The promise of a DNA taxonomy

DNA barcodes of Rosy Tetras and allied species (Characiformes: Characidae: Hyphessobrycon) from the Brazilian Amazon basin

DNA barcoding can be an effective tool for fast and accurate species-level identification based on sequencing of the mitochondrial cytochrome c oxidase subunit (COI) gene. The diversity of this fragment can be used to estimate the richness of the respective species. In this study, we explored the use of DNA barcoding in a group of ornamental freshwater fish of the genus Hyphessobrycon. We sequenced the COI from 10 species of Hyphessobrycon belonging to the "Rosy Tetra Clade" collected from the Amazon and Negro River basins and combined our results with published data. The average conspecific and congeneric Kimura 2-parameter distances were 2.3% and 19.3%, respectively. Six of the 10 species were easily distinguishable by DNA barcoding (H. bentosi, H. copelandi, H. eques, H. epicharis, H. pulchrippinis, and H. sweglesi), whereas the remaining species (H. erythrostigma, H. pyrrhonotus, H. rosaceus and H. socolofi) lacked reciprocal monophyly. Although the COI gene was not fully diagnostic, the discovery of distinct evolutionary units in certain Hyphessobrycon species under the same specific epithet as well as haplotype sharing between different species suggest that DNA barcoding is useful for species identification in this speciose genus.

Forest without prey: livestock sustain a leopard Panthera pardus population in Pakistan

Human–carnivore conflict is one of the major challenges in the management of populations of large carnivores. Concerns include the increasing human population; habitat loss as a result of degradation and fragmentation of forest; and livestock predation as a result of a lack of natural prey, leading to retaliatory killings of wild carnivores. Conflicts may be further aggravated by occasional attacks that result in injury and loss of human life. The level of consumption of prey species by a predator is a benchmark to evaluate the scale of this conflict. We used a newly developed DNA-based diet analysis to study the prey profile of common leopards Panthera pardus in Ayubia National Park, Pakistan. The results suggest that the common leopard is a generalist predator, subsisting mainly on domestic animals. Based on the frequency of occurrence of prey items in 57 faecal samples, the diet of the leopard is dominated by domestic goat Capra hircus (64.9%), followed by domestic dog Canis lupus familiaris (17.5%) and cow Bos taurus (12.3%). Domestic animals (goat, dog, cow, water buffalo Bubalus bubalis, horse Equus caballus and sheep Ovis aries) occurred in 54 (95%) of the 57 samples. We recommend a two-step strategy to mitigate this conflict: (1) introducing incentives for increased acceptance of leopards among local communities in the vicinity of the protected area and (2) increasing the availability of wild prey. We hope that the results of this study will contribute to the survival of the leopard in Pakistan.

So what is a species anyway? A primatological perspective

Since Darwin's time, the question "what a species" has provoked fierce disputes and a tremendous number of publications, from short opinion papers to thick volumes. The debates covered fundamental philosophical questions, such as: Do species exist at all independently of a human observer or are they just a construct of the human mind to categorize nature's organismic diversity and serve as a semantic tool in human communication about biodiversity? or: Are species natural kinds (classes) or individuals that are "born" by speciation, change in course of time, and finally "die" when they go extinct or diverge into new species? Also included was the problem of species as taxa (taxonomic) versus species as products of the speciation process (evolutionary). More pragmatic issues arose, such as: How can we reliably delineate and delimitate species? The great interest in what a species is reflects the importance of "species" as fundamental units in most fields of biology, especially evolutionary biology, ecology, and conservation.

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.

Schistosomiasis research in Africa: how the CONTRAST alliance made it happen

In May 2012, the World Health Assembly passed resolution WHA 65.21, calling upon member states to intensify schistosomiasis control and, wherever possible, to attempt transmission interruption and initiate interventions towards local elimination. It is now clear that CONTRAST--a multidisciplinary alliance to optimize schistosomiasis control and transmission surveillance in sub-Saharan Africa--was ahead of the game. Indeed, launched in October 2006, this 4-year project funded by the European Commission made important contributions for sustainable schistosomiasis control in the selected African countries through innovation, validation and application of new tools and locally adapted intervention strategies complementary to preventive chemotherapy. Moreover, CONTRAST articulated a research agenda for schistosomiasis elimination, framed by 10 key questions. Here, we provide a rationale for CONTRAST and discuss its overarching goal, the interrelated objectives, establishment and running of a research node network across Africa, partnership configuration and modus operandi of the project. A collection of 25 articles is presented that are grouped into five main themes: molecular, biological, spatial, social and cross-cutting issues pertaining to the epidemiology and control of schistosomiasis. We summarize key achievements made by CONTRAST, many of which are featured in this special issue of Acta Tropica. Together with an independent view put forth by an eminent schistosomiasis researcher, the current piece provides an umbrella for the 25-article collection, including current gaps and remaining research needs. Finally, post-CONTRAST initiatives are discussed and a speculative viewpoint is given on how schistosomiasis control/elimination will have evolved over the next several years.

How to describe a cryptic species? Practical challenges of molecular taxonomy

BACKGROUND

Molecular methods of species delineation are rapidly developing and widely considered as fast and efficient means to discover species and face the 'taxonomic impediment' in times of biodiversity crisis. So far, however, this form of DNA taxonomy frequently remains incomplete, lacking the final step of formal species description, thus enhancing rather than reducing impediments in taxonomy. DNA sequence information contributes valuable diagnostic characters and -at least for cryptic species - could even serve as the backbone of a taxonomic description. To this end solutions for a number of practical problems must be found, including a way in which molecular data can be presented to fulfill the formal requirements every description must meet. Multi-gene barcoding and a combined molecular species delineation approach recently revealed a radiation of at least 12 more or less cryptic species in the marine meiofaunal slug genus Pontohedyle (Acochlidia, Heterobranchia). All identified candidate species are well delimited by a consensus across different methods based on mitochondrial and nuclear markers.

RESULTS

The detailed microanatomical redescription of Pontohedyle verrucosa provided in the present paper does not reveal reliable characters for diagnosing even the two major clades identified within the genus on molecular data. We thus characterize three previously valid Pontohedyle species based on four genetic markers (mitochondrial cytochrome c oxidase subunit I, 16S rRNA, nuclear 28S and 18S rRNA) and formally describe nine cryptic new species (P. kepii sp. nov., P. joni sp. nov., P. neridae sp. nov., P. liliae sp. nov., P. wiggi sp. nov., P. wenzli sp. nov., P. peteryalli sp. nov., P. martynovi sp. nov., P. yurihookeri sp. nov.) applying molecular taxonomy, based on diagnostic nucleotides in DNA sequences of the four markers. Due to the minute size of the animals, entire specimens were used for extraction, consequently the holotype is a voucher of extracted DNA ('DNA-type'). We used the Character Attribute Organization System (CAOS) to determine diagnostic nucleotides, explore the dependence on input data and data processing, and aim for maximum traceability in our diagnoses for future research. Challenges, pitfalls and necessary considerations for applied DNA taxonomy are critically evaluated.

CONCLUSIONS

To describe cryptic species traditional lines of evidence in taxonomy need to be modified. DNA sequence information, for example, could even serve as the backbone of a taxonomic description. The present contribution demonstrates that few adaptations are needed to integrate into traditional taxonomy novel diagnoses based on molecular data. The taxonomic community is encouraged to join the discussion and develop a quality standard for molecular taxonomy, ideally in the form of an automated final step in molecular species delineation procedures.

Integrative species delimitation in photosynthetic sea slugs reveals twenty candidate species in three nominal taxa studied for drug discovery, plastid symbiosis or biological control

DNA barcoding can highlight taxa in which conventional taxonomy underestimates species richness, identifying mitochondrial lineages that may correspond to unrecognized species. However, key assumptions of barcoding remain untested for many groups of soft-bodied marine invertebrates with poorly resolved taxonomy. Here, we applied an integrative approach for species delimitation to herbivorous sea slugs in clade Sacoglossa, in which unrecognized diversity may complicate studies of drug discovery, plastid endosymbiosis, and biological control. Using the mitochondrial barcoding COI gene and the nuclear histone 3 gene, we tested the hypothesis that three widely distributed "species" each comprised a complex of independently evolving lineages. Morphological and reproductive characters were then used to evaluate whether each lineage was distinguishable as a candidate species. The "circumtropical" Elysia ornata comprised a Caribbean species and four Indo-Pacific candidate species that are potential sources of kahalalides, anti-cancer compounds. The "monotypic" and highly photosynthetic Plakobranchus ocellatus, used for over 60 years to study chloroplast symbiosis, comprised 10 candidate species. Finally, six candidate species were distinguished in the Elysia tomentosa complex, including potential biological control agents for invasive green algae (Caulerpa spp.). We show that a candidate species approach developed for vertebrates effectively categorizes cryptic diversity in marine invertebrates, and that integrating threshold COI distances with non-molecular character data can delimit species even when common assumptions of DNA barcoding are violated.

DNA barcoding a regional bee (Hymenoptera: Apoidea) fauna and its potential for ecological studies

DNA barcoding has been evaluated for many animal taxa and is now advocated as a reliable and rapid means for species-level identification. The coming-to-light of this identification tool is timely as we are now facing perhaps the greatest rate of species loss in recent millennia. This study contributes to an ever-increasing number of published accounts of DNA barcoding successfully and accurately distinguishing animal taxa, in this instance, the bee fauna of Nova Scotia, Canada. Most members of this well-known fauna were resolved with particular clarity; the average intraspecific divergence was less than 0.5%, and COI sequences from over 75% of the province's species are now in the Barcodes of Life Data System. DNA barcoding also revealed some surprises within this fauna, including the possible recognition of two undescribed genetically unique species, one in the genus Ceratina (subgenus Zadontomerus), the second in the genus Andrena (subgenus Larandrena); both are presently receiving further taxonomic study. In addition, DNA barcoding has allowed sex-associations among two pairs of cleptoparasitic species. The resulting utility of DNA barcoding for ecological studies of bee communities is discussed.

Integrative analysis of DNA phylogeography and morphology of the European rose chafer (Cetonia aurata) to infer species taxonomy and patterns of postglacial colonisation in Europe

Integrative taxonomy has been proposed as a framework to unify new conceptual and methodological developments in quantitative assessment of trait variation used in species delimitation, but empirical studies in this young branch of systematics are rare. Here we use standard phylogenetic and parsimony network analyses on nuclear and mitochondrial DNA (Cox1, ITS1) of 230 individuals from 65 European sampling sites in order to deduce population structure of Cetonia beetles from geno- and haplotypes. Statistical measures of population differentiation are inferred on genealogical and geographical scales to test hypotheses about species limits and population history. By combining results of phylogenetic structure with features of morphology, including genital shape morphometrics and discrete external body characters, as well as with measures of population genetics, we attempt to integrate the results as a test of the validity of species limits, in particular of currently recognised subspecies. Despite high Cox1 divergence between some haplotype lineages, even some sympatric lineages (9%, e.g. N2 vs. N4), nDNA and morphology, as well as pattern of geographical and genealogical divergence measured by AMOVA analysis did not support the hypothesis of separate species. Highest divergence in nuclear markers was found among Italian populations of C. aurata pisana and C. a. sicula, and moderately high fixation indices along measurable morphological divergence suggest the correctness of their status as 'subspecies'. Divergence time estimates of the lineages suggest a glacial divergence in different refugia between the major haplogroups, while population differentiation in mtDNA among these was primarily attributable to restricted gene flow caused by geographic isolation.

Exploring species level taxonomy and species delimitation methods in the facultatively self-fertilizing land snail genus Rumina (gastropoda: pulmonata)

Delimiting species in facultatively selfing taxa is a challenging problem of which the terrestrial pulmonate snail genus Rumina is a good example. These snails have a mixed breeding system and show a high degree of shell and color variation. Three nominal species (R. decollata, R. saharica and R. paivae) and two color morphs within R. decollata (dark and light) are currently recognized. The present study aims at evaluating to what extent these entities reflect evolutionary diverging taxonomic units, rather than fixed polymorphisms due to sustained selfing. Therefore, a phylogenetic analysis of nuclear (ITS1, ITS2) and mitochondrial DNA (COI, CytB, 12S rDNA, 16S rDNA) sequences was performed. Putative species in Rumina, inferred from the mitochondrial DNA phylogeny, were compared with those proposed on the basis of the COI gene by (1) DNA barcoding gap analysis, (2) Automatic Barcode Gap Discovery, (3) the species delimitation plug-in of the Geneious software, (4) the Genealogical Sorting Index, and (5) the General Mixed Yule Coalescent model. It is shown that these methods produce a variety of different species hypotheses and as such one may wonder to what extent species delimitation methods are really useful. With respect to Rumina, the data suggest at least seven species, one corresponding to R. saharica and six that are currently grouped under the name R. decollata. The species-level status of R. paivae is rejected.

Molecular identification of nematode larvae different from those of the Trichinella genus detected by muscle digestion

Although larvae of the genus Trichinella are the most common parasite species detected in vertebrate muscles using artificial digestion, nematode larvae belonging to other genera are sometimes detected and incorrectly identified as Trichinella. However, it is often very difficult to identify these larvae at the species, genus or family level using microscopy because of the absence of specific morphological characters or cuticle damage, and the only means of identification is PCR and sequencing of specific molecular markers (12S mtDNA; COI; 18S rDNA; and ITS1). From 2008 to 2011, 18 nematode isolates not belonging to the genus Trichinella were collected from different host species. Eleven of these isolates were successfully identified at the species, genus or superfamily level: larvae from two common kestrels, three hooded crows, a hen harrier and a domestic pig were identified as Toxocara cati; larvae from a badger were identified as Toxocara canis; larvae from a domestic pig were identified as a free-living nematode of the genus Panagrolaimus; larvae from a wild boar were identified as belonging to the Metastrongylus genus; and larvae from a rough-legged buzzard were identified as belonging to the superfamily Filarioidea. The recovery of nematodes belonging to genera other than Trichinella during routine meat inspection suggests that the persons performing the analyses need to be informed of the possibility of false positives and that a molecular-based identification system that allows for a rapid and reliable response must be adopted (i.e., a DNA barcoding-like system).

DNA barcodes for species identification in the hyperdiverse ant genus Pheidole (Formicidae: Myrmicinae)

DNA sequencing is increasingly being used to assist in species identification in order to overcome taxonomic impediment. However, few studies attempt to compare the results of these molecular studies with a more traditional species delineation approach based on morphological characters. Mitochondrial DNA Cytochrome oxidase subunit 1 (CO1) gene was sequenced, measuring 636 base pairs, from 47 ants of the genus Pheidole (Formicidae: Myrmicinae) collected in the Brazilian Atlantic Forest to test whether the morphology-based assignment of individuals into species is supported by DNA-based species delimitation. Twenty morphospecies were identified, whereas the barcoding analysis identified 19 Molecular Operational Taxonomic Units (MOTUs). Fifteen out of the 19 DNA-based clusters allocated, using sequence divergence thresholds of 2% and 3%, matched with morphospecies. Both thresholds yielded the same number of MOTUs. Only one MOTU was successfully identified to species level using the CO1 sequences of Pheidole species already in the Genbank. The average pairwise sequence divergence for all 47 sequences was 19%, ranging between 0-25%. In some cases, however, morphology and molecular based methods differed in their assignment of individuals to morphospecies or MOTUs. The occurrence of distinct mitochondrial lineages within morphological species highlights groups for further detailed genetic and morphological studies, and therefore a pluralistic approach using several methods to understand the taxonomy of difficult lineages is advocated.

Profiling nematode communities in unmanaged flowerbed and agricultural field soils in Japan by DNA barcode sequencing

Soil nematodes play crucial roles in the soil food web and are a suitable indicator for assessing soil environments and ecosystems. Previous nematode community analyses based on nematode morphology classification have been shown to be useful for assessing various soil environments. Here we have conducted DNA barcode analysis for soil nematode community analyses in Japanese soils. We isolated nematodes from two different environmental soils of an unmanaged flowerbed and an agricultural field using the improved flotation-sieving method. Small subunit (SSU) rDNA fragments were directly amplified from each of 68 (flowerbed samples) and 48 (field samples) isolated nematodes to determine the nucleotide sequence. Sixteen and thirteen operational taxonomic units (OTUs) were obtained by multiple sequence alignment from the flowerbed and agricultural field nematodes, respectively. All 29 SSU rDNA-derived OTUs (rOTUs) were further mapped onto a phylogenetic tree with 107 known nematode species. Interestingly, the two nematode communities examined were clearly distinct from each other in terms of trophic groups: Animal predators and plant feeders were markedly abundant in the flowerbed soils, in contrast, bacterial feeders were dominantly observed in the agricultural field soils. The data from the flowerbed nematodes suggests a possible food web among two different trophic nematode groups and plants (weeds) in the closed soil environment. Finally, DNA sequences derived from the mitochondrial cytochrome oxidase c subunit 1 (COI) gene were determined as a DNA barcode from 43 agricultural field soil nematodes. These nematodes were assigned to 13 rDNA-derived OTUs, but in the COI gene analysis were assigned to 23 COI gene-derived OTUs (cOTUs), indicating that COI gene-based barcoding may provide higher taxonomic resolution than conventional SSU rDNA-barcoding in soil nematode community analysis.

Deep sympatric mtDNA divergence in the autumnal moth (Epirrita autumnata)

Deep sympatric intraspecific divergence in mtDNA may reflect cryptic species or formerly distinct lineages in the process of remerging. Preliminary results from DNA barcoding of Scandinavian butterflies and moths showed high intraspecific sequence variation in the autumnal moth, Epirrita autumnata. In this study, specimens from different localities in Norway and some samples from Finland and Scotland, with two congeneric species as outgroups, were sequenced with mitochondrial and nuclear markers to resolve the discrepancy found between mtDNA divergence and present species-level taxonomy. We found five COI sub-clades within the E. autumnata complex, most of which were sympatric and with little geographic structure. Nuclear markers (ITS2 and Wingless) showed little variation and gave no indications that E. autumnata comprises more than one species. The samples were screened with primers for Wolbachia outer surface gene (wsp) and 12% of the samples tested positive. Two Wolbachia strains were associated with different mtDNA sub-clades within E. autumnata, which may indicate indirect selection/selective sweeps on haplotypes. Our results demonstrate that deep mtDNA divergences are not synonymous with cryptic speciation and this has important implications for the use of mtDNA in species delimitation, like in DNA barcoding.

Revision of the freshwater genus Atyaephyra (Crustacea, Decapoda, Atyidae) based on morphological and molecular data

Atyaephyra de Brito Capello, 1867 was described from the Mediterranean region almost 200 years ago. Since then, the genus has been recorded from various freshwater habitats in Europe, North Africa and the Middle East. Despite its long history, the taxonomic status of Atyaephyra species remains confusing and uncertain. Consequently numerous specimens from the known range of Atyaephyra were analysed using morphological characters and mitochondrial COI sequences in an attempt to clarify the taxonomy of this genus. The present study recognises seven Atyaephyra species, more than twice as many as previously recorded (three), four of which are considered as new. The new species are described, additional information to the original descriptions are provided for the remaining three taxa, while neotypes of Atyaephyra desmarestii Millet, 1831 and Atyaephyra stankoi Karaman, 1972 are designated to stabilize their taxonomy. Non-overlapping distinguishing morphological characters are used to discriminate the examined material into five species, e.g., Atyaephyra desmarestii, Atyaephyra stankoi, Atyaephyra orientalis Bouvier, 1913, Atyaephyra thyamisensissp. n., Atyaephyra strymonensissp. n. In addition, the genetic analysis supports the existence of multiple phylogenetic clades in the broader Mediterranean area and distinguishes two new cryptic species, namely Atyaephyra tuerkayisp. n. and Atyaephyra acheronensissp. n. The geographic distribution of these species is confirmed and their phylogenetic relationships are described.

Reverse taxonomy for elucidating diversity of insect-associated nematodes: a case study with termites

BACKGROUND

The molecular operational taxonomic unit (MOTU) has recently been applied to microbial and microscopic animal biodiversity surveys. However, in many cases, some of the MOTUs cannot be definitively tied to any of the taxonomic groups in current databases. To surmount these limitations, the concept of "reverse taxonomy" has been proposed, i.e. to primarily list the MOTUs with morphological information, and then identify and/or describe them at genus/species level using subsamples or by re-isolating the target organisms. Nevertheless, the application of "reverse taxonomy" has not been sufficiently evaluated. Therefore, the practical applicability of "reverse taxonomy" is tested using termite-associated nematodes as a model system for phoretic/parasitic organisms which have high habitat specificity and a potential handle (their termite host species) for re-isolation attempts.

METHODOLOGY

Forty-eight species (from 298 colonies) of termites collected from the American tropics and subtropics were examined for their nematode associates using the reverse taxonomy method and culturing attempts (morphological identification and further sequencing efforts). The survey yielded 51 sequence types ( =  MOTUs) belonging to 19 tentatively identified genera. Within these, four were identified based on molecular data with preliminary morphological observation, and an additional seven were identified or characterized from successful culturing, leaving eight genera unidentified.

CONCLUSIONS

That 1/3 of the genera were not successfully identified suggests deficiencies in the depth of available sequences in the database and biological characters, i.e. usually isolated as phoretic/parasitic stages which are not available for morphological identification, and too many undiscovered lineages of nematodes. Although there still is the issue of culturability of nematodes, culturing attempts could help to make reverse taxonomy methods more effective. However, expansion of the database, i.e., production of more DNA barcodes tied to biological information by finding and characterizing additional new and known lineages, is necessary for analyzing functional diversity.

Molecular Techniques for the Detection and Differentiation of Host and Parasitoid Species and the Implications for Fruit Fly Management

Parasitoid detection and identification is a necessary step in the development and implementation of fruit fly biological control strategies employing parasitoid augmentive release. In recent years, DNA-based methods have been used to identify natural enemies of pest species where morphological differentiation is problematic. Molecular techniques also offer a considerable advantage over traditional morphological methods of fruit fly and parasitoid discrimination as well as within-host parasitoid identification, which currently relies on dissection of immature parasitoids from the host, or lengthy and labour-intensive rearing methods. Here we review recent research focusing on the use of molecular strategies for fruit fly and parasitoid detection and differentiation and discuss the implications of these studies on fruit fly management.

Babesia: a world emerging

Babesia are tick-transmitted hemoprotozooans that infect mammals and birds, and which are acknowledged for their major impact on farm and pet animal health and associated economic costs worldwide. Additionally, Babesia infections of wildlife can be fatal if associated with stressful management practices; and human babesiosis, also transmitted by blood transfusion, is an increasing public-health concern. Due to the huge diversity of species reported to serve as Babesia hosts, all vertebrates might be potential carriers, as long as they are adequate hosts for Babesia-vector ticks. We here provide a comprehensive overview of the most relevant Babesia species, and a discussion of the classical taxonomic criteria. Babesia, Cytauxzoon and Theileria parasites are closely related and collectively referred to as piroplasmids. A possible scenario for the history of piroplasmids is presented in the context of recent findings, and its implications for future research avenues are outlined. Phylogenetic trees of all available 18S rRNA and hsp70 genes were generated, based on which we present a thoroughly revised molecular classification, comprising five monophyletic Babesia lineages, one Cytauxzoon clade, and one Theileria clade. Updated 18S rRNA and beta-tubulin gene trees of the B. microti isolates agree with those previously reported. To reconcile estimates of the origin of piroplasmids and ticks (~300 Ma, respectively), and mammalian radiation (60 Ma), we hypothesize that the dixenous piroplasmid life cycle evolved with the origin of ticks. Thus, the observed time gap between tick origin and mammalian radiation indicates the existence of hitherto unknown piroplasmid lineages and/or species in extant vertebrate taxa, including reptiles and possibly amphibians. The development and current status of the molecular taxonomy of Babesia, with emphasis on human-infecting species, is discussed. Finally, recent results from population genetic studies of Babesia parasites, and their implications for the development of pathogenicity, drug resistance and vaccines, are summarized.

Obtaining molecular data for all life stages of Typhlodromus (Typhlodromus) exhilaratus (Mesostigmata: Phytoseiidae): consequences for species identification

Several species of the family Phytoseiidae are known to control mite pests in many crops worldwide. However, biological control success greatly depends on the accurate identification of these predatory mites. Species diagnostics is essentially based on the morphological characters of females. Thus, when only immature stages and/or males are collected, their identification is poorly supported. Molecular tools could be of great help to overcome these difficulties, as molecular sequences are assumed to be identical for the life stage considered. However, one of the essential points is to extract a sufficient DNA amount from a single specimen of immature stages (eggs, protonymphs, deutonymphs) and males (less than 300 μm in length) to amplify and sequence DNA. The markers used were two mitochondrial DNA fragments (12S rRNA and Cytb mtDNA) and the species studied were Typhlodromus (Typhlodromus) exhilaratus and T. (T.) phialatus, two cryptic species, reported to control mite pests in crops of southern Europe and commonly found on the same plants. Despite a low quantity of DNA extracted, particularly for the egg, larva and protonymph stages, DNA was amplified and sequences were obtained from all the life stages considered with the two mtDNA fragments. Sequences from all the developmental stages of T. (T.) exhilaratus were identical and well differentiated from those of its sister-species. However, contaminations were observed especially for eggs and DNA amplified with the Cytb mt marker. Utility of the present results are discussed and protocol improvements are proposed.

Investigating the ecology and evolution of cryptic marine nematode species through quantitative real-time PCR of the ribosomal ITS region

The presence of morphologically similar but genetically distinct species has impacted biogeographical and ecological paradigms. In marine sediments, free-living nematodes form one of the most abundant and diverse faunal groups. Inferring the importance of nematode diversity for ecosystem functioning requires species-level identification, which is hampered by the lack of easily observable diagnostic characters and the presence of cryptic species. New techniques are urgently needed to adequately study the ecology and evolution of cryptic species. The aim of the present study was to evaluate the potential of a quantitative real-time PCR (qPCR) assay using the internal transcribed spacer (ITS) region of the ribosomal DNA to detect and quantify cryptic species of the R. (P.) marina complex. All primer pairs proved to be highly specific, and each primer pair was able to detect a single juvenile in a pool of 100 nematodes. C(t) values were significantly different between developmental stages for all species except for PmIII. Despite differences between developmental stages, a strong correlation was observed between the amount of extracted DNA and the number of nematodes present. Relative and absolute quantification estimates were comparable and resulted in strong positive correlations between the qPCR estimate and the actual number of nematodes present in the samples. The qPCR assay developed here provides the ability to quickly identify and quantify cryptic nematode species and will facilitate their study in laboratory and field settings.

Prey preference of snow leopard (Panthera uncia) in South Gobi, Mongolia

Accurate information about the diet of large carnivores that are elusive and inhabit inaccessible terrain, is required to properly design conservation strategies. Predation on livestock and retaliatory killing of predators have become serious issues throughout the range of the snow leopard. Several feeding ecology studies of snow leopards have been conducted using classical approaches. These techniques have inherent limitations in their ability to properly identify both snow leopard feces and prey taxa. To examine the frequency of livestock prey and nearly-threatened argali in the diet of the snow leopard, we employed the recently developed DNA-based diet approach to study a snow leopard population located in the Tost Mountains, South Gobi, Mongolia. After DNA was extracted from the feces, a region of ∼100 bp long from mitochondrial 12S rRNA gene was amplified, making use of universal primers for vertebrates and a blocking oligonucleotide specific to snow leopard DNA. The amplicons were then sequenced using a next-generation sequencing platform. We observed a total of five different prey items from 81 fecal samples. Siberian ibex predominated the diet (in 70.4% of the feces), followed by domestic goat (17.3%) and argali sheep (8.6%). The major part of the diet was comprised of large ungulates (in 98.8% of the feces) including wild ungulates (79%) and domestic livestock (19.7%). The findings of the present study will help to understand the feeding ecology of the snow leopard, as well as to address the conservation and management issues pertaining to this wild cat.

Exploring diversity in cryptorhynchine weevils (Coleoptera) using distance-, character- and tree-based species delineation

Species boundaries are studied in a group of beetles, the western Palaearctic Cryptorhynchinae. We test for congruence of 'traditionally' identified morphospecies with species inferred through parsimony networks, distance-based clustering and the ultrametric tree-based generalized mixed yule-coalescent (GMYC) approach. For that purpose, we sequenced two variable fragments of mitochondrial DNA (CO1 and 16S) for a total of 791 specimens in 217 species of Cryptorhynchinae. Parsimony networks, morphology-calibrated distance clusters and the different tree-based species inferences all achieved low congruence with morphospecies, at best 60%. Although the degree of match with morphospecies was often similar for the different approaches, the composition of clusters partially varied. A barcoding gap was absent in morphospecies-oriented distances as well as for GMYC species clusters. This demonstrates that not only erroneous taxonomic assignments, incomplete lineage sorting, hybridization, or insufficient sampling can compromise distance-based identification, but also differences in speciation rates and uneven tree structure. The initially low match between morphospecies and the different molecular species delineation methods in this case study shows the necessity of combining the output of various methods in an integrative approach. Thereby we obtain an idea about the reliability of the different results and signals, which enables us to fine-tune sampling, delineation technique and data collection, and to identify species that require taxonomic revision.

DNA barcoding of Caenogastropoda along coast of China based on the COI gene

DNA barcoding provides an efficient method for species-level identifications. In this study, we have amplified partial sequences of mitochondrial cytochrome c oxidase I (COI) gene from 110 specimens of 45 species of Caenogastropoda collected from the coast along China to evaluate whether DNA barcodes can distinguish these species accurately. The average Kimura 2-parameter (K2P) distances within species, genera and families were 0.44%, 13.96% and 22.27%, respectively. Both the neighbour-joining tree and the Bayesian tree showed a clear discrimination of all the species in our study with highly supported clades. These results proved that the species of Caenogastropoda can be efficiently and accurately identified by DNA barcoding based on the COI gene.

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages.

Recent discoveries of armyworms in Japan and their species identification using DNA barcoding

Long columns of migrating larval sciarid armyworms were discovered in central and northern Japan, specifically Kanagawa, Gunma, Miyagi and Akita prefectures, as well as Hokkaido. This is the first examination of armyworms in East Asia. In Europe, armyworms have been identified as Sciara militaris, belonging to the family Sciaridae (sciarid flies or black fungus gnats), by rearing them to adulthood. In Japan, we were unable to obtain live samples for rearing; therefore, DNA barcodes were obtained from the samples of armyworms collected in the Gunma and Miyagi prefectures. The DNA barcodes were compared with those obtained from the following samples: pupae of S. militaris from UK, adults of Sciara kitakamiensis, Sciara humeralis, Sciara hemerobioides, Sciara thoracica, Sciara helvola and Sciara melanostyla from Japan, and adults of one undescribed Sciara species from Malaysia. Neighbour-joining, maximum parsimony, and maximum likelihood analyses revealed that the armyworms discovered in Japan are S. kitakamiensis. Although adults of this species have been recorded in several locations in Japan, this is the first report of migrating larval armyworms. DNA barcodes were effectively used to link different life stages of this species. The average intraspecific and interspecific pairwise genetic distances of the genus Sciara were 0.3% and 12.6%, respectively. The present study illustrates that DNA barcodes are an effective means of identifying sciarid flies in Japan.

Establishment of a mitochondrial DNA sequence database for the identification of fish species commercially available in South Africa

The limitations intrinsic to morphology-based identification systems have created an urgent need for reliable genetic methods that enable the unequivocal recognition of fish species, particularly those that are prone to overexploitation and/or market substitution. The aim of this study was to develop a comprehensive reference library of DNA sequence data to allow the explicit identification of 53 commercially available fish species in South Africa, most of which were locally caught marine species. Sequences of approximately 655 base pairs were generated for all species from the cytochrome c oxidase I (COI) gene, the region widely adopted for DNA barcoding. Specimens of the genus Thunnus were examined in further detail, employing additional mitochondrial DNA control region sequencing. Cumulative analysis of the sequences from the COI region revealed mean conspecific, congeneric and confamilial Kimura 2-parameter distances of 0.10%, 4.58% and 15.43%, respectively. The results showed that the vast majority (98%) of fish species examined could be readily differentiated by their COI barcodes, but that supplementary control region sequencing was more useful for the discrimination of three Thunnus species. Additionally, the analysis of COI data raised the prospect that Thyrsites atun (snoek) could constitute a species pair. The present study has established the necessary genetic information to permit the unambiguous identification of 53 commonly marketed fish species in South Africa, the applications of which hold a plethora of benefits relating to ecology research, fisheries management and control of commercial practices.

DNA barcoding of nymphalid butterflies (Nymphalidae: Lepidoptera) from Western Ghats of India

We have checked the utility of DNA barcoding for species identification of nymphalid butterflies from Western Ghats of India by using 650 bp sequence of mitochondrial gene cytochrome c oxidase subunit I. Distinct DNA barcoding gap (i.e. difference between intraspecies and interspecies nucleotide divergence), exists between species studied here. When our sequences were compared with the sequences of the conspecifics submitted from different geographic regions, nine cases of deep intraspecies nucleotide divergences were observed. In spite of this, NJ (Neighbour Joining) clustering analysis successfully discriminated all species. Observed cases of deep intraspecies nucleotide divergences certainly warrant further study.

Tropical nematode diversity: vertical stratification of nematode communities in a Costa Rican humid lowland rainforest

Comparisons of nematode communities among ecosystems have indicated that, unlike many organisms, nematode communities have less diversity in the tropics than in temperate ecosystems. There are, however, few studies of tropical nematode diversity on which to base conclusions of global patterns of diversity. This study reports an attempt to estimate nematode diversity in the lowland tropical rainforest of La Selva Biological Research Station in Costa Rica. We suggest one reason that previous estimates of tropical nematode diversity were low is because habitats above the mineral soil are seldom sampled. As much as 62% of the overall genetic diversity, measured by an 18S ribosomal barcode, existed in litter and understorey habitats and not in soil. A maximum-likelihood tree of barcodes from 360 individual nematodes indicated most major terrestrial nematode lineages were represented in the samples. Estimated 'species' richness ranged from 464 to 502 within the four 40 x 40 m plots. Directed sampling of insects and their associated nematodes produced a second set of barcodes that were not recovered by habitat sampling, yet may constitute a major class of tropical nematode diversity. While the generation of novel nematode barcodes proved relatively easy, their identity remains obscure due to deficiencies in existing taxonomic databases. Specimens of Criconematina, a monophyletic group of soil-dwelling plant-parasitic nematodes were examined in detail to assess the steps necessary for associating barcodes with nominal species. Our results highlight the difficulties associated with studying poorly understood organisms in an understudied ecosystem using a destructive (i.e. barcode) sampling method.

jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units

Background

DNA barcoding and other DNA sequence-based techniques for investigating and estimating biodiversity require explicit methods for associating individual sequences with taxa, as it is at the taxon level that biodiversity is assessed. For many projects, the bioinformatic analyses required pose problems for laboratories whose prime expertise is not in bioinformatics. User-friendly tools are required for both clustering sequences into molecular operational taxonomic units (MOTU) and for associating these MOTU with known organismal taxonomies.

Results

Here we present jMOTU, a Java program for the analysis of DNA barcode datasets that uses an explicit, determinate algorithm to define MOTU. We demonstrate its usefulness for both individual specimen-based Sanger sequencing surveys and bulk-environment metagenetic surveys using long-read next-generation sequencing data. jMOTU is driven through a graphical user interface, and can analyse tens of thousands of sequences in a short time on a desktop computer. A companion program, Taxonerator, that adds traditional taxonomic annotation to MOTU, is also presented. Clustering and taxonomic annotation data are stored in a relational database, and are thus amenable to subsequent data mining and web presentation.

Conclusions

jMOTU efficiently and robustly identifies the molecular taxa present in survey datasets, and Taxonerator decorates the MOTU with putative identifications. jMOTU and Taxonerator are freely available from http://www.nematodes.org/.