Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group

Parthenogenesis in Darevskia lizards: A rare outcome of common hybridization, not a common outcome of rare hybridization

Hybridization is a common evolutionary process with multiple possible outcomes. In vertebrates, interspecific hybridization has repeatedly generated parthenogenetic hybrid species. However, it is unknown whether the generation of parthenogenetic hybrids is a rare outcome of frequent hybridization between sexual species within a genus or the typical outcome of rare hybridization events. Darevskia is a genus of rock lizards with both hybrid parthenogenetic and sexual species. Using capture sequencing, we estimate phylogenetic relationships and gene flow among the sexual species, to determine how introgressive hybridization relates to the origins of parthenogenetic hybrids. We find evidence for widespread hybridization with gene flow, both between recently diverged species and deep branches. Surprisingly, we find no signal of gene flow between parental species of the parthenogenetic hybrids, suggesting that the parental pairs were either reproductively or geographically isolated early in their divergence. The generation of parthenogenetic hybrids in Darevskia is, then, a rare outcome of the total occurrence of hybridization within the genus, but the typical outcome when specific species pairs hybridize. Our results question the conventional view that parthenogenetic lineages are generated by hybridization in a window of divergence. Instead, they suggest that some lineages possess specific properties that underpin successful parthenogenetic reproduction.

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of primary importance and species of low/negligible epidemiological relevance, of which distribution data in Italy are outdated.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.

Dynamics of Plasmodium vivax populations in border areas of the Greater Mekong sub-region during malaria elimination

Background

Countries within the Greater Mekong Sub-region (GMS) of Southeast Asia have committed to eliminating malaria by 2030. Although the malaria situation has greatly improved, malaria transmission remains at international border regions. In some areas, Plasmodium vivax has become the predominant parasite. To gain a better understanding of transmission dynamics, knowledge on the changes of P. vivax populations after the scale-up of control interventions will guide more effective targeted control efforts.

Methods

This study investigated genetic diversity and population structures in 206 P. vivax clinical samples collected at two time points in two international border areas: the China-Myanmar border (CMB) (n = 50 in 2004 and n = 52 in 2016) and Thailand-Myanmar border (TMB) (n = 50 in 2012 and n = 54 in 2015). Parasites were genotyped using 10 microsatellite markers.

Results

Despite intensified control efforts, genetic diversity remained high (H_E = 0.66–0.86) and was not significantly different among the four populations (P > 0.05). Specifically, H_E slightly decreased from 0.76 in 2004 to 0.66 in 2016 at the CMB and increased from 0.80 in 2012 to 0.86 in 2015 at the TMB. The proportions of polyclonal infections varied significantly among the four populations (P < 0.05), and showed substantial decreases from 48.0% in 2004 to 23.7 at the CMB and from 40.0% in 2012 to 30.7% in 2015 at the TMB, with corresponding decreases in the multiplicity of infection. Consistent with the continuous decline of malaria incidence in the GMS over time, there were also increases in multilocus linkage disequilibrium, suggesting more fragmented and increasingly inbred parasite populations. There were considerable genetic differentiation and sub-division among the four tested populations. Temporal genetic differentiation was observed at each site (F_ST = 0.081 at the CMB and F_ST = 0.133 at the TMB). Various degrees of clustering were evident between the older parasite samples collected in 2004 at the CMB and the 2016 CMB and 2012 TMB populations, suggesting some of these parasites had shared ancestry. In contrast, the 2015 TMB population was genetically distinctive, which may reflect a process of population replacement. Whereas the effective population size (N_e) at the CMB showed a decrease from 4979 in 2004 to 3052 in 2016 with the infinite allele model, the N_e at the TMB experienced an increase from 6289 to 10,259.

Conclusions

With enhanced control efforts on malaria, P. vivax at the TMB and CMB showed considerable spatial and temporal differentiation, but the presence of large P. vivax reservoirs still sustained genetic diversity and transmission. These findings provide new insights into P. vivax transmission dynamics and population structure in these border areas of the GMS. Coordinated and integrated control efforts on both sides of international borders are essential to reach the goal of regional malaria elimination.

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

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

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.

Population genetics of Anopheles funestus, the African malaria vector, Kenya

Background

Anopheles funestus is among the major malaria vectors in Kenya and sub-Saharan Africa and has been recently implicated in persistent malaria transmission. However, its ecology and genetic diversity remain poorly understood in Kenya.

Methods

Using 16 microsatellite loci, we examined the genetic structure of An. funestus sampled from 11 locations (n = 426 individuals) across a wide geographical range in Kenya spanning coastal, western and Rift Valley areas.

Results

Kenyan An. funestus resolved as three genetically distinct clusters. The largest cluster (FUN1) broadly included samples from western and Rift Valley areas of Kenya with two clusters identified from coastal Kenya (FUN2 and FUN3), not previously reported. Geographical distance had no effect on population differentiation of An. funestus. We found a significant variation in the mean Plasmodium infectivity between the clusters (χ² = 12.1, df = 2, P = 0.002) and proportional to the malaria prevalence in the different risk zones of Kenya. Notably, there was variation in estimated effective population sizes between the clusters, suggesting possible differential impact of anti-vector interventions in represented areas.

Conclusions

Heterogeneity among Kenyan populations of An. funestus will impact malaria vector control with practical implications for the development of gene-drive technologies. The difference in Plasmodium infectivity and effective population size between the clusters could suggest potential variation in phenotypic characteristics relating to competence or insecticide resistance. This is worth examining in future studies.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-3252-3) contains supplementary material, which is available to authorized users.

Molecular evidence for new sympatric cryptic species of Aedes albopictus (Diptera: Culicidae) in China: A new threat from Aedes albopictus subgroup?

Background

Aedes (Stegomyia) albopictus (Skuse) is an indigenous species and the predominant vector of dengue fever in China. Understanding of genetic diversity and structure of the mosquito would facilitate dengue prevention and vector control. Sympatric cryptic species have been identified in the Ae. albopictus subgroup in Southeast Asia; however, little is known about the presence and distribution of cryptic species in China. This study aimed to examine the genetic diversity, evaluate potential new cryptic sibling species, and assess the prevalence of Wolbachia infections in field populations.

Methods

Aedes adult female specimens were collected from five provinces in southern and central China during 2015–2016. Morphological identification was performed under dissection microscope. The mitochondrial DNA cytochrome c oxidase subunit 1 (cox1, DNA barcoding) locus and the ribosomal DNA internal transcribed spacer region 2 (ITS2) marker were used to examine the genetic variation, evaluate cryptic sibling species, and population structure in the field populations. Screening for the presence of Wolbachia was performed using multiplex PCR.

Results

A total of 140 individual specimens with morphological characteristics similar to Ae. albopictus were sequenced for DNA barcoding. Among these, 129 specimens (92.1%) were confirmed and identified as Ae. albopictus. The remaining 11 specimens, from 2 provinces, were identified as 2 distinct sequence groups, which were confirmed by ITS2 marker sequencing, suggesting the existence of potential cryptic species of Ae. albopictus. In Ae. albopictus, we found significant genetic differentiation and population structure between populations collected from different climate zones. Medium to high frequencies of Wolbachia infections were observed in natural Ae. albopictus populations, whereas Wolbachia was infrequent or absent in cryptic species populations.

Conclusions

Our findings highlight the population differentiation by climate zone and the presence of novel, cryptic Aedes species in China. The low prevalence of Wolbachia infections in cryptic species populations could reflect either a recent invasion of Wolbachia in Ae. albopictus or different host immune responses to this symbiont in the cryptic species. The study provides useful information for vector control and host-symbiont coevolution. Further study is needed to investigate the potential for arbovirus infection and disease transmission in the emerged cryptic species.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-2814-8) contains supplementary material, which is available to authorized users.

Human Interventions: Driving Forces of Mosquito Evolution

One of the most common strategies for controlling mosquito-borne diseases relies on the use of chemical pesticides to repel or kill the mosquito vector. Pesticide exposure interferes with several key biological functions in the mosquito and triggers a variety of adaptive responses whose underlying mechanisms are only partially elucidated. The availability of reference genome sequences opens up the possibility of tracking signatures of evolutionary changes, including the most recent, across the genomes of many vector species. In this review, we highlight the recent genomic changes, which contribute to the fascinating adaptation of malaria vectors of the sub-Saharan African region to intensive insecticide-based interventions. We emphasize the operational significance of detailed genomic knowledge for current monitoring and decision-making.

Genomic insights into adaptive divergence and speciation among malaria vectors of the Anopheles nili group

Ongoing speciation in the most important African malaria vectors gives rise to cryptic populations, which differ remarkably in their behavior, ecology, and capacity to vector malaria parasites. Understanding the population structure and the drivers of genetic differentiation among mosquitoes is crucial for effective disease control because heterogeneity within vector species contributes to variability in malaria cases and allow fractions of populations to escape control efforts. To examine population structure and the potential impacts of recent large-scale control interventions, we have investigated the genomic patterns of differentiation in mosquitoes belonging to the Anopheles nili group-a large taxonomic group that diverged ~3 Myr ago. Using 4,343 single nucleotide polymorphisms (SNPs), we detected strong population structure characterized by high-FST values between multiple divergent populations adapted to different habitats within the Central African rainforest. Delineating the cryptic species within the Anopheles nili group is challenging due to incongruence between morphology, ribosomal DNA, and SNP markers consistent with incomplete lineage sorting and/or interspecific gene flow. A very high proportion of loci are fixed (FST = 1) within the genome of putative species, which suggests that ecological and/or reproductive barriers are maintained by strong selection on a substantial number of genes.