Genetic isolation within the malaria mosquito Anopheles melas.

Anopheles melas is a brackish water-breeding member of the Anopheles gambiae complex that is distributed along the coast of West Africa and is a major malaria vector within its range. Because little is known about the population structure of this species, we analysed 15 microsatellite markers and 1161 bp of mtDNA in 11 A. melas populations collected throughout its range. Compared with its sibling species A. gambiae, A. melas populations have a high level of genetic differentiation between them, representing its patchy distribution due to its fragmented larval habitat that is associated with mangroves and salt marsh grass. Populations clustered into three distinct groups representing Western Africa, Southern Africa and Bioko Island populations that appear to be mostly isolated. Fixed differences in the mtDNA are present between all three clusters, and a Bayesian clustering analysis of the microsatellite data found no evidence for migration from mainland to Bioko Island populations, and little migration was evident between the Southern to the Western cluster. Surprisingly, mtDNA divergence between the three A. melas clusters is on par with levels of divergence between other species of the A. gambiae complex, and no support for monophyly was observed in a maximum-likelihood phylogenetic analysis. Finally, an approximate Bayesian analysis of microsatellite data indicates that Bioko Island A. melas populations were connected to the mainland populations in the past, but became isolated, presumably when sea levels rose after the last glaciation period (≥10 000-11 000 bp). This study has exposed species-level genetic divergence within A. melas and also has implications for control of this malaria vector.

Limited usefulness of microsatellite markers from the malaria vector Anopheles gambiae when applied to the closely related species Anopheles melas.

Anopheles melas is a brackish water mosquito found in coastal West Africa where it is a dominant malaria vector locally. In order to facilitate genetic studies of this species, 45 microsatellite loci originally developed for Anopheles gambiae were sequenced in An. melas. Those that were suitable based on repeat number and flanking regions were examined in 2 natural populations from Equatorial Guinea. Only 15 loci were eventually deemed suitable as polymorphic markers in An. melas populations. These loci were screened in 4 populations from a wider geographic range. Heterozygosity estimates ranged from 0.18 to 0.79, and 2.5-15 average alleles were observed per locus, yielding 13 highly polymorphic markers and 2 loci with lower variability. To examine the usefulness of microsatellite markers when applied in a sibling species, the original An. gambiae specific markers were used to amplify 5 loci in An. melas. Null alleles were found for 1 An. gambiae marker. We discuss the pitfalls of using microsatellite loci across closely related species and conclude that in addition to the problem of null alleles associated with this practice, many loci may prove to be of very limited use as polymorphic markers even when used in a sibling species.

The Genetic Architecture of Post-Zygotic Reproductive Isolation Between Anopheles coluzzii and An. quadriannulatus.

The Anopheles gambiae complex is comprised of eight morphologically indistinguishable species and has emerged as a model system for the study of speciation genetics due to the rapid radiation of its member species over the past two million years. Male hybrids between most An. gambiae complex species pairs are sterile, and some genotype combinations in hybrid males cause inviability. We investigated the genetic basis of hybrid male inviability and sterility between An. coluzzii and An. quadriannulatus by measuring segregation distortion and performing a QTL analysis of sterility in a backcross population. Hybrid males were inviable if they inherited the An. coluzzii X chromosome and were homozygous at one or more loci in 18.9 Mb region of chromosome 3. The An. coluzzii X chromosome has a disproportionately large effect on hybrid sterility when introgressed into an An. quadriannulatus genetic background. Additionally, an epistatic interaction between the An. coluzzii X and a 1.12 Mb, pericentric region of the An. quadriannulatus 3L chromosome arm has a statistically significant contribution to the hybrid sterility phenotype. This same epistatic interaction occurs when the An. coluzzii X is introgressed into the genetic background of An. arabiensis, the sister species of An. quadriannulatus, suggesting that this may represent one of the first Dobzhansky-Muller incompatibilities to evolve early in the radiation of the Anopheles gambiae species complex. We describe the additive effects of each sterility QTL, epistatic interactions between them, and genes within QTL with protein functions related to mating behavior, reproduction, spermatogenesis, and microtubule morphogenesis, whose divergence may contribute to post-zygotic reproductive isolation between An. coluzzii and An. quadriannulatus.

The Effect of Hybridization on Dosage Compensation in Member Species of the Anopheles gambiae Species Complex.

Dosage compensation has evolved in concert with Y-chromosome degeneration in many taxa that exhibit heterogametic sex chromosomes. Dosage compensation overcomes the biological challenge of a "half dose" of X chromosome gene transcripts in the heterogametic sex. The need to equalize gene expression of a hemizygous X with that of autosomes arises from the fact that the X chromosomes retain hundreds of functional genes that are actively transcribed in both sexes and interact with genes expressed on the autosomes. Sex determination and heterogametic sex chromosomes have evolved multiple times in Diptera, and in each case the genetic control of dosage compensation is tightly linked to sex determination. In the Anopheles gambiae species complex (Culicidae), maleness is conferred by the Y-chromosome gene Yob, which despite its conserved role between species is polymorphic in its copy number between them. Previous work demonstrated that male An. gambiae s.s. males exhibit complete dosage compensation in pupal and adult stages. In the present study, we have extended this analysis to three sister species in the An. gambiae complex: An. coluzzii, An. arabiensis, and An. quadriannulatus. In addition, we analyzed dosage compensation in bi-directional F1 hybrids between these species to determine if hybridization results in the mis-regulation and disruption of dosage compensation. Our results confirm that dosage compensation operates in the An. gambiae species complex through the hypertranscription of the male X chromosome. Additionally, dosage compensation in hybrid males does not differ from parental males, indicating that hybridization does not result in the mis-regulation of dosage compensation.

Genome-Wide Divergence in the West-African Malaria Vector Anopheles melas.

Anopheles melas is a member of the recently diverged An. gambiae species complex, a model for speciation studies, and is a locally important malaria vector along the West-African coast where it breeds in brackish water. A recent population genetic study of An. melas revealed species-level genetic differentiation between three population clusters. An. melas West extends from The Gambia to the village of Tiko, Cameroon. The other mainland cluster, An. melas South, extends from the southern Cameroonian village of Ipono to Angola. Bioko Island, Equatorial Guinea An. melas populations are genetically isolated from mainland populations. To examine how genetic differentiation between these An. melas forms is distributed across their genomes, we conducted a genome-wide analysis of genetic differentiation and selection using whole genome sequencing data of pooled individuals (Pool-seq) from a representative population of each cluster. The An. melas forms exhibit high levels of genetic differentiation throughout their genomes, including the presence of numerous fixed differences between clusters. Although the level of divergence between the clusters is on a par with that of other species within the An. gambiae complex, patterns of genome-wide divergence and diversity do not provide evidence for the presence of pre- and/or postmating isolating mechanisms in the form of speciation islands. These results are consistent with an allopatric divergence process with little or no introgression.

Large fluctuations in the effective population size of the malaria mosquito Anopheles gambiae s.s. during vector control cycle.

On Bioko Island, Equatorial Guinea, indoor residual spraying (IRS) has been part of the Bioko Island Malaria Control Project since early 2004. Despite success in reducing childhood infections, areas of high transmission remain on the island. We therefore examined fluctuations in the effective population size (N e ) of the malaria vector Anopheles gambiae in an area of persistent high transmission over two spray rounds. We analyzed data for 13 microsatellite loci from 791 An. gambiae specimens collected at six time points in 2009 and 2010 and reconstructed the demographic history of the population during this period using approximate Bayesian computation (ABC). Our analysis shows that IRS rounds have a large impact on N e , reducing it by 65%-92% from prespray round N e . More importantly, our analysis shows that after 3-5 months, the An. gambiae population rebounded by 2818% compared shortly following the spray round. Our study underscores the importance of adequate spray round frequency to provide continuous suppression of mosquito populations and that increased spray round frequency should substantially improve the efficacy of IRS campaigns. It also demonstrates the ability of ABC to reconstruct a detailed demographic history across only a few tens of generations in a large population.

Population genomics of resource exploitation: insights from gene expression profiles of two Daphnia ecotypes fed alternate resources.

Consumer-resource interactions are a central issue in evolutionary and community ecology because they play important roles in selection and population regulation. Most consumers encounter resource variation at multiple scales, and respond through phenotypic plasticity in the short term or evolutionary divergence in the long term. The key traits for these responses may influence resource acquisition, assimilation, and/or allocation. To identify relevant candidate genes, we experimentally assayed genome-wide gene expression in pond and lake Daphnia ecotypes exposed to alternate resource environments. One was a simple, high-quality laboratory diet, Ankistrodesmus falcatus. The other was the complex natural seston from a large lake. In temporary ponds, Daphnia generally experience high-quality, abundant resources, whereas lakes provide low-quality, seasonally shifting resources that are chronically limiting. For both ecotypes, we used replicate clones drawn from a number of separate populations. Fourteen genes were differentially regulated with respect to resources, including genes involved in gut processes, resource allocation, and activities with no obvious connection to resource exploitation. Three genes were differentially regulated in both ecotypes; the others may play a role in ecological divergence. Genes clearly linked to gut processes include two peritrophic matrix proteins, a Niemann-Pick type C2 gene, and a chymotrypsin. A pancreatic lipase, an epoxide hydrolase, a neuroparsin, and an UDP-dependent glucuronyltransferase are potentially involved in resource allocation through effects on energy processing and storage or hormone pathways. We performed quantitative rt-PCR for eight genes in independent samples of three clones of each of the two ecotypes. Though these largely confirmed observed differential regulation, some genes' expression was highly variable among clones. Our results demonstrate the value of matching the level of biological replication in genome-wide assays to the question, as it gave us insight into ecotype-level responses at ecological and evolutionary scales despite substantial variation within ecotypes.