Data from: Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex

A major goal in evolutionary biology is to uncover the genetic basis of
adaptation. Divergent selection exerted on ecological traits may result in
adaptive population differentiation and reproductive isolation and affect
differentially the level of genetic divergence along the genome.
Genome-wide scan of large sets of individuals from multiple populations is
a powerful approach to identify loci or genomic regions under ecologically
divergent selection. Here, we focused on the pea aphid, a species complex
of divergent host races, to explore the organization of the genomic
divergence associated with host-plant adaptation and ecological
speciation. We analyzed 390 microsatellite markers located at variable
distances from predicted genes in replicate samples of sympatric
populations of the pea aphid collected on alfalfa, red clover and pea,
which correspond to three common host-adapted races reported in this
species complex. Using a method that accounts for the hierarchical
structure of our dataset, we found a set of 11 outlier loci that show
higher genetic differentiation between host races than expected under the
null hypothesis of neutral evolution. Two of the outliers are close to
olfactory receptor genes and three other nearby genes encoding salivary
proteins. The remaining outliers are located in regions with genes of
unknown functions, or which functions are unlikely to be involved in
interactions with the host plant. This study reveals genetic signatures of
divergent selection across the genome and provides an inventory of
candidate genes responsible for plant specialization in the pea aphid,
thereby setting the stage for future functional studies.