Molecular systematics of Anopheles: from subgenera to subpopulations

Emerging West African Genotype Chikungunya Virus in Mosquito Virome

We studied the viromes of three dominant mosquito species in Wenzhou, a coastal city in Zhejiang Province, using metavirome sequencing, with 18 viral families identified. Viral sequences were verified by RT-PCR. The JEV E gene was most closely related to the 1988 Korean strain. DENV sequences were most closely related to the 1997 Australian strain. CHIKV-E1-1 was most closely related to the 1983 Senegal strain and belonged to West African genotype CHIKV. Remarkably, this is the first time that a West African genotype of CHIKV has been detected in Zhejiang Province. Mutations in the CHIKV-E1-1 protein A226V may increase infectivity in Ae. albopictus. Three non-conservative mutations of CHIKV-E1-1 (D45H, D70H and V290D) may have an impact on the function. In conclusion, our study reveals the diversity of mosquito-borne viruses and potential emerging outbreaks in the southeast coastal region of China, providing new perspectives for mining the ecological characterization of other important arboviruses.

Improved species assignments across the entire Anopheles genus using targeted sequencing

Accurate species identification of the mosquitoes in the genus Anopheles is of crucial importance to implement malaria control measures and monitor their effectiveness. We use a previously developed amplicon panel (ANOSPP) that retrieves sequence data from multiple short nuclear loci for any species in the genus. Species assignment is based on comparison of samples to a reference index using k-mer distance. Here, we provide a protocol to generate version controlled updates of the reference index and present its latest release, NNv2, which contains 91 species, compared to 56 species represented in its predecessor NNv1. With the updated reference index, we are able to assign samples to species level that previously could not be assigned. We discuss what happens if a species is not represented in the reference index and how this can be addressed in a future update. To demonstrate the increased power of NNv2, we showcase the assignments of 1789 wild-caught mosquitoes from Madagascar and demonstrate that we can detect within species population structure from the amplicon sequencing data.

A DNA barcode reference library of Croatian mosquitoes (Diptera: Culicidae): implications for identification and delimitation of species, with notes on the distribution of potential vector species

BACKGROUND

Mosquitoes pose a risk to human health worldwide, and correct species identification and detection of cryptic species are the most important keys for surveillance and control of mosquito vectors. In addition to traditional identification based on morphology, DNA barcoding has recently been widely used as a complementary tool for reliable identification of mosquito species. The main objective of this study was to create a reference DNA barcode library for the Croatian mosquito fauna, which should contribute to more accurate and faster identification of species, including cryptic species, and recognition of relevant vector species.

METHODS

Sampling was carried out in three biogeographical regions of Croatia over six years (2017-2022). The mosquitoes were morphologically identified; molecular identification was based on the standard barcoding region of the mitochondrial COI gene and the nuclear ITS2 region, the latter to identify species within the Anopheles maculipennis complex. The BIN-RESL algorithm assigned the COI sequences to the corresponding BINs (Barcode Index Number clusters) in BOLD, i.e. to putative MOTUs (Molecular Operational Taxonomic Units). The bPTP and ASAP species delimitation methods were applied to the genus datasets in order to verify/confirm the assignment of specimens to specific MOTUs.

RESULTS

A total of 405 mosquito specimens belonging to six genera and 30 morphospecies were collected and processed. Species delimitation methods assigned the samples to 31 (BIN-RESL), 30 (bPTP) and 28 (ASAP) MOTUs, with most delimited MOTUs matching the morphological identification. Some species of the genera Culex, Aedes and Anopheles were assigned to the same MOTUs, especially species that are difficult to distinguish morphologically and/or represent species complexes. In total, COI barcode sequences for 34 mosquito species and ITS2 sequences for three species of the genus Anopheles were added to the mosquito sequence database for Croatia, including one individual from the Intrudens Group, which represents a new record for the Croatian mosquito fauna.

CONCLUSION

We present the results of the first comprehensive study combining morphological and molecular identification of most mosquito species present in Croatia, including several invasive and vector species. With the exception of some closely related species, this study confirmed that DNA barcoding based on COI provides a reliable basis for the identification of mosquito species in Croatia.

Phylogenomics revealed migration routes and adaptive radiation timing of Holarctic malaria mosquito species of the Maculipennis Group

BACKGROUND

Phylogenetic analyses of closely related species of mosquitoes are important for better understanding the evolution of traits contributing to transmission of vector-borne diseases. Six out of 41 dominant malaria vectors of the genus Anopheles in the world belong to the Maculipennis Group, which is subdivided into two Nearctic subgroups (Freeborni and Quadrimaculatus) and one Palearctic (Maculipennis) subgroup. Although previous studies considered the Nearctic subgroups as ancestral, details about their relationship with the Palearctic subgroup, and their migration times and routes from North America to Eurasia remain controversial. The Palearctic species An. beklemishevi is currently included in the Nearctic Quadrimaculatus subgroup adding to the uncertainties in mosquito systematics.

RESULTS

To reconstruct historic relationships in the Maculipennis Group, we conducted a phylogenomic analysis of 11 Palearctic and 2 Nearctic species based on sequences of 1271 orthologous genes. The analysis indicated that the Palearctic species An. beklemishevi clusters together with other Eurasian species and represents a basal lineage among them. Also, An. beklemishevi is related more closely to An. freeborni, which inhabits the Western United States, rather than to An. quadrimaculatus, a species from the Eastern United States. The time-calibrated tree suggests a migration of mosquitoes in the Maculipennis Group from North America to Eurasia about 20-25 million years ago through the Bering Land Bridge. A Hybridcheck analysis demonstrated highly significant signatures of introgression events between allopatric species An. labranchiae and An. beklemishevi. The analysis also identified ancestral introgression events between An. sacharovi and its Nearctic relative An. freeborni despite their current geographic isolation. The reconstructed phylogeny suggests that vector competence and the ability to enter complete diapause during winter evolved independently in different lineages of the Maculipennis Group.

CONCLUSIONS

Our phylogenomic analyses reveal migration routes and adaptive radiation timing of Holarctic malaria vectors and strongly support the inclusion of An. beklemishevi into the Maculipennis Subgroup. Detailed knowledge of the evolutionary history of the Maculipennis Subgroup provides a framework for examining the genomic changes related to ecological adaptation and susceptibility to human pathogens. These genomic variations may inform researchers about similar changes in the future providing insights into the patterns of disease transmission in Eurasia.

Mosquito surveillance and the first record of morphological and molecular-based identification of invasive species Aedes (Stegomyia) aegypti (Diptera: Culicidae), southern Iran

Ae. aegypti is an important vector for transmission of some dangerous arboviral diseases, including Dengue Fever. The present study was conducted (from August 2017 to January 2020) to survey the fauna of Culicine mosquitoes, emphasizing the existence of this invasive species in oriental parts of the country located near the Persian Gulf. Different sampling methods were used to collect all life stages of the mosquito. After morphological identification, a molecular study based on Cytochrome Oxidase (COI) gene-specific primers was performed. Then, the COI gene was sequenced via the Sanger method. A total of 4843 adults and 11,873 larvae were collected (8 species of Culex, one species of Culiseta, and 5 species of Aedes). Fifty-five Ae. aegypti specimens (8 adults and 47 larvae) were identified.Based on the biology and ecological requirements of Ae. aegypti, the possibility of the permanent establishment of this species in the tropical climate of the region is very likely. Considering the detection of this invasive vector mosquito species in Iran and the high incidence of some arboviral diseases in the neighboring countries, and continuous movements of the settlers of these areas, potential outbreaks of arboviral diseases can be predicted. Planning and implementing an immediate surveillance and control program of the vector mosquito is vital to prevent the permanent establishment of this invasive vector mosquito species in southern Iran.

A targeted amplicon sequencing panel to simultaneously identify mosquito species and Plasmodium presence across the entire Anopheles genus

Anopheles is a diverse genus of mosquitoes comprising over 500 described species, including all known human malaria vectors. While a limited number of key vector species have been studied in detail, the goal of malaria elimination calls for surveillance of all potential vector species. Here, we develop a multilocus amplicon sequencing approach that targets 62 highly variable loci in the Anopheles genome and two conserved loci in the Plasmodium mitochondrion, simultaneously revealing both the mosquito species and whether that mosquito carries malaria parasites. We also develop a cheap, nondestructive, and high-throughput DNA extraction workflow that provides template DNA from single mosquitoes for the multiplex PCR, which means specimens producing unexpected results can be returned to for morphological examination. Over 1000 individual mosquitoes can be sequenced in a single MiSeq run, and we demonstrate the panel's power to assign species identity using sequencing data for 40 species from Africa, Southeast Asia, and South America. We also show that the approach can be used to resolve geographic population structure within An. gambiae and An. coluzzii populations, as the population structure determined based on these 62 loci from over 1000 mosquitoes closely mirrors that revealed through whole genome sequencing. The end-to-end approach is quick, inexpensive, robust, and accurate, which makes it a promising technique for very large-scale mosquito genetic surveillance and vector control.

Multiple Novel Clades of Anopheline Mosquitoes Caught Outdoors in Northern Zambia

Residual vector populations that do not come in contact with the most frequently utilized indoor-directed interventions present major challenges to global malaria eradication. Many of these residual populations are mosquito species about which little is known. As part of a study to assess the threat of outdoor exposure to malaria mosquitoes within the Southern and Central Africa International Centers of Excellence for Malaria Research, foraging female anophelines were collected outside households in Nchelenge District, northern Zambia. These anophelines proved to be more diverse than had previously been reported in the area. In order to further characterize the anopheline species, sequencing and phylogenetic approaches were utilized. Anopheline mosquitoes were collected from outdoor light traps, morphologically identified, and sent to Johns Hopkins Bloomberg School of Public Health for sequencing. Sanger sequencing from 115 field-derived samples yielded mitochondrial COI sequences, which were aligned with a homologous 488 bp gene segment from known anophelines (n = 140) retrieved from NCBI. Nuclear ITS2 sequences (n = 57) for at least one individual from each unique COI clade were generated and compared against NCBI’s nucleotide BLAST database to provide additional evidence for taxonomical identity and structure. Molecular and morphological data were combined for assignment of species or higher taxonomy. Twelve phylogenetic groups were characterized from the COI and ITS2 sequence data, including the primary vector species Anopheles funestus s.s. and An. gambiae s.s. An unexpectedly large proportion of the field collections were identified as An. coustani and An. sp. 6. Six phylogenetic groups remain unidentified to species-level. Outdoor collections of anopheline mosquitoes in areas frequented by people in Nchelenge, northern Zambia, proved to be extremely diverse. Morphological misidentification and underrepresentation of some anopheline species in sequence databases confound efforts to confirm identity of potential malaria vector species. The large number of unidentified anophelines could compromise the malaria vector surveillance and malaria control efforts not only in northern Zambia but other places where surveillance and control are focused on indoor-foraging and resting anophelines. Therefore, it is critical to continue development of methodologies that allow better identification of these populations and revisiting and cleaning current genomic databases.

Multiple evolutionary lineages for the main vector of Leishmania guyanensis, Lutzomyia umbratilis (Diptera: Psychodidae), in the Brazilian Amazon

Lutzomyia umbratilis is the main vector of Leishmania guyanensis in the Brazilian Amazon and in neighboring countries. Previous biological and molecular investigations have revealed significant differences between L. umbratilis populations from the central Brazilian Amazon region. Here, a phylogeographic survey of L. umbratilis populations collected from nine localities in the Brazilian Amazon was conducted using two mitochondrial genes. Statistical analyses focused on population genetics, phylogenetic relationships and species delimitations. COI genetic diversity was very high, whereas Cytb diversity was moderate. COI genealogical haplotypes, population structure and phylogenetic analyses identified a deep genetic differentiation and three main genetic groups. Cytb showed a shallower genetic structure, two main haplogroups and poorly resolved phylogenetic trees. These findings, allied to absence of isolation by distance, support the hypothesis that the Amazon and Negro Rivers and interfluves are the main evolutionary forces driving L. umbratilis diversification. The main three genetic groups observed represent three evolutionary lineages, possibly species. The first lineage occurs north of the Amazon River and east of Negro River, where Le. guyanensis transmission is intense, implying that L. umbratilis is an important vector there. The second lineage is in the interfluve between north of Amazon River and west of Negro River, an area reported to be free of Le. guyanensis transmission. The third lineage, first recorded in this study, is in the interfluve between south of Amazonas River and west of Madeira River, and its involvement in the transmission of this parasite remains to be elucidated.

Updating the bionomy and geographical distribution of Anopheles (Nyssorhynchus) albitarsis F: A vector of malaria parasites in northern South America

Anopheles albitarsis F is a putative species belonging to the Albitarsis Complex, recognized by rDNA, mtDNA, partial white gene, and microsatellites sequences. It has been reported from the island of Trinidad, Venezuela and Colombia, and incriminated as a vector of malaria parasites in the latter. This study examined mitochondrially encoded cytochrome c oxidase I (MT-CO1) sequences of An. albitarsis F from malaria-endemic areas in Colombia and Venezuela to understand its relations with other members of the Complex, revised and update the geographical distribution and bionomics of An. albitarsis F and explore hypotheses to explain its phylogenetic relationships and geographical expansion. Forty-five MT-CO1 sequences obtained in this study were analyzed to estimate genetic diversity and possible evolutionary relationships. Sequences generated 37 haplotypes clustered in a group where the genetic divergence of Venezuelan populations did not exceed 1.6% with respect to Colombian samples. Anopheles albitarsis F (π = 0.013) represented the most recent cluster located closer to An. albitarsis I (π = 0.009). Barcode gap was detected according to Albitarsis Complex lineages previously reported (threshold 0.014–0.021). Anopheles albitarsis F has a wide distribution in northern South America and might play an important role in the transmission dynamics of malaria due to its high expansion capacity. Future studies are required to establish the southern distribution of An. albitarsis F in Venezuela, and its occurrence in Guyana and Ecuador.

Molecular Characterization of Mosquito Diversity in the Balearic Islands

Several outbreaks of mosquito-borne diseases have taken place in Europe in recent years. In Spain, both active and passive surveillance have demonstrated that dengue and West Nile viruses are currently circulating, and seven autochthonous dengue cases have been reported in the last 2 yr. The effectiveness of vector control programs largely depends on the accuracy of the taxonomic identification of the species. However, in Spain, identification almost completely relies on the use of morphological keys to characterize the mosquito fauna. This study investigates the congruence between molecular and morphological species boundaries in 13 Spanish mosquito taxa. The Cytochrome c oxidase subunit I (COI) gene region was sequenced from 60 adult specimens collected in Mallorca, plus several representatives from other Spanish regions for comparative purposes. Phylogenetic relationships were established using Bayesian and maximum-likelihood approaches. Using three species delimitation algorithms (ABGD, mPTP, and GMYC), we found strong evidence for cryptic speciation within Anopheles algeriensis Theobald, a widespread mosquito in the Mediterranean basin. We also delimited the Mallorcan rock pool mosquito Aedes mariae (Sergent & Sergent), from mainland European populations. Finally, we found difficulties in the use of wing characters in species keys to distinguish Culiseta annulata (Schrk) from Culiseta subochrea (Edwards). Given that these species are vectors of pathogens of medical relevance and have veterinary importance, their accurate taxonomic identification is essential in European vector surveillance programs.

K-mer-Based Motif Analysis in Insect Species across Anopheles, Drosophila, and Glossina Genera and Its Application to Species Classification

Short k-mer sequences from DNA are both conserved and diverged across species owing to their functional significance in speciation, which enables their use in many species classification algorithms. In the present study, we developed a methodology to analyze the DNA k-mers of whole genome, 5' UTR, intron, and 3' UTR regions from 58 insect species belonging to three genera of Diptera that include Anopheles, Drosophila, and Glossina. We developed an improved algorithm to predict and score k-mers based on a scheme that normalizes k-mer scores in different genomic subregions. This algorithm takes advantage of the information content of the whole genome as opposed to other algorithms or studies that analyze only a small group of genes. Our algorithm uses k-mers of lengths 7-9 bp for the whole genome, 5' and 3' UTR regions as well as the intronic regions. Taxonomical relationships based on the whole-genome k-mer signatures showed that species of the three genera clustered together quite visibly. We also improved the scoring and filtering of these k-mers for accurate species identification. The whole-genome k-mer content correlation algorithm showed that species within a single genus correlated tightly with each other as compared to other genera. The genomes of two Aedes and one Culex species were also analyzed to demonstrate how newly sequenced species can be classified using the algorithm. Furthermore, working with several dozen species has enabled us to assign a whole-genome k-mer signature for each of the 58 Dipteran species by making all-to-all pairwise comparison of the k-mer content. These signatures were used to compare the similarity between species and to identify clusters of species displaying similar signatures.

Characterization of the complete mitogenome of Anopheles aquasalis, and phylogenetic divergences among Anopheles from diverse geographic zones

Whole mitogenome sequences (mtDNA) have been exploited for insect ecology studies, using them as molecular markers to reconstruct phylogenies, or to infer phylogeographic relationships and gene flow. Recent Anopheles phylogenomic studies have provided information regarding the time of deep lineage divergences within the genus. Here we report the complete 15,393 bp mtDNA sequences of Anopheles aquasalis, a Neotropical human malaria vector. When comparing its structure and base composition with other relevant and available anopheline mitogenomes, high similarity and conserved genomic features were observed. Furthermore, 22 mtDNA sequences comprising anopheline and Dipteran sibling species were analyzed to reconstruct phylogenies and estimate dates of divergence between taxa. Phylogenetic analysis using complete mtDNA sequences suggests that A. aquasalis diverged from the Anopheles albitarsis complex ~28 million years ago (MYA), and ~38 MYA from Anopheles darlingi. Bayesian analysis suggests that the most recent ancestor of Nyssorhynchus and Anopheles + Cellia was extant ~83 MYA, corroborating current estimates of ~79–100 MYA. Additional sampling and publication of African, Asian, and North American anopheline mitogenomes would improve the resolution of the Anopheles phylogeny and clarify early continental dispersal routes.

Vector bionomics and malaria transmission in an area of sympatry of An. arabiensis, An. coluzzii and An. gambiae

Despite extensive genetic studies on their variability and differentiation, few is known about the specific and relative role of An. coluzzii, An. gambiae and An. arabiensis in areas of sympatry. Indeed, their behavioral dissimilarities and divergent population dynamics can impact on malaria transmission level and intensity. This study was undertaken in four sympatric sites belonging to two different ecosystems with differential insecticide pressure to study the bionomics of these species and their relative role in malaria transmission. Mosquitoes were collected monthly from July to December 2011 when landing on human volunteers and by pyrethrum spray catches. Specimens belonging to the An. gambiae complex were further identified using molecular tools. Plasmodium falciparum infection and blood-feeding preferences were studied using the ELISA techniques. Overall, the three species were in sympatry in each of the four sites with the predominance of An. gambiae. Mosquito populations' dynamics varied temporally depending on the rainy season for each zone. The anthropophilic rates varied between 45.7 and 78.1% for An. arabiensis, 81.8 and 100% for An. coluzzii and 80 and 96.7% for An. gambiae. Plasmodium infection rates were higher in An. gambiae (range: 2.17%-6.54%) while for An. arabiensis and An. coluzzii it varied respectively between 0-1.24% and 0-3.66%. Malaria transmission occured in each of the four sites both indoors and outdoors and was due mainly to An. gambiae. An. arabiensis and An. coluzzii played a limited role due both to a low anthropophilic rate and a lower biting rate for An. coluzzii in comparison with An. gambiae. This study showed that, while present in sympatric areas, species from the An. gambiae complex could exhibit differential involvement in malaria transmission. Even less involved in malaria transmission, the occurrence of ecological and environmental changes tending to a good adaptation of An. coluzzii could lead to a great risk for malaria transmission in time and space in human populations.

Evidence of natural Wolbachia infections and molecular identification of field populations of Culex pipiens complex (Diptera: Culicidae) mosquitoes in western Turkey

Establishing reliable risk projection information about the distribution pattern of members of the Culex pipiens complex is of particular interest, as these mosquitoes are competent vectors for certain disease-causing pathogens. Wolbachia, a maternally inherited bacterial symbiont, are distributed in various arthropod species and can induce cytoplasmic incompatibility, i.e., reduced egg hatch, in certain crosses. It is being considered as a tool for population control of mosquito disease vectors. The Aegean region is characterized by highly populated, rural, and agricultural areas and is also on the route of the migratory birds. In this study, a fragment of the 658 bp of the mitochondrial cytochrome c oxidase subunit 1 (COI) gene, which includes the barcode region, was employed to differentiate Cx. pipiens complex species found in this region. Moreover, for the first time, the prevalence of Wolbachia endobacteria in these natural populations was examined using PCR amplification of a specific wsp gene. Our results revealed a widespread (more than 90%, n=121) presence of the highly efficient West Nile virus vector Cx. quinquefasciatus in the region. We also found that Wolbachia infection is widespread; the average prevalence was 62% in populations throughout the region. This study provided valuable information about the composition of Cx. pipiens complex mosquitoes and the prevalence of Wolbachia infection in these populations in the Aegean region. This information will be helpful in tracking mosquito-borne diseases and designing and implementing Wolbachia-based control strategies in the region.

Phylogeny of Anophelinae using mitochondrial protein coding genes

Malaria is a vector-borne disease that is a great burden on the poorest and most marginalized communities of the tropical and subtropical world. Approximately 41 species of Anopheline mosquitoes can effectively spread species of Plasmodium parasites that cause human malaria. Proposing a natural classification for the subfamily Anophelinae has been a continuous effort, addressed using both morphology and DNA sequence data. The monophyly of the genus Anopheles, and phylogenetic placement of the genus Bironella, subgenera Kerteszia, Lophopodomyia and Stethomyia within the subfamily Anophelinae, remain in question. To understand the classification of Anophelinae, we inferred the phylogeny of all three genera (Anopheles, Bironella, Chagasia) and major subgenera by analysing the amino acid sequences of the 13 protein coding genes of 150 newly sequenced mitochondrial genomes of Anophelinae and 18 newly sequenced Culex species as outgroup taxa, supplemented with 23 mitogenomes from GenBank. Our analyses generally place genus Bironella within the genus Anopheles, which implies that the latter as it is currently defined is not monophyletic. With some inconsistencies, Bironella was placed within the major clade that includes Anopheles, Cellia, Kerteszia, Lophopodomyia, Nyssorhynchus and Stethomyia, which were found to be monophyletic groups within Anophelinae. Our findings provided robust evidence for elevating the monophyletic groupings Kerteszia, Lophopodomyia, Nyssorhynchus and Stethomyia to genus level; genus Anopheles to include subgenera Anopheles, Baimaia, Cellia and Christya; Anopheles parvus to be placed into a new genus; Nyssorhynchus to be elevated to genus level; the genus Nyssorhynchus to include subgenera Myzorhynchella and Nyssorhynchus; Anopheles atacamensis and Anopheles pictipennis to be transferred from subgenus Nyssorhynchus to subgenus Myzorhynchella; and subgenus Nyssorhynchus to encompass the remaining species of Argyritarsis and Albimanus Sections.

Phylogeny of Anophelinae using mitochondrial protein coding genes

Malaria is a vector-borne disease that is a great burden on the poorest and most marginalized communities of the tropical and subtropical world. Approximately 41 species of Anopheline mosquitoes can effectively spread species of Plasmodium parasites that cause human malaria. Proposing a natural classification for the subfamily Anophelinae has been a continuous effort, addressed using both morphology and DNA sequence data. The monophyly of the genus Anopheles, and phylogenetic placement of the genus Bironella, subgenera Kerteszia, Lophopodomyia and Stethomyia within the subfamily Anophelinae, remain in question. To understand the classification of Anophelinae, we inferred the phylogeny of all three genera (Anopheles, Bironella, Chagasia) and major subgenera by analysing the amino acid sequences of the 13 protein coding genes of 150 newly sequenced mitochondrial genomes of Anophelinae and 18 newly sequenced Culex species as outgroup taxa, supplemented with 23 mitogenomes from GenBank. Our analyses generally place genus Bironella within the genus Anopheles, which implies that the latter as it is currently defined is not monophyletic. With some inconsistencies, Bironella was placed within the major clade that includes Anopheles, Cellia, Kerteszia, Lophopodomyia, Nyssorhynchus and Stethomyia, which were found to be monophyletic groups within Anophelinae. Our findings provided robust evidence for elevating the monophyletic groupings Kerteszia, Lophopodomyia, Nyssorhynchus and Stethomyia to genus level; genus Anopheles to include subgenera Anopheles, Baimaia, Cellia and Christya; Anopheles parvus to be placed into a new genus; Nyssorhynchus to be elevated to genus level; the genus Nyssorhynchus to include subgenera Myzorhynchella and Nyssorhynchus; Anopheles atacamensis and Anopheles pictipennis to be transferred from subgenus Nyssorhynchus to subgenus Myzorhynchella; and subgenus Nyssorhynchus to encompass the remaining species of Argyritarsis and Albimanus Sections.

Zooprophylaxis as a control strategy for malaria caused by the vector Anopheles arabiensis (Diptera: Culicidae): a systematic review

Background

Zooprophylaxis is the use of wild or domestic animals, which are not the reservoir host of a given disease, to divert the blood-seeking malaria vectors from human hosts. In this paper, we systematically reviewed zooprophylaxis to assess its efficacy as a malaria control strategy and to evaluate the possible methods of its application.

Methods

The electronic databases, PubMed Central®, Web of Science, Science direct, and African Journals Online were searched using the key terms: “zooprophylaxis” or “cattle and malaria”, and reports published between January 1995 and March 2016 were considered. Thirty-four reports on zooprophylaxis were retained for the systematic review.

Results

It was determined that Anopheles arabiensis is an opportunistic feeder. It has a strong preference for cattle odour when compared to human odour, but feeds on both hosts. Its feeding behaviour depends on the available hosts, varying from endophilic and endophagic to exophilic and exophagic. There are three essential factors for zooprophylaxis to be effective in practice: a zoophilic and exophilic vector, habitat separation between human and host animal quarters, and augmenting zooprophylaxis with insecticide treatment of animals or co-intervention of long-lasting insecticide-treated nets and/or indoor residual spraying. Passive zooprophylaxis can be applied only in malaria vector control if cattle and human dwellings are separated in order to avoid the problem of zoopotentiation.

Conclusions

The outcomes of using zooprophylaxis as a malaria control strategy varied across locations. It is therefore advised to conduct a site-specific evaluation of its effectiveness in vector control before implementing zooprophylaxis as the behaviour of Anopheles arabiensis mosquitoes varies across localities and circumstances.

Electronic supplementary material

The online version of this article (10.1186/s40249-017-0366-3) contains supplementary material, which is available to authorized users.

Immune Regulation of Plasmodium Is Anopheles Species Specific and Infection Intensity Dependent

Malaria parasite ookinetes must traverse the vector mosquito midgut epithelium to transform into sporozoite-producing oocysts. The Anopheles innate immune system is a key regulator of this process, thereby determining vector competence and disease transmission. The role of Anopheles innate immunity factors as agonists or antagonists of malaria parasite infection has been previously determined using specific single Anopheles-Plasmodium species combinations. Here we show that the two C-type lectins CTL4 and CTLMA2 exert differential agonistic and antagonistic regulation of parasite killing in African and South American Anopheles species. The C-type lectins regulate both parasite melanization and lysis through independent mechanisms, and their implication in parasite melanization is dependent on infection intensity rather than mosquito-parasite species combination. We show that the leucine-rich repeat protein LRIM1 acts as an antagonist on the development of Plasmodium ookinetes and as a regulator of oocyst size and sporozoite production in the South American mosquito Anopheles albimanus. Our findings explain the rare observation of human Plasmodium falciparum melanization and define a key factor mediating the poor vector competence of Anopheles albimanus for Plasmodium berghei and Plasmodium falciparum.

Malaria, one of the world’s deadliest diseases, is caused by Plasmodium parasites that are vectored to humans by the bite of Anopheles mosquitoes. The mosquito’s innate immune system is actively engaged in suppressing Plasmodium infection. Studies on mosquito immunity revealed multiple factors that act as either facilitators or inhibitors of Plasmodium infection, but these findings were mostly based on single Anopheles-Plasmodium species combinations, not taking into account the diversity of mosquito and parasite species. We show that the functions of CTL4 and CTLMA2 have diverged in different vector species and can be both agonistic and antagonistic for Plasmodium infection. Their protection against parasite melanization in Anopheles gambiae is dependent on infection intensity, rather than the mosquito-parasite combination. Importantly, we describe for the first time how LRIM1 plays an essential role in Plasmodium infection of Anopheles albimanus, suggesting it is a key regulator of the poor vector competence of this species.

Standardization of sample homogenization for mosquito identification using an innovative proteomic tool based on protein profiling

The rapid spread of vector-borne diseases demands the development of an innovative strategy for arthropod monitoring. The emergence of MALDI-TOF MS as a rapid, low-cost, and accurate tool for arthropod identification is revolutionizing medical entomology. However, as MS spectra from an arthropod can vary according to the body part selected, the sample homogenization method used and the mode and duration of sample storage, standardization of protocols is indispensable prior to the creation and sharing of an MS reference spectra database. In the present study, manual grinding of Anopheles gambiae Giles and Aedes albopictus mosquitoes at the adult and larval (L3) developmental stages was compared to automated homogenization. Settings for each homogenizer were optimized, and glass powder was found to be the best sample disruptor based on its ability to create reproducible and intense MS spectra. In addition, the suitability of common arthropod storage conditions for further MALDI-TOF MS analysis was kinetically evaluated. The conditions that best preserved samples for accurate species identification by MALDI-TOF MS were freezing at -20°C or in liquid nitrogen for up to 6 months. The optimized conditions were objectified based on the reproducibility and stability of species-specific MS profiles. The automation and standardization of mosquito sample preparation methods for MALDI-TOF MS analyses will popularize the use of this innovative tool for the rapid identification of arthropods with medical interest.

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.

Chromosome inversions and ecological plasticity in the main African malaria mosquitoes

Chromosome inversions have fascinated the scientific community, mainly because of their role in the rapid adaption of different taxa to changing environments. However, the ecological traits linked to chromosome inversions have been poorly studied. Here, we investigated the roles played by 23 chromosome inversions in the adaptation of the four major African malaria mosquitoes to local environments in Africa. We studied their distribution patterns by using spatially explicit modeling and characterized the ecogeographical determinants of each inversion range. We then performed hierarchical clustering and constrained ordination analyses to assess the spatial and ecological similarities among inversions. Our results show that most inversions are environmentally structured, suggesting that they are actively involved in processes of local adaptation. Some inversions exhibited similar geographical patterns and ecological requirements among the four mosquito species, providing evidence for parallel evolution. Conversely, common inversion polymorphisms between sibling species displayed divergent ecological patterns, suggesting that they might have a different adaptive role in each species. These results are in agreement with the finding that chromosomal inversions play a role in Anopheles ecotypic adaptation. This study establishes a strong ecological basis for future genome-based analyses to elucidate the genetic mechanisms of local adaptation in these four mosquitoes.

Implicating Cryptic and Novel Anophelines as Malaria Vectors in Africa

Entomological indices and bionomic descriptions of malaria vectors are essential to accurately describe and understand malaria transmission and for the design and evaluation of appropriate control interventions. In order to correctly assign spatio-temporal distributions, behaviors and responses to interventions to particular anopheline species, identification of mosquitoes must be accurately made. This paper reviews the current methods and their limitations in correctly identifying anopheline mosquitoes in sub-Saharan Africa, and highlights the importance of molecular methods to discriminate cryptic species and identify lesser known anophelines. The increasing number of reports of Plasmodium infections in assumed "minor", non-vector, and cryptic and novel species is reviewed. Their importance in terms of evading current control and elimination strategies and therefore maintaining malaria transmission is emphasized.

The mitochondrial genomes of Culex tritaeniorhynchus and Culex pipiens pallens (Diptera: Culicidae) and comparison analysis with two other Culex species

Background

Culex tritaeniorhynchus and Culex pipiens pallens are the major vectors of the Japanese encephalitis virus and Wuchereria bancrofti, the causative agent of filariasis. The knowledge of mitochondrial genomes has been widely useful for the studies on molecular evolution, phylogenetics and population genetics.

Methods

In this study, we sequenced and annotated the mitochondrial (mt) genomes of Cx. tritaeniorhynchus and Cx. p. pallens, and performed a comparative analysis including four known mt genomes of species of the subgenus Culex (Culex). The phylogenetic relationships of Cx. tritaeniorhynchus, Cx. p. pallens and four known Culex mt genome sequences were reconstructed by maximum likelihood based on concatenated protein-coding gene sequences.

Results

Culex tritaeniorhynchus and Cx. p. pallens mt genomes are 14,844 bp and 15,617 bp long, both consists of 13 PCGs, 22 tRNAs, 2 rRNAs and 1 CR (not sequenced for Cx. tritaeniorhynchus). The initiation and termination codons of PCGs are ATN and TAA, respectively, except for COI starting with TCG, and COI and COII terminated with T. tRNAs have the typical clover-leaf secondary structures except for trnS^(AGN) that is lacking the DHU stem. 16S rRNA and 12S rRNA secondary structures were drawn for the first time for mosquito mt genomes. The control region of Cx. p. pallens mt genome is 747 bp long and with four tandem repeat structures. Phylogenetic analyses demonstrated that the mt genome of Cx. tritaeniorhynchus was significantly separated from the remaining five mt genomes of Culex spp. Culex p. pipiens, Cx. p. pallens and Cx. p. quinquefasciatus formed a monophyletic clade with Cx. p. quinquefasciatus linked in the middle of the clade, and Cx. p. pallens should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus.

Conclusions

The mt genomes of Cx. tritaeniorhynchus and Cx. p. pallens share the same gene composition and order with those of two other Culex species. Culex p. pallens of the Pipiens complex should have the same taxonomic level as Culex p. pipiens and Cx. p. quinquefasciatus investigated. We enriched the Culex mt genome data and provided a reference basis for further Culex mt genome sequencing and analyses.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1694-z) contains supplementary material, which is available to authorized users.

Evidence of new species for malaria vector Anopheles nuneztovari sensu lato in the Brazilian Amazon region

BACKGROUND

Anopheles nuneztovari sensu lato comprises cryptic species in northern South America, and the Brazilian populations encompass distinct genetic lineages within the Brazilian Amazon region. This study investigated, based on two molecular markers, whether these lineages might actually deserve species status.

METHODS

Specimens were collected in five localities of the Brazilian Amazon, including Manaus, Careiro Castanho and Autazes, in the State of Amazonas; Tucuruí, in the State of Pará; and Abacate da Pedreira, in the State of Amapá, and analysed for the COI gene (Barcode region) and 12 microsatellite loci. Phylogenetic analyses were performed using the maximum likelihood (ML) approach. Intra and inter samples genetic diversity were estimated using population genetics analyses, and the genetic groups were identified by means of the ML, Bayesian and factorial correspondence analyses and the Bayesian analysis of population structure.

RESULTS

The Barcode region dataset (N = 103) generated 27 haplotypes. The haplotype network suggested three lineages. The ML tree retrieved five monophyletic groups. Group I clustered all specimens from Manaus and Careiro Castanho, the majority of Autazes and a few from Abacate da Pedreira. Group II clustered most of the specimens from Abacate da Pedreira and a few from Autazes and Tucuruí. Group III clustered only specimens from Tucuruí (lineage III), strongly supported (97 %). Groups IV and V clustered specimens of A. nuneztovari s.s. and A. dunhami, strongly (98 %) and weakly (70 %) supported, respectively. In the second phylogenetic analysis, the sequences from GenBank, identified as A. goeldii, clustered to groups I and II, but not to group III. Genetic distances (Kimura-2 parameters) among the groups ranged from 1.60 % (between I and II) to 2.32 % (between I and III). Microsatellite data revealed very high intra-population genetic variability. Genetic distances showed the highest and significant values (P = 0.005) between Tucuruí and all the other samples, and between Abacate da Pedreira and all the other samples. Genetic distances, Bayesian (Structure and BAPS) analyses and FCA suggested three distinct biological groups, supporting the barcode region results.

CONCLUSIONS

The two markers revealed three genetic lineages for A. nuneztovari s.l. in the Brazilian Amazon region. Lineages I and II may represent genetically distinct groups or species within A. goeldii. Lineage III may represent a new species, distinct from the A. goeldii group, and may be the most ancestral in the Brazilian Amazon. They may have differences in Plasmodium susceptibility and should therefore be investigated further.

Anopheles farauti is a homogeneous population that blood feeds early and outdoors in the Solomon Islands

BACKGROUND

In the 1970s, Anopheles farauti in the Solomon Island responded to indoor residual spraying with DDT by increasingly feeding more outdoors and earlier in the evening. Although long-lasting insecticidal nets (LLINs) are now the primary malaria vector control intervention in the Solomon Islands, only a small proportion of An. farauti still seek blood meals indoors and late at night where they are vulnerable to being killed by contract with the insecticides in LLINs. The effectiveness of LLINs and indoor residual spraying (IRS) in controlling malaria transmission where the vectors are exophagic and early biting will depend on whether the predominant outdoor or early biting phenotypes are associated with a subpopulation of the vectors present.

METHODS

Mark-release-recapture experiments were conducted in the Solomon Islands to determine if individual An. farauti repeat the same behaviours over successive feeding cycles. The two behavioural phenotypes examined were those on which the WHO recommended malaria vector control strategies, LLINs and IRS, depend: indoor and late night biting.

RESULTS

Evidence was found for An. farauti being a single population regarding time (early evening or late night) and location (indoor or outdoor) of blood feeding. Individual An. farauti did not consistently repeat behavioural phenotypes expressed for blood feeding (e.g., while most mosquitoes that fed early and outdoors, and would repeat those behaviours, some fed late at night or indoors in the next feeding cycle).

CONCLUSIONS

The finding that An. farauti is a homogeneous population is significant, because during the multiple feeding cycles required to complete the extrinsic incubation period, many individual female anophelines will enter houses late at night and be exposed to the insecticides used in LLINs or IRS. This explains, in part, the control that LLINs and IRS have exerted against a predominantly outdoor feeding vector, such as An. farauti. These findings may be relevant to many of the outdoor feeding vectors that dominate transmission in much of the malaria endemic world and justifies continued use of LLINs. However, the population-level tendency of mosquitoes to feed outdoors and early in the evening does require complementary interventions to accelerate malaria control towards elimination.

Deep Interisland Genetic Divergence in the Macaronesian Endemic Mosquito Ochlerotatus eatoni (Diptera: Culicidae), Indication of Cryptic Species

Ochlerotatus eatoni (Edwards, 1916) is a species endemic to Canary and Madeira Islands that, based on morphology, is considered to be single species. Mitochondrial 16S rRNA and cytochrome oxidase I (COI) sequence data demonstrate that the populations from Tenerife and Madeira Islands are highly differentiated (F(ST) = 0.93). The phylogenetic analysis also separates the two populations into two highly distinct groups. The sharp mitochondrial genetic differentiation between islands is congruent with the published nuclear (allozyme) data. However, mtDNA data did not reveal any significant genetic differentiation within islands. Extreme interisland genetic divergence, but lack of morphological variation, is indicative of the existence of cryptic species. I suggest the elevation of populations to at least incipient species status, designating the populations from Tenerife and Madeira Islands as Oc. eatoni. hewitti and Oc. eatoni. krimbasi, respectively.

The Seasonality and Ecology of the Anopheles gambiae complex (Dipetra: Culicidae) in Liberia Using Molecular Identification

Members of the Anopheles gambiae sensu lato (Giles) complex define a group of seven morphologically indistinguishable species, including the principal malaria vectors in Sub-Saharan Africa. Members of this complex differ in behavior and ability to transmit malaria; hence, precise identification of member species is critical to monitoring and evaluating malaria threat levels. We collected mosquitoes from five counties in Liberia every other month from May 2011 until May 2012, using various trapping techniques. A. gambiae complex members were identified using molecular techniques based on differences in the ribosomal DNA (rDNA) region between species and the molecular forms (S and M) of A. gambiae sensu stricto (s.s) specimens. In total, 1,696 A. gambiae mosquitoes were collected and identified. DNA was extracted from legs of each specimen with species identification determined by multiplex polymerase chain reaction using specific primers. The molecular forms (M or S) of A. gambiae s.s were determined by restriction fragment length polymorphism. Bivariate and multivariate logistic regression models identified environmental variables associated with genomic differentiation. Our results indicate widespread occurrence of A. gambiae s.s., the principal malaria vector in the complex, although two Anopheles melas Theobald/A. merus Donitz mosquitoes were detected. We found 72.6, 25.5, and 1.9% of A. gambiae s.s specimens were S, M, and hybrid forms, respectively. Statistical analysis indicates that the S form was more likely to be found in rural areas during rainy seasons and indoor catchments. This information will enhance vector control efforts in Liberia.

Genetic structuring and fixed polymorphisms in the gene period among natural populations of Lutzomyia longipalpis in Brazil

BACKGROUND

Even one hundred years after being originally identified, aspects of the taxonomy of the sand fly Lutzomyia longipalpis, the principal vector of Leishmania infantum in the Americas, remain unresolved for Brazilian populations of this vector. The diversity of morphological, behavioral, biochemical, and ethological characters, as well as the genetic variability detected by molecular markers are indicative of the presence of a complex of species.

METHODS

In this study, a 525 bp fragment of the period gene was used to evaluate sympatric populations of L. longipalpis. A combination of probabilistic methods such as maximum likelihood and genetic assignment approach to investigate sympatric species of L. longipalpis were applied in three populations of Northeast Brazil.

RESULTS

Fixed polymorphisms in geographically isolated populations of L. longipalpis from two localities in the state of Ceará and one in the state of Pernambuco, Brazil, was identified in a 525 bp fragment of the gene period (per). Our results suggest a direct relationship between the number of spots found in males' tergites and the genetic variation in cryptic species of L. longipalpis. The fragment used in this study revealed the nature of the ancestral morphotype 1S.

CONCLUSION

New polymorphisms were identified in the gene per which can be used as a genetic barcode to sympatric taxonomy of L. longipalpis. The per gene fragment confirmed the presence of two siblings species of L. longipalpis in Sobral and showed that these same species are present in two other localities, representing an expansion within the L. longipalpis species complex with regards to the states of Ceará and Pernambuco.

Whole-genome sequencing reveals absence of recent gene flow and separate demographic histories for Anopheles punctulatus mosquitoes in Papua New Guinea

Anopheles mosquitoes are the vectors of several human diseases including malaria. In many malaria endemic areas, several species of Anopheles coexist, sometimes in the form of related sibling species that are morphologically indistinguishable. Determining the size and organization of Anopheles populations, and possible ongoing gene flow among them is important for malaria control and, in particular, for monitoring the spread of insecticide resistance alleles. However, these parameters have been difficult to evaluate in most Anopheles species due to the paucity of genetic data available. Here, we assess the extent of contemporary gene flow and historical variations in population size by sequencing and de novo assembling the genomes of wild-caught mosquitoes from four species of the Anopheles punctulatus group of Papua New Guinea. Our analysis of more than 50 Mb of orthologous DNA sequences revealed no evidence of contemporary gene flow among these mosquitoes. In addition, investigation of the demography of two of the An. punctulatus species revealed distinct population histories. Overall, our analyses suggest that, despite their similarities in morphology, behaviour and ecology, contemporary sympatric populations of An. punctulatus are evolving independently.

Prominent intraspecific genetic divergence within Anopheles gambiae sibling species triggered by habitat discontinuities across a riverine landscape

The Anopheles gambiae complex of mosquitoes includes malaria vectors at different stages of speciation, whose study enables a better understanding of how adaptation to divergent environmental conditions leads to evolution of reproductive isolation. We investigated the population genetic structure of closely related sympatric taxa that have recently been proposed as separate species (An. coluzzii and An. gambiae), sampled from diverse habitats along the Gambia river in West Africa. We characterized putatively neutral microsatellite loci as well as chromosomal inversion polymorphisms known to be associated with ecological adaptation. The results revealed strong ecologically associated population subdivisions within both species. Microsatellite loci on chromosome-3L revealed clear differentiation between coastal and inland populations, which in An. coluzzii is reinforced by a unusual inversion polymorphism pattern, supporting the hypothesis of genetic divergence driven by adaptation to the coastal habitat. A strong reduction of gene flow was observed between An. gambiae populations west and east of an extensively rice-cultivated region apparently colonized exclusively by An. coluzzii. Notably, this 'intraspecific' differentiation is higher than that observed between the two species and involves also the centromeric region of chromosome-X which has previously been considered a marker of speciation within this complex, possibly suggesting that the two populations may be at an advanced stage of differentiation triggered by human-made habitat fragmentation. These results confirm ongoing ecological speciation within these most important Afro-tropical malaria vectors and raise new questions on the possible effect of this process in malaria transmission.

Phylogenetic study of six species of Anopheles mosquitoes in Peninsular Malaysia based on inter-transcribed spacer region 2 (ITS2) of ribosomal DNA

Background

Molecular techniques are invaluable for investigation on the biodiversity of Anopheles mosquitoes. This study aimed at investigating the spatial-genetic variations among Anopheles mosquitoes from different areas of Peninsular Malaysia, as well as deciphering evolutionary relationships of the local Anopheles mosquitoes with the mosquitoes from neighbouring countries using the anopheline ITS2 rDNA gene.

Methods

Mosquitoes were collected, identified, dissected to check infection status, and DNA extraction was performed for PCR with primers targeting the ITS2 rDNA region. Sequencing was done and phylogenetic tree was constructed to study the evolutionary relationship among Anopheles mosquitoes within Peninsular Malaysia, as well as across the Asian region.

Results

A total of 133 Anopheles mosquitoes consisting of six different species were collected from eight different locations across Peninsular Malaysia. Of these, 65 ITS2 rDNA sequences were obtained. The ITS2 rDNA amplicons of the studied species were of different sizes. One collected species, Anopheles sinensis, shows two distinct pools of population in Peninsular Malaysia, suggesting evolvement of geographic race or allopatric speciation.

Conclusion

Anopheles mosquitoes from Peninsular Malaysia show close evolutionary relationship with the Asian anophelines. Nevertheless, genetic differences due to geographical segregation can be seen. Meanwhile, some Anopheles mosquitoes in Peninsular Malaysia show vicariance, exemplified by the emergence of distinct cluster of An. sinensis population.

Analyzing mosquito (Diptera: culicidae) diversity in Pakistan by DNA barcoding

BACKGROUND

Although they are important disease vectors mosquito biodiversity in Pakistan is poorly known. Recent epidemics of dengue fever have revealed the need for more detailed understanding of the diversity and distributions of mosquito species in this region. DNA barcoding improves the accuracy of mosquito inventories because morphological differences between many species are subtle, leading to misidentifications.

METHODOLOGY/PRINCIPAL FINDINGS

Sequence variation in the barcode region of the mitochondrial COI gene was used to identify mosquito species, reveal genetic diversity, and map the distribution of the dengue-vector species in Pakistan. Analysis of 1684 mosquitoes from 491 sites in Punjab and Khyber Pakhtunkhwa during 2010-2013 revealed 32 species with the assemblage dominated by Culex quinquefasciatus (61% of the collection). The genus Aedes (Stegomyia) comprised 15% of the specimens, and was represented by six taxa with the two dengue vector species, Ae. albopictus and Ae. aegypti, dominant and broadly distributed. Anopheles made up another 6% of the catch with An. subpictus dominating. Barcode sequence divergence in conspecific specimens ranged from 0-2.4%, while congeneric species showed from 2.3-17.8% divergence. A global haplotype analysis of disease-vectors showed the presence of multiple haplotypes, although a single haplotype of each dengue-vector species was dominant in most countries. Geographic distribution of Ae. aegypti and Ae. albopictus showed the later species was dominant and found in both rural and urban environments.

CONCLUSIONS

As the first DNA-based analysis of mosquitoes in Pakistan, this study has begun the construction of a barcode reference library for the mosquitoes of this region. Levels of genetic diversity varied among species. Because of its capacity to differentiate species, even those with subtle morphological differences, DNA barcoding aids accurate tracking of vector populations.

Multigene phylogenetics reveals temporal diversification of major African malaria vectors

The major vectors of malaria in sub-Saharan Africa belong to subgenus Cellia. Yet, phylogenetic relationships and temporal diversification among African mosquito species have not been unambiguously determined. Knowledge about vector evolutionary history is crucial for correct interpretation of genetic changes identified through comparative genomics analyses. In this study, we estimated a molecular phylogeny using 49 gene sequences for the African malaria vectors An. gambiae, An. funestus, An. nili, the Asian malaria mosquito An. stephensi, and the outgroup species Culex quinquefasciatus and Aedes aegypti. To infer the phylogeny, we identified orthologous sequences uniformly distributed approximately every 5 Mb in the five chromosomal arms. The sequences were aligned and the phylogenetic trees were inferred using maximum likelihood and neighbor-joining methods. Bayesian molecular dating using a relaxed log normal model was used to infer divergence times. Trees from individual genes agreed with each other, placing An. nili as a basal clade that diversified from the studied malaria mosquito species 47.6 million years ago (mya). Other African malaria vectors originated more recently, and independently acquired traits related to vectorial capacity. The lineage leading to An. gambiae diverged 30.4 mya, while the African vector An. funestus and the Asian vector An. stephensi were the most closely related sister taxa that split 20.8 mya. These results were supported by consistently high bootstrap values in concatenated phylogenetic trees generated individually for each chromosomal arm. Genome-wide multigene phylogenetic analysis is a useful approach for discerning historic relationships among malaria vectors, providing a framework for the correct interpretation of genomic changes across species, and comprehending the evolutionary origins of this ubiquitous and deadly insect-borne disease.

New tools and insights to assist with the molecular identification of Simulium guianense s.l., main Onchocerca volvulus vector within the highland areas of the Amazonia onchocerciasis focus

Following the success of the Onchocerciasis Elimination Programme for the Americas (OEPA), there is now just one Latin American onchocerciasis focus where onchocerciasis transmission is described as 'on-going:' the Amazonia Onchocerciasis focus. In the hyperendemic highland areas of the Amazonia focus, Simulium guianense s.l. Wise are the most important vectors of the disease. Populations of S. guianense s.l. are, however, known to vary in their cytogenetics and in a range of behaviours, including in their biting habits. In the hypoendemic lowland areas of the Amazonia focus, for example, S. guianense s.l. are generally regarded as zoophilic and consequently unimportant to disease transmission. Robust tools, to discriminate among various populations of S. guianense s.l. have, however, not yet been developed. In the work reported here, we have assessed the utility of a ribosomal DNA sequence fragment spanning the nuclear ribosomal ITS-1, ITS-2 and 5.8S sequence regions and a ∼850 nucleotide portion of the mitochondrial cytochrome oxidase gene (CO1) for species-level identification and for resolving the within species substructuring. We report here how we have generated 78 CO1 sequences from a rich set of both zoophilic and anthropophilic populations of S. guianense s.l. that were collected from eight sites that are broadly distributed across Brazil. Consistent with previous findings, our analysis supports the genetic isolation of Simulium litobranchium from S. guianense s.l. In contrast with previous findings, however, our results did not provide support for the divergence of the two species prior to the radiation of S. guianense s.l. In our analysis of the S. guianense s.l. ribosomal DNA sequence trace files we generated, we provide clear evidence of multiple within-specimen single nucleotide polymorphisms and indels suggesting that S. guianense s.l. ribosomal DNA is not a good target for conventional DNA barcoding. This is the first report of S. guianense s.l. within individual ribosomal DNA variation and thus the first evidence that the species is not subject to the normal effects of concerted evolution. Collectively, these data illustrate the need for diverse sampling in the development of robust molecular tools for vector identification and suggest that ribosomal DNA might be able to assist with resolving S. guianense s.l. species substructuring that C01 barcoding has hitherto failed to.

Evidence for the occurrence of two sympatric sibling species within the Anopheles (Kerteszia) cruzii complex in southeast Brazil and the detection of asymmetric introgression between them using a multilocus analysis

BACKGROUND

Anopheles (Kerteszia) cruzii (Diptera: Culicidae) is a primary vector of human and simian malaria parasites in southern and southeastern Brazil. Earlier studies using chromosome inversions, isoenzymes and a number of molecular markers have suggested that An. cruzii is a species complex.

RESULTS

In this study, a multilocus approach using six loci, three circadian clock genes and three encoding ribosomal proteins, was carried out to investigate in more detail the genetic differentiation between the An. cruzii populations from Florianópolis-Santa Catarina (southern Brazil) and Itatiaia-Rio de Janeiro States (southeastern Brazil). The analyses were performed first comparing Florianópolis and Itatiaia, and then comparing the two putative sympatric incipient species from Itatiaia (Itatiaia A and Itatiaia B). The analysis revealed high FST values between Florianópolis and Itatiaia (considering Itatiaia A and B together) and also between the sympatric Itatiaia A and Itatiaia B, irrespective of their function. Also, using the IM program, no strong indication of migration was found between Florianópolis and Itatiaia (considering Itatiaia A and B together) using all loci together, but between Itatiaia A and Itatiaia B, the results show evidence of migration only in the direction of Itatiaia B.

CONCLUSIONS

The results of the multilocus analysis indicate that Florianópolis and Itatiaia represent different species of the An. cruzii complex that diverged around 0.6 Mya, and also that the Itatiaia sample is composed of two sympatric incipient species A and B, which diverged around 0.2 Mya. Asymmetric introgression was found between the latter two species despite strong divergence in some loci.

Molecular taxonomy of the two Leishmania vectors Lutzomyia umbratilis and Lutzomyia anduzei (Diptera: Psychodidae) from the Brazilian Amazon

BACKGROUND

Lutzomyia umbratilis (a probable species complex) is the main vector of Leishmania guyanensis in the northern region of Brazil. Lutzomyia anduzei has been implicated as a secondary vector of this parasite. These species are closely related and exhibit high morphological similarity in the adult stage; therefore, they have been wrongly identified, both in the past and in the present. This shows the need for employing integrated taxonomy.

METHODS

With the aim of gathering information on the molecular taxonomy and evolutionary relationships of these two vectors, 118 sequences of 663 base pairs (barcode region of the mitochondrial DNA cytochrome oxidase I - COI) were generated from 72 L. umbratilis and 46 L. anduzei individuals captured, respectively, in six and five localities of the Brazilian Amazon. The efficiency of the barcode region to differentiate the L. umbratilis lineages I and II was also evaluated. The data were analyzed using the pairwise genetic distances matrix and the Neighbor-Joining (NJ) tree, both based on the Kimura Two Parameter (K2P) evolutionary model.

RESULTS

The analyses resulted in 67 haplotypes: 32 for L. umbratilis and 35 for L. anduzei. The mean intra-specific genetic distance was 0.008 (0.002 to 0.010 for L. umbratilis; 0.008 to 0.014 for L. anduzei), whereas the mean interspecific genetic distance was 0.044 (0.041 to 0.046), supporting the barcoding gap. Between the L. umbratilis lineages I and II, it was 0.009 to 0.010. The NJ tree analysis strongly supported monophyletic clades for both L. umbratilis and L. anduzei, whereas the L. umbratilis lineages I and II formed two poorly supported monophyletic subclades.

CONCLUSIONS

The barcode region clearly separated the two species and may therefore constitute a valuable tool in the identification of the sand fly vectors of Leishmania in endemic leishmaniasis areas. However, the barcode region had not enough power to separate the two lineages of L. umbratilis, likely reflecting incipient species that have not yet reached the status of distinct species.

Mosquito fauna in municipal parks of São Paulo City, Brazil: a preliminary survey

A mosquito faunal survey was conducted from October 2010 to February 2011 in the municipal parks of São Paulo City, Brazil. A total of 7,015 specimens of 53 taxonomic categories grouped into 12 genera (Aedes, Anopheles, Coquilletidia, Culex, Limatus, Lutzia, Mansonia, Psorophora, Toxorhynchites, Trichoprosopon, Uranotaenia, and Wyeomyia) were collected. The largest and most peripheral parks showed greater species richness compared to smaller and more centralized parks.

Matrix-assisted laser desorption ionization--time of flight mass spectrometry: an emerging tool for the rapid identification of mosquito vectors

Background

The identification of mosquito vectors is typically based on morphological characteristics using morphological keys of determination, which requires entomological expertise and training. The use of protein profiling by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS), which is increasingly being used for the routine identification of bacteria, has recently emerged for arthropod identification.

Methods

To investigate the usefulness of MALDI-TOF-MS as a mosquito identification tool, we tested protein extracts made from mosquito legs to create a database of reference spectra. The database included a total of 129 laboratory-reared and field-caught mosquito specimens consisting of 20 species, including 4 Aedes spp., 9 Anopheles spp., 4 Culex spp., Lutzia tigripes, Orthopodomyia reunionensis and Mansonia uniformis. For the validation study, blind tests were performed with 76 specimens consisting of 1 to 4 individuals per species. A cluster analysis was carried out using the MALDI-Biotyper and some spectra from all mosquito species tested.

Results

Biomarker mass sets containing 22 and 43 masses have been detected from 100 specimens of the Anopheles, Aedes and Culex species. By carrying out 3 blind tests, we achieved the identification of mosquito vectors at the species level, including the differentiation of An. gambiae complex, which is possible using MALDI-TOF-MS with 1.8 as the cut-off identification score. A cluster analysis performed with all available mosquito species showed that MALDI-Biotyper can distinguish between specimens at the subspecies level, as demonstrated for An gambiae M and S, but this method cannot yet be considered a reliable tool for the phylogenetic study of mosquito species.

Conclusions

We confirmed that even without any specific expertise, MALDI-TOF-MS profiling of mosquito leg protein extracts can be used for the rapid identification of mosquito vectors. Therefore, MALDI-TOF-MS is an alternative, efficient and inexpensive tool that can accurately identify mosquitoes collected in the field during entomological surveys.

Molecular phylogenetic analysis of Anopheles and Cellia subgenus anophelines (Diptera: Culicidae) in temperate and tropical regions of Iran

Molecular studies on population genetics of speciation across Iran have recently started. Morphological and molecular studies have showed that 25 species of genus Anopheles are present in the country; however, relationships between vector and non-vector species as well as compatibility of morphological characters with molecular data have not been verified. Molecular phylogenetic analysis was undertaken on the Anopheles and Cellia subgenus members internal transcribed spacer 2 (ITS2) sequences submitted to GenBank among the Oriental and Palearctic members in north and southern Iran. rDNA-ITS2 sequences were extracted from the GenBank and analyzed using bioinformatics softwares: BLAST, ITS2 annotation tool (version 3.0.13), ClustalW, and MEGA5 in neighbor-joining and maximum likelihood algorithms. There are not any submitted sequences in GenBank from Iran for the following seven species: Anopheles algeriensis, Anopheles marteri, Anopheles plumbeus, Anopheles peditaeniatus, Anopheles melanoon, Anopheles subpictus, and Anopheles mongolensis; therefore, they have not been included in the study. Although these molecular-based phylogenetic trees match well enough with classical morphological taxonomy, the arrangement of species did not match with morphological classification in some cases. Correct species identification is essential for control of vector born disease such as malaria; therefore, phylogenetic methods will help to understand the relationship among the members of the target species within the genus Anopheles. It could also help us to design molecular markers for species differentiation particularly in cryptic species, which is difficult to classify them based on morphological features.

ITS2 characterization and Anopheles species identification of the subgenus Cellia

In Mizoram, the origin and molecular nature of Anopheles species is poorly understood, despite the region having high malarial incidence and rich biodiversity. A diagnostic PCR assay for distinguishing the Cellia subgenera members of Anopheles species was developed based on the interspecific ITS2 variation. No intraspecific variation was found and the size (362-604bp) and GC content (48.8-58.9%) of the ITS2 were highly variable among Anophelines. The ITS2 of A. vagus is significantly longer than those of other Anopheles species. Significant relationship was observed among repeats, minimum free energy and RNA secondary structures. Different types of microsatellites were identified and among them dinucleotide, pentanucleotide and polynucleotide microsatellites were predominant. Variation in the length of the ITS2 between species was due to indels in simple repeats. Four domain types of RNA secondary structures were identified and the lowest free energy values were predicted using the computer software, RNAfold. Types I and II were observed only in Neocellia and Myzomyia series and Types III and IV were common in Neocellia and Pyretophorus series. ITS2-based PCR protocol provides a means for vector ecologists, malaria epidemiologists and control personnel to accurately identify members of the subgenera Cellia and a better understanding of their genomic status in Mizoram.

Phylogeography of the neotropical Anopheles triannulatus complex (Diptera: Culicidae) supports deep structure and complex patterns

BACKGROUND

The molecular phylogenetic relationships and population structure of the species of the Anopheles triannulatus complex: Anopheles triannulatus s.s., Anopheles halophylus and the putative species Anopheles triannulatus C were investigated.

METHODS

The mitochondrial COI gene, the nuclear white gene and rDNA ITS2 of samples that include the known geographic distribution of these taxa were analyzed. Phylogenetic analyses were performed using Bayesian inference, Maximum parsimony and Maximum likelihood approaches.

RESULTS

Each data set analyzed septely yielded a different topology but none provided evidence for the seption of An. halophylus and An. triannulatus C, consistent with the hypothesis that the two are undergoing incipient speciation. The phylogenetic analyses of the white gene found three main clades, whereas the statistical parsimony network detected only a single metapopulation of Anopheles triannulatus s.l. Seven COI lineages were detected by phylogenetic and network analysis. In contrast, the network, but not the phylogenetic analyses, strongly supported three ITS2 groups. Combined data analyses provided the best resolution of the trees, with two major clades, Amazonian (clade I) and trans-Andean + Amazon Delta (clade II). Clade I consists of multiple subclades: An. halophylus + An. triannulatus C; trans-Andean Venezuela; central Amazonia + central Bolivia; Atlantic coastal lowland; and Amazon delta. Clade II includes three subclades: Panama; cis-Andean Colombia; and cis-Venezuela. The Amazon delta specimens are in both clades, likely indicating local sympatry. Spatial and molecular variance analyses detected nine groups, corroborating some of subclades obtained in the combined data analysis.

CONCLUSION

Combination of the three molecular markers provided the best resolution for differentiation within An. triannulatus s.s. and An. halophylus and C. The latest two species seem to be very closely related and the analyses performed were not conclusive regarding species differentiation. Further studies including new molecular markers would be desirable to solve this species status question. Besides, results of the study indicate a trans-Andean origin for An. triannulatus s.l. The potential implications for malaria epidemiology remain to be investigated.

Mitochondrial genome sequences reveal deep divergences among Anopheles punctulatus sibling species in Papua New Guinea

Background

Members of the Anopheles punctulatus group (AP group) are the primary vectors of human malaria in Papua New Guinea. The AP group includes 13 sibling species, most of them morphologically indistinguishable. Understanding why only certain species are able to transmit malaria requires a better comprehension of their evolutionary history. In particular, understanding relationships and divergence times among Anopheles species may enable assessing how malaria-related traits (e.g. blood feeding behaviours, vector competence) have evolved.

Methods

DNA sequences of 14 mitochondrial (mt) genomes from five AP sibling species and two species of the Anopheles dirus complex of Southeast Asia were sequenced. DNA sequences from all concatenated protein coding genes (10,770 bp) were then analysed using a Bayesian approach to reconstruct phylogenetic relationships and date the divergence of the AP sibling species.

Results

Phylogenetic reconstruction using the concatenated DNA sequence of all mitochondrial protein coding genes indicates that the ancestors of the AP group arrived in Papua New Guinea 25 to 54 million years ago and rapidly diverged to form the current sibling species.

Conclusion

Through evaluation of newly described mt genome sequences, this study has revealed a divergence among members of the AP group in Papua New Guinea that would significantly predate the arrival of humans in this region, 50 thousand years ago. The divergence observed among the mtDNA sequences studied here may have resulted from reproductive isolation during historical changes in sea-level through glacial minima and maxima. This leads to a hypothesis that the AP sibling species have evolved independently for potentially thousands of generations. This suggests that the evolution of many phenotypes, such as insecticide resistance will arise independently in each of the AP sibling species studied here.

Evidence for genetic differentiation at the microgeographic scale in Phlebotomus papatasi populations from Sudan

Background

Cutaneous Leishmaniasis (CL) is endemic in Sudan. It is caused by Leishmania major parasites and transmitted by Phlebotomus papatasi sandflies. Recently, uncommon clinical manifestations of CL have been reported. Moreover, L. donovani parasites that cause Visceral Leishmaniasis (VL) have been isolated from CL lesions of some patients who contracted the disease in Khartoum State, Central Sudan with no history of travelling to VL endemic sites on south-eastern Sudan. Because different clinical manifestations and the parasite behaviour could be related to genetic differentiation, or even sub-structuring within sandfly vector populations, a population genetic study was conducted on P. papatasi populations collected from different localities in Khartoum State known for their uncommon CL cases and characterized by contrasting environmental conditions.

Methods

A set of seven microsatellite loci was used to investigate the population structure of P. papatasi samples collected from different localities in Khartoum State, Central Sudan. Populations from Kassala State, Eastern Sudan and Egypt were also included in the analyses as outgroups. The level of genetic diversity and genetic differentiation among natural populations of P. papatasi was determined using F_ST statistics and Bayesian assignments.

Results

Genetic analyses revealed significant genetic differentiation (F_ST) between the Sudanese and the Egyptian populations. Within the Sudanese P. papatasi populations, one population from Gerif West, Khartoum State, exhibited significant genetic differentiation from all other populations including those collected as near as 22 km.

Conclusion

The significant genetic differentiation of Gerif West P. papatasi population from other Sudanese populations may have important implication for the epidemiology of leishmaniasis in Khartoum State and needs to be further investigated. Primarily, it could be linked to the unique location of Gerif West which is confined by the River Nile and its tributaries that may act as a natural barrier for gene flow between this site and the other rural sites. The observed high migration rates and lack of genetic differentiation among the other P. papatasi populations could be attributed to the continuous human and cattle movement between these localities.

A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites

Malaria morbidity and mortality caused by both Plasmodium falciparum and Plasmodium vivax extend well beyond the African continent, and although P. vivax causes between 80 and 300 million severe cases each year, vivax transmission remains poorly understood. Plasmodium parasites are transmitted by Anopheles mosquitoes, and the critical site of interaction between parasite and host is at the mosquito's luminal midgut brush border. Although the genome of the “model” African P. falciparum vector, Anopheles gambiae, has been sequenced, evolutionary divergence limits its utility as a reference across anophelines, especially non-sequenced P. vivax vectors such as Anopheles albimanus. Clearly, technologies and platforms that bridge this substantial scientific gap are required in order to provide public health scientists with key transcriptomic and proteomic information that could spur the development of novel interventions to combat this disease. To our knowledge, no approaches have been published that address this issue. To bolster our understanding of P. vivax–An. albimanus midgut interactions, we developed an integrated bioinformatic-hybrid RNA-Seq-LC-MS/MS approach involving An. albimanus transcriptome (15,764 contigs) and luminal midgut subproteome (9,445 proteins) assembly, which, when used with our custom Diptera protein database (685,078 sequences), facilitated a comparative proteomic analysis of the midgut brush borders of two important malaria vectors, An. gambiae and An. albimanus.

A new chromosomal phylogeny supports the repeated origin of vectorial capacity in malaria mosquitoes of the Anopheles gambiae complex

Understanding phylogenetic relationships within species complexes of disease vectors is crucial for identifying genomic changes associated with the evolution of epidemiologically important traits. However, the high degree of genetic similarity among sibling species confounds the ability to determine phylogenetic relationships using molecular markers. The goal of this study was to infer the ancestral–descendant relationships among malaria vectors and nonvectors of the Anopheles gambiae species complex by analyzing breakpoints of fixed chromosomal inversions in ingroup and several outgroup species. We identified genes at breakpoints of fixed overlapping chromosomal inversions 2Ro and 2Rp of An. merus using fluorescence in situ hybridization, a whole-genome mate-paired sequencing, and clone sequencing. We also mapped breakpoints of a chromosomal inversion 2La (common to An. merus, An. gambiae, and An. arabiensis) in outgroup species using a bioinformatics approach. We demonstrated that the “standard” 2R+^p arrangement and “inverted” 2Ro and 2La arrangements are present in outgroup species Anopheles stephensi, Aedes aegypti, and Culex quinquefasciatus. The data indicate that the ancestral species of the An. gambiae complex had the 2Ro, 2R+^p, and 2La chromosomal arrangements. The “inverted” 2Ro arrangement uniquely characterizes a malaria vector An. merus as the basal species in the complex. The rooted chromosomal phylogeny implies that An. merus acquired the 2Rp inversion and that its sister species An. gambiae acquired the 2R+^o inversion from the ancestral species. The karyotype of nonvectors An. quadriannulatus A and B was derived from the karyotype of the major malaria vector An. gambiae. We conclude that the ability to effectively transmit human malaria had originated repeatedly in the complex. Our findings also suggest that saltwater tolerance originated first in An. merus and then independently in An. melas. The new chromosomal phylogeny will facilitate identifying the association of evolutionary genomic changes with epidemiologically important phenotypes.

Malaria causes more than one million deaths every year, mostly among children in Sub-Saharan Africa. Anopheles mosquitoes are exclusive vectors of human malaria. Many malaria vectors belong to species complexes, and members within these complexes can vary significantly in their ecological adaptations and ability to transmit the parasite. To better understand evolution of epidemiologically important traits, we studied relationships among nonvector and vector species of the African Anopheles gambiae complex. We analyzed gene orders at genomic regions where evolutionary breaks of chromosomal inversions occurred in members of the complex and compared them with gene orders in species outside the complex. This approach allowed us to identify ancient and recent gene orders for three chromosomal inversions. Surprisingly, the more ancestral chromosomal arrangements were found in mosquito species that are vectors of human malaria, while the more derived arrangements were found in both nonvectors and vectors. Our finding strongly suggests that the increased ability to transmit human malaria originated repeatedly during the recent evolution of these African mosquitoes. This knowledge can be used to identify specific genetic changes associated with the human blood choice and ecological adaptations.

Dry season reproductive depression of Anopheles gambiae in the Sahel

The African malaria mosquito, Anopheles gambiae, is widespread south of the Sahara including in dry savannahs and semi-arid environments where no surface water exists for several months a year. Adults of the M form of An. gambiae persist through the long dry season, when no surface waters are available, by increasing their maximal survival from 4 weeks to 7 months. Dry season diapause (aestivation) presumably underlies this extended survival. Diapause in adult insects is intrinsically linked to depressed reproduction. To determine if reproduction of the Sahelian M form is depressed during the dry season, we assessed seasonal changes in oviposition, egg batch size, and egg development, as well as insemination rate and blood feeding in wild caught mosquitoes. Results from xeric Sahelian and riparian populations were compared. Oviposition response in the Sahelian M form dropped from 70% during the wet season to 20% during the dry season while the mean egg batch size among those that laid eggs fell from 173 to 101. Correspondingly, the fraction of females that exhibited gonotrophic dissociation increased over the dry season from 5% to 45%, while a similar fraction of the population retained developed eggs despite having access to water. This depression in reproduction the Sahelian M form was not caused by a reduced insemination rate. Seasonal variation in these reproductive parameters of the riparian M form population was less extreme and the duration of reproductive depression was shorter. Blood feeding responses did not change with the season in either population. Depressed reproduction during the dry season in the Sahelian M form of An. gambiae provides additional evidence for aestivation and illuminates the physiological processes involved. The differences between the Sahelian and riparian population suggest an adaptive cline in aestivation phenotypes between populations only 130 km apart.