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Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure

Though large multilocus genomic data sets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can ske...

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Detalles Bibliográficos
Autores principales: Koch, Hillary, DeGiorgio, Michael
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061232/
https://www.ncbi.nlm.nih.gov/pubmed/32022857
http://dx.doi.org/10.1093/gbe/evaa022
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author Koch, Hillary
DeGiorgio, Michael
author_facet Koch, Hillary
DeGiorgio, Michael
author_sort Koch, Hillary
collection PubMed
description Though large multilocus genomic data sets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI (Taxa with Ancestral structure Species Tree Inference), that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI’s performance in the three- and four-taxon settings and demonstrate the application of TASTI on a six-species Afrotropical mosquito data set. Finally, we have implemented TASTI in an open-source software package for ease of use by the scientific community.
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spelling pubmed-70612322020-03-12 Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure Koch, Hillary DeGiorgio, Michael Genome Biol Evol Research Article Though large multilocus genomic data sets have led to overall improvements in phylogenetic inference, they have posed the new challenge of addressing conflicting signals across the genome. In particular, ancestral population structure, which has been uncovered in a number of diverse species, can skew gene tree frequencies, thereby hindering the performance of species tree estimators. Here we develop a novel maximum likelihood method, termed TASTI (Taxa with Ancestral structure Species Tree Inference), that can infer phylogenies under such scenarios, and find that it has increasing accuracy with increasing numbers of input gene trees, contrasting with the relatively poor performances of methods not tailored for ancestral structure. Moreover, we propose a supertree approach that allows TASTI to scale computationally with increasing numbers of input taxa. We use genetic simulations to assess TASTI’s performance in the three- and four-taxon settings and demonstrate the application of TASTI on a six-species Afrotropical mosquito data set. Finally, we have implemented TASTI in an open-source software package for ease of use by the scientific community. Oxford University Press 2020-02-05 /pmc/articles/PMC7061232/ /pubmed/32022857 http://dx.doi.org/10.1093/gbe/evaa022 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Koch, Hillary
DeGiorgio, Michael
Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure
title Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure
title_full Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure
title_fullStr Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure
title_full_unstemmed Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure
title_short Maximum Likelihood Estimation of Species Trees from Gene Trees in the Presence of Ancestral Population Structure
title_sort maximum likelihood estimation of species trees from gene trees in the presence of ancestral population structure
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7061232/
https://www.ncbi.nlm.nih.gov/pubmed/32022857
http://dx.doi.org/10.1093/gbe/evaa022
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