Population Genetic Analysis of Aedes aegypti Mosquitoes From Sudan Revealed Recent Independent Colonization Events by the Two Subspecies

Abstract

Increases in arbovirus outbreaks in Sudan are vectored by Aedes aegypti, raising the medical importance of this mosquito. We genotyped 12 microsatellite loci in four populations of Ae. aegypti from Sudan, two from the East and two from the West, and analyzed them together with a previously published database of 31 worldwide populations to infer population structure and investigate the demographic history of this species in Sudan. Our results revealed the presence of two genetically distinct subspecies of Ae. aegypti in Sudan. These are Ae. aegypti aegypti in Eastern Sudan and Ae. aegypti formosus in Western Sudan. Clustering analysis showed that mosquitoes from East Sudan are genetically homogeneous, while we found population substructure in West Sudan. In the global context our results indicate that Eastern Sudan populations are genetically closer to Asian and American populations, while Western Sudan populations are related to East and West African populations. Approximate Bayesian Computation Analysis supports a scenario in which Ae. aegypti entered Sudan in at least two independent occasions nearly 70-80 years ago. This study provides a baseline database that can be used to determine the likely origin of new introductions for this invasive species into Sudan. The presence of the two subspecies in the country should be consider when designing interventions, since they display different behaviors regarding epidemiologically relevant parameters, such as blood feeding preferences and ability to transmit disease.

Keywords: Aedes aegypti; Sudan; genetic diversity; microsatellites; population genetics.

FIGURE 1

(A) Map of Sudan showing the locations of the two subspecies/forms of Ae. aegypti collected from four sites. AR = Allelic Richness and PAR = Private Allelic Richness. (B). Map showing locations of Ae. aegypti included in this study. Population codes are as labeled in Supplementary Table S1. Shapefile downloaded from https://mapcruzin.com/

FIGURE 2

Genetic structure of Ae. aegypti Sudan populations. STRUCTURE bar plot indicating genetic groupings of four geographic locations in Sudan based on 12 microsatellite loci. Each vertical bar represents an individual. The height of each bar represents the probability of assignment to each of K = 2 (A) and of K = 3 (B) clusters as determined using the Delta K method. Each cluster is indicated by different colours.

FIGURE 3

Principal Component Analysis (PCA) on the Sudan Ae. aegypti microsatellite dataset as implemented and plotted using the (GenAlEx) version 6.3. Populations that originated from different regions are presented with different colors.

FIGURE 4

Discriminant Analysis of Principal Components (DAPC) for the Ae. aegypti populations from Sudan based on the microsatellite dataset. The graph represents the individuals as dots and the groups as inertia ellipses. A bar plot of eigenvalues for the discriminant analysis (DA eigenvalues) is displayed in the inset. The number of bars represent the number of discriminant functions retained in the analysis and the eigenvalues correspond to the ratio of the variance between groups over the variance within groups for each discriminant function.

FIGURE 5

Global genetic structure of Ae. aegypti populations. STRUCTURE bar plot indicating genetic groupings of five continents (35 geographic locations) based on 12 microsatellite loci. Each vertical bar represents an individual. The height of each bar represents the probability of assignment to each of (A) K = 2 and (B) K = 3 clusters. The optimal number of clusters was determined using the Delta K method as K = 2. Each cluster is indicated by different colour: Aaa: orange and Aaf: blue.

FIGURE 6

Evolutionary scenarios of Ae. aegypti colonization of Sudan evaluated using Approximate Bayesian Computation inference, as implemented by the DIYABC software (Cornuet et al., 2014). Scenarios include four regions: Western Sudan, Eastern Sudan, Africa, out-of-Africa, N = 30 randomly chosen individuals for each region. t0 represents the most recent time, point. Increasing values of t are not to scale and are not necessarily be in chronological order. Posterior probabilities are shown for each scenario. For more details see Materials and Methods and Supplementary Table S3.