Monday, February 6, 2017

Monday reads

Welcome to another week -  a couple of interesting reads to get you started:

This study tested the effectiveness of COI barcodes for the discrimination of anuran species from the Amazon basin and other Neotropical regions. Barcodes were determined for a total of 59 species, with a further 58 species being included from GenBank. In most cases, distinguishing species using the barcodes was straightforward. Each species had a distinct COI barcode or codes, with intraspecific distances ranging from 0% to 9.9%. However, relatively high intraspecific divergence (11.4-19.4%) was observed in some species, such as Ranitomeya ventrimaculata, Craugastor fitzingeri, Hypsiboas leptolineatus, Scinax fuscomarginatus and Leptodactylus knudseni, which may reflect errors of identification or the presence of a species complex. Intraspecific distances recorded in species for which samples were obtained from GenBank (Engystomops pustulosus, Atelopus varius, Craugastor podiciferus, and Dendropsophus labialis) were greater than those between many pairs of species. Interspecific distances ranged between 11-39%. Overall, the clear differences observed between most intra- and inter-specific distances indicate that the COI barcode is an effective tool for the identification of Neotropical species in most of the cases analyzed in the present study.

In marine and estuarine benthic communities, the inventory and estimation of species richness are often hampered by the need for broad taxonomic expertise across several phyla. The use of DNA metabarcoding has emerged as a powerful tool for the fast assessment of species composition in a diversity of ecological communities. Here, we tested the amplification success of five primer sets targeting different COI-5P regions by 454 pyrosequencing to maximize the recovery of two simulated macrobenthic communities containing 21 species (SimCom1 and SimCom 2). Species identification was first performed against a compiled reference library of macrobenthic species. Reads with similarity results to reference sequences between 70% and 97% were then submitted to GenBank and BOLD to attempt the identification of concealed species in the bulk sample. The combination of at least three primer sets was able to recover more species than any primer set alone, achieving 85% of represented species in SimCom1 and 76% in SimCom2. Our approach was successful to detect low-frequency specimens, as well as concealed species, in the bulk sample, indicating the potential for the application of this approach on marine bioassessment and inventory, including the detection of "hidden" biodiversity that would hardly be possible based on morphology only.

Integrative taxonomy, a multi-disciplinary approach adding modern techniques to traditional morphology-based methods (e.g. molecular and morphological criteria), can play an important role in bioinvasion research to identify introduced taxa, discover pathways of introduction and inform authorities to control and prevent future introductions. The present study is the first on introduced populations of Callosciurus, Asiatic tree squirrels, known as potentially invasive species in Europe (Italy, Belgium and France). We combined molecular (mitochondrial DNA markers: CoxI, D-loop) and morphometric analysis on skulls, comparing them to the widest morphological and molecular datasets ever assembled for Callosciurus. Squirrels collected in Italy and Belgium share the same haplotypes and skull characteristics, but are conspicuously different from the French population in Antibes. Genetic data revealed close similarity between French squirrels and Pallas's squirrels, Callosciurus erythraeus, from Taiwan, China. Italian and Belgian squirrels formed an independent taxonomic lineage in genetic analyses, whose taxonomic rank needs further investigation. The morphological and morphometric characteristics of these 2 populations are, however, similar to known specimens assigned to Callosciurus erythraeus. These results may indicate a common origin for the populations found in Belgium and Italy. In contrast, French specimens suggest an independent introduction event of squirrels originating from Asia.

The E. dispunctella and E. triseriatella complexes sensu Traugott-Olsen are merged. The newly delineated E. dispunctella complex is re-defined and diagnosed. Until now, a total of 64 species has been assigned to this species complex. The taxonomy of the constituent species has been obscure owing to their identities based on unvalidated traits, in particular subtle differences on branching points of forewing veins. The taxonomy of the E. dispunctella complex is revised on the basis of new material, new and reevaluated information obtained from morphology and biology, as well as from the standard barcode region of COI, with at least partial barcode data derived from 194 recently collected specimens and 33 holotypes. As a result, the number of species considered valid is markedly reduced, with only 19 species now recognized. The following 43 new synonymies are established: Elachista dispunctella (Duponchel, 1843) = E. cahorsensis Traugott-Olsen, 1992, syn. nov., E. imbi Traugott-Olsen, 1992, syn. nov., E. karsholti Traugott-Olsen, 1992, syn. nov., E. mannella Traugott-Olsen, 1992, syn. nov., E. multipunctella Traugott-Olsen, 1992, syn. nov., E. pocopunctella Traugott-Olsen, 1992, syn. nov., E. povolnyi Traugott-Olsen, 1992, syn. nov., E. punctella Traugott-Olsen, 1992, syn. nov., E. hallini Traugott-Olsen, 1992, syn. nov., E. intrigella Traugott-Olsen, 1992, syn. nov., E. skulei Traugott-Olsen, 1992 and E. nielspederi Traugott-Olsen, 1992, syn. nov.; E. tribertiella Traugott-Olsen, 1985 = E. toveella Traugott-Olsen, 1985, syn. nov., E. baldizzonella Traugott-Olsen, 1985, syn. nov., E. veletaella Traugott-Olsen, 1992, syn. nov., E. bazaella Traugott-Olsen, 1992, syn. nov. and E. louiseae Traugott-Olsen, 1992, syn. nov.; E. parvula Parenti, 1978 = E. minusculella Traugott-Olsen, 1992, syn. nov. and E. blancella Traugott-Olsen, 1992, syn. nov.; E. maboulella Chr├ętien, 1915 = E. catalunella Traugott-Olsen, 1992, syn. nov., E. gerdmaritella Traugott-Olsen, 1992, syn. nov. and E. gielisi Traugott-Olsen, 1992, syn. nov.; E. glaseri Traugott-Olsen, 1992 = E. rikkeae Traugott-Olsen, 1992, syn. nov., E. totanaensis Traugott-Olsen, 1992, syn. nov., E. olemartini Traugott-Olsen, 1992, syn. nov., E. bengtssoni Traugott-Olsen, 1992, syn. nov., E. senecai Traugott-Olsen, 1992, syn. nov., E. wadielhiraensis Traugott-Olsen, 1992, syn. nov., E. rissaniensis Traugott-Olsen, 1992, syn. nov. and E. michelseni Traugott-Olsen, 1992, syn. nov.; E. hispanica Traugott-Olsen, 1992 = E. vivesi Traugott-Olsen, 1992, syn. nov., E. cuencaensis Traugott-Olsen, 1992, syn. nov., E. vanderwolfi Traugott-Olsen, 1992, syn. nov., E. amparoae Traugott-Olsen, 1992, syn. nov., E. varensis Traugott-Olsen, 1992, syn. nov., E. luqueti Traugott-Olsen, 1992, syn. nov., E. occidentella Traugott-Olsen, 1992, syn. nov. and E. clintoni Traugott-Olsen, 1992, syn. nov.; E. berndtiella Traugott-Olsen, 1985 = E. casascoensis Traugott-Olsen, 1992, syn. nov.; E. triseriatella Stainton, 1854 = E. contisella Chr├ętien, 1922, syn. nov., E. gregori Traugott-Olsen, 1988, syn. nov., and E. lerauti Traugott-Olsen, 1992, syn. nov.; E. elsaella Traugott-Olsen, 1988 = E. svenssoni Traugott-Olsen, 1988, syn. nov.; E. galactitella (Eversmann, 1844) = E. madridensis Traugott-Olsen, 1992, syn. nov. E. deresyensis Traugott-Olsen, 1988 is resurrected as a valid species, stat. rev. Evidence from DNA barcodes suggests that there may exist further species, but in the absence of distinct morphological differences, they are not formally described as new.


No comments:

Post a Comment