Cytotaxonomic characterization and estimation of migration patterns of onchocerciasis vectors (Simulium damnosum sensu lato) in northwestern Ethiopia based on RADSeq data

Abstract

Background: While much progress has been made in the control and elimination of onchocerciasis across Africa, the extent to which vector migration might confound progress towards elimination or result in re-establishment of endemism in areas where transmission has been eliminated remains unclear. In Northern Ethiopia, Metema and Metekel-two foci located near the Sudan border-exhibit continuing transmission. While progress towards elimination has been faster in Metema, there remains a problematic hotspot of transmission. Whether migration from Metekel contributes to this is currently unknown.

Methodology/principle findings: To assess the role of vector migration from Metekel into Metema, we present a population genomics study of 151 adult female vectors using 47,638 RADseq markers and mtDNA CoI sequencing. From additional cytotaxonomy data we identified a new cytoform in Metema, closely related to S. damnosum s.str, here called the Gondar form. RADseq data strongly indicate the existence of two distinctly differentiated clusters within S. damnosum s.l.: one genotypic cluster found only in Metema, and the second found predominantly in Metekel. Because blackflies from both clusters were found in sympatry (in all four collection sites in Metema), but hybrid genotypes were not detected, there may be reproductive barriers preventing interbreeding. The dominant genotype in Metema was not found in Metekel while the dominant genotype in Metekel was found in Metema, indicating that (at the time of sampling) migration is primarily unidirectional, with flies moving from Metekel to Metema. There was strong differentiation between clusters but little genetic differentiation within clusters, suggesting migration and gene flow of flies within the same genetic cluster are sufficient to prevent genetic divergence between sites.

Conclusions/significance: Our results confirm that Metekel and Metema represent different transmission foci, but also indicate a northward movement of vectors between foci that may have epidemiological importance, although its significance requires further study.

Fig 1. Map showing the Metema-Galabat and Metekel foci of onchocerciasis and collection sites sampled for Simulium in northwest Ethiopia.

Transmission zone borders are outlined in red. Numbers/red circles (1–5) indicate larval samples collected in 2013 for cytotaxonomy and letters/grey cicles indicate blood-seeking adult females collected in 2017–8 for DNA sequencing (see Tables 1 and S2). Basemap property of the Government of Ethiopia and supplied by the Ethiopian Ministry of Health.

Fig 2. Mitochondrial CoI haplotype network of 189 Simulium from Metema and Metekel foci.

Circles represent unique haplotypes; the size of the circles indicate the number of blackflies with that haplotype. Hatches along the lines connecting haplotypes indicate the number of sequence differences between them. Colors indicate the proportion of each haplotype found in each sampling location.

Fig 3. Population genetic structure of Simulium damnosum from Ethiopia genotyped at 23,860 variant sites.

A) First (7.17% of total variance) and second (1.25% of variance) principal components (PCs) of variation in the genetic data (third and fourth PCs are presented in S10 Fig) and B) discriminant analysis of principal components (DAPC): each dot represents a genotyped fly; its color represents the sampling location. Lines connect to the center of the inertia ellipse for each sampling location. C) Genotype assignment of 134 flies based on DAPC for 6 sampling locations (K = 6) and D) based on assignment of each fly to one of two clusters (purple or yellow; K = 2). The results of structure with two to eight populations were identical to (D): all flies from Metekel were assigned to a cluster containing only Metekel flies, but 9 flies collected in Metema were inferred to be from this Metekel cluster. Numbered samples on A-C are the six “query”-Simulium damnosum specimens identified through mtDNA barcoding.