Molecular data reveal cryptic lineages within the northeastern Atlantic and Mediterranean small mussel drills of the Ocinebrina edwardsii complex (Mollusca: Gastropoda: Muricidae)

We used a molecular phylogenetic approach to investigate species delimitations and diversification in the mussel drills of the Ocinebrina edwardsii complex by means of a combination of nuclear (internal transcribed spacer 2, ITS2) and mitochondrial [cytochrome oxidase subunit I (COI) and 16S] sequences. Our sample included 243 specimens ascribed to seven currently accepted species from 51 sites. Five of the samples were from either the type locality of a nominal species or a close nearby locality (O. edwardsii from Corsica, O. carmelae and O. piantonii from the Kerkennah Islands, O. hispidula from the Gulf of Gabès and O. leukos from the Canary Islands), one from the inferred original locality (O. ingloria from Venice Lagoon), and specimens assigned in the recent literature to O. nicolai. We used a combination of distance‐ and tree‐based species delimitation methods to identify Molecular Operational Taxonomic Units (MOTUs) to compare with the a priori species identifications. The consensus tree obtained by BEAST on the COI alignment allows the recognition of several distinct clades supported by the three species delimitation methods employed. The eight‐MOTUs scenario, shared by the Automatic Barcode Gap Discovery (ABGD) and Generalized Mixed Yule‐Coalescent (GMYC) methods, comprises the following major clades: clade A contains the south Tunisian species Ocinebrina piantonii Cecalupo, Buzzurro & Mariani from which the sympatric taxon O. carmelae Cecalupo, Buzzurro & Mariani (new synonym) cannot be separated; clades B and C bring together all populations from the Aegean Sea and some from the Ionian Sea, respectively; clade D groups, on the one hand, the south Tunisian samples morphologically assigned to O. hispidula Pallary and, on the other, Atlantic and Alboran Sea samples (including the Canarian taxon O. leukos Houart); clade E includes a sample from the type locality of O. edwardsii and several samples from the Tyrrhenian Sea; clades F and G correspond to a few samples from the Venice Lagoon and the Tyrrhenian Sea, respectively; clade H groups the bulk of samples from the Adriatic Sea, including samples from the Venice Lagoon morphologically identified as Ocinebrina ingloria (Crosse), and some from the Ionian Sea. No final conclusions could be reached to reconcile the currently recognized morphological taxa with the clades suggested by the COI data. The geographical structure proposed by the mitochondrial markers is similar to that found in other marine invertebrates and partially corresponds to the species defined by shell characters. We propose here a framework for the revision of the Ocinebrina edwardsii species complex, suggesting a geographical pattern for the diversification of this group in the studied area. © 2013 The Linnean Society of London     

An integrative approach to species discrimination in the Anagrus atomus group sensu stricto (Hymenoptera: Mymaridae), with a description of a new species

Egg parasitoids of the genus Anagrus Haliday (Hymenoptera: Mymaridae) are natural enemies of many pests around the world. We used an integrative approach to characterize some species belonging to the Anagrus atomus group, using specimens reared from leafhoppers infesting some Lamiaceae. Starting from morphological identifications based on available keys, we carried out a multi-locus genetic characterization using phylogenetic and species delimitation analyses, and integrated it with biological and morphometric evidence. This approach revealed the existence of a new species, A. nepetellae sp. nov., here described along with its phenological traits. The approach also allowed us to characterize the expected taxonomic stability of other putative species within the group. We propose two new species groups called the atomus group sensu stricto and the vilis group, with the goal of streamlining the taxonomy of the atomus group. We also present a key for the identification of females of the European species of the atomus group sensu stricto. Some specimens show heterozygosity in 28S-D2 sequences, suggesting hybridization between A. atomus and A. nepetellae, which, if it is common between other species as well, could partly explain the taxonomic problems in the genus Anagrus. DNA sequencing of specimens reared by the same biofactory at different times suggests involuntary contamination leading to the displacement of a laboratory strain of A. atomus by A. nepetellae, which may have resulted from undetected partial reproductive compatibility.http://zoobank.org/urn:lsid:zoobank.org:pub:DFCD7654-5AA5-4E4F-AE48-24377BAACEFE     

DNA条形码技术在河北保定、廊坊地区鳞翅目昆虫上的应用及小型区域数据库的构建

【目的】为了探究DNA条形码技术和小型区域数据库在蛾类鉴定上的可行性,本研究利用条形码通用引物扩增了采自河北保定、廊坊地区10种夜蛾82个样本的线粒体细胞色素c氧化酶亚基I(Mitochondrial cytochrome c oxidase subunit I,COⅠ)基因序列。【方法】基于进化树、距离、阈值和特征的方法。【结果】虽然整体分类效果较好,但基于进化树、距离、阈值的方法都无法将二点委夜蛾Athetis lepigone进行较好的分类;样本LF110802.008总是被分入标瑙夜蛾Maliattha signifera类群,与形态学分类结果发生分歧。基于特征的方法运用核基因28S进行分析,结果与形态分类一致。同时还探讨了基于特征方法得到的诊断特征数目与样本数量之间的关系,发现两者密切相关;基于特征的方法对小样本量的鉴定也比较有效。本研究建立了小型区域的DNA条形码数据库,使物种识别具有更强的针对性,有利于提高地区性蛾类病虫害防治效果。【结论】在蛾类鉴定中,DNA条形码有很好的分类效果,小型区域数据库很有实际应用价值。     

New Bathynellidae (Crustacea) taxa and their relationships in the Fortescue catchment aquifers of the Pilbara region,Western Australia

In the past 20?years, the number of subterranean taxa discovered in Australia, especially in the Pilbara bioregion, has considerably increased due to incidental environmental surveys often associated with mining development. Bathynellidae are an important component of stygofauna and they occur in most Australian aquifers, but their collection and identification are difficult due to their habitat, and small and fragile bodies with conservative morphology. The study of Pilbaranella ethelensis in the upper Fortescue catchment contributed to a better understanding of the group at local scale, but knowledge at larger catchment scale is still limited. Abundant material collected by different environmental consultant companies on behalf of mining companies allowed an accurate analysis of the populations of Central Hamersley Range bathynellids. A new genus and one new species from the lower Fortescue catchment, Fortescuenella serenitatis gen. et sp. nov., is described using an approach that integrates morphological and molecular data. Three additional lineages are defined through morphology and DNA sequencing, using Automatic Barcode Gap Discovery and Poisson Tree Processes species delimitation methods. Based on previous knowledge on bathynellids and other stygofauna we expected to find multiple taxa, geographically restricted, possibly related to each other and to Pilbaranella genus described upstream of the Fortescue catchment. The phylogenetic reconstruction of the relationships among known lineages of the family in the Pilbara highlights a pattern of distribution characterized by a complex evolutionary history that does not reflect contemporary surface water catchments, suggesting a diversification that preceded the aridification processes started in the north of Western Australia during the Miocene. This study also clarifies the status of the 'cosmopolitan' Bathynella by excluding the Australian bathynellids from this genus.

http://www.zoobank.org/urn:lsid:zoobank.org:act:E30796F4-1026-4278-BC13-45091DCB44CC     

The DNA barcoding of Mediterranean combtooth blennies suggests the paraphyly of some taxa (Perciformes,Blenniidae)

A dataset including novel and publicly available mtDNA COI sequences of 14 Mediterranean combtooth blenny species belonging to nine genera was assembled in order to provide a reference dataset for DNA barcoding studies. Some inconsistencies in the current taxonomy of some genera were observed. In particular, the monophyly of the genera Parablennius and Salaria is not supported by the present dataset and the absence of reciprocal monophyly between the morphospecies Salaria basilisca and S. pavo questions their status and stresses the need of a revision of the genus Salaria.     

A rosette by any other name: species diversity in the Bangiales (Rhodophyta) along the South African coast

The Bangiales is an order of Rhodophyta, widely distributed around the globe and best known for its economic value in the nori industry. The morphological simplicity of the group offers limited distinguishing characters for species identification. We therefore delimited species of the Bangiales along the South African coast based on two unlinked loci, the mitochondrial cox1 gene and the plastid rbcL gene, supplemented with additional sequence data from a third gene, the nuclear nSSU. Application of DNA-based species delimitation methods including the Automatic Barcode Gap Discovery (ABGD), General Mixed Yule Coalescent (GYMC) and Poisson Tree Processes (PTP), resulted in the recognition of 10 Porphyra and three Pyropia species in South Africa, only three of which had been previously described. Additional species of Bangiales previously recorded along the South African coast were added to our final species list despite not being found in the present study, resulting in an estimate of 14–16 Bangiales species occurring along this shoreline. Most of this extensive genetic diversity has been misidentified as the commonly rosette-forming species P. capensis. The name P. capensis currently refers to a species complex and cannot be attached to any one species with certainty. All species in this complex, confirmed using genetic data, are endemic to South Africa. Our results compare well with other Southern Hemisphere countries, such as Chile and New Zealand, where high genetic diversity, species richness and endemicity have also been found.     

Cryptic diversity and discordance in single‐locus species delimitation methods within horned lizards (Phrynosomatidae: Phrynosoma)

Biodiversity reduction and loss continues to progress at an alarming rate, and thus, there is widespread interest in utilizing rapid and efficient methods for quantifying and delimiting taxonomic diversity. Single‐locus species delimitation methods have become popular, in part due to the adoption of the DNA barcoding paradigm. These techniques can be broadly classified into tree‐based and distance‐based methods depending on whether species are delimited based on a constructed genealogy. Although the relative performance of these methods has been tested repeatedly with simulations, additional studies are needed to assess congruence with empirical data. We compiled a large data set of mitochondrial ND4 sequences from horned lizards (Phrynosoma) to elucidate congruence using four tree‐based (single‐threshold GMYC, multiple‐threshold GMYC, bPTP, mPTP) and one distance‐based (ABGD) species delimitation models. We were particularly interested in cases with highly uneven sampling and/or large differences in intraspecific diversity. Results showed a high degree of discordance among methods, with multiple‐threshold GMYC and bPTP suggesting an unrealistically high number of species (29 and 26 species within the P. douglasii complex alone). The single‐threshold GMYC model was the most conservative, likely a result of difficulty in locating the inflection point in the genealogies. mPTP and ABGD appeared to be the most stable across sampling regimes and suggested the presence of additional cryptic species that warrant further investigation. These results suggest that the mPTP model may be preferable in empirical data sets with highly uneven sampling or large differences in effective population sizes of species.     

SPdel: A pipeline to compare and visualize species delimitation methods for single-locus datasets

An accurate species delimitation is critical for biological studies. In this context, the use of molecular techniques along with species delimitation methods would help to a rapid and accurate biodiversity assessment. The species delimitation methods cluster data sets of orthologous sequences in molecular operational taxonomic units (MOTU). In particular, the methods based on a single gene are easily integrated with the widely used DNA barcoding approach. We developed SPdel a user-friendly pipeline to integrate different single-gene species delimitation methods. SPdel is designed to calculate and compare MOTUs obtained by different species delimitation approaches. SPdel also outputs diverse ready-to-publish quality figures, that facilitate the interpretation of results. SPdel aims to help researchers use species delimitation methods that would improve biodiversity studies.     

Genetic and morphological studies of species status for poorly known endemic Trochulus phorochaetius (Bourguignat, 1864) (Gastropoda: Pulmonata: Hygromiidae), and its comparison with closely related taxa

The taxonomic status of Trochulus phorochaetius and its phylogenetic relationships to Trochulus plebeius and Trochulus hispidus were evaluated based on molecular, morphological, and genital anatomy data. The canonical discriminant analysis (CDA) of shell morphology allowed the clear differentiation between these three nominal species, whereas the genitalia revealed their high similarity. Analyses of cytochrome c oxidase subunit I (COI) sequences were not always congruent with the differentiation between these three species by shell characters. None of them formed a monophyletic group covering all its sequences. Instead, many sequences obtained from individuals classified to the same morphospecies, and/or usually collected from the same region or country, created highly supported separate clades and delimited clusters. Three distinct clades containing sequences of two morphospecies originating from the same country were identified in molecular phylogenetic and species delimitation studies: (1) T. plebeius + T. hispidus from Great Britain; (2) T. plebeius + T. hispidus from Poland; and (3) T. phorochaetius + T. hispidus from France. In the latter case some of the sequences were even identical. Their genetic similarity could indicate the ability to hybridize, which may be evidenced by the lack of major differences in their reproductive system. The assignment of distinctive morphospecies, and thus existing taxonomic names, to genetically defined evolutionary lineages is premature and arbitrary to some extent at this stage. © 2013 The Linnean Society of London