Approximate Bayesian computational methods to estimate the strength of divergent selection in population genomics models

TL;DR

This paper explores using ABC methods to estimate divergent selection strength in population genomics models, comparing summary statistics and addressing confounding factors like recombination.

Contribution

The paper introduces a mechanistic model with variable migration and reproduction modes, and evaluates ABC's feasibility for inferring selection strength.

Findings

ABC can effectively estimate selection strength and locus positions under divergent selection.

Population differentiation and LD-based summary statistics show varying effectiveness in capturing selection.

Recombination rate significantly affects linkage disequilibrium and selection estimation accuracy.

Abstract

Statistical estimation of parameters in large models of evolutionary processes is often too computationally inefficient to pursue using exact model likelihoods, even with single-nucleotide polymorphism (SNP) data, which offers a way to reduce the size of genetic data while retaining relevant information. Approximate Bayesian Computation (ABC) to perform statistical inference about parameters of large models takes the advantage of simulations to bypass direct evaluation of model likelihoods. We develop a mechanistic model to simulate forward-in-time divergent selection with variable migration rates, modes of reproduction (sexual, asexual), length and number of migration-selection cycles. We investigate the computational feasibility of ABC to perform statistical inference and study the quality of estimates on the position of loci under selection and the strength of selection. To expand the parameter space of positions under selection, we enhance the model by implementing an outlier scan on summarized observed data. We evaluate the usefulness of summary statistics well-known to capture the strength of selection, and assess their informativeness under divergent selection. We also evaluate the effect of genetic drift with respect to an idealized deterministic model with single-locus selection. We discuss the role of the recombination rate as a confounding factor in estimating the strength of divergent selection, and emphasize its importance in break down of linkage disequilibrium (LD). We answer the question for which part of the parameter space of the model we recover strong signal for estimating the selection, and determine whether population differentiation-based summary statistics or LD–based summary statistics perform well in estimating selection.

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