Genetic diversity and population structure of the tsetse fly Glossina fuscipes fuscipes (Diptera: Glossinidae) in Northern Uganda: Implications for vector control

Abstract

Uganda is the only country where the chronic and acute forms of human African Trypanosomiasis (HAT) or sleeping sickness both occur and are separated by < 100 km in areas north of Lake Kyoga. In Uganda, Glossina fuscipes fuscipes is the main vector of the Trypanosoma parasites responsible for these diseases as well for the animal African Trypanosomiasis (AAT), or Nagana. We used highly polymorphic microsatellite loci and a mitochondrial DNA (mtDNA) marker to provide fine scale spatial resolution of genetic structure of G. f. fuscipes from 42 sampling sites from the northern region of Uganda where a merger of the two disease belts is feared. Based on microsatellite analyses, we found that G. f. fuscipes in northern Uganda are structured into three distinct genetic clusters with varying degrees of interconnectivity among them. Based on genetic assignment and spatial location, we grouped the sampling sites into four genetic units corresponding to northwestern Uganda in the Albert Nile drainage, northeastern Uganda in the Lake Kyoga drainage, western Uganda in the Victoria Nile drainage, and a transition zone between the two northern genetic clusters characterized by high level of genetic admixture. An analysis using HYBRIDLAB supported a hybrid swarm model as most consistent with tsetse genotypes in these admixed samples. Results of mtDNA analyses revealed the presence of 30 haplotypes representing three main haplogroups, whose location broadly overlaps with the microsatellite defined clusters. Migration analyses based on microsatellites point to moderate migration among the northern units located in the Albert Nile, Achwa River, Okole River, and Lake Kyoga drainages, but not between the northern units and the Victoria Nile drainage in the west. Effective population size estimates were variable with low to moderate sizes in most populations and with evidence of recent population bottlenecks, especially in the northeast unit of the Lake Kyoga drainage. Our microsatellite and mtDNA based analyses indicate that G. f. fuscipes movement along the Achwa and Okole rivers may facilitate northwest expansion of the Rhodesiense disease belt in Uganda. We identified tsetse migration corridors and recommend a rolling carpet approach from south of Lake Kyoga northward to minimize disease dispersal and prevent vector re-colonization. Additionally, our findings highlight the need for continuing tsetse monitoring efforts during and after control.

The population genomics of multiple tsetse fly (Glossina fuscipes fuscipes) admixture zones in Uganda

“…Figure shows the 18 sampling sites included in this study (details in Supporting Information Table ). Tsetse flies were collected using bi‐conical traps (Challier & Laveissiere, ) set out in groups of 10–15 traps within a radius of 2 km, a field protocol that reliably traps unrelated individuals (Echodu et al, ; Opiro et al, ). Sampling sites are a subset of sites from previous studies (Beadell et al, ; Echodu et al, ; Hyseni et al, ; Opiro et al, ) and were selected to represented the genetic diversity of the four geographic regions of genetically distinct populations found in Uganda (Figure : northwest, northeast, west and south; Beadell et al, ; Opiro et al, ) and the four admixture zones between them (Figure : “a” between the northwest and west, “b” between the northwest and northeast, “c” between the west and south, and “d” between the northeast and south).…”

“… Geographic region of origin and assignment to admixture zones “a”–“d” if applicable (Beadell et al, ; Echodu et al, ; Opiro et al, ), sample size ( N ) and statistics from stacks v.1.34 software (Catchen et al, ) including sample‐wide nucleotide diversity in the 55,267 representative SNPs (Pi; one SNP per ddRAD fragment), sample‐wide observed heterozygosity ( H O ), and sample‐wide expected heterozygosity ( H E ), statistics from plink version 1.9 (Purcell et al, ) including the proportion of locus pairs in linkage disequilibrium in this sample ( P LD ) and the proportion of loci in Hardy–Weinberg disequilibrium in this sample ( P HWD ), and sample‐wide inbreeding fixation index ( F IS ) calculated in the “ hierFSTAT ” R package (Goudet and Jombart, ). F IS values are marked with 1 if significantly different from zero with p < 0.02 based on 1,000 bootstrap replicates, with 1,2 if p < 0.02 after Benjamini–Hochberg correction for multiple testing, and with 1,2,3 if p < 0.02 after Bonferroni correction for multiple testing (Supporting Information Table ).…”

“…From the northwest cluster (Table ; Beadell et al, ; Opiro et al, ), we sampled from the Albert Nile watershed, which is characterized by lowland woodlands and gallery forest. This habitat extends north into South Sudan and west into the Democratic Republic of the Congo (DRC).…”

“…ddRAD data provided a genome‐wide analysis of hybridization and introgression. Microsatellites offered continuity with previous studies and reliable models of recent evolutionary history because of their well‐documented mutation rates, high molecular diversity and high minor allele frequencies (Beadell et al, ; Echodu et al, ; Hyseni et al, ; Opiro et al, ; Saarman et al, ). mtDNA sequences supplied inference of maternal inheritance, which can help distinguish asymmetrical reproductive barriers (Coyne & Orr, ) and past colonization patterns in hybrid zones (Currat, Ruedi, Petit, & Excoffier, ).…”

“…One prediction of this hypothesis is the rare occurrence of stable long‐lasting hybrid zones (Gompert et al, ), which implies rarity of first‐generation hybrids as well as intermediate levels of introgression in nature. Here, we investigate this prediction with a comparison of introgression patterns found in G. f. fuscipes , a unique system with four admixture zones that exist within a ~40,000 km 2 region in Uganda (Beadell et al, ; Echodu et al, ; Opiro et al, ; Saarman et al, ). Our goal was to investigate the biogeographic context and patterns of introgression in this unique system (Figure ) to provide insight on the evolutionary and ecological processes important in diversification.…”