Genomic Analysis Reveals a New Cryptic Taxon Within the Anopheles gambiae Complex With a Distinct Insecticide Resistance Profile in the Coast of East Africa

Abstract

Anopheles mosquitoes are major malaria vectors, encompassing several species complexes with diverse life histories, transmission risks and insecticide resistance profiles that challenge malaria control efforts. This study investigated the genetic structure and insecticide resistance profiles of Anopheles gambiae complex mosquitoes in Tanzania. We analysed whole-genome sequence data of 300 mosquitoes collected between 2012 and 2015 across four regions in northern Tanzania and identified An. gambiae s.s., An. arabiensis and a distinct taxonomic group that was previously unknown. This distinct taxon has a unique profile of genetic diversity and appears restricted to the coastal region, and we refer to it as the Pwani molecular form. Analysis of insecticide resistance based on target-site mutations and copy number variations (CNV) showed that these markers were strikingly absent from the Pwani molecular form in contrast to other taxa. Our analysis also revealed a pattern of geographical isolation in the An. gambiae s.s. populations, with samples from the north-western site (Muleba) clustering separately from those collected in the north-eastern site (Muheza). These geographically isolated subpopulations also had differing resistance and selection profiles, with An. gambiae s.s. from the north-western site showing genomic evidence of higher resistance to pyrethroids compared with the north-eastern population. Conversely, An. arabiensis showed no geographical population structuring, with a similar insecticide resistance profile across all sampling locations, suggesting unrestricted gene flow. Our findings underscore the need to incorporate genetic data into malaria vector surveillance and control decisions and could inform the development and deployment of new interventions.

Keywords: Anopheles gambiae complex; cryptic species; insecticide resistance; population structure; whole‐genome sequencing.

FIGURE 1

Map of Tanzania showing mosquito collection sites with the distribution of provisional species assigned using ancestry informative markers (AIMs) in each region and the Köppen climate classification in Tanzania.

FIGURE 2

Principal component analysis (PCA) plot showing the population structure of Anopheles gambiae complex mosquitoes from Tanzania as provisionally assigned by AIMs, computed using SNPs from chromosome arm 3L.

FIGURE 3

Neighbour Joining Trees (NJT) plots showing the population structure of Anopheles gambiae, An. arabiensis, and Pwani molecular form from (A) Tanzania, (B) Tanzania, Kenya and Uganda, (C) including An. merus, An. melas and An. quadriannulatus, and An. coluzzii, (D) including the most recent cryptic taxa such as An. fontenillei, Goundry and Tengrella from West Africa, computed using SNPs from chromosome arm 3L.

FIGURE 4

Genetic diversity summary statistics (A) Nucleotide diversity, (B) Watterson estimator, (C) Tajima's D and (D) Plot comparing all the estimators showing the diversity differentiation between different population cohorts of Anopheles gambiae complex mosquitoes collected in Tanzania.

FIGURE 5

Heat map showing non‐synonymous amino acid substitutions within the pyrethroid insecticide target Vgsc; the target site of dieldrin known as Rdl and the Ace‐1 organophosphate/carbamate target site in An. gambiae complex mosquitoes collected from selected sites in Tanzania.

FIGURE 6

(A) Heat map showing copy number variation (CNV) frequencies of Cytochrome P450 and GSTe, and COE gene clusters associated with metabolic insecticide resistance (B). diplotype clustering in Anopheles gambiae complex mosquitoes collected from selected sites in Tanzania.

FIGURE 7

Genome‐wide selection scans (GWSS) showing selection sweeps labelled with the likely drivers of the respective selections on chromosome 2 of Anopheles gambiae complex mosquito populations collected across four sites in Tanzania.

FIGURE 8

Haplotype networks showing the sharing of haplotypes at the Cyp6aa/p locus associated with metabolic resistance, across (A) All taxa, (B) An. arabiensis, (C) An. gambiae and (D) Pwani molecular form mosquitoes collected from four selected sites in Tanzania.