Population genetic structure of Anopheles arabiensis mosquitoes in Ethiopia and Eritrea

Genomic Analysis Reveals a New Cryptic Taxon Within the Anopheles gambiae Complex With a Distinct Insecticide Resistance Profile in the Coast of East Africa

Anopheles mosquitoes are major malaria vectors, encompassing several species complexes with diverse life histories, transmission risks and insecticide resistance profiles that challenge malaria control efforts. This study investigated the genetic structure and insecticide resistance profiles of Anopheles gambiae complex mosquitoes in Tanzania. We analysed whole-genome sequence data of 300 mosquitoes collected between 2012 and 2015 across four regions in northern Tanzania and identified An. gambiae s.s., An. arabiensis and a distinct taxonomic group that was previously unknown. This distinct taxon has a unique profile of genetic diversity and appears restricted to the coastal region, and we refer to it as the Pwani molecular form. Analysis of insecticide resistance based on target-site mutations and copy number variations (CNV) showed that these markers were strikingly absent from the Pwani molecular form in contrast to other taxa. Our analysis also revealed a pattern of geographical isolation in the An. gambiae s.s. populations, with samples from the north-western site (Muleba) clustering separately from those collected in the north-eastern site (Muheza). These geographically isolated subpopulations also had differing resistance and selection profiles, with An. gambiae s.s. from the north-western site showing genomic evidence of higher resistance to pyrethroids compared with the north-eastern population. Conversely, An. arabiensis showed no geographical population structuring, with a similar insecticide resistance profile across all sampling locations, suggesting unrestricted gene flow. Our findings underscore the need to incorporate genetic data into malaria vector surveillance and control decisions and could inform the development and deployment of new interventions.

Fine-scale adaptive divergence and population genetic structure of Aedes aegypti in Metropolitan Manila, Philippines

BACKGROUND

The adaptive divergence of Aedes aegypti populations to heterogeneous environments can be a driving force behind the recent expansion of their habitat distribution and outbreaks of dengue disease in urbanized areas. In this study, we investigated the population genomics of Ae. aegypti at a regional scale in Metropolitan Manila, Philippines.

METHODS

We used the Pool-Seq double digestion restriction-site association DNA sequencing (ddRAD-Seq) approach to generate a high number of single nucleotide polymorphisms (SNPs), with the aim to determine local adaptation and compare the population structure with 11 microsatellite markers. A total of 217 Ae. aegypti individuals from seven female and seven male populations collected from Metropolitan Manila were used in the assays.

RESULTS

We detected 65,473 SNPs across the populations, of which 76 were non-neutral SNPs. Of these non-neutral SNPs, the multivariate regression test associated 50 with eight landscape variables (e.g. open space, forest, etc.) and 29 with five climate variables (e.g. air temperature, humidity, etc.) (P-value range 0.005-0.045) in female and male populations separately. Male and female populations exhibited contrasting spatial divergence, with males exhibiting greater divergence than females, most likely reflecting the different dispersal abilities of male and female mosquitoes. In the comparative analysis of the same Ae. aegypti individuals, the pairwise FST values of 11 microsatellite markers were lower than those of the neutral SNPs, indicating that the neutral SNPs generated via pool ddRAD-Seq were more sensitive in terms of detecting genetic differences between populations at fine-spatial scales.

CONCLUSIONS

Overall, our study demonstrates the utility of pool ddRAD-Seq for examining genetic differences in Ae. aegypti populations in areas at fine-spatial scales that could inform vector control programs such as Wolbachia-infected mosquito mass-release programs. This in turn would provide information on mosquito population dispersal patterns and the potential barriers to mosquito movement within and around the release area. In addition, the potential of environmental adaptability observed in Ae. aegypti could help population control efforts.

Cryptic Diversity and Demographic Expansion of Plasmodium knowlesi Malaria Vectors in Malaysia

Although Malaysia is considered free of human malaria, there has been a growing number of Plasmodium knowlesi cases. This alarming trend highlighted the need for our understanding of this parasite and its associated vectors, especially considering the role of genetic diversity in the adaptation and evolution among vectors in endemic areas, which is currently a significant knowledge gap in their fundamental biology. Thus, this study aimed to investigate the genetic diversity of Anopheles balabacensis, Anopheles cracens, Anopheles introlatus, and Anopheles latens-the vectors for P. knowlesi malaria in Malaysia. Based on cytochrome c oxidase 1 (CO1) and internal transcribed spacer 2 (ITS2) markers, the genealogic networks of An. latens showed a separation of the haplotypes between Peninsular Malaysia and Malaysia Borneo, forming two distinct clusters. Additionally, the genetic distances between these clusters were high (2.3-5.2% for CO1) and (2.3-4.7% for ITS2), indicating the likely presence of two distinct species or cryptic species within An. latens. In contrast, no distinct clusters were observed in An. cracens, An. balabacensis, or An. introlatus, implying a lack of pronounced genetic differentiation among their populations. It is worth noting that there were varying levels of polymorphism observed across the different subpopulations, highlighting some levels of genetic variation within these mosquito species. Nevertheless, further analyses revealed that all four species have undergone demographic expansion, suggesting population growth and potential range expansion for these vectors in this region.

Bioactivity of select essential oil constituents against life stages of Anopheles arabiensis (Diptera: Culicidae)

Malaria is transmitted by infected female Anopheles mosquitoes, and An. arabiensis is a main malaria vector in arid African countries. Like other anophelines, its life cycle comprises of three aquatic stages; egg, larva, and pupa, followed by a free flying adult stage. Current vector control interventions using synthetic insecticides target these stages using adulticides or less commonly, larvicides. With escalating insecticide resistance against almost all conventional insecticides, identification of agents that simultaneously act at multiple stages of Anopheles life cycle presents a cost-effective opportunity. A further cost-effective approach would be the discovery of such insecticides from natural origin. Interestingly, essential oils present as potential sources of cost-effective and eco-friendly bioinsecticides. This study aimed to identify essential oil constituents (EOCs) with potential toxic effects against multiple stages of An. arabiensis life cycle. Five EOCs were assessed for inhibition of Anopheles egg hatching and ability to kill larvae, pupae and adult mosquitoes of An. arabiensis species. One of these EOCs, namely methyleugenol, exhibited potent Anopheles egg hatchability inhibition with an IC₅₀ value of 0.51 ± 0.03 μM compared to propoxur (IC₅₀: 5.13 ± 0.62 μM). Structure-activity relationship study revealed that methyleugenol and propoxur share a 1,2-dimethoxybenze moiety that may be responsible for the observed egg-hatchability inhibition. On the other hand, all five EOCs exhibited potent larvicidal activity with LC₅₀ values less than 5 μM, with four of them; cis-nerolidol, trans-nerolidol, (-)-α-bisabolol, and farnesol, also possessing potent pupicidal effects (LC₅₀ < 5 μM). Finally, all EOCs showed only moderate lethality against adult mosquitoes. This study reports for the first time, methyleugenol, (-)-α-bisabolol and farnesol as potent bioinsecticides against early life stages of An. arabiensis. This synchronized activity against Anopheles aquatic stages shows a prospect to integrate EOCs into existing adulticide-based vector control interventions.

Fine-scale spatial distribution of deltamethrin resistance and population structure of Anopheles funestus and Anopheles arabiensis populations in Southern Mozambique

BACKGROUND

Insecticide resistance in malaria vectors can be spatially highly heterogeneous, yet population structure analyses frequently find relatively high levels of gene flow among mosquito populations. Few studies have contemporaneously assessed phenotypic, genotypic and population structure analysis on mosquito populations and none at fine geographical scales. In this study, genetic diversity, population structure, and insecticide resistance profiles of Anopheles funestus and Anopheles arabiensis were examined across mosquito populations from and within neighbouring villages.

METHODS

Mosquitoes were collected from 11 towns in southern Mozambique, as well as from different neighbourhoods within the town of Palmeira, during the peak malaria transmission season in 2016. CDC bottle bioassay and PCR assays were performed with Anopheles mosquitoes at each site to determine phenotypic and molecular insecticide resistance profiles, respectively. Microsatellite analysis was conducted on a subsample of mosquitoes to estimate genetic diversity and population structure.

RESULTS

Phenotypic insecticide resistance to deltamethrin was observed in An. funestus sensu stricto (s.s.) throughout the area, though a high level of mortality variation was seen. However, 98% of An. funestus s.s. were CYP6P9a homozygous resistant. An. arabiensis was phenotypically susceptible to deltamethrin and 99% were kdr homozygous susceptible. Both Anopheles species exhibited high allelic richness and heterozygosity. Significant deviations from Hardy-Weinberg equilibrium were observed, and high linkage disequilibrium was seen for An. funestus s.s., supporting population subdivision. However, the FST values were low for both anophelines (- 0.00457 to 0.04213), Nm values were high (9.4-71.8 migrants per generation), AMOVA results showed almost 100% genetic variation among and within individuals, and Structure analysis showed no clustering of An. funestus s.s. and An. arabiensis populations. These results suggest high gene flow among mosquito populations.

CONCLUSION

Despite a relatively high level of phenotypic variation in the An. funestus population, molecular analysis shows the population is admixed. These data indicate that CYP6P9a resistance markers do not capture all phenotypic variation in the area, but also that resistance genes of high impact are likely to easily spread in the area. Conversely, other strategies, such as transgenic mosquito release programmes will likely not face challenges in this locality.

Population genetics of Anopheles arabiensis, the primary malaria vector in the Republic of Sudan

Background

Anopheles arabiensis is a member of Anopheles gambiae complex and the main malaria vector in Sudan. There is insufficient population genetics data available on An. arabiensis for an understanding of vector population structure and genetics, which are important for the malaria vector control programmes in this country. The objective of this investigation is to study the population structure, gene flow and isolation by distance among An. arabiensis populations for developing control strategies.

Methods

Mosquitoes were collected from six sites located in three different states in Sudan, Khartoum, Kassala and Sennar, using pyrethrum spray catch of indoor resting mosquitoes. Anopheline mosquitoes were identified morphologically and based on species specific nucleotide sequences in the ribosomal DNA intergenic spacers (IGS). Seven published An. gambiae microsatellite loci primers were used to amplify the DNA of An. arabiensis samples.

Results

PCR confirmed that An. arabiensis was the main malaria vector found in the six localities. Of the seven microsatellite loci utilized, six were found to be highly polymorphic across populations, with high allelic richness and heterozygosity with the remaining one being monomorphic. Deviation from Hardy–Weinberg expectations were found in 21 out of 42 tests in the six populations due to heterozygote deficiency. Bayesian clustering analysis revealed two gene pools, grouping samples into two population clusters; one includes four and the other includes two populations. The clusters were not grouped according to the three states but were instead an admixture. The genetic distances between pairs of populations ranged from 0.06 to 0.24. Significant F_ST was observed between all pairwise analyses of An. arabiensis populations. The Kassala state population indicated high genetic differentiation (F_ST ranged from 0.17 to 0.24) from other populations, including one which is also located in the same state. High gene flow (Nm = 1.6–8.2) was detected among populations within respective clusters but limited between clusters particularly with respect to Kassala state. There was evidence of a bottleneck event in one of the populations (Al Haj Yousif site). No isolation by distance pattern was detected among populations.

Conclusions

This study revealed low levels of population differentiation with high gene flow among the An. arabiensis populations investigated in Sudan, with the exception of Kassala state.

Population genetic structure of the malaria vector Anopheles minimus in Thailand based on mitochondrial DNA markers

BACKGROUND

The malaria vector Anopheles minimus has been influenced by external stresses affecting the survival rate and vectorial capacity of the population. Since An. minimus habitats have continuously undergone ecological changes, this study aimed to determine the population genetic structure and the potential gene flow among the An. minimus populations in Thailand.

METHODS

Anopheles minimus was collected from five malaria transmission areas in Thailand using Centers for Disease Control and Prevention (CDC) light traps. Seventy-nine females from those populations were used as representative samples. The partial mitochondrial cytochrome c oxidase subunit I (COI), cytochrome c oxidase subunit II (COII) and cytochrome b (Cytb) gene sequences were amplified and analyzed to identify species and determine the current population genetic structure. For the past population, we determined the population genetic structure from the 60 deposited COII sequences in GenBank of An. minimus collected from Thailand 20 years ago.

RESULTS

The current populations of An. minimus were genetically divided into two lineages, A and B. Lineage A has high haplotype diversity under gene flow similar to the population in the past. Neutrality tests suggested population expansion of An. minimus, with the detection of abundant rare mutations in all populations, which tend to arise from negative selection.

CONCLUSIONS

This study revealed that the population genetic structure of An. minimus lineage A was similar between the past and present populations, indicating high adaptability of the species. There was substantial gene flow between the eastern and western An. minimus populations without detection of significant gene flow barriers.

Predicting distribution of malaria vector larval habitats in Ethiopia by integrating distributed hydrologic modeling with remotely sensed data

Larval source management has gained renewed interest as a malaria control strategy in Africa but the widespread and transient nature of larval breeding sites poses a challenge to its implementation. To address this problem, we propose combining an integrated high resolution (50 m) distributed hydrological model and remotely sensed data to simulate potential malaria vector aquatic habitats. The novelty of our approach lies in its consideration of irrigation practices and its ability to resolve complex ponding processes that contribute to potential larval habitats. The simulation was performed for the year of 2018 using ParFlow-Common Land Model (CLM) in a sugarcane plantation in the Oromia region, Ethiopia to examine the effects of rainfall and irrigation. The model was calibrated using field observations of larval habitats to successfully predict ponding at all surveyed locations from the validation dataset. Results show that without irrigation, at least half of the area inside the farms had a 40% probability of potential larval habitat occurrence. With irrigation, the probability increased to 56%. Irrigation dampened the seasonality of the potential larval habitats such that the peak larval habitat occurrence window during the rainy season was extended into the dry season. Furthermore, the stability of the habitats was prolonged, with a significant shift from semi-permanent to permanent habitats. Our study provides a hydrological perspective on the impact of environmental modification on malaria vector ecology, which can potentially inform malaria control strategies through better water management.

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.

Genetic diversity and population structure of malaria vector mosquitoes Anopheles subpictus, Anopheles peditaeniatus, and Anopheles vagus in five districts of Sri Lanka

Background

Although Sri Lanka is considered as a malaria-free nation, the threat of re-emergence of outbreaks still remains due to the high prevalence and abundance of malaria vectors. Analysis of population genetic structure of malaria vectors is considered to be one of the vital components in implementing successful vector control programmes. The present study was conducted to determine the population genetic structure of three abundant malaria vectors; Anopheles subpictus sensu lato (s.l.), Anopheles peditaneatus and Anopheles vagus from five administrative districts in two climatic zones; intermediate zone (Badulla and Kurunegala districts) and dry zone (Ampara, Batticoloa and Jaffna districts) of Sri Lanka using the mitochondrial gene, cytochrome c oxidase subunit I (COI).

Methods

Adult mosquitoes of An. subpictus s.l., An. peditaeniatus, and An. vagus were collected from five study sites located in five districts using cattle baited traps and backpack aspirators. Representative samples of each species that were morphologically confirmed were selected from each locality in generating COI sequences (> 6 good quality sequences per species per locality).

Results

Anopheles subpictus s.l. specimens collected during the study belonged to two sibling species; An. subpictus ‘A’ (from all study sites except from Jaffna) and An. subpictus ‘B’ (only from Jaffna). The results of haplotype and nucleotide diversity indices showed that all the three species are having high genetic diversity. Although a high significant pairwise difference was observed between An. subpictus ‘A’ and ‘B’ (F_st> 0.950, p < 0.05), there were no significant genetic population structures within An. peditaeniatus, An. vagus and An. subpictus species A (p > 0.05), indicating possible gene flow between these populations.

Conclusions

Gene flow among the populations of An. peditaeniatus, An. vagus and An. subpictus species A was evident. Application of vector control measures against all mosquito species must be done with close monitoring since gene flow can assist the spread of insecticide resistance genes over a vast geographical area.

Electronic supplementary material

The online version of this article (10.1186/s12936-018-2419-x) contains supplementary material, which is available to authorized users.

The implementation of long-lasting insecticidal bed nets has differential effects on the genetic structure of the African malaria vectors in the Anopheles gambiae complex in Dielmo, Senegal

BACKGROUND

Mosquitoes belonging to the Anopheles gambiae complex are the main vectors of malaria in sub-Saharan Africa. Among these, An. gambiae, Anopheles coluzzii and Anopheles arabiensis are the most efficient vectors and are largely distributed in sympatric locations. However, these species present ecological and behavioural differences that impact their vectorial capacity and complicate vector-control efforts, mainly based on long-lasting insecticidal bed nets (LLINs) and indoor residual spraying (IRS). In this study, the genetic structure of these three species in a Senegalese village (Dielmo) was investigated using microsatellite data in samples collected in 2006 before implementation of LLINs, in 2008, when they were introduced, and in 2010, 2 years after the use of LLINs.

RESULTS

In this study 611 individuals were included, namely 136 An. coluzzii, 101 An. gambiae, 6 An. coluzzii/An. gambiae hybrids and 368 An. arabiensis. According to the species, the effect of the implementation of LLINs in Dielmo is differentiated. Populations of the sister species An. coluzzii and An. gambiae regularly experienced bottleneck events, but without significant inbreeding. The Fst values suggested in 2006 a breakdown of assortative mating resulting in hybrids, but the introduction of LLINs was followed by a decrease in the number of hybrids. This suggests a decrease in mating success of hybrids, ecological maladaptation, or a lesser probability of mating between species due to a decrease in An. coluzzii population size. By contrast, the introduction of LLINs has favoured the sibling species An. arabiensis. In this study, some spatial and temporal structuration between An. arabiensis populations were detected, especially in 2008, and the higher genetic diversity observed could result from a diversifying selection.

CONCLUSIONS

This work demonstrates the complexity of the malaria context and shows the need to study the genetic structure of Anopheles populations to evaluate the effectiveness of vector-control tools and successful management of malaria vector control.

Similar trends of susceptibility in Anopheles arabiensis and Anopheles pharoensis to Plasmodium vivax infection in Ethiopia

Background

Around half of the global population is living in areas at risk of malaria infection. Plasmodium vivax malaria has become increasingly prevalent and responsible for a high health and socio-economic burden in Ethiopia. The availability of gametocyte carriers and mosquito species susceptible to P. vivax infection are vital for malaria transmission. Determining the susceptibility of vector species to parasite infection in space and time is important in vector control programs. This study assesses the susceptibility of Anopheles arabiensis, An. pharoensis and An. coustani group to Plasmodium vivax infection in Ethiopia.

Methods

Larvae of An. arabiensis, An. pharoensis and An. coustani group were collected from an array of breeding sites and reared to adult under controlled conditions. Batches of adult female mosquitoes of the three species were allowed to feed in parallel on the same infected blood with gametocytes drawn from Plasmodium vivax infected patients by Direct Membrane Feeding Assays (DMFA). Fed mosquitoes were kept in an incubator under controlled laboratory conditions. Seven days after each feeding assay, mosquitoes were dissected for midgut oocyst microscopy and enumeration. Data were analysed using R statistical software package version 3.1.0.

Results

Over all, 8,139 adult female mosquitoes were exposed to P. vivax infection. Of the exposed mosquitoes 16.64 % (95 % CI: 1,354–8,139) were properly fed and survived until dissection. The infection rate in An. arabiensis and An. pharoensis was 31.72 % (95 % CI: 28.35–35.08) and 28.80 % (95 % CI: 25.31–32.28), respectively. The intensity of infection for An. arabiensis and An. pharoensis was 2.5 (95 % CI: 1.9–3.2) and 1.4 (95 % CI: 1.1–1.8), respectively. Gametocyte density was positively correlated to infection rate and intensity of infection in An. arabiensis as well as An. pharoensis. No An. coustani group mosquitoes were found infected, though almost four hundred mosquitoes were successfully fed and dissected. All groups received blood from the same infected blood source containing gametocytes in parallel. There was no significant difference in susceptibility rates between An. arabiensis and An. pharoensis (P = 0.215).

Conclusions

Anopheles arabiensis and An. pharoensis showed similar susceptibility to P. vivax infection. However, An. coustani group was not permissive for the development of P. vivax parasites.

A genotypically distinct, melanic variant of Anopheles arabiensis in Sudan is associated with arid environments

BACKGROUND

Anopheles arabiensis, an important malaria vector in Sudan and other countries in sub-Saharan Africa, exhibits considerable ecological and behavioural plasticity allowing it to survive in the harsh conditions of arid regions. It has been shown that adult populations of An. arabiensis in the semi-desert habitat of western Khartoum State survive through the long dry season in a state of partial aestivation, characterized by limited feeding activity and a degree of arrested ovarian development. Anopheles arabiensis in these sites occurs in two phenotypic forms. One is large and heavily melanized, the other has the typical characteristics of An. arabiensis as found elsewhere in Africa. The extent of genetic variation in these forms was examined in widely separated locations in Sudan, including Kassala, Gedaref and the Northern States between 1998 and 1999 and 2004 and 2006.

METHODS

Each mosquito specimen was identified using standard morphological keys and a species-specific PCR test. Sequence variation in a 660 bp fragment of the mtDNA ND5 coding region was examined and the extent of genetic divergence between the forms was estimated from FST values using DNASP version 4.9. TCS 1.13 software was used to determine the genealogical relationships and to reflect clustering among mtDNA haplotypes.

RESULTS

The melanic and normal forms were found in sympatry in Kassala, Gedaref and Khartoum states, with the melanic form commonest in the hottest and most arid areas. Both forms were encountered in the periods of study: 1998-1999, and 2004-2006. Only ten specimens of An. arabiensis were collected from the Northern State in February 2006, all of which were of the normal form.Based on the ND5 analysis, there was a marked subdivision between the normal and melanic forms (FST = 0.59). Furthermore, the melanic form showed more genetic variability, as measured by haplotype diversity (0.95) compared with the normal form (0.57), suggesting larger effective population.

CONCLUSIONS

This is the first demonstration of correspondent phenotypic and genetic structuring in An. arabiensis. The high level of genetic differentiation shown by the mtDNA ND5 locus suggests that the two forms may represent separate species. It is hypothesized that the melanic form is better adapted to hot and arid environments.

Islands and stepping-stones: comparative population structure of Anopheles gambiae sensu stricto and Anopheles arabiensis in Tanzania and implications for the spread of insecticide resistance

Population genetic structures of the two major malaria vectors Anopheles gambiae s.s. and An. arabiensis, differ markedly across Sub-Saharan Africa, which could reflect differences in historical demographies or in contemporary gene flow. Elucidation of the degree and cause of population structure is important for predicting the spread of genetic traits such as insecticide resistance genes or artificially engineered genes. Here the population genetics of An. gambiae s.s. and An. arabiensis in the central, eastern and island regions of Tanzania were compared. Microsatellite markers were screened in 33 collections of female An. gambiae s.l., originating from 22 geographical locations, four of which were sampled in two or three years between 2008 and 2010. An. gambiae were sampled from six sites, An. arabiensis from 14 sites, and both species from two sites, with an additional colonised insectary sample of each species. Frequencies of the knock-down resistance (kdr) alleles 1014S and 1014F were also determined. An. gambiae exhibited relatively high genetic differentiation (average pairwise FST = 0.131), significant even between nearby samples, but without clear geographical patterning. In contrast, An. arabiensis exhibited limited differentiation (average FST = 0.015), but strong isolation-by-distance (Mantel test r = 0.46, p = 0.0008). Most time-series samples of An. arabiensis were homogeneous, suggesting general temporal stability of the genetic structure. An. gambiae populations from Dar es Salaam and Bagamoyo were found to have high frequencies of kdr 1014S (around 70%), with almost 50% homozygote but was at much lower frequency on Unguja Island, with no. An. gambiae population genetic differentiation was consistent with an island model of genetic structuring with highly restricted gene flow, contrary to An. arabiensis which was consistent with a stepping-stone model of extensive, but geographically-restricted gene flow.

Diversity, differentiation, and linkage disequilibrium: prospects for association mapping in the malaria vector Anopheles arabiensis

Association mapping is a widely applied method for elucidating the genetic basis of phenotypic traits. However, factors such as linkage disequilibrium and levels of genetic diversity influence the power and resolution of this approach. Moreover, the presence of population subdivision among samples can result in spurious associations if not accounted for. As such, it is useful to have a detailed understanding of these factors before conducting association mapping experiments. Here we conducted whole-genome sequencing on 24 specimens of the malaria mosquito vector, Anopheles arabiensis, to further understanding of patterns of genetic diversity, population subdivision and linkage disequilibrium in this species. We found high levels of genetic diversity within the An. arabiensis genome, with ~800,000 high-confidence, single- nucleotide polymorphisms detected. However, levels of nucleotide diversity varied significantly both within and between chromosomes. We observed lower diversity on the X chromosome, within some inversions, and near centromeres. Population structure was absent at the local scale (Kilombero Valley, Tanzania) but detected between distant populations (Cameroon vs. Tanzania) where differentiation was largely restricted to certain autosomal chromosomal inversions such as 2Rb. Overall, linkage disequilibrium within An. arabiensis decayed very rapidly (within 200 bp) across all chromosomes. However, elevated linkage disequilibrium was observed within some inversions, suggesting that recombination is reduced in those regions. The overall low levels of linkage disequilibrium suggests that association studies in this taxon will be very challenging for all but variants of large effect, and will require large sample sizes.

Genomic analyses of three malaria vectors reveals extensive shared polymorphism but contrasting population histories

Anopheles gambiae s.l. are important malaria vectors, but little is known about their genomic variation in the wild. Here, we present inter- and intraspecies analysis of genome-wide RADseq data, in three Anopheles gambiae s.l. species collected from East Africa. The mosquitoes fall into three genotypic clusters representing described species (A. gambiae, A. arabiensis, and A. merus) with no evidence of cryptic breeding units. Anopheles merus is the most divergent of the three species, supporting a recent new phylogeny based on chromosomal inversions. Even though the species clusters are well separated, there is extensive shared polymorphism, particularly between A. gambiae and A. arabiensis. Divergence between A. gambiae and A. arabiensis does not vary across the autosomes but is higher in X-linked inversions than elsewhere on X or on the autosomes, consistent with the suggestion that this inversion (or a gene within it) is important in reproductive isolation between the species. The 2La/2L+(a) inversion shows no more evidence of introgression between A. gambiae and A. arabiensis than the rest of the autosomes. Population differentiation within A. gambiae and A. arabiensis is weak over approximately 190-270 km, implying no strong barriers to dispersal. Analysis of Tajima's D and the allele frequency spectrum is consistent with modest population increases in A. arabiensis and A. merus, but a more complex demographic history of expansion followed by contraction in A. gambiae. Although they are less than 200 km apart, the two A. gambiae populations show evidence of different demographic histories.

Agro-ecosystems impact malaria prevalence: large-scale irrigation drives vector population in western Ethiopia

Background

Development strategies in Ethiopia have largely focused on the expansion of irrigated agriculture in the last decade to reduce poverty and promote economic growth. However, such irrigation schemes can worsen the socio-economic state by aggravating the problem of mosquito-borne diseases. In this study, the effect of agro-ecosystem practices on malaria prevalence and the risk of malaria transmission by the primary vector mosquito, Anopheles arabiensis, in Ethiopia were investigated.

Methods

In three villages in western Ethiopia practising large-scale sugarcane irrigation, traditional smallholder irrigation and non-irrigated farming, cross-sectional parasitological surveys were conducted during the short rains, after the long rains and during the dry season. Entomological surveys were undertaken monthly (February 2010-January 2011) in each village using light traps, pyrethrum spray collections and artificial pit shelters.

Results

Malaria prevalence and the risk of transmission by An. arabiensis assessed by the average human biting rate, mean sporozoite rate and estimated annual entomological inoculation rate were significantly higher in the irrigated sugarcane agro-ecosystem compared to the traditionally irrigated and non-irrigated agro-ecosystems. The average human biting rate was significantly elevated by two-fold, while the mean sporozoite rate was 2.5-fold higher, and the annual entomological inoculation rate was 4.6 to 5.7-fold higher in the irrigated sugarcane compared to the traditional and non-irrigated agro-ecosystems. Active irrigation clearly affected malaria prevalence by increasing the abundance of host seeking Anopheles mosquitoes year-round and thus increasing the risk of infective bites. The year-round presence of sporozoite-infected vectors due to irrigation practices was found to strengthen the coupling between rainfall and risk of malaria transmission, both on- and off-season.

Conclusion

This study demonstrates the negative impact of large-scale irrigation expansion on malaria transmission by increasing the abundance of mosquito vectors and indicates the need for effective vector monitoring and control strategies in the implementation of irrigation projects.

A global map of dominant malaria vectors

Background

Global maps, in particular those based on vector distributions, have long been used to help visualise the global extent of malaria. Few, however, have been created with the support of a comprehensive and extensive evidence-based approach.

Methods

Here we describe the generation of a global map of the dominant vector species (DVS) of malaria that makes use of predicted distribution maps for individual species or species complexes.

Results

Our global map highlights the spatial variability in the complexity of the vector situation. In Africa, An. gambiae, An. arabiensis and An. funestus are co-dominant across much of the continent, whereas in the Asian-Pacific region there is a highly complex situation with multi-species coexistence and variable species dominance.

Conclusions

The competence of the mapping methodology to accurately portray DVS distributions is discussed. The comprehensive and contemporary database of species-specific spatial occurrence (currently available on request) will be made directly available via the Malaria Atlas Project (MAP) website from early 2012.

Single-nucleotide polymorphisms for high-throughput genotyping of Anopheles arabiensis in East and southern Africa

Anopheles arabiensis Patton is one of the principal vectors of malaria in sub-Saharan Africa, occupying a wide variety of ecological zones. This species is increasingly responsible for malaria transmission in Africa and is becoming the dominant vector species in some localities. Despite its growing importance, little is known about genetic polymorphisms in this species. Multiple sequences of various gene fragments from An. arabiensis isolates from Cameroon were obtained from GenBank. In total, 20 gene fragments containing single-nucleotide polymorphisms (SNPs) at moderate density were selected for direct sequencing from field collected specimens from Tanzania and Zambia. We obtained 301 SNPs in total from the 20 gene fragments, 60 of which were suitable for Illumina GoldenGate SNP genotyping. A greater number of SNPs (n = 185) was suitable for analysis using Sequenom iPLEX, an alternative high-throughput genotyping technology using mass spectrometry. An SNP was present every 59 (+/- 44.5) bases on average. Overall, An. arabiensis from Tanzania and Zambia are genetically closer (mean F(ST) = 0.075) than either is to populations in Cameroon (F(ST, TZ-CM) = 0.250, F(ST,ZA-CM) = 0.372). A fixed polymorphism between East/southern and Central Africa was identified on AGAP000574, a gene on the X chromosome. We have identified SNPs in natural populations of An. arabiensis. SNP densities in An. arabiensis were higher than Anopheles gambiae s.s., suggesting a greater challenge in the development of high-throughput SNP analysis for this species. The SNP markers provided in this study are suitable for a high-throughput genotyping analysis and can be used for population genetic studies and association mapping efforts.

Population genetic structure of Anopheles arabiensis and Anopheles gambiae in a malaria endemic region of southern Tanzania

BACKGROUND

Genetic diversity is a key factor that enables adaptation and persistence of natural populations towards environmental conditions. It is influenced by the interaction of a natural population's dynamics and the environment it inhabits. Anopheles gambiae s.s. and Anopheles arabiensis are the two major and widespread malaria vectors in sub-Saharan Africa. Several studies have examined the ecology and population dynamics of these vectors. Ecological conditions along the Kilombero valley in Tanzania influence the distribution and population density of these two vector species. It remains unclear whether the ecological diversity within the Kilombero valley has affected the population structure of An. gambiae s.l. populations. The goal of this study was to characterise the genetic structure of sympatric An. gambiae s.s and An. arabiensis populations along the Kilombero valley.

METHODOLOGY

Mosquitoes were collected from seven locations in Tanzania: six from the Kilombero valley and one outside the valley (-700 km away) as an out-group. To archive a genome-wide coverage, 13 microsatellite markers from chromosomes X, 2 and 3 were used.

RESULTS

High levels of genetic differentiation among An. arabiensis populations was observed, as opposed to An. gambiae s.s., which was genetically undifferentiated across the 6,650 km2 of the Kilombero valley landscape. It appears that genetic differentiation is not attributed to physical barriers or distance, but possibly by ecological diversification within the Kilombero valley. Genetic divergence among An. arabiensis populations (FST = 0.066) was higher than that of the well-known M and S forms of An. gambiae s. s. in West and Central Africa (FST = 0.035), suggesting that these populations are maintained by some level of reproductive isolation.

CONCLUSION

It was hypothesized that ecological diversification across the valley may be a driving force for observed An. arabiensis genetic divergence. The impact of the observed An. arabiensis substructure to the prospects for new vector control approaches is discussed.

Population genetic structure of Anopheles gambiae and Anopheles arabiensis in Niger

The increasing usage of long-lasting insecticide-treated nets allows protection of millions of people from malaria infection. Monitoring studies should be planned during any wide-scale malaria control program integrating insecticide-treated materials, to evaluate their effects and effectiveness on epidemiologically relevant parameters. Such operational control interventions may be challenged by insecticide resistance spread within vector populations, as a result of wide insecticide pressure. A nationwide distribution of long-lasting insecticidal nets was implemented throughout Niger in 2005. We studied the population genetic structure of major malaria vectors across Nigerien Sahel, and investigated potential effects of this large malaria control intervention. Wild-caught Anopheles gambiae sensu lato females from seven villages and two wet seasons were genotyped at 12 microsatellite loci. The genetic diversity within both species appeared homogenous between villages and years. The estimated genetic differentiation among samples was very low within both species, indicating high gene flow across the area. An absence of differentiation was also found between 2005 and 2006 wet seasons, for all samples but one, showing that the net distribution did not impact significantly the genetic diversity and structure of vector populations in a single year. We provide valuable results participating to document effects of large malaria control programs, to maximize the efficiency of available tools in future interventions.

Monooxygenase levels and knockdown resistance (kdr) allele frequencies in Anopheles gambiae and Anopheles arabiensis in Kenya

Pyrethroid-treated bed-nets and indoor spray are important components of malaria control strategies in Kenya. Information on resistance to pyrethroid insecticides in Anopheles gambiae and An. arabiensis populations is essential to the selection of appropriate insecticides and the management of insecticide resistance. Monooxygenase activity and knockdown resistance (kdr) allele frequency are biochemical and molecular indicators of mosquito resistance to pyrethroids. This study determined baseline information on monooxygenase activity and kdr allele frequency in anopheline mosquitoes in the western region, the Great Rift Valley-central region, and the coastal region of Kenya. In total, 1,990 field-collected individuals, representing 12 An. gambiae and 22 An. arabiensis populations were analyzed. We found significant among-population variation in monooxygenase activity in An. gambiae and An. arabiensis and substantial variability among individuals within populations. Nine of 12 An. gambiae populations exhibited significantly higher average monooxygenase activity than the susceptible Kisumu reference strain. The kdr alleles (L1014S) were detected in three An. gambiae populations, and one An. arabiensis population in western Kenya, but not in the Rift Valley-central region and the coastal Kenya region. All genotypes with the kdr alleles were heterozygous, and the conservative estimation of kdr allele frequency was below 1% in these four populations. Information on monooxygenase activity and kdr allele frequency reported in this study provided baseline data for monitoring insecticide resistance changes in Kenya during the era when large-scale insecticide-treated bed-net and indoor residual spray campaigns were being implemented.

Evidence for late Pleistocene population expansion of the malarial mosquitoes, Anopheles arabiensis and Anopheles gambiae in Nigeria

Anopheles gambiae Giles s.s. and Anopheles arabiensis Patton (Diptera: Culicidae) are major vectors of malaria in Nigeria. We used 1115 bp of the mitochondrial COI gene to assess their population genetic structures based on samples from across Nigeria (n = 199). The mtDNA neighbour-joining tree, based on F(ST) estimates, separated An. gambiae M and S forms, except that samples of An. gambiae M from Calabar clustered with all the An. gambiae S form. Anopheles arabiensis and An. gambiae could be combined into a single star-shaped, parsimonious haplotype network, and shared three haplotypes. Haplotype diversity values were high in An. arabiensis and An. gambiae S, and intermediate in An. gambiae M; all nucleotide diversities were relatively low. Taken together, patterns of haplotype diversity, the star-like genealogy of haplotypes, five of seven significant neutrality tests, and the violation of the isolation-by-distance model indicate population expansion in An. arabiensis and An. gambiae S, but the signal was weak in An. gambiae M. Selection is supported as an important factor shaping genetic structure in An. gambiae in Nigeria. There were two geographical subdivisions in An. arabiensis: one included all southern localities and all but two central localities; the other included all northern and two central localities. Re-analysing an earlier microsatellite dataset of An. arabiensis using a Bayesian method determined that there were two distinctive clusters, northern and southern, that were fairly congruent with the mtDNA subdivisions. There was a trend towards decreasing genetic diversity in An. arabiensis from the northern savannah to the southern rainforest that corroborated previous data from microsatellites and polytene chromosomes.

Dynamics of gene introgression in the African malaria vector Anopheles gambiae

Anopheles gambiae is a major malaria vector in Africa and a popular model species for a variety of ecological, evolutionary, and genetic studies on vector control. Genetic manipulation of mosquito vectorial capacity is a promising new weapon for the control of malaria. However, the release of exotic transgenic mosquitoes will bring in novel alleles in addition to the parasite-inhibiting genes, which may have unknown effects on the local population. Therefore, it is necessary to develop methodologies that can be used to evaluate the spread rate of introduced genes in A. gambiae. In this study, the effects and dynamics of genetic introgression between two geographically distinct A. gambiae populations from western Kenya (Mbita) and eastern Tanzania (Ifakara) were investigated with amplified fragment length polymorphisms (AFLPs) and microsatellite markers. Microsatellites and polymorphic cDNA markers revealed a large genetic differentiation between the two populations (average F(ST) = 0.093, P < 0.001). When the two strains were crossed in random mating between the two populations, significant differences in the rate of genetic introgression were found in the mixed populations. Allele frequencies of 18 AFLP markers (64.3%) for Mbita and of 26 markers (92.9%) for Ifakara varied significantly from F5 to F20. This study provides basic information on how a mosquito release program would alter the genetic makeup of natural populations, which is critical for pilot field testing and ecological risk evaluation of transgenic mosquitoes.