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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 .

SUBMITTER: Beeravolu CR

PROVIDER: S-EPMC6156964 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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

Beeravolu Champak R CR Hickerson Michael J MJ Frantz Laurent A F LAF Lohse Konrad K

Genome biology 20180925 1

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 ...[more]

PMID: 30253810

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