Cargando…
Inference of Historical Population-Size Changes with Allele-Frequency Data
With up to millions of nearly neutral polymorphisms now being routinely sampled in population-genomic surveys, it is possible to estimate the site-frequency spectrum of such sites with high precision. Each frequency class reflects a mixture of potentially unique demographic histories, which can be r...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Genetics Society of America
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6945023/ https://www.ncbi.nlm.nih.gov/pubmed/31699776 http://dx.doi.org/10.1534/g3.119.400854 |
_version_ | 1783485111241539584 |
---|---|
author | Lynch, Michael Haubold, Bernhard Pfaffelhuber, Peter Maruki, Takahiro |
author_facet | Lynch, Michael Haubold, Bernhard Pfaffelhuber, Peter Maruki, Takahiro |
author_sort | Lynch, Michael |
collection | PubMed |
description | With up to millions of nearly neutral polymorphisms now being routinely sampled in population-genomic surveys, it is possible to estimate the site-frequency spectrum of such sites with high precision. Each frequency class reflects a mixture of potentially unique demographic histories, which can be revealed using theory for the probability distributions of the starting and ending points of branch segments over all possible coalescence trees. Such distributions are completely independent of past population history, which only influences the segment lengths, providing the basis for estimating average population sizes separating tree-wide coalescence events. The history of population-size change experienced by a sample of polymorphisms can then be dissected in a model-flexible fashion, and extension of this theory allows estimation of the mean and full distribution of long-term effective population sizes and ages of alleles of specific frequencies. Here, we outline the basic theory underlying the conceptual approach, develop and test an efficient statistical procedure for parameter estimation, and apply this to multiple population-genomic datasets for the microcrustacean Daphnia pulex. |
format | Online Article Text |
id | pubmed-6945023 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Genetics Society of America |
record_format | MEDLINE/PubMed |
spelling | pubmed-69450232020-01-09 Inference of Historical Population-Size Changes with Allele-Frequency Data Lynch, Michael Haubold, Bernhard Pfaffelhuber, Peter Maruki, Takahiro G3 (Bethesda) Investigations With up to millions of nearly neutral polymorphisms now being routinely sampled in population-genomic surveys, it is possible to estimate the site-frequency spectrum of such sites with high precision. Each frequency class reflects a mixture of potentially unique demographic histories, which can be revealed using theory for the probability distributions of the starting and ending points of branch segments over all possible coalescence trees. Such distributions are completely independent of past population history, which only influences the segment lengths, providing the basis for estimating average population sizes separating tree-wide coalescence events. The history of population-size change experienced by a sample of polymorphisms can then be dissected in a model-flexible fashion, and extension of this theory allows estimation of the mean and full distribution of long-term effective population sizes and ages of alleles of specific frequencies. Here, we outline the basic theory underlying the conceptual approach, develop and test an efficient statistical procedure for parameter estimation, and apply this to multiple population-genomic datasets for the microcrustacean Daphnia pulex. Genetics Society of America 2019-11-07 /pmc/articles/PMC6945023/ /pubmed/31699776 http://dx.doi.org/10.1534/g3.119.400854 Text en Copyright © 2020 Lynch et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Investigations Lynch, Michael Haubold, Bernhard Pfaffelhuber, Peter Maruki, Takahiro Inference of Historical Population-Size Changes with Allele-Frequency Data |
title | Inference of Historical Population-Size Changes with Allele-Frequency Data |
title_full | Inference of Historical Population-Size Changes with Allele-Frequency Data |
title_fullStr | Inference of Historical Population-Size Changes with Allele-Frequency Data |
title_full_unstemmed | Inference of Historical Population-Size Changes with Allele-Frequency Data |
title_short | Inference of Historical Population-Size Changes with Allele-Frequency Data |
title_sort | inference of historical population-size changes with allele-frequency data |
topic | Investigations |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6945023/ https://www.ncbi.nlm.nih.gov/pubmed/31699776 http://dx.doi.org/10.1534/g3.119.400854 |
work_keys_str_mv | AT lynchmichael inferenceofhistoricalpopulationsizechangeswithallelefrequencydata AT hauboldbernhard inferenceofhistoricalpopulationsizechangeswithallelefrequencydata AT pfaffelhuberpeter inferenceofhistoricalpopulationsizechangeswithallelefrequencydata AT marukitakahiro inferenceofhistoricalpopulationsizechangeswithallelefrequencydata |