TY  - JOUR
AU  - Achurra, A.
AU  - Erséus, C.
PY  - 2013
TI  - DNA barcoding and species delimitation: the Stylodrilus heringianus case (Annelida : Clitellata : Lumbriculidae)
SP  - 118-128
JF  - Invertebrate Systematics
VL  - 27
IS  - 1Mar 2013
N2  - Individuals of the aquatic oligochaete species Stylodrilus heringianus Claparède, 1862 were collected across a part of this species’ distribution range in Sweden, Estonia, Great Britain and Spain to test whether they represent a single metapopulation or several separately evolving lineages. Using sequences of the barcoding gene cytochrome c oxidase subunit I (COI) and two nuclear genes (internal transcribed spacer region and histone 3), three different approaches were conducted: pairwise distance-method, Bayesian inference and network analysis. Both the COI phylogeny and network analyses were concordant in recovering six haplotype clusters, which showed a maximum genetic distance of 7.7% (K2P) among each other. Nevertheless, nuclear genes failed to confirm any lineage separation, and we conclude that the sampled specimens all belong to the same species. A phylogeographic history with allopatric divergence and secondary contact is suggested to explain this intraspecific pattern of mitochondrial divergence and nuclear non-divergence. The study shows that a mitochondrial single-locus approach can be problematic for the accurate delimitation of species, and we emphasise the need for nuclear genes as supplementary markers, when taxonomic resolution is assessed with COI barcodes.
UR  - http://www.publish.csiro.au/paper/IS12049
ID  - 3060
ER  - 

TY  - JOUR
AU  - Alcántar-Escalera, F.J.
AU  - García-Varela, M.
AU  - Vázquez-Domínguez, E.
AU  - Pérez-Ponce de León, G.
PY  - 2013
TI  - Using DNA barcoding to link cystacanths and adults of the acanthocephalan Polymorphus brevis in central Mexico
SP  - n/a-n/a
JF  - Molecular Ecology Resourcesparasites
N1  - Mar 2013
KW  - acanthocephala
cytochrome c oxidase subunit I
endoparasite
life cycle
polymorphidae
N2  - In parasitic organisms, particularly helminths, the usage of the mitochondrial cytochrome c oxidase subunit I gene as the standard DNA barcoding region for species identification and discovery has been very limited. Here, we present an integrated study, based on both DNA barcoding and morphological analyses, for acanthocephalans belonging to the genus Polymorphus, whose larvae (cystacanths) are commonly found in the mesentery of freshwater fishes, while adults are found in the intestine of fish-eating birds. The alpha taxonomy of parasitic helminths is based on adult morphological traits, and because of that larval forms cannot be identified to species level based on morphology alone. DNA barcoding offers an alternative tool for linking larval stages of parasitic organisms to known adults. We sequenced cystacanths collected from freshwater fishes in localities across central Mexico and adults obtained from fish-eating birds, to determine whether they were conspecific. To corroborate the molecular results, we conducted a morphometric analysis with ‘Proboscis profiler’, which is a software tool developed to detect heterogeneity in morphologically similar acanthocephalans based on the multivariate statistical analysis of proboscis hook dimensions. Both sources of information indicate that cystacanths infecting freshwater fishes in central Mexico belong to a single species, Polymorphus brevis.
UR  - http://dx.doi.org/10.1111/1755-0998.12090
ID  - 3049
ER  - 

TY  - JOUR
AU  - Ashfaq, M.
AU  - Asif, M.
AU  - Anjum, Z.I.
AU  - Zafar, Y.
PY  - 2013
TI  - Evaluating the capacity of plant DNA barcodes to discriminate species of cotton (Gossypium: Malvaceae)
SP  - n/a-n/a
JF  - Molecular Ecology ResourcesMar 2013
KW  - DNA barcoding
Gossypium
ITS2
matK
rbcL
species discrimination
N2  - Although two plastid regions have been adopted as the standard markers for plant DNA barcoding, their limited resolution has provoked the consideration of other gene regions, especially in taxonomically diverse genera. The genus Gossypium (cotton) includes eight diploid genome groups (A–G, and K) and five allotetraploid species which are difficult to discriminate morphologically. In this study, we tested the effectiveness of three widely used markers (matK, rbcL, and ITS2) in the discrimination of 20 diploid and five tetraploid species of cotton. Sequences were analysed locus-wise and in combinations to determine the most effective strategy for species identification. Sequence recovery was high, ranging from 92% to 100% with mean pairwise interspecific distance highest for ITS2 (3.68%) and lowest for rbcL (0.43%). At a 0.5% threshold, the combination of matK+ITS2 produced the greatest number of species clusters. Based on ‘best match’ analysis, the combination of matK+ITS2 was best, while based on ‘all species barcodes’ analysis, ITS2 gave the highest percentage of correct species identifications (98.93%). The combination of sequences for all three markers produced the best resolved tree. The disparity index test based on matK+rbcL+ITS2 was significant (P < 0.05) for a higher number of species pairs than the individual gene sequences. Although all three barcodes separated the species with respect to their genome type, no single combination of barcodes could differentiate all the Gossypium species, and tetraploid species were particularly difficult.
UR  - http://dx.doi.org/10.1111/1755-0998.12089
ID  - 3043
ER  - 

TY  - JOUR
AU  - Bayer, S.
AU  - Schönhofer, A.L.
PY  - 2013
TI  - Phylogenetic relationships of the spider family Psechridae inferred from molecular data, with comments on the Lycosoidea (Arachnida : Araneae)
SP  - 53-80
JF  - Invertebrate Systematics
VL  - 27
IS  - 1spiders
N1  - Mar 2013
KW  -, , , , , , Desidae, Thomisidae, Ctenidae, Miturgidae, Lycosidae, Pisauridae, Oxyopidae, Zoropsidae, Zorocratidae, COI, 28S rRNA, calamistrum, Laos, Thailand, DNA barcoding.
N2  - We investigated the relative phylogenetic position of the spider genera Psechrus Thorell, 1878 and Fecenia Simon, 1887 comprising the family Psechridae Simon, 1890 within the order Araneae (plus 50 outgroup taxa) using molecular data of the nuclear 28S rRNA gene and the mitochondrial cytochrome c oxidase subunit I (COI) gene. We further revised the placement of genera formerly hypothesised in Psechridae and tested morphological species and species-group hypotheses recently proposed for Psechrus and Fecenia. Our results showed both genera as monophyletic and included within Lycosoidea but indicated no support for a monophyletic family Psechridae. Support for relationships to particular genera of other families (Lycosidae, Pisauridae) was found to be equally low. Previous removal of the genera Stiphidion Simon, 1902, Poaka Forster &amp; Wilton, 1973, Tengella Dahl, 1901 (Metafecenia F. O. Pickard-Cambridge, 1902) and Themacrys Simon, 1906 from Psechridae is confirmed by recovering most of them outside Lycosoidea. For Tengella (part of Lycosoidea) a close relation to Psechridae is not supported. In the species-rich genus Psechrus, morphologically predefined species groups were generally recovered as monophyletic. COI information was applied to test the morphological species hypotheses for 28 Psechridae species, most of them represented by more than one specimen. Our analyses corroborated all proposed species and indicated COI as reliable for barcoding both Psechrus and Fecenia. COI enabled assignment of a juvenile specimen to Fecenia protensa, establishing the first species record for Brunei.
UR  - http://www.publish.csiro.au/paper/IS12017
ID  - 3061
ER  - 

TY  - JOUR
AU  - Bhargava, M.
AU  - Sharma, A.
PY  - 2013
TI  - DNA Barcoding in plants: Evolution and applications of in silico approaches and resources
JF  - Molecular Phylogenetics and Evolution
IS  - 0informatics
N1  - Mar 2013
KW  - DNA barcoding
Plants
Bioinformatics
Softwares
Databases
N2  - Abstract Bioinformatics has played an important role in the analysis of DNA barcoding data. The process of DNA barcoding initially involves the available data collection from the existing databases. Many databases have been developed in recent years eg. MMDBD [Medicinal Materials DNA Barcode Database], BioBarcode etc. In case of non-availability of sequences, sequencing has to be done in vitro for which a recently developed software ecoPrimers can be helpful. This is followed by multiple sequence alignment. Further, basic sequence statistics computation and phylogenetic analysis can be performed by MEGA and PHYLIP/PAUP tools respectively. Some of the recent tools for in silico and statistical analysis specifically designed for barcoding viz. CAOS (Character Based DNA Barcoding), BRONX (DNA Barcode Sequence Identification Incorporating Taxonomic Hierarchy and within Taxon Variability), Spider (Analysis of species identity and evolution, particularly DNA barcoding), jMOTU and Taxonerator (Turning DNA Barcode Sequences into Annotated OTUs), OTUbase (Analysis of OTU data and taxonomic data), SAP (Statistical Assignment Package) etc. have been discussed and analysed in this review. The paper presents a comprehensive overview of the various in silico methods, tools, softwares and databases used for DNA barcoding of plants.
UR  - http://dx.doi.org/10.1016/j.ympev.2013.03.002
ID  - 3044
ER  - 

TY  - JOUR
AU  - Blank, S.M.
AU  - Shinohara, A.
AU  - Altenhofer, E.
PY  - 2013
TI  - The Eurasian species of Xyela (Hymenoptera, Xyelidae): taxonomy, host plants and distribution
SP  - 1-+
JF  - Zootaxa
JO  - Zootaxa
VL  - 3629
IS  - 1
Y2  - Mar
N1  - CCC:000316173600001
N1  - ISI Document Delivery No.: 106VU
Blank, Stephan M. Shinohara, Akihiko Altenhofer, Ewald
Magnolia press
Auckland
Mar 2013
KW  - Palearctic, Oriental, new species, Pinaceae, Pinus, barcoding
sawflies hymenoptera, united-states, dna barcodes, symphyta,
tenthredinidae, pamphiliidae, orussidae, america, history
N2  - The 28 Eurasian species of Xyela Dalman, 1819 are revised based on material of ca 7,500 imagines including about 10 % reared specimens. Larvae of Eurasian Xyela usually are monophagous and feed inside the staminate cones of pines (Pinus spp., Pinaceae). Based on the reared material, on identification by barcoding and on additional collection observations, the larval host associations for the Xyela species are summarized and additional biological observations are noted. An illustrated key to the species and distribution maps are presented. Eight species are described as new: X. altenhoferi Blank, sp. nov. (Croatia), X. heldreichii Blank, sp. nov. (Albania, Greece), X. koraiensis Blank & Shinohara, sp. nov. (Russia, South Korea), X. peuce Blank, sp. nov. (Bulgaria), X. pumilae Blank & Shinohara, sp. nov. (Japan), X. rasnitsyni Blank & Shinohara, sp. nov. (China, Russia, South Korea), X. sibiricae Blank, sp. nov. (Mongolia, Russia), and X. uncinatae Blank, sp. nov. (Andorra, France, Spain, Switzerland). For the other species redescriptions are given. A lectotype is designated for X. longula Dalman, 1819, and neotypes are designated for X. graeca J. P. E. F. Stein, 1876 and Pinicola julii Brebisson, 1818. The following new synonymies are proposed: X. lii Xiao, 1988, syn. nov. of X. sinicola Maa, 1947; X. nigroabscondita Haris & Gyurkovics, 2011, syn. nov. of X. lugdunensis (Berland, 1943); and X. suwonae Ryu & Lee, 1992, syn. nov. of X. ussuriensis Rasnitsyn, 1965.
AD  - [Blank, SM] Senckenberg Deutsch Entomol Inst, D-15374 Muncheberg, Germany [Shinohara, A] Natl Museum Nat & Sci, Dept Zool, Tsukuba, Ibaraki 3050005, Japan
Blank, Stephan M. (reprint author), Senckenberg Deutsch Entomol Inst, Eberswalder Str 90, D-15374 Muncheberg, Germany
stephan.blank@senckenberg.de shinohar@kahaku.go.jp ewald.altenhofer@aon.at
UR  - http://dx.doi.org/10.11646/zootaxa.3629.1.1
ID  - 3073
ER  - 

TY  - JOUR
AU  - Bribiesca-Contreras, G.
AU  - Solís-Marín, F.A.
AU  - Laguarda-Figueras, A.
AU  - Zaldívar-Riverón, A.
PY  - 2013
TI  - Identification of echinoderms (Echinodermata) from an anchialine cave in Cozumel Island, Mexico, using DNA barcodes
JF  - Molecular Ecology Resources
VL  - online earlymarine
N1  - Mar 2013
KW  - anchialine cave
barcoding
Caribbean
cox1
Echinodermata
N2  - The echinoderm species richness of the Aerolito de Paraiso anchialine cave, on Cozumel Island, in the Mexican Caribbean, is assessed on the basis of morphological and DNA barcoding data. We included specimens from this cave system and from different open sea areas, and employed two different approaches for species delineation based on DNA barcoding data: a 2% cox1 divergence and the general mixed Yule-coalescent (GMYC) approaches. We subsequently compared the results derived from these approaches with our morphospecies discrimination. A total of 188 cox1 sequences belonging to specimens of four echinoderm classes were examined. The 2% cox1 divergence and GMYC approaches recovered 78 and 70 putative species, respectively, 24 and 22 of which corresponded to specimens from the anchialine system. Of 26 echinoderm species identified in the cave system, seven appear to be endemic to it. Among these are Copidaster carvenicola Solís-Marín & Laguarda-Figueras, 2010, two morphologically distinctive, undescribed species belonging to Asterinides and Ophionereis and four probably cryptic undescribed species originally assigned to Amphipholis squamata (Delle Chiaje, 1839), Astropecten duplicatus Gray, 1840, Copidaster lymani (AH Clark, 1948) and Ophiothrix angulata (Say, 1825). Further research and protection of this particularly fragile ecosystem becomes urgent because construction of tourism developments is planned nearby.
UR  - http://dx.doi.org/10.1111/1755-0998.12098
ID  - 3052
ER  - 

TY  - JOUR
AU  - Deagle, B.E.
AU  - Thomas, A.C.
AU  - Shaffer, A.K.
AU  - Trites, A.W.
AU  - Jarman, S.N.
PY  - 2013
TI  - Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?
JF  - Molecular Ecology Resources
VL  - online earlyMar 2013
KW  - DNA barcoding
Ion Torrent
metabarcoding
next-generation sequencing
pinniped diet
N2  - A goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals’ diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis.
UR  - http://dx.doi.org/10.1111/1755-0998.12103
ID  - 3084
ER  - 

TY  - JOUR
AU  - Delong, J.P.
AU  - Cox, N.S.
AU  - Cox, S.W.
AU  - Hurst, Z.M.
AU  - Smith, J.P.
PY  - 2013
TI  - DNA Sequencing Reveals Patterns of Prey Selection in Migrating Sharp-Shinned Hawks
SP  - 40-46
JF  - The Condor
VL  - 115
IS  - 1
Y2  - 2013/02/01birds
N1  - Mar 2013
N2  - Prey selection of migrating raptors has been documented only rarely. Here we used a genetic approach to identify avian prey of Sharp-shinned Hawks (Accipiter striatus) migrating through central New Mexico. We identified species by comparing profiles of a section of the 16S rRNA mitochondrial gene extracted from feathers of prey of known species to profiles from feathers of prey found on the feet and beaks of migrating hawks. We also quantified prey availability along the migration route with multi-year sampling by mist net at two sites near the raptor-sampling site. Sharp-shinned Hawks took most prey species in proportion to their availability, but they took some species, particularly medium-sized species, more frequently than expected. This pattern may indicate selection for energetically rewarding prey, or the pattern also could arise from differences between our sample of potential prey and the potential prey as viewed by the hawks themselves. The co-occurrence of migrating predators and their prey suggests interesting feedbacks that likely influenced the evolution of migration strategies of both hawks and songbirds in this area.
UR  - http://dx.doi.org/10.1525/cond.2012.120016
ID  - 3104
ER  - 

TY  - JOUR
AU  - Durgante, F.M.
AU  - Higuchi, N.
AU  - Almeida, A.
AU  - Vicentini, A.
PY  - 2013
TI  - Species Spectral Signature: Discriminating closely related plant species in the Amazon with Near-Infrared Leaf-Spectroscopy
SP  - 240-248
JF  - Forest Ecology and Management
VL  - 291
IS  - 0Mar 2013
blog?
KW  - Plant identification
Forest inventory
Lecythidaceae
Eschweilera
Corythophora
N2  - Abstract The combined use of high technology instruments and appropriate techniques for discriminating tree species is necessary to improve the biodiversity inventory system in tropical countries. The Fourier-Transform Near-Infrared (FT-NIR) Leaf Spectroscopy appears to be a promising tool for plant species discrimination. In this study, we demonstrate an outstanding performance of FT-NIR, extracted from dried whole leaves, to discriminate closely related species of Eschweilera and Corythophora, Lecythidaceae, a major component of Amazonian forests. We obtained 36 spectral readings, from the adaxial and abaxial surfaces of dried leaves, for 159 individuals representing 10 species. Each spectrum consisted of 1557 FT-NIR absorbance values. We compared the rate of correct specimen (individual tree) identification to species for different datasets and discriminant models, in which individual spectrum consisted of different combinations as to the number of variables (all, stepwise selected), different number of reads per specimen (all reads, adaxial, abaxial, randomly selected), and discriminant models (cross-validation, test set validation). The best results indicated 99.4% of correct specimen identification when we used the average of all 36 spectral readings per specimen and stepwise selected variables. The lowest rate was on average 96.6% when a single spectral reading was used per individual tree (randomly sampled over 100 replicates). Overall, the rate of correct species discrimination was always high and insensible to variable selection, to the different datasets, and to the two major validation models we used. These Species Spectral Signature (SSS) provided better results than current DNA barcoding for plant identification in tropical forests, and represents a fast, low-cost sampling technique. Although further tests are required to assess the potential of FT-NIR spectroscopy for plant identification at broader geographical and phylogenetic scales, the results presented in this paper indicate that SSS extracted from herbarium specimens can be a powerful reference to identify specimens, even when lacking reproductive structures, an so of particular interest for forest inventory and management.
UR  - http://dx.doi.org/10.1016/j.foreco.2012.10.045
ID  - 3068
ER  - 

TY  - JOUR
AU  - Eurlings, M.C.M.
AU  - Lens, F.
AU  - Pakusza, C.
AU  - Peelen, T.
AU  - Wieringa, J.J.
AU  - Gravendeel, B.
PY  - 2013
TI  - Forensic Identification of Indian Snakeroot (Rauvolfia serpentina Benth. ex Kurz) Using DNA Barcoding
SP  - n/a-n/a
JF  - Journal of Forensic SciencesMar 2013
KW  - forensic science
DNA typing
Apocynaceae
CITES
medicinal plants
Rauvolfia
rps16 intron
N2  - Indian snakeroot (Rauvolfia serpentina) is a valuable forest product, root extracts of which are used as an antihypertensive drug. Increasing demand led to overharvesting in the wild. Control of international trade is hampered by the inability to identify root samples to the species level. We therefore evaluated the potential of molecular identification by searching for species-specific DNA polymorphisms. We found two species-specific indels in the rps16 intron region for R. serpentina. Our DNA barcoding method was tested for its specificity, reproducibility, sensitivity and stability. We included samples of various tissues and ages, which had been treated differently for preservation. DNA extractions were tested in a range of amplification settings and dilutions. Species-specific rps16 intron sequences were obtained from 79 herbarium accessions and one confiscated root, encompassing 39 different species. Our results demonstrate that molecular analysis provides new perspectives for forensic identification of Indian snakeroot.
UR  - http://dx.doi.org/10.1111/1556-4029.12072
ID  - 3040
ER  - 

TY  - JOUR
AU  - Federici, S.
AU  - Galimberti, A.
AU  - Bartolucci, F.
AU  - Bruni, I.
AU  - De mattia, F.
AU  - Cortis, P.
AU  - Labra, M.
PY  - 2013
TI  - DNA barcoding to analyse taxonomically complex groups in plants: the case of Thymus (Lamiaceae)
SP  - 687-699
JF  - Botanical Journal of the Linnean Society
VL  - 171
IS  - 4Mar 2013
KW  - matK
rbcL
species delimitation
trnH-psbA
N2  - We evaluated the utility of the core barcode regions (matK and rbcL) and the plastid intergenic spacer trnH-psbA to distinguish between Thymus spp. This is a taxonomically complex group that has been investigated so far mainly using morphological approaches. Thirty-six samples representing nine different morphospecies were collected and used for molecular analysis. The three markers showed clear amplification and sequencing. However, the genetic variation and the resulting haplotype networks showed that only Thymus capitatus forms a well-defined ‘barcoding gap’ compared with the other taxa. The identification problems observed in the other Thymus spp. may be related to reduced gene flow among populations, resulting in high intraspecific and low interspecific genetic variation. This situation does not permit the definition of species-specific barcodes. A second hypothesis suggests that morphological traits used for the delimitation of Thymus spp. do not reflect real biological and molecular species boundaries. If this is the case, the taxonomy of Thymus should be revised through extensive sampling and analyses with different tools (i.e. molecular variability, morphology, geographical distribution, etc.) to define the natural units at the species level. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 171, 687–699.
UR  - http://dx.doi.org/10.1111/boj.12034
ID  - 3075
ER  - 

TY  - JOUR
AU  - Fernández-Flores, S.
AU  - Fernández-Triana, J.L.
AU  - Martínez, J.J.
AU  - Zaldívar-Riverón, A.
PY  - 2013
TI  - DNA barcoding species inventory of Microgastrinae wasps (Hymenoptera, Braconidae) from a Mexican tropical dry forest
SP  - n/a-n/a
JF  - Molecular Ecology ResourcesMar 2013
KW  - COI
GYMC model
Mexico
Microgastrinae
parasitoid
N2  - The cosmopolitan Microgastrinae is probably the most diverse braconid subfamily of parasitoid wasps, yet its species diversity is far from being known. As part of a global initiative for DNA barcoding Microgastrinae species, here we show the results of a study that assessed the species richness of this subfamily in a Mexican tropical dry forest located in the Chamela region, near the Pacific coast of Jalisco. Barcoding sequences of a total of 551 microgastrine specimens were generated, corresponding to 238 haplotypes. Performance of two species delineation approaches, a 2% corrected pairwise distance criterion and the general mixed Yule-coalescent (GMYC) method, yielded 100 and 112 putative species, respectively, which belong to 13 genera. The species delimited by the above two approaches were mostly congruent with our morphospecies identification. Ten molecular operational taxonomic units (MOTUs) were split into twenty-two species by the GMYC approach. We found morphological differences between the GMYC species corresponding to three of these MOTUs. Thus, a total of 103 microgastrine species were confirmed for the region of study. Thirty-three species were only represented by males, and therefore, their generic assignment is only tentatively proposed. A new record for the country is provided for the Diolcogaster-basimacula species group. Based on a comparison of nearly 20 000 barcoding sequences released for Microgastrinae from 75 countries, only five microgastrine species from Chamela were found to occur in other countries, four in Costa Rica and one in Canada and the United States.
UR  - http://dx.doi.org/10.1111/1755-0998.12102
ID  - 3085
ER  - 

TY  - JOUR
AU  - Glowska, E.
AU  - Dragun-Damian, A.
AU  - Dabert, J.
PY  - 2013
TI  - DNA-barcoding contradicts morphology in quill mite species Torotrogla merulae and T. rubeculi (Prostigmata: Syringophilidae)
SP  - 51-60
JF  - Folia Parasitol (Praha)
VL  - 60
IS  - 1
Y2  - Feb
N1  - 23539952
N1  - Glowska, Eliza
Dragun-Damian, Anna
Dabert, Jacek
Research Support, Non-U.S. Gov't
Czech Republic
Folia parasitologica
Folia Parasitol (Praha). 2013 Feb;60(1):51-60.
Mar 2013
N2  - Torotrogla merulae Skoracki, Dabert et Ehrnsberger, 2000 and T. rubeculi Skoracki, 2004 have been considered as distinct steno- and monoxenous quill mite species (Acari: Prostigmata: Syringophilidae) parasitizing the thrushes of the genus Turdus Linnaeus and the European robin Erithacus rubecula (Linnaeus), respectively. Morphological and molecular studies on the taxonomical status of these two species provided contradictory results. Well defined differences in morphology were not supported by substantial genetic distance in nucleotide sequences of the DNA barcode (mitochondrial cytochrome c oxidase subunit I, COI, and D2 domain of the nuclear 28S rRNA gene), by the topology of the phylogenetic trees (neighbor-joining, maximum parsimony, maximum likelihood) and the network analyses of the COI haplotype genealogy (median-joining, statistical parsimony) that reveal rubeculi populations nested within merulae haplotypes. Since detected differences between T. merulae and T. rubeculi populations (1.6-2.4% for COI and 0.1% for D2) are comparable to the intraspecific level observed in majority of currently recognized European Torotrogla species and are much lower than the interspecific distances observed in the genus, we postulate their conspecificity. Because main morphological distinctions concern the structures used for feeding, we hypothesize that they are the result of phenotypic plasticity evoked by specific and different environmental conditions prevailing on the host bodies (thickness of the feather quill wall).
AD  - Department of Animal Morphology, Faculty of Biology, A. Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland. glowska@amu.edu.pl
UR  - http://folia.paru.cas.cz/detail.php?id=22107
ID  - 3053
ER  - 

TY  - JOUR
AU  - Gwiazdowski, R.A.
AU  - Elkinton, J.S.
AU  - Dewaard, J.R.
AU  - Sremac, M.
PY  - 2013
TI  - Phylogeographic Diversity of the Winter Moths Operophtera brumata and O. bruceata (Lepidoptera: Geometridae) in Europe and North America
SP  - 143-151
JF  - Annals of the Entomological Society of America
VL  - 106
IS  - 2
Y2  - 2013/03/01leps
N1  - Mar 2013
N2  - The European winter moth, Operophtera brumata (L.), an invasive forest defoliator, is undergoing a rapid range expansion in northeastern North America. The source of this invasion, and phylogeographic diversity throughout its native range, has not been explored. To do this, we used samples from a pheromone-baited trap survey of O. brumata collected across its native range in Europe, and invasive range in North America. Traps in North America also attract a congeneric species, the Bruce spanworm O. bruceata (Hulst), and the western Bruce spanworm O. b. occidentalis (Hulst). From this sampling, we sequenced two regions of the cytochrome c oxidase subunit I mitochondrial gene; one region corresponds to the DNA ‘barcode’ region, the other is a nonoverlapping section. We used these sequences, in combination with sequence data from a recent survey of the Geometridae in western North America, for phylogenetic and phylogeographic analyses to characterize genetic divergence and variation for O. brumata in North America and Europe, and O. bruceata and O. b. occidentalis in North America. We found O. brumata mtDNA diversity to be dominated by a single widespread, and common haplotype. In contrast, O. bruceata shows high haplotype diversity that is evenly distributed throughout North America. Phylogeographic patterns indicate an introduction of O. brumata in British Columbia likely originated from Germany, and suggest the invasive population in northeastern North America may have its origins in the United Kingdom, and/or Germany. We found uncorrected pairwise sequence divergence between Operophtera species to be ≈7%. O. b. occidentalis is ≈ 5% divergent from O. bruceata, has a restricted range in the Pacific Northwest, and has unique morphological characters. Together these lines of evidence suggest O. b. occidentalis may be deserving of species status. Additionally, a single morphologically unique Operophtera specimen, similar to O. bruceata, was collected in southern Arizona, far outside the known range of O. bruceata. This suggests that North America may contain further, unsampled, Operophtera diversity.
UR  - http://dx.doi.org/10.1603/AN12033
ID  - 3059
ER  - 

TY  - JOUR
AU  - Han, J.
AU  - Zhu, Y.
AU  - Chen, X.
AU  - Liao, B.
AU  - Yao, H.
AU  - Song, J.
AU  - Chen, S.
AU  - Meng, F.
PY  - 2013
TI  - The Short ITS2 Sequence Serves as an Efficient Taxonomic Sequence Tag in Comparison with the Full-Length ITS
SP  - 741476
JF  - Biomed Res Int
VL  - 2013
N1  - 23484151
N1  - plants
N1  - Han, Jianping
Zhu, Yingjie
Chen, Xiaochen
Liao, Baoshen
Yao, Hui
Song, Jingyuan
Chen, Shilin
Meng, Fanyun
United States
BioMed research international
Biomed Res Int. 2013;2013:741476. doi: 10.1155/2013/741476. Epub 2013 Jan 17.
Mar 2013
N2  - An ideal DNA barcoding region should be short enough to be amplified from degraded DNA. In this paper, we discuss the possibility of using a short nuclear DNA sequence as a barcode to identify a wide range of medicinal plant species. First, the PCR and sequencing success rates of ITS and ITS2 were evaluated based entirely on materials from dry medicinal product and herbarium voucher specimens, including some samples collected back to 90 years ago. The results showed that ITS2 could recover 91% while ITS could recover only 23% efficiency of PCR and sequencing by using one pair of primer. Second, 12861 ITS and ITS2 plant sequences were used to compare the identification efficiency of the two regions. Four identification criteria (BLAST, inter- and intradivergence Wilcoxon signed rank tests, and TaxonDNA) were evaluated. Our results supported the hypothesis that ITS2 can be used as a minibarcode to effectively identify species in a wide variety of specimens and medicinal materials.
AD  - Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100094, China.
UR  - http://dx.doi.org/10.1155/2013/741476
ID  - 3048
ER  - 

TY  - JOUR
AU  - Hardisty, A.
AU  - Roberts, D.
AU  - Community, T.B.I.
PY  - 2013
TI  - A decadal view of biodiversity informatics: challenges and priorities
SP  - 16
JF  - BMC Ecology
VL  - 13
IS  - 1
N1  - doi:10.1186/1472-6785-13-16
N1  - Mar 2013
N2  - Biodiversity informatics plays a central enabling role in the research community's efforts to address scientific conservation and sustainability issues. Great strides have been made in the past decade establishing a framework for sharing data, where taxonomy and systematics has been perceived as the most prominent discipline involved. To some extent this is inevitable, given the use of species names as the pivot around which information is organised. To address the urgent questions around conservation, land-use, environmental change, sustainability, food security and ecosystem services that are facing Governments worldwide, we need to understand how the ecosystem works. So, we need a systems approach to understanding biodiversity that moves significantly beyond taxonomy and species observations. Such an approach needs to look at the whole system to address species interactions, both with their environment and with other species.It is clear that some barriers to progress are sociological, basically persuading people to use the technological solutions that are already available. This is best addressed by developing more effective systems that deliver immediate benefit to the user, hiding the majority of the technology behind simple user interfaces. An infrastructure should be a space in which activities take place and, as such, should be effectively invisible.This community consultation paper positions the role of biodiversity informatics, for the next decade, presenting the actions needed to link the various biodiversity infrastructures invisibly and to facilitate understanding that can support both business and policy-makers. The community considers the goal in biodiversity informatics to be full integration of the biodiversity research community, including citizens' science, through a commonly-shared, sustainable e-infrastructure across all sub-disciplines that reliably serves science and society alike.
UR  - http://dx.doi.org/10.1186/1472-6785-13-16
ID  - 3106
ER  - 

TY  - JOUR
AU  - Hertz, A.
AU  - Lotzkat, S.
AU  - Kohler, G.
PY  - 2013
TI  - A new species of Bolitoglossa (Caudata, Plethodontidae) from the continental divide of western Panama
SP  - 463-475
JF  - Zootaxa
JO  - Zootaxa
VL  - 3636
IS  - 3
Y2  - Apr
N1  - CCC:000317096600005
N1  - herps
N1  - ISI Document Delivery No.: 119KQ
Hertz, Andreas Lotzkat, Sebastian Koehler, Gunther
Magnolia press
Auckland
Mar 2013
KW  - Bolitoglossa jugivagans sp nov., B. robinsoni clade, La Fortuna Forest
Reserve, Protected Forest Palo Seco, DNA barcoding, Eladinea, Serrania
de Talamanca
genus bolitoglossa, costa-rica, salamanders, evolutionary, inventory,
amphibia
N2  - We describe the new salamander species Bolitoglossa jugivagans from the Atlantic slopes of the Fortuna depression in western Panama on the basis of morphological and molecular data. Based on mtDNA data, the new species seems to be closely related to B. aureogularis and B. robinsoni, with which it forms a subclade within the subgenus Eladinea.
AD  - [Hertz, A; Lotzkat, S; Kohler, G] Senckenberg Forschungsinst & Nat Museum, D-60325 Frankfurt, Germany [Hertz, A; Lotzkat, S] Goethe Univ Frankfurt, Inst Ecol Evolut & Divers, D-60438 Frankfurt, Germany
Hertz, Andreas (reprint author), Senckenberg Forschungsinst & Nat Museum, Senckenberganlage 25, D-60325 Frankfurt, Germany
ahertz@senckenberg.de
UR  - http://dx.doi.org/10.11646%2Fzootaxa.3636.3.5
ID  - 3066
ER  - 

TY  - JOUR
AU  - Hou, D.Y.
AU  - Song, J.Y.
AU  - Yao, H.
AU  - Han, J.P.
AU  - Pang, X.H.
AU  - Shi, L.C.
AU  - Wang, X.C.
AU  - Chen, S.L.
PY  - 2013
TI  - Molecular identification of Corni Fructus and its adulterants by ITS/ITS2 sequences
SP  - 121-127
JF  - Chinese Journal of Natural Medicines
JO  - Chin. J. Nat. Med.
VL  - 11
IS  - 2
Y2  - Mar
N1  - WOS:000317091000003
N1  - ISI Document Delivery No.: 119IM
Times Cited: 0
Cited Reference Count: 25
Hou Dian-Yun Song Jing-Yuan Yao Hui Han Jian-Ping Pang Xiao-Hui Shi Lin-Chun Wang Xiao-Chen Chen Shi-Lin
National High-tech R&D Program of China (863 Program) [2012AA021602]; Fundamental Research Funds for the Central Universities [2012C02]; National Natural Science Foundation of China [81073001]
The project was supported by the National High-tech R&D Program of China (863 Program) (No. 2012AA021602) and the Fundamental Research Funds for the Central Universities (No. 2012C02) and the National Natural Science Foundation of China (No. 81073001).
Chinese journal natural medicines
Nanjing
Mar 2013
KW  - Corni Fructus
ITS/ITS2
DNA barcoding
Molecular identification
dna barcode
plants
its2
N2  - The DNA barcoding method was used to accurately and rapidly identify Corni Fructus and its adulterants. METHODS: Genomic DNA extracted from Conn Fructus and its adulterants were used as templates. The ITS (internal trascribed spacer) regions were amplified using polymerase chain reaction. Sequence assembly was performed using CodonCode Aligner V 3.5.4. Genetic distances were computed using MEGA V 5.0. Species identification was conducted using neighbor-joining (NJ) trees. RESULTS: The ITS sequence length of Conn Fructus was 659 bp. The average intra-specific genetic distance of Corni Fructus was 0.005, markedly lower than the inter-specific genetic distance between Conn Fructus and its adulterants (0.357). The ITS2 sequence length of Corni Fructus was 250 bp. No variation was found among the different samples. The interspecific genetic distance of ITS2 between Conn Fructus and its adulterants was 0.571. NJ trees and BLAST results indicated that Corni Fructus and its adulterants can be easily differentiated with monophyly. CONCLUSION: ITS/ITS2 regions can accurately and efficiently distinguish Corni Fructus and its adulterants. In addition, the results not only established the foundation for the clinical safety in the utilization of Corni Fructus, but also provided reference for molecular identification of other Chinese herbal medicine and Chinese herbal pieces.
AD  - Chinese Acad Med Sci, Inst Med Plant Dev IMPLAD, Beijing 100193, Peoples R China. Peking Union Med Coll, Beijing 100193, Peoples R China. Henan Univ Sci & Technol, Coll Agr, Luoyang 471003, Peoples R China. China Acad Chinese Med Sci, Inst Chinese Mat Med, Beijing 100700, Peoples R China. Inst Cornus Officinalis, Nanyang 474550, Peoples R China.
Chen, SL (reprint author), Chinese Acad Med Sci, Inst Med Plant Dev IMPLAD, Beijing 100193, Peoples R China.
slchen@implad.ac.cn
UR  - http://www.cpucjnm.com/zgtryw/ch/reader/view_abstract.aspx?file_no=201302003&flag=1
ID  - 3098
ER  - 

TY  - JOUR
AU  - Hsu, T.-H.
AU  - Ning, Y.
AU  - Gwo, J.-C.
AU  - Zeng, Z.-N.
PY  - 2013
TI  - DNA barcoding reveals cryptic diversity in the peanut worm Sipunculus nudus
JF  - Molecular Ecology Resources
VL  - early onlineMar 2013
KW  - COI
cryptic species
mtDNA
Sipunculidae
speciation
N2  - Peanut worm (Sipunculus nudus) is a cosmopolitan species mainly distributed in tropical and subtropical coastal waters. Analysis of the mitochondrial cytochrome c oxidase subunit I (COI) gene sequences among S. nudus from GenBank revealed high genetic variation (p-distance, 0.115–0.235; k2p, 0.128–0.297) and paraphyletic relationships. These indicated misidentification and/or cryptic diversity may be present in the genus Sipunculus. To understand the genetic diversity and to manage the recourse of S. nudus, we collected specimens from coastal waters of southern China and Taiwan. In the phylogenetic topology, specimens can be separated into four distinct clades; three of these clades (clade A, B and C) were only represented from this region (southern China and Taiwan), but the clade D grouped with individuals from Central America (Atlantic coast). Furthermore, individuals of clades A and D were collected at the same location, which does not support the hypothesis that this genetic break reflects contemporary geographical isolation. The four distinct clades observed among coastal waters of southern China and Taiwan indicated underestimated diversity. It is noteworthy that the cryptic diversity is vulnerable under high pressure of human activity.
UR  - http://dx.doi.org/10.1111/1755-0998.12097
ID  - 3091
ER  - 

TY  - BOOK
AU  - Huemer, P.
PY  - 2013
BT  - Die Schmetterlinge Österreichs (Lepidoptera)
CY  - Innsbruck
PB  - Tiroler Landesmuseen-Betriebsgesellschaft m.b.H.
SP  - 304
ED  - Meighörner, P.D.W.
VL  - 12Mar 2013
VL  - 12
UR  - http://www.tiroler-landesmuseum.at/shop.php/de/druckwerke_alle_/studiohefte_12
ID  - 3097
ER  - 

TY  - JOUR
AU  - James, E.R.
AU  - Okamoto, N.
AU  - Burki, F.
AU  - Scheffrahn, R.H.
AU  - Keeling, P.J.
PY  - 2013
TI  - Cthulhu Macrofasciculumque n. g., n. sp. and Cthylla Microfasciculumque n. g., n. sp., a Newly Identified Lineage of Parabasalian Termite Symbionts
SP  - e58509
JF  - PLoS ONE
VL  - 8
IS  - 3Mar 2013
N2  - <p>The parabasalian symbionts of lower termite hindgut communities are well-known for their large size and structural complexity. The most complex forms evolved multiple times independently from smaller and simpler flagellates, but we know little of the diversity of these small flagellates or their phylogenetic relationships to more complex lineages. To understand the true diversity of Parabasalia and how their unique cellular complexity arose, more data from smaller and simpler flagellates are needed. Here, we describe two new genera of small-to-intermediate size and complexity, represented by the type species <italic>Cthulhu macrofasciculumque</italic> and <italic>Cthylla microfasciculumque</italic> from <italic>Prorhinotermes simplex</italic> and <italic>Reticulitermes virginicus</italic>, respectively (both hosts confirmed by DNA barcoding). Both genera have a single anterior nucleus embeded in a robust protruding axostyle, and an anterior bundle flagella (and likely a single posterior flagellum) that emerge slightly subanteriorly and have a distinctive beat pattern. <italic>Cthulhu</italic> is relatively large and has a distinctive bundle of over 20 flagella whereas <italic>Cthylla</italic> is smaller, has only 5 anterior flagella and closely resembles several other parababsalian genera. Molecular phylogenies based on small subunit ribosomal RNA (SSU rRNA) show both genera are related to previously unidentified environmental sequences from other termites (possibly from members of the Tricercomitidae), which all branch as sisters to the Hexamastigitae. Altogether, <italic>Cthulhu</italic> likely represents another independent origin of relatively high cellular complexity within parabasalia, and points to the need for molecular characterization of other key taxa, such as <italic>Tricercomitus</italic>.</p>
UR  - http://dx.doi.org/10.1371%2Fjournal.pone.0058509
ID  - 3055
ER  - 

TY  - JOUR
AU  - Jiang, F.
AU  - Li, Z.H.
AU  - Deng, Y.L.
AU  - Wu, J.J.
AU  - Liu, R.S.
AU  - Buahom, N.
PY  - 2013
TI  - Rapid diagnosis of the economically important fruit fly, Bactrocera correcta (Diptera: Tephritidae) based on a species-specific barcoding cytochrome oxidase I marker
SP  - 1-9
JF  - Bulletin of Entomological Research
VL  - FirstViewMar 2013
KW  -, molecular diagnosis, species-specific PCR, mtDNA COI, DNA barcode
N2  - The guava fruit fly, Bactrocera correcta (Bezzi) (Diptera: Tephritidae), is an invasive pest of fruit and vegetable crops that primarily inhabits Southeast Asia and which has the potential to become a major threat within both the Oriental and Australian oceanic regions as well as California and Florida. In light of the threat posed, it is important to develop a rapid, accurate and reliable method to identify B. correcta in quarantine work in order to provide an early warning to prevent its widespread invasion. In the present study, we describe a species-specific polymerase chain reaction assay for the diagnosis of B. correcta using mitochondrial DNA cytochrome oxidase I (mtDNA COI) barcoding genes. A B. correcta-specific primer pair was designed according to variations in the mtDNA COI barcode sequences among 14 fruit fly species. The specificity and sensitivity of the B. correcta-specific primer pair was tested based on the presence or absence of a band in the gel profile. A pair of species-specific B. correcta primers was successfully designed and named BCOR-F/BCOR-R. An ∼280 bp fragment was amplified from specimens belonging to 17 geographical populations and four life stages of B. correcta, while no such diagnostic bands were present in any of the 14 other related fruit fly species examined. Sensitivity test results demonstrated that successful amplification can be obtained with as little as 1 ng μl−1 of template DNA. The species-specific PCR analysis was able to successfully diagnose B. correcta, even in immature life stages, and from adult body parts. This method proved to be a robust single-step molecular technique for the diagnosis of B. correcta with respect to potential plant quarantine.
UR  - http://dx.doi.org/10.1017/S0007485312000806
ID  - 3039
ER  - 

TY  - JOUR
AU  - Jorger, K.
AU  - Norenburg, J.
AU  - Wilson, N.
AU  - Schrodl, M.
PY  - 2012
TI  - Barcoding against a paradox? Combined molecular species delineations reveal multiple cryptic lineages in elusive meiofaunal sea slugs
SP  - 245
JF  - BMC Evolutionary Biology
VL  - 12
IS  - 1
N1  - doi:10.1186/1471-2148-12-245
N1  - Mar 2013
N2  - BACKGROUND:Many marine meiofaunal species are reported to have wide distributions, which creates a paradox considering their hypothesized low dispersal abilities. Correlated with this paradox is an especially high taxonomic deficit for meiofauna, partly related to a lower taxonomic effort and partly to a high number of putative cryptic species. Molecular-based species delineation and barcoding approaches have been advocated for meiofaunal biodiversity assessments to speed up description processes and uncover cryptic lineages. However, these approaches show sensitivity to sampling coverage (taxonomic and geographic) and the success rate has never been explored on mesopsammic Mollusca.RESULTS:We collected the meiofaunal sea-slug Pontohedyle (Acochlidia, Heterobranchia) from 28 localities worldwide. With a traditional morphological approach, all specimens fall into two morphospecies. However, with a multi-marker genetic approach, we reveal multiple lineages that are reciprocally monophyletic on single and concatenated gene trees in phylogenetic analyses. These lineages are largely concordant with geographical and oceanographic parameters, leading to our primary species hypothesis (PSH). In parallel, we apply four independent methods of molecular based species delineation: General Mixed Yule Coalescent model (GMYC), statistical parsimony, Bayesian Species Delineation (BPP) and Automatic Barcode Gap Discovery (ABGD). The secondary species hypothesis (SSH) is gained by relying only on uncontradicted results of the different approaches ('minimum consensus approach'), resulting in the discovery of a radiation of (at least) 12 mainly cryptic species, 9 of them new to science, some sympatric and some allopatric with respect to ocean boundaries. However, the meiofaunal paradox still persists in some Pontohedyle species identified here with wide coastal and trans-archipelago distributions.CONCLUSIONS:Our study confirms extensive, morphologically cryptic diversity among meiofauna and accentuates the taxonomic deficit that characterizes meiofauna research. We observe for Pontohedyle slugs a high degree of morphological simplicity and uniformity, which we expect might be a general rule for meiofauna. To tackle cryptic diversity in little explored and hard-to-sample invertebrate taxa, at present, a combined approach seems most promising, such as multi-marker-barcoding (i.e., molecular systematics using mitochondrial and nuclear markers and the criterion of reciprocal monophyly) combined with a minimum consensus approach across independent methods of molecular species delineation to define candidate species.
UR  - http://dx.doi.org/10.1186/1471-2148-12-245
ID  - 3089
ER  - 

TY  - JOUR
AU  - Kermarrec, L.
AU  - Franc, A.
AU  - Rimet, F.
AU  - Chaumeil, P.
AU  - Humbert, J.F.
AU  - Bouchez, A.
PY  - 2013
TI  - Next-generation sequencing to inventory taxonomic diversity in eukaryotic communities: a test for freshwater diatoms
SP  - n/a-n/a
JF  - Molecular Ecology ResourcesMar 2013
blog
KW  - benthic diatom diversity
environmental communities
high-throughput sequencing
molecular ecology
species inventories
N2  - The recent emergence of barcoding approaches coupled to those of next-generation sequencing (NGS) has raised new perspectives for studying environmental communities. In this framework, we tested the possibility to derive accurate inventories of diatom communities from pyrosequencing outputs with an available DNA reference library. We used three molecular markers targeting the nuclear, chloroplast and mitochondrial genomes (SSU rDNA, rbcL and cox1) and three samples of a mock community composed of 30 known diatom strains belonging to 21 species. In the goal to detect methodological biases, one sample was constituted directly from pooled cultures, whereas the others consisted of pooled PCR products. The NGS reads obtained by pyrosequencing (Roche 454) were compared first to a DNA reference library including the sequences of all the species used to constitute the mock community, and second to a complete DNA reference library with a larger taxonomic coverage. A stringent taxonomic assignation gave inventories that were compared to the real one. We detected biases due to DNA extraction and PCR amplification that resulted in false-negative detection. Conversely, pyrosequencing errors appeared to generate false positives, especially in case of closely allied species. The taxonomic coverage of DNA reference libraries appears to be the most crucial factor, together with marker polymorphism which is essential to identify taxa at the species level. RbcL offers a high resolving power together with a large DNA reference library. Although needing further optimization, pyrosequencing is suitable for identifying diatom assemblages and may find applications in the field of freshwater biomonitoring.
UR  - http://dx.doi.org/10.1111/1755-0998.12105
ID  - 3083
ER  - 

TY  - JOUR
AU  - Keshavmurthy, S.
AU  - Yang, S.-Y.
AU  - Alamaru, A.
AU  - Chuang, Y.-Y.
AU  - Pichon, M.
AU  - Obura, D.
AU  - Fontana, S.
AU  - De Palmas, S.
AU  - Stefani, F.
AU  - Benzoni, F.
AU  - MacDonald, A.
AU  - Noreen, A.M.E.
AU  - Chen, C.
AU  - Wallace, C.C.
AU  - Pillay, R.M.
AU  - Denis, V.
AU  - Amri, A.Y.
AU  - Reimer, J.D.
AU  - Mezaki, T.
AU  - Sheppard, C.
AU  - Loya, Y.
AU  - Abelson, A.
AU  - Mohammed, M.S.
AU  - Baker, A.C.
AU  - Mostafavi, P.G.
AU  - Suharsono, B.A.
AU  - Chen, C.A.
PY  - 2013
TI  - DNA barcoding reveals the coral “laboratory-rat”, Stylophora pistillata encompasses multiple identities
JF  - Sci. Rep.
VL  - 3Mar 2013
N2  - Stylophora pistillata is a widely used coral “lab-rat” species with highly variable morphology and a broad biogeographic range (Red Sea to western central Pacific). Here we show, by analysing Cytochorme Oxidase I sequences, from 241 samples across this range, that this taxon in fact comprises four deeply divergent clades corresponding to the Pacific-Western Australia, Chagos-Madagascar-South Africa, Gulf of Aden-Zanzibar-Madagascar, and Red Sea-Persian/Arabian Gulf-Kenya. On the basis of the fossil record of Stylophora, these four clades diverged from one another 51.5-29.6 Mya, i.e., long before the closure of the Tethyan connection between the tropical Indo-West Pacific and Atlantic in the early Miocene (16–24 Mya) and should be recognised as four distinct species. These findings have implications for comparative ecological and/or physiological studies carried out using Stylophora pistillata as a model species, and highlight the fact that phenotypic plasticity, thought to be common in scleractinian corals, can mask significant genetic variation.
UR  - http://dx.doi.org/10.1038/srep01520
ID  - 3056
ER  - 

TY  - JOUR
AU  - Keskin, E.
AU  - Atar, H.H.
PY  - 2012
TI  - Molecular identification of fish species from surimi-based products labeled as Alaskan pollock
SP  - 811-814
JF  - Journal of Applied Ichthyology
VL  - 28
IS  - 5fish, marine
N1  - Mar 2013
N2  - Sequence analysis of the cytochrome c oxidase I gene was used to confirm the identity of species in 50 commercial surimi products labeled as Alaskan pollock (Theragra chalcogramma). All sequences (655 base pairs long) produced from the samples were aligned and compared with reference sequences from the GenBank database. A Neighbor Joining tree clustered samples into eight groups. Results showed that only 16% (8/50) of the surimi samples were made from Alaskan pollock as declared. The remaining species detected in samples belonged to the families Sciaenidae (12%), Synodontidae (16%), Merlucciidae (38%), Nemipteridae (8%), Priacanthidae (2%), Mullidae (2%), and two species of Gadidae (4%).
UR  - http://dx.doi.org/10.1111/j.1439-0426.2012.02031.x
ID  - 3096
ER  - 

TY  - JOUR
AU  - Laforest, B.
AU  - Winegardner, A.
AU  - Zaheer, O.
AU  - Jeffery, N.
AU  - Boyle, E.
AU  - Adamowicz, S.
PY  - 2013
TI  - Insights into biodiversity sampling strategies for freshwater microinvertebrate faunas through bioblitz campaigns and DNA barcoding
SP  - 13
JF  - BMC Ecology
VL  - 13
IS  - 1
N1  - doi:10.1186/1472-6785-13-13
N1  - Mar 2013
N2  - BACKGROUND:Biodiversity surveys have long depended on traditional methods of taxonomy to inform sampling protocols and to determine when a representative sample of a given species pool of interest has been obtained. Questions remain as to how to design appropriate sampling efforts to accurately estimate total biodiversity. Here we consider the biodiversity of freshwater ostracods (crustacean class Ostracoda) from the region of Churchill, Manitoba, Canada. Through an analysis of observed species richness and complementarity, accumulation curves, and richness estimators, we conduct an a posteriori analysis of five bioblitz-style collection strategies that differed in terms of total duration, number of sites, protocol flexibility to heterogeneous habitats, sorting of specimens for analysis, and primary purpose of collection. We used DNA barcoding to group specimens into molecular operational taxonomic units for comparison.RESULTS:Forty-eight provisional species were identified through genetic divergences, up from the 30 species previously known and documented in literature from the Churchill region. We found differential sampling efficiency among the five strategies, with liberal sorting of specimens for molecular analysis, protocol flexibility (and particularly a focus on covering diverse microhabitats), and a taxon-specific focus to collection having strong influences on garnering more accurate species richness estimates.CONCLUSIONS:Our findings have implications for the successful design of future biodiversity surveys and citizen-science collection projects, which are becoming increasingly popular and have been shown to produce reliable results for a variety of taxa despite relying on largely untrained collectors. We propose that efficiency of biodiversity surveys can be increased by non-experts deliberately selecting diverse microhabitats; by conducting two rounds of molecular analysis, with the numbers of samples processed during round two informed by the singleton prevalence during round one; and by having sub-teams (even if all non-experts) focus on select taxa. Our study also provides new insights into subarctic diversity of freshwater Ostracoda and contributes to the broader "Barcoding Biotas" campaign at Churchill. Finally, we comment on the associated implications and future research directions for community ecology analyses and biodiversity surveys through DNA barcoding, which we show here to be an efficient technique enabling rapid biodiversity quantification in understudied taxa.
UR  - http://www.biomedcentral.com/1472-6785/13/13
ID  - 3093
ER  - 

TY  - JOUR
AU  - Lawton, S.P.
AU  - Majoros, G.
PY  - 2013
TI  - A foreign invader or a reclusive native? DNA bar coding reveals a distinct European lineage of the zoonotic parasite Schistosoma turkestanicum (syn. Orientobilharzia turkestanicum ())
SP  - 186-193
JF  - Infection, Genetics and Evolution
VL  - 14
IS  - 0Mar 2013
KW  - European
Schistosoma
Cox1
DNA barcoding
Red deer
Divergence
N2  - Natural foci of Schistosoma turkestanicum (syn. Orientobilharzia turkestanicum) has been identified in the Gemenc Forest regions of Hungary utilising red deer as the definitive host. In order to identify the origins of this parasite in Europe standard DNA bar coding techniques were employed to sequence fragments of the cytochrome oxidase 1 (cox1) and the nuclear ribosomal internal transcribed region (ITS) from 10 individual adult male worms. Phylogenetic reconstruction using maximum likelihood phylogenetic reconstruction and haplotype networks of the cox1 showed all the worms to be of a distinct unique Hungarian lineage although some ITS haplotypes were shared with worms from populations in China and Iran. Molecular clock analysis suggests an early divergence event around 270,000 years before present (YBP) between all S. turkestanicum populations giving rise to the Chinese, Iranian and Hungarian lineages. However, divergence of the sequences within the Hungarian population appears to have occurred approximately 63,000 YBP suggesting a long established population of S. turkestanicum in Europe. This suggests that the Hungarian population of S. turkestanicum has been native since the Ice Age and probably established itself during the last interglacial period as red deer moved into Europe from North Africa and the Middle East. This may also indicate that the parasite may have unknown populations established in several other countries in Eastern, Central and Southern Europe.
UR  - http://dx.doi.org/10.1016/j.meegid.2012.11.013
ID  - 3065
ER  - 

TY  - JOUR
AU  - Lee, M.Y.
AU  - Munroe, T.A.
AU  - Shao, K.T.
PY  - 2013
TI  - Symphurus orientalis (Bleeker) redefined based on morphological and molecular characters (Pleuronectiformes: Cynoglossidae)
SP  - 379-403
JF  - Zootaxa
JO  - Zootaxa
VL  - 3620
IS  - 3
Y2  - Mar
N1  - WOS:000315937200003
N1  - fish, marine
N1  - ISI Document Delivery No.: 103RS
Times Cited: 0
Cited Reference Count: 117
Lee, Mao-Ying Munroe, Thomas A. Shao, Kwang-Tsao
National Science Council [NSC 96-2628-B-001-006-MY3, NSC 99-2621-B-001-008-MY3]; Biodiversity Research Center, Academia Sinica.
This work represents a portion of a collecting activities grant investigating the biodiversity and systematics of deep-sea fishes in Taiwanese waters supported by the National Science Council (NSC 96-2628-B-001-006-MY3 and NSC 99-2621-B-001-008-MY3) and awarded to K.-T. Shao, Biodiversity Research Center, Academia Sinica. We thank H.-M. Yeh, Coastal and Offshore Resource Research Center, Fisheries Research Institute, who kindly provided trawl station data from research vessels. H.-C. Ho, P.-F. Lee, Y.-C. Liao and L.-P. Lin assisted with collecting specimens and kindly provided other specimens used in this study. K.-C. Hsu advised M.-Y. Lee regarding molecular aspects of this research study. A. Collins, NSL, kindly provided information and helpful editorial suggestions regarding molecular approaches used in this study. L.-P. Lin and C.-W. Chang assisted with loans and shipments of specimens. M. Nizinski provided assistance and support during M.-Y. Lee's visit to the National Museum of Natural History, Smithsonian Institution. H. Endo, N. Nakayama, and R. Asaoka provided assistance and support during M.-Y. Lee's visit to the Department of Biology, Faculty of Science, Kochi University. They also provided two important fresh specimens of S. orientalis from Japan to help with molecular comparisons. K. Matsuura and G. Shinohara provided loan of Suruga Bay specimens during M.-Y. Lee's visit to the Department of Zoology, National Science Museum. K. Murphy (USNM) assisted with specimen and catalogue information. K. Nakaya, Hokkaido University, provided the photograph of the holotype of S. septemstriatus. K. Vinnikov, University of Hawaii at Manoa, graciously provided translations of Russian literature. L. Willis, NMFS-NSL, assisted with literature. H.-M. Chen provided comments on an early draft of the manuscript. M.-Y. Lee extends his appreciation to all members of the Laboratory of Fish Ecology and Evolution for their support, especially H. Lee for helping to draw the distribution map and assistance during this study.
Magnolia press
Auckland
Mar 2013
KW  - Symphurus orientalis
Symphurus novemfasciatus
flatfish
redescription
synonym
tonguefish
species complex
cryptic species
16s ribosomal-rna
dna barcoding reveals
tonguefish pleuronectiformes
taxonomic status
western pacific
identification
australia
teleostei
flatfish
pattern
N2  - Aphoristia (= Symphurus) orientalis Bleeker 1879, collected from an unspecified depth and location in Japanese waters, is the first described species of symphurine tonguefish from Indo-Pacific waters. The original description with accompanying illustration is based on the unique holotype specimen and provides limited diagnostic characters for this taxon. Subsequent to its description, the holotype of A. orientalis has been lost. Limited diagnostic information and loss of the holotype have caused considerable confusion to subsequent systematic studies regarding the identity of this and similar tonguefish species occurring in the Indo-West Pacific region. Several, often-cited, taxonomic accounts purportedly redescribing S. orientalis are erroneous because they include more than one species in these redescriptions. These erroneous redescriptions not only confused the species concept of S. orientalis (Bleeker), but also confounded the systematics of similar Indo-West Pacific tonguefishes. Symphurus novemfasciatus Shen and Lin, described on two specimens collected in southern Taiwan, shares many morphological and pigmentation features similar to those of S. orientalis. Morphological data from a large series of tonguefishes collected in Taiwanese and Japanese waters, as well as molecular data from a smaller number of specimens from these locations, including the type locality of S. novemfasciatus, confirm the presence of only one species, S. orientalis (Bleeker), among these specimens. Symphurus novemfasciatus Shen and Lin is therefore regarded as a junior subjective synonym of S. orientalis. Symphurus orientalis is redefined based on a large series of specimens identified by a consistent set of morphological criteria, and a neotype is designated to stabilize nomenclature and systematics of this species. Symphurus orientalis differs from congeners by its combination of: a predominant 1-2-2-2-2 pattern of interdigitation of proximal dorsal-fin pterygiophores and neural spines, 12 caudal-fin rays, 9 abdominal and 52-55 total vertebrae, four hypurals, 96-101 dorsal-fin rays, 82-89 anal-fin rays, 87-99 longitudinal scale rows, 37-42 transverse scales, 5-11 (usually) distinct, complete or incomplete, blackish-brown crossbands on the ocular side, uniformly white blind side, and conspicuous bluish-black peritoneum. Documenting morphological variation for S. orientalis represents the most important step towards clarification of the identity of this and other symphurine tonguefish species from this region. Reliable identification of specimens of S. orientalis also provides the foundation for evaluating the status of several other, poorly-known, nominal species of Indo-West Pacific tonguefishes that have features similar to those of S. orientalis. Improved identifications will lead to better knowledge on the geographic distribution of S. orientalis and these other species, as well as to improve estimates of biodiversity and the biogeography of Indo-West Pacific symphurine tonguefishes.
AD  - Natl Taiwan Ocean Univ, Dept Aquaculture, Keelung 20224, Taiwan. NOAA, Natl Marine Fisheries Serv, Natl Systemat Lab, Smithsonian Inst,Natl Museum Nat Hist, Washington, DC 20013 USA. Acad Sinica, Biodivers Res Ctr, Lab Fish Ecol & Evolut, Taipei 11529, Taiwan.
Shao, KT (reprint author), Acad Sinica, Biodivers Res Ctr, Lab Fish Ecol & Evolut, Taipei 11529, Taiwan.
coleoptera@gmail.com; munroet@si.edu; zoskt@gate.sinica.edu.tw
UR  - http://dx.doi.org/10.11646/zootaxa.3620.3.3
ID  - 3103
ER  - 

TY  - JOUR
AU  - Linse, K.
AU  - Jackson, J.A.
AU  - Fitzcharles, E.
AU  - Sands, C.J.
AU  - Buckeridge, J.S.
PY  - 2013
TI  - Phylogenetic position of Antarctic Scalpelliformes (Crustacea: Cirripedia: Thoracica)
SP  - 99-116
JF  - Deep Sea Research Part I: Oceanographic Research Papers
VL  - 73
IS  - 0Mar 2013
KW  - Cirripedia
Scalpellidae
Barcoding
28S
18S
CO1
Scotia Sea
N2  - The phylogenetic relationships of seven Antarctic barnacle species, one verrucomorph and six scalpelliforms from the Scotia, Weddell and Ross seas were investigated using DNA sequences from two nuclear genes (18 S and 28 S) and one mitochondrial gene (COI), with a combined total length of 3,151 base pairs. Analyses of these new sequences, together with those of previously published ibliform, lepadiform, scalpelliform, balanomorph and verrucomorph species, confirm that the Scalpelliformes are not monophyletic. Bayesian and maximum likelihood analyses consistently recovered a monophyletic group which comprised Ornatoscalpellum stroemii (Sars) and the Southern Ocean scalpellomorphs; Arcoscalpellum sp. from the Weddell Sea, Arcoscalpellum africanum from Elephant Island, A. bouveti from Bouvet Island, the circum-Antarctic Litoscalpellum discoveryi, Litoscalpellum sp. from Shag Rocks and Scalpellum sp. from the Falkland Trough. We also used multiple fossil constraints in a relaxed clock Bayesian framework to estimate divergence times for the 18 S+28 S phylogeny. Our results indicate a mid Cretaceous divergence for the Weddell Sea Arcoscalpellum sp, followed by a late Cretaceous divergence from the North Atlantic O. stroemii. Subsequent to this, the Antarctic scalpellomorphs began to radiate at the Cretaceous-Tertiary boundary. Monophyly within the scalpellid genera Arcoscalpellum, Litoscalpellum and Scalpellum was strongly rejected by all loci. Our results show incongruence between taxonomy and molecular systematics and highlight the need for more species to be sequenced as well as taxonomic revisions to resolve uncertainties in the phylogenetic relationships of the stalked barnacles.
UR  - http://dx.doi.org/10.1016/j.dsr.2012.11.006
ID  - 3101
ER  - 

TY  - JOUR
AU  - Lis, B.
AU  - Lis, J.A.
AU  - Ziaja, D.J.
PY  - 2013
TI  - Identification of the nymphal stages of two European seed bugs, L. equestris and L. simulans (Hemiptera: Heteroptera: Lygaeidae), using DNA barcodes
SP  - 147-150
JF  - Zootaxa
VL  - 3608
IS  - 2
Y2  - Jan 17
N1  - ZOOREC:ZOOR14904015915
N1  - Zoor14904015915
Mar 2013
KW  - Systematics
Nomenclature
Diagnosis
Techniques
Genetics
Lygaeus equestris
Lygaeus simulans [Identification techniques / /
nymph] [Molecular genetics / DNA barcoding / ].
Lygaeus equestris - (Linnaeus 1758) (Lygaeidae): [Diagnostic characters,
P. 148].
Lygaeus simulans - Deckert 1985 (Lygaeidae): [Diagnostic characters, P.
148].
AD  - Lis, Jerzy A.; Opole Univ, Dept Biosystemat, Oleska 22, Opole, PL-45052, Poland, Poland.
cydnus@uni.opole.pl
UR  - http://dx.doi.org/10.11646/zootaxa.3608.2.5
ID  - 3050
ER  - 

TY  - JOUR
AU  - López-Caballero, J.
AU  - Oceguera-Figueroa, A.
AU  - León-Règagnon, V.
PY  - 2013
TI  - Detection of multiple species of human Paragonimus from Mexico using morphological data and molecular barcodes
SP  - n/a-n/a
JF  - Molecular Ecology ResourcesMar 2013
blog
KW  - Barcoding
DNA
lung parasites
Mexico
Paragonimus
Zoonosis
N2  - Paragonimus mexicanus is the causal agent of human paragonimiasis in several countries of the Americas. It is considered to be the only species of the genus present in Mexico, where it is responsible for human infection. Through the investigation of P. mexicanus specimens from several places throughout Mexico, we provide morphological, molecular and geographical evidence that strongly suggests the presence of at least three species from this genus in Mexico. These results raise questions regarding the diagnosis, treatment, prophylaxis and control of human paragonimiasis in Mexico. We also provide a brief discussion regarding biodiversity inventories and the convenience of providing molecular and morphological information in biodiversity studies.
UR  - http://dx.doi.org/10.1111/1755-0998.12093
ID  - 3105
ER  - 

TY  - JOUR
AU  - Lv, J.
AU  - Wu, S.
AU  - Zhang, Y.
AU  - Zhang, T.
AU  - Feng, C.
AU  - Jia, G.
AU  - Lin, X.
PY  - 2013
TI  - Development of a DNA barcoding system for the Ixodida (Acari: Ixodida)
SP  - 1-8
JF  - Mitochondrial DNA
VL  - 0
IS  - 0
N1  - 23631370
N1  - Mar 2013
N2  - To control the spread of tick-borne diseases, there is an urgent need to develop a reliable technique that can distinguish different species of ticks. DNA barcoding has been proved to be a powerful tool to identify species of arthropods, but this technique has not yet been developed for identifying ticks. Here, we screened and analyzed 1082 sequences of ticks from BOLD system and GenBank, consisting of 647 16S, 325 COI, and 110 18S. These sequences are reported in previous studies and considered to be correctly identified at the species level. Through the analyses of genetic divergences and neighbor-joining (NJ) phylogenetic relationships between the species of ticks, our results show that COI and 16S are reliable in discriminating species of ticks and the 18S could discriminate ticks at the genera level. New universal primers for 16S, 18S, and COI of ticks were designed and a DNA barcoding system for the Ixodida was developed. To assess the performance of this system, 57 specimens of ticks were collected within China. Our results show that DNA barcoding system could correctly identify the species of specimens in adult and subadult stages. This system would assist non-taxonomists to conveniently identify the species of Ixodida based on DNA sequences rather than morphological traits. However, there are still serious deficiencies in the information of 16S and COI of some species of ticks, and additional research is needed to resolve this problem.

UR  - http://dx.doi.org/10.3109/19401736.2013.792052
ID  - 3081
ER  - 

TY  - JOUR
AU  - Ma, M.-y.
AU  - Yan, Y.
AU  - Wang, Y.-w.
AU  - Li, J.
AU  - Cai, Y.-s.
AU  - Li, J.-l.
PY  - 2012
TI  - A Study of DNA Barcoding on 32 Species of Bird in China
SP  - 729-733
JF  - Sichuan Journal of Zoology
VL  - 31
IS  - 5
Y2  - September 28
N1  - ZOOREC:ZOOR14904015478
N1  - Zoor14904015478
Mar 2013
KW  - Systematics
Techniques
Biochemistry
Genetics
Aves [Genetic techniques / DNA barcoding / ] [Identification techniques
/ Species identification / ] [Nucleic acids / mtDNA sequences / ]
[Molecular genetics / CO1 gene characterization / ].
Aves (Vertebrata).
N2  - DNA barcoding has been proposed as a promising tool for the rapid species identification in a wide range of animal taxa. In this study, the ~648 bp mitochondrial cytochrome c oxidase subunit I (CO I) gene of 61 individuals from 32 bird species was analyzed. By applying three methods (distance based method, monophyly-based method, and diagnostic characters), our result shows that CO I is able to distinguish all species studied. The present study validated the effectiveness of barcoding for the identification of birds.
AD  - Li, Jing; Key Laboratory of Conservation Biology on Endangered Wildlife, Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610064, China, China.
ljtjf71@hotmail.com
UR  - http://www.scdwzz.com/viewmulu_en.aspx?qi_id=825&mid=23667
ID  - 3051
ER  - 

TY  - JOUR
AU  - Maranan, F.S.
AU  - Diaz, M.G.Q.
PY  - 2013
TI  - Molecular Diversity and DNA Barcode Identification of Selected Philippine Endemic Hoya Species (Apocynaceae)
SP  - 86-92
JF  - Philippine Agricultural Scientist
JO  - Philipp. Agric. Sci.
VL  - 96
IS  - 1
Y2  - Mar
N1  - CCC:000316826500010
N1  - plants
N1  - ISI Document Delivery No.: 115QH
Maranan, Faith S. Diaz, Ma. Genaleen Q.
Univ philippines los banos
Laguna
Mar 2013
KW  - DNA barcode, Hoya, matK, molecular diversity, rbcL
neighbor-joining method, land plants, sequences, marsdenieae,
phylogenies, primers, complex, markers, region, spacer
N2  - Although several Hoya species are endemic to the Philippines, their limited geographical distribution makes some species more vulnerable to extinction. Likewise, a number of species were also reported to exhibit phenotypic plasticity, which makes it difficult to distinguish them using morphological characters. DNA barcoding, together with morphological traits, may help in the proper identification and protection of this group of plants. Determination of molecular diversity, through analysis of the sequence variation of selected genes and identification of DNA barcodes for five Hoya species, was conducted using the recommended standard gene barcoding regions in the plant-maturase K gene (matK) and in the ribulose 1,5-bisphosphate carboxylase oxygenase large sub-unit gene (rbcL). Gene amplification was done using a single primer pair for each gene which generated product sizes of 535 bp and 809-815 bp for rbcL and matK, respectively. Phylogenetic trees were generated using the partial gene sequences. The Neighbour-Joining (NJ) method was likewise used with Maximum Likelihood as the measure of evolutionary distance. Distinctive clades with high bootstrap support (95-99%) were generated for three Hoya species using the matK sequences and for two species for rbcL with low support (63-64%). Pair-wise sequence analysis of rbcL sequences showed 0-1% level of sequence variability while matK sequences had 0-2%, indicating high sequence homology for both genes. Potential barcoding regions in the Hoya species were identified through haplotype construction. MatK sequences exhibited a higher number of variable sites, which is 21, while only two were observed in the rbcL sequences. The maximum number of haplotypes constructed for matK was four and three for rbcL. Greater resolution and discrimination among species was achieved when haplotypes from both genes were combined.
AD  - [Maranan, FS] Univ Philippines Los Banos, Coll Arts & Sci, Inst Biol Sci, Environm Biol Div, College Los Banos 4031, Laguna, Philippines [Diaz, MGQ] Univ Philippines Los Banos, Coll Arts & Sci, Inst Biol Sci, Genet & Mol Biol Div, College Los Banos 4031, Laguna, Philippines
Maranan, Faith S. (reprint author), Univ Philippines Los Banos, Coll Arts & Sci, Inst Biol Sci, Environm Biol Div, College Los Banos 4031, Laguna, Philippines
fsmaranan@gmail.com
UR  - http://journals.uplb.edu.ph/index.php/PAS/article/view/882
ID  - 3070
ER  - 

TY  - JOUR
AU  - Martin, B.T.
AU  - Bernstein, N.P.
AU  - Birkhead, R.D.
AU  - Koukl, J.F.
AU  - Mussmann, S.M.
AU  - Placyk Jr, J.S.
PY  - 2013
TI  - Sequence-based molecular phylogenetics and phylogeography of the American box turtles (Terrapene spp.) with support from DNA barcoding
JF  - Molecular Phylogenetics and Evolution
IS  - 0Mar 2013
KW  - Box turtle
DNA barcoding
Molecular phylogenetics
Phylogeography
Terrapene
Emydidae
N2  - Abstract The classification of the American box turtles (Terrapene spp.) has remained enigmatic to systematists. Previous comprehensive phylogenetic studies focused primarily on morphology. The goal of this study was to re-assess the classification of Terrapene spp. by obtaining DNA sequence data from a broad geographic range and from all four recognized species and 11 subspecies within the genus. Tissue samples were obtained for all taxa except for Terrapene nelsoni klauberi. DNA was extracted, and the mitochondrial DNA (mtDNA) cytochrome b (Cytb) and nuclear DNA (nucDNA) glyceraldehyde-3-phosphate-dehydrogenase (GAPD) genes were amplified via polymerase chain reaction and sequenced. In addition, the mtDNA gene commonly used for DNA barcoding (cytochrome oxidase c subunit I; COI) was amplified and sequenced to calculate pairwise percent DNA sequence divergence comparisons for each Terrapene taxon. The sequence data were analyzed using maximum likelihood and Bayesian phylogenetic inference, a molecular clock, AMOVAs, SAMOVAs, haplotype networks, and pairwise percent sequence divergence comparisons. Terrapene carolina mexicana and T. c. yucatana formed a monophyletic clade with T. c. triunguis, and this clade was paraphyletic to the rest of T. carolina. Terrapene ornata ornata and T. o. luteola lacked distinction phylogenetically, and Terrapene nelsoni was confirmed to be the sister taxon of T. ornata. Terrapene c. major, T. c. bauri, and Terrapene coahuila were not well resolved for some of the analyses. The DNA barcoding results indicated that all taxa were different species (&gt; 2% sequence divergence) except for T. c. triunguis - T. c. mexicana and T. o. ornata - T. o. luteola. The results suggest that T. c. triunguis should be elevated to species status (Terrapene mexicana), and mexicana and yucatana should be included in this group as subspecies. In addition, T. o. ornata and T. o. luteola should not be considered separate subspecies. The DNA barcoding data support these recommended taxonomic revisions. Because conservation efforts are typically species-based, these results will be important for facilitating successful conservation management strategies.
UR  - http://dx.doi.org/10.1016/j.ympev.2013.03.006
ID  - 3045
ER  - 

TY  - JOUR
AU  - Matheny, P.B.
AU  - Norvell, L.L.
AU  - Giles, E.C.
PY  - 2013
TI  - A common new species of Inocybe in the Pacific Northwest with a diagnostic PDAB reaction
SP  - 436-446
JF  - Mycologia
VL  - 105
IS  - 2
Y2  - March 1, 2013fungi
N1  - Mar 2013
N2  - A species of Inocybe common in Washington, Oregon and British Columbia is documented and described as new. The species, I. chondroderma, is characterized by these features: pileus with a fulvous disk and ochraceous to chamois margin, presence of a cortina, densely mycelioid stipe base, smooth spores and fall phenology. The most reliable and distinctive feature of the species is a blue-green or turquoise reaction in response to application of a solution of p-dimethylaminobenzaldehyde (PDAB), indicating the presence of what is most likely an indole alkaloid. PDAB use provides a quick and diagnostic character easily implemented in a laboratory setting. ITS sequences from recent collections of I. chondroderma and from materials collected in the 1940s in Washington and Oregon fully match numerous mislabeled sequences from specimens in British Columbia and Oregon. The species is most closely related to an unclarified taxon from Colorado and Japan (I. cf. chondroderma) and a rare European species, I. subnudipes. Nine different species names in Inocybe and one in Hebeloma attributed to I. chondroderma based on GenBank BLASTN searches of the ITS locus match with 99–100% similarity, reinforcing concerns about taxonomic inaccuracies in public DNA sequence databases. A complete morphological description, illustrations and phylogenetic assessment are provided.
UR  - http://www.mycologia.org/content/105/2/436.abstract
ID  - 3067
ER  - 

TY  - JOUR
AU  - Muchlisin, Z.A.
AU  - Thomy, Z.
AU  - Fadli, N.
AU  - Sarong, M.A.
AU  - Siti-Azizah, M.N.
PY  - 2013
TI  - DNA Barcoding of Freshwater Fishes from Lake Laut Tawar, Aceh Province, Indonesia
SP  - 21-29
JF  - Acta Ichthyologica Et Piscatoria
JO  - Acta Ichthyol. Piscat.
VL  - 43
IS  - 1
N1  - WOS:000317035600004
N1  - fish
N1  - ISI Document Delivery No.: 118OT
Times Cited: 0
Cited Reference Count: 44
Muchlisin, Zainal A. Thomy, Zairin Fadli, Nur Sarong, Muhammad A. Siti-Azizah, Mohd N.
Directorate General of Higher Education (DGHE), Republic of Indonesia [139/UN11/A.01/APBN-P2T/2012]
The work described in this paper was partially supported by a grant from the Directorate General of Higher Education (DGHE), Republic of Indonesia (Project no. 139/UN11/A.01/APBN-P2T/2012). We wish to express our appreciation to anonymous reviewers for their critical comments and suggestions. The technical assistance by all members of Aquaculture Research Group (308 Biotech Lab), University Sains Malaysia, Penang, Malaysia and Syiah Kuala University, Banda Aceh, Indonesia are also acknowledged.
Wydawnictwo akad rolniczej w szczecinie
Szczecin
Mar 2013
KW  - genetic distance
COX1 gene
depik
Cyprinidae
cyprinus-carpio l.
genetic-characterization
diversity
identification
wild
populations
australia
taxonomy
river
life
N2  - Muchlisin Z.A., Thomy Z., Fadli N., Sarong M. A., Siti-Azizah M. N. 2013. DNA barcoding of freshwater fishes from Lake Laut Tawar, Aceh Province, Indonesia. Acta Ichthyol. Piscat. 43 (1): 21-29. Background. DNA barcoding has been recognised for its usefulness in species identification. The method is used for fast and accurate species identifications by focusing analysis on a short standardized segment of the genome. The main objective of the barcode of life project is to provide a database of genetic sequences which can be used as a tool for universal species identification. Indonesia has at least 1300 freshwater fish species, however unfortunately no species has been barcoded as yet. In the presently reported study, we subjected to barcoding a total of 14 species of freshwater fishes from Lake Laut Tawar, Indonesia. Materials and methods. On average, 10 random samples from each species were processed for DNA analysis. Approximately 655-bp were amplified from the 5' region of the mitochondrial cytochrome C oxidase subunit I (COX1) gene. All obtained sequences were edited and aligned using MEGA 4.0 program. Nucleotide divergence among sequences was estimated based on Kimura 2-parameter distances. Unique haplotypes were determined using DnaSP Version 5.10.02 software, and the genetic relations among haplotypes were assessed by constructing a phenogram using the neighbour-joining method. Results. A total of 31 haplotypes from 14 freshwater fish species were produced in this study. The read lengths were 626-bp, where 259 sites were polymorphic, 254 sites parsimony informative, and five singletons. No stop codons, deletions, or insertions were observed in any of the sequences. The nucleotide distance between species ranged from 7.1%-between Puntius brevis (Bleeker, 1850) and Poropuntius tawarensis (Weber et de Beaufort, 1916)to 30.4%-between Channa gachua (Hamilton, 1822) and Homaloptera sp.-indicating that P. brevis and P. tawarensis are very closely related. Conclusion. This study confirms the utility of COX1 gene in accurate identification of 14 species of freshwater fishes from Lake Laut Tawar, however, three species could not be identified to species level namely Rasbora sp. (local name: relo), Homaloptera sp. (ilie) and Clarias sp. (mud). It is suggested that future studies should incorporate morphometric methods to resolve the taxonomic status of these undetermined species.
AD  - Syiah Kuala Univ, Fac Marine & Fishery Sci, Dept Aquaculture, Banda Aceh 23111, Aceh Province, Indonesia. Syiah Kuala Univ, Dept Biol, Fac Sci, Banda Aceh 23111, Indonesia. Syiah Kuala Univ, Fac Educ & Teacher Training, Dept Educ Biol, Banda Aceh 23111, Indonesia. Univ Sains Malaysia, Sch Biol Sci, George Town 11800, Malaysia.
Muchlisin, ZA (reprint author), Syiah Kuala Univ, Fac Marine & Fishery Sci, Dept Aquaculture, Banda Aceh 23111, Aceh Province, Indonesia.
muchlisinza@yahoo.com
UR  - http://dx.doi.org/10.3750/AIP2013.43.1.04
ID  - 3100
ER  - 

TY  - JOUR
AU  - Newmaster, S.G.
AU  - Ragupathy, S.
AU  - Dhivya, S.
AU  - Jijo, C.J.
AU  - Sathishkumar, R.
AU  - Patel, K.
PY  - 2013
TI  - Genomic valorization of the fine scale classification of small millet landraces in southern India
SP  - 123-127
JF  - Genome
VL  - 56
IS  - 2
Y2  - 2013/02/01Mar 2013
N2  - Our research seeks to investigate genomic diversity of landraces of millet, addressing a key uncertainty that will provide a framework for (i) a DNA barcode method that could be used for fast, sensitive, and accurate identification of millet landraces, and (ii) millet landrace conservation including biocultural diversity. We found considerable intraspecific variation among 15 landraces representing six species of small millets using nuclear regions (ITS, ITS1, and ITS2); there was no variation in plastid regions (rbcL, matK, and trnH-psbA). An efficacious ITS2 DNA barcode was used to make 100% accurate landrace assignments for 150 blind samples representing 15 landraces. Our research revealed that genomic variation is aligned with a fine-scale classification of landraces using traditional knowledge (TK) of local farmers. The landrace classification was highly correlated with traits (morphological, agricultural, and cultural utility) associated with considerable factors such as yield, drought tolerance, growing season, medicinal properties, and nutrition. This could provide a DNA-based model for conservation of genetic diversity and the associated bicultural diversity (TK) of millet landraces, which has sustained marginal farming communities in harsh environments for many generations.
UR  - http://dx.doi.org/10.1139/gen-2012-0183
ID  - 3074
ER  - 

TY  - JOUR
AU  - Osmundson, T.W.
AU  - Robert, V.A.
AU  - Schoch, C.L.
AU  - Baker, L.J.
AU  - Smith, A.
AU  - Robich, G.
AU  - Mizzan, L.
AU  - Garbelotto, M.M.
PY  - 2013
TI  - Filling Gaps in Biodiversity Knowledge for Macrofungi: Contributions and Assessment of an Herbarium Collection DNA Barcode Sequencing Project
SP  - e62419
JF  - PLoS ONE
VL  - 8
IS  - 4fungi
N1  - Mar 2013
N2  - <p>Despite recent advances spearheaded by molecular approaches and novel technologies, species description and DNA sequence information are significantly lagging for fungi compared to many other groups of organisms. Large scale sequencing of vouchered herbarium material can aid in closing this gap. Here, we describe an effort to obtain broad ITS sequence coverage of the approximately 6000 macrofungal-species-rich herbarium of the Museum of Natural History in Venice, Italy. Our goals were to investigate issues related to large sequencing projects, develop heuristic methods for assessing the overall performance of such a project, and evaluate the prospects of such efforts to reduce the current gap in fungal biodiversity knowledge. The effort generated 1107 sequences submitted to GenBank, including 416 previously unrepresented taxa and 398 sequences exhibiting a best BLAST match to an unidentified environmental sequence. Specimen age and taxon affected sequencing success, and subsequent work on failed specimens showed that an ITS1 mini-barcode greatly increased sequencing success without greatly reducing the discriminating power of the barcode. Similarity comparisons and nonmetric multidimensional scaling ordinations based on pairwise distance matrices proved to be useful heuristic tools for validating the overall accuracy of specimen identifications, flagging potential misidentifications, and identifying taxa in need of additional species-level revision. Comparison of within- and among-species nucleotide variation showed a strong increase in species discriminating power at 1–2% dissimilarity, and identified potential barcoding issues (same sequence for different species and vice-versa). All sequences are linked to a vouchered specimen, and results from this study have already prompted revisions of species-sequence assignments in several taxa.</p>
UR  - http://dx.doi.org/10.1371%2Fjournal.pone.0062419
ID  - 3078
ER  - 

TY  - JOUR
AU  - Parducci, L.
AU  - Matetovici, I.
AU  - Fontana, S.L.
AU  - Bennett, K.D.
AU  - Suyama, Y.
AU  - Haile, J.
AU  - Kjær, K.H.
AU  - Larsen, N.K.
AU  - Drouzas, A.D.
AU  - Willerslev, E.
PY  - 2013
TI  - Molecular- and pollen-based vegetation analysis in lake sediments from central Scandinavia
SP  - n/a-n/a
JF  - Molecular EcologyMar 2013
KW  - ancient DNA
barcoding
environmental DNA
palaeoecology
pollen
N2  - Plant and animal biodiversity can be studied by obtaining DNA directly from the environment. This new approach in combination with the use of generic barcoding primers (metabarcoding) has been suggested as complementary or alternative to traditional biodiversity monitoring in ancient soil sediments. However, the extent to which metabarcoding truly reflects plant composition remains unclear, as does its power to identify species with no pollen or macrofossil evidence. Here, we compared pollen-based and metabarcoding approaches to explore the Holocene plant composition around two lakes in central Scandinavia. At one site, we also compared barcoding results with those obtained in earlier studies with species-specific primers. The pollen analyses revealed a larger number of taxa (46), of which the majority (78%) was not identified by metabarcoding. The metabarcoding identified 14 taxa (MTUs), but allowed identification to a lower taxonomical level. The combined analyses identified 52 taxa. The barcoding primers may favour amplification of certain taxa, as they did not detect taxa previously identified with species-specific primers. Taphonomy and selectiveness of the primers are likely the major factors influencing these results. We conclude that metabarcoding from lake sediments provides a complementary, but not an alternative, tool to pollen analysis for investigating past flora. In the absence of other fossil evidence, metabarcoding gives a local and important signal from the vegetation, but the resulting assemblages show limited capacity to detect all taxa, regardless of their abundance around the lake. We suggest that metabarcoding is followed by pollen analysis and the use of species-specific primers to provide the most comprehensive signal from the environment.
UR  - http://dx.doi.org/10.1111/mec.12298
ID  - 3087
ER  - 

TY  - JOUR
AU  - Parmentier, I.
AU  - Duminil, J.
AU  - Kuzmina, M.
AU  - Philippe, M.
AU  - Thomas, D.W.
AU  - Kenfack, D.
AU  - Chuyong, G.B.
AU  - Cruaud, C.
AU  - Hardy, O.J.
PY  - 2013
TI  - How Effective Are DNA Barcodes in the Identification of African Rainforest Trees?
SP  - e54921
JF  - PLoS ONE
VL  - 8
IS  - 4plants
N1  - Mar 2013
N2  - <sec><title>Background</title><p>DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of <italic>rbcL</italic>, <italic>matK</italic> and <italic>trnH</italic>-<italic>psbA</italic> plastid DNA markers to identify rain forest trees at two sites in Atlantic central Africa under the assumption that a database is exhaustive in terms of species content, but not necessarily in terms of haplotype diversity within species.</p></sec><sec><title>Methodology/Principal Findings</title><p>We assess the accuracy of identification to species or genus using a genetic distance matrix between samples either based on a global multiple sequence alignment (GD) or on a basic local alignment search tool (BLAST). Where a local database is available (within a 50 ha plot), barcoding was generally reliable for genus identification (95–100% success), but less for species identification (71–88%). Using a single marker, best results for species identification were obtained with <italic>trnH-psbA</italic>. There was a significant decrease of barcoding success in species-rich clades. When the local database was used to identify the genus of trees from another region and did include all genera from the query individuals but not all species, genus identification success decreased to 84–90%. The GD method performed best but a global multiple sequence alignment is not applicable on <italic>trnH-psbA</italic>.</p></sec><sec><title>Conclusions/Significance</title><p>Barcoding is a useful tool to assign unidentified African rain forest trees to a genus, but identification to a species is less reliable, especially in species-rich clades, even using an exhaustive local database. Combining two markers improves the accuracy of species identification but it would only marginally improve genus identification. Finally, we highlight some limitations of the BLAST algorithm as currently implemented and suggest possible improvements for barcoding applications.</p></sec>
UR  - http://dx.doi.org/10.1371%2Fjournal.pone.0054921
ID  - 3092
ER  - 

TY  - JOUR
AU  - Pereira, L.
AU  - Hanner, R.
AU  - Foresti, F.
AU  - Oliveira, C.
PY  - 2013
TI  - Can DNA barcoding accurately discriminate megadiverse Neotropical freshwater fish fauna?
SP  - 20
JF  - BMC Genetics
VL  - 14
IS  - 1
N1  - doi:10.1186/1471-2156-14-20
N1  - Mar 2013
N2  - BACKGROUND:The megadiverse Neotropical freshwater ichthyofauna is the richest in the world with approximately 6,000 recognized species. Interestingly, they are distributed among only 17 orders, and almost 80% of them belong to only three orders: Characiformes, Siluriformes and Perciformes. Moreover, evidence based on molecular data has shown that most of the diversification of the Neotropical ichthyofauna occurred recently. These characteristics make the taxonomy and identification of this fauna a great challenge, even when using molecular approaches. In this context, the present study aimed to test the effectiveness of the barcoding methodology (COI gene) to identify the mega diverse freshwater fish fauna from the Neotropical region. For this purpose, 254 species of fishes were analyzed from the Upper Parana River basin, an area representative of the larger Neotropical region.RESULTS:Of the 254 species analyzed, 252 were correctly identified by their barcode sequences (99.2%). The main K2P intra- and inter-specific genetic divergence values (0.3% and 6.8%, respectively) were relatively low compared with similar values reported in the literature, reflecting the higher number of closely related species belonging to a few higher taxa and their recent radiation. Moreover, for 84 pairs of species that showed low levels of genetic divergence (<2%), application of a complementary character-based nucleotide diagnostic approach proved useful in discriminating them. Additionally, 14 species displayed high intra-specific genetic divergence (>2%), pointing to at least 23 strong candidates for new species.CONCLUSIONS:Our study is the first to examine a large number of freshwater fish species from the Neotropical area, including a large number of closely related species. The results confirmed the efficacy of the barcoding methodology to identify a recently radiated, megadiverse fauna, discriminating 99.2% of the analyzed species. The power of the barcode sequences to identify species, even with low interspecific divergence, gives us an idea of the distribution of inter-specific genetic divergence in these megadiverse fauna. The results also revealed hidden genetic divergences suggestive of reproductive isolation and putative cryptic speciation in some species (23 candidates for new species). Finally, our study constituted an important contribution to the international Barcoding of Life (iBOL.org) project, providing barcode sequences for use in identification of these species by experts and non-experts, and allowing them to be available for use in other applications.
UR  - http://dx.doi.org/10.1186/1471-2156-14-20
ID  - 3042
ER  - 

TY  - JOUR
AU  - Pohjoismaki, J.
AU  - Kahanpaa, J.
AU  - Mutanen, M.
PY  - 2013
TI  - DNA barcodes for north European Tachinidae: preliminary results and material request
SP  - 17-19
JF  - Tachinid Times
VL  - 26
Y2  - February
N1  - ZOOREC:ZOOR14905018538
N1  - Zoor14905018538
Mar 2013
KW  - Systematics
Biochemistry
Genetics
Evolution
Land zones
Palaearctic
region
Eurasia
Tachinidae [Nucleic acids / DNA barcoding / taxonomic implications]
[Molecular genetics / / ] [Phylogeny / Molecular phylogeny / ] [Europe
/ North / ].
Tachinidae (Cyclorrhapha).
AD  - Pohjoismaki, Jaakko; Department of Biology, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland, Finland.
jaakko.pohjoismaki@uef.fi
UR  - http://www.nadsdiptera.org/Tach/TTimes/TT26_e-prints/Pohjoismaki-et-al2013_17-19_TTT_Barcoding.pdf
ID  - 3094
ER  - 

TY  - JOUR
AU  - Prévot, V.
AU  - Jordaens, K.
AU  - Sonet, G.
AU  - Backeljau, T.
PY  - 2013
TI  - Exploring Species Level Taxonomy and Species Delimitation Methods in the Facultatively Self-Fertilizing Land Snail Genus Rumina (Gastropoda: Pulmonata)
SP  - e60736
JF  - PLoS ONE
VL  - 8
IS  - 4Mar 2013
N2  - <p>Delimiting species in facultatively selfing taxa is a challenging problem of which the terrestrial pulmonate snail genus <italic>Rumina</italic> is a good example. These snails have a mixed breeding system and show a high degree of shell and color variation. Three nominal species (<italic>R. decollata, R. saharica</italic> and <italic>R. paivae</italic>) and two color morphs within <italic>R. decollata</italic> (dark and light) are currently recognized. The present study aims at evaluating to what extent these entities reflect evolutionary diverging taxonomic units, rather than fixed polymorphisms due to sustained selfing. Therefore, a phylogenetic analysis of nuclear (ITS1, ITS2) and mitochondrial DNA (COI, CytB, 12S rDNA, 16S rDNA) sequences was performed. Putative species in <italic>Rumina,</italic> inferred from the mitochondrial DNA phylogeny, were compared with those proposed on the basis of the COI gene by (1) DNA barcoding gap analysis, (2) Automatic Barcode Gap Discovery, (3) the species delimitation plug-in of the Geneious software, (4) the Genealogical Sorting Index, and (5) the General Mixed Yule Coalescent model. It is shown that these methods produce a variety of different species hypotheses and as such one may wonder to what extent species delimitation methods are really useful. With respect to <italic>Rumina</italic>, the data suggest at least seven species, one corresponding to <italic>R. saharica</italic> and six that are currently grouped under the name <italic>R. decollata</italic>. The species-level status of <italic>R. paivae</italic> is rejected.</p>
UR  - http://dx.doi.org/10.1371%2Fjournal.pone.0060736
ID  - 3088
ER  - 

TY  - JOUR
AU  - Riedel, A.
AU  - Sagata, K.
AU  - Surbakti, S.
AU  - Tänzler, R.
AU  - Balke, M.
PY  - 2013
TI  - One hundred and one new species of Trigonopterus weevils from New Guinea
SP  - 1-150
JF  - ZooKeys
VL  - 280
IS  - 0Mar 2013
blog
N2  - <p>A species discovery and description pipeline to accelerate and improve taxonomy is outlined, relying on concise expert descriptions, combined with DNA sequencing, digital imaging, and automated wiki species page creation from the journal. One hundred and one new species of Trigonopterus Fauvel, 1862 are described to demonstrate the feasibility of this approach: T. aeneipennis sp. n., T. aeneus sp. n., T. agathis sp. n., T. agilis sp. n., T. amplipennis sp. n., T. ancoruncus sp. n., T. angulatus sp. n., T. angustus sp. n., T. apicalis sp. n., T. armatus sp. n., T. ascendens sp. n., T. augur sp. n., T. balimensis sp. n., T. basalis sp. n., T. conformis sp. n., T. constrictus sp. n., T. costatus sp. n., T. costicollis sp. n., T. crassicornis sp. n., T. cuneipennis sp. n., T. cyclopensis sp. n., T. dentirostris sp. n., T. discoidalis sp. n., T. dromedarius sp. n., T. durus sp. n., T. echinus sp. n., T. edaphus sp. n., T. eremitus sp. n., T. euops sp. n., T. ferrugineus sp. n., T. fusiformis sp. n., T. glaber sp. n., T. gonatoceros sp. n., T. granum sp. n., T. helios sp. n., T. hitoloorum sp. n., T. imitatus sp. n., T. inflatus sp. n., T. insularis sp. n., T. irregularis sp. n., T. ixodiformis sp. n., T. kanawiorum sp. n., T. katayoi sp. n., T. koveorum sp. n., T. kurulu sp. n., T. lekiorum sp. n., T. lineatus sp. n., T. lineellus sp. n., T. maculatus sp. n., T. mimicus sp. n., T. monticola sp. n., T. montivagus sp. n., T. moreaorum sp. n., T. myops sp. n., T. nangiorum sp. n., T. nothofagorum sp. n., T. ovatus sp. n., T. oviformis sp. n., T. parumsquamosus sp. n., T. parvulus sp. n., T. phoenix sp. n., T. plicicollis sp. n., T. politoides sp. n., T. pseudogranum sp. n., T. pseudonasutus sp. n., T. ptolycoides sp. n., T. punctulatus sp. n., T. ragaorum sp. n., T. rhinoceros sp. n., T. rhomboidalis sp. n., T. rubiginosus sp. n., T. rubripennis sp. n., T. rufibasis sp. n., T. scabrosus sp. n., T. scissops sp. n., T. scharfi sp. n., T. signicollis sp. n., T. simulans sp. n., T. soiorum sp. n., T sordidus sp. n., T. squamirostris sp. n., T. striatus sp. n., T. strigatus sp. n., T. strombosceroides sp. n., T. subglabratus sp. n., T. sulcatus sp. n., T. taenzleri sp. n., T. talpa sp. n., T. taurekaorum sp. n., T. tialeorum sp. n., T. tibialis sp. n., T. tridentatus sp. n., T. uniformis sp. n., T. variabilis sp. n., T. velaris sp. n., T. verrucosus sp. n., T. violaceus sp. n., T. viridescens sp. n., T. wamenaensis sp. n., T. wariorum sp. n., T. zygops sp. n.. All new species are authored by the taxonomist-in-charge, Alexander Riedel.</p>
UR  - http://dx.doi.org/10.3897/zookeys.280.3906
ID  - 3072
ER  - 

TY  - JOUR
AU  - Robe, L.J.
AU  - Cenzi de Re, F.
AU  - Ludwig, A.
AU  - Loreto, E.L.
PY  - 2013
TI  - The Drosophila flavopilosa species group (Diptera, Drosophilidae): An array of exciting questions
JF  - Fly (Austin)
VL  - 7
IS  - 2
Y2  - Mar 4
N1  - 23459119
N1  - Robe, Lizandra J
Cenzi de Re, Francine
Ludwig, Adriana
Loreto, Elgion L S
Journal article
Fly
Fly (Austin). 2013 Mar 4;7(2).
Mar 2013
N2  - The D. flavopilosa group encompasses an ecologically restricted set of species strictly adapted to hosting flowers of Cestrum (Solanaceae). This group presents potential to be used as a model to the study of different questions regarding ecologically restricted species macro and microevolutionary responses, geographical vs. ecological speciation and intra and interspecific competition. This review aims to revisit and reanalyze the patterns and processes that are subjacent to the interesting ecological and evolutionary properties of these species. Biotic and abiotic niche properties of some species were reanalyzed in face of ecological niche modeling approaches in order to get some insights into their ecological evolution. A test of the potential of DNA-Barcoding provided evidences that this technology may be a way of overcoming difficulties related to cryptic species differentiation. The new focus replenishes the scenario with new questions, presenting a case where neither geographical nor ecological speciation may be as yet suggested.
AD  - Programa de Pos-Graduacao em Biologia de Ambientes Aquaticos Continentais (PPGBAC); Universidade Federal do Rio Grande (FURG); Rio Grande, Rio Grande do Sul, Brazil; Programa de Pos-Graduacao em Biodiversidade Animal (PPGBA); Universidade Federal de Santa Maria (UFSM); Rio Grande, Rio Grande do Sul, Brazil.
UR  - https://www.landesbioscience.com/journals/fly/article/23923/?show_full_text=true&
ID  - 3038
ER  - 

TY  - JOUR
AU  - Rolo, E.A.
AU  - Oliveira, A.R.
AU  - Dourado, C.G.
AU  - Farinha, A.
AU  - Rebelo, M.T.
AU  - Dias, D.
PY  - 2013
TI  - Identification of sarcosaprophagous Diptera species through DNA barcoding in wildlife forensics
SP  - 160-164
JF  - Forensic Science International
VL  - 228
IS  - 1Mar 2013
KW  - Wildlife forensic entomology
Cytochrome c oxidase I
DNA barcoding
DNA databases
Diptera
Iberian Peninsula
N2  - In recent years, forensic entomology has been applied in wildlife crimes, such as neglect cases, animal cruelty and illegal poaching. Likewise in human death investigations, in which insects can help to provide information about postmortem interval (PMI) and corpse transfer, entomology may be an important source of information in animal murder suspicion. The use of insects in forensic context relies primarily on its identification at the species level. To overcome some problems of morphological determination, molecular identification has gained relevance and has been applied frequently in forensic areas. Cytochrome c oxidase I (COI) gene was adopted in DNA barcoding approach. This methodology intends to unify the DNA-based identification using a specific region of mitochondrial DNA. COI sequences have been collected into the BOLD online database, allowing the molecular identification of sequences from unknown specimens. Nonetheless, to achieve a correct identification of an unknown sample, it is necessary that sequences from species under study exist, for comparison, in online databases. Due to the geographic differences, it is of huge importance to have samples from a certain species from its distribution range. In that sense, the aim of this research is to contribute to the potential and accuracy improvement of such databases in identification of species commonly found in wildlife carcasses. A portion of COI was sequenced from 95 specimens of seven species belonging to two families of Diptera (Calliphoridae and Muscidae) found in wildlife carcasses-baited traps in Serra da Estrela (Portugal). All specimens were identified at species level with a high specimen similarity and maximum identity percentage (through BOLD Systems and GenBank online databases, respectively). We also demonstrate the correct discrimination of all species through phylogenic and sequence divergence analyses proposed in DNA barcoding studies, reinforcing the suitability of this marker.
UR  - http://linkinghub.elsevier.com/retrieve/pii/S0379073813001242?showall=true
ID  - 3082
ER  - 

TY  - JOUR
AU  - Sasakawa, K.
PY  - 2013
TI  - A Novel Technique for Identifying the Instar of Field-Collected Insect Larvae
SP  - e57836
JF  - PLoS ONE
VL  - 8
IS  - 2Mar 2013
N2  - <p>Many field studies of insects have focused on the adult stage alone, likely because immature stages are unknown in most insect species. Molecular species identification (e.g., DNA barcoding) has helped ascertain the immature stages of many insects, but larval developmental stages (instars) cannot be identified. The identification of the growth stages of collected individuals is indispensable from both ecological and taxonomic perspectives. Using a larval–adult body size relationship across species, I present a novel technique for identifying the instar of field-collected insect larvae that are identified by molecular species identification technique. This method is based on the assumption that classification functions derived from discriminant analyses, performed with larval instar as a response variable and adult and larval body sizes as explanatory variables, can be used to determine the instar of a given larval specimen that was not included in the original data set, even at the species level. This size relationship has been demonstrated in larval instars for many insects (Dyar’s rule), but no attempt has been made to include the adult stage. Analysis of a test data set derived from the beetle family Carabidae (Coleoptera) showed that classification functions obtained from data sets derived from related species had a correct classification rate of 81–100%. Given that no reliable method has been established to identify the instar of field-collected insect larvae, these values may have sufficient accuracy as an analytical method for field-collected samples. The chief advantage of this technique is that the instar can be identified even when only one specimen is available per species if classification functions are determined for groups to which the focal species belongs. Similar classification functions should be created for other insect groups. By using those functions together with molecular species identification, future studies could include larval stages as well as adults.</p>
UR  - http://dx.doi.org/10.1371%2Fjournal.pone.0057836
ID  - 3057
ER  - 

TY  - JOUR
AU  - Saunders, G.
AU  - McDevit, D.
PY  - 2013
TI  - DNA barcoding unmasks overlooked diversity improving knowledge on the composition and origins of the Churchill algal flora
SP  - 9
JF  - BMC Ecology
VL  - 13
IS  - 1
N1  - doi:10.1186/1472-6785-13-9
N1  - Mar 2013
N2  - BACKGROUND:Sampling expeditions to Churchill in the Canadian subarctic were completed with the aim of compiling a molecular-assisted survey of the macroalgal flora (seaweeds) for comparison to published accounts for this area, which are based on morphological identifications. Further, because the Churchill region was covered by ice until recently (~10,000 before present), the current algal flora has had to migrate from adjacent waters into that region. We used our DNA barcode data to predict the relative contribution of the North Atlantic and North Pacific floras (Likely Source Region) in repopulating the Churchill region following the most recent glacial retreat.RESULTS:We processed 422 collections representing ~50 morpho-species, which is the approximate number reported for this region, and generated DNA barcode data for 346 of these. In contrast to the morpho-species count, we recovered 57 genetic groups indicating overlooked species (this despite failing to generate barcode data for six of the ~50 morpho-species). However, we additionally uncovered numerous inconsistencies between the species that are currently listed in the Churchill flora (again as a result of overlooked species diversity, but combined with taxonomic confusion) and those identified following our molecular analyses including eight new records and another 17 genetic complexes in need of further study. Based on a comparison of DNA barcode data from the Churchill flora to collections from the contiguous Atlantic and Pacific floras we estimate that minimally 21% (possibly as much as 44%) of the Churchill flora was established by migration from the Pacific region with the balance of species arriving from the Atlantic (predominantly North American populations) following the last glacial retreat.CONCLUSIONS:Owing to difficulties associated with the morphological identification of macroalgae, our results indicate that current comprehension of the Canadian Arctic flora is weak. We consider that morphology-based field-identifications are ill-advised in carrying out floristic and ecological surveys for macroalgae and that much of the current data, at least for the Canadian Arctic, should be used with caution. Our efforts to use DNA barcode data to identify the most Likely Source Regions for macroalgal species currently found in Churchill suggests that migration from both the Atlantic and the Pacific have played important roles in establishing the Canadian Arctic flora. This result has significance for understanding both the current and future biodiversity and biogeography of macroalgae in these waters.
UR  - http://dx.doi.org/10.1186/1472-6785-13-9
ID  - 3047
ER  - 

TY  - JOUR
AU  - Shirak, A.
AU  - Barkai, O.
AU  - Lernau, O.
AU  - Kahanov, Y.
AU  - Seroussi, E.
AU  - Ron, M.
PY  - 2013
TI  - DNA Barcoding Analysis of Fish Bones from a Shipwreck found at Dor, Israel
SP  - 873-873
JF  - Israeli Journal of Aquaculture-Bamidgeh
JO  - Isr. J. Aquac.-Bamidgeh
VL  - 65
N1  - CCC:000316866000001
N1  - fish
N1  - ISI Document Delivery No.: 116ER
Shirak, Andrey Barkai, Ofra Lernau, Omri Kahanov, Yaacov Seroussi, Eyal Ron, Micha
Israeli journal of aquaculture-bamidgeh
Ashrat
Mar 2013
blog?
KW  - Oreochromis aureus, Sarotherodon galilaeus, Tantura F shipwreck,
mini-barcoding, mitochondrial DNA
extraction
N2  - The Tantura F shipwreck, found in Dor lagoon, was dated to the Early Islamic period of Israel (8th century). Ovoid amphorae found in the shipwreck contained fish bones that were morphologically assigned to the genus Tilapia. A mini-barcode sequence of a 140-bp fragment of the cytochrome oxidase subunit I mitochondrial gene was analyzed for DNA-based taxonomy of the ancient fish. A single transition m. 5573 G>A of Oreochromis aureus and Sarotherodon galilaeus further identified the ancient fish as tilapia. This nucleotide transition suggests that the ancient fish belonged to an extinct species or sub-species closely related to contemporary O. aureus or S. galilaeus. Within the archeological and historical context, the DNA-based identification of the ancient fish as tilapia may aid in understanding the fish industry and trade in the region during the Islamic period.
AD  - [Shirak, A; Seroussi, E; Ron, M] Agr Res Org, Volcani Ctr, Inst Anim Sci, Dept Quantitat & Mol Genet, IL-50250 Bet Dagan, Israel [Barkai, O; Kahanov, Y] Univ Haifa, Dept Maritime Civilizat, IL-31905 Haifa, Israel [Lernau, O] Univ Haifa, Zinman Inst Archaeol, IL-31905 Haifa, Israel [Kahanov, Y] Univ Haifa, Leon Recanati Inst Maritime Studies, IL-31905 Haifa, Israel
Shirak, Andrey (reprint author), Agr Res Org, Volcani Ctr, Inst Anim Sci, Dept Quantitat & Mol Genet, POB 6, IL-50250 Bet Dagan, Israel
shiraka@agri.gov.il
UR  - http://www.siamb.org.il/article-1305,1187-IJA-65-2013-873.aspx
ID  - 3069
ER  - 

TY  - JOUR
AU  - Tai, V.
AU  - James, E.R.
AU  - Perlman, S.J.
AU  - Keeling, P.J.
PY  - 2013
TI  - Single-Cell DNA Barcoding Using Sequences from the Small Subunit rRNA and Internal Transcribed Spacer Region Identifies New Species of Trichonympha and Trichomitopsis from the Hindgut of the Termite Zootermopsis angusticollis
SP  - e58728
JF  - PLoS ONE
VL  - 8
IS  - 3Mar 2013
N2  - <p>To aid in their digestion of wood, lower termites are known to harbour a diverse community of prokaryotes as well as parabasalid and oxymonad protist symbionts. One of the best-studied lower termite gut communities is that of <italic>Zootermopsis angusticollis</italic> which has been known for almost 100 years to possess 3 species of <italic>Trichonympha</italic> (<italic>T. campanula</italic>, <italic>T. collaris</italic>, and <italic>T. sphaerica</italic>), 1 species of <italic>Trichomitopsis</italic> (<italic>T. termopsidis),</italic> as well as smaller flagellates. We have re-assessed this community by sequencing the small subunit (SSU) rRNA gene and the internal transcribed spacer (ITS) region from a large number of single <italic>Trichonympha</italic> and <italic>Trichomitopsis</italic> cells for which morphology was also documented. Based on phylogenetic clustering and sequence divergence, we identify 3 new species: <italic>Trichonympha postcylindrica</italic>, <italic>Trichomitopsis minor</italic>, and <italic>Trichomitopsis parvus</italic> spp. nov. Once identified by sequencing, the morphology of the isolated cells for all 3 new species was re-examined and found to be distinct from the previously described species: <italic>Trichonympha postcylindrica</italic> can be morphologically distinguished from the other <italic>Trichonympha</italic> species by an extension on its posterior end, whereas <italic>Trichomitopsis minor</italic> and <italic>T. parvus</italic> are smaller than <italic>T. termopsidis</italic> but similar in size to each other and cannot be distinguished based on morphology using light microscopy. Given that <italic>Z. angusticollis</italic> has one of the best characterized hindgut communities, the near doubling of the number of the largest and most easily identifiable symbiont species suggests that the diversity of hindgut symbionts is substantially underestimated in other termites as well. Accurate descriptions of the diversity of these microbial communities are essential for understanding hindgut ecology and disentangling the interactions among the symbionts, and molecular barcoding should be a priority for these systems.</p>
UR  - http://dx.doi.org/10.1371%2Fjournal.pone.0058728
ID  - 3054
ER  - 

TY  - JOUR
AU  - Thompson, K.F.
AU  - Millar, C.D.
AU  - Scott Baker, C.
AU  - Dalebout, M.
AU  - Steel, D.
AU  - van Helden, A.L.
AU  - Constantine, R.
PY  - 2013
TI  - A novel conservation approach provides insights into the management of rare cetaceans
SP  - 331-340
JF  - Biological Conservation
VL  - 157
IS  - 0mammals, marine
N1  - Mar 2013
KW  - Strandings
Beaked whales
Ziphiidae
Cetaceans
Distribution
Mesoplodon grayi
N2  - The conservation of rare or cryptic species in inaccessible habitats represents a particular challenge to biologists. Since 1991, a collaborative research program involving members of the public, indigenous communities, the Museum of New Zealand Te Papa Tongarewa (NMNZ) and the Department of Conservation has provided tissue samples for genetic analysis of stranded, or beach-cast cetaceans. The New Zealand Cetacean Tissue Archive (NZCeTA), initiated and maintained by the University of Auckland, is now one of the largest archives of its kind in the world, with tissue samples or extracted DNA from 1982 individuals. Species identity has been confirmed by DNA barcoding, using mtDNA control region sequences for 65% of the samples representing 35 species, 11 of which are from the poorly known beaked whale family, Ziphiidae. Although these animals regularly strand around the coastline of New Zealand there are no known areas at sea where they can be reliably found and very few reported live sightings. Samples collected from strandings of three species: Gray’s (Mesoplodon grayi); straptoothed (Mesoplodon layardii) and Cuvier’s beaked whale (Ziphius cavirostris), represent 83% (n = 225) of all ziphiids in the NZCeTA (n = 272). As an example of the archives utility, we used the spatial and temporal distribution of these records to provide new evidence for key habitat of these cryptic species and for seasonal and sex-biased patterns of stranding mortality. As beaked whales are known to be threatened by anthropogenic activity in other parts of the world, these records provide a critical baseline for understanding the future impacts of planned development in New Zealand’s near and offshore waters.
UR  - http://dx.doi.org/10.1016/j.biocon.2012.07.017
ID  - 3071
ER  - 

TY  - JOUR
AU  - Wang, L.-J.
AU  - Cherng, J.-J.
AU  - Chang, Y.-J.
AU  - Jiang, J.-L.
PY  - 2013
TI  - Description of Rhinocypha taiwana sp. nov. from Taiwan, with a preliminary molecular phylogenetic analysis of the Rhinocypha drusilla-group (Odonata: Chlorocyphidae)
SP  - 93-107
JF  - International Journal of Odonatology
VL  - 16
IS  - 1
Y2  - 2013/03/01Mar 2013
N2  - Rhinocypha taiwana Wang & Chang, sp. nov. is described and illustrated for both sexes. The genetic distance of the cytochrome c oxidase I (COI) gene in R. taiwana and related species ranges from 4.2% to 10.4%. R. taiwana is shown to be a good species based on morphological and genetic criteria. It also is clearly retrieved as a distinct species based on COI phylogenetic analysis. The R. drusilla group is proposed and defined by a combination of characteristics which distinguish them from all other Rhinocypha species: male abdomen with reddish orange markings and S2 with a unique dorsal spade-shaped or similar marking. A key to the males of the six species of the R. drusilla group is provided. Two morphologically distinct continental species, R. drusilla and R. arguta, are shown to have a rather small genetic distance, only 1.2?1.7%. More material from the continental populations of this group is needed for further morphological and molecular studies.
UR  - http://dx.doi.org/10.1080/13887890.2012.763152
ID  - 3077
ER  - 

TY  - JOUR
AU  - Yacoub, H.A.
AU  - Fathi, M.M.
AU  - Mahmoud, W.M.
PY  - 2013
TI  - DNA barcode through cytochrome b gene information of mtDNA in native chicken strains
SP  - null
JF  - Mitochondrial DNA
VL  - 0
IS  - 0
N1  - 23464748
N1  - Mar 2013
N2  - This study was carried out to figure out the potentiality of a cytochrome b gene as a barcoding tool in discriminating native chicken strains and other Gallus gallus species. We performed PCR amplification using universal primer to amplify around 415 bp fragment of cytochrome b gene of mtDNA. The results revealed that all Saudi chicken strains were identical to each other but when compared with other species of Gallus the differences were exciting. The phylogenetic tree revealed that there were seven clusters represented for native strains and were clustered together especially in black strain and dark brown ones. The results have confirmed that using cytochrome b gene to discriminate between Saudi chicken strains and other species of G. gallus fowl was a very sufficient tool. Moreover, we can consider short fragment of cytochrome b gene of mtDNA as a universal DNA barcode region. It was a much more accurate and efficient tool to discriminate interspecies than intraspecies. We think it needs more studies to confirm this concept, and we have to apply that tool for many species of vertebrate and invertebrate as well.

UR  - http://dx.doi.org/10.3109/19401736.2013.770489
ID  - 3058
ER  - 

TY  - JOUR
AU  - Yamamoto, N.
AU  - Bibby, K.
AU  - Qian, J.
AU  - Hospodsky, D.
AU  - Rismani-Yazdi, H.
AU  - Nazaroff, W.W.
AU  - Peccia, J.
PY  - 2012
TI  - Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air
SP  - 1801-1811
JF  - ISME J
VL  - 6
IS  - 10fungi
N1  - Mar 2013
blog?
N2  - Fungi are ubiquitous in outdoor air, and their concentration, aerodynamic diameters and taxonomic composition have potentially important implications for human health. Although exposure to fungal allergens is considered a strong risk factor for asthma prevalence and severity, limitations in tracking fungal diversity in air have thus far prevented a clear understanding of their human pathogenic properties. This study used a cascade impactor for sampling, and quantitative real-time PCR plus 454 pyrosequencing for analysis to investigate seasonal, size-resolved fungal communities in outdoor air in an urban setting in the northeastern United States. From the 20 libraries produced with an average of ~800 internal transcribed spacer (ITS) sequences (total 15 326 reads), 12 864 and 11 280 sequences were determined to the genus and species levels, respectively, and 558 different genera and 1172 different species were identified, including allergens and infectious pathogens. These analyses revealed strong relationships between fungal aerodynamic diameters and features of taxonomic compositions. The relative abundance of airborne allergenic fungi ranged from 2.8% to 10.7% of total airborne fungal taxa, peaked in the fall, and increased with increasing aerodynamic diameter. Fungi that can cause invasive fungal infections peaked in the spring, comprised 0.1–1.6% of fungal taxa and typically increased in relative abundance with decreasing aerodynamic diameter. Atmospheric fungal ecology is a strong function of aerodynamic diameter, whereby through physical processes, the size influences the diversity of airborne fungi that deposit in human airways and the efficiencies with which specific groups of fungi partition from outdoor air to indoor environments.
UR  - http://dx.doi.org/10.1038/ismej.2012.30
ID  - 3079
ER  - 

TY  - JOUR
AU  - Yoo, H.
AU  - Eah, J.-Y.
AU  - Kim, J.
AU  - Kim, Y.-J.
AU  - Min, M.-S.
AU  - Paek, W.
AU  - Lee, H.
AU  - Kim, C.-B.
PY  - 2013
TI  - Retraction note: DNA barcoding Korean birds
SP  - 357-357
JF  - Molecules and Cells
JO  - Mol Cells
VL  - 35
IS  - 4
Y2  - 2013/04/01Mar 2013
UR  - http://dx.doi.org/10.1007/s10059-013-3151-6
ID  - 3090
ER  - 

TY  - JOUR
AU  - Young, M.K.
AU  - McKelvey, K.S.
AU  - Pilgrim, K.L.
AU  - Schwartz, M.K.
PY  - 2013
TI  - DNA barcoding at riverscape scales: assessing biodiversity among fishes of the genus Cottus (Teleostei) in northern Rocky Mountain streams
SP  - n/a-n/a
JF  - Molecular Ecology ResourcesMar 2013
KW  - Cottidae
cryptic species
sculpins
species discovery
N2  - There is growing interest in broad-scale biodiversity assessments that can serve as benchmarks for identifying ecological change. Genetic tools have been used for such assessments for decades, but spatial sampling considerations have largely been ignored. Here, we demonstrate how intensive sampling efforts across a large geographical scale can influence identification of taxonomic units. We used sequences of mtDNA cytochrome c oxidase subunit 1 and cytochrome b, analysed with maximum parsimony networks, maximum-likelihood trees and genetic distance thresholds, as indicators of biodiversity and species identity among the taxonomically challenging fishes of the genus Cottus in the northern Rocky Mountains, USA. Analyses of concatenated sequences from fish collected in all major watersheds of this area revealed eight groups with species-level differences that were also geographically circumscribed. Only two of these groups, however, were assigned to recognized species, and these two assignments resulted in intraspecific genetic variation (>2.0%) regarded as atypical for individual species. An incomplete inventory of individuals from throughout the geographical ranges of many species represented in public databases, as well as sample misidentification and a poorly developed taxonomy, may have hampered species assignment and discovery. We suspect that genetic assessments based on spatially robust sampling designs will reveal previously unrecognized biodiversity in many other taxa.
UR  - http://dx.doi.org/10.1111/1755-0998.12091
ID  - 3046
ER  - 

TY  - JOUR
AU  - Zhou, X.
AU  - Li, Y.
AU  - Liu, S.
AU  - Yang, Q.
AU  - Su, X.
AU  - Zhou, L.
AU  - Tang, M.
AU  - Fu, R.
AU  - Li, J.
AU  - Huang, Q.
PY  - 2013
TI  - Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification
SP  - 4
JF  - GigaScience
VL  - 2
IS  - 1
N1  - doi:10.1186/2047-217X-2-4
N1  - pyro
N1  - Mar 2013
N2  - BACKGROUND:Next-generation-sequencing (NGS) technologies combined with a classic DNA barcoding approach have enabled fast and credible measurement for biodiversity of mixed environmental samples. However, the PCR amplification involved in nearly all existing NGS protocols inevitably introduces taxonomic biases. In the present study, we developed new Illumina pipelines without PCR amplifications to analyze terrestrial arthropod communities.RESULTS:Mitochondrial enrichment directly followed by Illumina shotgun sequencing, at an ultra-high sequence volume, enabled the recovery of Cytochrome c Oxidase subunit 1 (COI) barcode sequences, which allowed for the estimation of species composition at high fidelity for a terrestrial insect community. With 15.5 Gbp Illumina data, approximately 97% and 92% were detected out of the 37 input Operational Taxonomic Units (OTUs), whether the reference barcode library was used or not, respectively, while only 1 novel OTU was found for the latter. Additionally, relatively strong correlation between the sequencing volume and the total biomass was observed for species from the bulk sample, suggesting a potential solution to reveal relative abundance.CONCLUSIONS:The ability of the new Illumina PCR-free pipeline for DNA metabarcoding to detect small arthropod specimens and its tendency to avoid most, if not all, false positives suggests its great potential in biodiversity-related surveillance, such as in biomonitoring programs. However, further improvement for mitochondrial enrichment is likely needed for the application of the new pipeline in analyzing arthropod communities at higher diversity.
UR  - http://dx.doi.org/10.1186/2047-217X-2-4
ID  - 3086
ER  -