ABLE: blockwise site frequency spectrafor inferring complex population histories and recombination

Authors

Champak R. Beeravolu, CUNY City College
Michael J. Hickerson, CUNY City CollegeFollow
Laurent A. F. Frantz, University of Oxford
Konrad Lohse, University of Edinburgh

Document Type

Article

Publication Date

9-25-2018

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.

Comments

This article was originally published in BMC Genome Biology, available at DOI: 10.1186/s13059-018-1517-y.

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0).