Population genetics as a tool to select tsetse control strategies: suppression or eradication of Glossina palpalis gambiensis in the Niayes of Senegal.
TL;DR: In this article, the authors used population genetics to measure genetic differentiation between Glossina palpalis gambiensis from the Niayes and those from the southern tsetse belt (Missira).
Abstract: Background: The Government of Senegal has initiated the ''Projet de lutte contre les glossines dans les Niayes'' to remove the trypanosomosis problem from this area in a sustainable way. Due to past failures to sustainably eradicate Glossina palpalis gambiensis from the Niayes area, controversies remain as to the best strategy implement, i.e. ''eradication'' versus ''suppression.'' To inform this debate, we used population genetics to measure genetic differentiation between G. palpalis gambiensis from the Niayes and those from the southern tsetse belt (Missira). Methodology/Principal Findings: Three different markers (microsatellite DNA, mitochondrial CO1 DNA, and geometric morphometrics of the wings) were used on 153 individuals and revealed that the G. p. gambiensis populations of the Niayes were genetically isolated from the nearest proximate known population of Missira. The genetic differentiation measured between these two areas (h = 0.12 using microsatellites) was equivalent to a between-taxa differentiation. We also demonstrated that within the Niayes, the population from Dakar - Hann was isolated from the others and had probably experienced a bottleneck. Conclusion/Significance: The information presented in this paper leads to the recommendation that an eradication strategy for the Niayes populations is advisable. This kind of study may be repeated in other habitats and for other tsetse species to (i) help decision on appropriate tsetse control strategies and (ii) find other possible discontinuities in tsetse distribution. (Resume d'auteur)
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TL;DR: It is argued that sustainable tsetse-free zones can be created on Africa mainland provided certain managerial and technical prerequisites are in place and the principles of area-wide integrated pest management (AW-IPM) and the phased-conditional approach with the tsete project in Senegal as a recent example are argued.
147 citations
TL;DR: The integration of the sterile insect technique has proven successful to manage crop pests and disease vectors, particularly tsetse flies, and is likely to prove effective against mosquito vectors,particularly once sex-separation methods are improved.
146 citations
TL;DR: It is argued that the methodology developed should be integrated into future tsetse control efforts that are planned under the umbrella of the PATTEC initiative and have a generic value for vector and pest control campaigns, especially when eradication is contemplated.
Abstract: Tsetse flies are vectors of human and animal trypanosomoses in sub-Saharan Africa and are the target of the Pan African Tsetse and Trypanosomiasis Eradication Campaign (PATTEC). Glossina palpalis gambiensis (Diptera: Glossinidae) is a riverine species that is still present as an isolated metapopulation in the Niayes area of Senegal. It is targeted by a national eradication campaign combining a population reduction phase based on insecticide-treated targets (ITTs) and cattle and an eradication phase based on the sterile insect technique. In this study, we used species distribution models to optimize control operations. We compared the probability of the presence of G. p. gambiensis and habitat suitability using a regularized logistic regression and Maxent, respectively. Both models performed well, with an area under the curve of 0.89 and 0.92, respectively. Only the Maxent model predicted an expert-based classification of landscapes correctly. Maxent predictions were therefore used throughout the eradication campaign in the Niayes to make control operations more efficient in terms of deployment of ITTs, release density of sterile males, and location of monitoring traps used to assess program progress. We discuss how the models’ results informed about the particular ecology of tsetse in the target area. Maxent predictions allowed optimizing efficiency and cost within our project, and might be useful for other tsetse control campaigns in the framework of the PATTEC and, more generally, other vector or insect pest control programs.
104 citations
Cites background from "Population genetics as a tool to se..."
...Bouyer J, et al. (2010) Stratified entomological sampling in preparation for an areawide integrated pest management program: The example of Glossina palpalis gambiensis (Diptera: Glossinidae) in the Niayes of Senegal....
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...Glossina palpalis gambiensis (Diptera: Glossinidae) is a riverine species that is still present as an isolated metapopulation in the Niayes area of Senegal....
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...Before the availability of the Maxent model in the Senegal project, operational choices such as selection of trap sites were made using a vegetation classification obtained from a Landsat 7 Enhanced Thematic Mapper Plus (ETM+) image of April 2001....
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...Using species distribution models to optimize vector control in the framework of the tsetse eradication campaign in Senegal...
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...As part of this global effort, the government of Senegal embarked in 2007 on a tsetse eradication campaign in a 1,000-km2 target area of the Niayes region, neighboring the capital Dakar....
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TL;DR: A PCP for tsetse-transmitted animal trypanosomosis, the scourge of poor livestock keepers in tropical Africa, is outlined, with a mixed-record of success and failure in past efforts.
84 citations
Cites background from "Population genetics as a tool to se..."
...In particular, if a fast-tracking to the elimination pathway is envisaged (Stage 3 and beyond), genetics studies are likely to be needed to establish the degree of isolation of the target tsetse populations [33,34] and the related risk of reinvasion (Box 1)....
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...In the selection of target areas for tsetse elimination, the level of isolation should be assessed [33,34], and isolated populations should be given priority....
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79 citations
References
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TL;DR: In this paper, a simple and widely accepted multiple test procedure of the sequentially rejective type is presented, i.e. hypotheses are rejected one at a time until no further rejections can be done.
Abstract: This paper presents a simple and widely ap- plicable multiple test procedure of the sequentially rejective type, i.e. hypotheses are rejected one at a tine until no further rejections can be done. It is shown that the test has a prescribed level of significance protection against error of the first kind for any combination of true hypotheses. The power properties of the test and a number of possible applications are also discussed.
20,459 citations
"Population genetics as a tool to se..." refers methods in this paper
...The Bonferronni procedure [53] was used each time multiple testing was done and individual tests significance required....
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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-
17,890 citations
Book•
01 Feb 1987
TL;DR: Recent developments of statistical methods in molecular phylogenetics are reviewed and it is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used.
Abstract: Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies exlensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining'the accuracy of trees obtained by neighborjoining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.
15,840 citations
"Population genetics as a tool to se..." refers methods in this paper
...12 in [58], Pi, the nucleotide diversity, which is the average number of nucleotide differences per site between two sequences, and its sampling variance was calculated using equations 10....
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...7 in [58], K, the average number of nucleotide differences and the total variance of K is (sampling plus stochastic), assuming no recombination were calculated using equations from [59]....
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TL;DR: An overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA is provided.
Abstract: With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
12,124 citations
"Population genetics as a tool to se..." refers methods in this paper
...1 [35] from a chord distance matrix (noted DC-S&E) [36], as recommended by [37], and computed using Genetix V4 [38]....
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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.
11,408 citations
"Population genetics as a tool to se..." refers methods in this paper
...To evaluate the correlation between distance matrices we undertook three Mantel tests [68] with the ‘‘Mantelize it’’ option of Fstat 2....
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