Résumé
The molecular mechanisms and genetic architecture that facilitate adaptive
radiation of lineages remain elusive. Polymorphic chromosomal inversions,
due to their recombination-reducing effect, are proposed instruments of
ecotypic differentiation. Here we study an ecologically diversifying
lineage of An. gambiae, known as the Bamako chromosomal form based on its
unique complement of three chromosomal inversions, to explore the impact
of these inversions on ecotypic differentiation. We used pooled and
individual genome sequencing of Bamako, typical (non-Bamako) An. gambiae,
and the sister species An. coluzzii to investigate evolutionary
relationships and genome-wide patterns of nucleotide diversity and
differentiation among lineages. Despite extensive shared polymorphism and
limited differentiation from the other taxa, Bamako clusters apart from
the other taxa, and forms a maximally supported clade in neighbor-joining
trees based on whole genome data (including inversions) or solely on
collinear regions. Nevertheless, FST outlier analysis reveals that the
majority of differentiated regions between Bamako and typical An. gambiae
are located inside chromosomal inversions, consistent with their role in
the ecological isolation of Bamako. Exceptionally differentiated genomic
regions were enriched for genes implicated in nervous system development
and signaling. Candidate genes associated with a selective sweep unique to
Bamako contain substitutions not observed in sympatric samples of the
other taxa, and several insecticide resistance gene alleles shared between
Bamako and other taxa segregate at sharply different frequencies in these
samples. Bamako represents a useful window into the initial stages of
ecological and genomic differentiation from sympatric populations in this
important group of malaria vectors.