High Levels of Admixture in Anopheles gambiae Populations from Côte d’Ivoire Revealed by Multilocus Genotyping

SIMPLE SUMMARY: Anopheles gambiae and An. coluzzii are two mosquito species with the most prominent role in transmitting malaria parasites to humans in the Afrotropical region. They are morphologically indistinguishable, but their ecological and behavioral differences affect their geographical distribution and may impact their role as malaria vectors and their response to malaria control interventions. A few genomic markers differentiate the two species and allow them to be consistently identified across most of their range. We here report the presence of two populations in Côte d’Ivoire characterized by an admixed pattern of these markers and try to understand their nature. Results do not support the hypothesis that the observed patterns are due to the current crossing between the two species, highlighting the constraints of currently available markers in clarifying the origin of the “unusual” populations in the country. Further analysis exploiting a larger set of markers will eventually solve this puzzle and allow a better understanding of its potential impact on malaria transmission and control. ABSTRACT: Anopheles coluzzii and An. gambiae—the two most recently radiated species of the An. gambiae complex and the major Afrotropical malaria vector species—are identified by markers in the X-centromeric IGS rDNA region. Putative IGS-hybrids are rarely found in the field, except in restricted areas where genomic studies have led to the hypothesis that the observed IGS-patterns are due to cryptic taxa rather than to hybridization between the two species. We investigated the genome-wide levels of admixture in two villages in Côte d’Ivoire where high levels of IGS-hybrids have been detected, confirming unparalleled high frequencies in the coastal village. Genotyping of 24 Ancestry Informative Markers (AIMs) along the three chromosomes produced discordant results between the IGS-marker and the multilocus genotype obtained for AIMs across the whole genome (29%) as well as AIMs on chromosome-X (considered to be fundamental for species reproductive isolation) only (21%). Results highlight a complicated pattern of admixture that deserves deeper genomic analyses to understand better possible underlying causes (from extensive processes of hybridization to the existence of different cryptic taxa), and stress the need of developing advanced diagnostics for An. coluzzii, An. gambiae and putative new taxa, instrumental for assessing taxon-specific epidemiological characters.