title: Chromosomal inversions and ecotypic differentiation in Anopheles gambiae: the perspective from whole-genome sequencing.
abstract: 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 Anopheles 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 Anopheles coluzzii to investigate evolutionary relationships and genomewide 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 neighbour-joining trees based on whole-genome data (including inversions) or solely on collinear regions. Nevertheless, FSToutlier 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 signalling. 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.
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.|Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA.
authors.forename: R Rebecca
authors.initials: RR
authors.lastname: Love
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.|Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.
authors.forename: Aaron M
authors.initials: AM
authors.lastname: Steele
authors.affiliation: Malaria Research and Training Centre, Faculty of Medicine Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
authors.forename: Mamadou B
authors.initials: MB
authors.lastname: Coulibaly
authors.affiliation: Malaria Research and Training Centre, Faculty of Medicine Pharmacy and Dentistry, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali.
authors.forename: Sékou F
authors.initials: SF
authors.lastname: Traore
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.|Department of Computer Science and Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.
authors.forename: Scott J
authors.initials: SJ
authors.lastname: Emrich
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.|Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA.|Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
authors.forename: Michael C
authors.initials: MC
authors.lastname: Fontaine
authors.affiliation: Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, 46556, USA.|Department of Biological Sciences, University of Notre Dame, Galvin Life Sciences Center, Notre Dame, IN, 46556, USA.
authors.forename: Nora J
authors.initials: NJ
authors.lastname: Besansky
mesh_terms: D000483:Alleles; D000818:Animals; D000852:Anopheles / Q000235:genetics*; D007446:Chromosome Inversion; D060146:Ecotype; D049750:Genome, Insect; D007305:Insecticide Resistance / Q000235:genetics; D000072138:Mosquito Vectors / Q000235:genetics; D011110:Polymorphism, Genetic
keywords: 
  Anopheles gambiae
  ; adaptive radiation; chromosomal inversions; ecological divergence; genome scan; population genomics; selective sweeps