Transcontinental dispersal of Anopheles gambiae occurred from West African origin via serial founder events

Abstract

The mosquito Anopheles gambiae s.s. is distributed across most of sub-Saharan Africa and is of major scientific and public health interest for being an African malaria vector. Here we present population genomic analyses of 111 specimens sampled from west to east Africa, including the first whole genome sequences from oceanic islands, the Comoros. Genetic distances between populations of A. gambiae are discordant with geographic distances but are consistent with a stepwise migration scenario in which the species increases its range from west to east Africa through consecutive founder events over the last ~200,000 years. Geological barriers like the Congo River basin and the East African rift seem to play an important role in shaping this process. Moreover, we find a high degree of genetic isolation of populations on the Comoros, confirming the potential of these islands as candidate sites for potential field trials of genetically engineered mosquitoes for malaria control.

The origin of island populations of the African malaria mosquito, Anopheles coluzzii

“…Concerning the cross-coalescence analysis, we observed a split that occurred˜200,000 years ago separating west African populations (Mali and Benin) firstly from Angola, then from all others (RCC< .5; Figure 4), consistent with observations ofA. gambiae which were correlated with the Congo River basin as a geological barrier to dispersal (Schmidt et al, 2019;Voelker et al, 2013).…”

“…For this analysis, SNPs were phased with SHAPEIT2 v2.9 (Delaneau, Marchini, Genomes Project, & Genomes Project, 2014) using an A. gambiae recombination map (Anopheles gambiae 1000 Genomes et al, 2017). Four samples per population (except Bioko; N =3) were randomly selected and used for population size and two per population for cross-coalescence inter-population, as described in Schmidt et al, 2019. The results were plotted in R, assuming 10 generations per year and mutation rate of 2.85 x 10 -9 (median between mutation rates in insects as used in Schmidt et al (2019).…”

“…Four samples per population (except Bioko; N =3) were randomly selected and used for population size and two per population for cross-coalescence inter-population, as described in Schmidt et al, 2019. The results were plotted in R, assuming 10 generations per year and mutation rate of 2.85 x 10 -9 (median between mutation rates in insects as used in Schmidt et al (2019).…”

“…Based on our analyses of historical population size and cross-coalescence, we hypothesize that, like A. gambiae (Schmidt et al 2019) the geographical origin of A. coluzzii was from a west African ancestral population represented by the current Mali and Benin groups (Figure 4). West African and Cameroonian populations have no sign of strong historical fluctuations in population size, whereas Gabon and Angola populations each experienced a decrease in effective population size.…”

Abundance of conserved CRISPR-Cas9 target sites within the highly polymorphic genomes of Anopheles and Aedes mosquitoes

“…Recently, several population genomic studies have amassed a large volume of genomic data from natural populations of An. gambiae 20,21 , An. coluzzii 21 , and Ae.…”