Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex

Population genomic evidence of a putative 'far-west' African cryptic taxon in the Anopheles gambiae complex

The two main Afrotropical malaria vectors - Anopheles coluzzii and An. gambiae - are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as "intermediate" between the two species by whole genome sequence (WGS) data, and as hybrid forms by conventional molecular diagnostics. By exploiting WGS data from 1190 specimens collected across west Africa via the Anopheles gambiae 1000 Genomes network, we identified a putative taxon in the far-west (provisionally named Bissau molecular form), which did not arise by admixture but rather may have originated at the same time as the split between An. coluzzii and An. gambiae. Intriguingly, this taxon lacks insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches.

Mitochondrial Variation in Anopheles gambiae and Anopheles coluzzii: Phylogeographic Legacy and Mitonuclear Associations With Metabolic Resistance to Pathogens and Insecticides

Mitochondrial DNA has been a popular marker in phylogeography, phylogeny, and molecular ecology, but its complex evolution is increasingly recognized. Here, we investigated mitochondrial DNA variation in Anopheles gambiae and Anopheles coluzzii, in relation to other species in the Anopheles gambiae complex, by assembling the mitogenomes of 1,219 mosquitoes across Africa. The mitochondrial DNA phylogeny of the Anopheles gambiae complex was consistent with previously reported highly reticulated evolutionary history, revealing important discordances with the species tree. The three most widespread species (An. gambiae, An. coluzzii, and Anopheles arabiensis), known for extensive historical introgression, could not be discriminated based on mitogenomes. Furthermore, a monophyletic clustering of the three saltwater-tolerant species (Anopheles merus, Anopheles melas, and Anopheles bwambae) in the Anopheles gambiae complex also suggested that introgression and possibly selection shaped mitochondrial DNA evolution. Mitochondrial DNA variation in An. gambiae and An. coluzzii across Africa revealed significant partitioning among populations and species. A peculiar mitochondrial DNA lineage found predominantly in An. coluzzii and in the hybrid taxon of the African "far-west" exhibited divergence comparable to the interspecies divergence in the Anopheles gambiae complex, with a geographic distribution matching closely An. coluzzii's geographic range. This phylogeographic relict of the An. coluzzii and An. gambiae split was associated with population and species structure, but not with the rare Wolbachia occurrence. The lineage was significantly associated with single nucleotide polymorphisms in the nuclear genome, particularly in genes associated with pathogen and insecticide resistance. These findings underline potential mitonuclear coevolution history and the role played by mitochondria in shaping metabolic responses to pathogens and insecticides in Anopheles.

Speciation within the Anopheles gambiae complex: high-throughput whole genome sequencing reveals evidence of a putative new cryptic taxon in 'far-west' Africa

The two main Afrotropical malaria vectors - Anopheles coluzzii and An. gambiae - are genetically distinct and reproductively isolated across West Africa. However, populations at the western extreme of their range are assigned as "intermediate" between the two species by whole genome sequence (WGS) data, and as hybrid forms by conventional molecular diagnostics. By exploiting WGS data from 1,190 specimens collected across west Africa via the Anopheles gambiae 1000 Genomes network, we identify a novel putative taxon in the far-west (provisionally named Bissau molecular form), which did not arise by admixture but rather originated at the same time as the split between An. coluzzii and An. gambiae. Intriguingly, these populations lack insecticide resistance mechanisms commonly observed in the two main species. These findings lead to a change of perspective on malaria vector species in the far-west region with potential for epidemiological implications, and a new challenge for genetic-based mosquito control approaches.

Reproductive isolation in a three-way contact zone

Contact zones between divergent forms within a species provide insight into the role of gene flow in adaptation and speciation. Previous work has focused on contact zones involving only two divergent forms, but in nature, many more than two populations may overlap simultaneously and experience gene flow. Patterns of introgression in wild populations are, therefore, likely much more complicated than is often assumed. We begin to address this gap in current knowledge by investigating patterns of divergence and introgression across a complex natural contact zone. We use phenotypic and genomic data to confirm the existence of a three-way contact zone among divergent freshwater resident, saltwater resident and saltwater migratory three-spined stickleback (Gasterosteus aculeatus) on the island of North Uist, Scottish Western Isles. We find evidence for hybridization, mostly between saltwater resident and saltwater migratory forms. Despite hybridization, genomic analyses reveal pairwise islands of divergence between all forms that are maintained across the contact zone. Genomic cline analyses also provide evidence for selection and/or hybrid incompatibilities in divergent regions. Divergent genomic regions occur across multiple chromosomes and involve many known adaptive loci and several chromosomal inversions. We also identify distinct immune gene expression profiles between forms, but no evidence for transgressive expression in hybrids. Our results suggest that reproductive isolation is maintained in this three-way contact zone, despite some hybridization, and that reduced recombination in chromosomal inversions may play an important role in maintaining this isolation.

Conceptual risk assessment of mosquito population modification gene-drive systems to control malaria transmission: preliminary hazards list workshops

The field-testing and eventual adoption of genetically-engineered mosquitoes (GEMs) to control vector-borne pathogen transmission will require them meeting safety criteria specified by regulatory authorities in regions where the technology is being considered for use and other locales that might be impacted. Preliminary risk considerations by researchers and developers may be useful for planning the baseline data collection and field research used to address the anticipated safety concerns. Part of this process is to identify potential hazards (defined as the inherent ability of an entity to cause harm) and their harms, and then chart the pathways to harm and evaluate their probability as part of a risk assessment. The University of California Malaria Initiative (UCMI) participated in a series of workshops held to identify potential hazards specific to mosquito population modification strains carrying gene-drive systems coupled to anti-parasite effector genes and their use in a hypothetical island field trial. The hazards identified were placed within the broader context of previous efforts discussed in the scientific literature. Five risk areas were considered i) pathogens, infections and diseases, and the impacts of GEMs on human and animal health, ii) invasiveness and persistence of GEMs, and interactions of GEMs with target organisms, iii) interactions of GEMs with non-target organisms including horizontal gene transfer, iv) impacts of techniques used for the management of GEMs and v) evolutionary and stability considerations. A preliminary hazards list (PHL) was developed and is made available here. This PHL is useful for internal project risk evaluation and is available to regulators at prospective field sites. UCMI project scientists affirm that the subsequent processes associated with the comprehensive risk assessment for the application of this technology should be driven by the stakeholders at the proposed field site and areas that could be affected by this intervention strategy.

Introgression of a synthetic sex ratio distortion transgene into different genetic backgrounds of Anopheles coluzzii

The development of genetically modified mosquitoes (GMM) and their subsequent field release offers innovative approaches for vector control of malaria. A non-gene drive self-limiting male-bias Ag(PMB)1 strain has been developed in a 47-year-old laboratory G3 strain of Anopheles gambiae s.l. When Ag(PMB)1 males are crossed to wild-type females, expression of the endonuclease I-PpoI during spermatogenesis causes the meiotic cleavage of the X chromosome in sperm cells, leading to fertile offspring with a 95% male bias. However, World Health Organization states that the functionality of the transgene could differ when inserted in different genetic backgrounds of Anopheles coluzzii which is currently a predominant species in several West-African countries and thus a likely recipient for a potential release of self-limiting GMMs. In this study, we introgressed the transgene from the donor Ag(PMB)1 by six serial backcrosses into two recipient colonies of An. coluzzii that had been isolated in Mali and Burkina Faso. Scans of informative Single Nucleotide Polymorphism (SNP) markers and whole-genome sequencing analysis revealed a nearly complete introgression of chromosomes 3 and X, but a remarkable genomic divergence in a large region of chromosome 2 between the later backcrossed (BC6) transgenic offspring and the recipient paternal strains. These findings suggested to extend the backcrossing breeding strategy beyond BC6 generation and increasing the introgression efficiency of critical regions that have ecological and epidemiological implications through the targeted selection of specific markers. Disregarding differential introgression efficiency, we concluded that the phenotype of the sex ratio distorter is stable in the BC6 introgressed An. coluzzii strains.

Gene drive in species complexes: defining target organisms

Engineered gene drives, which bias their own inheritance to increase in frequency in target populations, are being developed to control mosquito malaria vectors. Such mosquitoes can belong to complexes of both vector and nonvector species that can produce fertile interspecific hybrids, making vertical gene drive transfer (VGDT) to sibling species biologically plausible. While VGDT to other vectors could positively impact human health protection goals, VGDT to nonvectors might challenge biodiversity ones. Therefore, environmental risk assessment of gene drive use in species complexes invites more nuanced considerations of target organisms and nontarget organisms than for transgenes not intended to increase in frequency in target populations. Incorporating the concept of target species complexes offers more flexibility when assessing potential impacts from VGDT.

High Levels of Admixture in Anopheles gambiae Populations from Côte d'Ivoire Revealed by Multilocus Genotyping

Anopheles coluzzii and An. gambiae-the two most recently radiated species of the An. gambiae complex and the major Afrotropical malaria vector species-are identified by markers in the X-centromeric IGS rDNA region. Putative IGS-hybrids are rarely found in the field, except in restricted areas where genomic studies have led to the hypothesis that the observed IGS-patterns are due to cryptic taxa rather than to hybridization between the two species. We investigated the genome-wide levels of admixture in two villages in Côte d'Ivoire where high levels of IGS-hybrids have been detected, confirming unparalleled high frequencies in the coastal village. Genotyping of 24 Ancestry Informative Markers (AIMs) along the three chromosomes produced discordant results between the IGS-marker and the multilocus genotype obtained for AIMs across the whole genome (29%) as well as AIMs on chromosome-X (considered to be fundamental for species reproductive isolation) only (21%). Results highlight a complicated pattern of admixture that deserves deeper genomic analyses to understand better possible underlying causes (from extensive processes of hybridization to the existence of different cryptic taxa), and stress the need of developing advanced diagnostics for An. coluzzii, An. gambiae and putative new taxa, instrumental for assessing taxon-specific epidemiological characters.

Spatial modelling for population replacement of mosquito vectors at continental scale

Malaria is one of the deadliest vector-borne diseases in the world. Researchers are developing new genetic and conventional vector control strategies to attempt to limit its burden. Novel control strategies require detailed safety assessment to ensure responsible and successful deployments. Anopheles gambiae sensu stricto (s.s.) and Anopheles coluzzii, two closely related subspecies within the species complex Anopheles gambiae sensu lato (s.l.), are among the dominant malaria vectors in sub-Saharan Africa. These two subspecies readily hybridise and compete in the wild and are also known to have distinct niches, each with spatially and temporally varying carrying capacities driven by precipitation and land use factors.

We model the spread and persistence of a population-modifying gene drive system in these subspecies across sub-Saharan Africa by simulating introductions of genetically modified mosquitoes across the African mainland and its offshore islands. We explore transmission of the gene drive between the two subspecies that arise from different hybridisation mechanisms, the effects of both local dispersal and potential wind-aided migration to the spread, and the development of resistance to the gene drive. Given the best current available knowledge on the subspecies’ life histories, we find that an introduced gene drive system with typical characteristics can plausibly spread from even distant offshore islands to the African mainland with the aid of wind-driven migration, with resistance beginning to take over within a decade. Our model accounts for regional to continental scale mechanisms, and demonstrates a range of realistic dynamics including the effect of prevailing wind on spread and spatio-temporally varying carrying capacities for subspecies. As a result, it is well-placed to answer future questions relating to mosquito gene drives as important life history parameters become better understood.

Conventional control methods have dramatically reduced malaria, but it still kills over 300,000 children in Africa each year, and this number could increase as their effectiveness wanes. Novel control methods using gene drives rapidly reduce or modify malaria vector populations in laboratory settings, and hence are now being considered for field applications. We use modelling to assess how a gene drive might spread and persist in the malaria-carrying subspecies Anopheles gambiae sensu stricto (s.s.) and Anopheles coluzzii. These two subspecies interbreed and compete, so we model how these interactions affect the spread of the drive at a continental scale. In scenarios that allow mosquitoes to travel on prevailing wind currents, we find that a gene drive can potentially spread across national borders—and jump from offshore islands to the African mainland—but spread is eventually arrested when the drive allele is ousted by a resistant allele. As we learn more about the population dynamics of both genetically modified and wild mosquitoes, and as gene drive systems are further developed to allow local containment and evade resistance, our model will be able to answer more detailed questions about how they can be applied in the field effectively and safely.

Is Côte D'Ivoire a new high hybridization zone for the two major malaria vectors, Anopheles coluzzii and An. gambiae (Diptera, Culicidae)?

Anopheles gambiae and An. coluzzii are very closely related and recently differentiated species representing the main malaria vectors in the Afrotropical region and responsible of up to >3 infective bites/person/night in Côte D'Ivoire, where prevention and control has stagnated in recent years. The aim of the present study was to genetically and ecologically characterize An. gambiae and An. coluzzii populations from two villages of Côte D'Ivoire, lying in the coastal forest belt and 250 km inland in the Guinean savannah mosaic belt, respectively. Results reveal high frequencies of both species in both study sites and high frequencies of hybrids (4-33%) along the whole year of sampling. Consistently with observations for the well-known high hybridization zone at the far-west of the species range, hybrid frequencies were higher in the coastal village and highest when the two species occurred at more balanced frequencies, supporting the "frequency-dependent hybridization" ecological speciation theory. Pilot genotyping revealed signatures of genomic admixture in both chromosome-X and -3. Coupled with previous reports of hybrids in the region, the results point to the coastal region of Côte D'Ivoire as a possible regions of high hybridization. Preliminary characterization of parameters relevant for malaria transmission and control (e.g. possibly higher sporozoite rates and indoor biting preferences in hybrids than in the parental species) highlight the possible relevance of the breakdown of reproductive barriers between An. gambiae and An. coluzzii not only in the field of ecological evolution, but also in malaria epidemiology and control.

Modelling spatiotemporal trends in the frequency of genetic mutations conferring insecticide target-site resistance in African mosquito malaria vector species

BACKGROUND

Resistance in malaria vectors to pyrethroids, the most widely used class of insecticides for malaria vector control, threatens the continued efficacy of vector control tools. Target-site resistance is an important genetic resistance mechanism caused by mutations in the voltage-gated sodium channel (Vgsc) gene that encodes the pyrethroid target-site. Understanding the geographic distribution of target-site resistance, and temporal trends across different vector species, can inform strategic deployment of vector control tools.

RESULTS

We develop a Bayesian statistical spatiotemporal model to interpret species-specific trends in the frequency of the most common resistance mutations, Vgsc-995S and Vgsc-995F, in three major malaria vector species Anopheles gambiae, An. coluzzii, and An. arabiensis over the period 2005-2017. The models are informed by 2418 observations of the frequency of each mutation in field sampled mosquitoes collected from 27 countries spanning western and eastern regions of Africa. For nine selected countries, we develop annual predictive maps which reveal geographically structured patterns of spread of each mutation at regional and continental scales. The results show associations, as well as stark differences, in spread dynamics of the two mutations across the three vector species. The coverage of ITNs was an influential predictor of Vgsc allele frequencies, with modelled relationships between ITN coverage and allele frequencies varying across species and geographic regions. We found that our mapped Vgsc allele frequencies are a significant partial predictor of phenotypic resistance to the pyrethroid deltamethrin in An. gambiae complex populations.

CONCLUSIONS

Our predictive maps show how spatiotemporal trends in insecticide target-site resistance mechanisms in African An. gambiae vary across individual vector species and geographic regions. Molecular surveillance of resistance mechanisms will help to predict resistance phenotypes and track their spread.

Preferred reporting items for systematic reviews and meta-analyses in ecology and evolutionary biology: a PRISMA extension

Since the early 1990s, ecologists and evolutionary biologists have aggregated primary research using meta-analytic methods to understand ecological and evolutionary phenomena. Meta-analyses can resolve long-standing disputes, dispel spurious claims, and generate new research questions. At their worst, however, meta-analysis publications are wolves in sheep's clothing: subjective with biased conclusions, hidden under coats of objective authority. Conclusions can be rendered unreliable by inappropriate statistical methods, problems with the methods used to select primary research, or problems within the primary research itself. Because of these risks, meta-analyses are increasingly conducted as part of systematic reviews, which use structured, transparent, and reproducible methods to collate and summarise evidence. For readers to determine whether the conclusions from a systematic review or meta-analysis should be trusted - and to be able to build upon the review - authors need to report what they did, why they did it, and what they found. Complete, transparent, and reproducible reporting is measured by 'reporting quality'. To assess perceptions and standards of reporting quality of systematic reviews and meta-analyses published in ecology and evolutionary biology, we surveyed 208 researchers with relevant experience (as authors, reviewers, or editors), and conducted detailed evaluations of 102 systematic review and meta-analysis papers published between 2010 and 2019. Reporting quality was far below optimal and approximately normally distributed. Measured reporting quality was lower than what the community perceived, particularly for the systematic review methods required to measure trustworthiness. The minority of assessed papers that referenced a guideline (~16%) showed substantially higher reporting quality than average, and surveyed researchers showed interest in using a reporting guideline to improve reporting quality. The leading guideline for improving reporting quality of systematic reviews is the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) statement. Here we unveil an extension of PRISMA to serve the meta-analysis community in ecology and evolutionary biology: PRISMA-EcoEvo (version 1.0). PRISMA-EcoEvo is a checklist of 27 main items that, when applicable, should be reported in systematic review and meta-analysis publications summarising primary research in ecology and evolutionary biology. In this explanation and elaboration document, we provide guidance for authors, reviewers, and editors, with explanations for each item on the checklist, including supplementary examples from published papers. Authors can consult this PRISMA-EcoEvo guideline both in the planning and writing stages of a systematic review and meta-analysis, to increase reporting quality of submitted manuscripts. Reviewers and editors can use the checklist to assess reporting quality in the manuscripts they review. Overall, PRISMA-EcoEvo is a resource for the ecology and evolutionary biology community to facilitate transparent and comprehensively reported systematic reviews and meta-analyses.

Urban malaria in sub-Saharan Africa: dynamic of the vectorial system and the entomological inoculation rate

Sub-Saharan Africa is registering one of the highest urban population growth across the world. It is estimated that over 75% of the population in this region will be living in urban settings by 2050. However, it is not known how this rapid urbanization will affect vector populations and disease transmission. The present study summarizes findings from studies conducted in urban settings between the 1970s and 2020 to assess the effects of urbanization on the entomological inoculation rate pattern and anopheline species distribution. Different online databases such as PubMed, ResearchGate, Google Scholar, Google were screened. A total of 90 publications were selected out of 1527. Besides, over 200 additional publications were consulted to collate information on anopheline breeding habitats and species distribution in urban settings. The study confirms high malaria transmission in rural compared to urban settings. The study also suggests that there had been an increase in malaria transmission in most cities after 2003, which could also be associated with an increase in sampling, resources and reporting. Species of the Anopheles gambiae complex were the predominant vectors in most urban settings. Anopheline larvae were reported to have adapted to different aquatic habitats. The study provides updated information on the distribution of the vector population and the dynamic of malaria transmission in urban settings. The study also highlights the need for implementing integrated control strategies in urban settings.

Unravelling population structure heterogeneity within the genome of the malaria vector Anopheles gambiae

Background

Whole genome re-sequencing provides powerful data for population genomic studies, allowing robust inferences of population structure, gene flow and evolutionary history. For the major malaria vector in Africa, Anopheles gambiae, other genetic aspects such as selection and adaptation are also important. In the present study, we explore population genetic variation from genome-wide sequencing of 765 An. gambiae and An. coluzzii specimens collected from across Africa. We used t-SNE, a recently popularized dimensionality reduction method, to create a 2D-map of An. gambiae and An. coluzzii genes that reflect their population structure similarities.

Results

The map allows intuitive navigation among genes distributed throughout the so-called “mainland” and numerous surrounding “island-like” gene clusters. These gene clusters of various sizes correspond predominantly to low recombination genomic regions such as inversions and centromeres, and also to recent selective sweeps. Because this mosquito species complex has been studied extensively, we were able to support our interpretations with previously published findings. Several novel observations and hypotheses are also made, including selective sweeps and a multi-locus selection event in Guinea-Bissau, a known intense hybridization zone between An. gambiae and An. coluzzii.

Conclusions

Our results present a rich dataset that could be utilized in functional investigations aiming to shed light onto An. gambiae s.l genome evolution and eventual speciation. In addition, the methodology presented here can be used to further characterize other species not so well studied as An. gambiae, shortening the time required to progress from field sampling to the identification of genes and genomic regions under unique evolutionary processes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07722-y.

Novel genotyping approaches to easily detect genomic admixture between the major Afrotropical malaria vector species, Anopheles coluzzii and An. gambiae

The two most efficient and most recently radiated Afrotropical vectors of human malaria - Anopheles coluzzii and An. gambiae - are identified by single-locus diagnostic PCR assays based on species-specific markers in a 4 Mb region on chromosome-X centromere. Inherently, these diagnostic assays cannot detect interspecific autosomal admixture shown to be extensive at the westernmost and easternmost extremes of the species range. The main aim of this study was to develop novel, easy-to-implement tools for genotyping An. coluzzii and An. gambiae-specific ancestral informative markers (AIMs) identified from the Anopheles gambiae 1000 genomes (Ag1000G) project. First, we took advantage of this large set of data in order to develop a multilocus approach to genotype 26 AIMs on all chromosome arms valid across the species range. Second, we tested the multilocus assay on samples from Guinea Bissau, The Gambia and Senegal, three countries spanning the westernmost hybridization zone, where conventional species diagnostic is problematic due to the putative presence of a novel "hybrid form". The multilocus assay was able to capture patterns of admixture reflecting those revealed by the whole set of AIMs and provided new original data on interspecific admixture in the region. Third, we developed an easy-to-use, cost-effective PCR approach for genotyping two AIMs on chromosome-3 among those included in the multilocus approach, opening the possibility for advanced identification of species and of admixed specimens during routine large scale entomological surveys, particularly, but not exclusively, at the extremes of the range, where WGS data highlighted unexpected autosomal admixture.

Mosquitoes of the Maculipennis complex in Northern Italy

The correct identification of mosquito vectors is often hampered by the presence of morphologically indiscernible sibling species. The Maculipennis complex is one of these groups that include both malaria vectors of primary importance and species of low/negligible epidemiological relevance, of which distribution data in Italy are outdated. Our study was aimed at providing an updated distribution of Maculipennis complex in Northern Italy through the sampling and morphological/molecular identification of specimens from five regions. The most abundant species was Anopheles messeae (2032), followed by Anopheles maculipennis s.s. (418), Anopheles atroparvus (28) and Anopheles melanoon (13). Taking advantage of ITS2 barcoding, we were able to finely characterize tested mosquitoes, classifying all the Anopheles messeae specimens as Anopheles daciae, a taxon with debated rank to which we referred as species inquirenda (sp. inq.). The distribution of species was characterized by Ecological Niche Models (ENMs), fed by recorded points of presence. ENMs provided clues on the ecological preferences of the detected species, with An. daciae sp. inq. linked to stable breeding sites and An. maculipennis s.s. more associated to ephemeral breeding sites. We demonstrate that historical Anopheles malaria vectors are still present in Northern Italy.

Control of malaria-transmitting mosquitoes using gene drives

Gene drives are selfish genetic elements that can be re-designed to invade a population and they hold tremendous potential for the control of mosquitoes that transmit disease. Much progress has been made recently in demonstrating proof of principle for gene drives able to suppress populations of malarial mosquitoes, or to make them refractory to the Plasmodium parasites they transmit. This has been achieved using CRISPR-based gene drives. In this article, I will discuss the relative merits of this type of gene drive, as well as barriers to its technical development and to its deployment in the field as malaria control. This article is part of the theme issue 'Novel control strategies for mosquito-borne diseases'.

Unveiling mosquito cryptic species and their reproductive isolation

Mosquitoes are major vectors of many infectious pathogens or parasites. Understanding cryptic species and the speciation of disease vectors has important implications for vector management, evolution and host-pathogen and/or host-parasite interactions. Currently, mosquito cryptic species have been reported in many studies, most of which focus on the reproductive isolation of cryptic species and mainly on Anopheles gambiae sensu lato complex. Emerging species within the primary malaria vector Anopheles gambiae show different ecological preferences and significant prezygotic reproductive isolation, while Aedes mariae and Aedes zammitii show postmating reproductive isolation. However, data reporting the reproductive isolation in Culex and Aedes albopictus mosquito cryptic species is absent. The lack of systematic studies leaves many questions open, such as whether cryptic species are more common in particular habitats, latitudes or taxonomic groups; what mosquito cryptic species evolutionary processes bring about reproductive isolation in the absence of morphological differentiation? How does Wolbachia infection affect in mosquitoes' reproductive isolation? In this review, we provide a summary of recent advances in the discovery and identification of sibling or cryptic species within mosquito genera.

Leveraging big data for public health: Mapping malaria vector suitability in Malawi with Google Earth Engine

In an era of big data, the availability of satellite-derived global climate, terrain, and land cover imagery presents an opportunity for modeling the suitability of malaria disease vectors at fine spatial resolutions, across temporal scales, and over vast geographic extents. Leveraging cloud-based geospatial analytical tools, we present an environmental suitability model that considers water resources, flow accumulation areas, precipitation, temperature, vegetation, and land cover. In contrast to predictive models generated using spatially and temporally discontinuous mosquito presence information, this model provides continuous fine-spatial resolution information on the biophysical drivers of suitability. For the purposes of this study the model is parameterized for Anopheles gambiae s.s. in Malawi for the rainy (December-March) and dry seasons (April-November) in 2017; however, the model may be repurposed to accommodate different mosquito species, temporal periods, or geographical boundaries. Final products elucidate the drivers and potential habitat of Anopheles gambiae s.s. Rainy season results are presented by quartile of precipitation; Quartile four (Q4) identifies areas most likely to become inundated and shows 7.25% of Malawi exhibits suitable water conditions (water only) for Anopheles gambiae s.s., approximately 16% for water plus another factor, and 8.60% is maximally suitable, meeting suitability thresholds for water presence, terrain characteristics, and climatic conditions. Nearly 21% of Malawi is suitable for breeding based on land characteristics alone and 28.24% is suitable according to climate and land characteristics. Only 6.14% of the total land area is suboptimal. Dry season results show 25.07% of the total land area is suboptimal or unsuitable. Approximately 42% of Malawi is suitable based on land characteristics alone during the dry season, and 13.11% is suitable based on land plus another factor. Less than 2% meets suitability criteria for climate, water, and land criteria. Findings illustrate environmental drivers of suitability for malaria vectors, providing an opportunity for a more comprehensive approach to malaria control that includes not only modeled species distributions, but also the underlying drivers of suitability for a more effective approach to environmental management.

Male swarming aggregation pheromones increase female attraction and mating success among multiple African malaria vector mosquito species

Accumulating behavioural data indicate that aggregation pheromones may mediate the formation and maintenance of mosquito swarms. However, chemical cues possibly luring mosquitoes to swarms have not been adequately investigated, and the likely molecular incitants of these complex reproductive behaviours remain unknown. Here we show that males of the important malaria vector species Anopheles arabiensis and An. gambiae produce and release aggregation pheromones that attract individuals to the swarm and enhance mating success. We found that males of both species released significantly higher amounts of 3-hydroxy-2-butanone (acetoin), 6-methyl-5-hepten-2-one (sulcatone), octanal, nonanal and decanal during swarming in the laboratory. Feeding males with stable-isotope-labelled glucose revealed that the males produced these five compounds. A blend composed of synthetic analogues to these swarming odours proved highly attractive to virgin males and females of both species under laboratory conditions and substantially increased mating in five African malaria vectors (An. gambiae, An. coluzzii, An. arabiensis, An. merus and An. funestus) in semi-field experiments. Our results not only narrow a conspicuous gap in understanding a vital aspect of the chemical ecology of male mosquitoes but also demonstrate fundamental roles of rhythmic and metabolic genes in the physiology and behavioural regulation of these vectors. These identified aggregation pheromones have great potential for exploitation against these highly dangerous insects. Manipulating such pheromones could increase the efficacy of malaria-vector control programmes.

Behavioural plasticity of Anopheles coluzzii and Anopheles arabiensis undermines LLIN community protective effect in a Sudanese-savannah village in Burkina Faso

BACKGROUND

Despite the overall major impact of long-lasting insecticide treated nets (LLINs) in eliciting individual and collective protection to malaria infections, some sub-Saharan countries, including Burkina Faso, still carry a disproportionately high share of the global malaria burden. This study aims to analyse the possible entomological bases of LLIN limited impact, focusing on a LLIN-protected village in the Plateau Central region of Burkina Faso.

METHODS

Human landing catches (HLCs) were carried out in 2015 for 12 nights both indoors and outdoors at different time windows during the highest biting activity phase for Anopheles gambiae (s.l.). Collected specimens were morphologically and molecularly identified and processed for Plasmodium detection and L1014F insecticide-resistance allele genotyping.

RESULTS

Almost 2000 unfed An. gambiae (s.l.) (54% Anopheles coluzzii and 44% Anopheles arabiensis) females landing on human volunteers were collected, corresponding to a median number of 23.5 females/person/hour. No significant differences were observed in median numbers of mosquitoes collected indoors and outdoors, nor between sporozoite rates in An. coluzzii (6.1%) and An. arabiensis (5.5%). The estimated median hourly entomological inoculation rate (EIR) on volunteers was 1.4 infective bites/person/hour. Results do not show evidence of the biting peak during night hours typical for An. gambiae (s.l.) in the absence of bednet protection. The frequency of the L1014F resistant allele (n = 285) was 66% in An. coluzzii and 38% in An. arabiensis.

CONCLUSIONS

The observed biting rate and sporozoite rates are in line with the literature data available for An. gambiae (s.l.) in the same geographical area before LLIN implementation and highlight high levels of malaria transmission in the study village. Homogeneous biting rate throughout the night and lack of preference for indoor-biting activity, suggest the capacity of both An. coluzzii and An. arabiensis to adjust their host-seeking behaviour to bite humans despite bednet protection, accounting for the maintenance of high rates of mosquito infectivity and malaria transmission. These results, despite being limited to a local situation in Burkina Faso, represent a paradigmatic example of how high densities and behavioural plasticity in the vector populations may contribute to explaining the limited impact of LLINs on malaria transmission in holo-endemic Sudanese savannah areas in West Africa.

Genetic analysis and population structure of the Anopheles gambiae complex from different ecological zones of Burkina Faso

The Anopheles gambiae complex (Diptera: Culicidae) is the most important vector for malaria in Sub-Saharan Africa, besides other vectors such as Anopheles funestus. Malaria vector control should encompass specific identification, genetic diversity and population structure of An. gambiae to design vector control strategies. The aim of this study was to determine the distribution of sibling species of the An. gambiae complex according to climatic regions related to cotton-growing or cotton-free areas by using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Then, variation in mitochondrial cytochrome c oxidase 1 (COI) was used to assess the genetic structure within and between populations from our selected ecological zones. At the sibling species level, the following proportions were found across all samples (n = 180): An. coluzzii 65.56%, An. gambiae stricto sensu (s.s). 21.11%, and An. arabiensis 3.33%. Hybrids between An. gambiae s.s. and An. coluzzii (7.78%) and hybrids between An. coluzzii and An. arabiensis (2.22%) were found. The phylogenetic tree and Integer Neighbour-Joining (IntNJ) haplotype network did not reveal any distinct genetic structure pattern related to climatic or agricultural conditions in Burkina Faso. The Fst (Wright's F-statistic) values close to zero showed a free gene flow and no differentiation in An. gambiae complex populations. Furthermore, neutrality indices calculated by Tajima's D, Fu and Li's D^⁎, Fu and Li's F^⁎, Fu's Fs tests suggested an excess of rare mutations in the populations. Overall, variation in the proportions of An. gambiae s.s., An. coluzzii and An. arabiensis was found according to climatic regions, but COI analysis did not evidence any population structuring of the An. gambiae complex. These scientific contributions can be used as a basis for further in-depth study of the genetic diversity of the An. gambiae complex for epidemiological risk assessment of malaria in Burkina Faso.

Sex aggregation and species segregation cues in swarming mosquitoes: role of ground visual markers

BACKGROUND

Mating swarm segregation in closely related insect species may contribute to reproductive isolation. Visual markers are used for swarm formation; however, it is unknown whether they play a key role in swarm location, species segregation and sex aggregation.

METHODS

Using two sympatric closely related species of the Anopheles gambiae complex, An. coluzzii and An. gambiae (s.s.), we investigated in both laboratory and semi-field conditions (i) whether males of the two species use visual markers (black cloths) to locate their swarm; and (ii) whether the presence/absence and size of the marker may differentially affect swarm characteristics. We also investigated whether conspecific virgin females use these markers to join male swarm sites.

RESULTS

We showed that males of the two species used visual markers but in different ways: An. coluzzii swarm right above the marker whereas An. gambiae (s.s.) locate their swarm at a constant distance of 76.4 ± 0.6 cm from a 20 × 20 cm marker in the laboratory setup and at 206 ± 6 cm from a 60 × 60 cm marker in the semi-field setup. Although increased marker size recruited more mosquitoes and consequently increased the swarm size in the two species, An. coluzzii swarms flew higher and were stretched both vertically and horizontally, while An. gambiae (s.s.) swarms were only stretched horizontally. Virgin females displayed a swarm-like behavior with similar characteristics to their conspecific males.

CONCLUSIONS

Our results provided experimental evidence that both An. coluzzii and An. gambiae (s.s.) males use ground visual markers to form and locate their swarm at species-specific locations. Moreover, the marker size differentially affected swarm characteristics in the two species. Our results also showed that virgin females displayed a swarm-like behavior. However, these "swarms" could be due to the absence of males in our experimental conditions. Nevertheless, the fact that females displayed these "swarms" with the same characteristics as their respective males provided evidence that visual markers are used by the two sexes to join mating spots. Altogether, this suggests that visual markers and the way species and sexes use them could be key cues in species segregation, swarm location and recognition.

Review of malaria situation in Cameroon: technical viewpoint on challenges and prospects for disease elimination

Malaria still has a devastating impact on public health and welfare in Cameroon. Despite the increasing number of studies conducted on disease prevalence, transmission patterns or treatment, there are to date, not enough studies summarising findings from previous works in order to identify gaps in knowledge and areas of interest where further evidence is needed to drive malaria elimination efforts. The present study seeks to address these gaps by providing a review of studies conducted so far on malaria in Cameroon since the 1940s to date. Over 250 scientific publications were consulted for this purpose. Although there has been increased scale-up of vector control interventions which significantly reduced the morbidity and mortality to malaria across the country from a prevalence of 41% of the population reporting at least one malaria case episode in 2000 to a prevalence of 24% in 2017, the situation is not yet under control. There is a high variability in disease endemicity between epidemiological settings with prevalence of Plasmodium parasitaemia varying from 7 to 85% in children aged 6 months to 15 years after long-lasting insecticidal nets (LLINs) scale-up. Four species of Plasmodium have been recorded across the country: Plasmodium falciparum, P. malariae, P. ovale and P. vivax. Several primate-infecting Plasmodium spp. are also circulating in Cameroon. A decline of artemisinin-based combinations therapeutic efficacy from 97% in 2006 to 90% in 2016 have been reported. Several mutations in the P. falciparum chloroquine resistance (Pfcrt) and P. falciparum multidrug resistance 1 (Pfmdr1) genes conferring resistance to either 4-amino-quinoleine, mefloquine, halofanthrine and quinine have been documented. Mutations in the Pfdhfr and Pfdhps genes involved in sulfadoxine-pyrimethamine are also on the rise. No mutation associated with artemisinin resistance has been recorded. Sixteen anopheline species contribute to malaria parasite transmission with six recognized as major vectors: An. gambiae, An. coluzzii, An. arabiensis, An. funestus, An. nili and An. moucheti. Studies conducted so far, indicated rapid expansion of DDT, pyrethroid and carbamate resistance in An. gambiae, An. coluzzii, An. arabiensis and An. funestus threatening the performance of LLINs. This review highlights the complex situation of malaria in Cameroon and the need to urgently implement and reinforce integrated control strategies in different epidemiological settings, as part of the substantial efforts to consolidate gains and advance towards malaria elimination in the country.

A new species in the major malaria vector complex sheds light on reticulated species evolution

Complexes of closely related species provide key insights into the rapid and independent evolution of adaptive traits. Here, we described and studied Anopheles fontenillei sp.n., a new species in the Anopheles gambiae complex that we recently discovered in the forested areas of Gabon, Central Africa. Our analysis placed the new taxon in the phylogenetic tree of the An. gambiae complex, revealing important introgression events with other members of the complex. Particularly, we detected recent introgression, with Anopheles gambiae and Anopheles coluzzii, of genes directly involved in vectorial capacity. Moreover, genome analysis of the new species allowed us to clarify the evolutionary history of the 3La inversion. Overall, An. fontenillei sp.n. analysis improved our understanding of the relationship between species within the An. gambiae complex, and provided insight into the evolution of vectorial capacity traits that are relevant for the successful control of malaria in Africa.

Natural Wolbachia infections are common in the major malaria vectors in Central Africa

During the last decade, the endosymbiont bacterium Wolbachia has emerged as a biological tool for vector disease control. However, for long time, it was believed that Wolbachia was absent in natural populations of Anopheles. The recent discovery that species within the Anopheles gambiae complex host Wolbachia in natural conditions has opened new opportunities for malaria control research in Africa. Here, we investigated the prevalence and diversity of Wolbachia infection in 25 African Anopheles species in Gabon (Central Africa). Our results revealed the presence of Wolbachia in 16 of these species, including the major malaria vectors in this area. The infection prevalence varied greatly among species, confirming that sample size is a key factor to detect the infection. Moreover, our sequencing and phylogenetic analyses showed the important diversity of Wolbachia strains that infect Anopheles. Co-evolutionary analysis unveiled patterns of Wolbachia transmission within some Anopheles species, suggesting that past independent acquisition events were followed by co-cladogenesis. The large diversity of Wolbachia strains that infect natural populations of Anopheles offers a promising opportunity to select suitable phenotypes for suppressing Plasmodium transmission and/or manipulating Anopheles reproduction, which in turn could be used to reduce the malaria burden in Africa.

A framework for estimating the effects of sequential reproductive barriers: Implementation using Bayesian models with field data from cryptic species

Determining how reproductive barriers modulate gene flow between populations represents a major step toward understanding the factors shaping the course of speciation. Although many indices quantifying reproductive isolation (RI) have been proposed, they do not permit the quantification of cross-direction-specific RI under varying species frequencies and over arbitrary sequences of barriers. Furthermore, techniques quantifying associated uncertainties are lacking, and statistical methods unrelated to biological process are still preferred for obtaining confidence intervals and P-values. To address these shortcomings, we provide new RI indices that model changes in gene flow for both directions of hybridization, and we implement them in a Bayesian model. We use this model to quantify RI between two species of the psyllid Cacopsylla pruni based on field genotypic data for mating individuals, inseminated spermatophores and progeny. The results showed that preinsemination isolation was strong, mildly asymmetric, and indistinguishably different between study sites despite large differences in species frequencies; that postinsemination isolation strongly affected the more common hybrid type; and that cumulative isolation was close to complete. In the light of these results, we discuss how these developments can strengthen comparative RI studies.

Unexpectedly high Plasmodium sporozoite rate associated with low human blood index in Anopheles coluzzii from a LLIN-protected village in Burkina Faso

Despite the effectiveness of mass distribution of long-lasting insecticidal nets (LLINs) in reducing malaria transmission in Africa, in hyperendemic areas such as Burkina Faso the burden of malaria remains high. We here report the results of a 4-month survey on the feeding habits and Plasmodium infection in malaria vectors from a village in Burkina Faso one year following a national LLIN distribution programme. Low values of human blood index (HBI) observed in the major malaria vectors in the area (Anopheles coluzzii: N = 263, 20.1%; An. arabiensis: 5.8%, N = 103) are consistent with the hypothesis that LLINs reduced the availability of human hosts to mosquitoes. A regression meta-analysis of data from a systematic review of published studies reporting HBI and sporozoite rates (SR) for An. gambiae complex revealed that the observed SR values (An. coluzzii: 7.6%, N = 503; An. arabiensis: 5.3%, N = 225) are out of the ranges expected based on the low HBI observed. We hypothesize that a small fraction of inhabitants unprotected by bednets acts as a "core group" repeatedly exposed to mosquito bites, representing the major Plasmodium reservoir for the vectors, able to maintain a high risk of transmission even in a village protected by LLINs.

Analysis of natural female post-mating responses of Anopheles gambiae and Anopheles coluzzii unravels similarities and differences in their reproductive ecology

Anopheles gambiae and An. coluzzii, the two most important malaria vectors in sub-Saharan Africa, are recently radiated sibling species that are reproductively isolated even in areas of sympatry. In females from these species, sexual transfer of male accessory gland products, including the steroid hormone 20-hydroxyecdysone (20E), induces vast behavioral, physiological, and transcriptional changes that profoundly shape their post-mating ecology, and that may have contributed to the insurgence of post-mating, prezygotic reproductive barriers. As these barriers can be detected by studying transcriptional changes induced by mating, we set out to analyze the post-mating response of An. gambiae and An. coluzzii females captured in natural mating swarms in Burkina Faso. While the molecular pathways shaping short- and long-term mating-induced changes are largely conserved in females from the two species, we unravel significant inter-specific differences that suggest divergent regulation of key reproductive processes such as egg development, processing of seminal secretion, and mating behavior, that may have played a role in reproductive isolation. Interestingly, a number of these changes occur in genes previously shown to be regulated by the sexual transfer of 20E and may be due to divergent utilization of this steroid hormone in the two species.

Dissecting functional components of reproductive isolation among closely related sympatric species of the Anopheles gambiae complex

Explaining how and why reproductive isolation evolves and determining which forms of reproductive isolation have the largest impact on the process of population divergence are major goals in the study of speciation. By studying recent adaptive radiations in incompletely isolated taxa, it is possible to identify barriers involved at early divergence before other confounding barriers emerge after speciation is complete. Sibling species of the Anopheles gambiae complex offer opportunities to provide insights into speciation mechanisms. Here, we studied patterns of reproductive isolation among three taxa, Anopheles coluzzii, An. gambiae s.s. and Anopheles arabiensis, to compare its strength at different spatial scales, to dissect the relative contribution of pre‐ versus postmating isolation, and to infer the involvement of ecological divergence on hybridization. Because F1 hybrids are viable, fertile and not uncommon, understanding the dynamics of hybridization in this trio of major malaria vectors has important implications for how adaptations arise and spread across the group, and in planning studies of the safety and efficacy of gene drive as a means of malaria control. We first performed a systematic review and meta‐analysis of published surveys reporting on hybrid prevalence, showing strong reproductive isolation at a continental scale despite geographically restricted exceptions. Second, we exploited our own extensive field data sets collected at a regional scale in two contrasting environmental settings, to assess: (i) levels of premating isolation; (ii) spatio/temporal and frequency‐dependent dynamics of hybridization, (iii) relationship between reproductive isolation and ecological divergence and (iv) hybrid viability penalty. Results are in accordance with ecological speciation theory predicting a positive association between the strength of reproductive isolation and degree of ecological divergence, and indicate that postmating isolation does contribute to reproductive isolation among these species. Specifically, only postmating isolation was positively associated with ecological divergence, whereas premating isolation was correlated with phylogenetic distance.