Journal
JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS
Volume 26, Issue 1, Pages 182-194Publisher
AMER STATISTICAL ASSOC
DOI: 10.1080/10618600.2016.1159212
Keywords
Coalescent; Demographic inference; Population genetics; Sum-product algorithm
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Funding
- NIH [R01-GM109454, R01-GM108805]
- Packard Fellowship for Science and Engineering
- Miller Research Professorship
- Citadel Graduate Fellowship
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A wide range of studies in population genetics have employed the sample frequency spectrum (SFS), a summary statistic which describes the distribution of mutant alleles at a polymorphic site in a sample of DNA sequences and provides a highly efficient dimensional reduction of large-scale population genomic variation data. Recently, there has been much interest in analyzing the joint SFS data from multiple populations to infer parameters of complex demographic histories, including variable population sizes, population split times, migration rates, admixture proportions, and so on. SFS-based inference methods require accurate computation of the expected SFS under a given demographic model. Although much methodological progress has been made, existing methods suffer from numerical instability and high computational complexity when multiple populations are involved and the sample size is large. In this article, we present new analytic formulas and algorithms that enable accurate, efficient computation of the expected joint SFS for thousands of individuals sampled from hundreds of populations related by a complex demographic model with arbitrary population size histories (including piecewise-exponential growth). Our results are implemented in a new software package called momi (MOran Models for Inference). Through an empirical study, we demonstrate our improvements to numerical stability and computational complexity.
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