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

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

Research output: Contribution to journalArticlepeer-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 languageEnglish
Article number145
Number of pages16
JournalGenome Biology
Volume19
DOIs
Publication statusPublished - 25 Sep 2018

Keywords

  • Admixture
  • Composite likelihood
  • Inference
  • Orangutan
  • Population history
  • Recombination

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