Complete DNA barcode reference library for a country's butterfly fauna reveals high performance for temperate Europe

Unique among high passes: Phylogenetic inferences from DNA barcoding of the butterfly fauna of Ladakh Trans-Himalaya, India

The butterfly assemblage of Ladakh Trans-Himalaya demands a thorough analysis of their population genetic structure owing to their typical biogeographic affinity and their adaptability to extreme cold-desert climates. No such effort has been taken till date, and in this backdrop, we created a barcode reference library of 60 specimens representing 23 species. Barcodes were generated from freshly collected leg samples using the Sanger sequencing method, followed by phylogenetic clade analyses and divergence calculation. Our data represents 22% of Ladakh's Rhopaloceran fauna with the novel barcode submission for six species, including one Schedule II species, Paralasa mani . Contrary to the 3% threshold rule, the interspecific divergence between two species pairs of typical mountain genus Hyponephele and Karanasa was found to be 2.3% and 2.2%, respectively. The addition of conspecific global barcodes revealed that most species showed little increase in divergence value, while a two-fold increase was noted in a few species. Bayesian clade clustering outcomes largely aligned with current morphological classifications, forming monophyletic clades of conspecific barcodes, with only minor exceptions observed for the taxonomically complicated genus Polyommatus and misidentified records of Aulocera in the database. We also observed variations within the same phylogenetic clades forming nested lineages, which may be attributed to the taxonomic intricacies present at the subspecies level globally, mostly among Eurasian species. Overall, our effort not only substantiated the effectiveness of DNA Barcoding for the identification and conservation of this climatically vulnerable assemblage but also highlighted the significance of deciphering the unique genetic composition among this geographically isolated population of Ladakh butterflies.

Integrative analysis reveals the divergence and speciation between sister Sooty Copper butterflies Lycaena bleusei and L. tityrus

The comparison of closely related taxa is cornerstone in biology, as understanding mechanisms leading up to differentiation in relation to extant shared characters are powerful tools in interpreting the evolutionary process. Hotspots of biodiversity such as the west-Mediterranean, where many lineages meet are ideal grounds to study these processes. We set to explore the interesting example of Sooty Copper butterflies: widespread Eurasian Lycaena tityrus (Poda, 1761) comes into contact in Iberia with closely related and local endemic, L. bleusei (Oberthür, 1884), which hasn't always been considered a distinct species. An integrative analysis was designed, combining the use of extensive molecular data (five genes), geometric morphometrics analyses, verified and up-to-date distribution data, and environmental niche modelling, aimed at deciphering their true relationship, their placement within European Lycaena and trace their evolutionary history. We revealed several levels of differentiation: L. bleusei and L. tityrus appear to be reciprocally monophyletic independent gene-pools, distinct in all genes analysed, having mutually diverged 4.8 Ma ago. L. tityrus but not L. bleusei, further displays a genetic structure compatible with several glacial refugia, where populations assignable to infraspecific taxa surface. Conversely, L. bleusei shows a loss in mtDNA diversity in relation to nuDNA. Morphological analyses differentiate both species according to size and shape but also discriminate strong seasonal and sexual traits and a geographical phenotype segregation in L. tityrus. Finally, updated distribution and its modelling for current and glacial timeframes reveal both species respond differently to environmental variables, defining a mostly parapatric distribution and an overlapping belt where sympatry was recovered. During the last glacial maximum, a wider expansion in L. bleusei distribution explains current isolated populations. Our study highlights the importance of gathering several lines of evidence when deciphering the relationships between closely related populations in the fringe of cryptic species realm.

From DNA barcodes to ecology: Meta-analysis of central European beetles reveal link with species ecology but also to data pattern and gaps

DNA barcoding has been used worldwide to identify biological specimens and to delimit species. It represents a cost-effective, fast, and efficient way to assess biodiversity with help of the public Barcode of Life Database (BOLD) accounting for more than 236,000 animal species and more than 10 million barcode sequences. Here, we performed a meta-analysis of available barcode data of central European Coleoptera to detect intraspecific genetic patterns among ecological groups in relation to geographic distance with the aim to investigate a possible link between infraspecific variation and species ecology. We collected information regarding feeding style, body size, as well as habitat and biotope preferences. Mantel tests and two variants of Procrustes analysis, both involving the Principal Coordinates Neighborhood Matrices (PCNM) approach, were applied on genetic and geographic distance matrices. However, significance levels were too low to further use the outcome for further trait investigation: these were in mean for all ecological guilds only 7.5, 9.4, or 15.6% for PCNM + PCA, NMDS + PCA, and Mantel test, respectively, or at best 28% for a single guild. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. Results suggest that increased numbers of species, sampling localities, and specimens for a chosen area of interest may give new insights to explore barcode data and species ecology for the scope of conservation on a larger scale. We performed a meta-analysis of available barcode data of central European beetles to detect intraspecific genetic patterns among ecological groups in relation to geographic distance, regarding feeding style, body size, as well as habitat and biotope preferences. Our study confirmed that certain ecological traits were associated with higher species diversity and foster stronger genetic differentiation. However, significance levels were too low to further use the outcome for further trait investigation.

Butterfly–parasitoid–hostplant interactions in Western Palaearctic Hesperiidae: a DNA barcoding reference library

The study of ecological interactions between plants, phytophagous insects and their natural enemies is an essential but challenging component for understanding ecosystem dynamics. Molecular methods such as DNA barcoding can help elucidate these interactions. In this study, we employed DNA barcoding to establish hostplant and parasitoid interactions with hesperiid butterflies, using a complete reference library for Hesperiidae of continental Europe and north-western Africa (53 species, 100% of those recorded) based on 2934 sequences from 38 countries. A total of 233 hostplant and parasitoid interactions are presented, some recovered by DNA barcoding larval remains or parasitoid cocoons. Combining DNA barcode results with other lines of evidence allowed 94% species-level identification for Hesperiidae, but success was lower for parasitoids, in part due to unresolved taxonomy. Potential cases of cryptic diversity, both in Hesperiidae and Microgastrinae, are discussed. We briefly analyse the resulting interaction networks. Future DNA barcoding initiatives in this region should focus attention on north-western Africa and on parasitoids, because in these cases barcode reference libraries and taxonomy are less well developed.

Longer mtDNA Fragments Provide a Better Insight into the Genetic Diversity of the Sycamore Lace Bug, Corythucha ciliata (Say, 1832) (Tingidae, Hemiptera), Both in Its Native and Invaded Areas

Simple Summary

The sycamore lace bug (Corythucha ciliata Say, 1832) is one of the most abundant and widespread pests on plane trees (Platanus spp.) across the globe. The native range of the species is in North America, but it has been introduced to Europe (1964), South America (1985), Asia (1995), Australia (2006), and Africa (2014). To understand the genetic background behind this successful colonisation, we analysed a fragment (1356 bp) of the mitochondrial DNA. The 327 individuals revealed 17 haplotypes forming two separated groups. One group includes North American and Japanese individuals, while the other group comprises North American, European, and Asian individuals. We found a much higher genetic diversity in the native area (North America, 12 haplotypes) than in the invaded areas (Europe, five and Asia, four). The longer DNA fragment provided detailed information about the genetic structure of the species both in its native range and in the invaded areas, but the shorter DNA fragment could not provide a clear link between the genetic variation and the geographic origin.

Abstract

The sycamore lace bug (Corythucha ciliata Say, 1832) is of North American origin, but after its introduction to Europe (1964), South America (1985), Asia (1995), Australia (2006), and Africa (2014), it became an abundant and widespread pest on plane (Platanus spp.) trees. We analysed a 1356 bp long fragment of the mtDNA (COI gene) of 327 sycamore lace bug individuals from 38 geographic locations from Europe, Asia, and North America. Seventeen haplotypes (17 HTs) were detected. C. ciliata populations from North America exhibited higher haplotype diversity (12 HTs) than populations from Europe (6 HTs), Asia (4 HTs), or Japan (2 HTs). The haplotypes formed two haplogroups separated by at least seven mutation steps. One of these mutation steps includes HTs from North America and Japan. Another includes HTs from North America, Europe, and Asia. Haplotypes from Asia Minor, the Caucasus, and Central Asia are linked to haplotypes from Europe, while haplotypes found in Japan are linked to haplotypes found in North America only. The incorporation of published data from the GenBank into our dataset (altogether 517 individuals from 57 locations, but only 546 bp long fragment of the mtDNA) did not show any structure according to the geographic origin of the individuals.

Genomics Reveal Admixture and Unexpected Patterns of Diversity in a Parapatric Pair of Butterflies

We studied the evolutionary relationship of two widely distributed parapatric butterfly species, Melitaea athalia and Melitaea celadussa, using the ddRAD sequencing approach, as well as genital morphology and mtDNA data. M. athalia was retrieved as paraphyletic with respect to M. celadussa. Several cases of mito-nuclear discordance and morpho-genetic mismatch were found in the contact zone. A strongly diverged and marginally sympatric clade of M. athalia from the Balkans was revealed. An in-depth analysis of genomic structure detected high levels of admixture between M. athalia and M. celadussa at the contact zone, though not reaching the Balkan clade. The demographic modelling of populations supported the intermediate genetic make-up of European M. athalia populations with regards to M. celadussa and the Balkan clade. However, the dissimilarity matrix of genotype data (PCoA) suggested the Balkan lineage having a genetic component that is unrelated to the athalia-celadussa group. Although narrowly sympatric, almost no signs of gene flow were found between the main M. athalia group and the Balkan clade. We propose two possible scenarios on the historical evolution of our model taxa and the role of the last glacial maximum in shaping their current distribution. Finally, we discuss the complexities regarding the taxonomic delimitation of parapatric taxa.

Paraphyly and low levels of genetic divergence in morphologically distinct taxa: revision of the Pseudoanthidium scapulare complex of carder bees (Apoidea: Megachilidae: Anthidiini)

The Palaearctic complex of anthidiine bees closely related to Pseudoanthidium scapulare has long been a source of unresolved taxonomic and systematic issues. Until now, the number of species in the complex and their geographical distributions were largely unclear, thus complicating the compilation of accurate species checklists and hindering conservation efforts. In order to address these issues, we use morphology and mitochondrial cytochrome c oxidase subunit I (COI) sequences, combined with a thorough examination of the relevant literature and type material, to delimit species within this complex, assign names to species and clarify geographical ranges. An unexpected result was that a certain number of morphologically distinct taxa exhibited low levels of genetic divergence at the COI locus, resulting in species paraphyly. A set of ultra-conserved elements (UCEs) was also sequenced in order to further investigate relationships among these taxa. One morphologically distinct species was also paraphyletic using UCE data, hinting at recent species divergences and genetic exchange at zones of contact between morphologically well-differentiated taxa. The results of our study reveal the presence of ten species in this complex, including a previously overlooked species for western continental Europe. A complete diagnosis of the males and females of these species is provided, as are maps detailing the geographic distributions of each. An illustrated identification key to the males and females of each species is presented. Two new species are described, Pseudoanthidium kaspareki sp. nov. and P. rozeni sp. nov. New synonymy is established for several species and Pseudoanthidium palestinicum and P. tropicum are raised to species level. The new combination, Icteranthidium floripetum comb. nov. is also established. Lectotypes are designated for the following species: Anthidium eversmanni, A. floripetum, A. frontale, A. karakalense, A. nanum and A. reptans. Previously unpublished lectotype designations are published here for A. sinuatum and A. tenellum.

A DNA barcode library for the butterflies of North America

Although the butterflies of North America have received considerable taxonomic attention, overlooked species and instances of hybridization continue to be revealed. The present study assembles a DNA barcode reference library for this fauna to identify groups whose patterns of sequence variation suggest the need for further taxonomic study. Based on 14,626 records from 814 species, DNA barcodes were obtained for 96% of the fauna. The maximum intraspecific distance averaged 1/4 the minimum distance to the nearest neighbor, producing a barcode gap in 76% of the species. Most species (80%) were monophyletic, the others were para- or polyphyletic. Although 15% of currently recognized species shared barcodes, the incidence of such taxa was far higher in regions exposed to Pleistocene glaciations than in those that were ice-free. Nearly 10% of species displayed high intraspecific variation (>2.5%), suggesting the need for further investigation to assess potential cryptic diversity. Aside from aiding the identification of all life stages of North American butterflies, the reference library has provided new perspectives on the incidence of both cryptic and potentially over-split species, setting the stage for future studies that can further explore the evolutionary dynamics of this group.

High resolution DNA barcode library for European butterflies reveals continental patterns of mitochondrial genetic diversity

The study of global biodiversity will greatly benefit from access to comprehensive DNA barcode libraries at continental scale, but such datasets are still very rare. Here, we assemble the first high-resolution reference library for European butterflies that provides 97% taxon coverage (459 species) and 22,306 COI sequences. We estimate that we captured 62% of the total haplotype diversity and show that most species possess a few very common haplotypes and many rare ones. Specimens in the dataset have an average 95.3% probability of being correctly identified. Mitochondrial diversity displayed elevated haplotype richness in southern European refugia, establishing the generality of this key biogeographic pattern for an entire taxonomic group. Fifteen percent of the species are involved in barcode sharing, but two thirds of these cases may reflect the need for further taxonomic research. This dataset provides a unique resource for conservation and for studying evolutionary processes, cryptic species, phylogeography, and ecology.

Wolbachia affects mitochondrial population structure in two systems of closely related Palaearctic blue butterflies

The bacterium Wolbachia infects many insect species and spreads by diverse vertical and horizontal means. As co-inherited organisms, these bacteria often cause problems in mitochondrial phylogeny inference. The phylogenetic relationships of many closely related Palaearctic blue butterflies (Lepidoptera: Lycaenidae: Polyommatinae) are ambiguous. We considered the patterns of Wolbachia infection and mitochondrial diversity in two systems: Aricia agestis/Aricia artaxerxes and the Pseudophilotes baton species complex. We sampled butterflies across their distribution ranges and sequenced one butterfly mitochondrial gene and two Wolbachia genes. Both butterfly systems had uninfected and infected populations, and harboured several Wolbachia strains. Wolbachia was highly prevalent in A. artaxerxes and the host's mitochondrial structure was shallow, in contrast to A. agestis. Similar bacterial alleles infected both Aricia species from nearby sites, pointing to a possible horizontal transfer. Mitochondrial history of the P. baton species complex mirrored its Wolbachia infection and not the taxonomical division. Pseudophilotes baton and P. vicrama formed a hybrid zone in Europe. Wolbachia could obscure mitochondrial history, but knowledge on the infection helps us to understand the observed patterns. Testing for Wolbachia should be routine in mitochondrial DNA studies.

DNA barcoding reveals cryptic diversity in the underestimated genus Triplophysa (Cypriniformes: Cobitidae, Nemacheilinae) from the northeastern Qinghai-Tibet Plateau

Background

The northeastern part of the Qinghai-Tibet Plateau (QTP) presents a high number of plateau loach species. As one of the three major groups of fishes distributed on the QTP, plateau loach has high ecological value. However, the taxonomy and systematics of these fish are still controversial, and a large number of new species have been reported. The reason for this phenomenon is that the degree of morphological variation is low, the phylogenetic information provided by morphological and anatomical features used for species identification is relatively poor, and many cryptic species are observed. Based on the high-density sampling points from the biodiversity hotspots surveyed, this study aims to evaluate the biodiversity of plateau loach in the northeastern part of the QTP and reveal the hidden diversity by comparing morphological species with molecular operational taxonomic units (MOTUs).

Results

After careful identification and comparison of the morphology and DNA barcoding of 1630 specimens, 22 species were identified, with 20 considered valid local species and two identified as new species that had not been previously described. Based on the combination of morphological and molecular methods, a total of 24 native species were found, two of which were cryptic species: Triplophysa robusta sp1 and Triplophysa minxianensis sp1. Fourteen of the 24 species form clusters of barcodes that allow them to be reliably identified. The remaining cases involved 10 closely related species, including rapidly differentiated species and species that seemed to have experienced incomplete lineage sorting or showed introgressions.

Conclusions

The results highlight the need to combine traditional taxonomies with molecular methods to correctly identify species, especially closely related species, such as the plateau loach. This study provides a basis for protecting the biodiversity of plateau loach.

Phylogenetic position and taxonomic rearrangement of Davidina (Lepidoptera: Nymphalidae), an enigmatic butterfly genus new for Europe and America

Davidina, an enigmatic butterfly genus described from China in the 19th century, has for a long time been considered a member of the family Pieridae due to its pierid-like wing pattern. In the 20th century, it was transferred to Satyridae (now subfamily Satyrinae of Nymphalidae) based on analysis of the structure of genitalia and placed next to the species-rich genus Oeneis (subtribe Satyrina), being separated from the latter by supposed differences in wing venation. We have conducted a phylogenetic and taxonomic study of the subtribe Satyrina using analysis of molecular and morphological characters. We show that the genus Oeneis is not monophyletic, and consists of two genetically diverged and morphologically differentiated groups that are not sister-groups (Oeneis s.s. and Protoeneis). We also demonstrate that Davidina is closely related to Protoeneis, but not to Oeneis s.s. To resolve this newly discovered non-monophyly and morphological heterogeneity, several species should be removed from Oeneis and transferred to the genus Davidina. As a consequence, we synonymize the name ProtoeneisGorbunov, 2001 with DavidinaOberthür, 1879. We conclude that Davidina is not a monotypic Chinese endemic genus, as has been previously supposed, but is composed of nine species that have a broad distribution area across the Holarctic region, extending to Europe and America.

Molecular and morphometric divergence of four species of butterflies (Nymphalidae and Pieridae) from the Western Himalaya, India

Morphometric and molecular divergence among four butterfly species of the families Nymphalidae and Pieridae from the western Himalaya region were investigated using molecular tools, traditional morphometric measures and a truss network system. The considered species were Danaus chrysippus, Vanessa cardui, Pieris brassicae and Pieris canidia. Traditional taxonomy is sometimes unable to discriminate cryptic species or species that have close morphological features. Although taxonomists carefully examine external body features to differentiate the species; however, there is a risk for misidentification during a visual assessment of cryptic species. Therefore, we aimed to use the truss network system of 14 morphological landmarks interconnected to yield 90 variables about molecular taxonomy. Principal component analysis (PCA), discriminant function analysis (DFA) and cluster analysis (CA) were employed to determine morphometric variations. In the traditional analysis, 79, 68, 16 and 5 characters out of 90 were found significant (p < 0.05) for D. chrysippus, V. cardui, P. brassicae and P. canidia, respectively. One to seven principal components were extracted through PCA; they explained 87.5-100% of the total variance in samples. Notably, DFA correctly classified 100% of the original grouped cases and 100% of the cross-validated grouped cases. However, the variations were not the same for the two different methods (truss and traditional) employed for the analysis. We correctly identified all the species; the interspecies sequence divergence was between 0.1034 and 0.1398, and the intra-species sequence divergence range was 0.0001 to 0.0128 using the Cytochrome c oxidase subunit-I (COI) gene. The present study provides useful information about the application and complementary role of traditional with truss morphometric analysis for the precise identification and classification of the selected species.

A complete time-calibrated multi-gene phylogeny of the European butterflies

With the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localised endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to eleven nuclear gene fragments, using Bayesian inferences of phylogeny. To avoid analytical biases that could result from our region-focussed sampling, our European tree was grafted upon a global genus-level backbone butterfly phylogeny for analyses. In addition to a consensus tree, the posterior distribution of trees and the fully concatenated alignment are provided for future analyses. Altogether a complete phylogenetic framework of European butterflies for use by the ecological and evolutionary communities is presented.

High functionality of DNA barcodes and revealed cases of cryptic diversity in Korean curved-horn moths (Lepidoptera: Gelechioidea)

Curved-horn moths or gelechioid moths (Lepidoptera: Gelechioidea) represent one of the most diverse lepidopteran groups. Due to the large number of species, generally small size of adults and subtle morphological differences, their confident identification requires tenacious and long-term dedication on their diversity. Over the past decade, DNA barcoding has repeatedly been used to elucidate boundaries of species in many large and difficult groups. Here, we conducted a test of DNA barcoding with the diverse fauna of Korean Gelechioidea with very little prior information of COI gene region from the area. Altogether 509 specimens representing 154 morphospecies were included in the study. The species assignments of all three tested species delimitation methods (ABGD, bPTP and PTP) were consistent with morphological identifications for 117 species (75.97%). A threshold of 2.5% genetic divergence was observed to differentiate the morphological species efficiently. Careful morphological examination of morphospecies exceeding 2.5% intraspecific variability prove cryptic diversity in three species (Neoblastobasis biceratala, Evippe albidoesella and Promalactis atriplagata). One morphospecies, Promalactis odaiensis, showed high intraspecific divergence while consisted of only a single MOTU. Overall, DNA barcoding was shown to provide a powerful tool to discriminate species of Korean Gelechioidea and reveal cases of cryptic diversity.

Regional assemblages shaped by historical and contemporary factors: Evidence from a species-rich insect group

Understanding diversity patterns requires accounting for the roles of both historical and contemporary factors in the assembly of communities. Here, we compared diversity patterns of two moth assemblages sampled from Taihang and Yanshan mountains in Northern China and performed ancestral range reconstructions using the Multi-State Speciation and Extinction model, to track the origins of these patterns. Further, we estimated diversification rates of the two moth assemblages and explored the effects of contemporary ecological factors. From 7,788 specimens we identified 835 species belonging to 23 families, using both DNA barcode analysis and morphology. Moths in Yanshan mountains showed higher species diversity than in Taihang mountains. Ancestral range analysis indicated Yanshan as the origin, with significant historical dispersals from Yanshan to Taihang. Asymmetrical diversification, population expansion, along with frequent and considerable gene flow were detected between communities. Moreover, dispersal limitation or the joint effect of environment filtering and dispersal limitation were inferred as main driving forces shaping current diversity patterns. In summary, we demonstrate that a multiscale (community, population and species level) analysis incorporating both historical and contemporary factors can be useful in delineating factors contributing to community assembly and patterning in diversity.

Testing the Effectiveness of DNA Barcoding for Biodiversity Assessment of Moths from Nigeria

Comprehensive biodiversity assessment of moths in Nigeria rely greatly on accurate species identification. While most of the Nigerian moths are identified effortlessly using their morphological traits, some taxa are morphologically indistinguishable, which makes it difficult for taxon diagnosis. We investigated the efficiency of the DNA barcode, a fragment of the mitochondrial Cytochrome C oxidase subunit I, as a tool for the identification of Nigerian moths. We barcoded 152 individuals comprising 18 morphospecies collected from one of the remaining and threatened rainforest blocks of Nigeria – the Cross River National Park. Phenetic neighbor-joining tree and phylogenetic Maximum Likelihood approach were employed for the molecular-based species identification. Results showed that DNA barcodes enabled species-level identification of most of the individuals collected from the Park. Additionally, DNA barcoding unraveled the presence of at least six potential new and yet undescribed species—Amnemopsyche sp., Arctia sp., Deinypena sp., Hodebertia sp., Otroeda sp., and Palpita sp. The phylogenetic Maximum Likelihood using the combined dataset of all the newly assembled sequences from Nigeria showed that all species formed unique clades. The phylogenetic analyses provided evidence of population divergence in Euchromia lethe, Nyctemera leuconoe, and Deinypena lacista. This study thus illustrates the efficacy of DNA barcoding for species identification and discovery of potential new species, which demonstrates its relevance in biodiversity documentation of Nigerian moths. Future work should, therefore, extend to the creation of an exhaustive DNA barcode reference library comprising all species of moths from Nigeria to have a comprehensive insight on the diversity of moths in the country. Finally, we propose integrated taxonomic methods that would combine morphological, ecological, and molecular data in the identification and diversity studies of moths in Nigeria.

Assembling a DNA barcode reference library for the spiders (Arachnida: Araneae) of Pakistan

Morphological study of 1,795 spiders from sites across Pakistan placed these specimens in 27 families and 202 putative species. COI sequences >400 bp recovered from 1,782 specimens were analyzed using neighbor-joining trees, Bayesian inference, barcode gap, and Barcode Index Numbers (BINs). Specimens of 109 morphological species were assigned to 123 BINs with ten species showing BIN splits, while 93 interim species included representatives of 98 BINs. Maximum conspecific divergences ranged from 0-5.3% while congeneric distances varied from 2.8-23.2%. Excepting one species pair (Oxyopes azhari-Oxyopes oryzae), the maximum intraspecific distance was always less than the nearest-neighbor (NN) distance. Intraspecific divergence values were not significantly correlated with geographic distance. Most (75%) BINs detected in this study were new to science, while those shared with other nations mainly derived from India. The discovery of many new, potentially endemic species and the low level of BIN overlap with other nations highlight the importance of constructing regional DNA barcode reference libraries.

funbarRF: DNA barcode-based fungal species prediction using multiclass Random Forest supervised learning model

BACKGROUND

Identification of unknown fungal species aids to the conservation of fungal diversity. As many fungal species cannot be cultured, morphological identification of those species is almost impossible. But, DNA barcoding technique can be employed for identification of such species. For fungal taxonomy prediction, the ITS (internal transcribed spacer) region of rDNA (ribosomal DNA) is used as barcode. Though the computational prediction of fungal species has become feasible with the availability of huge volume of barcode sequences in public domain, prediction of fungal species is challenging due to high degree of variability among ITS regions within species.

RESULTS

A Random Forest (RF)-based predictor was built for identification of unknown fungal species. The reference and query sequences were mapped onto numeric features based on gapped base pair compositions, and then used as training and test sets respectively for prediction of fungal species using RF. More than 85% accuracy was found when 4 sequences per species in the reference set were utilized; whereas it was seen to be stabilized at ~88% if ≥7 sequence per species in the reference set were used for training of the model. The proposed model achieved comparable accuracy, while evaluated against existing methods through cross-validation procedure. The proposed model also outperformed several existing models used for identification of different species other than fungi.

CONCLUSIONS

An online prediction server "funbarRF" is established at http://cabgrid.res.in:8080/funbarrf/ for fungal species identification. Besides, an R-package funbarRF ( https://cran.r-project.org/web/packages/funbarRF/ ) is also available for prediction using high throughput sequence data. The effort put in this work will certainly supplement the future endeavors in the direction of fungal taxonomy assignments based on DNA barcode.

Linking karyotypes with DNA barcodes: proposal for a new standard in chromosomal analysis with an example based on the study of Neotropical Nymphalidae (Lepidoptera)

Chromosomal data are important for taxonomists, cytogeneticists and evolutionary biologists; however, the value of these data decreases sharply if they are obtained for individuals with inaccurate species identification or unclear species identity. To avoid this problem, here we suggest linking each karyotyped sample with its DNA barcode, photograph and precise geographic data, providing an opportunity for unambiguous identification of described taxa and for delimitation of undescribed species. Using this approach, we present new data on chromosome number diversity in neotropical butterflies of the subfamily Biblidinae (genus Vila Kirby, 1871) and the tribe Ithomiini (genera Oleria Hübner, 1816, Ithomia Hübner, 1816, Godyris Boisduval, 1870, Hypothyris Hübner, 1821, Napeogenes Bates, 1862, Pseudoscada Godman et Salvin, 1879 and Hyposcada Godman et Salvin, 1879). Combining new and previously published data we show that the species complex Oleria onega (Hewitson, [1852]) includes three discrete chromosomal clusters (with haploid chromosome numbers n = 15, n = 22 and n = 30) and at least four DNA barcode clusters. Then we discuss how the incomplete connection between these chromosomal and molecular data (karyotypes and DNA barcodes were obtained for different sets of individuals) complicates the taxonomic interpretation of the discovered clusters.

DNA barcoding in quarantine inspection: a case study on quarantine insect monitoring for Lepidoptera obtained through quarantine inspection on foreign vessels

We conducted quarantine insect species diversity monitoring using DNA barcoding with 517 lepidopteran samples that were obtained from quarantine inspections of foreign vessels entering Korea. For species delimitation and species identification of the analyzed samples, we applied a 2% cutoff rule. Consequently, 145 (368 samples) were considered taxonomically identified. Therefore the number of samples that were identified to the species level was relatively low, at approximately 71%. Thirty of 145 species were not known in Korea, three, i.e., Noctua pronuba (Noctuidae), Orthosia hibisci (Noctuidae), and Pieris brassicae (Pieridae), were checked as ‘Regulated pests’ in Korea.

A DNA barcode reference library for Swiss butterflies and forester moths as a tool for species identification, systematics and conservation

Butterfly monitoring and Red List programs in Switzerland rely on a combination of observations and collection records to document changes in species distributions through time. While most butterflies can be identified using morphology, some taxa remain challenging, making it difficult to accurately map their distributions and develop appropriate conservation measures. In this paper, we explore the use of the DNA barcode (a fragment of the mitochondrial gene COI) as a tool for the identification of Swiss butterflies and forester moths (Rhopalocera and Zygaenidae). We present a national DNA barcode reference library including 868 sequences representing 217 out of 224 resident species, or 96.9% of Swiss fauna. DNA barcodes were diagnostic for nearly 90% of Swiss species. The remaining 10% represent cases of para- and polyphyly likely involving introgression or incomplete lineage sorting among closely related taxa. We demonstrate that integrative taxonomic methods incorporating a combination of morphological and genetic techniques result in a rate of species identification of over 96% in females and over 98% in males, higher than either morphology or DNA barcodes alone. We explore the use of the DNA barcode for exploring boundaries among taxa, understanding the geographical distribution of cryptic diversity and evaluating the status of purportedly endemic taxa. Finally, we discuss how DNA barcodes may be used to improve field practices and ultimately enhance conservation strategies.

Phylogeographic pattern of the plane leaf miner, Phyllonorycter platani (STAUDINGER, 1870) (Lepidoptera: Gracillariidae) in Europe

Background

The plane leaf miner, Phyllonorycter platani is a widely distributed insect species on plane trees and has a well-documented colonisation history in Europe over the last century. However, phylogeographic data of the species are lacking.

Results

We analysed 284 individuals from 38 populations across Europe, Asia, and North America. A 1242 bp fragment of the mitochondrial COI gene and an 893 bp fragment of the 28S rDNA has been Sanger sequenced. Twenty-four haplotypes were detected on the COI gene, and two alleles were identified on the 28S rDNA. We revealed two distinct clades for both markers reflecting the geographic origins, Asia and Europe. The genetic distance between the two main clades is 2.08% on the COI gene and 0.10% on the nuclear DNA.

An overlapping zone of the two clades was found across Eastern Europe and the Anatolian Peninsula. We detected heterozygote individuals of the 28S rDNA gene in Moldavia, Ukraine and in the southern part of Turkey. These suggest that the two clades can hybridise. Furthermore, the presence of European type homozygote individuals has been confirmed in the southern part of Turkey as well.

Conclusions

We have shown that both post-glacial recolonization and recent expansion events influenced the present genetic structure of P. platani. The genetic patterns revealed at least two refugia during the last ice age: one in the Balkan Peninsula and the other in the Caucasus region. Recent expansion was detected in some European and Central Asian populations. The two main clades (Europe/Asia) show definite genetic differences; however, several hybrid individuals were found in the overlapping zone as well (stretching over Eastern Europe and the Anatolian Peninsula). Discrepancies in mitochondrial and nuclear data indicate introgressions in the southern part of the Anatolian Peninsula.

Electronic supplementary material

The online version of this article (10.1186/s12862-018-1240-z) contains supplementary material, which is available to authorized users.

Fish DNA barcoding around large marine infrastructure for improved biodiversity assessment and monitoring

Accurate species-level identification is pivotal for environmental assessments and monitoring. The PERU LNG terminal is composed of large marine infrastructure located on the central coast of Peru. Since construction, taxonomically challenging species such as drum fishes (Sciaenidae) have been attracted to the new hard-bottom habitat. We conducted a DNA barcoding study to investigate fish diversity and constructed a DNA barcode reference library. We examined 56 vouchered specimens and identified 24 unique species. Intra- and interspecific divergence estimates ranged between 0 and 0.64% and 11 and 35.5%, respectively. We assessed the efficiency of the reference library to identify 29 non-vouchered specimens. We had 82.5% efficiency by using both our reference library (n = 17) and GenBank (n = 24). We highlight the importance of implementing molecular barcoding for complementing biodiversity assessments in marine environments. This study represents a first step towards generating a comprehensive DNA barcode reference library for marine fishes in Peru.

Barcoding the butterflies of southern South America: Species delimitation efficacy, cryptic diversity and geographic patterns of divergence

Because the tropical regions of America harbor the highest concentration of butterfly species, its fauna has attracted considerable attention. Much less is known about the butterflies of southern South America, particularly Argentina, where over 1,200 species occur. To advance understanding of this fauna, we assembled a DNA barcode reference library for 417 butterfly species of Argentina, focusing on the Atlantic Forest, a biodiversity hotspot. We tested the efficacy of this library for specimen identification, used it to assess the frequency of cryptic species, and examined geographic patterns of genetic variation, making this study the first large-scale genetic assessment of the butterflies of southern South America. The average sequence divergence to the nearest neighbor (i.e. minimum interspecific distance) was 6.91%, ten times larger than the mean distance to the furthest conspecific (0.69%), with a clear barcode gap present in all but four of the species represented by two or more specimens. As a consequence, the DNA barcode library was extremely effective in the discrimination of these species, allowing a correct identification in more than 95% of the cases. Singletons (i.e. species represented by a single sequence) were also distinguishable in the gene trees since they all had unique DNA barcodes, divergent from those of the closest non-conspecific. The clustering algorithms implemented recognized from 416 to 444 barcode clusters, suggesting that the actual diversity of butterflies in Argentina is 3%-9% higher than currently recognized. Furthermore, our survey added three new records of butterflies for the country (Eurema agave, Mithras hannelore, Melanis hillapana). In summary, this study not only supported the utility of DNA barcoding for the identification of the butterfly species of Argentina, but also highlighted several cases of both deep intraspecific and shallow interspecific divergence that should be studied in more detail.

DNA Barcoding of an Assembly of Montane Andean Butterflies (Satyrinae): Geographical Scale and Identification Performance

DNA barcoding is a technique used primarily for the documentation and identification of biological diversity based on mitochondrial DNA sequences. Butterflies have received particular attention in DNA barcoding studies, although varied performance may be obtained due to different scales of geographic sampling and speciation processes in various groups. The montane Andean Satyrinae constitutes a challenging study group for taxonomy. The group displays high richness, with more of 550 species, and remarkable morphological similarity among taxa, which renders their identification difficult. In the present study, we evaluated the effectiveness of DNA barcodes in the identification of montane Andean satyrines and the effect of increased geographical scale of sampling on identification performance. Mitochondrial sequences were obtained from 104 specimens of 39 species and 16 genera, collected in a forest remnant in the northwest Andes. DNA barcoding has proved to be a useful tool for the identification of the specimens, with a well-defined gap and producing clusters with unambiguous identifications for all the morphospecies in the study area. The expansion of the geographical scale with published data increased genetic distances within species and reduced those among species, but did not generally reduce the success of specimen identification. Only in Forsterinaria rustica (Butler, 1868), a taxon with high intraspecific variation, the barcode gap was lost and low support for monophyly was obtained. Likewise, expanded sampling resulted in a substantial increase in the intraspecific distance in Morpho sulkowskyi (Kollar, 1850); Panyapedaliodes drymaea (Hewitson, 1858); Lymanopoda obsoleta (Westwood, 1851); and Lymanopoda labda Hewitson, 1861; but for these species, the barcode gap was maintained. These divergent lineages are nonetheless worth a detailed study of external and genitalic morphology variation, as well as ecological features, in order to determine the potential existence of cryptic species. Even including these cases, DNA barcoding performance in specimen identification was 100% successful based on monophyly, an unexpected result in such a taxonomically complicated group.

Close congruence between Barcode Index Numbers (bins) and species boundaries in the Erebidae (Lepidoptera: Noctuoidea) of the Iberian Peninsula

The DNA barcode reference library for Lepidoptera holds much promise as a tool for taxonomic research and for providing the reliable identifications needed for conservation assessment programs. We gathered sequences for the barcode region of the mitochondrial cytochrome c oxidase subunit I gene from 160 of the 176 nominal species of Erebidae moths (Insecta: Lepidoptera) known from the Iberian Peninsula. These results arise from a research project which constructing a DNA barcode library for the insect species of Spain. New records for 271 specimens (122 species) are coupled with preexisting data for 38 species from the Iberian fauna. Mean interspecific distance was 12.1%, while the mean nearest neighbour divergence was 6.4%. All 160 species possessed diagnostic barcode sequences, but one pair of congeneric taxa (Eublemma rosea and Eublemma rietzi) were assigned to the same BIN. As well, intraspecific sequence divergences higher than 1.5% were detected in four species which likely represent species complexes. This study reinforces the effectiveness of DNA barcoding as a tool for monitoring biodiversity in particular geographical areas and the strong correspondence between sequence clusters delineated by BINs and species recognized through detailed taxonomic analysis.

Probing planetary biodiversity with DNA barcodes: The Noctuoidea of North America

This study reports the assembly of a DNA barcode reference library for species in the lepidopteran superfamily Noctuoidea from Canada and the USA. Based on the analysis of 69,378 specimens, the library provides coverage for 97.3% of the noctuoid fauna (3565 of 3664 species). In addition to verifying the strong performance of DNA barcodes in the discrimination of these species, the results indicate close congruence between the number of species analyzed (3565) and the number of sequence clusters (3816) recognized by the Barcode Index Number (BIN) system. Distributional patterns across 12 North American ecoregions are examined for the 3251 species that have GPS data while BIN analysis is used to quantify overlap between the noctuoid faunas of North America and other zoogeographic regions. This analysis reveals that 90% of North American noctuoids are endemic and that just 7.5% and 1.8% of BINs are shared with the Neotropics and with the Palearctic, respectively. One third (29) of the latter species are recent introductions and, as expected, they possess low intraspecific divergences.

When COI barcodes deceive: complete genomes reveal introgression in hairstreaks

Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon About 2.3% of each C. cecrops genome has probably (p-value < 0.01, FDR < 0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. cecrops. The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery.

Chromosomal and mitochondrial diversity in Melitaea didyma complex (Lepidoptera, Nymphalidae): eleven deeply diverged DNA barcode groups in one non-monophyletic species?

It is generally accepted that cases of species' polyphyly in COI trees arising as a result of deep intraspecific divergence are negligible, and the detected cases reflect misidentifications or/and methodological errors. Here we studied the problem of species' non-monophyly through chromosomal and molecular analysis of butterfly taxa close to Melitaea didyma (Esper, 1779) (Lepidoptera, Nymphalidae). We found absence or low interspecific chromosome number variation and presence of intraspecific variation, therefore we conclude that in this group, chromosome numbers have relatively low value as taxonomic markers. Despite low karyotype variability, the group was found to have unexpectedly high mitochondrial haplotype diversity. These haplotypes were clustered in 23 highly diverged haplogroups. Twelve of these haplogroups are associated with nine traditionally recognized and morphologically distinct species Melitaea chitralensis Moore, 1901, Melitaea deserticola Oberthür, 1909, Melitaea didymoides Eversmann, 1847, Melitaea gina Higgins, 1941, Melitaea interrupta Colenati, 1846, Melitaea latonigena Eversmann, 1847, Melitaea mixta Evans, 1912, Melitaea saxatilis Christoph, 1873 and Melitaea sutschana Staudinger, 1892. The rest of the haplogroups (11 lineages) belong to a well-known west-palaearctic species Melitaea didyma. The last species is particularly unusual in the haplotypes we obtained. First, it is clearly polyphyletic with respect to COI gene. Second, the differentiation in COI gene between these mostly allopatric (but in few cases sympatric) eleven lineages is extremely high (up to 7.4%), i.e. much deeper than the "standard" DNA barcode species threshold (2.7-3%). This level of divergence normally could correspond not even to different species, but to different genera. Despite this divergence, the bearers of these haplogroups were found to be morphologically indistinguishable and, most importantly, to share absolutely the same ecological niches, i.e. demonstrating the pattern which is hardly compatible with hypothesis of multiple cryptic species. Most likely such a profound irregularity in barcodes is caused by reasons other than speciation and represents an extraordinary example of intra-species barcode variability. Given the deep level of genetic differentiation between the lineages, we assume that there was a long period (up to 5.0 My) of allopatric differentiation when the lineages were separated by geographic or/and ecological barriers and evolved in late Pliocene and Pleistocene refugia of north Africa, the Iberian and Balkan Peninsulas, the Middle East and Central Asia. We discuss the refugia-within-refugia concept as a mechanism explaining the presence of additional diverged minor haplogroups within the areas of the major haplogroups. We also provide the first record of Melitaea gina in Azerbaijan and the record of Melitaea didyma turkestanica as a new taxon for Russia and Europe.

Mitochondrial chromosome as a marker of animal migratory routes: DNA barcoding revealed Asian (non-African) origin of a tropical migrant butterfly Junonia orithya in south Israel

The blue pansy Junonia orithya Linnaeus, 1758 (Lepidoptera, Nymphalidae) is widely distributed along the tropical areas of Africa, Asia and Australia. It is also known as a migrant species in the Levant. Here we record Junonia orithya in south Israel and provide a DNA-barcode-based evidence for its Asian (non-African) origin.

A DNA Barcode Library for North American Pyraustinae (Lepidoptera: Pyraloidea: Crambidae)

Although members of the crambid subfamily Pyraustinae are frequently important crop pests, their identification is often difficult because many species lack conspicuous diagnostic morphological characters. DNA barcoding employs sequence diversity in a short standardized gene region to facilitate specimen identifications and species discovery. This study provides a DNA barcode reference library for North American pyraustines based upon the analysis of 1589 sequences recovered from 137 nominal species, 87% of the fauna. Data from 125 species were barcode compliant (>500bp, <1% n), and 99 of these taxa formed a distinct cluster that was assigned to a single BIN. The other 26 species were assigned to 56 BINs, reflecting frequent cases of deep intraspecific sequence divergence and a few instances of barcode sharing, creating a total of 155 BINs. Two systems for OTU designation, ABGD and BIN, were examined to check the correspondence between current taxonomy and sequence clusters. The BIN system performed better than ABGD in delimiting closely related species, while OTU counts with ABGD were influenced by the value employed for relative gap width. Different species with low or no interspecific divergence may represent cases of unrecognized synonymy, whereas those with high intraspecific divergence require further taxonomic scrutiny as they may involve cryptic diversity. The barcode library developed in this study will also help to advance understanding of relationships among species of Pyraustinae.

Identification of species based on DNA barcode using k-mer feature vector and Random forest classifier

DNA barcoding is a molecular diagnostic method that allows automated and accurate identification of species based on a short and standardized fragment of DNA. To this end, an attempt has been made in this study to develop a computational approach for identifying the species by comparing its barcode with the barcode sequence of known species present in the reference library. Each barcode sequence was first mapped onto a numeric feature vector based on k-mer frequencies and then Random forest methodology was employed on the transformed dataset for species identification. The proposed approach outperformed similarity-based, tree-based, diagnostic-based approaches and found comparable with existing supervised learning based approaches in terms of species identification success rate, while compared using real and simulated datasets. Based on the proposed approach, an online web interface SPIDBAR has also been developed and made freely available at http://cabgrid.res.in:8080/spidbar/ for species identification by the taxonomists.

Species delimitation in the Grayling genus Pseudochazara (Lepidoptera, Nymphalidae, Satyrinae) supported by DNA barcodes

The Palaearctic Grayling genus Pseudochazara encompasses a number of petrophilous butterfly species, most of which are local endemics especially in their centre of radiation in SW Asia and the Balkans. Due to a lack of consistent morphological characters, coupled with habitat induced variability, their taxonomy is poorly understood and species delimitation is hampered. We employed a DNA barcoding approach to address the question of separate species status for several European taxa and provide first insight into the phylogeny of the genus. Unexpectedly we found conflicting patterns with deep divergences between presumably conspecific taxa and lack of divergence among well-defined species. We propose separate species status for Pseudochazara tisiphone, Pseudochazara amalthea, Pseudochazara amymone, and Pseudochazara kermana all of which have separate well supported clades, with the majority of them becoming local endemics. Lack of resolution in the 'Mamurra' species group with well-defined species (in terms of wing pattern and coloration) such as Pseudochazara geyeri, Pseudochazara daghestana and Pseudochazara alpina should be further explored using nuclear molecular markers with higher genetic resolution.

A DNA barcode library for ground beetles (Insecta, Coleoptera, Carabidae) of Germany: The genus Bembidion Latreille, 1802 and allied taxa

As molecular identification method, DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has been proven to be a useful tool for species determination in many insect taxa including ground beetles. In this study we tested the effectiveness of DNA barcodes to discriminate species of the ground beetle genus Bembidion and some closely related taxa of Germany. DNA barcodes were obtained from 819 individuals and 78 species, including sequences from previous studies as well as more than 300 new generated DNA barcodes. We found a 1:1 correspondence between BIN and traditionally recognized species for 69 species (89%). Low interspecific distances with maximum pairwise K2P values below 2.2% were found for three species pairs, including two species pairs with haplotype sharing (Bembidion atrocaeruleum/Bembidion varicolor and Bembidion guttula/Bembidion mannerheimii). In contrast to this, deep intraspecific sequence divergences with distinct lineages were revealed for two species (Bembidion geniculatum/Ocys harpaloides). Our study emphasizes the use of DNA barcodes for the identification of the analyzed ground beetles species and represents an important step in building-up a comprehensive barcode library for the Carabidae in Germany and Central Europe as well.

Can butterflies cope with city life? Butterfly diversity in a young megacity in southern China

During 30 years of unprecedented urbanization, plant diversity in Shenzhen, a young megacity in southern China, has increased dramatically. Although strongly associated with plant diversity, butterfly diversity generally declines with urbanization, but this has not been investigated in Shenzhen. Considering the speed of urbanization in Shenzhen and the large number of city parks, we investigated butterfly diversity in Shenzhen parks. We measured butterfly species richness in four microhabitats (groves, hedges, flowerbeds, and unmanaged areas) across 10 parks and examined the relationship with three park variables: park age, park size, and distance from the central business district. Butterflies were identified based on wing morphology and DNA barcoding. We collected 1933 butterflies belonging to 74 species from six families; 20% of the species were considered rare. Butterfly species richness showed weak negative correlations with park age and distance from the central business district, but the positive correlation with park size was statistically significant (p = 0.001). Among microhabitat types, highest species richness was recorded in unmanaged areas. Our findings are consistent with others in suggesting that to promote urban butterfly diversity it is necessary to make parks as large as possible and to set aside areas for limited management. In comparison to neighbouring cities, Shenzhen parks have high butterfly diversity.

Turning Up the Heat on a Hotspot: DNA Barcodes Reveal 80% More Species of Geometrid Moths along an Andean Elevational Gradient

We sampled 14,603 geometrid moths along a forested elevational gradient from 1020-3021 m in the southern Ecuadorian Andes, and then employed DNA barcoding to refine decisions on species boundaries initially made by morphology. We compared the results with those from an earlier study on the same but slightly shorter gradient that relied solely on morphological criteria to discriminate species. The present analysis revealed 1857 putative species, an 80% increase in species richness from the earlier study that detected only 1010 species. Measures of species richness and diversity that are less dependent on sample size were more than twice as high as in the earlier study, even when analysis was restricted to an identical elevational range. The estimated total number of geometrid species (new dataset) in the sampled area is 2350. Species richness at single sites was 32-43% higher, and the beta diversity component rose by 43-51%. These impacts of DNA barcoding on measures of richness reflect its capacity to reveal cryptic species that were overlooked in the first study. The overall results confirmed unique diversity patterns reported in the first investigation. Species diversity was uniformly high along the gradient, declining only slightly above 2800 m. Species turnover also showed little variation along the gradient, reinforcing the lack of evidence for discrete faunal zones. By confirming these major biodiversity patterns, the present study establishes that incomplete species delineation does not necessarily conceal trends of biodiversity along ecological gradients, but it impedes determination of the true magnitude of diversity and species turnover.

Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago

Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra's most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8-54.4%. This has implications in the species' ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.

Determining threshold values for barcoding fungi: lessons from Cortinarius (Basidiomycota), a highly diverse and widespread ectomycorrhizal genus

Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by >3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and lineage based-alignments. Our study indicates that 1%-2% more species can be distinguished by using the full-length ITS barcode as compared to either the ITS1 or ITS2 regions alone. Optimal threshold values for different picking approaches and genetic marker lengths inferred from a subset of species containing major lineages ranged from 97.0% to 99.5% sequence similarity using clustering optimization and UNITE SH, and from 1% to 2% sequence dissimilarity with CROP. Errors for the optimal cutoff ranged from 0% to 70%, and these can be reduced to a maximum of 22% when excluding species lacking a barcode gap. A threshold value of 99% is suitable for distinguishing species in the majority of lineages in the genus using the entire ITS region but only 90% of the species could be identified using just the ITS1 or ITS2 region. Prior identification of species, lacking barcode gaps and their subsequent separate analyses, maximized the accuracy of threshold approaches.

Fast Census of Moth Diversity in the Neotropics: A Comparison of Field-Assigned Morphospecies and DNA Barcoding in Tiger Moths

The morphological species delimitations (i.e. morphospecies) have long been the best way to avoid the taxonomic impediment and compare insect taxa biodiversity in highly diverse tropical and subtropical regions. The development of DNA barcoding, however, has shown great potential to replace (or at least complement) the morphospecies approach, with the advantage of relying on automated methods implemented in computer programs or even online rather than in often subjective morphological features. We sampled moths extensively for two years using light traps in a patch of the highly endangered Atlantic Forest of Brazil to produce a nearly complete census of arctiines (Noctuoidea: Erebidae), whose species richness was compared using different morphological and molecular approaches (DNA barcoding). A total of 1,075 barcode sequences of 286 morphospecies were analyzed. Based on the clustering method Barcode Index Number (BIN) we found a taxonomic bias of approximately 30% in our initial morphological assessment. However, a morphological reassessment revealed that the correspondence between morphospecies and molecular operational taxonomic units (MOTUs) can be up to 94% if differences in genitalia morphology are evaluated in individuals of different MOTUs originated from the same morphospecies (putative cases of cryptic species), and by recording if individuals of different genders in different morphospecies merge together in the same MOTU (putative cases of sexual dimorphism). The results of two other clustering methods (i.e. Automatic Barcode Gap Discovery and 2% threshold) were very similar to those of the BIN approach. Using empirical data we have shown that DNA barcoding performed substantially better than the morphospecies approach, based on superficial morphology, to delimit species of a highly diverse moth taxon, and thus should be used in species inventories.

Interpretation of mitochondrial diversity in terms of taxonomy: a case study of Hyponephele lycaon species complex in Israel (Lepidoptera, Nymphalidae, Satyrinae)

It is difficult to interpret mitochondrial diversity in terms of taxonomy even in cases in which a concordance exists between mitochondrial, ecological and morphological markers. Here we demonstrate this difficulty through a study of Israeli Hyponephele butterflies. We show that samples commonly identified as Hyponephelelycaon are represented on Mount Hermon in Israel by two sympatric groups of individuals distinct both in mitochondrial DNA-barcodes (uncorrected p-distance = 3.5%) and hindwing underside pattern. These two groups were collected in different biotopes. They also tended to be different in length of brachia in male genitalia, although the latter character is variable. We reject the hypothesis that the discovered COI haplogroups are selectively neutral intraspecific characters. We hypothesize that they represent: either (1) two different biological species, or (2) a consequence of a strong positive selection acting at intraspecific level and resulting in two intraspecific clusters adapted to low and to high elevations. If we accept the first hypothesis, then provisionally these two haplogroups can be attributed to transpalearctic Hyponephelelycaon sensu stricto and to Hyponephelelycaonoides, previously known from Iran and East Turkey.

Looking back on a decade of barcoding crustaceans

Species identification represents a pivotal component for large-scale biodiversity studies and conservation planning but represents a challenge for many taxa when using morphological traits only. Consequently, alternative identification methods based on molecular markers have been proposed. In this context, DNA barcoding has become a popular and accepted method for the identification of unknown animals across all life stages by comparison to a reference library. In this review we examine the progress of barcoding studies for the Crustacea using the Web of Science data base from 2003 to 2014. All references were classified in terms of taxonomy covered, subject area (identification/library, genetic variability, species descriptions, phylogenetics, methods, pseudogenes/numts), habitat, geographical area, authors, journals, citations, and the use of the Barcode of Life Data Systems (BOLD). Our analysis revealed a total number of 164 barcoding studies for crustaceans with a preference for malacostracan crustaceans, in particular Decapoda, and for building reference libraries in order to identify organisms. So far, BOLD did not establish itself as a popular informatics platform among carcinologists although it offers many advantages for standardized data storage, analyses and publication.