Temporal genetic differentiation in Glossina pallidipes tsetse fly populations in Kenya

Abstract

Background Glossina pallidipes is a major vector of both Human and Animal African Trypanosomiasis (HAT and AAT) in Kenya. The disease imposes economic burden on endemic regions in Kenya, including south-western Kenya, which has undergone intense but unsuccessful tsetse fly control measures. We genotyped 387 G. pallidipes flies at 13 microsatellite markers to evaluate levels of temporal genetic variation in two regions that have been subjected to intensive eradication campaigns from the 1960s to the 1980s. One of the regions, Nguruman Escarpment, has been subject to habitat alteration due to human activities, while the other, Ruma National Park, has not. In addition, Nguruman Escarpment is impacted by the movement of grazing animals into the area from neighboring regions during the drought season. We collected our samples from three geographically close sampling sites for each of the two regions. Samples were collected between the years 2003 and 2015, spanning ~96 tsetse fly generations.ResultsWe established that allelic richness averaged 3.49 and 3.63, and temporal Ne estimates averaged 594 in Nguruman Escarpment and 1120 in Ruma National Park. This suggests that genetic diversity is similar to what was found in previous studies of G. pallidipes in Uganda and Kenya, implying that we could not detect a reduction in genetic diversity following the extensive control efforts during the 1960s to the 1980s. However, we did find differences in temporal patterns of genetic variation between the two regions, indicated by clustering analysis, pairwise FST, and Fisher’s exact tests for changes in allele and genotype frequencies. In Nguruman Escarpment, findings indicated differentiation among samples collected in different years, and evidence of local genetic bottlenecks in two locations previous to 2003, and between 2009 and 2015. In contrast, there was no consistent evidence of differentiation among samples collected in different years, and no evidence of local genetic bottlenecks in Ruma National Park.ConclusionOur findings suggest that, despite extensive control measures especially between the 1960s and the 1980s, tsetse flies in these regions persist with levels of genetic diversity similar to that found in populations that did not experience extensive control measures. Our findings also indicate temporal genetic differentiation in Nguruman Escarpment detected at a scale of > 80 generations, and no similar temporal differentiation in Ruma National Park. The different level of temporal differentiation between the two regions indicates that genetic drift is stronger in Nugruman Escarpment, for as-yet unknown reasons, which may include differences in land management. This suggests land management may have an impact on G. pallidipes population genetics, and reinforces the importance of long term monitoring of vector populations in estimates of parameters needed to model and plan effective species-specific control measures.Electronic supplementary materialThe online version of this article (10.1186/s13071-017-2415-y) contai...

Detecting Wahlund effects together with amplification problems: Cryptic species, null alleles and short allele dominance in Glossina pallidipes populations from Tanzania

“…Effective population sizes obtained in Kenya with temporal methods (N e ≈ 100-2,000), a method for which we did not have appropriate sampling, suggests much bigger G. pallidipes densities (Okeyo et al, 2017;Ouma et al, 2006) than what we found, unless tsetse subpopulations in Kenya occupy larger surfaces as compared to Tanzania. Nevertheless, in these studies, superficial analyses of heterozygote deficits causes and/or the use of pooling of some of the available subsamples makes any comparison quite uneasy.…”

“…The reversed relation when more than 40% pairs of loci are in LD comes from the same mechanism described in a previous paper (Prugnolle & De Meeûs, 2010) (Ouma, Marquez, & Krafsur, 2005). Isolation by distance was never accurately explored in the literature for this species, either because it was not really studied (Ouma et al, , 2005Ouma, Marquez, & Krafsur, 2006) or because it was analyzed with temporally heterogeneous subsamples (Okeyo et al, 2017). Clade B contained few and very small subsamples and the differences observed with Clade A might not be significant.…”

“…In clade A, for which we disposed of a reasonable sample size, isolation by distance slope and effective population size analyses suggested relatively small densities but quite large dispersal distances (2–8 km per generations on average and up to 14 km), which is not so different to what mark‐release recapture suggests for this species (Ouma, Marquez, & Krafsur, ). Isolation by distance was never accurately explored in the literature for this species, either because it was not really studied (Ouma et al, ; Ouma, Marquez, & Krafsur, ) or because it was analyzed with temporally heterogeneous subsamples (Okeyo et al, ). Clade B contained few and very small subsamples and the differences observed with Clade A might not be significant.…”

“…Some studies were published but with either timely heterogeneous samples and/or light analyses of local population structure and/or unexplained variation of parameter estimates (e.g. F IS , F ST …) across loci (Okeyo et al, 2017;Ouma et al, 2011;Ouma & Krafsur, 2010;Ouma, Marquez, & Krafsur, 2005, 2006, resulting in limited inference accuracy. In this paper, we apply our new analytic strategy on 190 G. pallidipes from seven sites and two cohorts in the Serengeti region in Tanzania.…”

Genetic Differentiation of Glossina pallidipes Tsetse Flies in Southern Kenya

“…38 Previous work has also shown that G. pallidipes populations undergo temporal changes in allele frequencies because of both natural (such as seasonal environmental fluctuations), and humaninduced factors (such as control measures). 42 Nonetheless, there remain gaps in our knowledge of the population structure of this dangerous vector in Kenya, especially at a regional scale.…”