ABLE: blockwise site frequency spectra for inferring complex population histories and recombination

We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genom...

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Detalles Bibliográficos
Autores principales: Beeravolu, Champak R., Hickerson, Michael J., Frantz, Laurent A. F., Lohse, Konrad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2018
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156964/
https://www.ncbi.nlm.nih.gov/pubmed/30253810
http://dx.doi.org/10.1186/s13059-018-1517-y
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author Beeravolu, Champak R.
Hickerson, Michael J.
Frantz, Laurent A. F.
Lohse, Konrad
author_facet Beeravolu, Champak R.
Hickerson, Michael J.
Frantz, Laurent A. F.
Lohse, Konrad
author_sort Beeravolu, Champak R.
collection PubMed
description We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide multi-locus data (for example, RADSeq) and can also accommodate arbitrarily large samples. We use simulations to demonstrate the accuracy of this method to infer complex histories of divergence and gene flow and reanalyze whole genome data from two species of orangutan. ABLE is available for download at https://github.com/champost/ABLE. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1517-y) contains supplementary material, which is available to authorized users.
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spelling pubmed-61569642018-09-27 ABLE: blockwise site frequency spectra for inferring complex population histories and recombination Beeravolu, Champak R. Hickerson, Michael J. Frantz, Laurent A. F. Lohse, Konrad Genome Biol Method We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel simulation-based composite likelihood method that uses the blockwise site frequency spectrum to jointly infer past demography and recombination. ABLE is explicitly designed for a wide variety of data from unphased diploid genomes to genome-wide multi-locus data (for example, RADSeq) and can also accommodate arbitrarily large samples. We use simulations to demonstrate the accuracy of this method to infer complex histories of divergence and gene flow and reanalyze whole genome data from two species of orangutan. ABLE is available for download at https://github.com/champost/ABLE. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-018-1517-y) contains supplementary material, which is available to authorized users. BioMed Central 2018-09-25 /pmc/articles/PMC6156964/ /pubmed/30253810 http://dx.doi.org/10.1186/s13059-018-1517-y Text en © The Author(s) 2018 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 Method
Beeravolu, Champak R.
Hickerson, Michael J.
Frantz, Laurent A. F.
Lohse, Konrad
ABLE: blockwise site frequency spectra for inferring complex population histories and recombination
title ABLE: blockwise site frequency spectra for inferring complex population histories and recombination
title_full ABLE: blockwise site frequency spectra for inferring complex population histories and recombination
title_fullStr ABLE: blockwise site frequency spectra for inferring complex population histories and recombination
title_full_unstemmed ABLE: blockwise site frequency spectra for inferring complex population histories and recombination
title_short ABLE: blockwise site frequency spectra for inferring complex population histories and recombination
title_sort able: blockwise site frequency spectra for inferring complex population histories and recombination
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6156964/
https://www.ncbi.nlm.nih.gov/pubmed/30253810
http://dx.doi.org/10.1186/s13059-018-1517-y
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