Statistical inconsistency of the unrooted minimize deep coalescence criterion.

Species trees, which describe the evolutionary relationships between species, are often inferred from gene trees, which describe the ancestral relationships between sequences sampled at different loci from the species of interest. A common approach to inferring species trees from gene trees is motiv...

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Autores principales:	Ayed A R Alanzi, James H Degnan
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3e51e79f96b44df7a89adb634d45f012
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spelling	oai:doaj.org-article:3e51e79f96b44df7a89adb634d45f0122021-12-02T20:11:25ZStatistical inconsistency of the unrooted minimize deep coalescence criterion.1932-620310.1371/journal.pone.0251107https://doaj.org/article/3e51e79f96b44df7a89adb634d45f0122021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0251107https://doaj.org/toc/1932-6203Species trees, which describe the evolutionary relationships between species, are often inferred from gene trees, which describe the ancestral relationships between sequences sampled at different loci from the species of interest. A common approach to inferring species trees from gene trees is motivated by supposing that gene tree variation is due to incomplete lineage sorting, also known as deep coalescence. One of the earliest methods motivated by deep coalescence is to find the species tree that minimizes the number of deep coalescent events needed to explain discrepancies between the species tree and input gene trees. This minimize deep coalescence (MDC) criterion can be applied in both rooted and unrooted settings. where either rooted or unrooted gene trees can be used to infer a rooted species tree. Previous work has shown that MDC is statistically inconsistent in the rooted setting, meaning that under a probabilistic model for deep coalescence, the multispecies coalescent, for some species trees, increasing the number of input gene trees does not make the method more likely to return a correct species tree. Here, we obtain analogous results in the unrooted setting, showing conditions leading to inconsistency of the MDC criterion using the multispecies coalescent model with unrooted gene trees for four taxa and five taxa.Ayed A R AlanziJames H DegnanPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 5, p e0251107 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Ayed A R Alanzi James H Degnan Statistical inconsistency of the unrooted minimize deep coalescence criterion.
description	Species trees, which describe the evolutionary relationships between species, are often inferred from gene trees, which describe the ancestral relationships between sequences sampled at different loci from the species of interest. A common approach to inferring species trees from gene trees is motivated by supposing that gene tree variation is due to incomplete lineage sorting, also known as deep coalescence. One of the earliest methods motivated by deep coalescence is to find the species tree that minimizes the number of deep coalescent events needed to explain discrepancies between the species tree and input gene trees. This minimize deep coalescence (MDC) criterion can be applied in both rooted and unrooted settings. where either rooted or unrooted gene trees can be used to infer a rooted species tree. Previous work has shown that MDC is statistically inconsistent in the rooted setting, meaning that under a probabilistic model for deep coalescence, the multispecies coalescent, for some species trees, increasing the number of input gene trees does not make the method more likely to return a correct species tree. Here, we obtain analogous results in the unrooted setting, showing conditions leading to inconsistency of the MDC criterion using the multispecies coalescent model with unrooted gene trees for four taxa and five taxa.
format	article
author	Ayed A R Alanzi James H Degnan
author_facet	Ayed A R Alanzi James H Degnan
author_sort	Ayed A R Alanzi
title	Statistical inconsistency of the unrooted minimize deep coalescence criterion.
title_short	Statistical inconsistency of the unrooted minimize deep coalescence criterion.
title_full	Statistical inconsistency of the unrooted minimize deep coalescence criterion.
title_fullStr	Statistical inconsistency of the unrooted minimize deep coalescence criterion.
title_full_unstemmed	Statistical inconsistency of the unrooted minimize deep coalescence criterion.
title_sort	statistical inconsistency of the unrooted minimize deep coalescence criterion.
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/3e51e79f96b44df7a89adb634d45f012
work_keys_str_mv	AT ayedaralanzi statisticalinconsistencyoftheunrootedminimizedeepcoalescencecriterion AT jameshdegnan statisticalinconsistencyoftheunrootedminimizedeepcoalescencecriterion
_version_	1718374877620076544

Statistical inconsistency of the unrooted minimize deep coalescence criterion.

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