Whole-genome resequencing confirms reproductive isolation between
sympatric demes of brown trout (Salmo trutta) detected with allozymes
Abstract
The sympatric existence of genetically distinct populations of the same
species remains a puzzle in ecology. Coexisting salmonid fish
populations are known from over 100 freshwater lakes. Most studies of
sympatric populations have used limited numbers of genetic markers
making it unclear if genetic divergence involves only certain parts of
the genome. We return to the first reported case of salmonid sympatry,
initially detected through contrasting homozygosity at a single allozyme
locus (lactate dehydrogenase, LDH-A1) in brown trout in the small Lakes
Bunnersjöarna, central Sweden. We use DNA from samples collected in the
1970s and a 96 SNP fluidigm array to verify the existence of the
coexisting demes. We then apply whole-genome resequencing of pooled DNA
to explore genome-wide diversity within and between these demes; strong
genetic divergence is observed with genome-wide FST=0.13. Nucleotide
diversity is estimated to 0.0013 in Deme I but only 0.0005 in Deme II.
Individual whole-genome resequencing of two individuals per deme
suggests considerably higher inbreeding in Deme II vs. Deme I. Comparing
with similar data from other lakes we find that the genome-wide
divergence between the demes is similar to that between reproductively
isolated populations. We located two genes for LDH-A and found
divergence between the demes in a regulatory section of one of the
genes, but we could not find a perfect fit between allozyme and sequence
data. Our data demonstrate genome-wide divergence governed by genetic
drift and diversifying selection, confirming reproductive isolation
between the sympatric demes.