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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

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

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Author(s):
Beeravolu, Champak R. [1, 2] ; Hickerson, Michael J. [3, 4, 2] ; Frantz, Laurent A. F. [5, 6] ; Lohse, Konrad [7]
Total Authors: 4
Affiliation:
[1] Univ Zurich, Dept Evolutionary Biol & Environm Studies, CH-8057 Zurich - Switzerland
[2] CUNY, Biol Dept, New York, NY 10031 - USA
[3] Amer Museum Nat Hist, Div Invertebrate Zool, New York, NY 10024 - USA
[4] CUNY, Grad Ctr, New York, NY 10016 - USA
[5] Queen Mary Univ London, Sch Biol & Chem Sci, London E1 4NS - England
[6] Univ Oxford, Res Lab Archeol & Hist Art, Paleogen & Bioarchaeol Res Network, Oxford OX1 3QY - England
[7] Univ Edinburgh, Inst Evolutionary Biol, Kings Bldg, Edinburgh EH9 3FL, Midlothian - Scotland
Total Affiliations: 7
Document type: Journal article
Source: Genome Biology; v. 19, SEP 25 2018.
Web of Science Citations: 3
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. (AU)

FAPESP's process: 13/50297-0 - Dimensions US-BIOTA São Paulo: a multidisciplinary framework for biodiversity prediction in the Brazilian Atlantic forest hotspot
Grantee:Cristina Yumi Miyaki
Support type: BIOTA-FAPESP Program - Thematic Grants