Inference with selection, varying population size and evolving population structure: Application of ABC to a forward-backward coalescent process with interactions

TL;DR

This paper introduces a stochastic birth-death model with interactions and trait structures to infer ecological, demographic, and genetic parameters from genetic data, using an ABC framework, and applies it to both simulated and real human population data.

Contribution

It develops a novel phylogenetic model with trait interactions and multiple mergers, and an ABC-based inference method for complex demographic and genetic scenarios.

Findings

Genetic diversity relates to birth, death, and competition rates.

The model captures multiple lineage mergers in phylogenies.

Application to human Y-chromosome data reveals social organization impacts fertility.

Abstract

Genetic data are often used to infer demographic history and changes or detect genes under selection. Inferential methods are commonly based on models making various strong assumptions: demography and population structures are supposed \textit{a priori} known, the evolution of the genetic composition of a population does not affect demography nor population structure, and there is no selection nor interaction between and within genetic strains. In this paper, we present a stochastic birth-death model with competitive interactions and asexual reproduction. We develop an inferential procedure for ecological, demographic and genetic parameters. We first show how genetic diversity and genealogies are related to birth and death rates, and to how individuals compete within and between strains. {This leads us to propose an original model of phylogenies, with trait structure and interactions, that allows multiple merging}. Second, we develop an Approximate Bayesian Computation framework to use our model for analyzing genetic data. We apply our procedure to simulated data from a toy model, and to real data by analyzing the genetic diversity of microsatellites on Y-chromosomes sampled from Central Asia human populations in order to test whether different social organizations show significantly different fertility.