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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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Detalles Bibliográficos
Autores principales: Alanzi, Ayed A. R., Degnan, James H.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8109837/
https://www.ncbi.nlm.nih.gov/pubmed/33970931
http://dx.doi.org/10.1371/journal.pone.0251107
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author Alanzi, Ayed A. R.
Degnan, James H.
author_facet Alanzi, Ayed A. R.
Degnan, James H.
author_sort Alanzi, Ayed A. R.
collection PubMed
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.
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spelling pubmed-81098372021-05-21 Statistical inconsistency of the unrooted minimize deep coalescence criterion Alanzi, Ayed A. R. Degnan, James H. PLoS One Research Article 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. Public Library of Science 2021-05-10 /pmc/articles/PMC8109837/ /pubmed/33970931 http://dx.doi.org/10.1371/journal.pone.0251107 Text en © 2021 Alanzi, Degnan https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Alanzi, Ayed A. R.
Degnan, James H.
Statistical inconsistency of the unrooted minimize deep coalescence criterion
title 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_short Statistical inconsistency of the unrooted minimize deep coalescence criterion
title_sort statistical inconsistency of the unrooted minimize deep coalescence criterion
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8109837/
https://www.ncbi.nlm.nih.gov/pubmed/33970931
http://dx.doi.org/10.1371/journal.pone.0251107
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