Exploring the origin and degree of genetic isolation of Anopheles gambiae from the islands of São Tomé and Príncipe, potential sites for testing transgenic-based vector control

Mitogenome Analyses Reveal Limited Introduction of Anopheles coluzzii Into the Central African Islands of São Tomé and Príncipe

Islands possess physical characteristics that make them uniquely well-suited for initial field trials of new genetic-based technologies applied to African malaria vectors. This has led to efforts to characterize the degree of isolation of island mosquito populations. São Tomé and Príncipe (STP) is a country composed of two small islands in the Gulf of Guinea (Central Africa) where Anopheles coluzzii is the primary malaria vector. Several studies have shown a relatively high degree of genetic isolation between A. coluzzii populations in STP and the mainland compared with pairs of mainland populations separated by equivalent distances. Here, we analyzed complete mitochondrial genomes of individual A. coluzzii specimens from STP and neighboring mainland countries. The objectives are to describe the history of A. coluzzii establishment in STP, specifically to address several questions germane to their suitability as sites for a field trial release of genetically engineered mosquitoes (GEMs). These questions include: (i) What are the origins of A. coluzzii populations in STP?; (ii) How many introductions occurred?; (iii) When was A. coluzzii introduced into STP? and (iv) Is there ongoing, contemporary gene flow into STP from mainland populations? Phylogenetic analysis and haplotype networks were constructed from sequences of 345 A. coluzzii from STP, and 107 individuals from 10 countries on or near the west coast of Africa. Analysis of these data suggest that there have been two introductions of A. coluzzii onto the island of São Tomé that occurred roughly 500 years ago and that these originated from mainland West Africa. It appears that A. coluzzii has never been introduced into Príncipe Island directly from mainland Africa, but there have been at least four introductions originating from São Tomé. Our findings provide further support for the notion that contemporary populations of A. coluzzii on São Tomé and Príncipe are genetically isolated from mainland populations of this mosquito species.

The origin of island populations of the African malaria mosquito, Anopheles coluzzii

Anopheles coluzzii is a major malaria vector throughout its distribution in west-central Africa. Here we present a whole-genome study of 142 specimens from nine countries in continental Africa and three islands in the Gulf of Guinea. This sample set covers a large part of this species' geographic range. Our population genomic analyses included a description of the structure of mainland populations, island populations, and connectivity between them. Three genetic clusters are identified among mainland populations and genetic distances (F_ST) fits an isolation-by-distance model. Genomic analyses are applied to estimate the demographic history and ancestry for each island. Taken together with the unique biogeography and history of human occupation for each island, they present a coherent explanation underlying levels of genetic isolation between mainland and island populations. We discuss the relationship of our findings to the suitability of São Tomé and Príncipe islands as candidate sites for potential field trials of genetic-based malaria control strategies.

Updated list of Anopheles species (Diptera: Culicidae) by country in the Afrotropical Region and associated islands

The distributions of the Afrotropical Anopheles mosquitoes were first summarized in 1938. In 2017, an extensive geo-coded inventory was published for 48 sub-Saharan African countries, including information such as sampling methods, collection dates, geographic co-ordinates and the literature consulted to produce the database. Using the information from the 2017 inventory, earlier distribution lists, museum collections and publications since 2016, this paper presents an updated, simplified list of Anopheles species by mainland countries and associated Afrotropical islands, with comments where applicable. It is intended as a supplement to the 2017 geo-coded inventory.

Assessing connectivity despite high diversity in island populations of a malaria mosquito

Documenting isolation is notoriously difficult for species with vast polymorphic populations. High proportions of shared variation impede estimation of connectivity, even despite leveraging information from many genetic markers. We overcome these impediments by combining classical analysis of neutral variation with assays of the structure of selected variation, demonstrated using populations of the principal African malaria vector Anopheles gambiae. Accurate estimation of mosquito migration is crucial for efforts to combat malaria. Modeling and cage experiments suggest that mosquito gene drive systems will enable malaria eradication, but establishing safety and efficacy requires identification of isolated populations in which to conduct field testing. We assess Lake Victoria islands as candidate sites, finding one island 30 km offshore is as differentiated from mainland samples as populations from across the continent. Collectively, our results suggest sufficient contemporary isolation of these islands to warrant consideration as field-testing locations and illustrate shared adaptive variation as a useful proxy for connectivity in highly polymorphic species.

Effects of indoor residual spraying and outdoor larval control on Anopheles coluzzii from São Tomé and Príncipe, two islands with pre-eliminated malaria

Background

Vector control is a key component of malaria prevention. Two major vector control strategies have been implemented in São Tomé and Príncipe (STP), indoor residual spraying (IRS) and outdoor larval control using Bacillus thuringiensis israelensis (Bti). This study evaluated post-intervention effects of control strategies on vector population density, composition, and knockdown resistance mutation, and their implications for malaria epidemiology in STP.

Methods

Mosquitoes were collected by indoor and outdoor human landing catches and mosquito light traps in seven districts. Mosquito density was calculated by numbers of captured adult mosquitoes/house/working hour. Mitochondrial cytochrome c oxidase subunit I (COI) was PCR amplified and sequenced to understand the spatial–temporal population composition of malaria vector in STP. Knockdown resistance L1014F mutation was detected using allele-specific PCR. To estimate the malaria transmission risks in STP, a negative binomial regression model was constructed. The response variable was monthly incidence, and the explanatory variables were area, rainfall, entomological inoculation rate (EIR), and kdr mutation frequency.

Results

Malaria vector in STP is exophilic Anopheles coluzzii with significant population differentiation between Príncipe and São Tomé (mean F_ST = 0.16, p < 0.001). Both vector genetic diversity and knockdown resistance mutation were relatively low in Príncipe (mean of kdr frequency = 15.82%) compared to São Tomé (mean of kdr frequency = 44.77%). Annual malaria incidence rate in STP had been rapidly controlled from 37 to 2.1% by three rounds of country-wide IRS from 2004 to 2007. Long-term application of Bti since 2007 kept the mosquito density under 10 mosquitoes/house/hr/month, and malaria incidence rate under 5% after 2008, except for a rising that occurred in 2012 (incidence rate = 6.9%). Risk factors of area (São Tomé compared to Príncipe), rainfall, outdoor EIR, and kdr mutation frequency could significantly increase malaria incidence by 9.33–11.50, 1.25, 1.07, and 1.06 fold, respectively.

Conclusions

Indoor residual spraying could rapidly decrease Anopheles density and malaria incidence in STP. Outdoor larval control using Bti is a sustainable approach for controlling local vector with exophilic feature and insecticide resistance problem. Vector control interventions should be intensified especially at the north-eastern part of São Tomé to minimize impacts of outbreaks.

Spatio-temporal genetic structure of Anopheles gambiae in the Northwestern Lake Victoria Basin, Uganda: implications for genetic control trials in malaria endemic regions

Background

Understanding population genetic structure in the malaria vector Anopheles gambiae (s.s.) is crucial to inform genetic control and manage insecticide resistance. Unfortunately, species characteristics such as high nucleotide diversity, large effective population size, recent range expansion, and high dispersal ability complicate the inference of genetic structure across its range in sub-Saharan Africa. The ocean, along with the Great Rift Valley, is one of the few recognized barriers to gene flow in this species, but the effect of inland lakes, which could be useful sites for initial testing of genetic control strategies, is relatively understudied. Here we examine Lake Victoria as a barrier between the Ugandan mainland and the Ssese Islands, which lie up to 60 km offshore. We use mitochondrial DNA (mtDNA) from populations sampled in 2002, 2012 and 2015, and perform Bayesian cluster analysis on mtDNA combined with microsatellite data previously generated from the same 2002 mosquito DNA samples.

Results

Hierarchical analysis of molecular variance and Bayesian clustering support significant differentiation between the mainland and lacustrine islands. In an mtDNA haplotype network constructed from this and previous data, haplotypes are shared even between localities separated by the Rift Valley, a result that more likely reflects retention of shared ancestral polymorphism than contemporary gene flow.

Conclusions

The relative genetic isolation of An. gambiae on the Ssese Islands, their small size, level terrain and ease of access from the mainland, the relative simplicity of the vectorial system, and the prevalence of malaria, are all attributes that recommend these islands as possible sites for the testing of genetic control strategies.

Population Genetic Structure of the Malaria Vector Anopheles sinensis (Diptera: Culicidae) Sensu Stricto and Evidence for Possible Introgression in the Republic of Korea

Anopheles sinensis Wiedemann sensu stricto (s.s.) is a dominant mosquito and considered a secondary malaria vector in the Republic of Korea (ROK). Despite the potential significance for malaria control, population genetics studies have been conducted using only mitochondrial DNA (mtDNA), and studies of the genetics of hybridization have never been attempted. In this study, 346 specimens from 23 localities were subject to experiments. Among them, 305 An. sinensis s.s. specimens from 20 localities were used for mtDNA analysis, and 346 specimens comprising 341 An. sinensis s.s. from 22 localities and five Anopheles kleini Rueda from one locality were examined in the microsatellite study. Neighbor-joining analysis of pairwise FST and RST based on microsatellite results showed that the populations are divided into two groups, as did the mtDNA results. However, the Bayesian analysis and factorial correspondence analysis plots showed three distinct clusters. Among the mtDNA and microsatellite results, only microsatellites represented small but positive and significant isolation-by-distance patterns. Both molecular markers show the Taebaek and Sobaek Mountain ranges as barriers between the northern and southern parts of the ROK. The newly recognized third group suggests possible introgressive hybridization of An. sinensis s.s. with closely related species. The slightly different composition of populations in each group based on different markers is probably because of different population dynamics in each group. These results imply that there is restricted gene flow of epidemiologically important malaria-related genes between the northern and southern parts of the ROK.

Engaging scientists: An online survey exploring the experience of innovative biotechnological approaches to controlling vector-borne diseases

Background

Pioneering technologies (e.g., nanotechnology, synthetic biology or climate engineering) are often associated with potential new risks and uncertainties that can become sources of controversy. The communication of information during their development and open exchanges between stakeholders is generally considered a key issue in their acceptance. While the attitudes of the public to novel technologies have been widely considered there has been relatively little investigation of the perceptions and awareness of scientists working on human or animal diseases transmitted by arthropods.

Methods

Consequently, we conducted a global survey on 1889 scientists working on aspects of vector-borne diseases, exploring, under the light of a variety of demographic and professional factors, their knowledge and awareness of an emerging biotechnology that has the potential to revolutionize the control of pest insect populations.

Results

Despite extensive media coverage of key developments (including releases of manipulated mosquitoes into human communities) this has in only one instance resulted in scientist awareness exceeding 50 % on a national or regional scale. We document that awareness of pioneering releases significantly relied on private communication sources that were not equally accessible to scientists from countries with endemic vector-borne diseases (dengue and malaria). In addition, we provide quantitative analysis of the perceptions and knowledge of specific biotechnological approaches to controlling vector-borne disease, which are likely to impact the way in which scientists around the world engage in the debate about their value.

Conclusions

Our results indicate that there is scope to strengthen already effective methods of communication, in addition to a strong demand by scientists (expressed by 79.9 % of respondents) to develop new, creative modes of public engagement.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-015-0996-x) contains supplementary material, which is available to authorized users.

Glossina palpalis palpalis populations from Equatorial Guinea belong to distinct allopatric clades

Background

Luba is one of the four historical foci of Human African Trypanosomiasis (HAT) on Bioko Island, in Equatorial Guinea. Although no human cases have been detected since 1995, T. b. gambiense was recently observed in the vector Glossina palpalis palpalis. The existence of cryptic species within this vector taxon has been previously suggested, although no data are available regarding the evolutionary history of tsetse flies populations in Bioko.

Methods

A phylogenetic analysis of 60 G. p. palpalis from Luba was performed sequencing three mitochondrial (COI, ND2 and 16S) and one nuclear (rDNA-ITS1) DNA markers. Phylogeny reconstruction was performed by Distance Based, Maximum Likelihood and Bayesian Inference methods.

Results

The COI and ND2 mitochondrial genes were concatenated and revealed 10 closely related haplotypes with a dominant one found in 61.1% of the flies. The sequence homology of the other 9 haplotypes compared to the former ranged from 99.6 to 99.9%. Phylogenetic analysis clearly clustered all island samples with flies coming from the Western African Clade (WAC), and separated from the flies belonging to the Central Africa Clade (CAC), including samples from Mbini and Kogo, two foci of mainland Equatorial Guinea. Consistent with mitochondrial data, analysis of the microsatellite motif present in the ITS1 sequence exhibited two closely related genotypes, clearly divergent from the genotypes previously identified in Mbini and Kogo.

Conclusions

We report herein that tsetse flies populations circulating in Equatorial Guinea are composed of two allopatric subspecies, one insular and the other continental. The presence of these two G. p. palpalis cryptic taxa in Equatorial Guinea should be taken into account to accurately manage vector control strategy, in a country where trypanosomiasis transmission is controlled but not definitively eliminated yet.

An analysis of two island groups as potential sites for trials of transgenic mosquitoes for malaria control

Considerable technological advances have been made towards the generation of genetically modified mosquitoes for vector control. In contrast, less progress has been made towards field evaluations of transformed mosquitoes which are critical for evaluating the success of, and hazards associated with, genetic modification. Oceanic islands have been highlighted as potentially the best locations for such trials. However, population genetic studies are necessary to verify isolation. Here, we used a panel of genetic markers to assess for evidence of genetic isolation of two oceanic island populations of the African malaria vector, Anopheles gambiae s.s. We found no evidence of isolation between the Bijagós archipelago and mainland Guinea-Bissau, despite separation by distances beyond the known dispersal capabilities of this taxon. Conversely, the Comoros Islands appear to be genetically isolated from the East African mainland, and thus represent a location worthy of further investigation for field trials. Based on assessments of gene flow within and between the Comoros islands, the island of Grande Comore was found to be genetically isolated from adjacent islands and also exhibited local population structure, indicating that it may be the most suitable site for trials with existing genetic modification technologies.

New insights into the population structure of Anopheles gambiae s.s. in the Gulf of Guinea Islands revealed by Herves transposable elements

Transposable elements (TEs) are mobile portions of DNA that are able to replicate and spread in the genome of many organisms. TEs can be used as a means to insert transgenes in insects, being stably inherited throughout generations. Anopheles gambiae is the main vector of human malaria in Sub-Saharan Africa. Given the extraordinary burden this disease imposes, the mosquito became a choice target for genetic control approaches with the purpose of reducing malaria transmission. In this study, we investigated the abundance and distribution of Herves TE in An. gambiae s.s. from Cameroon and four islands in the Gulf of Guinea, in order to determine their genetic structure. We have detected a population subdivision between Equatorial Guinea islands and the islands of São Tomé, Príncipe and mainland. This partitioning associates more with political rather than geographic boundaries, possibly reflecting different mainland source populations colonizing the islands.

Stability properties of underdominance in finite subdivided populations

IN ISOLATED populations underdominance leads to bistable evolutionary dynamics: below a certain mutant allele frequency the wildtype succeeds. Above this point, the potentially underdominant mutant allele fixes. In subdivided populations with gene flow there can be stable states with coexistence of wildtypes and mutants: polymorphism can be maintained because of a migration-selection equilibrium, i.e., selection against rare recent immigrant alleles that tend to be heterozygous. We focus on the stochastic evolutionary dynamics of systems where demographic fluctuations in the coupled populations are the main source of internal noise. We discuss the influence of fitness, migration rate, and the relative sizes of two interacting populations on the mean extinction times of a group of potentially underdominant mutant alleles. We classify realistic initial conditions according to their impact on the stochastic extinction process. Even in small populations, where demographic fluctuations are large, stability properties predicted from deterministic dynamics show remarkable robustness. Fixation of the mutant allele becomes unlikely but the time to its extinction can be long.