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Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola

Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) techniq...

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Autores principales: Balmori-de la Puente, Alfonso, Ventura, Jacint, Miñarro, Marcos, Somoano, Aitor, Hey, Jody, Castresana, Jose
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8904462/
https://www.ncbi.nlm.nih.gov/pubmed/35260719
http://dx.doi.org/10.1038/s41598-022-07877-y
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author Balmori-de la Puente, Alfonso
Ventura, Jacint
Miñarro, Marcos
Somoano, Aitor
Hey, Jody
Castresana, Jose
author_facet Balmori-de la Puente, Alfonso
Ventura, Jacint
Miñarro, Marcos
Somoano, Aitor
Hey, Jody
Castresana, Jose
author_sort Balmori-de la Puente, Alfonso
collection PubMed
description Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species.
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spelling pubmed-89044622022-03-09 Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola Balmori-de la Puente, Alfonso Ventura, Jacint Miñarro, Marcos Somoano, Aitor Hey, Jody Castresana, Jose Sci Rep Article Molecular dating methods of population splits are crucial in evolutionary biology, but they present important difficulties due to the complexity of the genealogical relationships of genes and past migrations between populations. Using the double digest restriction-site associated DNA (ddRAD) technique and an isolation-with-migration (IM) model, we studied the evolutionary history of water vole populations of the genus Arvicola, a group of complex evolution with fossorial and semi-aquatic ecotypes. To do this, we first estimated mutation rates of ddRAD loci using a phylogenetic approach. An IM model was then used to estimate split times and other relevant demographic parameters. A set of 300 ddRAD loci that included 85 calibrated loci resulted in good mixing and model convergence. The results showed that the two populations of A. scherman present in the Iberian Peninsula split 34 thousand years ago, during the last glaciation. In addition, the much greater divergence from its sister species, A. amphibius, may help to clarify the controversial taxonomy of the genus. We conclude that this approach, based on ddRAD data and an IM model, is highly useful for analyzing the origin of populations and species. Nature Publishing Group UK 2022-03-08 /pmc/articles/PMC8904462/ /pubmed/35260719 http://dx.doi.org/10.1038/s41598-022-07877-y Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Balmori-de la Puente, Alfonso
Ventura, Jacint
Miñarro, Marcos
Somoano, Aitor
Hey, Jody
Castresana, Jose
Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
title Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
title_full Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
title_fullStr Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
title_full_unstemmed Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
title_short Divergence time estimation using ddRAD data and an isolation-with-migration model applied to water vole populations of Arvicola
title_sort divergence time estimation using ddrad data and an isolation-with-migration model applied to water vole populations of arvicola
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8904462/
https://www.ncbi.nlm.nih.gov/pubmed/35260719
http://dx.doi.org/10.1038/s41598-022-07877-y
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