DNA probes for identifying the members of the Anopheles punctulatus complex in Papua New Guinea

The mosquito Anopheles (Cellia) oreios sp. n., formerly species 6 of the Australasian Anopheles farauti complex, and a critical review of its biology and relation to disease

Species 6 of the Australasian Anopheles farauti sibling species complex (Diptera: Culicidae) is described and formally named Anopheles oreios Bangs & Harbach, sp. n. Adult, pupal and fourth-instar larval specimens collected in the Baliem Valley, Papua Province, Indonesia, are characterized and compared with those of Anopheles farauti, Anopheles hinesorum, Anopheles irenicus and Anopheles torresiensis (formerly informally denoted as species 1, 2, 7 and 3, respectively). The variable wings of adult females, the male genitalia, the pupa and the fourth-instar larva of An. oreios are illustrated and DNA sequence data are included for regions coding for sections of the mitochondrial COI and COII genes. The biology of An. oreios and its relation to malaria transmission are discussed in detail and contrasted with the biology and disease relations of some members of the An. farauti and Anopheles punctulatus sibling species complexes.

Anopheles punctulatus group: evolution, distribution, and control

The major malaria vectors of the Southwest Pacific belong to a group of closely related mosquitoes known as the Anopheles punctulatus group. The group comprises 13 co-occurring species that either are isomorphic or carry overlapping morphological features, and today several species remain informally named. The advent of species-diagnostic molecular tools in the 1990s permitted a new raft of studies into the newly differentiated mosquitoes of this group, and these have revealed five species as the region's primary malaria vectors: An. farauti, An. hinesorum, An. farauti 4, An. koliensis, and An. punctulatus. Species' distributions are now well established across Papua New Guinea, northern Australia, and the Solomon Archipelago, but little has been documented thus far in eastern Indonesia. As each species reveals significant differences in distribution and biology, the relative paucity of knowledge of their biology or ecology in relation to malaria transmission is brought into clearer focus. Only three of the species have undergone some form of spatial or population genetics analyses, and this has revealed striking differences in their genetic signatures throughout the region. This review compiles and dissects the key findings for this important mosquito group and points to where future research should focus to maximize the output of field studies in developing relevant knowledge on these malaria vectors.

Microsatellite and mitochondrial markers reveal strong gene flow barriers for Anopheles farauti in the Solomon Archipelago: implications for malaria vector control

Anopheles farauti is the primary malaria vector throughout the coastal regions of the Southwest Pacific. A shift in peak biting time from late to early in the night occurred following widespread indoor residue spraying of dichlorodiphenyltrichloro-ethane (DDT) and has persisted in some island populations despite the intervention ending decades ago. We used mitochondrial cytochrome oxidase I (COI) sequence data and 12 newly developed microsatellite markers to assess the population genetic structure of this malaria vector in the Solomon Archipelago. With geographically distinct differences in peak A. farauti night biting time observed in the Solomon Archipelago, we tested the hypothesis that strong barriers to gene flow exist in this region. Significant and often large fixation index (FST) values were found between different island populations for the mitochondrial and nuclear markers, suggesting highly restricted gene flow between islands. Some discordance in the location and strength of genetic breaks was observed between the mitochondrial and microsatellite markers. Since early night biting A. farauti individuals occur naturally in all populations, the strong gene flow barriers that we have identified in the Solomon Archipelago lend weight to the hypothesis that the shifts in peak biting time from late to early night have appeared independently in these disconnected island populations. For this reason, we suggest that insecticide impregnated bed nets and indoor residue spraying are unlikely to be effective as control tools against A. farauti occurring elsewhere, and if used, will probably result in peak biting time behavioural shifts similar to that observed in the Solomon Islands.

Multilocus population genetic analysis of the Southwest Pacific malaria vector Anopheles punctulatus

The population structure and history of the cryptic malaria vector species, Anopheles punctulatus (Doenitz), was investigated throughout Papua New Guinea and the Solomon Islands with the aim of detailing genetic subdivisions and the potential for movement through this biogeographically complex region. We obtained larval collections from over 80 sites and utilised a diverse array of molecular markers that evolve through different processes. Individuals were initially identified to species and genotyped using the ribosomal DNA second internal transcribed spacer. DNA sequencing of a single copy nuclear ribosomal protein S9 and the mitochondrial cytochrome oxidase I loci were then investigated and 12 nuclear microsatellite markers were developed and analysed. Our data revealed three genetically distinct populations--one in Papua New Guinea, the second on Buka Island (Bougainville Province, Papua New Guinea), and the third on Guadalcanal Island (Solomon Islands). Genetic differentiation within Papua New Guinea was much lower than that found in studies of other closely related species in the region. The data does suggest that A. punctulatus has undergone a population bottleneck followed by a recent population and range expansion in Papua New Guinea. Humans and regional economic growth may be facilitating this population expansion, as A. punctulatus is able to rapidly occupy human modified landscapes and traverse unsealed roads. We therefore anticipate extensive movement of this species through New Guinea--particularly into the highlands, with a potential increase in malaria frequency in a warming climate--as well as relatively unrestricted gene flow of advantageous alleles that may confound vector control efforts.

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.

Population structure, mitochondrial polyphyly and the repeated loss of human biting ability in anopheline mosquitoes from the southwest Pacific

Australia and New Guinea contain high levels of endemism and biodiversity, yet there have been few evaluations of population-level genetic diversity in fauna occurring throughout the Australo-Papuan region. Using extensive geographical sampling, we examined and compared the phylogenetic relationships, phylogeography and population structure of Anopheles farauti, An. hinesorum and An. irenicus throughout their ranges in the southwest Pacific using mitochondrial (mtDNA COI) and nuclear (ribosomal protein S9 and ribosomal DNA ITS2) loci. Phylogenetic analyses suggest that the ability to utilize humans as hosts has been lost repeatedly, coincident with independent colonizations of the Solomon Islands. As some of the species under investigation transmit malaria in the region, this is a medically important finding. Maximum likelihood and Bayesian phylogenetic analyses of nuclear loci also showed that the three species are monophyletic. However, putative introgression of An. hinesorum mtDNA onto a nuclear background of An. farauti was evident in populations from Queensland, Torres Strait and southern New Guinea. Haplotype networks and pairwise F(ST) values show that there is significant genetic structure within New Guinea and Australia in both An. farauti and An. hinesorum, consistent with a long-term history of low gene flow among populations.

High throughput multiplex assay for species identification of Papua New Guinea malaria vectors: members of the Anopheles punctulatus (Diptera: Culicidae) species group

Malaria and filariasis are transmitted in the Southwest Pacific region by Anopheles punctulatus sibling species including An. punctulatus, An. koliensis, the An. farauti complex 1-8 (includes An. hinesorum [An. farauti 2], An. torresiensis [An. farauti 3]). Distinguishing these species from each other requires molecular diagnostic methods. We developed a multiplex polymerase chain reaction (PCR)-based assay specific for known species-specific nucleotide differences in the internal transcribed spacer 2 region and identified the five species most frequently implicated in transmitting disease (An. punctulatus, An. koliensis, An. farauti 1, An. hinesorum, and An. farauti 4). A set of 340 individual mosquitoes obtained from seven Papua New Guinea provinces representing a variety of habitats were analyzed by using this multiplex assay. Concordance between molecular and morphological diagnosis was 56.4% for An. punctulatus, 85.3% for An. koliensis, and 88.9% for An. farauti. Among 158 mosquitoes morphologically designated as An. farauti, 33 were re-classified by PCR as An. punctulatus, 4 as An. koliensis, 26 as An. farauti 1, 49 as An. hinesorum, and 46 as An. farauti 4. Misclassification results from variable coloration of the proboscis and overlap of An. punctulatus, An. koliensis, the An. farauti 4. This multiplex technology enables further mosquito strain identification and simultaneous detection of microbial pathogens.

Malaria vectors of Papua New Guinea

Understanding malaria transmission in Papua New Guinea (PNG) requires exact knowledge of which Anopheles species are transmitting malaria and is complicated by the cryptic species status of many of these mosquitoes. To identify the malaria vectors in PNG we studied Anopheles specimens from 232 collection localities around human habitation throughout PNG (using CO(2) baited light traps and human bait collections). A total of 22,970mosquitoes were individually assessed using a Plasmodium sporozoite enzyme-linked immunosorbent assay to identify Plasmodiumfalciparum, Plasmodiumvivax and Plasmodiummalariae circumsporozoite proteins. All mosquitoes were identified to species by morphology and/or PCR. Based on distribution, abundance and their ability to develop sporozoites, we identified five species as major vectors of malaria in PNG. These included: Anophelesfarauti, Anopheleshinesorum (incriminated here, to our knowledge, for the first time), Anophelesfarauti 4, Anopheleskoliensis and Anophelespunctulatus. Anopheleslongirostris and Anophelesbancroftii were also incriminated in this study. Surprisingly, An. longirostris showed a high incidence of infections in some areas. A newly identified taxon within the Punctulatus Group, tentatively called An. farauti 8, was also found positive for circumsporozoite protein. These latter three species, together with Anopheleskarwari and Anophelessubpictus, incriminated in other studies, appear to be only minor vectors, while Anophelesfarauti 6 appears to be the major vector in the highland river valleys (>1500m above sea level). The nine remaining Anopheles species found in PNG have been little studied and their bionomics are unknown; most appear to be uncommon with limited distribution and their possible role in malaria transmission has yet to be determined.

Distribution and evolution of the Anopheles punctulatus group (Diptera: Culicidae) in Australia and Papua New Guinea

The members of the Anopheles punctulatus group are major vectors of malaria and Bancroftian filariasis in the southwest Pacific region. The group is comprised of 12 cryptic species that require DNA-based tools for species identification. From 1984 to 1998 surveys were carried out in northern Australia, Papua New Guinea and on islands in the southwest Pacific to determine the distribution of the A. punctulatus group. The results of these surveys have now been completed and have generated distribution data from more than 1500 localities through this region. Within this region several climatic and geographical barriers were identified that restricted species distribution and gene flow between geographic populations. This information was further assessed in light of a molecular phylogeny derived from the ssrDNA (18S). Subsequently, hypotheses have been generated on the evolution and distribution of the group so that future field and laboratory studies may be approached more systematically. This study suggested that the ability for widespread dispersal was found to have appeared independently in species that show niche-specific habitat preference (Anopheles farauti s.s. and A. punctulatus) and conversely in species that showed diversity in their larval habitat (Anopheles farauti 2). Adaptation to the monsoonal climate of northern Australia and southwest Papua New Guinea was found to have appeared independently in A. farauti s.s., A. farauti 2 and Anopheles farauti 3. Shared or synapomorphic characters were identified as saltwater tolerance (A. farauti s.s. and Anopheles farauti 7) and elevational affinities above 1500 m (Anopheles farauti 5, Anopheles farauti 6 and A. farauti 2).

Speciation and distribution of the members of the Anopheles punctulatus (Diptera: Culicidae) group in Papua New Guinea

Mosquito collections were made throughout the mainland of Papua New Guinea to identify the members of the Anopheles punctulatus group present and to determine their distribution. Identification was made using morphology, DNA hybridization, and polymerase chain reaction (PCR)-RFLP analysis. Nine members of the group were identified: An. farauti s.s. Laveran, An. farauti 2, An. koliensis Owen, and An. punctulatus Dönitz, were common and widespread; An. farauti 4 was restricted to the north of the central ranges where it was common; An. farauti 6 was found only in the highlands above 1,000 m; and An. farauti 3, An. sp. near punctulatus and An. clowi Rozeboom & Knight were uncommon and had restricted distributions. Identification of An. koliensis and An. punctulatus using proboscis morphology was found to be unreliable wherever An. farauti 4 occurred. The distribution and dispersal of the members of the An. punctulatus group is discussed in regard to climate, larval habitats, distance from the coast, elevation, and proximity to human habitation.

Descriptions of the Anopheles (Cellia) farauti complex of sibling species (Diptera: Culicidae) in Australia

Descriptions of the three sibling species of the Anopheles farauti complex in Australia, A. farauti Laveran (formerly A. farauti No. 1), A. hinesorum Schmidt sp.n. (formerly A. farauti No. 2) and A. torresiensis Schmidt sp.n. (formerly A. farauti No. 3) are provided. These species form a part of the punctulatus group, which contains the major malaria vectors in the southwest Pacific. Morphological markers are described for adult females, fourth instar larvae and pupae which identify most specimens, and are presented in keys.

Shared salinity tolerance invalidates a test for the malaria vector Anopheles farauti s.s. on Guadalcanal, Solomon Islands [corrected]

Among the Punctulatus Group of Anopheles mosquitoes (Diptera: Culicidae), first-instar larvae of the medically unimportant freshwater Anopheles farauti species No. 7 survives a seawater tolerance test (STT) that was previously thought to be diagnostic for the saltwater-tolerant malaria vector species, An. farauti Laveran s.s. Salt tolerance in these two closely related isomorphic species appears to be a shared derived character within the Farauti Complex. Failure to differentiate An. farauti s.s. from An. farauti No.7 will overestimate potential malaria vector numbers and waste limited larval control resources. Use of the STT should therefore be discontinued on Guadalcanal and other techniques such as allozyme electrophoresis used instead [corrected].

Rediscovery of Anopheles (Cellia) clowi (Diptera: Culicidae), a rarely recorded member of the Anopheles punctulatus group

Anopheline specimens collected in Papua New Guinea were morphologically identified as the rarely recorded Anopheles clowi Rozeboom & Knight. Amplification of the rDNA ITS2 region of this material revealed a fragment of 750 bp confirming its placement in the Anopheles punctulatus group. This group contains 12 species and includes the major malaria vectors in the islands of the southwest Pacific. Digestion of the ITS2 with the restriction enzyme MspI produced restriction fragment-length polymorphism with bands at 380, 300, and 150 bp, a pattern shared by no other members of this group. Phylogenetic analysis involving the sequencing of a 2 kb region of the rDNA 18S gene indicated that An. clowi was monophyletic and basal to the rest of the group and showed considerable independent evolution from the other members. This is the first record of An. clowi in Papua New Guinea and only the third collection of this species since its discovery in 1945.

Ribosomal DNA internal transcribed spacer (ITS2) sequences differentiate Anopheles funestus and An. rivulorum, and uncover a cryptic taxon

Differentiation among the closely related Afrotropical species comprising the Funestus Group is difficult by traditional taxonomic measures. Anopheles rivulorum is the second most abundant and widespread species in the Funestus Group, and is occasionally collected indoors along with the dominant member and major malaria vector, An. funestus. The prospect of misidentification of An. rivulorum as An. funestus prompted the development of a rapid, polymerase chain reaction (PCR)-based method for identifying these two species. The ribosomal internal transcribed spacer 2 (ITS2) was amplified from thirty-five specimens of An. rivulorum collected from the extremes of its range: Eastern Africa (Kenya), Southern Africa (South Africa) and Western Africa (Burkina Faso). The ITS2 region of An. rivulorum ( approximately 380 bp) is sufficiently different in size from the ITS2 of An. funestus ( approximately 700 bp) that these species can be distinguished by agarose gel electrophoresis of PCR products without further manipulation. Comparison of the An. rivulorum and An. funestus ITS2 nucleotide sequences revealed such extensive divergence that meaningful alignment was impossible, except for a 25 bp island near the 5' end. Intraspecific sequence comparisons revealed no variation among An. rivulorum individuals collected from the same country. However, sequence divergence was 2% between specimens from South Africa and Kenya, and nearly tenfold higher ( approximately 19%) between specimens from Burkina Faso and either South Africa or Kenya, an unprecedented level of intraspecific ITS2 divergence in Anopheles. Taken together, these data suggest that the Burkina Faso sample is not An. rivulorum, but rather a cryptic taxon within the Funestus Group.

Shared salinity tolerance invalidates a test for the malaria vector Anopheles farauti s.s. on Guadalcanal, Solomon Islands

Among the Punctulatus Group of Anopheles mosquitoes (Diptera: Culicidae), first-instar larvae of the medically unimportant freshwater Anopheles farauti species No. 7 survives a seawater tolerance test (SST) that was previously thought to be diagnostic for the saltwater-tolerant malaria vector species, An. farauti Laveran s.s. Salt tolerance in these two closely related isomorphic species appears to be a shared derived character within the Farauti Complex. Failure to differentiate An. farauti s.s. from An. farauti No. 7 will overestimate potential malaria vector numbers and waste limited larval control resources. Use of the SST should therefore be discontinued on Guadalcanal and other techniques such as allozyme electrophoresis used instead.

Systematics of malaria vectors with particular reference to the Anopheles punctulatus group

The appearance of groups and complexes of closely related cryptic or sibling species in many of the anopheline taxa has impeded studies on malaria transmission and the evaluation of control strategies which have relied on morphological characters to identify the vector species involved. The advantages of morphological identification are low cost, speed and simplicity, which allow large numbers of specimens to be processed rapidly in the field. The need for accurate identification is crucial, as time and money may be wasted in studying and controlling species of no medical importance. Various techniques such as cross-mating, chromosome studies and allozyme analysis have been developed to resolve problems of identifying sibling species, though none, as yet, can match the speed and simplicity afforded by morphology markers. The latest of these identification methods comes from advances that have been made in DNA-based technology. Although costly and requiring fairly sophisticated laboratory support, methods such as DNA probe hybridisation and PCR are the quickest and most user-friendly to date. The use of DNA has other advantages in the study of intraspecific differences and in providing characters for phylogenetic studies. This review looks at the development of DNA-based techniques for taxonomic and systematic studies of anopheline mosquitoes. The Anopheles punctulatus group of the southwest Pacific is featured as an example of how this technology has been applied and how it has progressed.

Seasonal abundance of Anopheles farauti (Diptera: Culicidae) sibling species in far north Queensland, Australia

In the Cairns area of far north Queensland, Australia, the seasonal abundance of Anopheles farauti Laveran sibling species was studied at 6 locations, representing 3 habitat types, between August 1995 and September 1997. A total of 45,401 An. farauti s.l. was collected using CO2 + octenol baited CDC light traps, and consisted of 29,565 An. farauti No. 2, 14,214 An. farauti No. 3, and 1,622 An. farauti s.s. The relative abundance of all 3 species differed significantly by season and location. An. farauti No.2 was the dominant species except in Cairns, where An. farauti s.s. was most abundant, and at Ninds Creek, where An. farauti No. 3 predominated. The dominant species at each location was present year round, although peaks in seasonal abundance were observed. An. farauti s.s. populations were highest during the wet season (January-April). In lowland freshwater swamp habitats and 1 brackish location, An. farauti No. 2 was more abundant during the wet season. However, at the highland freshwater swamp habitat, populations of An. farauti No. 2 were highest during the late dry season and early wet season (October-December). There was a significant positive correlation of both temperature and rainfall with An. farauti s.s. and An. farauti No. 2 trap collections. There was a negative correlation between An. farauti No. 3 and temperature, indicating that this species may be more abundant during cool weather. Although there were significant relationships among weather variables and An. farauti s.l. collections, correlation values were generally low, indicating that other factors may contribute to variability among An. farauti sibling species trap collections.

A review of the use of ribosomal DNA (rDNA) to differentiate among cryptic Anopheles species

Cryptic species complexes are groups of closely related species that are difficult or impossible to distinguish by morphological traits. These complexes are known from a wide variety of arthropods and are common among the well-studied, medically-important insects. For example, many of the anopheline vectors of malaria parasites are members of cryptic species complexes. Complexes typically include both vector and non-vector species, and two or more member species are often found sympatrically. Until the late 1950, only two such Anopheles complexes were known, the A. gambiae complex from Africa and the A. maculipennis complex from Europe. Today, dozens of Anopheles cryptic species complexes are recognized, and accumulating evidence suggests that most important malaria vectors are likely to be members of such complexes. A variety of methods have been developed for identifying the species of individual specimens from these complexes, although until recently only those based on species-specific allozymes and polytene chromosome inversions were widely used. The limitations inherent in these methods have been circumvented with DNA-based procedures, which are especially useful because both sexes and all developmental stages can be identified, and DNA can be recovered from samples stored by a wide variety of simple methods. Several DNA-based identification techniques have been developed, including hybridization assays based on species-specific repeat sequences, and diagnostic PCR fragments produced either by the use of random PCR primers or by amplifying DNA with primers based on known species-specific sequences. In this review we discuss the relative marks of different methods of cryptic species identification, with emphasis on the use of ribosomal DNA as a target for species-diagnostic PCR assays.

The value of vector-based estimates of malaria transmission

Estimating malaria transmission in the human is fraught with problems of reconciling clinical illness with parasitological status. It follows that there is a role for entomological assessments as an independent outcome variable and as a process indicator. Advances in DNA technology have expanded our capacity to identify vectors rapidly, while immunoassays allow the inoculation rate to be measured simultaneously in a number of villages with a precision 3-fold greater than measurements of vectorial capacity. The rapid specific identification of parasites in vectors has been utilized to estimate survivorship in mosquitoes per extrinsic incubation period (EIP), circumventing the need for estimates of survivorship per feeding cycle, lengths of feeding cycles or the length of the EIP. While lack of accuracy does not universally preclude the utility of estimates of the components of vectorial capacity in serving as relative estimates of transmission, particularly as process indicators, more accurate estimates of these parameters, particularly for density-dependent variables, may diminish the associated bias in their measurement. When this is accomplished, we will come closer to obtaining true rather than relative estimates of transmission.

The Anopheles punctulatus group of mosquitoes in the Solomon Islands and Vanuatu surveyed by allozyme electrophoresis

Four species within the Anopheles punctulatus group of mosquitoes (Diptera: Culicidae) were identified by allozyme analysis of samples collected from thirty-three localities in Guadalcanal, Makira, Malaita, Temotu and Western Provinces in the Solomon Islands and six localities on Efate, Espiritu Santo, Maewo and Malekula Islands in Vanuatu. Three of these species are members of the An.farauti complex. A key is given to identify five species of the An.punctulatus group known to occur in the Solomon Islands using their isoenzyme characteristics. An.farauti No. 1 was widespread in coastal areas of the Solomon Islands and was the only species detected in Vanuatu, including Efate Island (where Faureville is the type locality of An.farauti Laveran sensu stricto). An.farauti No. 2 and An.punctulatus were common in the Solomon Islands in more inland areas. An.farauti No. 7, reported here for the first time, was found as larvae in freshwater at six localities on north Guadalcanal. Three other members of the An.punctulatus group which have been reported previously from the Solomon Islands: An.koliensis, An.renellensis and an electrophoretic variant of An.farauti sensu lato, were not found in our samples. Previously recognized vectors of malaria and bancroftian filariasis in the Solomon Islands are An.farauti No. 1 (i.e. An.farauti s.s.), An.koliensis and An.punctulatus s.s. Adult females of An.farauti No. 2 and An.farauti No. 7 were not attracted to human bait in areas where their larvae occurred, indicating that these two species are not anthropophilic and therefore unlikely to transmit human pathogens.