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Reconstructing past changes in locus-specific recombination rates

BACKGROUND: Recombination rates vary at the level of the species, population and individual. Now recognized as a transient feature of the genome, recombination rates at a given locus can change markedly over time. Existing inferential methods, predominantly based on linkage disequilibrium patterns,...

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Autores principales: Cox, Murray P, Holland, Barbara R, Wilkins, Matthew C, Schmid, Jan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605148/
https://www.ncbi.nlm.nih.gov/pubmed/23442125
http://dx.doi.org/10.1186/1471-2156-14-11
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author Cox, Murray P
Holland, Barbara R
Wilkins, Matthew C
Schmid, Jan
author_facet Cox, Murray P
Holland, Barbara R
Wilkins, Matthew C
Schmid, Jan
author_sort Cox, Murray P
collection PubMed
description BACKGROUND: Recombination rates vary at the level of the species, population and individual. Now recognized as a transient feature of the genome, recombination rates at a given locus can change markedly over time. Existing inferential methods, predominantly based on linkage disequilibrium patterns, return a long-term average estimate of past recombination rates. Such estimates can be misleading, but no analytical framework to infer recombination rates that have changed over time is currently available. RESULTS: We apply coalescent modeling in conjunction with a suite of summary statistics to show that the recombination history of a locus can be reconstructed from a time series of genetic samples. More usefully, we describe a new method, based on n-tuple dataset subsampling, to infer past changes in recombination rate from DNA sequences taken at a single time point. This subsampling strategy can correctly assign simulated loci to constant, increasing and decreasing recombination models with an accuracy of 84%. CONCLUSIONS: While providing an important stepping-stone to determining past recombination rates, n-tuple subsampling still exhibits a moderate error rate. Theoretical limitations indicated by coalescent theory suggest that highly accurate inference of past recombination rates will remain challenging. Nevertheless, we show for the first time that reconstructing historic recombination rates is possible in principle.
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spelling pubmed-36051482013-03-26 Reconstructing past changes in locus-specific recombination rates Cox, Murray P Holland, Barbara R Wilkins, Matthew C Schmid, Jan BMC Genet Research Article BACKGROUND: Recombination rates vary at the level of the species, population and individual. Now recognized as a transient feature of the genome, recombination rates at a given locus can change markedly over time. Existing inferential methods, predominantly based on linkage disequilibrium patterns, return a long-term average estimate of past recombination rates. Such estimates can be misleading, but no analytical framework to infer recombination rates that have changed over time is currently available. RESULTS: We apply coalescent modeling in conjunction with a suite of summary statistics to show that the recombination history of a locus can be reconstructed from a time series of genetic samples. More usefully, we describe a new method, based on n-tuple dataset subsampling, to infer past changes in recombination rate from DNA sequences taken at a single time point. This subsampling strategy can correctly assign simulated loci to constant, increasing and decreasing recombination models with an accuracy of 84%. CONCLUSIONS: While providing an important stepping-stone to determining past recombination rates, n-tuple subsampling still exhibits a moderate error rate. Theoretical limitations indicated by coalescent theory suggest that highly accurate inference of past recombination rates will remain challenging. Nevertheless, we show for the first time that reconstructing historic recombination rates is possible in principle. BioMed Central 2013-02-25 /pmc/articles/PMC3605148/ /pubmed/23442125 http://dx.doi.org/10.1186/1471-2156-14-11 Text en Copyright ©2013 Cox et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Cox, Murray P
Holland, Barbara R
Wilkins, Matthew C
Schmid, Jan
Reconstructing past changes in locus-specific recombination rates
title Reconstructing past changes in locus-specific recombination rates
title_full Reconstructing past changes in locus-specific recombination rates
title_fullStr Reconstructing past changes in locus-specific recombination rates
title_full_unstemmed Reconstructing past changes in locus-specific recombination rates
title_short Reconstructing past changes in locus-specific recombination rates
title_sort reconstructing past changes in locus-specific recombination rates
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605148/
https://www.ncbi.nlm.nih.gov/pubmed/23442125
http://dx.doi.org/10.1186/1471-2156-14-11
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