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

Champak R Beeravolu; Michael J Hickerson; Laurent A F Frantz; Konrad Lohse

doi:10.1186/s13059-018-1517-y

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

Champak R Beeravolu, Michael J Hickerson, Laurent A F Frantz, Konrad Lohse

School of Biological Sciences

Research output: Contribution to journal › Article › peer-review

Abstract

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 .

Original language	English
Article number	145
Number of pages	16
Journal	Genome Biology
Volume	19
DOIs	https://doi.org/10.1186/s13059-018-1517-y
Publication status	Published - 25 Sept 2018

Keywords / Materials (for Non-textual outputs)

Admixture
Composite likelihood
Inference
Orangutan
Population history
Recombination

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10.1186/s13059-018-1517-yLicence: Creative Commons: Attribution (CC-BY)

LohseEtalGB2018ABLEBlockwiseSiteFrequencySpectraForInferringComplexPopulation
© 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
Final published version, 1.61 MBLicence: Creative Commons: Attribution (CC-BY)

Using genomes to dissect the speciation process - a comparative approach
Lohse, K. (Principal Investigator)
NERC
31/12/14 → 30/11/21
Project: Research

Konrad Lohse
- School of Biological Sciences - Senior Lecturer
Person: Academic: Research Active

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title = "ABLE: Blockwise site frequency spectra for inferring complex population histories and recombination",

abstract = "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 .",

keywords = "Admixture, Composite likelihood, Inference, Orangutan, Population history, Recombination",

author = "Beeravolu, \{Champak R\} and Hickerson, \{Michael J\} and Frantz, \{Laurent A F\} and Konrad Lohse",

year = "2018",

month = sep,

day = "25",

doi = "10.1186/s13059-018-1517-y",

language = "English",

volume = "19",

journal = "Genome Biology",

issn = "1465-6906",

publisher = "BioMed Central",

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TY - JOUR

T1 - ABLE

T2 - Blockwise site frequency spectra for inferring complex population histories and recombination

AU - Beeravolu, Champak R

AU - Hickerson, Michael J

AU - Frantz, Laurent A F

AU - Lohse, Konrad

PY - 2018/9/25

Y1 - 2018/9/25

N2 - 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 .

AB - 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 .

KW - Admixture

KW - Composite likelihood

KW - Inference

KW - Orangutan

KW - Population history

KW - Recombination

U2 - 10.1186/s13059-018-1517-y

DO - 10.1186/s13059-018-1517-y

M3 - Article

C2 - 30253810

SN - 1465-6906

VL - 19

JO - Genome Biology

JF - Genome Biology

M1 - 145

ER -

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

Abstract

Keywords / Materials (for Non-textual outputs)

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Using genomes to dissect the speciation process - a comparative approach

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Konrad Lohse

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