The genomic signature of trophic divergence along the benthic-limnetic
axis in allopatric and sympatric threespine stickleback
Abstract
The repeated occurrence of similar phenotypes in independent lineages
(i.e., parallel evolution) in response to similar ecological conditions
can provide compelling insights into the process of adaptive evolution.
An intriguing question is to what extent repeated phenotypic changes are
underlain by repeated changes at the genomic level and whether patterns
of genomic divergence differ with the geographic context in which
populations evolve. Here, we combine genomic, morphological and
ecological datasets to investigate the genomic signatures of divergence
across populations of threespine stickleback (Gasterosteus aculeatus)
that adapted to contrasting trophic niches (benthic or limnetic) in
either sympatry or allopatry. We found that genome-wide differentiation
(FST) was an order of magnitude higher and substantially more repeatable
for sympatric benthic and limnetic specialists compared to allopatric
populations with similar levels of trophic divergence. We identified 55
genomic regions consistently differentiated between sympatric ecotypes
that were also associated with benthic vs. limnetic niche across
allopatric populations. These candidate regions were enriched on three
chromosomes known to be involved in the benthic-limnetic divergence of
threespine stickleback. Some candidate regions overlapped with QTL for
body shape and trophic traits such as number of gill rakers, traits that
strongly differ between benthic and limnetic ecotypes. In sum, our study
shows that magnitude and repeatability of genomic signatures of trophic
divergence in threespine stickleback highly depend on the geographical
context. The identified candidate regions provide starting points to
identify functionally important genes for the adaptation to benthic and
limnetic trophic niches.