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Inferring number of populations and changes in connectivity under the n-island model
Inferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, ignoring population structure. Alternatively, when structure is assumed, it is defined a priori as a population tree and not inferre...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8178352/ https://www.ncbi.nlm.nih.gov/pubmed/33846579 http://dx.doi.org/10.1038/s41437-021-00426-9 |
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author | Arredondo, Armando Mourato, Beatriz Nguyen, Khoa Boitard, Simon Rodríguez, Willy Mazet, Olivier Chikhi, Lounès |
author_facet | Arredondo, Armando Mourato, Beatriz Nguyen, Khoa Boitard, Simon Rodríguez, Willy Mazet, Olivier Chikhi, Lounès |
author_sort | Arredondo, Armando |
collection | PubMed |
description | Inferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, ignoring population structure. Alternatively, when structure is assumed, it is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate). The IICR can be estimated for a single diploid individual using the PSMC method of Li and Durbin (2011). For an isolated panmictic population, the IICR matches the population size history, and this is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme with limited connection to population size changes. Our method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise stationary symmetrical island models. In our models we assume a fixed number of time periods during which gene flow is constant, but gene flow is allowed to change between time periods. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent. |
format | Online Article Text |
id | pubmed-8178352 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-81783522021-06-07 Inferring number of populations and changes in connectivity under the n-island model Arredondo, Armando Mourato, Beatriz Nguyen, Khoa Boitard, Simon Rodríguez, Willy Mazet, Olivier Chikhi, Lounès Heredity (Edinb) Article Inferring the demographic history of species is one of the greatest challenges in populations genetics. This history is often represented as a history of size changes, ignoring population structure. Alternatively, when structure is assumed, it is defined a priori as a population tree and not inferred. Here we propose a framework based on the IICR (Inverse Instantaneous Coalescence Rate). The IICR can be estimated for a single diploid individual using the PSMC method of Li and Durbin (2011). For an isolated panmictic population, the IICR matches the population size history, and this is how the PSMC outputs are generally interpreted. However, it is increasingly acknowledged that the IICR is a function of the demographic model and sampling scheme with limited connection to population size changes. Our method fits observed IICR curves of diploid individuals with IICR curves obtained under piecewise stationary symmetrical island models. In our models we assume a fixed number of time periods during which gene flow is constant, but gene flow is allowed to change between time periods. We infer the number of islands, their sizes, the periods at which connectivity changes and the corresponding rates of connectivity. Validation with simulated data showed that the method can accurately recover most of the scenario parameters. Our application to a set of five human PSMCs yielded demographic histories that are in agreement with previous studies using similar methods and with recent research suggesting ancient human structure. They are in contrast with the view of human evolution consisting of one ancestral population branching into three large continental and panmictic populations with varying degrees of connectivity and no population structure within each continent. Springer International Publishing 2021-04-12 2021-06 /pmc/articles/PMC8178352/ /pubmed/33846579 http://dx.doi.org/10.1038/s41437-021-00426-9 Text en © The Author(s) 2021, corrected publication 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Arredondo, Armando Mourato, Beatriz Nguyen, Khoa Boitard, Simon Rodríguez, Willy Mazet, Olivier Chikhi, Lounès Inferring number of populations and changes in connectivity under the n-island model |
title | Inferring number of populations and changes in connectivity under the n-island model |
title_full | Inferring number of populations and changes in connectivity under the n-island model |
title_fullStr | Inferring number of populations and changes in connectivity under the n-island model |
title_full_unstemmed | Inferring number of populations and changes in connectivity under the n-island model |
title_short | Inferring number of populations and changes in connectivity under the n-island model |
title_sort | inferring number of populations and changes in connectivity under the n-island model |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8178352/ https://www.ncbi.nlm.nih.gov/pubmed/33846579 http://dx.doi.org/10.1038/s41437-021-00426-9 |
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