A taxonomic study of genus Teleogryllus from East Asia (Insecta: Orthoptera: Gryllidae)

Crickets belonging to Teleogryllus spp. are widely distributed in East Asia and they are difficult to distinguish. In this study, a phylogenetic tree of Teleogryllus is reconstructed by COI gene, and all species can be distinguished well. The possible evolutionary histories of male genitalia, songs and life history are discussed. The result supports establishing subgenera Macroteleogryllus and Brachyteleogryllus of Teleogryllus spp. from East Asia. T. boninensis is moved to Brachyteleogryllus. The calling song of four species includes both long and short chirps, and the rest just have single chirps. The species inhabit sympatrically trend to have different type of calling song. Egg overwinter type evolved several times independently.     

Which moss is which? Identification of the threatened moss Orthodontium gracile using molecular and morphological techniques

Taxonomic misidentification has potentially serious consequences for the management of threatened species. Closely related moss species are often difficult to distinguish from each other using morphological characteristics. Here we compared the use of molecular (DNA barcoding of the trnL-F intron, AFLPs) and morphological techniques to demonstrate that ex situ cultures, held for re-introduction trails, of the UK critically endangered moss Orthodontium gracile were contaminated with the potentially invasive species O. lineare. Barcoding techniques and AFLPs were both successful in determining Orthodontium species identity. There was some discrepancy between determinations from molecular and morphological techniques and some individuals were misidentified using morphological characteristics alone. When species identity is critical, for example prior to re-establishment or re-introduction programmes, we recommend that identity of mosses and other bryophytes be established by molecular techniques, in particular barcoding of the trnL-F intron.     

Integrative taxonomy at work: DNA barcoding of taeniids harboured by wild and domestic cats

In modern taxonomy, DNA barcoding is particularly useful where biometric parameters are difficult to determine or useless owing to the poor quality of samples. These situations are frequent in parasitology. Here, we present an integrated study, based on both DNA barcoding and morphological analysis, on cestodes belonging to the genus Taenia, for which biodiversity is still largely underestimated. In particular, we characterized cestodes from Italian wildcats (Felis silvestris silvestris), free‐ranging domestic cats (Felis silvestris catus) and hybrids populations. Adult taeniids were collected by post‐mortem examinations of the hosts and morphologically identified as Taenia taeniaeformis. We produced cox1 barcode sequences for all the analysed specimens, and we compared them with reference sequences of individuals belonging to the genus Taenia retrieved from GenBank. In order to evaluate the performance of a DNA barcoding approach to discriminate these parasites, the strength of correlation between species identification based on classical morphology and the molecular divergence of cox1 sequences was measured. Our study provides clear evidence that DNA barcoding is highly efficient to reveal the presence of cryptic lineages within already‐described taeniid species. Indeed, we detected three well‐defined molecular lineages within the whole panel of specimens morphologically identified as T. taeniaeformis. Two of these molecular groups were already identified by other authors and should be ranked at species level. The third molecular group encompasses only samples collected in Italy during this study, and it represents a third candidate species, still morphologically undescribed.     

Molecular identification of mosquitoes (Diptera: Culicidae) in southeastern Australia

DNA barcoding is a modern species identification technique that can be used to distinguish morphologically similar species, and is particularly useful when using small amounts of starting material from partial specimens or from immature stages. In order to use DNA barcoding in a surveillance program, a database containing mosquito barcode sequences is required. This study obtained Cytochrome Oxidase I (COI) sequences for 113 morphologically identified specimens, representing 29 species, six tribes and 12 genera; 17 of these species have not been previously barcoded. Three of the 29 species ─ Culex palpalis, Macleaya macmillani, and an unknown species originally identified as Tripteroides atripes ─ were initially misidentified as they are difficult to separate morphologically, highlighting the utility of DNA barcoding. While most species grouped separately (reciprocally monophyletic), the Cx. pipiens subgroup could not be genetically separated using COI. The average conspecific and congeneric p‐distance was 0.8% and 7.6%, respectively. In our study, we also demonstrate the utility of DNA barcoding in distinguishing exotics from endemic mosquitoes by identifying a single intercepted Stegomyia aegypti egg at an international airport. The use of DNA barcoding dramatically reduced the identification time required compared with rearing specimens through to adults, thereby demonstrating the value of this technique in biosecurity surveillance. The DNA barcodes produced by this study have been uploaded to the ‘Mosquitoes of Australia–Victoria’ project on the Barcode of Life Database (BOLD), which will serve as a resource for the Victorian Arbovirus Disease Control Program and other national and international mosquito surveillance programs.     

DNA barcoding reveals a cryptic nemertean invasion in Atlantic and Mediterranean waters

For several groups, like nemerteans, morphology-based identification is a hard discipline, but DNA barcoding may help non-experts in the identification process. In this study, DNA barcoding is used to reveal the cryptic invasion of Pacific Cephalothrix cf. simula into Atlantic and Mediterranean coasts. Although DNA barcoding is a promising method for the identification of Nemertea, only 6 % of the known number of nemertean species is currently associated with a correct DNA barcode. Therefore, additional morphological and molecular studies are necessary to advance the utility of DNA barcoding in the characterisation of possible nemertean alien invasions.     

A review of the subgenus Epicterodes of Arichanna (Lepidoptera,Geometridae, Ennominae), with description of one new species

The subgenus Epicterodes Wehrli, 1933 of Arichanna Moore, 1868 is reviewed. Six species are recognized, of which, A. (E). denticularia sp. nov. is described as new to science from China. One new synonym is established based on morphological and genetic similarity: A. (E.) flavomacularia Leech, 1897 (=A. (E.) perimelaina Wehrli, 1933 syn. nov.). Results of DNA barcoding for Epicterodes are briefly discussed. Diagnoses for all the species are provided and illustrations of adults, genitalia and distribution map are presented.     

DNA Barcoding as an Effective Tool in Improving a Digital Plant Identification System: A Case Study for the Area of Mt. Valerio, Trieste (NE Italy)

Background

Identification keys are decision trees which require the observation of one or more morphological characters of an organism at each step of the process. While modern digital keys can overcome several constraints of classical paper-printed keys, their performance is not error-free. Moreover, identification cannot be always achieved when a specimen lacks some morphological features (i.e. because of season, incomplete development or miss-collecting). DNA barcoding was proven to have great potential in plant identification, while it can be ineffective with some closely related taxa, in which the relatively brief evolutionary distance did not produce differences in the core-barcode sequences.

Methodology/Principal Findings

In this paper, we investigated how the DNA barcoding can support the modern digital approaches to the identification of organisms, using as a case study a local flora, that of Mt. Valerio, a small hill near the centre of Trieste (NE Italy). The core barcode markers (plastidial rbcL and matK), plus the additional trnH-psbA region, were used to identify vascular plants specimens. The usefulness of DNA barcoding data in enhancing the performance of a digital identification key was tested on three independent simulated scenarios.

Conclusions/Significance

Our results show that the core barcode markers univocally identify most species of our local flora (96%). The trnH-psbA data improve the discriminating power of DNA barcoding among closely related plant taxa. In the multiparametric digital key, DNA barcoding data improves the identification success rate; in our simulation, DNA data overcame the absence of some morphological features, reaching a correct identification for 100% of the species. FRIDA, the software used to generate the digital key, has the potential to combine different data sources: we propose to use this feature to include molecular data as well, creating an integrated identification system for plant biodiversity surveys.     

DNA barcodes of eight species in genus Sebastes

DNA barcode is effective for biological taxonomy and is able to identify species from any life-history stage. In the present study, eight species which belong to four different subgenera of genus Sebastes found in China sea waters were identified by cytochrome c oxidase I (COI) barcode. The results indicated that the intra-species variation in DNA barcode was less than inter-species variation. When the phylogenetic trees were reconstructed by neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian methods, all the species clustered in their groups distinguishable by high bootstrap values, which proved that COI barcode is a powerful means to differentiate species of Sebastes and supports their identification. When the molecular tree was compared to the morphological tree, only Sebastes trivittatus in subgenus Sebastocles settled in the different positions. It is suggested that S. trivittatus is one of the shallowest occurring species in the Northwest Pacific due to its life characters.     

The dark side of pseudoscorpion diversity: The German Barcode of Life campaign reveals high levels of undocumented diversity in European false scorpions

DNA barcoding is particularly useful for identification and species delimitation in taxa with conserved morphology. Pseudoscorpions are arachnids with high prevalence of morphological crypsis. Here, we present the first comprehensive DNA barcode library for Central European Pseudoscorpiones, covering 70% of the German pseudoscorpion fauna (35 out of 50 species). For 21 species, we provide the first publicly available COI barcodes, including the rare Anthrenochernes stellae Lohmander, a species protected by the FFH Habitats Directive. The pattern of intraspecific COI variation and interspecific COI variation (i.e., presence of a barcode gap) generally allows application of the DNA barcoding approach, but revision of current taxonomic designations is indicated in several taxa. Sequences of 36 morphospecies were assigned to 74 BINs (barcode index numbers). This unusually high number of intraspecific BINs can be explained by the presence of overlooked cryptic species and by the accelerated substitution rate in the mitochondrial genome of pseudoscorpions, as known from previous studies. Therefore, BINs may not be an appropriate proxy for species numbers in pseudoscorpions, while partitions built with the ASAP algorithm (Assemble Species by Automatic Partitioning) correspond well with putative species. ASAP delineated 51 taxonomic units from our data, an increase of 42% compared with the present taxonomy. The Neobisium carcionoides complex, currently considered a polymorphic species, represents an outstanding example of cryptic diversity: 154 sequences from our dataset were allocated to 23 BINs and 12 ASAP units.     

蒟蒻薯属 (薯蓣科) 植物DNA条形码研究

蒟蒻薯属（Tacca）植物种间在形态上差别不大,导致分类上存在一定的困难。DNA条形码是一种利用短的DNA标准片段来鉴别和发现物种的方法。本研究利用核基因ITS片段和叶绿体基因trnH psbA, rbcL, matK片段对蒟蒻薯属6个种的DNA条形码进行研究,对4个DNA片段可用性,种内种间变异,barcode gap进行了分析,采用Tree based和BBA两种方法比较不同序列的鉴定能力。结果显示：单片段ITS正确鉴定率最高,片段组合rbcL+matK正确鉴定率最高。支持CBOL植物工作组推荐的条码组合rbcL+matK可作为蒟蒻薯属物种鉴定的标准条码,建议ITS片段作为候选条码。丝须蒟蒻薯Tacca integrifolia采自西藏的居群与马来西亚居群形成了2个不同的遗传分支,且两者在形态上也存在一定的差异,很可能是一个新种。     

中国冠果蝇属一新种和二新记录种及DNA条形码信息(双翅目:果蝇科)

基于形态学和分子遗传学证据,描述了冠果蝇属1新种Stegana(Stegana)helvippecta sp.nov.和2中国新记录种:S.(S.)furta(Linnaeus,1767)和 S.(S.)taba Okada,1971;利用41 条 DNA 条形码信息,分析了18种冠果蝇的遗传距离,并提供了中国产全部1...     

Identifying Chinese species of Gammarus （Crustacea： Amphipoda） using DNA barcoding

Using a standard cytochrome c oxidase I sequence, DNA barcoding has been shown to be effective to distinguish known species and to discover cryptic species. Here we assessed the efficiency of DNA barcoding for the amphipod genus Gammarus from China. The maximum intraspecific divergence for widespread species, Gammarus lacustris, was 3.5%, and mean interspecific divergence reached 21.9%. We presented a conservative benchmark for determining provisional species using maximum intraspecific divergence of Gammarus lacustris. Thirty-one species possessed distinct barcode clusters. Two species were comprised of highly divergent clades with strong neighbor-joining bootstrap values, and likely indicated the presence of cryptic species. Although DNA barcoding is effective, future identification of species of Gammarus should incorporate DNA barcoding and morphological detection[Current Zoology 55(2):158-164,2009].     

Validation of the ITS2 Region as a Novel DNA Barcode for Identifying Medicinal Plant Species

Background

The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL + matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over.

Methodology/Principal Findings

Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level.

Conclusions

The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.     

Authentication of five <Emphasis Type="Italic">Barilius</Emphasis> species from Indian waters using DNA barcoding

Authentic identification of fish species is essential for conserving them as a valuable genetic resource in our environment. DNA barcoding of living beings has become an important and ultimate tool for establishing their molecular identity. Among cyprinids, Barilius is an important genus having nearly 23 species in Indian region whose morphological identification is often difficult due to minute differences in their features. Five species collected from Indian waters and primarily identified as Opsarius bakeri (syn. Barilius bakeri), B. gatensis, B. vagra, B. bendelisis and B. ngawa were authenticated by their DNA barcoding based on mitochondrial COI gene sequences. Five individuals of each species were taken for barcode preparation by COI gene sequencing which yielded one barcode for B. ngawa, two barcodes each for O. bakeri, B. gatensis, B. bendelisis and three barcodes for B. vagra. The order of inter and intra-specific variation was estimated to know a preliminary status of variation prevailing in these cold stream fish species significant for evolution and conservation of these valued species of our ichthyofauna. Average variation within genera was found to be 13.6% with intra-specific variation ranging from 0.0% (B. ngawa) to 0.6% (B. gatensis). These distance data are in the same order found by various researchers globally using COI barcode sequences in different fish species. Phylogenetic relatedness among Barilius species and some other cyprinids validate their status of individual species as established by conventional taxonomy.     

Barcoding bushmeat: molecular identification of Central African and South American harvested vertebrates

The creation and use of a globally available database of DNA sequences from a standardized gene region has been proposed as a tool for species identification, assessing genetic diversity and monitoring the legal and illegal trade in wildlife species. Here, we contribute to the Barcode of Life Data System and test whether a short region of the mitochondrial cytochrome c oxidase subunit 1 (COX1) gene would reliably distinguish among a suite of commonly hunted African and South American mammal and reptile species. We used universal primers to generate reference barcode sequences of 645 bp for 23 species from five vertebrate families (Crocodilidae, Alligatoridae, Bovidae, Suidae and Cercopithecidae). Primer cocktails yielded high quality barcode sequences for 179 out of 204 samples (87.7%) from all species included in the study. For most taxa, we sequenced multiple individuals to estimate intraspecific sequence variability and document fixed diagnostic characters for species identification. Polymorphism in the COX1 fragment was generally low (mean = 0.24%), while differences between congeneric species averaged 9.77%. Both fixed character differences and tree-based maximum likelihood distance methods unambiguously identified unknown and misidentified samples with a high degree of certainty. Barcode sequences also differentiated among newly identified lineages of African crocodiles and identified unusually high levels of genetic diversity in one species of African duiker. DNA barcoding offers promise as an effective tool for monitoring poaching and commercial trade in endangered species, especially when investigating semi-processed or morphologically indistinguishable wildlife products. We discuss additional benefits of barcoding to ecology and conservation.     

DNA Barcoding for Identification of Sugarcane Borers in China

Sugarcane borers are economically damaging insects with species that vary in distribution patterns both geographically and temporally, and vary based on ecological niche. Currently, identification of sugarcane borers is mostly based on morphological characters. However, morphological identification requires taxonomic expertise. An alternative method to identify sugarcane borers is the use of molecular data. DNA barcoding based on partial cytochrome c oxidase subunit 1 (COI) sequences has proven to be a useful tool for rapid and accurate species determination in many insect taxa. This study was conducted to test the effectiveness of DNA barcodes to discriminate among sugarcane borer species in China. Partial sequences of the COI gene (709 bp) were obtained from six species collected from different geographic areas. Results showed that the pairwise intraspecies genetic distance was < 0.02, whereas the interspecies genetic distance ranged from 0.117 to 0.182. Results from a neighbor-joining tree showed that the six sugarcane borer species were certainly separated. These results suggested that the partial COI sequences had high barcoding resolution in discriminating among sugarcane borer species. Our study emphasized the use of DNA barcodes for identification of the analyzed sugarcane borer species and represents an important step for building a comprehensive barcode library for sugarcane borers in China.