Genetic differentiation of the malaria vector Anopheles gambiae across Nigeria suggests that selection limits gene flow

Population Dynamics of Anopheles gambiae s.l. and Culex quinquefasciatus in Rural and Urban Settings Before an Indoor Residual Spraying Campaign in Northern Benin

Background: The purpose of this report is to provide information on Culicidae diversity; biting behavior and spatio-seasonal variation of abundance of Anopheles gambiae s.l. and Culex quinquefasciatus in rural and urban settings of the Alibori and Donga regions, Northern Benin, where an indoor residual spraying (IRS) campaign to control malaria is planned. Methods: Both human landing catches, associated with pyrethrum spray catches were used to monitor the mosquito populations in 12 sites with 1 urban and 1 rural located in each of the 6 districts randomly selected in the two targeted regions. After morphological identification of all mosquito specimens, biting behavior and density of An. gambiae s.l. and Cx quinquefasciatus were studied. PCR was also performed on An. gambiae s.l., to identify sibling species and its seasonal variation. Results: A total of 10,367 mosquitoes were captured, related to 14 species of the genera, Anopheles, Aedes, Culex and Mansonia. Of the total species collection, 40.39% were An. gambiae s.l. and 56.85% were Cx. quinquefasciatus. An. gambiae s.l. was more abundant in Donga (2521 specimens) compared with Alibori (1666 specimens). The opposite trend was observed with Cx. quinquefasciatus (2162 specimens in Donga against 4028 in Alibori). An. gambiae s.l. was predominant and displayed a higher blood feeding rate in rural areas, whereas Cx. quinquefasciatus was in majority in urban areas. An. gambiae s.l. was more endophagic, whereas Cx. quinquefasciatus showed similar indoor and outdoor biting behavior. An. gambiae s.l. was composed of An. coluzzii found in majority in the drought, and An. gambiae, which was predominant in the rainy season. Conclusion: The predominance of the malaria vector, An. gambiae s.l. and their higher blood feeding rate and their significantly high endophagy in rural areas indicate that these areas should be primarily targeted with the IRS operations to have a substantial impact on malaria transmission. Endophagy, characteristic of An. gambiae s.l. in our study area, suggests that IRS will have a positive impact on vector control if implemented 1 week before June that is the onset of the rainy season.

Microgeographical structure in the major Neotropical malaria vector Anopheles darlingi using microsatellites and SNP markers

BACKGROUND

In recent decades, throughout the Amazon Basin, landscape modification contributing to profound ecological change has proceeded at an unprecedented rate. Deforestation that accompanies human activities can significantly change aspects of anopheline biology, though this may be site-specific. Such local changes in anopheline biology could have a great impact on malaria transmission. The aim of this study was to investigate population genetics of the main malaria vector in Brazil, Anopheles darlingi, from a microgeographical perspective.

METHODS

Microsatellites and ddRADseq-derived single nucleotide polymorphisms (SNPs) were used to assess levels of population genetic structuring among mosquito populations from two ecologically distinctive agricultural settlements (~60 km apart) and a population from a distant (~700 km) urban setting in the western Amazon region of Brazil.

RESULTS

Significant microgeographical population differentiation was observed among Anopheles darlingi populations via both model- and non-model-based analysis only with the SNP dataset. Microsatellites detected moderate differentiation at the greatest distances, but were unable to differentiate populations from the two agricultural settlements. Both markers showed low polymorphism levels in the most human impacted sites.

CONCLUSIONS

At a microgeographical scale, signatures of genetic heterogeneity and population divergence were evident in Anopheles darlingi, possibly related to local environmental anthropic modification. This divergence was observed only when using high coverage SNP markers.

Three sympatric clusters of the malaria vector Anopheles culicifacies E (Diptera: Culicidae) detected in Sri Lanka

Background

The disease re-emergence threat from the major malaria vector in Sri Lanka, Anopheles culicifacies, is currently increasing. To predict malaria vector dynamics, knowledge of population genetics and gene flow is required, but this information is unavailable for Sri Lanka. This study was carried out to determine the population structure of An. culicifacies E in Sri Lanka.

Methods

Eight microsatellite markers were used to examine An. culicifacies E collected from six sites in Sri Lanka during 2010-2012. Standard population genetic tests and analyses, genetic differentiation, Hardy-Weinberg equilibrium, linkage disequilibrium, Bayesian cluster analysis, AMOVA, SAMOVA and isolation-by-distance were conducted using five polymorphic loci.

Results

Five microsatellite loci were highly polymorphic with high allelic richness. Hardy-Weinberg Equilibrium (HWE) was significantly rejected for four loci with positive F_IS values in the pooled population (p < 0.0100). Three loci showed high deviations in all sites except Kataragama, which was in agreement with HWE for all loci except one locus (p < 0.0016). Observed heterozygosity was less than the expected values for all sites except Kataragama, where reported negative F_IS values indicated a heterozygosity excess. Genetic differentiation was observed for all sampling site pairs and was not supported by the isolation by distance model. Bayesian clustering analysis identified the presence of three sympatric clusters (gene pools) in the studied population. Significant genetic differentiation was detected in cluster pairs with low gene flow and isolation by distance was not detected between clusters. Furthermore, the results suggested the presence of a barrier to gene flow that divided the populations into two parts with the central hill region of Sri Lanka as the dividing line.

Conclusions

Three sympatric clusters were detected among An. culicifacies E specimens isolated in Sri Lanka. There was no effect of geographic distance on genetic differentiation and the central mountain ranges in Sri Lanka appeared to be a barrier to gene flow.

Coalescent patterns for chromosomal inversions in divergent populations

Chromosomal inversions allow genetic divergence of locally adapted populations by reducing recombination between chromosomes with different arrangements. Divergence between populations (or hybridization between species) is expected to leave signatures in the neutral genetic diversity of the inverted region. Quantitative expectations for these patterns, however, have not been obtained. Here, we develop coalescent models of neutral sites linked to an inversion polymorphism in two locally adapted populations. We consider two scenarios of local adaptation: selection on the inversion breakpoints and selection on alleles inside the inversion. We find that ancient inversion polymorphisms cause genetic diversity to depart dramatically from neutral expectations. Other situations, however, lead to patterns that may be difficult to detect; important determinants are the age of the inversion and the rate of gene flux between arrangements. We also study inversions under genetic drift, finding that they produce patterns similar to locally adapted inversions of intermediate age. Our results are consistent with empirical observations, and provide the foundation for quantitative analyses of the roles that inversions have played in speciation.

An integrated chromosome map of microsatellite markers and inversion breakpoints for an Asian malaria mosquito, Anopheles stephensi

Anopheles stephensi is one of the major vectors of malaria in the Middle East and Indo-Pakistan subcontinent. Understanding the population genetic structure of malaria mosquitoes is important for developing adequate and successful vector control strategies. Commonly used markers for inferring anopheline taxonomic and population status include microsatellites and chromosomal inversions. Knowledge about chromosomal locations of microsatellite markers with respect to polymorphic inversions could be useful for better understanding a genetic structure of natural populations. However, fragments with microsatellites used in population genetic studies are usually too short for successful labeling and hybridization with chromosomes. We designed new primers for amplification of microsatellite loci identified in the A. stephensi genome sequenced with next-generation technologies. Twelve microsatellites were mapped to polytene chromosomes from ovarian nurse cells of A. stephensi using fluorescent in situ hybridization. All microsatellites hybridized to unique locations on autosomes, and 7 of them localized to the largest arm 2R. Ten microsatellites were mapped inside the previously described polymorphic chromosomal inversions, including 4 loci located inside the widespread inversion 2Rb. We analyzed microsatellite-based population genetic data available for A. stephensi in light of our mapping results. This study demonstrates that the chromosomal position of microsatellites may affect estimates of population genetic parameters and highlights the importance of developing physical maps for nonmodel organisms.

Genetic structure of Anopheles (Nyssorhynchus) marajoara (Diptera: Culicidae) in Colombia

Five Anopheles marajoara Galvão and Damasceno populations, representing diverse ecological conditions, were sampled throughout Colombia and analyzed using nine hypervariable DNA microsatellite loci. The overall genetic diversity (H = 0.58) was lower than that determined for some Brazilian populations using the same markers. The Caquetá population (Colombia) had the lowest gene diversity (H = 0.48), and it was the only population at Hardy-Weinberg equilibrium. Hardy-Weinberg disequilibrium in the remaining four populations was probably caused by the Wahlund effect. The assignment analyses showed two incompletely isolated gene pools separated by the Eastern Andean cordillera. However, other possible geographical barriers (rivers and other mountains) did not play any role in the moderate genetic heterogeneity found among these populations (F(ST) = 0.069). These results are noteworthy, because this species is a putative malaria vector in Colombia.

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia

BACKGROUND

Anopheles albimanus is an important malaria vector in some areas throughout its distribution in the Caribbean and the Pacific regions of Colombia, covering three biogeographic zones of the neotropical region, Maracaibo, Magdalena and Chocó.

METHODS

This study was conducted to estimate intra-population genetic diversity, genetic differentiation and demographic history of An. albimanus populations because knowledge of vector population structure is a useful tool to guide malaria control programmes. Analyses were based on mtDNA COI gene sequences and four microsatellite loci of individuals collected in eight populations from the Caribbean and the Pacific regions of Colombia.

RESULTS

Two distinctive groups were consistently detected corresponding to COI haplotypes from each region. A star-shaped statistical parsimony network, significant and unimodal mismatch distribution, and significant negative neutrality tests together suggest a past demographic expansion or a selective sweep in An. albimanus from the Caribbean coast approximately 21,994 years ago during the late Pleistocene. Overall moderate to low genetic differentiation was observed between populations within each region. However, a significant level of differentiation among the populations closer to Buenaventura in the Pacific region was observed. The isolation by distance model best explained genetic differentiation among the Caribbean region localities: Los Achiotes, Santa Rosa de Lima and Moñitos, but it could not explain the genetic differentiation observed between Turbo (Magdalena providence), and the Pacific region localities (Nuquí, Buenaventura, Tumaco). The patterns of differentiation in the populations from the different biogeographic provinces could not be entirely attributed to isolation by distance.

CONCLUSION

The data provide evidence for limited past gene flow between the Caribbean and the Pacific regions, as estimated by mtDNA sequences and current gene flow patterns among An. albimanus populations as measured by MS loci which may be mainly influenced by semi-permeable natural barriers in each biogeographical region that lead to the genetic differences and effective population sizes detected. The relatively high genetic differentiation in the port city of Buenaventura may be the result of specific ecological conditions, human migration and activities and/or differences in effective population sizes. This knowledge could serve to evaluate and coordinate vector control strategies in these regions of Colombia.

Desiccation resistance among subpopulations of Anopheles gambiae s.s. from Selinkenyi, Mali

Certain forms of Anopheles gambiae s.s. actively maintain malaria transmission in the driest areas and months of the year because of considerable drought tolerance. We monitored desiccation resistance of F1 offspring of both the M and S forms of field-collected An. gambiae s.s. Our results indicate that the geographic cline in the distribution of the two forms, as observed in Mali, corresponds to a physiological difference in response to arid environments. In addition, female mosquitoes survived significantly longer than males, enhancing the vector competence for the malaria parasite. Our study supports a genetic link to the drought tolerance phenotype, a phenotype with important consequences to malaria transmission in many places in Africa.

Revisiting the Impact of Inversions in Evolution: From Population Genetic Markers to Drivers of Adaptive Shifts and Speciation?

There is a growing appreciation that chromosome inversions affect rates of adaptation, speciation, and the evolution of sex chromosomes. Comparative genomic studies have identified many new paracentric inversion polymorphisms. Population models suggest that inversions can spread by reducing recombination between alleles that independently increase fitness, without epistasis or coadaptation. Areas of linkage disequilibrium extend across large inversions but may be interspersed by areas with little disequilibrium. Genes located within inversions are associated with a variety of traits including those involved in climatic adaptation. Inversion polymorphisms may contribute to speciation by generating underdominance owing to inviable gametes, but an alternative view gaining support is that inversions facilitate speciation by reducing recombination, protecting genomic regions from introgression. Likewise, inversions may facilitate the evolution of sex chromosomes by reducing recombination between sex determining alleles and alleles with sex-specific effects. However, few genes within inversions responsible for fitness effects or speciation have been identified.

A test of the chromosomal theory of ecotypic speciation in Anopheles gambiae

The role of chromosomal inversions in speciation has long been of interest to evolutionists. Recent quantitative modeling has stimulated reconsideration of previous conceptual models for chromosomal speciation. Anopheles gambiae, the most important vector of human malaria, carries abundant chromosomal inversion polymorphism nonrandomly associated with ecotypes that mate assortatively. Here, we consider the potential role of paracentric inversions in promoting speciation in A. gambiae via "ecotypification," a term that refers to differentiation arising from local adaptation. In particular, we focus on the Bamako form, an ecotype characterized by low inversion polymorphism and fixation of an inversion, 2Rj, that is very rare or absent in all other forms of A. gambiae. The Bamako form has a restricted distribution by the upper Niger River and its tributaries that is associated with a distinctive type of larval habitat, laterite rock pools, hypothesized to be its optimal breeding site. We first present computer simulations to investigate whether the population dynamics of A. gambiae are consistent with chromosomal speciation by ecotypification. The models are parameterized using field observations on the various forms of A. gambiae that exist in Mali, West Africa. We then report on the distribution of larvae of this species collected from rock pools and more characteristic breeding sites nearby. Both the simulations and field observations support the thesis that speciation by ecotypification is occurring, or has occurred, prompting consideration of Bamako as an independent species.

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.

Genetic population structure of Anopheles gambiae in Equatorial Guinea

BACKGROUND

Patterns of genetic structure among mosquito vector populations in islands have received particular attention as these are considered potentially suitable sites for experimental trials on transgenic-based malaria control strategies. In this study, levels of genetic differentiation have been estimated between populations of Anopheles gambiae s.s. from the islands of Bioko and Annobón, and from continental Equatorial Guinea (EG) and Gabon.

METHODS

Genotyping of 11 microsatellite loci located in chromosome 3 was performed in three island samples (two in Bioko and one in Annobón) and three mainland samples (two in EG and one in Gabon). Four samples belonged to the M molecular form and two to the S-form. Microsatellite data was used to estimate genetic diversity parameters, perform demographic equilibrium tests and analyse population differentiation.

RESULTS

High levels of genetic differentiation were found between the more geographically remote island of Annobón and the continent, contrasting with the shallow differentiation between Bioko island, closest to mainland, and continental localities. In Bioko, differentiation between M and S forms was higher than that observed between island and mainland samples of the same molecular form.

CONCLUSION

The observed patterns of population structure seem to be governed by the presence of both physical (the ocean) and biological (the M-S form discontinuity) barriers to gene flow. The significant degree of genetic isolation between M and S forms detected by microsatellite loci located outside the "genomic islands" of speciation identified in A. gambiae s.s. further supports the hypothesis of on-going incipient speciation within this species. The implications of these findings regarding vector control strategies are discussed.

The distribution of M and S molecular forms of Anopheles gambiae in Nigeria

The distribution of M and S molecular forms of Anopheles gambiae sensu stricto across Nigeria was determined. The molecular form of 40 to 45 specimens per locality from 9 localities was determined using mostly the same specimens from our recent study of genetic differentiation of A. gambiae across Nigeria (Onyabe & Conn, 2001). These samples were previously genotyped at 10 microsatellite loci, 5 located within chromosome inversions and 5 outside inversions. Both molecular forms occurred throughout the country, with no apparent relationship to the ecological transition from dry savannah in the north to humid forest in southern Nigeria. In all localities, however, 1 form or the other occurred virtually exclusively. No hybrids between forms were found. Across all loci, F(ST) values were as high within molecular forms as between forms. Regardless of molecular form, F(ST) values calculated across loci within inversions were much higher (range 0.0016 to 0.1988) than those calculated across loci outside inversions (range -0.0035 to 0.0260). Genetic distance was not significantly correlated with geographical distance within either form (P> 0.05). These observations suggest that, in addition to partial reproductive barriers between molecular forms, selection is a major factor shaping genetic differentiation of A. gambiae across Nigeria.

Population structure of the malaria vector Anopheles funestus in Senegal based on microsatellite and cytogenetic data

The study of chromosomal inversions distribution within natural Anopheles funestus populations from West Africa revealed high levels of genetic structuring. In Burkina Faso, this was interpreted as evidence for incipient speciation, and two chromosomal forms were described, namely 'Folonzo' and 'Kiribina'. Assignation of field collected specimens to one chromosomal form depends upon application of an algorithm based on chromosomal inversions. We assessed relevance and applicability of this algorithm on An. funestus populations from Senegal, where both forms occur. Furthermore, we estimated the level of genetic differentiation between populations using microsatellite loci spread over the whole genome. Significant genetic differentiation was revealed between geographical populations of An. funestus, and the pattern observed suggested isolation by distance. Chromosomal heterogeneity was not detected by microsatellite markers. Thus, although incipient speciation could not be ruled out by our data, our results suggest that differential environmental selection pressure acting on inversions should be considered a major factor in shaping their distribution in wild An. funestus populations.

Malaria control with genetically manipulated insect vectors

At a recent workshop, experts discussed the benefits, risks, and research priorities associated with using genetically manipulated insects in the control of vector-borne diseases.

Molecular systematics of Anopheles: from subgenera to subpopulations

The century-old discovery of the role of Anopheles in human malaria transmission precipitated intense study of this genus at the alpha taxonomy level, but until recently little attention was focused on the systematics of this group. The application of molecular approaches to systematic problems ranging from subgeneric relationships to relationships at and below the species level is helping to address questions such as anopheline phylogenetics and biogeography, the nature of species boundaries, and the forces that have structured genetic variation within species. Current knowledge in these areas is reviewed, with an emphasis on the Anopheles gambiae model. The recent publication of the genome of this anopheline mosquito will have a profound impact on inquiries at all taxonomic levels, supplying better tools for estimating phylogeny and population structure in the short term, and ultimately allowing the identification of genes and/or regulatory networks underlying ecological differentiation, speciation, and vectorial capacity.