A universal mechanism generating clusters of differentiated loci during divergence-with-migration

TL;DR

This paper proposes a universal mechanism where stochastic loss and gain of local differentiation, influenced by recombination distance, lead to the formation of tightly-linked divergence clusters during adaptation with gene flow.

Contribution

It introduces a new theoretical framework explaining how stochastic loss combined with gain drives divergence clusters, addressing limitations of previous models.

Findings

Divergence clusters form due to a balance between stochastic loss and gain.

Critical recombination distance determines the rate of local divergence loss.

The mechanism applies universally across genomes during divergence with gene flow.

Abstract

Genome-wide patterns of genetic divergence reveal mechanisms of adaptation under gene flow. Empirical data show that divergence is mostly concentrated in narrow genomic regions. This pattern may arise because differentiated loci protect nearby mutations from gene flow, but recent theory suggests this mechanism is insufficient to explain the emergence of concentrated differentiation during biologically realistic timescales. Critically, earlier theory neglects an inevitable consequence of genetic drift: stochastic loss of local genomic divergence. Here we demonstrate that the rate of stochastic loss of weak local differentiation increases with recombination distance to a strongly diverged locus and, above a critical recombination distance, local loss is faster than local `gain' of new differentiation. Under high migration and weak selection this critical recombination distance is much smaller than the total recombination distance of the genomic region under selection. Consequently, divergence between populations increases by net gain of new differentiation within the critical recombination distance, resulting in tightly-linked clusters of divergence. The mechanism responsible is the balance between stochastic loss and gain of weak local differentiation, a mechanism acting universally throughout the genome. Our results will help to explain empirical observations and lead to novel predictions regarding changes in genomic architectures during adaptive divergence.