Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: Arredondo, Armando, Mourato, Beatriz, Nguyen, Khoa, Boitard, Simon, Rodríguez, Willy, Mazet, Olivier, Chikhi, Lounès
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2021
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
_version_ 1783703555990880256
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
work_keys_str_mv AT arredondoarmando inferringnumberofpopulationsandchangesinconnectivityunderthenislandmodel
AT mouratobeatriz inferringnumberofpopulationsandchangesinconnectivityunderthenislandmodel
AT nguyenkhoa inferringnumberofpopulationsandchangesinconnectivityunderthenislandmodel
AT boitardsimon inferringnumberofpopulationsandchangesinconnectivityunderthenislandmodel
AT rodriguezwilly inferringnumberofpopulationsandchangesinconnectivityunderthenislandmodel
AT mazetolivier inferringnumberofpopulationsandchangesinconnectivityunderthenislandmodel
AT chikhilounes inferringnumberofpopulationsandchangesinconnectivityunderthenislandmodel