Speciation within the Anopheles gambiae complex: high-throughput whole genome sequencing reveals evidence of a putative new cryptic taxon in 'far-west' Africa

Abstract

The two main Afrotropical malaria vectors - Anopheles coluzzii and An. gambiae - are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as "intermediate" between the two species by whole genome sequence (WGS) data, and as hybrid forms by conventional molecular diagnostics. By exploiting WGS data from 1,190 specimens collected across west Africa via the Anopheles gambiae 1000 Genomes network, we identify a novel putative taxon in the far-west (provisionally named Bissau molecular form), which did not arise by admixture but rather originated at the same time as the split between An. coluzzii and An. gambiae. Intriguingly, these populations lack insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches.

Keywords: Anopheles; admixture; gene-flow; malaria vectors; reproductive barriers.

Figure 1.. Genomic structure of Phase-3 Ag1000G Anopheles gambiae s.l. from West and Far-West Africa.

A - Distribution and numbers of Phase-3 Ag1000G individuals included in the analysis (right) with focus on the Far-West region (left). Classification based on Ancestry Informative Marker (AIM): FW individuals classified as “intermediate” as they show An. coluzzii AIM-fraction >5% and <95%. Details on population codes, AIM proportions, and total number of individuals/country are Table S1. Updated and modified from Anopheles gambiae 1000 Genomes, 2020. B - Principal component analysis based on SNPs on chromosome-X, −3 and −2. Specimens coloured by AIM-fraction. Circles = Anopheles coluzzii and Anopheles gambiae; crosses=Far-West individuals. C - ADMIXTURE Bayesian ancestry most parsimonious models for chromosome-X (K=3) and chromosome-3 (K=3). Anopheles coluzzii: BFcol (Burkina Faso), CIcol (Côte d’Ivoire), GHcol (Ghana), GNcol (Guinea), MAcol (Mali); An. gambiae: BFgam (Burkina Faso), GHgam (Ghana), GNgam (Guinea), GWgam (Guinea-Bissau), MAgam (Mali).

Figure 2.. Genome-wide F_ST per 100k accessible bases between FW-clusters and An. gambiae

(upper panel) or An. coluzzii (intermediate panel), and between An. coluzzii and An. gambiae (lower panel) gcx2=orange=; gcx1-GM=green; gcx1-GW=light green.

Figure 3.. Patterns of west-African An. gambiae s.l. population splits and mixtures as inferred by TreeMix based on SNPs in the euchromatic region of chromosome-3.

Branch lengths are proportional to the evolutionary change (the drift parameter) and terminal nodes were labelled with clusters codes. Migration edges were coloured according to migration weight.

Figure 4.. Demographic models explored by ∂a∂i analysis:

1) Admixed origin model; 2) Simultaneous split model, the best supported model depicted by the analysis; 3) Simple split model with gcx1-GM stemming from GA (3a) or CO (3b).

Figure 5.. gcx1-GM vs Anopheles gambiae markers plot.

Rows represent individual mosquitoes (grouped by population) and columns represent SNPs (grouped by chromosome arm). Approximate chromosomal position is given below the graph. Colours represent gcx1-GM related (Purple), An. gambiae (GA; Green), gcx1-GM/GA (cyan) heterozygous genotypes; Missing genotypes in black. The column at the far right shows the individual allelic percentage (A.P.).