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Journal ArticleDOI

Population genetics of Glossina palpalis palpalis from central African sleeping sickness foci

18 Jul 2011-Parasites & Vectors (BioMed Central)-Vol. 4, Iss: 1, pp 140-140

TL;DR: This first investigation of population genetic structure of G. p.

AbstractBackground: Glossina palpalis palpalis (Diptera: Glossinidae) is widespread in west Africa, and is the main vector of sleeping sickness in Cameroon as well as in the Bas Congo Province of the Democratic Republic of Congo. However, little is known on the structure of its populations. We investigated G. p. palpalis population genetic structure in five sleeping sickness foci (four in Cameroon, one in Democratic Republic of Congo) using eight microsatellite DNA markers. Results: A strong isolation by distance explains most of the population structure observed in our sampling sites of Cameroon and DRC. The populations here are composed of panmictic subpopulations occupying fairly wide zones with a very strong isolation by distance. Effective population sizes are probably between 20 and 300 individuals and if we assume densities between 120 and 2000 individuals per km 2 , dispersal distance between reproducing adults and their parents extends between 60 and 300 meters. Conclusions: This first investigation of population genetic structure of G. p. palpalis in Central Africa has evidenced random mating subpopulations over fairly large areas and is thus at variance with that found in West African populations of G. p. palpalis. This study brings new information on the isolation by distance at a macrogeographic scale which in turn brings useful information on how to organise regional tsetse control. Future investigations should be directed at temporal sampling to have more accurate measures of demographic parameters in order to help vector control decision.

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Citations
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Journal ArticleDOI
TL;DR: It is shown that, for organisms collected in a single sample, Wahlund effects and null alleles affect the values of both FIS and FST though in the opposite direction, and a determination key is proposed to interpret data with heterozygote deficits.
Abstract: Null alleles and Wahlund effects are well known causes of heterozygote deficits in empirical population genetics studies as compared to Hardy-Weinberg genotypic expectations. Some authors have theoretically studied the relationship of Wright's FIS computed from subsamples displaying a Wahlund effect and FST before the Wahlund effect, as can occasionally be obtained from populations of long-lived organisms. In the 2 subsample case, a positive relationship between these 2 parameters across loci would represent a signature of Wahlund effects. Nevertheless, for most organisms, getting 2 independent subsamples of the same cohort and population, one with a Wahlund effect and the other without, is almost never achieved and most of the time, empirical population geneticists only collect a single sample, with or without a Wahlund effect, or with or without null alleles. Another issue is that null allele increase FIS and FST altogether and thus may also create such correlation. In this article, I show that, for organisms collected in a single sample, which corresponds to the most common situation, Wahlund effects and null alleles affect the values of both FIS and FST though in the opposite direction. I also show that Wahlund effect produces no or weak positive correlation between the 2 F-statistics, while null alleles generate a strong positive correlation between them. Variation of these F-statistics is small and even minimized for FST under Wahlund effects as compared to null alleles. I finally propose a determination key to interpret data with heterozygote deficits.

36 citations


Journal ArticleDOI
TL;DR: Population genetic analyses of Theileria parva from Isoka and Petauke districts showed a low level of genotype exchange between the districts, but a high level of genetic diversity within each district population, implying genetic and geographic sub-structuring between the Districts.
Abstract: Theileriosis, caused by Theileria parva, is an economically important disease in Africa. It is a major constraint to the development of the livestock industry in some parts of eastern, central and southern Africa. In Zambia, theileriosis causes losses of up to 10,000 cattle annually. Cattle blood samples were collected for genetic analysis of Theileria parva from Isoka and Petauke districts in Zambia. Microsatellite analysis was then performed on all Theileria parva positive samples for PCR using a panel of 9 microsatellite markers. Microsatellite data was analyzed using microsatellite toolkit, GenAlEx ver. 6, Fstat ver. 2.9.3.2, and LIAN computer softwares. The combined percentage of positive samples in both districts determined by PCR using the p104 gene primers was 54.9% (95% CI: 46.7 – 63.1%, 78/142), while in each district, it was 44.8% (95% CI: 34.8 – 54.8%) and 76.1% (95% CI = 63.9 – 88.4%) for Isoka and Petauke districts, respectively. We analyzed the population genetic structure of Theileria parva from a total of 61 samples (33 from Isoka and 28 from Petauke) using a panel of 9 microsatellite markers encompassing the 4 chromosomes of Theileria parva. Wright’s F index (FST = 0.178) showed significant differentiation between the Isoka and Petauke populations. Linkage disequilibrium was observed when populations from both districts were treated as a single population. When analyzed separately, linkage disequilibrium was observed in Kanyelele and Kalembe areas in Isoka district, Isoka district overall and in Petauke district. Petauke district had a higher multiplicity of infection than Isoka district. Population genetic analyses of Theileria parva from Isoka and Petauke districts showed a low level of genotype exchange between the districts, but a high level of genetic diversity within each district population, implying genetic and geographic sub-structuring between the districts. The sub-structuring observed, along with the lack of panmixia in the populations, could have been due to low transmission levels at the time of sampling. However, the Isoka population was less diverse than the Petauke population.

31 citations


Cites background from "Population genetics of Glossina pal..."

  • ...Micro- and mini-satellite markers have been used to genotype several species of apicomplexan parasites and their vectors, revealing different population structures [18,21,26-30]....

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Journal ArticleDOI
24 May 2017-Heredity
TL;DR: This simulation study analyzes the behavior of different genetic distances in Island and stepping stone models displaying varying neighborhood sizes and shows that the proportion of null allelic states interact with the slope of the regression of FST/(1−FST) as a function of geographic distance.
Abstract: Studying isolation by distance can provide useful demographic information. To analyze isolation by distance from molecular data, one can use some kind of genetic distance or coalescent simulations. Molecular markers can often display technical caveats, such as PCR-based amplification failures (null alleles, allelic dropouts). These problems can alter population parameter inferences that can be extracted from molecular data. In this simulation study, we analyze the behavior of different genetic distances in Island (null hypothesis) and stepping stone models displaying varying neighborhood sizes. Impact of null alleles of increasing frequency is also studied. In stepping stone models without null alleles, the best statistic to detect isolation by distance in most situations is the chord distance DCSE. Nevertheless, for markers with genetic diversities HS<0.4-0.5, all statistics tend to display the same statistical power. Marginal sub-populations behave as smaller neighborhoods. Metapopulations composed of small sub-population numbers thus display smaller neighborhood sizes. When null alleles are introduced, the power of detection of isolation by distance is significantly reduced and DCSE remains the most powerful genetic distance. We also show that the proportion of null allelic states interact with the slope of the regression of FST/(1-FST) as a function of geographic distance. This can have important consequences on inferences that can be made from such data. Nevertheless, Chapuis and Estoup's FreeNA correction for null alleles provides very good results in most situations. We finally use our conclusions for reanalyzing and reinterpreting some published data sets.

29 citations


Journal ArticleDOI
TL;DR: This study suggests that different control strategies should be implemented for the three PATTEC blocks and that, given the high potential for re-invasion from island sites, mainland and offshore sites in each block should be targeted at the same time.
Abstract: Glossina fuscipes fuscipes is the primary vector of trypanosomiasis in humans and livestock in Uganda. The Lake Victoria basin has been targeted for tsetse eradication using a rolling carpet initiative, from west to east, with four operational blocks (3 in Uganda and 1 in Kenya), under a Pan-African Tsetse and Trypanosomiasis Eradication Campaign (PATTEC). We screened tsetse flies from the three Ugandan PATTEC blocks for genetic diversity at 15 microsatellite loci from continental and offshore populations to provide empirical data to support this initiative. We collected tsetse samples from 11 sites across the Lake Victoria basin in Uganda. We performed genetic analyses on 409 of the collected tsetse flies and added data collected for 278 individuals in a previous study. The flies were screened across 15 microsatellite loci and the resulting data were used to assess the temporal stability of populations, to analyze patterns of genetic exchange and structuring, to estimate dispersal rates and evaluate the sex bias in dispersal, as well as to estimate demographic parameters (NE and NC). We found that tsetse populations in this region were stable over 4-16 generations and belong to 4 genetic clusters. Two genetic clusters (1 and 2) corresponded approximately to PATTEC blocks 1 and 2, while the other two (3 and 4) fell within PATTEC block 3. Island populations grouped into the same genetic clusters as neighboring mainland sites, suggesting presence of gene flow between these sites. There was no evidence of the stretch of water separating islands from the mainland forming a significant barrier to dispersal. Dispersal rates ranged from 2.5 km per generation in cluster 1 to 14 km per generation in clusters 3 and 4. We found evidence of male-biased dispersal. Few breeders are successfully dispersing over large distances. Effective population size estimates were low (33–310 individuals), while census size estimates ranged from 1200 (cluster 1) to 4100 (clusters 3 and 4). We present here a novel technique that adapts an existing census size estimation method to sampling without replacement, the scheme used in sampling tsetse flies. Our study suggests that different control strategies should be implemented for the three PATTEC blocks and that, given the high potential for re-invasion from island sites, mainland and offshore sites in each block should be targeted at the same time.

27 citations


Cites background or result from "Population genetics of Glossina pal..."

  • ...Solano P, Ravel S, de Meeus T: How can tsetse population genetics contribute to African trypanosomiasis control?...

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  • ...Aylesbury: East Africa European Commission; 2005....

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  • ...Vreysen MJB, Marc JB: Prospects for area-wide integrated control of tsetse flies (Diptera: Glossinidae) and trypanosomosis in sub-Saharan Africa....

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  • ...palpalis palpalis in west and central Africa [17] have provided information that is useful for control efforts at a regional scale....

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  • ...The extent of genetic connectivity of fly populations in this study is congruent with the general finding of other genetic studies on Gff [16,26] and other riverine species of tsetse [13,14,17,80]....

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Journal ArticleDOI
TL;DR: Blue-black 0.25 m2 cloth targets show promise as simple cost effective devices for management of G. p.
Abstract: Background Glossina palpalis palpalis (G. p. palpalis) is one of the principal vectors of sleeping sickness and nagana in Africa with a geographical range stretching from Liberia in West Africa to Angola in Central Africa. It inhabits tropical rain forest but has also adapted to urban settlements. We set out to standardize a long-lasting, practical and cost-effective visually attractive device that would induce the strongest landing response by G. p. palpalis for future use as an insecticide-impregnated tool in area-wide population suppression of this fly across its range. Methodology/Principal Findings Trials were conducted in wet and dry seasons in the Ivory Coast, Cameroon, the Democratic Republic of Congo and Angola to measure the performance of traps (biconical, monoconical and pyramidal) and targets of different sizes and colours, with and without chemical baits, at different population densities and under different environmental conditions. Adhesive film was used as a practical enumerator at these remote locations to compare landing efficiencies of devices. Independent of season and country, both phthalogen blue-black and blue-black-blue 1 m2 targets covered with adhesive film proved to be as good as traps in phthalogen blue or turquoise blue for capturing G. p. palpalis. Trap efficiency varied (8–51%). There was no difference between the performance of blue-black and blue-black-blue 1 m2 targets. Baiting with chemicals augmented the overall performance of targets relative to traps. Landings on smaller phthalogen blue-black 0.25 m2 square targets were not significantly different from either 1 m2 blue-black-blue or blue-black square targets. Three times more flies were captured per unit area on the smaller device. Conclusions/Significance Blue-black 0.25 m2 cloth targets show promise as simple cost effective devices for management of G. p. palpalis as they can be used for both control when impregnated with insecticide and for population sampling when covered with adhesive film.

18 citations


Cites background from "Population genetics of Glossina pal..."

  • ...palpalis cannot be ascribed to known population structuring in this species across its West and Central African range [18,19,54] as inconsistencies in the performance of the same pyramidal trap were recorded in successive years at two sites in this study....

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  • ...geographical distance at a macro-geographical scale [18] and that...

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References
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Journal ArticleDOI
TL;DR: The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973).
Abstract: This journal frequently contains papers that report values of F-statistics estimated from genetic data collected from several populations. These parameters, FST, FIT, and FIS, were introduced by Wright (1951), and offer a convenient means of summarizing population structure. While there is some disagreement about the interpretation of the quantities, there is considerably more disagreement on the method of evaluating them. Different authors make different assumptions about sample sizes or numbers of populations and handle the difficulties of multiple alleles and unequal sample sizes in different ways. Wright himself, for example, did not consider the effects of finite sample size. The purpose of this discussion is to offer some unity to various estimation formulae and to point out that correlations of genes in structured populations, with which F-statistics are concerned, are expressed very conveniently with a set of parameters treated by Cockerham (1 969, 1973). We start with the parameters and construct appropriate estimators for them, rather than beginning the discussion with various data functions. The extension of Cockerham's work to multiple alleles and loci will be made explicit, and the use of jackknife procedures for estimating variances will be advocated. All of this may be regarded as an extension of a recent treatment of estimating the coancestry coefficient to serve as a mea-

16,821 citations


"Population genetics of Glossina pal..." refers methods in this paper

  • ...Population parameters were assessed through Weir and Cockerham’s unbiased estimators [21] of Wright’s F-statistics [22] and their significance assessed through 10000 permutations with Fstat 2....

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Journal Article
TL;DR: The technic to be given below for imparting statistical validity to the procedures already in vogue can be viewed as a generalized form of regression with possible useful application to problems arising in quite different contexts.
Abstract: The problem of identifying subtle time-space clustering of disease, as may be occurring in leukemia, is described and reviewed. Published approaches, generally associated with studies of leukemia, not dependent on knowledge of the underlying population for their validity, are directed towards identifying clustering by establishing a relationship between the temporal and the spatial separations for the n ( n - 1)/2 possible pairs which can be formed from the n observed cases of disease. Here it is proposed that statistical power can be improved by applying a reciprocal transform to these separations. While a permutational approach can give valid probability levels for any observed association, for reasons of practicability, it is suggested that the observed association be tested relative to its permutational variance. Formulas and computational procedures for doing so are given. While the distance measures between points represent symmetric relationships subject to mathematical and geometric regularities, the variance formula developed is appropriate for arbitrary relationships. Simplified procedures are given for the case of symmetric and skew-symmetric relationships. The general procedure is indicated as being potentially useful in other situations as, for example, the study of interpersonal relationships. Viewing the procedure as a regression approach, the possibility for extending it to nonlinear and multivariate situations is suggested. Other aspects of the problem and of the procedure developed are discussed. Similarly, pure temporal clustering can be identified by a study of incidence rates in periods of widespread epidemics. In point of fact, many epidemics of communicable diseases are somewhat local in nature and so these do actually constitute temporal-spatial clusters. For leukemia and similar diseases in which cases seem to arise substantially at random rather than as clear-cut epidemics, it is necessary to devise sensitive and efficient procedures for detecting any nonrandom component of disease occurrence. Various ingenious procedures which statisticians have developed for the detection of disease clustering are reviewed here. These procedures can be generalized so as to increase their statistical validity and efficiency. The technic to be given below for imparting statistical validity to the procedures already in vogue can be viewed as a generalized form of regression with possible useful application to problems arising in quite different contexts.

10,970 citations


"Population genetics of Glossina pal..." refers methods in this paper

  • ...The significance of this regression was assessed with a Mantel test of randomization of cells of one matrix [42]....

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Journal ArticleDOI
TL;DR: MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis.
Abstract: DNA degradation, low DNA concentrations and primer-site mutations may result in the incorrect assignment of microsatellite genotypes, potentially biasing population genetic analyses. MICRO - CHECKER is WINDOWS ®-based software that tests the genotyping of microsatellites from diploid populations. The program aids identification of genotyping errors due to nonamplified alleles (null alleles), short allele dominance (large allele dropout) and the scoring of stutter peaks, and also detects typographic errors. MICRO - CHECKER estimates the frequency of null alleles and, importantly, can adjust the allele and genotype frequencies of the amplified alleles, permitting their use in further population genetic analysis. MICRO CHECKER can be freely downloaded from http://www.microchecker.hull.ac.uk/.

9,353 citations


"Population genetics of Glossina pal..." refers methods in this paper

  • ...’s method [26] and Brookfield’s second method [27]....

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Journal ArticleDOI
TL;DR: This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options.
Abstract: This note summarizes developments of the genepop software since its first description in 1995, and in particular those new to version 4.0: an extended input format, several estimators of neighbourhood size under isolation by distance, new estimators and confidence intervals for null allele frequency, and less important extensions to previous options. genepop now runs under Linux as well as under Windows, and can be entirely controlled by batch calls.

7,572 citations


"Population genetics of Glossina pal..." refers methods in this paper

  • ...All these isolation by distance procedures were undertaken with Genepop 4 [43] with 1000000 iterations for the Mantel test and georeferenced coordinates in Km of traps....

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