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  • 1
    Online Resource
    Online Resource
    Enhanced primers for amplification of DNA barcodes from a broad range of marine metazoans
    Springer Science and Business Media LLC ; 2013
    In:  BMC Ecology Vol. 13, No. 1 ( 2013), p. 34-
    Details
    In: BMC Ecology, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2013), p. 34-
    Type of Medium: Online Resource
    ISSN: 1472-6785
    URL: Article
    DOI: 10.1186/1472-6785-13-34
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2013
    detail.hit.zdb_id: 2050430-5
    SSG: 12
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  • 2
    Online Resource
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    With a little help from DNA barcoding: investigating the diversity of Gastropoda from the Portuguese coast
    Springer Science and Business Media LLC ; 2016
    In:  Scientific Reports Vol. 6, No. 1 ( 2016-02-15)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2016-02-15)
    Abstract: The Gastropoda is one of the best studied classes of marine invertebrates. Yet, most species have been delimited based on morphology only. The application of DNA barcodes has shown to be greatly useful to help delimiting species. Therefore, sequences of the cytochrome c oxidase I gene from 108 specimens of 34 morpho-species were used to investigate the molecular diversity within the gastropods from the Portuguese coast. To the above dataset, we added available COI-5P sequences of taxonomically close species, in a total of 58 morpho-species examined. There was a good match between ours and sequences from independent studies, in public repositories. We found 32 concordant (91.4%) out of the 35 Barcode Index Numbers (BINs) generated from our sequences. The application of a ranking system to the barcodes yield over 70% with top taxonomic congruence, while 14.2% of the species barcodes had insufficient data. In the majority of the cases, there was a good concordance between morphological identification and DNA barcodes. Nonetheless, the discordance between morphological and molecular data is a reminder that even the comparatively well-known European marine gastropods can benefit from being probed using the DNA barcode approach. Discordant cases should be reviewed with more integrative studies.
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/srep20226
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2016
    detail.hit.zdb_id: 2615211-3
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  • 3
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    Online Resource
    Starting a DNA barcode reference library for shallow water polychaetes from the southern European Atlantic coast
    Wiley ; 2016
    In:  Molecular Ecology Resources Vol. 16, No. 1 ( 2016-01), p. 298-313
    Details
    In: Molecular Ecology Resources, Wiley, Vol. 16, No. 1 ( 2016-01), p. 298-313
    Abstract: Annelid polychaetes have been seldom the focus of dedicated DNA barcoding studies, despite their ecological relevance and often dominance, particularly in soft‐bottom estuarine and coastal marine ecosystems. Here, we report the first assessment of the performance of DNA barcodes in the discrimination of shallow water polychaete species from the southern European Atlantic coast, focusing on specimens collected in estuaries and coastal ecosystems of Portugal. We analysed cytochrome oxidase I DNA barcodes ( COI ‐5P) from 164 specimens, which were assigned to 51 morphospecies. To our data set from Portugal, we added available published sequences selected from the same species, genus or family, to inspect for taxonomic congruence among studies and collection location. The final data set comprised 290 specimens and 79 morphospecies, which generated 99 Barcode Index Numbers ( BIN s) within Barcode of Life Data Systems ( BOLD ). Among these, 22 BIN s were singletons, 47 other BIN s were concordant, confirming the initial identification based on morphological characters, and 30 were discordant, most of which consisted on multiple BIN s found for the same morphospecies. Some of the most prominent cases in the latter category include Hediste diversicolor (O.F. Müller, 1776) (7), Eulalia viridis (Linnaeus, 1767) (2) and Owenia fusiformi s (delle Chiaje, 1844) (5), all of them reported from Portugal and frequently used in ecological studies as environmental quality indicators. Our results for these species showed discordance between molecular lineages and morphospecies, or added additional relatively divergent lineages. The potential inaccuracies in environmental assessments, where underpinning polychaete species diversity is poorly resolved or clarified, demand additional and extensive investigation of the DNA barcode diversity in this group, in parallel with alpha taxonomy efforts.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    URL: Article
    DOI: 10.1111/men.2016.16.issue-1
    DOI: 10.1111/1755-0998.12441
    Language: English
    Publisher: Wiley
    Publication Date: 2016
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    Contrasting morphological and DNA barcode-suggested species boundaries among shallow-water amphipod fauna from the southern European Atlantic coast
    Canadian Science Publishing ; 2017
    In:  Genome Vol. 60, No. 2 ( 2017-02), p. 147-157
    Details
    In: Genome, Canadian Science Publishing, Vol. 60, No. 2 ( 2017-02), p. 147-157
    Abstract: In this study we compared DNA barcode-suggested species boundaries with morphology-based species identifications in the amphipod fauna of the southern European Atlantic coast. DNA sequences of the cytochrome c oxidase subunit I barcode region (COI-5P) were generated for 43 morphospecies (178 specimens) collected along the Portuguese coast which, together with publicly available COI-5P sequences, produced a final dataset comprising 68 morphospecies and 295 sequences. Seventy-five BINs (Barcode Index Numbers) were assigned to these morphospecies, of which 48 were concordant (i.e., 1 BIN = 1 species), 8 were taxonomically discordant, and 19 were singletons. Twelve species had matching sequences ( 〈 2% distance) with conspecifics from distant locations (e.g., North Sea). Seven morphospecies were assigned to multiple, and highly divergent, BINs, including specimens of Corophium multisetosum (18% divergence) and Dexamine spiniventris (16% divergence), which originated from sampling locations on the west coast of Portugal (only about 36 and 250 km apart, respectively). We also found deep divergence (4%–22%) among specimens of seven species from Portugal compared to those from the North Sea and Italy. The detection of evolutionarily meaningful divergence among populations of several amphipod species from southern Europe reinforces the need for a comprehensive re-assessment of the diversity of this faunal group.
    Type of Medium: Online Resource
    ISSN: 0831-2796 , 1480-3321
    URL: Article
    DOI: 10.1139/gen-2016-0009
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2017
    detail.hit.zdb_id: 2020635-5
    SSG: 12
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  • 5
    Online Resource
    Online Resource
    Priming of a DNA metabarcoding approach for species identification and inventory in marine macrobenthic communities
    Canadian Science Publishing ; 2017
    In:  Genome Vol. 60, No. 3 ( 2017-03), p. 260-271
    Details
    In: Genome, Canadian Science Publishing, Vol. 60, No. 3 ( 2017-03), p. 260-271
    Abstract: In marine and estuarine benthic communities, the inventory and estimation of species richness are often hampered by the need for broad taxonomic expertise across several phyla. The use of DNA metabarcoding has emerged as a powerful tool for the fast assessment of species composition in a diversity of ecological communities. Here, we tested the amplification success of five primer sets targeting different COI-5P regions by 454 pyrosequencing to maximize the recovery of two simulated macrobenthic communities containing 21 species (SimCom1 and SimCom 2). Species identification was first performed against a compiled reference library of macrobenthic species. Reads with similarity results to reference sequences between 70% and 97% were then submitted to GenBank and BOLD to attempt the identification of concealed species in the bulk sample. The combination of at least three primer sets was able to recover more species than any primer set alone, achieving 85% of represented species in SimCom1 and 76% in SimCom2. Our approach was successful to detect low-frequency specimens, as well as concealed species, in the bulk sample, indicating the potential for the application of this approach on marine bioassessment and inventory, including the detection of “hidden” biodiversity that would hardly be possible based on morphology only.
    Type of Medium: Online Resource
    ISSN: 0831-2796 , 1480-3321
    URL: Article
    DOI: 10.1139/gen-2015-0220
    Language: English
    Publisher: Canadian Science Publishing
    Publication Date: 2017
    detail.hit.zdb_id: 2020635-5
    SSG: 12
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