Genetic Diversity and the Structure of Genealogies in Rapidly Adapting Populations

TL;DR

This paper introduces a new coalescent theory to understand how rapid adaptation and clonal interference shape genealogical structures and genetic variation in populations.

Contribution

It develops a fitness-class coalescent model that captures the effects of multiple linked beneficial mutations on genealogies and genetic diversity.

Findings

The model predicts unique genetic signatures of rapid adaptation.

Simulations show how clonal interference alters molecular evolution patterns.

The theory provides a framework for analyzing genetic variation in evolving populations.

Abstract

Positive selection distorts the structure of genealogies and hence alters patterns of genetic variation within a population. Most analyses of these distortions focus on the signatures of hitchhiking due to hard or soft selective sweeps at a single genetic locus. However, in linked regions of rapidly adapting genomes, multiple beneficial mutations at different loci can segregate simultaneously within the population, an effect known as clonal interference. This leads to a subtle interplay between hitchhiking and interference effects, which leads to a unique signature of rapid adaptation on genetic variation both at the selected sites and at linked neutral loci. Here, we introduce an effective coalescent theory (a "fitness-class coalescent") that describes how positive selection at many perfectly linked sites alters the structure of genealogies. We use this theory to calculate several simple statistics describing genetic variation within a rapidly adapting population, and to implement efficient backwards-time coalescent simulations which can be used to predict how clonal interference alters the expected patterns of molecular evolution.