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Efficiently inferring the demographic history of many populations with allele count data.

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Kamm, Jack 
Terhorst, Jonathan 
Song, Yun S 

Abstract

The sample frequency spectrum (SFS), or histogram of allele counts, is an important summary statistic in evolutionary biology, and is often used to infer the history of population size changes, migrations, and other demographic events affecting a set of populations. The expected multipopulation SFS under a given demographic model can be efficiently computed when the populations in the model are related by a tree, scaling to hundreds of populations. Admixture, back-migration, and introgression are common natural processes that violate the assumption of a tree-like population history, however, and until now the expected SFS could be computed for only a handful of populations when the demographic history is not a tree. In this article, we present a new method for efficiently computing the expected SFS and linear functionals of it, for demographies described by general directed acyclic graphs. This method can scale to more populations than p reviously possible for complex demographic histories including admixture. We apply our method to an 8-population SFS to estimate the timing and strength of a proposed "basal Eurasian" admixture event in human history. We implement and release our method in a new open-source software package momi2.

Description

Keywords

coalescent theory, demographic inference, frequency spectrum, population genetics

Journal Title

J Am Stat Assoc

Conference Name

Journal ISSN

0162-1459
1537-274X

Volume Title

115

Publisher

Informa UK Limited

Rights

All rights reserved
Sponsorship
Wellcome Trust (unknown)