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Article Reference DNA analyses reveal abundant homoplasy in taxonomically important morphological characters of Eusiroidea (Crustacea, Amphipoda)
Located in Library / RBINS Staff Publications 2016
Article Reference DNA barcodes and phylogenetic affinities of the terrestrial slugs Arion gilvus and A. ponsi (Gastropoda, Pulmonata, Arionidae)
Located in Library / RBINS Staff Publications
Incollection Reference DNA Barcoding Amphibians and Reptiles
Only a few major research programs are currently targeting COI barcoding of amphibians and reptiles (including chelonians and crocodiles), two major groups of tetrapods. Amphibian and reptile species are typically old, strongly divergent, and contain deep conspecifi c lineages which might lead to problems in species assignment with incomplete reference databases. As far as known, there is no single pair of COI primers that will guarantee a suffi cient rate of success across all amphibian and reptile taxa, or within major subclades of amphibians and reptiles, which means that the PCR amplifi cation strategy needs to be adjusted depending on the specifi c research question. In general, many more amphibian and reptile taxa have been sequenced for 16S rDNA, which for some purposes may be a suitable complementary marker, at least until a more comprehensive COI reference database becomes available. DNA barcoding has successfully been used to identify amphibian larval stages (tadpoles) in species-rich tropical assemblages. Tissue sampling, DNA extraction, and amplifi cation of COI is straightforward in amphibians and reptiles. Single primer pairs are likely to have a failure rate between 5 and 50\% if taxa of a wide taxonomic range are targeted; in such cases the use of primer cocktails or subsequent hierarchical usage of different primer pairs is necessary. If the target group is taxonomically limited, many studies have followed a strategy of designing specifi c primers which then allow an easy and reliable amplifi cation of all samples.
Located in Library / RBINS Staff Publications
Inproceedings Reference DNA barcoding and diversity of groundwater oligochaetes in Benin (West Africa)
Located in Library / RBINS Staff Publications 2017
Inproceedings Reference Dna barcoding and ecological surveys of the ants of southern Atlantic forest: looking at the tip of the iceberg in a biodiversity hotspot
Located in Library / RBINS Staff Publications 2017
Inproceedings Reference DNA barcoding and ecological survey of the ants of Iguazu National Park: looking at the tip of the iceberg in a biodiversity hotspot
Understanding patterns of species diversity can only be achieved by long-term research and the integration of taxonomical, ecological and behavioral data. Here we studied the diversity and ecology of ants of Iguazu National Park (INP), Argentina, using six sampling techniques. DNA barcodes were used to uncover cryptic diversity, test species/morphospecies delimitation accuracy, and link unidentified male and queen specimens with their worker caste. Results: INP houses 195 described ant species and an additional 49 morphospecies. Leaf litter sampling and pitfall traps were the most efficient sampling methods, while surface baiting revealed the prevalence of large predatory species at different times of the day. Comparing baiting to other sampling methods provided information on species co-existence and the presence of possible dominance hierarchies among ant species. We obtained the DNA barcodes of 312 specimens from 124 species (51% of the ants of INP). Our analyses evidenced a clear barcode gap in all species but two, with an average distance to the nearest neighbor of 15.75%, almost eight times larger than the mean distance to the furthest conspecific (2.07%). Eighty-three percent of the sequence clusters obtained with different clustering algorithms (ABGD, RESL, TCS) matched the reference species or morphospecies, while 10% highlighted possible cryptic diversity. In terms of efficacy, this barcode library allowed a correct identification in more than 94% of the species/morphospecies, and to assign a species name to 69% of the unidentified males and queens. Significance: This study evidences that DNA barcodes are a valuable tool for identifying the ants of the Atlantic Forest, a global diversity hotspot. Furthermore, our project provides a framework for understanding the ecology and the taxonomic diversity of the ants of this region, including the identification of currently undescribed reproductive castes and the discovery of possible cryptic species.
Located in Library / RBINS Staff Publications 2017
Article Reference DNA barcoding and evolutionary relationships in Accipiter Brisson, 1760 (Aves, Falconiformes: Accipitridae) with a focus on African and Eurasian representatives
Located in Library / RBINS Staff Publications
Article Reference DNA barcoding and male genital morphology reveal five new cryptic species in the West palearctic bee Seladonia smaragdula (Vachal, 1895) (Hypmenoptera: Apoidea: Halictidae)
Located in Library / RBINS Staff Publications
Article Reference DNA barcoding and the differentiation between North American and West European Phormia regina (Diptera, Calliphoridae, Chrysomyinae)
Located in Library / RBINS Staff Publications
Article Reference DNA barcoding echinoderms from the East Coast of South Africa. The challenge to maintain DNA data connected with taxonomy
Echinoderms are marine water invertebrates that are represented by more than 7000 extant species, grouped in five classes and showing diverse morphologies (starfish, sea lilies, feather stars, sea urchins, sea cucumbers, brittle and basket stars). In an effort to further study their diversity, DNA barcodes (DNA fragments of the 5’ end of the cytochrome c oxidase subunit I gene, COI) have been used to complement morphological examination in identifying evolutionary lineages. Although divergent clusters of COI sequences were reported to generally match morphological species delineations, they also revealed some discrepancies, suggesting overlooked species, ecophenotypic variation or multiple COI lineages within one species. Here, we sequenced COI fragments of 312 shallow-water echinoderms of the East Coast of South Africa (KwaZulu-Natal Province) and compared morphological identifications with species delimitations obtained with four methods that are exclusively based on COI sequences. We identified a total of 103 morphospecies including 18 that did not exactly match described species. We also report 46 COI sequences that showed large divergences (>5% p-distances) with those available to date and publish the first COI sequences for 30 species. Our analyses also identified discordances between morphological identifications and COI-based species delimitations for a considerable proportion of the morphospecies studied here (49/103). For most of them, further investigation is necessary to keep a sound connection between taxonomy and the growing importance of DNA-based research.
Located in Library / RBINS Staff Publications 2022