  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.
