchontoglires
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Coalescent-based genome analyses resolve the early branches of the euarchontoglires.

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