Identification of Nearctic black flies using DNA barcodes (Diptera: Simuliidae)

Co-occurrence of dual lineages within Simulium (Gomphostilbia) atratum De Meijere in the Indonesian Archipelago along Wallace's Line

Mitochondrial cytochrome c oxidase subunit I (COI) sequences were utilized to infer the population genetic structure of Simulium (Gomphostilbia) atratum De Meijere, an endemic simulid species to Indonesia. Both median-joining haplotype network and maximum-likelihood tree revealed two genetic lineages (A and B) within the species, with an overlap distribution in Lombok, which is situated along Wallace's line. Genetic differentiation and gene flow with varying frequencies (FST = 0.02-0.967; Nm = 0.01-10.58) were observed between populations of S. (G.) atratum, of which population pairs of different lineages showed high genetic differentiation. Notably, the high genetic distance of up to 5.92 % observed within S. (G.) atratum in Lombok was attributed to the existence of two genetically distinct lineages. The co-occurrence of distinct lineages in Lombok indicated that Wallace's line did not act as faunistic border for S. (G.) atratum in the present study. Moreover, both lineages also exhibited unimodal distributions and negative values of neutrality tests, suggesting a pattern of population expansion. The expansion and divergence time estimation suggested that the two lineages of S. (G.) atratum diverged and expanded during the Pleistocene era in Indonesia.

Comparative Study of Potential Habitats for Simulium qinghaiense (Diptera: Simuliidae) in the Huangshui River Basin, Qinghai-Tibet Plateau: An Analysis Using Four Ecological Niche Models and Optimized Approaches

The Huangshui River, a vital tributary in the upper reaches of the Yellow River within the eastern Qinghai-Tibet Plateau, is home to the endemic black fly species S. qinghaiense. In this study, we conducted a systematic survey of the distribution of the species in the Huangshui River basin, revealing its predominant presence along the river's main stem. Based on four ecological niche models-MaxEnt with parameter optimization; GARP; BIOCLIM; and DOMAIN-we conduct a comparative analysis; evaluating the accuracy of AUC and Kappa values. Our findings indicate that optimizing parameters significantly improves the MaxEnt model's predictive accuracy by reducing complexity and overfitting. Furthermore, all four models exhibit higher accuracy compared to a random model, with MaxEnt demonstrating the highest AUC and Kappa values (0.9756 and 0.8118, respectively), showcasing significant superiority over the other models (p < 0.05). Evaluation of predictions from the four models elucidates that potential areas of S. qinghaiense in the Huangshui River basin are primarily concentrated in the central and southern areas, with precipitation exerting a predominant influence. Building upon these results, we utilized the MaxEnt model to forecast changes in suitable areas and distribution centers during the Last Interglacial (LIG), Mid-Holocene (MH), and future periods under three climate scenarios. The results indicate significantly smaller suitable areas during LIG and MH compared to the present, with the center of distribution shifting southeastward from the Qilian Mountains to the central part of the basin. In the future, suitable areas under different climate scenarios are expected to contract, with the center of distribution shifting southeastward. These findings provide important theoretical references for monitoring, early warning, and control measures for S. qinghaiense in the region, contributing to ecological health assessment.

Fast-evolving nuclear genes as barcoding markers for black flies (Diptera: Simuliidae) in Thailand

Rapid and accurate identification is a prerequisite for the study of all aspects of species, particularly for pests and vectors. Black flies are economically significant blood-sucking insects, as many species are pests and vectors that transmit parasites to humans and other animals. We examined the efficiency of two fast-evolving nuclear genes, elongator complex protein 1 (ECP1) and big zinc finger (BZF), for identifying 13 nominal species in three species-groups of black flies, the Simulium multistriatum, S. striatum, and S. tuberosum groups, in Thailand where the mitochondrial cytochrome c oxidase I (COI) gene has not been successful for differentiating many nominal species. ECP1 gene sequences were highly effective for identification, with >96% (181 of 188) of the specimens correctly identified. Unsuccessful identifications based on ECP1 were between S. nakhonense and S. chiangmaiense, which are members of the S. striatum species-group, whereas all identifications of nominal species of the S. multistriatum and S. tuberosum species-groups were successful. In contrast, BZF had successful rates for the S. striatum species-group, with >93% (71 of 76) of the specimens correctly identified. This gene also successfully assigned unknown larvae of the S. striatum group to species. Phylogenetic analyses and molecular species delimitations based on the BZF gene uncovered cryptic diversity in two nominal species, S. nakhonense and S. wangkwaiense, which will require resolution through further study.

Cryptic Species in Ecotoxicology

The advent of genetic methods has led to the discovery of an increasing number of species that previously could not be distinguished from each other on the basis of morphological characteristics. Even though there has been an exponential growth of publications on cryptic species, such species are rarely considered in ecotoxicology. Thus, the particular question of ecological differentiation and the sensitivity of closely related cryptic species is rarely addressed. Tackling this question, however, is of key importance for evolutionary ecology, conservation biology, and, in particular, regulatory ecotoxicology. At the same time, the use of species with (known or unknown) cryptic diversity might be a reason for the lack of reproducibility of ecotoxicological experiments and implies a false extrapolation of the findings. Our critical review includes a database and literature search through which we investigated how many of the species most frequently used in ecotoxicological assessments show evidence of cryptic diversity. We found a high proportion of reports indicating overlooked species diversity, especially in invertebrates. In terrestrial and aquatic realms, at least 67% and 54% of commonly used species, respectively, were identified as cryptic species complexes. The issue is less prominent in vertebrates, in which we found evidence for cryptic species complexes in 27% of aquatic and 6.7% of terrestrial vertebrates. We further exemplified why different evolutionary histories may significantly determine cryptic species' ecology and sensitivity to pollutants. This in turn may have a major impact on the results of ecotoxicological tests and, consequently, the outcome of environmental risk assessments. Finally, we provide a brief guideline on how to deal practically with cryptic diversity in ecotoxicological studies in general and its implementation in risk assessment procedures in particular. Environ Toxicol Chem 2023;42:1889-1914. © 2023 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.

From bites to barcodes: uncovering the hidden diversity of black flies (Diptera: Simuliidae) in Vietnam

BACKGROUND

Prompt and precise identification of black flies (Simuliidae) is crucial, given their biting behaviour and significant impact on human and animal health. To address the challenges presented by morphology and chromosomes in black fly taxonomy, along with the limited availability of molecular data pertaining to the black fly fauna in Vietnam, this study employed DNA-based approaches. Specifically, we used mitochondrial and nuclear-encoded genes to distinguish nominal species of black flies in Vietnam.

METHODS

In this study, 135 mitochondrial cytochrome c oxidase subunit I (COI) sequences were established for 45 species in the genus Simulium in Vietnam, encompassing three subgenera (Gomphostilbia, Nevermannia, and Simulium), with 64 paratypes of 27 species and 16 topotypes of six species. Of these COI sequences, 71, representing 27 species, are reported for the first time.

RESULTS

Combined with GenBank sequences of specimens from Malaysia, Myanmar, Thailand, and Vietnam, a total of 234 DNA barcodes of 53 nominal species resulted in a 71% success rate for species identification. Species from the non-monophyletic Simulium asakoae, S. feuerborni, S. multistriatum, S. striatum, S. tuberosum, and S. variegatum species groups were associated with ambiguous or incorrect identifications. Pairwise distances, phylogenetics, and species delimitation analyses revealed a high level of cryptic diversity, with discovery of 15 cryptic taxa. The current study also revealed the limited utility of a fast-evolving nuclear gene, big zinc finger (BZF), in discriminating closely related, morphologically similar nominal species of the S. asakoae species group.

CONCLUSION

This study represents the first comprehensive molecular genetic analysis of the black fly fauna in Vietnam to our knowledge, providing a foundation for future research. DNA barcoding exhibits varying levels of differentiating efficiency across species groups but is valuable in the discovery of cryptic diversity.

DNA barcoding of black flies (Diptera: Simuliidae) in Indonesia

BACKGROUND

DNA barcoding is a valuable taxonomic tool for rapid and accurate species identification and cryptic species discovery in black flies. Indonesia has 143 nominal species of black flies, but information on their biological aspects, including vectorial capacity and biting habits, remains underreported, in part because of identification problems. The current study represents the first comprehensive DNA barcoding of Indonesian black flies using mitochondrial cytochrome c oxidase subunit I (COI) gene sequences.

METHODS

Genomic DNA of Indonesian black fly samples were extracted and sequenced, producing 86 COI sequences in total. Two hundred four COI sequences, including 118 GenBank sequences, were analysed. Maximum likelihood (ML) and Bayesian inference (BI) trees were constructed and species delimitation analyses, including ASAP, GMYC and single PTP, were performed to determine whether the species of Indonesian black flies could be delineated. Intra- and interspecific genetic distances were also calculated and the efficacy of COI sequences for species identification was tested.

RESULTS

The DNA barcodes successfully distinguished most morphologically distinct species (> 80% of sampled taxa). Nonetheless, high maximum intraspecific distances (3.32-13.94%) in 11 species suggested cryptic diversity. Notably, populations of the common taxa Simulium (Gomphostilbia) cheongi, S. (Gomphostilbia) sheilae, S. (Nevermannia) feuerborni and S. (Simulium) tani in the islands of Indonesia were genetically distinct from those on the Southeast Asian mainland (Malaysia and Thailand). Integrated morphological, cytogenetic and nuclear DNA studies are warranted to clarify the taxonomic status of these more complex taxa.

CONCLUSIONS

The findings showed that COI barcoding is a promising taxonomic tool for Indonesian black flies. The DNA barcodes will aid in correct identification and genetic study of Indonesian black flies, which will be helpful in the control and management of potential vector species.

Molecular circumscription of the blackfly Simulium oyapockense from South America

Problems related to the identity of Simuliidae species are impediments to effective disease control in Amazonia. Some of these species, such as Simulium oyapockense Floch & Abonnenc, 1946 (Diptera: Simuliidae), are vectors of the organisms that cause onchocerciasis and mansonellosis diseases. This blackfly species has a wide distribution in South America, and it is suspected of being a complex of cryptic species. The aim of this study is to characterize the nominal species S. oyapockense using partial COI gene sequences. Seven populations of S. oyapockense (morphologically identified) were analysed, including one from its type-locality. The other six populations were collected in Brazil and in Argentina. A taxon collected in Amazonas state, Brazil, with adults similar to S. oyapockense but with distinct pupae, was also included in the analysis (Simulium 'S'). The nominal species S. oyapockense is circumscribed, and its geographical distribution is restricted to areas north of the Amazon River. Populations of S. oyapockense s.l. collected south of the Amazon River comprise a species complex that needs to be evaluated using integrative taxonomy. Simulium 'S' represents a species with unique morphological and molecular characteristics. Distinguishing cryptic species is a prerequisite for reducing the taxonomic impediment, especially in medically important taxa.

North–South Differentiation of Black Flies in the Western Cordillera of North America: A New Species of Prosimulium (Diptera: Simuliidae)

Glaciation has been a powerful determiner of species distributions and the genetic structure of populations. Contemporary distributions of many organisms in North America’s Western Cordillera reflect the influence of Pleistocene glaciation. We identified a pattern of north–south differentiation in the genus Prosimulium of western North America, which reflects the separation of northern and southern populations by the North American Ice Sheet during the Pleistocene Epoch. The taxonomic implication is that new species exist within nominal species, requiring formal description or revalidation of names currently in synonymy. We morphologically and cytogenetically examined populations of one nominal species of black fly, Prosimulium esselbaughi Sommerman, over its known range from Alaska south to California and Colorado. Chromosomal and morphological evidence supports the presence of two species, P. esselbaughi sensu stricto from Alaska to at least southern British Columbia, and a new species, Prosimulium supernum in the central Rocky Mountains and high Sierra Nevada range of the United States. The new species is described in all life stages above the egg, along with its polytene chromosomes. The existence of differentiated populations of other nominal species of black flies in northern and southern North America provides a system for investigating possible co-differentiation of vectors and parasites.

Chromosomes as Barcodes: Discovery of a New Species of Black Fly (Diptera: Simuliidae) from California, USA

One of the most popular tools for species discovery and resolution is the DNA barcode, typically based on the cytochrome c oxidase I (COI) gene. However, other non-genic barcodes are available for Diptera. The banding sequence of polytene chromosomes in some dipteran cells, particularly of the larval silk glands, can provide a unique species barcode. We used the sequence of bands to reveal a new species of black fly in the Simulium (Boreosimulium) annulus species group from California, USA. To further characterize the species and provide more integrated taxonomy, we morphologically described all life stages above the egg, formally named the species Simulium ustulatum n. sp., and provided a conventional COI barcode. The COI barcode confirmed the chromosomal and morphological evidence that the species is a new member of the S. annulus group, and enabled identification of the larva and female, which are structurally similar to those of other species. The chromosomal barcode shows that this species has the most rearranged complement, compared with the eight other North American members of its species group, with up to 12 times the number of fixed rearrangements. Up to six chromosomal rearrangements, including autosomal polymorphisms and sex-linked phenomena, are shared with other members of the group. The most unique and conspicuous chromosomal feature of this new species is a large, pale-staining chromocenter from which the six chromosomal arms radiate. The distribution of this univoltine species in lowland rivers of California's Central Valley could make it vulnerable, given climate change and increasing land development.

Associating life stages and sexes of Nearctic Polycentropus Curtis, 1835 (Trichoptera: Polycentropodidae) using mitochondrial DNA barcoding

Alpha taxonomy of caddisflies (order Trichoptera) is based primarily on male genital morphology. As such, associations of adult females and other life stages typically require conclusive association with the species' identifiable male. The aim of this study was to use molecular methods to associate females and larvae of Polycentropus species represented in the Nearctic. Analysis of mtCOI sequences using distance- and tree-based methods resulted in the association of larvae for 14 species of Polycentropus (P. alabamensis Hamilton, Harris & Lago, 1990, P. blicklei Ross & Yamamoto 1965, P. carlsoni Morse 1971, P. carolinensis Banks 1905, P. colei Ross 1941, P. confusus Hagen 1861, P. denningi Smith 1962, P. elarus Ross 1944, P. gertschi Denning 1950, Polycentropus halidus Milne 1936, P. maculatus Banks 1908, P. pentus Ross 1941, P. rickeri Yamamoto 1966, and P. variegatus Banks 1900) and females for 2 species (P. carolinensis and P. chelatus Ross & Yamamoto 1965). Searches for, and descriptions of, diagnostic morphological characters for these previously unidentifiable life forms are now possible. The identity of the larva of P. centralis Banks, 1914 is confirmed and some interesting phylogenetic relationships and a possible cryptic species and potential synonyms are implied in the results. Targets for future immature- and female-male associations are discussed along with a preliminary assessment of morphological differences among larvae.

Surveillance along the Rio Grande during the 2020 Vesicular Stomatitis Outbreak Reveals Spatio-Temporal Dynamics of and Viral RNA Detection in Black Flies

Vesicular stomatitis virus (VSV) emerges periodically from its focus of endemic transmission in southern Mexico to cause epizootics in livestock in the US. The ecology of VSV involves a diverse, but largely undefined, repertoire of potential reservoir hosts and invertebrate vectors. As part of a larger program to decipher VSV transmission, we conducted a study of the spatiotemporal dynamics of Simulium black flies, a known vector of VSV, along the Rio Grande in southern New Mexico, USA from March to December 2020. Serendipitously, the index case of VSV-Indiana (VSIV) in the USA in 2020 occurred at a central point of our study. Black flies appeared soon after the release of the Rio Grande’s water from an upstream dam in March 2020. Two-month and one-year lagged precipitation, maximum temperature, and vegetation greenness, measured as Normalized Difference Vegetation Index (NDVI), were associated with increased black fly abundance. We detected VSIV RNA in 11 pools comprising five black fly species using rRT-PCR; five pools yielded a VSIV sequence. To our knowledge, this is the first detection of VSV in the western US from vectors that were not collected on premises with infected domestic animals.

Integrative taxonomy uncovers a new Culicoides (Diptera: Ceratopogonidae) biting midge species from Thailand

Fully understanding biodiversity often requires an integrated approach especially for small insects because species diagnostic morphological characters are limited. In this study, morphological characters and DNA barcodes were used to examine previously recognized genetically divergent lineages detected in the biting midge, Culicoides arakawae (Arakawa), from Thailand. Morphological examinations revealed that specimens belonging to one lineage are morphologically different from C. arakawae in shape of the paramere in males, and in the leg color pattern of both sexes. Therefore, a formal description is provided for this new species, Culicoides mahasarakhamense sp. nov. Based on morphological characters including a large and shallow palpal pit, one sac like spermatheca and male with parameres bent at base with large basal knob, the new species was assigned into the subgenus Meijerehelea Wirth and Hubert. Morphological differentiation including wing pattern and shape of spermatheca of the new species are discussed and compared with other members of this subgenus. Mitochondrial cytochrome c oxidase I sequence analysis indicated that this new species is different from other members of the subgenus Meijerehelea with minimum interspecific genetic divergence of 3.92%. Automatic Barcode Gap Discovery species delimitation analysis also supported the recognition of a new species. Phylogenetic analyses revealed that the new species is closely related to C. arakawae, consistent with morphological similarity of these species. Results of this study highlight the necessity of using integrated approach for Culicoides taxonomy.

The biology of Simulium noelleri and Simulium dolini: morphological, ecological and molecular data

Molecular genetic research has revolutionized the taxonomy and systematics of the Simuliidae family. Simulium noelleri Friederichs, 1920 is a species of blackfly, common in the Holarctic, reported for 33 countries. In 1954, Topchiev recorded it in Ukraine for the first time. Simulium dolini Usova et Sukhomlin, 1989 has been recorded at the borders of Ukraine and Belarus. It was described for the first time by Usova and Sukhomlin in 1989 from the collection from the territory of Volyn region in 1985. Usova and Sukhomlin, Yankovsky, Adler state that S. noelleri and S. dolini are different species by the morphological characteristics that differ in all phases of development. Adults differ in the structure of the genital appendages, palps, the margin and shape of the face and forehead, the colour of the legs; the larva – in the pattern on the frontal capsule, the number of rays in the fans, mandibular teeth and the hypostoma, the structure of the hind organ of attachment; pupae – in the branching way of gills. Molecular data are becoming an increasingly important tool in insect taxonomy. Therefore, we had to check that these two closely related species also have genetic difference. The development of S. noelleri and S. dolini was studied in four small rivers of Volyn region, Ukraine (Chornohuzka, Konopelka, Putylivka, Omelyanivka) in the period from 2017 to 2019. During initial processing of insect samples, we used the standard protocols EPPO PM7/129. We obtained the nucleotide sequence of S. dolini. It was proved that the populations of S. noelleri and S. dolini from medium and small rivers of Volyn differ in biological, morphological, behavioural and genetic characteristics. Comparison of the species S. noelleri with the data of the GenBank confirms the identification of three distinct morphotypes from Volyn, Great Britain and Canada. As a result of the conducted researches, it was confirmed that two close species of S. dolini and S. noelleri from the noelleri species group differ in the structure of mitochondrial DNA, which confirms their independent taxonomic status. Additional studies comprising more individuals from larger areas of Europe are required to verify the taxonomic position of these two species.

Genetic variation, DNA barcoding and blood meal identification of Culicoides Latreille biting midges (Diptera: Ceratopogonidae) in Thailand

Biting midges of the genus Culicoides Latreille are blood sucking insects of medical and veterinary importance. Many species are vectors of disease agents transmitted to humans and other animals. Therefore, rapid and accurate species identification is essential for appreciation of all aspects of these insects. In this study, DNA barcode efficacy and molecular identification of host blood sources were examined in biting midges from Thailand. A total of 203 barcoding sequences were obtained from 16 Culicoides taxa. Intraspecific genetic divergence varied from 0.28% to 9.90% for specimens collected in Thailand. Despite this high level of genetic variation, DNA barcode identifications in the Barcoding of Life Data System had a considerable success rate (90%). Phylogenetic analyses and distance-based species delimitation methods indicated the possibility of cryptic species in four taxa, namely, Culicoides actoni Smit, C. arakawae Arakawa, C. huffi Causey and C. jacobsoni Macfie. Further investigations will be required to examine the species status of these lineages. Host blood meal identifications from 42 blood engorged females of 10 Culicoides taxa revealed three animal hosts: chicken, cattle and buffalo. Most of this information agrees with previous knowledge but this is the first report of C. actoni, C. fulvus and C. huffi feeding on chicken.

Foretelling the Phenotype of a Genomic Sequence

Estimating phenotypic features (physical and biochemical traits) in a biological organism from their genomic sequence alone and/or environmental conditions has major applications in anthropological paleontology and criminal forensics, for example. To what extent do genomic sequences generally and causally determine phenotypic features of organisms, environmental conditions aside? We present results of two studies, one in blackfly (Insecta:Diptera:Simuliidae) larvae in two species (Simulium ignescens and S. tunja) with four phenotypic features, including the area and spot pattern of the cephalic apotome (in the form of a latin cross on the dorsal side of the head), the postgenal cleft (area under the head on the ventral side) and general body color in larva specimens; the second in strains of Arabidopsis thaliana. They establish that a substantial component of these phenotypic features (over 75 percent) are at least logically inferable, if not causally determined, by genomic fragments alone, despite the fact that these phenotypic features are not 100 percent determined entirely by genetic traits. These results suggest that it is possible to infer the genetic contribution in the determination of specific phenotypic features of a biological organism, without recourse to the causal chain of metabolomics and proteomic events leading to them from genomic sequences.

New records and DNA barcoding of deer flies, Chrysops (Diptera: Tabanidae) in Thailand

Chrysops spp. or deer flies (Diptera: Tabanidae) are hematophagous flies of medical and veterinary importance and some species are important vectors of Trypanosoma evansi, the causative agent of surra in Thailand. However, data regarding deer fly species and their molecular identification are limited. Accurate species identification will indicate the appropriate control measures. In this study, an entomological survey of deer flies from different sites in Thailand between May 2018 and June 2019 were conducted. In addition, mitochondrial cytochrome oxidase subunit I (COI) barcoding region was used for species identification. A total of 82 females were collected and 6 species were identified. Of these, three species are new records for Thailand: C. designatus, C. fuscomarginalis and C. vanderwulpi bringing the species total found in Thailand to nine. The COI sequences revealed an intraspecific divergence of 0.0%-2.65% and an interspecific divergence of 7.03%-13.47%. Phylogenetic analysis showed that all deer fly species were clearly separated into distinct clusters according to morphologically identified species. These results indicated that COI barcodes were capable in discriminating between deer fly species on the basis of the barcoding gap and phylogenetic analysis. Therefore, DNA barcoding is a valuable tool for species identification of deer flies in Thailand.

Black flies (Diptera: Simuliidae) of the Aras River Basin: Species composition and floral visitation

Black flies are insects of medical, veterinary, and environmental significance. Historically, they have attacked humans and caused simuliotoxicosis in livestock in the Aras River Basin in northwest Iran. However, information on the species and their bionomics is limited in the region. Adult flies were collected from diverse ecotopes of the Aras River Basin. After morphological identification, representative specimens of each morphological group were subjected to mtDNA COI gene sequence analysis for species diagnosis and to infer relationships. Flies also were examined for pollinia. A total of 1880 specimens representing 12 morphotaxa in two genera (Simulium and Metacnephia) were identified: Simulium turgaicum (n=1834), S. kiritshenkoi (n=12), S. bezzii (n=7), S. brevitarse (n=7), S. pseudequinum (n=5), S. aureum species group (n=4), S. vernum species group (n=3), S. transcaspicum (n=1), three unidentified species of the subgenus Simulium (n=5), and Metacnephia possibly persica (n=2). Fifty two haplotypes were detected for the 65 COI sequences analyzed. Intraspecific genetic divergence was 0.19-8.83%, whereas the mean interspecific genetic distances among the morphotaxa were 1.41-19.58%. Molecular analyses recovered three well-supported lineages within S. turgaicum. One lineage included black flies collected from agricultural fields, a second lineage involved black flies captured from animals, and a third lineage included specimens that had visited flowers, as evidenced by presence of pollinia. The relative abundance (97%) and observations of the S. turgaicum complex biting humans are important epidemiological factors. Future studies are needed to define the potential epidemiological risk of simulids in Khoda-Afarin County of Iran.

A new species in Simulium (Trichodagmia) (Diptera: Simuliidae) from Chapada Diamantina region, Brazil: cryptic diversity revealed by morphological and molecular evidence

We describe new species of black fly that had previously been identified as S. scutistriatum Lutz due to morphological similarities at the pupal stage. The description of the new species, Simulium (Trichogamia) itajara n. sp., is based on molecular and morphological evidences. The known distribution of the new species is currently restricted to the Paraguaçu River hydrographic basin in Chapada Diamantina National Park and the surrounded area in Bahia state, Brazil. The distribution record for S. scutistriatum in the northeast region of Brazil needs to be removed, since the previous records were based on occurrence of S. itajara n. sp.

Genetic diversity and differentiation in the blackflies Simulium cheongi, Simulium jeffreyi and Simulium vanluni (Diptera: Simuliidae) in Peninsular Malaysia

The population genetic structures of S. vanluni, S. cheongi and S. jeffreyi were determined from mitochondria-encoded sequences of cytochrome c oxidase subunits I (COI) across different states in Peninsular Malaysia. High levels of genetic diversity and genetic differentiation were observed among three species. All three species revealed an intermediate level of gene flow among the populations. Negative values of Fu's Fs and low values of Raggedness index supported the hypothesis of population expansion in S. vanluni, S. cheongi and S. jeffreyi.

Highly variable COI haplotype diversity between three species of invasive pest fruit fly reflects remarkably incongruent demographic histories

Distance decay principles predict that species with larger geographic ranges would have greater intraspecific genetic diversity than more restricted species. However, invasive pest species may not follow this prediction, with confounding implications for tracking phenomena including original ranges, invasion pathways and source populations. We sequenced an 815 base-pair section of the COI gene for 441 specimens of Bactrocera correcta, 214 B. zonata and 372 Zeugodacus cucurbitae; three invasive pest fruit fly species with overlapping hostplants. For each species, we explored how many individuals would need to be included in a study to sample the majority of their haplotype diversity. We also tested for phylogeographic signal and used demographic estimators as a proxy for invasion potency. We find contrasting patterns of haplotype diversity amongst the species, where B. zonata has the highest diversity but most haplotypes were represented by singletons; B. correcta has ~7 dominant haplotypes more evenly distributed; Z. cucurbitae has a single dominant haplotype with closely related singletons in a 'star-shape' surrounding it. We discuss how these differing patterns relate to their invasion histories. None of the species showed meaningful phylogeographic patterns, possibly due to gene-flow between areas across their distributions, obscuring or eliminating substructure.

Simulium reptans (Linnaeus, 1758) and Simulium reptantoides Carlsson, 1962 from the Balkan Peninsula

Simulium reptans (Linnaeus, 1758) and Simulium reptantoides Carlsson, 1962 are two species of the Simulium reptans group whose distribution is unclear because of their confusing taxonomy and systematics. Their genetic variability is well known for populations in northern and central Europe and shows that both species have two forms; however, the genetic variability of these species in southern and eastern Europe is unknown. To identify the status of these two species in southeast Europe, mtDNA was extracted from 19 individuals from 12 localities across the Balkan Peninsula. Phylogenetic analysis confirmed the existence of two species with 7.38-7.94% divergence. Each species was comprised of two clades, with 2.31% and 1.43% interclade divergence for S. reptans and S. reptantoides, respectively. This study revealed the presence of both species across the Balkans and that S. reptans occurs in this area in only one form (S. reptans B), while S. reptantoides is found in two genetic forms (A and B).

Hidden biodiversity revealed by DNA barcoding in black fly genus Simulium

BACKGROUND & OBJECTIVES

The black fly genus Simulium Latreille is one of the most important medical insect group of the family Simuliidae (Diptera) and many species of this genus are important pests of human and animals, while some of them also represent vectors of pathogens. Correct species identification is essential to the implementation of control measures for species of medical or agricultural importance.

METHODS

In this study, the usefulness of DNA barcoding was discussed in distinguishing species of Simulium.

RESULTS

Analysis showed hidden biodiversity, usually referred to in Simuliidae as cryptic species, which was detected in 15 species. Firstly, intraspecific divergences of eleven species was unexpectedly high and the maximum distances of them ranged from 5.1-16.8%. Based on the differential of K2P (Kimura 2-Parameter) distances, sequences were subdivided into two or three groups, respectively. Secondly, extremely low interspecific divergences were detected in eight groups of species, and shared haplotypes were also found among them. Furthermore, the subdivision within species and shared haplotypes among some species were all supported by the NJ (Neighbour-Joining) analysis.

INTERPRETATION & CONCLUSION

Our results confirmed that DNA barcoding was a powerful tool for revealing hidden species diversity of black flies. Further work is needed to reveal ambiguous species delimitation in some problematic species groups.

Molecular characterization of black flies (Diptera: Simuliidae) in areas with pest outbreaks and simuliotoxicosis in Northeast Anatolia Region, Turkey

Accurate species identification provides the foundation for successful pest management and vector control of black flies. Accordingly, we examined the mitochondrial DNA cytochrome oxidase I (COI) gene sequences of four morphologically and chromosomally identified species of black flies (Simulium vernumgroup sp., S. bergi Rubtsov, S. bezzii (Corti), and S. kiritshenkoi Rubtsov) in Northeast Anatolia Region of Turkey where simuliid pest problems and simuliotoxicosis cases have been reported among cattle. COI gene sequences of these species and closely related species available in GenBank were used to provide species-level diagnoses and infer relationships. Both subgenera (Nevermannia and Simulium) were monophyletic, and subclades generally corresponded with species groups. Intraspecific genetic divergence was 0.2-1.6%, whereas the mean interspecific genetic divergence among the four species was 11.2-14.5%. The COI analysis produced results congruent with morphological concepts of the nominal species S. bergi and S. bezzii. Probable misidentifications in GenBank were revealed, especially for species in the S. ornatum and S. vernum groups, complicating identification capability. Sequence variation in the COI barcode region also might not be adequate for species delineation and identification among some species in these two species groups.

Who is biting you? DNA barcodes reveal cryptic diversity in human-biting black flies (Diptera: Simuliidae)

Black flies (Simuliidae) are important biting insects and vectors of diseases agents of humans and livestock. Thus, understanding the taxonomy and biodiversity of these insects is crucial for control and management of these diseases. In this study, we used mitochondrial cytochrome c oxidase I sequences to examine genetic diversity of three human-biting and possible vector black fly taxa; the Simulium asakoae species-complex, S. chamlongi and S. nigrogilvum. High levels of genetic diversity (>3.5% intraspecific genetic divergence) were found in all three taxa. Phylogenetic analyses indicated that the S. asakoae complex can be divided into seven groups with the largest group consisting of specimens from Thailand, Malaysia and Myanmar. This group most likely represents true S. asakoae. The remaining haplotypes formed groups with conspecific haplotypes or with other closely related species. Among these groups, one including S. monglaense and another including S. myanmarense suggest that certain specimens identified as S. asakoae most likely belong to those species. Therefore, they constitute new locality records for Thailand and also represent new records of anthropophily. Members of S. chamlongi are not monophyletic as its clade also included S. hackeri. A median joining network revealed strong geographic associations of the haplotypes of S. nigrogilvum suggesting limitation of gene flow. Because this species occurs mainly in high elevation habitats, low land areas could present a barrier to gene flow.

A DNA barcode library for 5,200 German flies and midges (Insecta: Diptera) and its implications for metabarcoding-based biomonitoring

This study summarizes results of a DNA barcoding campaign on German Diptera, involving analysis of 45,040 specimens. The resultant DNA barcode library includes records for 2,453 named species comprising a total of 5,200 barcode index numbers (BINs), including 2,700 COI haplotype clusters without species‐level assignment, so called “dark taxa.” Overall, 88 out of 117 families (75%) recorded from Germany were covered, representing more than 50% of the 9,544 known species of German Diptera. Until now, most of these families, especially the most diverse, have been taxonomically inaccessible. By contrast, within a few years this study provided an intermediate taxonomic system for half of the German Dipteran fauna, which will provide a useful foundation for subsequent detailed, integrative taxonomic studies. Using DNA extracts derived from bulk collections made by Malaise traps, we further demonstrate that species delineation using BINs and operational taxonomic units (OTUs) constitutes an effective method for biodiversity studies using DNA metabarcoding. As the reference libraries continue to grow, and gaps in the species catalogue are filled, BIN lists assembled by metabarcoding will provide greater taxonomic resolution. The present study has three main goals: (a) to provide a DNA barcode library for 5,200 BINs of Diptera; (b) to demonstrate, based on the example of bulk extractions from a Malaise trap experiment, that DNA barcode clusters, labelled with globally unique identifiers (such as OTUs and/or BINs), provide a pragmatic, accurate solution to the “taxonomic impediment”; and (c) to demonstrate that interim names based on BINs and OTUs obtained through metabarcoding provide an effective method for studies on species‐rich groups that are usually neglected in biodiversity research projects because of their unresolved taxonomy.

Diptera of Canada

The Canadian Diptera fauna is updated. Numbers of species currently known from Canada, total Barcode Index Numbers (BINs), and estimated numbers of undescribed or unrecorded species are provided for each family. An overview of recent changes in the systematics and Canadian faunistics of major groups is provided as well as some general information on biology and life history. A total of 116 families and 9620 described species of Canadian Diptera are reported, representing more than a 36% increase in species numbers since the last comparable assessment by JF McAlpine et al. (1979). Almost 30,000 BINs have so far been obtained from flies in Canada. Estimates of additional number of species remaining to be documented in the country range from 5200 to 20,400.

The complete mitochondrial genome of Orancistrocerusaterrimusaterrimus and comparative analysis in the family Vespidae (Hymenoptera, Vespidae, Eumeninae)

To date, only one mitochondrial genome (mitogenome) in the Eumeninae has been reported in the world and this is the first report in China. The mitogenome of O.a.aterrimus is 17 972 bp long, and contains 38 genes, including 13 protein coding genes (PCGs), 23 tRNA genes, two rRNA genes, a long non-coding region (NCR), and a control region (CR). The mitogenome has 79.43% A + T content, its 13 PCGs use ATN as the initiation codon except for cox1 using TTG, and nine genes used complete translation termination TAA and four genes have incomplete stop codon T (cox2, cox3, nad4, and cytb). Twenty-two of 23 tRNAs can form the typical cloverleaf secondary structure except for trnS1. The CR is 1 078 bp long with 84.69% A+T content, comprising 28 bp tandem repeat sequences and 13 bp T-strech. There are two gene rearrangements which are an extra trnM2 located between trnQ and nad2 and the trnL2 in the upstream of nad1. Within all rearrangements of these mitogenomes reported in the family Vespidae, the translocation between trnS1 and trnE genes only appears in Vespinae, and the translocation of trnY in Polistinae and Vespinae. The absent codons of 13 PCGs in Polistinae are more than those both in Vespinae and Eumeninae in the family Vespidae. The study reports the complete mitogenome of O.a.aterrimus, compares the characteristics and construct phylogenetic relationships of the mitogenomes in the family Vespidae.

DNA barcoding of blackflies (Diptera: Simuliidae) as a tool for species identification and detection of hidden diversity in the eastern regions of Spain

Background

Blackflies have negative impact on public and animal health due to the haematophagous habit of females. In recent times, in some regions in Spain, blackfly outbreaks are becoming more and more frequent, threatening the public health. However, there is still a paucity of data concerning the Spanish blackfly fauna. Correct identification of species is of paramount importance in order to provide correct information on species distribution, biology and behaviour, so that control measures could be implemented appropriately.

Methods

Blackflies specimens (larvae, pupae, reared adults and biting females) were collected in the period 2015–2017 in and near rivers and streams from different regions in Spain. A modified Hotshot technique was used for the DNA extraction and the cox1 DNA barcoding region of the cytochrome c oxidase subunit 1 was sequenced from the specimens collected.

Results

In total, we collected 239 specimens representing 22 species. Of these, six species are new records for the Aragón region: P. tomosvaryi, S. bertrandi, S. galloprovinciale, S. lineatum, S. rubzovianum and S. xanthinum. Cox1 DNA barcode sequences for 21 species were recovered, including four species of the genus Prosimulium and 17 species of the genus Simulium [Boophthora (1 species), Eusimulium (1 species), Nevermannia (4 species), Simulium (s.s.) (6 species), Trichodagmia (1 species) and Wilhelmia (4 species)]. For the first time the complete DNA barcodes for five species (P. tomosvaryi, S. carthusiense, S. brevidens, S. monticola and S. sergenti) were registered. Most of the specimens belonging to the same recognized species were clustered together in the neighbour-joining tree, except for S. argyreatum, S. monticola and S. variegatum. The overall genetic distance in the dataset was 0.14%. The average of the intraspecific genetic divergence within the different taxa was 1.47% (0.05–3.96%). In contrast, the interspecific divergence varied between 2.50–22.0%.

Conclusions

In this study we assessed the use of the cox1 DNA barcoding region for the identification of species of blackflies in Spain. Our results showed that combining DNA barcoding with morphology enhanced our taxonomic rationale in identifying the blackflies in the country.

Electronic supplementary material

The online version of this article (10.1186/s13071-018-3046-7) contains supplementary material, which is available to authorized users.

Species identification of horse flies (Diptera: Tabanidae) in Thailand using DNA barcoding

Horse flies (Diptera: Tabanidae) are of medical and veterinary importance because they are known to transmit pathogens. Approximately 80 species of horse flies have been reported in Thailand. Monitoring the distribution of horse fly species is important to control the spread of diseases transmitted by them. Currently, the species identification of horse flies is based on their morphology; this requires considerable skills and taxonomic expertise, and it may be difficult to identify morphologically similar species. DNA-based identification methods are increasingly being developed for rapid and accurate identification of various insect species. In this study, we used mitochondrial cytochrome oxidase subunit I (COI) for species identification of horse flies in Thailand. A 658 bp fragment of COI was amplified from 145 adult horse flies belonging to 48 morphologically distinct species and sequenced. Sequence analysis revealed an intraspecific divergence of 0.0%-4.4% and an interspecific divergence of 0.0%-16.2%. Our results showed that COI barcodes were effective in discriminating a majority of horse flies in Thailand on the basis of the barcoding gap and phylogenetic analyses. However, COI barcodes were unable to distinguish among members of the Tabanus striatus complex and some species within the T. ceylonicus group.

Vector species-specific association between natural Wolbachia infections and avian malaria in black fly populations

Artificial infection of mosquitoes with the endosymbiont bacteria Wolbachia can interfere with malaria parasite development. Therefore, the release of Wolbachia-infected mosquitoes has been proposed as a malaria control strategy. However, Wolbachia effects on vector competence are only partly understood, as indicated by inconsistent effects on malaria infection reported under laboratory conditions. Studies of naturally-occurring Wolbachia infections in wild vector populations could be useful to identify the ecological and evolutionary conditions under which these endosymbionts can block malaria transmission. Here we demonstrate the occurrence of natural Wolbachia infections in three species of black fly (genus Simulium), which is a main vector of the avian malaria parasite Leucocytozoon. Prevalence of Leucocytozoon was high (25%), but the nature and magnitude of its association with Wolbachia differed between black fly species. Wolbachia infection was positively associated with avian malaria infection in S. cryophilum, negatively associated in S. aureum, and unrelated in S. vernum. These differences suggest that Wolbachia interacts with the parasite in a vector host species-specific manner. This provides a useful model system for further study of how Wolbachia influences vector competence. Such knowledge, including the possibility of undesirable positive association, is required to guide endosymbiont based control methods.

A New Anthropophilic Species of Simulium (Trichodagmia) (Diptera: Simuliidae) From Amazonia: Morphology, Chromosomes, and DNA Sequences

The black fly Simulium (Trichodagmia) hirtipupa Lutz (Diptera: Simuliidae) is widely distributed in southern Brazil, with one report from Amapá state in the northern region of Brazilian Amazonia. Morphological comparison of northern and southern populations revealed differences in all life stages, corroborated by chromosomal and molecular analyses, and indicated that the population previously identified as S. hirtipupa from Amapá state represents an undescribed species. This new species is described based on all life stages above the egg, and its chromosomal and molecular divergence from S. hirtipupa is highlighted. Simulium criniferum n. sp. can be diagnosed by the deeply concave male ventral plate with a prominent median projection bearing a ventral keel; female anal lobe in lateral view with a broadly rounded, distal membranous area about as long as wide; pupa with a boot-shaped cocoon bearing a minutely bubbled surface, cephalic plate and thorax with abundant hair-like tubercles, and gill of 12 translucent filaments with darkly sclerotized, acuminate tips; and larva with the body cuticle bearing spiniform setae, abdomen truncated posteriorly, and gill histoblast in situ with the filament tips directed ventrally. Chromosomally, the new species has five unique fixed inversions and uniquely shares three additional fixed inversions with its nearest relative, S. hirtipupa. Partial COI sequences indicate a genetic distance of ~9% between the new species and S. hirtipupa. Females of the new species are anthropophilic.

DNA barcoding a nightmare taxon: assessing barcode index numbers and barcode gaps for sweat bees

There is an ongoing campaign to DNA barcode the world’s >20 000 bee species. Recent revisions of Lasioglossum (Dialictus) (Hymenoptera: Halictidae) for Canada and the eastern United States were completed using integrative taxonomy. DNA barcode data from 110 species of L. (Dialictus) are examined for their value in identification and discovering additional taxonomic diversity. Specimen identification success was estimated using the best close match method. Error rates were 20% relative to current taxonomic understanding. Barcode Index Numbers (BINs) assigned using Refined Single Linkage Analysis (RESL) and barcode gaps using the Automatic Barcode Gap Discovery (ABGD) method were also assessed. RESL was incongruent for 44.5% of species, although some cryptic diversity may exist. Forty-three of 110 species were part of merged BINs with multiple species. The barcode gap is non-existent for the data set as a whole and ABGD showed levels of discordance similar to the RESL. The viridatum species-group is particularly problematic, so that DNA barcodes alone would be misleading for species delimitation and specimen identification. Character-based methods using fixed nucleotide substitutions could improve specimen identification success in some cases. The use of DNA barcoding for species discovery for standard taxonomic practice in the absence of a well-defined barcode gap is discussed.

Phylogeography and population diversity of Simulium hirtipupa Lutz (Diptera: Simuliidae) based on mitochondrial COI sequences

High morphological homogeneity and cryptic speciation may cause the diversity within Simuliidae to be underestimated. Recent molecular studies on population genetics and phylogeography have contributed to reveal which factors influenced the diversity within this group. This study aimed at examining the genetic diversity of Simulium hirtipupa Lutz, 1910 in populations from the biomes Caatinga, Cerrado, and Atlantic Forest. In this study, we carried out phylogeographic and population genetic analyses using a fragment of the mitochondrial gene COI. The 19 populations studied were clustered into seven groups, most of which are associated with geography indicating certain genetic structure. The northern region of the state of Minas Gerais is most likely the center of origin of this species. The average intergroup genetic distance was 3.7%, indicating the presence of cryptic species. The species tree as well as the haplotype network recovered all groups forming two major groups: the first comprises groups Gr-Bahia (in which the São Francisco river has not acted as geographical barrier), Gr-Pernambuco, and Gr-Mato Grosso do Sul. The second included groups comprising populations of the states of Goiás, Tocantins, Minas Gerais, Bahia, São Paulo, and Espírito Santo. The mismatch distribution for groups was consistent with the model of demographic expansion, except for the Gr-Central-East_1 group. The diversification in this group occurred about 1.19 Mya during the Pleistocene, influenced by paleoclimatic oscillations during the Quaternary glacial cycles.

Genetic Diversity and Identification of Palearctic Black Flies in the Subgenus Wilhelmia (Diptera: Simuliidae)

Accurate species identifications are the essential first step in understanding the medical, economic, and ecological importance of black flies. The utility of DNA barcoding based on cytochrome c oxidase subunit 1 (COI) sequences was evaluated for identifying six common species of Palearctic black flies in the subgenus Wilhelmia, including several that are virulent pests. Chromosomally identified larvae from Turkey and Germany and COI sequences in GenBank were analyzed. Intraspecific genetic divergence was 0.7-3.5% (mean 1.6%), whereas interspecific genetic divergence was 2.7-16.9%. On the basis of COI barcodes, the six nominal species of Simulium (Wilhelmia) were clustered in three distinct clades with high levels of genetic divergence, using maximum likelihood and Bayesian analyses. All specimens of Simulium equinum (L.), Simulium pseudequinum Séguy, and Simulium paraequinum Puri were correctly identified. However, >75% of identifications were ambiguous for Simulium lineatum (Meigen) and Simulium turgaicum Rubtsov (Meigen) because of overlapping intra- and interspecific divergence of the two species and Simulium balcanicum (Enderlein), all three of which are chromosomally similar and nearly isomorphic. Phylogenetic evaluation showed that S. balcanicum, S. equinum, S. pseudequinum, and S. paraequinum were monophyletic, with high bootstrap and posterior probability values, but it also showed that S. lineatum and S. turgaicum were paraphyletic, each clustering in two distinct groups, suggesting the presence of cryptic taxa. Although DNA barcoding provided a partial means of identification and indications of additional biodiversity, other molecular markers are needed to clarify the limits of all pest species of the subgenus Wilhelmia.

Taxonomy and polytene chromosomes of the Neotropical black fly Simulium perplexum (Diptera: Simuliidae)

Simulium perplexum Shelley, Maia-Herzog, Luna Dias & Couch is structurally similar in the pupal stage to Simulium guianense Wise, the main vector in the onchocerciasis foci of Amazonian Brazil and Venezuela. We report S. perplexum for the first time beyond its type locality (Guyana, Potaro River), describe its larva, redescribe its pupa, and provide a chromosomal comparison with S. guianense and other morphologically similar species. We collected it in two rivers in Rurópolis municipality, Pará state, Brazil. The larvae can be distinguished from those of related species by having body cuticle with microscopic, translucent, and lanceolate setae. Chromosomal comparisons of S. perplexum and similar Brazilian species with available chromosome information (S. guianense, S. hirtipupa Lutz, and S. litobranchium Hamada, Pepinelli, Mattos-Glória & Luz), using S. guianense Cytoform A as the standard, show that S. perplexum has the nucleolar organizer uniquely in the middle of the short arm of chromosome I, whereas the other three species have this marker at the base of the long arm of chromosome I. All chromosome arms, except IIS and IIIS, of S. perplexum are rearranged, compared with S. guianense Cytoform A, suggesting that it is not closely related to this species or to S. litobranchium, as suggested by some authors, based on morphological features.

DNA barcoding as an aid for species identification in austral black flies (Insecta: Diptera: Simuliidae)

In this paper, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies in the austral region was assessed. Twenty-eight morphospecies were analyzed: eight of the genus Austrosimulium (four species in the subgenus Austrosimulium s. str., three species in the subgenus Novaustrosimulium, and one species unassigned to subgenus), two of the genus Cnesia, eight of Gigantodax, three of Paracnephia, one of Paraustrosimulium, and six of Simulium (subgenera Morops, Nevermannia, and Pternaspatha). The neighbour-joining tree derived from the DNA barcode sequences grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0% to 1.8%, while higher divergences (2%–4.2%) in certain species suggested the presence of cryptic diversity. The existence of well-defined groups within S. simile revealed the likely inclusion of cryptic diversity. DNA barcodes also showed that specimens identified as C. dissimilis, C. nr. pussilla, and C. ornata might be conspecific, suggesting possible synonymy. DNA barcoding combined with a sound morphotaxonomic framework would provide an effective approach for the identification of black flies in the region.

Isolation of Novel Trypanosomatid, Zelonia australiensis sp. nov. (Kinetoplastida: Trypanosomatidae) Provides Support for a Gondwanan Origin of Dixenous Parasitism in the Leishmaniinae

The genus Leishmania includes approximately 53 species, 20 of which cause human leishmaniais; a significant albeit neglected tropical disease. Leishmaniasis has afflicted humans for millennia, but how ancient is Leishmania and where did it arise? These questions have been hotly debated for decades and several theories have been proposed. One theory suggests Leishmania originated in the Palearctic, and dispersed to the New World via the Bering land bridge. Others propose that Leishmania evolved in the Neotropics. The Multiple Origins theory suggests that separation of certain Old World and New World species occurred due to the opening of the Atlantic Ocean. Some suggest that the ancestor of the dixenous genera Leishmania, Endotrypanum and Porcisia evolved on Gondwana between 90 and 140 million years ago. In the present study a detailed molecular and morphological characterisation was performed on a novel Australian trypanosomatid following its isolation in Australia’s tropics from the native black fly, Simulium (Morops) dycei Colbo, 1976. Phylogenetic analyses were conducted and confirmed this parasite as a sibling to Zelonia costaricensis, a close relative of Leishmania previously isolated from a reduviid bug in Costa Rica. Consequently, this parasite was assigned the name Zelonia australiensis sp. nov. Assuming Z. costaricensis and Z. australiensis diverged when Australia and South America became completely separated, their divergence occurred between 36 and 41 million years ago at least. Using this vicariance event as a calibration point for a phylogenetic time tree, the common ancestor of the dixenous genera Leishmania, Endotrypanum and Porcisia appeared in Gondwana approximately 91 million years ago. Ultimately, this study contributes to our understanding of trypanosomatid diversity, and of Leishmania origins by providing support for a Gondwanan origin of dixenous parasitism in the Leishmaniinae.

The genus Leishmania includes approximately 53 species, 20 of which cause human leishmaniais, a significant disease that has afflicted humans for millennia. But how ancient is Leishmania and where did it arise? Some suggest Leishmania originated in the Palearctic. Others suggest it appeared in the Neotropics. The Multiple Origins theory proposes that separation of certain Old World and Neotropical species occurred following the opening of the Atlantic. Others suggest that an ancestor to the Euleishmania and Paraleishmania appeared on Gondwana 90 to 140 million years ago (MYA). We performed a detailed molecular and morphological characterisation of a novel Australian trypanosomatid. This parasite is a sibling to the Neotropical Zelonia costaricensis, a close relative of Leishmania, and designated as Zelonia australiensis sp. nov. Assuming Z. costaricensis and Z. australiensis split when Australia and South America separated, their divergence occurred between 36 and 41 MYA. Using this event as a calibration point for a phylogenetic time tree, an ancestor of the dixenous Leishmaniinae appeared in Gondwana ~ 91 MYA. This study contributes to our understanding of trypanosomatid diversity by describing a unique Australian trypanosomatid and to our understanding of Leishmania evolution by inferring a Gondwanan origin for dixenous parasitism in the Leishmaniinae.

Species-level identification of the blowfly Chrysomya megacephala and other Diptera in China by DNA barcoding

The blowfly Chrysomya megacephala, or oriental latrine fly, is the most common human-associated fly of the oriental and Australasian regions. Chrysomya megacephala is of particular interest for its use in forensic entomology and because it is a disease vector. The larvae are economically important as feed for livestock and in traditional Chinese medicine. Identification of adults is straightforward, but larvae and fragments of adults are difficult to identify. We collected C. megacephala, its allies Chrysomya pinguis and Protophormia terraenovae, as well as flies from 11 other species from 52 locations around China, then sequenced 658 base pairs of the COI barcode region from 645 flies of all 14 species, including 208 C. megacephala, as the basis of a COI barcode library for flies in China. While C. megacephala and its closest relative C. pinguis are closely related (mean K2P divergence of 0.022), these species are completely non-overlapping in their barcode divergences, thus demonstrating the utility of the COI barcode region for the identification of C. megacephala. We combined the 208 C. megacephala sequences from China with 98 others from public databases and show that worldwide COI barcode diversity is low, with 70% of all individuals belonging to one of three haplotypes that differ by one or two substitutions from each other, reflecting recent anthropogenic dispersal from its native range in Eurasia.

DNA barcoding of human-biting black flies (Diptera: Simuliidae) in Thailand

Black flies (Diptera: Simuliidae) are important insect vectors and pests of humans and animals. Accurate identification, therefore, is important for control and management. In this study, we used mitochondrial cytochrome oxidase I (COI) barcoding sequences to test the efficiency of species identification for the human-biting black flies in Thailand. We used human-biting specimens because they enabled us to link information with previous studies involving the immature stages. Three black fly taxa, Simulium nodosum, S. nigrogilvum and S. doipuiense complex, were collected. The S. doipuiense complex was confirmed for the first time as having human-biting habits. The COI sequences revealed considerable genetic diversity in all three species. Comparisons to a COI sequence library of black flies in Thailand and in a public database indicated a high efficiency for specimen identification for S. nodosum and S. nigrogilvum, but this method was not successful for the S. doipuiense complex. Phylogenetic analyses revealed two divergent lineages in the S. doipuiense complex. Human-biting specimens formed a separate clade from other members of this complex. The results are consistent with the Barcoding Index Number System (BINs) analysis that found six BINs in the S. doipuiense complex. Further taxonomic work is needed to clarify the species status of these human-biting specimens.

DNA barcodes for bio-surveillance: regulated and economically important arthropod plant pests

Many of the arthropod species that are important pests of agriculture and forestry are impossible to discriminate morphologically throughout all of their life stages. Some cannot be differentiated at any life stage. Over the past decade, DNA barcoding has gained increasing adoption as a tool to both identify known species and to reveal cryptic taxa. Although there has not been a focused effort to develop a barcode library for them, reference sequences are now available for 77% of the 409 species of arthropods documented on major pest databases. Aside from developing the reference library needed to guide specimen identifications, past barcode studies have revealed that a significant fraction of arthropod pests are a complex of allied taxa. Because of their importance as pests and disease vectors impacting global agriculture and forestry, DNA barcode results on these arthropods have significant implications for quarantine detection, regulation, and management. The current review discusses these implications in light of the presence of cryptic species in plant pests exposed by DNA barcoding.

DNA Barcoding of Gypsy Moths From China (Lepidoptera: Erebidae) Reveals New Haplotypes and Divergence Patterns Within Gypsy Moth Subspecies

The gypsy moth from Asia (two subspecies) is considered a greater threat to North America than European gypsy moth, because of a broader host range and females being capable of flight. Variation within and among gypsy moths from China (nine locations), one of the native countries of Asian gypsy moth, were compared using DNA barcode sequences (658 bp of mtDNA cytochrome c oxidase subunit 1 [COI] sequence), together with two restriction site mtDNA markers (NlaIII and BamHI in COI), which is the standard system used to distinguish European gypsy moths from Asian gypsy moths. Relatedness of these populations to gypsy moths from seven other world areas was also examined. The restriction site markers showed that two Chinese populations had both Asian and European haplotypes. DNA barcode sequence divergence between the Asian populations and the European populations was three times greater than the variation within each group. Using Bayesian and parsimonious network analyses, nine previously unknown barcode haplotypes were documented from China and a single haplotype was found to be shared by 55% of the Chinese and some Far Eastern Russian and Japanese individuals. Some gypsy moths from two Chinese populations showed genetic affinity with mtDNA haplotypes from Siberia, Russia, suggesting there could be a cryptic new subspecies in Lymantria dispar (L.) or human-aided movement of moths between these two locations at an earlier point in time. The previously unknown haplotype patterns may complicate efforts to identify Asian gypsy moth introductions and require changes in monitoring and exclusion programs.

DNA Barcoding of Neotropical Sand Flies (Diptera, Psychodidae, Phlebotominae): Species Identification and Discovery within Brazil

DNA barcoding has been an effective tool for species identification in several animal groups. Here, we used DNA barcoding to discriminate between 47 morphologically distinct species of Brazilian sand flies. DNA barcodes correctly identified approximately 90% of the sampled taxa (42 morphologically distinct species) using clustering based on neighbor-joining distance, of which four species showed comparatively higher maximum values of divergence (range 4.23–19.04%), indicating cryptic diversity. The DNA barcodes also corroborated the resurrection of two species within the shannoni complex and provided an efficient tool to differentiate between morphologically indistinguishable females of closely related species. Taken together, our results validate the effectiveness of DNA barcoding for species identification and the discovery of cryptic diversity in sand flies from Brazil.