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The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure

In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of populati...

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Autores principales: Rodríguez, Willy, Mazet, Olivier, Grusea, Simona, Arredondo, Armando, Corujo, Josué M., Boitard, Simon, Chikhi, Lounès
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6221895/
https://www.ncbi.nlm.nih.gov/pubmed/30293985
http://dx.doi.org/10.1038/s41437-018-0148-0
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author Rodríguez, Willy
Mazet, Olivier
Grusea, Simona
Arredondo, Armando
Corujo, Josué M.
Boitard, Simon
Chikhi, Lounès
author_facet Rodríguez, Willy
Mazet, Olivier
Grusea, Simona
Arredondo, Armando
Corujo, Josué M.
Boitard, Simon
Chikhi, Lounès
author_sort Rodríguez, Willy
collection PubMed
description In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362–371, 2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T(2) (the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective.
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spelling pubmed-62218952019-04-12 The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure Rodríguez, Willy Mazet, Olivier Grusea, Simona Arredondo, Armando Corujo, Josué M. Boitard, Simon Chikhi, Lounès Heredity (Edinb) Article In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362–371, 2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T(2) (the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective. Springer International Publishing 2018-10-07 2018-12 /pmc/articles/PMC6221895/ /pubmed/30293985 http://dx.doi.org/10.1038/s41437-018-0148-0 Text en © The Author(s) 2018 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/.
spellingShingle Article
Rodríguez, Willy
Mazet, Olivier
Grusea, Simona
Arredondo, Armando
Corujo, Josué M.
Boitard, Simon
Chikhi, Lounès
The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure
title The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure
title_full The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure
title_fullStr The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure
title_full_unstemmed The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure
title_short The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure
title_sort iicr and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6221895/
https://www.ncbi.nlm.nih.gov/pubmed/30293985
http://dx.doi.org/10.1038/s41437-018-0148-0
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