Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions
Abstract
:1. Introduction
2. Materials and Methods
2.1. Compilation of the List of Non-Indigenous Invertebrate Marine Species Occurring in Europe
2.2. Compilation of the Genetic Data and Curation
- BINs were tagged SYN if the identifications (IDs) were synonyms of the accepted species name (confirmed using the WoRMS database) and were considered RELIABLE.
- BINs were tagged AMBIG and UNCERTAIN if:
- The BIN comprises more than 3 different IDs (i.e., species, genus, incomplete classification);
- The BIN comprises 3 IDs, but one of the two IDs with the lowest number of records still contains ≥ 10 records.
- BINs were tagged MISID, and the discordance was solved if:
- When there are only two IDs, and the number of records of the putative “incorrect ID” is ≤ 5% of all records in the BIN (rounded up to the unit), the species with the highest number of records is considered the correct ID;
- The ID with the highest number of records is close to other BINs of the same species (when analyzing the NJ tree for the genus), then it is considered the correct ID;
- The ID with the lowest number of records is from a different genus than the one that is considered the “correct ID”, then it is considered the incorrect ID;
- When analyzing the NJ tree for the genus, the ID with the lowest number of records is in a different cluster, containing only records of that same ID, then it is considered the incorrect ID.
2.3. Testing the Impact of the Curated Reference Library on the Accuracy and Amount of NIS Detected through DNA Metabarcoding of Natural Communities
3. Results
3.1. List of Non-Indigenous Invertebrate Marine Species Occurring in Europe
3.2. Curation of the Taxonomic Assignments of Barcode Records
3.3. Impact of the Curated Reference Library on the Accuracy and Amount of NIS Detected through DNA Metabarcoding of Natural Communities
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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Phylum | Species | Authority | Non-Curated | Audited | Audited + Curated |
---|---|---|---|---|---|
Arthropoda | Amphibalanus amphitrite | (Darwin, 1854) | 0 | 499 | 499 |
Arthropoda | Amphibalanus improvisus | (Darwin, 1854) | 0 | 0 | 698 |
Arthropoda | Ampithoe valida | Smith, 1873 | 4 | 4 | 4 |
Arthropoda | Austrominius modestus | (Darwin, 1854) | 0 | 469 | 469 |
Bryozoa | Bugula neritina | (Linnaeus, 1758) | 1 | 0 | 1 |
Arthropoda | Carcinus maenas | (Linnaeus, 1758) | 93 | 93 | 93 |
Cnidaria | Ectopleura crocea | (Agassiz, 1862) | 657 | 0 | 657 |
Cnidaria | Haliclystus tenuis* | Kishinouye, 1910 | 2 | 0 | 0 |
Arthropoda | Monocorophium acherusicum | (Costa, 1853) | 3677 | 3676 | 3676 |
Mollusca | Mya arenaria | Linnaeus, 1758 | 1 | 0 | 1 |
Arthropoda | Mytilicola intestinalis | Steuer, 1902 | 0 | 1 | 1 |
Mollusca | Ostrea stentina | Payraudeau, 1826 | 6 | 0 | 6 |
Arthropoda | Paracalanus indicus | Wolfenden, 1905 | 0 | 0 | 54 |
Arthropoda | Perforatus perforatus | (Bruguière, 1789) | 0 | 207 | 209 |
Annelida | Polydora cornuta | Bosc, 1802 | 5 | 5 | 5 |
Arthropoda | Pseudodiaptomus marinus | Sato, 1913 | 0 | 54 | 54 |
Mollusca | Ruditapes philippinarum | (A. Adams and Reeve, 1850) | 0 | 0 | 51 |
Bryozoa | Scruparia ambigua * | (d’Orbigny, 1841) | 1 | 0 | 0 |
Annelida | Syllidia armata * | Quatrefages, 1866 | 4 | 0 | 0 |
Annelida | Terebella lapidaria * | Linnaeus, 1767 | 76 | 0 | 0 |
Total NIS | 12 | 9 | 16 |
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Lavrador, A.S.; Fontes, J.T.; Vieira, P.E.; Costa, F.O.; Duarte, S. Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions. Diversity 2023, 15, 174. https://doi.org/10.3390/d15020174
Lavrador AS, Fontes JT, Vieira PE, Costa FO, Duarte S. Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions. Diversity. 2023; 15(2):174. https://doi.org/10.3390/d15020174
Chicago/Turabian StyleLavrador, Ana S., João T. Fontes, Pedro E. Vieira, Filipe O. Costa, and Sofia Duarte. 2023. "Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions" Diversity 15, no. 2: 174. https://doi.org/10.3390/d15020174