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.     

Identification of Swedish mosquitoes based on molecular barcoding of the COI gene and SNP analysis

Mosquito‐borne infectious diseases are emerging in many regions of the world. Consequently, surveillance of mosquitoes and concomitant infectious agents is of great importance for prediction and prevention of mosquito‐borne infectious diseases. Currently, morphological identification of mosquitoes is the traditional procedure. However, sequencing of specified genes or standard genomic regions, DNA barcoding, has recently been suggested as a global standard for identification and classification of many different species. Our aim was to develop a genetic method to identify mosquitoes and to study their relationship. Mosquitoes were captured at collection sites in northern Sweden and identified morphologically before the cytochrome c oxidase subunit I (COI) gene sequences of 14 of the most common mosquito species were determined. The sequences obtained were then used for phylogenetic placement, for validation and benchmarking of phenetic classifications and finally to develop a hierarchical PCR‐based typing scheme based on single nucleotide polymorphism sites (SNPs) to enable rapid genetic identification, circumventing the need for morphological characterization. The results showed that exact phylogenetic relationships between mosquito taxa were preserved at shorter evolutionary distances, but at deeper levels, they could not be inferred with confidence using COI gene sequence data alone. Fourteen of the most common mosquito species in Sweden were identified by the SNP/PCR‐based typing scheme, demonstrating that genetic typing using SNPs of the COI gene is a useful method for identification of mosquitoes with potential for worldwide application.     

Nuclear simple sequence repeat markers are superior to DNA barcodes for identification of closely related Rhododendron species on the same mountain

Accurate species delimitation of sampled biological material is critical for a range of studies. Although the DNA barcodes developed in recent years are useful for identifying numerous well differentiated species that have not experienced frequent gene flow, they fail to delimit recently diverged species, especially those with extensive introgressions. Here we use five Rhododendron species growing together on the same mountain as a model system to compare the species delimitation effectiveness of the DNA barcodes (internal transcribed spacer, matK, psbA‐trnH, and rbcL) previously proposed versus 15 pairs of microsatellite markers. Using these markers, we genotyped 129 individuals, which were members of five species according to morphological identification. We identified five simple sequence repeat genetic clusters (independently evolving lineages) corresponding to the morphological identification. However, we found that numerous individuals contained cryptic hybrid introgressions from the other species. The four DNA barcodes could not delimit three out of four closely related species that showed clear morphological differentiation and cryptic introgressions. Even after excluding all cryptic hybrids, two closely related species could not be successfully identified. The low discrimination ability of the DNA barcodes for closely related Rhododendron species could result from two, not mutually exclusive factors: introgressive hybridization and incomplete lineage sorting. Our results highlight the importance of simple sequence repeat markers in delimiting closely related species and identifying cryptic introgressions in the absence of morphological changes.     

Analysis of trapped mosquito excreta as a noninvasive method to reveal biodiversity and arbovirus circulation

Emerging and endemic mosquito-borne viruses can be difficult to detect and monitor because they often cause asymptomatic infections in human or vertebrate animals or cause nonspecific febrile illness with a short recovery waiting period. Some of these pathogens circulate into complex cryptic cycles involving several animal species as reservoir or amplifying hosts. Detection of cases in vertebrate hosts can be complemented by entomological surveillance, but this method is not adapted to low infection rates in mosquito populations that typically occur in low or nonendemic areas. We identified West Nile virus circulation in Camargue, a wetland area in South of France, using a cost-effective xenomonitoring method based on the molecular detection of virus in excreta from trapped mosquitoes. We also succeeded at identifying the mosquito species community on several sampling sites, together with the vertebrate hosts on which they fed prior to being captured using amplicon-based metabarcoding on mosquito excreta without processing any mosquitoes. Mosquito excreta-based virus surveillance can complement standard surveillance methods because it is cost-effective and does not require personnel with a strong background in entomology. This strategy can also be used to noninvasively explore the ecological network underlying arbovirus circulation.     

Modeling Dynamics of Culex pipiens Complex Populations and Assessing Abatement Strategies for West Nile Virus

The primary mosquito species associated with underground stormwater systems in the United States are the Culex pipiens complex species. This group represents important vectors of West Nile virus (WNV) throughout regions of the continental U.S. In this study, we designed a mathematical model and compared it with surveillance data for the Cx. pipiens complex collected in Beaufort County, South Carolina. Based on the best fit of the model to the data, we estimated parameters associated with the effectiveness of public health insecticide (adulticide) treatments (primarily pyrethrin products) as well as the birth, maturation, and death rates of immature and adult Cx. pipiens complex mosquitoes. We used these estimates for modeling the spread of WNV to obtain more reliable disease outbreak predictions and performed numerical simulations to test various mosquito abatement strategies. We demonstrated that insecticide treatments produced significant reductions in the Cx. pipiens complex populations. However, abatement efforts were effective for approximately one day and the vector mosquitoes rebounded until the next treatment. These results suggest that frequent insecticide applications are necessary to control these mosquitoes. We derived the basic reproductive number (ℜ₀) to predict the conditions under which disease outbreaks are likely to occur and to evaluate mosquito abatement strategies. We concluded that enhancing the mosquito death rate results in lower values of ℜ₀, and if ℜ₀<1, then an epidemic will not occur. Our modeling results provide insights about control strategies of the vector populations and, consequently, a potential decrease in the risk of a WNV outbreak.     

Resolving genetic diversity in Australasian Culex mosquitoes: Incongruence between the mitochondrial cytochrome c oxidase I and nuclear acetylcholine esterase 2

Insects that vector pathogens are under constant surveillance in Australasia although the repertoire of genetic markers to distinguish what are often cryptic mosquito species remains limited. We present a comparative assessment of the second exon–intron region of the acetylcholine esterase 2 gene (ace-2) and the mitochondrial DNA cytochrome c oxidase I (COI) using two closely related Australasia mosquitoes Culex annulirostris and Culex palpalis. The COI revealed eight divergent lineages of which four were confirmed with the ace-2. We dissect out the nuclear chromosomal haplotypes of the ace-2 as well as the exon–intron regions by assessing the protein’s tertiary structure to reveal a hypervariable 5’-exon that forms part of an external protein loop and displays a higher polymorphic rate than the intron. We retrace the evolutionary history of these mosquitoes by phylogenetic inference and by testing different evolutionary hypotheses. We conclude that DNA barcoding using COI may overestimate the diversity of Culex mosquitoes in Australasia and should be applied cautiously with support from the nuclear DNA such as the ace-2. Together the COI and ace-2 provide robust evidence for distinct cryptic Culex lineages—one of which correlates exactly with the southern limit of Japanese encephalitis virus activity in Australasia.     

Species richness estimates of Blattodea s.s. (Insecta: Dictyoptera) from northern Guyana vary depending upon methods of species delimitation

Cockroaches (Order: Blattodea) comprise a taxon that, although very abundant in tropical forests, remains largely unstudied. Making sense of the diversity of species is a challenging task hindered by the large numbers of species and the abundance of cryptic or polymorphic forms. Here, we estimated species richness of cockroaches (s.s.) from northern Guyana while applying a method to deal with these confounding factors. We utilized two interpretations of abundance data, the first using only morphological information, and the second using both morphological and genetic barcode information. The two methods of species delimitation greatly influenced the resulting estimates of species richness. When incorporating genetic barcodes, our total species richness estimate decreased by 26%. Our results emphasize the importance of using independent datasets to delimit species boundaries and expert identification of specimens when possible.     

Usefulness and accuracy of MALDI‐TOF mass spectrometry as a supplementary tool to identify mosquito vector species and to invest in development of international database

Arthropod‐borne diseases are important causes of morbidity and mortality. The identification of vector species relies mainly on morphological features and/or molecular biology tools. The first method requires specific technical skills and may result in misidentifications, and the second method is time‐consuming and expensive. The aim of the present study is to assess the usefulness and accuracy of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF MS) as a supplementary tool with which to identify mosquito vector species and to invest in the creation of an international database. A total of 89 specimens belonging to 10 mosquito species were selected for the extraction of proteins from legs and for the establishment of a reference database. A blind test with 123 mosquitoes was performed to validate the MS method. Results showed that: (a) the spectra obtained in the study with a given species differed from the spectra of the same species collected in another country, which highlights the need for an international database; (b) MALDI‐TOF MS is an accurate method for the rapid identification of mosquito species that are referenced in a database; (c) MALDI‐TOF MS allows the separation of groups or complex species, and (d) laboratory specimens undergo a loss of proteins compared with those isolated in the field. In conclusion, MALDI‐TOF MS is a useful supplementary tool for mosquito identification and can help inform vector control.     

Avian Plasmodium lineages found in spot surveys of mosquitoes from 2007 to 2010 at Sakata wetland,Japan: do dominant lineages persist for multiple years?

The ecology and geographical distribution of disease vectors are major determinants of spatial and temporal variations in the transmission dynamics of vector‐borne pathogens. However, there are limited studies on the ecology of vectors that contribute to the natural transmission of most vector‐borne pathogens. Avian Plasmodium parasites are multihost mosquito‐borne pathogens transmitted by multiple mosquito species, which might regulate the diversity and persistence of these parasites. From 2007 to 2010, we conducted entomological surveys at Sakata wetland in central Japan, to investigate temporal variation in mosquito occurrence and prevalence of avian Plasmodium lineages in the mosquito populations. A polymerase chain reaction (PCR)‐based method was used to detect Plasmodium parasites and identify the blood sources of mosquitoes. Culex inatomii and C. pipiens pallens represented 60.0% and 34.8% of 11 mosquito species collected, respectively. Our results showed that the two dominant mosquito species most likely serve as principal vectors of avian Plasmodium parasites during June, which coincides with the breeding season of bird species nesting in the wetland reed beds. Fourteen animal species were identified as blood sources of mosquitoes, with the oriental reed warbler (Acrocephalus orientalis) being the commonest blood source. Although there was significant temporal variation in the occurrence of mosquitoes and prevalence of Plasmodium lineages in the mosquitoes, the dominant Plasmodium lineages shared by the two dominant mosquito species were consistently found at the same time during transmission seasons. Because vector competence cannot be confirmed solely by PCR approaches, experimental demonstration is required to provide definitive evidence of transmission suggested in this study.     

Impact of population age structure on Wolbachia transgene driver efficacy: ecologically complex factors and release of genetically modified mosquitoes

Wolbachia symbionts hold theoretical promise as a way to drive transgenes into insect vector populations for disease prevention. For simplicity, current models of Wolbachia dynamics and spread ignore ecologically complex factors such as the age structure of vector populations and overlapping vector generations. We developed a model including these factors to assess their impact on the process of Wolbachia spread into populations of three mosquito species (Anopheles gambiae, Aedes aegypti and Culex pipiens). Depending on the mosquito species, Wolbachia parameters, released mosquito life stage and initial age structure of the target population, the number of Wolbachia-infected mosquitoes that we predict would need to be released ranged from less than the threshold calculated by the simple model to a 10-30-fold increase. Transgenic releases into age-structured populations, which is an expectation for wild mosquitoes, will be difficult and depending on the circumstances may not be economically or logistically feasible due to the large number of infected mosquitoes that must be released. Our results support the perspective that understanding ecological factors is critical for designing transgenic vector-borne disease control strategies.     

Species diversity of freshwater shrimp in Henan Province,China, based on morphological characters and COI mitochondrial gene

Freshwater shrimp are a rich species group, with a long and problematic taxonomic history attributed to their wide distribution and similar morphological characteristics. Shrimp diversity and species identification are important cornerstones for fisheries management. However, identification based on morphological characteristics is a difficult task for a nonspecialist. Abundant freshwater shrimp species are distributed in the waters of Henan Province, but investigations of freshwater shrimp are limited in this region, especially concerning molecular features. Here, we combined morphology and DNA barcodes to reveal the species diversity of freshwater shrimp in Henan province. A total of 1,200 freshwater shrimp samples were collected from 46 sampling sites, and 222 samples were chosen for further microscopic examination and molecular delimitation. We used tree‐based methods (NJ, ML, and bPTP) and distance‐based methods (estimation of the paired genetic distances and ABGD) to delimit species. The results showed that there were nine morphospecies based on morphological characteristics; all could effectively be defined by molecular methods, among which bPTP and ABGD defined 13 and 8 MOTUs, respectively. The estimation of the paired genetic distances of K2P and the p‐distances had similar results. Mean K2P distances and p‐distances within species were both equal to 1.2%. The maximum intraspecific genetic distances of all species were less than 2%, with the exception of Palaemon modestus and M. maculatum. Various analyses have shown that P. modestus and M. maculatum have a large genetic differentiation, which may indicate the existence of cryptic species. By contrast, DNA barcoding could unambiguously discriminate 13 species and detect cryptic diversity. Our results demonstrate the high efficiency of DNA barcoding to delimit freshwater shrimp diversity and detect the presence of cryptic species.     

Empirical?Evidence?Supporting Frequent Cryptic Speciation in Epiphyllous Liverworts:?A Case Study of the Cololejeunea lanciloba Complex

Cryptic species are frequently recovered in plant lineages, and considered an important cause for divergent of morphological disparity and species diversity. The identification of cryptic species has important implications for the assessment of conservation needs of species aggregates. The mechanisms and processes of the origin of cryptic species diversity are still poorly understand based on the lack of studies especially in context of environment factors. Here we explored evidence for cryptic species within the epiphyllous liverworts Cololejeunea lanciloba complex based on two loci, the plastid trnL-F region and the nuclear ribosomal ITS region. Several analytic approaches were employed to delimit species based on DNA sequence variation including phylogenetic reconstruction, statistical parsimony networks analysis and two recently introduced species delimitation criteria: Rosenberg’s reciprocal monophyly and Rodrigo’s randomly distinct. We found evidence for thirteen genetically distinct putative species, each consisting of more than one haplotype, rather than four morphologically-circumscribed species. The results implied that the highly conserved phenotypes are not congruent with the genetic differentiation, contributing to incorrect assessments of the biodiversity of epiphyllous liverworts. We hypothesize that evolution of cryptic species recovered may be caused by selection of traits critical to the survival in epiphyllous habitats combined with limited developmental options designed in the small body.     

Mosquito distribution in a saltmarsh: determinants of eggs in a variable environment

Two saltmarsh mosquitoes dominate the transmission of Ross River virus (RRV, Togoviridae: Alphavirus), one of Australia's most prominent mosquito‐borne diseases. Ecologically, saltmarshes vary in their structure, including habitat types, hydrological regimes, and diversity of aquatic fauna, all of which drive mosquito oviposition behavior. Understanding the distribution of vector mosquitoes within saltmarshes can inform early warning systems, surveillance, and management of vector populations. The aim of this study was to identify the distribution of Ae. camptorhynchus, a known vector for RRV, across a saltmarsh and investigate the influence that other invertebrate assemblage might have on Ae. camptorhynchus egg dispersal. We demonstrate that vegetation is a strong indicator for Ae. camptorhynchus egg distribution, and this was not correlated with elevation or other invertebrates located at this saltmarsh. Also, habitats within this marsh are less frequently inundated, resulting in dryer conditions. We conclude that this information can be applied in vector surveillance and monitoring of temperate saltmarsh environments and also provides a baseline for future investigations into understanding mosquito vector habitat requirements.     

Evidence for a conspecific relationship between two morphologically and cytologically different forms of Korean Anopheles pullus mosquito

Despite the medical importance of anopheline mosquitoes as vectors of Korean vivax malaria, differentiation between Korean anopheline mosquitoes by traditional morphological taxonomic criteria is difficult. An. yatsushiroensis is the second most common Anopheles mosquito species in Korea and a possible vector of Korean vivax malaria together with An. sinensis, the predominant anopheline species. Recently, An. yatsushiroensis has been declared a synonym of An. pullus, based on comparisons of egg morphology and adult progeny, although they differ in ecology and morphology. To verify the species status of these two ambiguous forms, we established isofemale lines of Korean An. pullus and An. yatsushiroensis (An. pullus form yatsushiroensis) mosquitoes and investigated their genetic relationship by metaphase karyotype analysis, comparing the DNA sequences of rDNA internal transcribed spacer 2 (ITS2) and mitochondrial cytochrome c oxidase subunits I (COI) and II (COII), and by hybridization experiments. Two isofemale lines had differently shaped X and Y chromosomes. However reciprocal crosses between them yielded viable progeny with completely synaptic salivary gland polytene chromosomes. DNA analyses also strongly supported their conspecificity. The two strains also showed great sequence similarity in the ITS2, COI and COII regions (variation rate = 0.0 to 0.8%). Based on these findings, we conclude that the two forms, though differing distinctly in morphological, cytological and ecological traits, remain interfertile.     

Effective mosquito and arbovirus surveillance using metabarcoding

Effective vector and arbovirus surveillance requires timely and accurate screening techniques that can be easily upscaled. Next‐generation sequencing (NGS) is a high‐throughput technology that has the potential to modernize vector surveillance. When combined with DNA barcoding, it is termed ‘metabarcoding.’ The aim of our study was to establish a metabarcoding protocol to characterize pools of mosquitoes and screen them for virus. Pools contained 100 morphologically identified individuals, including one Ross River virus (RRV) infected mosquito, with three species present at different proportions: 1, 5, 94%. Nucleic acid extracted from both crude homogenate and supernatant was used to amplify a 269‐bp section of the mitochondrial cytochrome c oxidase subunit I (COI) locus. Additionally, a 67‐bp region of the RRV E2 gene was amplified from synthesized cDNA to screen for RRV. Amplicon sequencing was performed using an Illumina MiSeq, and bioinformatic analysis was performed using a DNA barcode database of Victorian mosquitoes. Metabarcoding successfully detected all mosquito species and RRV in every positive sample tested. The limits of species detection were also examined by screening a pool of 1000 individuals, successfully identifying the species and RRV from a single mosquito. The primers used for amplification, number of PCR cycles and total number of individuals present all have effects on the quantification of species in mixed bulk samples. Based on the results, a number of recommendations for future metabarcoding studies are presented. Overall, metabarcoding shows great promise for providing a new alternative approach to screening large insect surveillance trap catches.     

Direct PCR of indigenous and invasive mosquito species: a time‐ and cost‐effective technique of mosquito barcoding

Millions of people die each year as a result of pathogens transmitted by mosquitoes. However, the morphological identification of mosquito species can be difficult even for experts. The identification of morphologically indistinguishable species, such as members of the Anopheles maculipennis complex (Diptera: Culicidae), and possible hybrids, such as Culex pipiens pipiens/Culex pipiens molestus (Diptera: Culicidae), presents a major problem. In addition, the detection and discrimination of newly introduced species can be challenging, particularly to researchers without previous experience. Because of their medical importance, the clear identification of all relevant mosquito species is essential. Using the direct polymerase chain reaction (PCR) method described here, DNA amplification without prior DNA extraction is possible and thus species identification after sequencing can be achieved. Different amounts of tissue (leg, head; larvae or adult) as well as different storage conditions (dry, ethanol, ?20 and ?80 °C) and storage times were successfully applied and showed positive results after amplification and gel electrophoresis. Overall, 28 different indigenous and non‐indigenous mosquito species were analysed using a gene fragment of the COX1 gene for species differentiation and identification by sequencing this 658‐bp fragment. Compared with standard PCR, this method is time‐ and cost‐effective and could thus improve existing surveillance and control programmes.     

Ribosomal DNA sequence variation among sympatric strains of the Cyclotella meneghiniana complex (Bacillariophyceae) reveals cryptic diversity

Cyclotella meneghiniana Kützing is one of the most commonly found and intensively studied freshwater diatom species. However, it is considered taxonomically problematic because of its unusually wide ecological range and large frustule ultrastructural variation. As part of a study of morphological and genetic variation in this morphospecies, we surveyed nucleotide variation in the hypervariable D1/D2 regions of the 28S rDNA, in the ribosomal internal transcribed spacer region (containing ITS1, the 5.8S rDNA and ITS2) and in the 18S rDNA in a collection of 20 sympatric strains. High genetic variability and strong indications of genetic structure among the Cyclotella meneghiniana strains were found. Representatives of four genetically distinct--apparently reproductively isolated--groups were revealed among them. The random distribution of ITS variation within these four groups indicated that the genetic structure in Cyclotella meneghiniana can probably be explained by the presence of cryptic sexual species rather than by the lack of allogamous sexual reproduction. The morphological features traditionally used for species identification in this group cannot distinguish these putative cryptic species.     

Cryptic or pseudocryptic: can morphological methods inform copepod taxonomy? An analysis of publications and a case study of the Eurytemora affinis species complex

Interest in cryptic species has increased significantly with current progress in genetic methods. The large number of cryptic species suggests that the resolution of traditional morphological techniques may be insufficient for taxonomical research. However, some species now considered to be cryptic may, in fact, be designated pseudocryptic after close morphological examination. Thus the “cryptic or pseudocryptic” dilemma speaks to the resolution of morphological analysis and its utility for identifying species. We address this dilemma first by systematically reviewing data published from 1980 to 2013 on cryptic species of Copepoda and then by performing an in‐depth morphological study of the former Eurytemora affinis complex of cryptic species. Analyzing the published data showed that, in 5 of 24 revisions eligible for systematic review, cryptic species assignment was based solely on the genetic variation of forms without detailed morphological analysis to confirm the assignment. Therefore, some newly described cryptic species might be designated pseudocryptic under more detailed morphological analysis as happened with Eurytemora affinis complex. Recent genetic analyses of the complex found high levels of heterogeneity without morphological differences; it is argued to be cryptic. However, next detailed morphological analyses allowed to describe a number of valid species. Our study, using deep statistical analyses usually not applied for new species describing, of this species complex confirmed considerable differences between former cryptic species. In particular, fluctuating asymmetry (FA), the random variation of left and right structures, was significantly different between forms and provided independent information about their status. Our work showed that multivariate statistical approaches, such as principal component analysis, can be powerful techniques for the morphological discrimination of cryptic taxons. Despite increasing cryptic species designations, morphological techniques have great potential in determining copepod taxonomy.     

Fusing multi-season UAS images with convolutional neural networks to map tree species in Amazonian forests

Remote sensing images obtained by unoccupied aircraft systems (UAS) across different seasons enabled capturing of species-specific phenological patterns of tropical trees. The application of UAS multi-season images to classify tropical tree species is still poorly understood. In this study, we used RGB images from different seasons obtained by a low-cost UAS and convolutional neural networks (CNNs) to map tree species in an Amazonian forest. Individual tree crowns (ITC) were outlined in the UAS images and identified to the species level using forest inventory data. The CNN model was trained with images obtained in February, May, August, and November. The classification accuracy in the rainy season (November and February) was higher than in the dry season (May and August). Fusing images from multiple seasons improved the average accuracy of tree species classification by up to 21.1 percentage points, reaching 90.5%. The CNN model can learn species-specific phenological characteristics that impact the classification accuracy, such as leaf fall in the dry season, which highlights its potential to discriminate species in various conditions. We produced high-quality individual tree crown maps of the species using a post-processing procedure. The combination of multi-season UAS images and CNNs has the potential to map tree species in the Amazon, providing valuable insights for forest management and conservation initiatives.