With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast

Borges, Luísa M. S.; Hollatz, Cláudia; Lobo, Jorge; Cunha, Ana Margarida; Vilela, Ana Paula Pessoa; Calado, Gonçalo; Coelho, Rita; Costa, Ana C.; Ferreira, Miguel; Costa, Maria Helena; Costa, Filipe O.

doi:10.1038/srep20226

Cited by 38 publications

(18 citation statements)

References 54 publications

(96 reference statements)

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“…Eumida 18%, Eulalia 17%), but it is within the average congeneric distances reported for other marine invertebrates (e.g. Borges et al, 2016;Costa et al 2009;Matzen da Silva et al 2011;Radulovici et al 2010). The relatively high substitution rates in COI may mask deep phylogenies and preclude good resolution of taxonomic ranks higher than species.…”

Section: Molecular Analysessupporting

confidence: 57%

Taxonomy, distribution and ecology of the order Phyllodocida (Annelida, Polychaeta) in deep-sea habitats around the Iberian margin

Ravara

Ramos

Teixeira

et al. 2017

Deep Sea Research Part II: Topical Studies in Oceanography

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The polychaetes of the order Phyllodocida (excluding Nereidiformia and Phyllodociformia incertae sedis) collected from deep-sea habitats of the Iberian margin (Bay of Biscay, Horseshoe continental rise, Gulf of Cadiz and Alboran Sea), and Atlantic seamounts (Gorringe Bank, Atlantis and Nameless) are reported herein. Thirty-six species belonging to seven families-Acoetidae, Pholoidae, Polynoidae, Sigalionidae, Glyceridae, Goniadidae and Phyllodocidae, were identified. Amended descriptions and/or new illustrations are given for the species Allmaniella setubalensis, Anotochaetonoe michelbhaudi, Lepidasthenia brunnea and Polynoe sp.. Relevant taxonomical notes are provided for other seventeen species. Allmaniella setubalensis, Anotochaetonoe michelbhaudi, Harmothoe evei, Eumida longicirrata and Glycera noelae, previously known only from their type localities were found in different deep-water places of the studied areas and constitute new records for the Iberian margin. The geographic distributions and the bathymetric range of thirteen and fifteen species, respectively, are extended. The morphology-based biodiversity inventory was complemented with DNA sequences of the mitochondrial barcode region (COI barcodes) providing a molecular tag for future reference. Twenty new sequences were obtained for nine species in the families Acoetidae, Glyceridae and Polynoidae and for three lineages within the Phylodoce madeirensis complex (Phyllodocidae). A brief analysis of the newly obtained sequences and publicly available COI barcode data for the genera herein reported, highlighted several cases of unclear taxonomic assignments, which need further study.

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Section: Molecular Analysessupporting

confidence: 57%

Taxonomy, distribution and ecology of the order Phyllodocida (Annelida, Polychaeta) in deep-sea habitats around the Iberian margin

Ravara

Ramos

Teixeira

et al. 2017

Deep Sea Research Part II: Topical Studies in Oceanography

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“…In order to assess the level of taxonomic reliability in the library, species‐specific DNA barcode subsets were ranked from grade A to E, as described below (Costa et al , ; Borges et al , ). The basis of such rating systems is that taxonomic reliability is greater if barcode sequences from independent researchers cluster unambiguously and consistently for a given species.…”

Section: Methodsmentioning

confidence: 99%

Assembling and auditing a comprehensive DNA barcode reference library for European marine fishes

Oliveira

Knebelsberger

Landi

et al. 2016

Journal of Fish Biology

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A large-scale comprehensive reference library of DNA barcodes for European marine fishes was assembled, allowing the evaluation of taxonomic uncertainties and species genetic diversity that were otherwise hidden in geographically restricted studies. A total of 4118 DNA barcodes were assigned to 358 species generating 366 Barcode Index Numbers (BIN). Initial examination revealed as much as 141 BIN discordances (more than one species in each BIN). After implementing an auditing and five-grade (A-E) annotation protocol, the number of discordant species BINs was reduced to 44 (13% grade E), while concordant species BINs amounted to 271 (78% grades A and B) and 14 other had insufficient data (grade D). Fifteen species displayed comparatively high intraspecific divergences ranging from 2·6 to 18·5% (grade C), which is biologically paramount information to be considered in fish species monitoring and stock assessment. On balance, this compilation contributed to the detection of 59 European fish species probably in need of taxonomic clarification or re-evaluation. The generalized implementation of an auditing and annotation protocol for reference libraries of DNA barcodes is recommended.

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“…18S, 16S, cytB ) for biodiversity assessment of benthic and marine ecosystems, whereas detection of OTUs was possible, a delineation of species was not perfectly applicable due to lack of available marker libraries [ 13 – 15 ]. Especially for ecosystems like soil or benthos the reference libraries are still not representative, whereas first pioneering studies analyzing selected taxa have been published [ 16 – 22 ]. Furthermore, the necessity of generation and maintenance of individually barcoded and curated specimens in museum collections to link metabarcoding sequences to species was discussed [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix

et al. 2016

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The German Barcoding initiatives BFB and GBOL have generated a reference library of more than 16,000 metazoan species, which is now ready for applications concerning next generation molecular biodiversity assessments. To streamline the barcoding process, we have developed a meta-barcoding pipeline: We pre-sorted a single malaise trap sample (obtained during one week in August 2014, southern Germany) into 12 arthropod orders and extracted DNA from pooled individuals of each order separately, in order to facilitate DNA extraction and avoid time consuming single specimen selection. Aliquots of each ordinal-level DNA extract were combined to roughly simulate a DNA extract from a non-sorted malaise sample. Each DNA extract was amplified using four primer sets targeting the CO1-5’ fragment. The resulting PCR products (150-400bp) were sequenced separately on an Illumina Mi-SEQ platform, resulting in 1.5 million sequences and 5,500 clusters (coverage ≥10; CD-HIT-EST, 98%). Using a total of 120,000 DNA barcodes of identified, Central European Hymenoptera, Coleoptera, Diptera, and Lepidoptera downloaded from BOLD we established a reference sequence database for a local CUSTOM BLAST. This allowed us to identify 529 Barcode Index Numbers (BINs) from our sequence clusters derived from pooled Malaise trap samples. We introduce a scoring matrix based on the sequence match percentages of each amplicon in order to gain plausibility for each detected BIN, leading to 390 high score BINs in the sorted samples; whereas 268 of these high score BINs (69%) could be identified in the combined sample. The results indicate that a time consuming presorting process will yield approximately 30% more high score BINs compared to the non-sorted sample in our case. These promising results indicate that a fast, efficient and reliable analysis of next generation data from malaise trap samples can be achieved using this pipeline.

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With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast

Cited by 38 publications

References 54 publications

Taxonomy, distribution and ecology of the order Phyllodocida (Annelida, Polychaeta) in deep-sea habitats around the Iberian margin

Taxonomy, distribution and ecology of the order Phyllodocida (Annelida, Polychaeta) in deep-sea habitats around the Iberian margin

Assembling and auditing a comprehensive DNA barcode reference library for European marine fishes

Species Identification in Malaise Trap Samples by DNA Barcoding Based on NGS Technologies and a Scoring Matrix

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