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Estimates of introgression as a function of pairwise distances

BACKGROUND: Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation by natural and/or sexual selection. Fueled by research in a few model systems...

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Autores principales: Pfeifer, Bastian, Kapan, Durrell D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6480520/
https://www.ncbi.nlm.nih.gov/pubmed/31014244
http://dx.doi.org/10.1186/s12859-019-2747-z
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author Pfeifer, Bastian
Kapan, Durrell D.
author_facet Pfeifer, Bastian
Kapan, Durrell D.
author_sort Pfeifer, Bastian
collection PubMed
description BACKGROUND: Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation by natural and/or sexual selection. Fueled by research in a few model systems where phenotypic hybrids are easily identified, research into hybridization and introgression (the flow of genes between species) has exploded with the advent of whole-genome sequencing and emerging methods to detect the signature of hybridization at the whole-genome or chromosome level. Amongst these are a general class of methods that utilize patterns of single-nucleotide polymorphisms (SNPs) across a tree as markers of hybridization. These methods have been applied to a variety of genomic systems ranging from butterflies to Neanderthals to detect introgression, however, when employed at a fine genomic scale these methods do not perform well to quantify introgression in small sample windows. RESULTS: We introduce a novel method to detect introgression by combining two widely used statistics: pairwise nucleotide diversity d(xy) and Patterson’s D. The resulting statistic, the distance fraction (d(f)), accounts for genetic distance across possible topologies and is designed to simultaneously detect and quantify introgression. We also relate our new method to the recently published f(d) and incorporate these statistics into the powerful genomics R-package PopGenome, freely available on GitHub (pievos101/PopGenome) and the Comprehensive R Archive Network (CRAN). The supplemental material contains a wide range of simulation studies and a detailed manual how to perform the statistics within the PopGenome framework. CONCLUSION: We present a new distance based statistic d(f) that avoids the pitfalls of Patterson’s D when applied to small genomic regions and accurately quantifies the fraction of introgression (f) for a wide range of simulation scenarios. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2747-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-64805202019-05-01 Estimates of introgression as a function of pairwise distances Pfeifer, Bastian Kapan, Durrell D. BMC Bioinformatics Methodology Article BACKGROUND: Research over the last 10 years highlights the increasing importance of hybridization between species as a major force structuring the evolution of genomes and potentially providing raw material for adaptation by natural and/or sexual selection. Fueled by research in a few model systems where phenotypic hybrids are easily identified, research into hybridization and introgression (the flow of genes between species) has exploded with the advent of whole-genome sequencing and emerging methods to detect the signature of hybridization at the whole-genome or chromosome level. Amongst these are a general class of methods that utilize patterns of single-nucleotide polymorphisms (SNPs) across a tree as markers of hybridization. These methods have been applied to a variety of genomic systems ranging from butterflies to Neanderthals to detect introgression, however, when employed at a fine genomic scale these methods do not perform well to quantify introgression in small sample windows. RESULTS: We introduce a novel method to detect introgression by combining two widely used statistics: pairwise nucleotide diversity d(xy) and Patterson’s D. The resulting statistic, the distance fraction (d(f)), accounts for genetic distance across possible topologies and is designed to simultaneously detect and quantify introgression. We also relate our new method to the recently published f(d) and incorporate these statistics into the powerful genomics R-package PopGenome, freely available on GitHub (pievos101/PopGenome) and the Comprehensive R Archive Network (CRAN). The supplemental material contains a wide range of simulation studies and a detailed manual how to perform the statistics within the PopGenome framework. CONCLUSION: We present a new distance based statistic d(f) that avoids the pitfalls of Patterson’s D when applied to small genomic regions and accurately quantifies the fraction of introgression (f) for a wide range of simulation scenarios. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-019-2747-z) contains supplementary material, which is available to authorized users. BioMed Central 2019-04-23 /pmc/articles/PMC6480520/ /pubmed/31014244 http://dx.doi.org/10.1186/s12859-019-2747-z Text en © The Author(s) 2019 Open Access This article is 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 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 Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Methodology Article
Pfeifer, Bastian
Kapan, Durrell D.
Estimates of introgression as a function of pairwise distances
title Estimates of introgression as a function of pairwise distances
title_full Estimates of introgression as a function of pairwise distances
title_fullStr Estimates of introgression as a function of pairwise distances
title_full_unstemmed Estimates of introgression as a function of pairwise distances
title_short Estimates of introgression as a function of pairwise distances
title_sort estimates of introgression as a function of pairwise distances
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6480520/
https://www.ncbi.nlm.nih.gov/pubmed/31014244
http://dx.doi.org/10.1186/s12859-019-2747-z
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