DNA barcoding supports reclassification of Japanese Chironomus species (Diptera: Chironomidae)

Non‐biting midges (Diptera: Chironomidae) adapt to species‐specific environmental conditions and hence are promising bioindicators for aquatic and ecotoxicological monitoring. Although their utility for these purposes was historically limited by difficulties in their morphological identification, DNA barcoding offers a possible solution. Here, eight Japanese species of the genus Chironomus, which is characterized by its worldwide distribution and abundance among Chironomidae, were subjected to DNA barcoding using cytochromec oxidase subunit I (COI). To examine whether this DNA barcode is a useful indicator for Japanese species of Chironomus, we calculated genetic distances within and between the COI sequences of Chironomus species both from this study and worldwide and constructed phylogenetic trees. Based on 415 bp COI sequences and the Kimura two‐parameter model, the average genetic distances within 37 species and between 72 species were 2.6% and 17.2%, respectively. Although the ranges of genetic distances within and between species overlapped from 0.8% to 17.3%, 99.7% of average genetic distances between species were >3.0%. Some of this overlap is attributable to distances within species that were “too large” as well as those between species that were “too small”. Of eight Japanese species examined, two showed genetic distances between species that were below a 3.0% threshold, and four had distances within species that were greater than 3.0%. These results suggest a possible reclassification of these species and the need for further sampling to unveil biogeographic variations among different countries and regions.     

Jenynsia lineata species complex,revision and new species description (Cyprinodontiformes: Anablepidae)

The Jenynsia lineata species complex comprises J. lineata from Montevideo, Uruguay and Jenynsia multidentata, from coastal basins of Brazil, Uruguay and Argentina up to 1200 m a.s.l. Taxonomic divisions within this group were tested using three different species delimitation methods, which found the two existing names to be synonyms and revealed a new cryptic species. Jenynsia darwini sp. nov. is distinguished from all congeners by having a unique combination of character states, including the shape of the dorsal postcleithrum (three times higher than wide v. less than two times higher than wide) and female colour pattern in the half of the caudal peduncle with rows of chromatophores segmented in unaligned spots (v. aligned spots forming lines). The new species also differs from J. lineata by having 26 nucleotide substitutions in the mitochondrial gene cytochrome c oxidase I (coI). Phylogenetic analysis of the genus based on morphological characters proposed by previous studies corroborates monophyly of the subgenera Plesiojenynsia and Jenynsia, with the new species being allocated to the subgenus Jenynsia as the sister group of J. lineata.     

The subgenus Ashima (Diptera,Drosophildae, Phortica) from China,with DNA barcoding and descriptions of three new species

In the present study, three new species found in Yunnan, Southwest China were described as members of the subgenus Phortica (Ashima): P. (A.) haba An & Chen, sp. nov., P. (A.) montipagana An & Chen, sp. nov. and P. (A.) qingsongi An & Chen, sp. nov. Barcode sequences (partial sequences of the mitochondrial COI gene) were collected from 61 specimens of 16 known and the above-mentioned three new Ashima species. The intra- and interspecific pairwise K-2P (Kimura two-parameter) COI distances were analysed and a phylogenetic tree was constructed based on the barcode sequences. Species delimitation in this subgenus was supported by integrating barcodes with morphological information, in particular for the three new species, considered to be cryptic species. In addition, the diversification of lineages in the subgenus Ashima was proposed to occur in southern China and adjacent areas, suggesting specific adaptation of Ashima species to the high plateau environments.

http://zoobank.org/urn:lsid:zoobank.org:pub:69A81D0E-5993-426D-9B59-A2AC5E52BD84     

甘肃省鱼类资源现状及DNA条形码在鱼类物种鉴定中的应用

为了摸清甘肃省土著鱼类资源与分布现状, 探索DNA条形码在鱼类辅助物种鉴定中的适用性, 2012年6-9月对甘肃境内黄河水系、嘉陵江水系和河西内陆河水系进行了较全面的鱼类调查。共采集鱼类标本3,087尾, 隶属于5目10科38属64种, 以鲤科种类最多, 为30种, 占总种数的46.88%。物种多样性分析表明, 在黄河水系的夏河和庄浪河多样性指数是所有调查点中最低的, 分别为1.38和1.09。嘉陵江水系各河段的多样性指数较高(H = 2.15-3.27), 其次为河西内陆河水系(H = 2.01-2.83)。在河西内陆河水系中, 疏勒河的均匀度指数最高, 为1.10, 黑河最低(0.68)。庄浪河的优势度指数最高, 为0.34, 而嘉陵江干流两当段的优势度指数在所有调查点中最低, 为0.04。利用DNA条形码分析了49种662尾标本的COI基因部分序列, 大部分种类在neighbor-joining系统树中形成各自的单系, 种内平均遗传距离0.88%, 种间平均遗传距离为9.99%, 在种内和种间COI序列遗传距离之间形成明显的条形码间隙, 斯氏高原鳅(Triplophysa stoliczkae)与达里湖高原鳅(T. dalaica), 甘肃高原鳅(T. robusta)与似鲇高原鳅(T. siluroides), 嘉陵裸裂尻鱼(Schizopygopsis kialingensis)与黄河裸裂尻鱼(S. pylzovi)之间的遗传距离低于2%, 甘肃高原鳅与似鲇高原鳅不能通过COI基因片段区分开, 其他两对物种可以采用核苷酸诊断法来进一步区分。斯氏高原鳅和拉氏鱼岁(Phoxinus lagowskii)种内遗传分歧较大, 揭示种内可能存在隐存种。结果表明, 对某些近缘种和不同地理种群差异较大的物种, 要将分子、形态和地理分布特点结合起来才能准确鉴定。     

Systematics of treefrogs of the Hypsiboas calcaratus and Hypsiboas fasciatus species complex (Anura,Hylidae) with the description of four new species

We review the systematics of the Hypsiboas calcaratus species complex, a group of widely distributed Amazonian hylid frogs. A comprehensive analysis of genetic, morphological, and bioacoustic datasets uncovered the existence of eleven candidate species, six of which are confirmed. Two of them correspond to Hypsiboas fasciatus and Hypsiboas calcaratus and the remaining four are new species that we describe here. Hypsiboas fasciatus sensu stricto has a geographic range restricted to the eastern Andean foothills of southern Ecuador while Hypsiboas calcaratus sensu stricto has a wide distribution in the Amazon basin. Hypsiboas almendarizae sp. n. occurs at elevations between 500 and 1950 m in central and northern Ecuador; the other new species (H. maculateralis sp. n., H. alfaroi sp. n., and H. tetete sp. n.) occur at elevations below 500 m in Amazonian Ecuador and Peru. The new species differ from H. calcaratus and H. fasciatus in morphology, advertisement calls, and mitochondrial and nuclear DNA sequences. Five candidate species from the Guianan region, Peru, and Bolivia are left as unconfirmed. Examination of the type material of Hyla steinbachi, from Bolivia, shows that it is not conspecific with H. fasciatus and thus is removed from its synonymy.     

DNA barcoding provides support for a cryptic species complex within the globally distributed and fishery important opah (Lampris guttatus)

The cornerstone of fisheries management relies on a solid taxonomic base and an understanding of how animals can be grouped into coherent management units. Surprisingly, little is known about the basic biology and ecology of opah (Lampris guttatus), a globally distributed species that is commercially exploited and regionally common in the North Pacific. Recent efforts to collect life history data on this species uncovered evidence of two North Pacific morphotypes. Sequencing of the mitochondrial cytochrome c oxidase I gene (655 bp) for these morphotypes and other specimens collected worldwide (n = 480) produced five strongly diverged and well‐supported clades. Additional sequence data from the cytochrome b gene (1141 bp) as well as the nuclear recombination activating gene 1 (1323 bp) corroborated these results, suggesting these five clades probably represent separate species. Our conclusion that opah is a complex of five separate species has implications for management and indicates a need to gather additional data on these poorly understood fishes.     

Barcoding of Central European Cryptops centipedes reveals large interspecific distances with ghost lineages and new species records from Germany and Austria (Chilopoda,Scolopendromorpha)

In order to evaluate the diversity of Central European Myriapoda species in the course of the German Barcode of Life project, 61 cytochrome c oxidase I sequences of the genus Cryptops Leach, 1815, a centipede genus of the order Scolopendromorpha, were successfully sequenced and analyzed. One sequence of Scolopendracingulata Latreille, 1829 and one of Theatopserythrocephalus Koch, 1847 were utilized as outgroups. Instead of the expected three species (Cryptopsparisi Brolemann, 1920; Cryptopsanomalans Newport, 1844; Cryptopshortensis (Donovan, 1810)), analyzed samples included eight to ten species. Of the eight clearly distinguishable morphospecies of Cryptops, five (Cryptopsparisi; Cryptopscroaticus Verhoeff, 1931; Cryptopsanomalans; Cryptopsumbricus Verhoeff, 1931; Cryptopshortensis) could be tentatively determined to species level, while a further three remain undetermined (one each from Germany, Austria and Croatia, and Slovenia). Cryptopscroaticus is recorded for the first time from Austria. A single specimen (previously suspected as being Cryptopsanomalans), was redetermined as Cryptopsumbricus Verhoeff, 1931, a first record for Germany. All analyzed Cryptops species are monophyletic and show large genetic distances from one another (p-distances of 13.7–22.2%). Clear barcoding gaps are present in lineages represented by >10 specimens, highlighting the usefulness of the barcoding method for evaluating species diversity in centipedes. German specimens formally assigned to Cryptopsparisi are divided into three clades differing by 8.4–11.3% from one another; their intra-lineage genetic distance is much lower at 0–1.1%. The three clades are geographically separate, indicating that they might represent distinct species. Aside from Cryptopsparisi, intraspecific distances of Cryptops spp. in Central Europe are low (<3.3%).     

Taxonomy and molecular phylogeny of the Neotropical genus Atlantoscia (Oniscidea,Philosciidae): DNA barcoding and description of two new species

Identification to the species level using morphology is challenging when usual diagnostic characters are similar amongst related taxa. Within the Neotropical genus Atlantoscia, differences between nominal species are generally small and restricted to a few characters. Despite the power of DNA sequencing to identify and distinguish between species, molecular phylogenies of terrestrial isopods from the Neotropics have not been determined. In this study, two new species of Atlantoscia were described and molecular markers were used to verify both the validity of the current taxonomy and the relationships amongst the species within this genus. All of the recognized Atlantoscia species were strongly supported in the generated phylogenetic trees. The average congeneric distance was 14.7%, with Atlantoscia ituberasensis and Atlantoscia rubromarginata showing the highest genetic divergence. Our results demonstrate the utility of the cytochrome c oxidase subunit I gene together with DNA barcoding to reliably distinguish Atlantoscia species. They also show that DNA barcoding may be helpful in those cases in which classical taxonomy does not provide clear‐cut species resolution. © 2015 The Linnean Society of London     

Diversity of Porifera in the Mediterranean coralligenous accretions,with description of a new species

Temperate reefs, built by multilayers of encrusting algae accumulated during hundreds to thousands of years, represent one of the most important habitats of the Mediterranean Sea. These bioconstructions are known as “coralligenous” and their spatial complexity allows the formation of heterogeneous microhabitats offering opportunities for a large number of small cryptic species hardly ever considered.Although sponges are the dominant animal taxon in the coralligenous rims with both insinuating and perforating species, this group is until now poorly known. Aim of this work is to develop a reference baseline about the taxonomic knowledge of sponges and, considering their high level of phenotypic plasticity, evaluate the importance of coralligenous accretions as a pocket for biodiversity conservation.Collecting samples in four sites along the coast of the Ligurian Sea, we recorded 133 sponge taxa (115 of them identified at species level and 18 at genus level). One species, Eurypon gracilis is new for science; three species, Paratimea oxeata, Clathria (Microciona) haplotoxa and Eurypon denisae are new records for the Italian sponge fauna, eleven species are new findings for the Ligurian Sea. Moreover, seventeen species have not been recorded before from the coralligenous community. The obtained data, together with an extensive review of the existing literature, increase to 273 the number of sponge species associated with the coralligenous concretions and confirm that this habitat is an extraordinary reservoir of biodiversity still largely unexplored, not only taxonomically, but also as to peculiar adaptations and life histories.     

DNA barcoding and morphology reveal two common species in one: Pimpla molesta stat. rev. separated from P. croceipes (Hymenoptera, Ichneumonidae)

Correct species identification is the basis of ecological studies. Nevertheless, morphological examination alone may not be enough to tell species apart. Here, our integrated molecular and morphological studies demonstrate that the relatively widespread and common neotropical parasitoid wasp Pimpla croceipes Cresson, 1874 (Hymenoptera: Ichneumonidae: Pimplinae) actually consists of two distinct species. The name Pimpla molesta (Smith, 1879), stat. rev. is available for the second species. The two species were identified by DNA barcoding and minor differences in morphology and colouration. Our results support the previous notions that DNA barcoding can complement morphological identification and aid the discovery of cryptic species complexes.     

Review and redescription of species in the Oecetis avara group,with the description of 15 new species (Trichoptera,Leptoceridae)

The O. avara group of Oecetis is formally defined to include 4 described species, O. avara (Banks), O. disjuncta (Banks), O. elata Denning & Sykora, and O. metlacenis Bueno-Soria, and 15 new species. Oecetis marquesi Bueno-Soria, previously considered a member of the O. avara group, is treated as incertae sedis to species group, but is also redescribed and treated in the current work. New species described here (with their respective distributions) include: O. acciptrina (Costa Rica, Panama, Ecuador), O. agosta (Mexico), O. angularis (Guatemala to Ecuador), O. apache (SW USA), O. campana (Ecuador), O. constricta (Mexico to Ecuador, Venezuela, and Trinidad), O. houghtoni (North America), O. maritza (Costa Rica), O. mexicana (Mexico to Ecuador), O. patula (Guatemala, Nicaragua), O. protrusa (Mexico to Ecuador), O. sordida (Mexico, USA, Canada), O. tumida (Costa Rica), O. uncata (Costa Rica), and O. verrucula (Mexico to Costa Rica). A key to the species is also provided.     

DNA barcoding of euryglossine bees and the description of new species of Euhesma Michener (Hymenoptera,Colletidae, Euryglossinae)

This paper launches an open access DNA barcoding project “AUSBS” under the Barcoding of Life Datasystems (BOLD). The aims of the project are to help scientists who lack the necessary morphological knowledge to identify known species using molecular markers, to aid native bee specialists with the recognition of species groups that morphologically are difficult to define, and, eventually, to assist with the recognition of new species among known species. Using integrative taxonomy, i.e. morphological comparison to type specimens in Australian museum collections combined with phylogenetic analysis of a fragment of the mitochondrial DNA cytochrome c oxidase subunit I (mtCOI) gene sequences led to the recognition of four new species of Euhesma Michener (Hymenoptera: Colletidae: Euryglossini) collected during intensive surveys in remote Australian conservation areas, which are described. The new species are Euhesma micans, Euhesma lyngouriae, and Euhesma aulaca in a species group associated with Eremophila flowers, and Euhesma albamala in the walkeriana species group.     

Cryptic species within the Chydorus sphaericus species complex (Crustacea: Cladocera) revealed by molecular markers and sexual stage morphology

The cosmopolitanism paradigm in the biogeography of freshwater invertebrates is currently being replaced by non-cosmopolitanism or continental endemism. Benthic water fleas (Cladocera) from the family Chydoridae were the first group of freshwater invertebrates for which non-cosmopolitanism and cryptic diversity was substantiated by morphological studies. Yet, little is known about genetic differentiation and evolutionary history of chydorid species complexes. Here we present the first analysis of the genetic versus morphological differentiation in a benthic cladoceran species complex—Chydorus sphaericus s. str. using sequence variation in a nuclear (ribosomal internal transcribed spacer 2, ITS-2) and a mitochondrial (cytochrome c oxidase subunit I, COI) genes in 50 Holarctic localities. We tested for continental endemism and cryptic diversity predicted by previous morphological studies. We found evidence for the presence of at least seven putative regional species in the Holarctic, at least three of them being distributed beyond a single continent. While the molecular and sexual stage characters showed general concordance on species lineages, parthenogenetic female characters lacked resolution or were unassociated with molecular lineages. We conclude that cryptic regional lineages of benthic cladocerans are apparent and that the sexual stages represent the most informative morphological source of species characters for this environmental indicator group.     

Cutting the Gordian Knot: Phylogenetic and ecological diversification of the Mesalina brevirostris species complex (Squamata,Lacertidae)

Mesalina are small lacertid lizards occurring in the Saharo‐Sindian deserts from North Africa to the east of the Iranian plateau. Earlier phylogenetic studies indicated that there are several species complexes within the genus and that thorough taxonomic revisions are needed. In this study, we aim at resolving the phylogeny and taxonomy of the M. brevirostris species complex distributed from the Middle East to the Arabian/Persian Gulf region and Pakistan. We sequenced three mitochondrial and three nuclear gene fragments, and in combination with species delimitation and species‐tree estimation, we infer a time‐calibrated phylogeny of the complex. The results of the genetic analyses support the presence of four clearly delimited species in the complex that diverged approximately between the middle Pliocene and the Pliocene/Pleistocene boundary. Species distribution models of the four species show that the areas of suitable habitat are geographically well delineated and nearly allopatric, and that most of the species have rather divergent environmental niches. Morphological characters also confirm the differences between the species, although sometimes minute. As a result of all these lines of evidence, we revise the taxonomy of the Mesalina brevirostris species complex. We designate a lectotype for Mesalina brevirostris Blanford, 1874; resurrect the available name Eremias bernoullii Schenkel, 1901 from the synonymy of M. brevirostris; elevate M. brevirostris microlepis (Angel, 1936) to species status; and describe Mesalina saudiarabica, a new species from Saudi Arabia.     

Evolutionary systematics of the Australian Cyzicidae (Crustacea,Branchiopoda, Spinicaudata) with the description of a new genus

In Australia's arid and semi‐arid zone, most aquatic habitats are nonpermanent. Although approximately 70% of its land surface belongs to these zones, very little is known of the iconic ‘large branchiopods’ that inhabit these important and widespread habitats. In the present study, we investigated 737 Australian specimens of the spinicaudatan taxa Caenestheria and Caenestheriella with a combination of one mitochondrial (cytochrome oxidase subunit I; COI) and three nuclear (elongation factor 1α, internal transcribed spacer 2, and 28S) markers to assess the diversity of species, their phylogenetic relationships, and phylogeographical history. The initial species delimitation was based on COI employing a combination of phylogenetic analyses and two automated approaches to species delimitation (general mixed Yule coalescent model and Automated Barcode Gap Discovery). The outcome was tested by the nuclear markers and considered under differing species concepts. The number of delineated species ranged from 14–27, in no case being in full agreement with any of the two automated approaches. The lower numbers resulted if inferred reproductive isolation, as required for the biological or Hennigian species concept, was employed. Although nuclear markers did not indicate ongoing reproduction, the lack of sympatric co‐occurrences inhibited inferences of definitive reproductive isolation in several instances. If monophyly or an ‘independent evolutionary fate’ was employed, as required for the phylogenetic or evolutionary species concepts, the species' distribution was of no importance and up to 27 species could be delimitated. Because the Australian representatives of both studied genera could not be clearly separated from each other but constitute a single monophyletic clade separated from all available non‐Australian representatives of these genera, we describe a new spinicaudatan genus Ozestheria gen. nov. to accommodate these species. Populations revealed relatively small levels of genetic differentiation over large areas of central and eastern Australia. By far the most pronounced levels of genetic differentiation were observed towards the north‐eastern regions, a pattern possibly explainable by ecological conditions and the movement of nomadic water birds that disperse resting eggs. © 2015 The Linnean Society of London     

DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species

There is currently international interest in the application of DNA barcoding as a tool for plant species discrimination and identification. In this study, we evaluated the utility of five candidate plant DNA barcoding regions [rbcL, matK, trnH-psbA, trnL-F and internal transcribed spacer (ITS)] in Eurasian yews. This group of species is taxonomically difficult because of a lack of clear-cut morphologically differences between species and hence represents a good test case for DNA barcoding. Forty-seven accessions were analysed, representing all taxa treated in current floristic works and covering most of the distribution range of Taxus in Eurasia. As single loci, trnL-F and ITS showed the highest species discriminatory power, each resolving 11 of 11 lineages (= barcode taxa). Species discrimination using matK, trnH-psbA and rbcL individually was lower, with matK resolving 8 of 10, trnH-psbA 7 of 11 and rbcL 5 of 11 successfully sequenced lineages. The proposed CBOL core barcode (rbcL + matK) resolved 8 of 11 lineages. Combining loci generally increased the robustness (measured by clade support) of the barcoding discrimination. Based on overall performance, trnL-F and ITS, separately or combined, are proposed as barcode for Eurasian Taxus. DNA barcoding discriminated recognized taxa of Eurasian Taxus, namely T. baccata, T. cuspidata, T. fuana and T. sumatrana, and identified seven lineages among the T. wallichiana group, some with distinct geographical distributions and morphologies, and potentially representing new species. Using the proposed DNA barcode, a technical system can be established to rapidly and reliably identify Taxus species in Eurasia for conservation protection and for monitoring illegal trade.     

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...