Cargando…

Inference of recombination maps from a single pair of genomes and its application to ancient samples

Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefor...

Descripción completa

Detalles Bibliográficos
Autores principales: V. Barroso, Gustavo, Puzović, Nataša, Dutheil, Julien Y.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879166/
https://www.ncbi.nlm.nih.gov/pubmed/31725722
http://dx.doi.org/10.1371/journal.pgen.1008449
_version_ 1783473569006616576
author V. Barroso, Gustavo
Puzović, Nataša
Dutheil, Julien Y.
author_facet V. Barroso, Gustavo
Puzović, Nataša
Dutheil, Julien Y.
author_sort V. Barroso, Gustavo
collection PubMed
description Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datasets cannot be generated easily, such as non-model or ancient species. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the spatial variation in recombination rate. Using extensive simulations and sequence data from humans, fruit-flies and a fungal pathogen, we demonstrate that iSMC accurately infers recombination maps under a wide range of scenarios–remarkably, even from a single pair of unphased genomes. We exploit this possibility and reconstruct the recombination maps of ancient hominins. We report that the ancient and modern maps are correlated in a manner that reflects the established phylogeny of Neanderthals, Denisovans, and modern human populations.
format Online
Article
Text
id pubmed-6879166
institution National Center for Biotechnology Information
language English
publishDate 2019
publisher Public Library of Science
record_format MEDLINE/PubMed
spelling pubmed-68791662019-12-06 Inference of recombination maps from a single pair of genomes and its application to ancient samples V. Barroso, Gustavo Puzović, Nataša Dutheil, Julien Y. PLoS Genet Research Article Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datasets cannot be generated easily, such as non-model or ancient species. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the spatial variation in recombination rate. Using extensive simulations and sequence data from humans, fruit-flies and a fungal pathogen, we demonstrate that iSMC accurately infers recombination maps under a wide range of scenarios–remarkably, even from a single pair of unphased genomes. We exploit this possibility and reconstruct the recombination maps of ancient hominins. We report that the ancient and modern maps are correlated in a manner that reflects the established phylogeny of Neanderthals, Denisovans, and modern human populations. Public Library of Science 2019-11-14 /pmc/articles/PMC6879166/ /pubmed/31725722 http://dx.doi.org/10.1371/journal.pgen.1008449 Text en © 2019 V. Barroso et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
V. Barroso, Gustavo
Puzović, Nataša
Dutheil, Julien Y.
Inference of recombination maps from a single pair of genomes and its application to ancient samples
title Inference of recombination maps from a single pair of genomes and its application to ancient samples
title_full Inference of recombination maps from a single pair of genomes and its application to ancient samples
title_fullStr Inference of recombination maps from a single pair of genomes and its application to ancient samples
title_full_unstemmed Inference of recombination maps from a single pair of genomes and its application to ancient samples
title_short Inference of recombination maps from a single pair of genomes and its application to ancient samples
title_sort inference of recombination maps from a single pair of genomes and its application to ancient samples
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6879166/
https://www.ncbi.nlm.nih.gov/pubmed/31725722
http://dx.doi.org/10.1371/journal.pgen.1008449
work_keys_str_mv AT vbarrosogustavo inferenceofrecombinationmapsfromasinglepairofgenomesanditsapplicationtoancientsamples
AT puzovicnatasa inferenceofrecombinationmapsfromasinglepairofgenomesanditsapplicationtoancientsamples
AT dutheiljulieny inferenceofrecombinationmapsfromasinglepairofgenomesanditsapplicationtoancientsamples