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Castro N, Félix PM, Gestoso I, Costa JL, Canning-Clode J. Management of non-indigenous species in Macaronesia: Misconceptions and alerts to decision-makers. MARINE POLLUTION BULLETIN 2024; 204:116506. [PMID: 38796992 DOI: 10.1016/j.marpolbul.2024.116506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 05/15/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Abstract
Human-induced pressures have led to substantial changes in marine ecosystems worldwide, with the introduction of non-indigenous species (NIS) emerging as a significant threat to ecological, economic, and social aspects. The Macaronesian islands, comprising the Azores, Madeira, Canary Islands, and Cabo Verde archipelagos, are regions where the regional economy is dependent on marine resources (e.g., marine traffic, ecotourism and fisheries). Despite their importance, concerted efforts to manage marine biological invasions in Macaronesia have been scarce. In this context, the current study aims to contribute to the much-needed debate on biosecurity measures in this unique insular ecosystem to prevent and mitigate the impact of NIS. By adhering to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) criteria, this work validated and analyzed 260 documents providing insights into the management of NIS in Macaronesia until 2022. These documents revealed the presence of 29 Invasive Alien Species (IAS), most of which are misconceptions regarding this terminology. Most studies focused on the stages of early detection, rapid response, and eradication across the archipelagos. Cabo Verde had comparatively fewer studies. The most common techniques include monitoring/sampling, literature reviews, and taxonomic reviews. NIS introduction pathways were mainly attributed to transport (stowaway) and unaided migration, with ship fouling, ballast water, rafting, ocean currents, and tropicalization being also identified as significant contributors. This systematic review highlights the current efforts to establish robust biosecurity protocols in Macaronesia and emphasizes the urgent need to safeguard the region's ecological, economic, and social well-being.
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Affiliation(s)
- Nuno Castro
- MARE - Marine and Environmental Sciences Centre/ARNET - Aquatic Research Network, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Funchal, Madeira, Portugal; Faculty of Life Sciences, University of Madeira, Funchal, Portugal; MARE - Marine and Environmental Sciences Centre/ARNET - Aquatic Research Network, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
| | - Pedro M Félix
- MARE - Marine and Environmental Sciences Centre/ARNET - Aquatic Research Network, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Ignacio Gestoso
- MARE - Marine and Environmental Sciences Centre/ARNET - Aquatic Research Network, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Funchal, Madeira, Portugal; Faculty of Life Sciences, University of Madeira, Funchal, Portugal; Department of Biology, Faculty of Marine and Environmental Sciences & Marine Research Institute (INMAR), University of Cadiz (UCA), Puerto Real, Cadiz, Spain; Smithsonian Environmental Research Center, Edgewater, MD, USA
| | - José L Costa
- MARE - Marine and Environmental Sciences Centre/ARNET - Aquatic Research Network, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - João Canning-Clode
- MARE - Marine and Environmental Sciences Centre/ARNET - Aquatic Research Network, Agência Regional para o Desenvolvimento da Investigação Tecnologia e Inovação (ARDITI), Funchal, Madeira, Portugal; Faculty of Life Sciences, University of Madeira, Funchal, Portugal; Smithsonian Environmental Research Center, Edgewater, MD, USA
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Compilation, Revision, and Annotation of DNA Barcodes of Marine Invertebrate Non-Indigenous Species (NIS) Occurring in European Coastal Regions. DIVERSITY 2023. [DOI: 10.3390/d15020174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The introduction of non-indigenous species (NIS) is one of the major threats to the integrity of European coastal ecosystems. DNA-based assessments have been increasingly adopted for monitoring NIS. However, the accuracy of DNA-based taxonomic assignments is largely dependent on the completion and reliability of DNA barcode reference libraries. As such, we aimed to compile and audit a DNA barcode reference library for marine invertebrate NIS occurring in Europe. To do so, we compiled a list of NIS using three databases: the European Alien Species Information Network (EASIN), the Information System on Aquatic Non-indigenous and Cryptogenic Species (AquaNIS), and the World Register of Introduced Marine Species (WRiMS). For each species, we retrieved the available cytochrome c oxidase subunit I (COI) mitochondrial gene sequences from the Barcode of Life Data System (BOLD) and used the Barcode, Audit & Grade System (BAGS) to check congruence between morphospecies names and Barcode Index Numbers (BINs). From the 1249 species compiled, approximately 42% had records on BOLD, among which 56% were discordant. We further analyzed these cases to determine the causes of the discordances and attributed additional annotation tags. Of the 622 discordant BINs, after revision, 35% were successfully solved, which increased the number of NIS detected in metabarcoding datasets from 12 to 16. However, a fair number of BINs remained discordant. Reliability of reference barcode records is particularly critical in the case of NIS, where erroneous identification may trigger action or inaction when not required.
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Klimova A, Rodríguez‐Estrella R, Meng G, Gutiérrez‐Rivera JN, Jimenez‐Jimenez ML, Liu S. Metabarcoding reveals seasonal and spatial patterns of arthropod community assemblages in two contrasting habitats: Desert and oasis of the Baja California Peninsula, Mexico. DIVERS DISTRIB 2023. [DOI: 10.1111/ddi.13672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Anastasia Klimova
- Centro de Investigaciones Biológicas del Noroeste S.C. La Paz Mexico
| | | | - Guanliang Meng
- Zoological Research Museum Alexander Koenig, Leibniz Institute for the Analysis of Biodiversity Change Bonn Germany
| | | | | | - Shanlin Liu
- Department of Entomology, College of Plant Protection China Agricultural University Beijing China
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Baptista L, Berning B, Curto M, Waeschenbach A, Meimberg H, Santos AM, Ávila SP. Morphospecies and molecular diversity of ‘lace corals’: the genus Reteporella (Bryozoa: Cheilostomatida) in the central North Atlantic Azores Archipelago. BMC Ecol Evol 2022; 22:128. [PMCID: PMC9635095 DOI: 10.1186/s12862-022-02080-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
Background As in most bryozoans, taxonomy and systematics of species in the genus Reteporella Busk, 1884 (family Phidoloporidae) has hitherto almost exclusively been based on morphological characters. From the central North Atlantic Azores Archipelago, nine Reteporella species have historically been reported, none of which have as yet been revised. Aiming to characterise the diversity and biogeographic distribution of Azorean Reteporella species, phylogenetic reconstructions were conducted on a dataset of 103 Azorean Reteporella specimens, based on the markers cytochrome C oxidase subunit 1, small and large ribosomal RNA subunits. Morphological identification was based on scanning electron microscopy and complemented the molecular inferences. Results Our results reveal two genetically distinct Azorean Reteporella clades, paraphyletic to eastern Atlantic and Mediterranean taxa. Moreover, an overall concordance between morphological and molecular species can be shown, and the actual bryozoan diversity in the Azores is greater than previously acknowledged as the dataset comprises three historically reported species and four putative new taxa, all of which are likely to be endemic. The inclusion of Mediterranean Reteporella specimens also revealed new species in the Adriatic and Ligurian Sea, whilst the inclusion of additional phidoloporid taxa hints at the non-monophyly of the genus Reteporella. Conclusion Being the first detailed genetic study on the genus Reteporella, the high divergence levels inferred within the genus Reteporella and family Phidoloporidae calls for the need of further revision. Nevertheless, the overall concordance between morphospecies and COI data suggest the potential adequacy of a 3% cut-off to distinguish Reteporella species. The discovery of new species in the remote Azores Archipelago as well as in the well-studied Mediterranean Sea indicates a general underestimation of bryozoan diversity. This study constitutes yet another example of the importance of integrative taxonomical approaches on understudied taxa, contributing to cataloguing genetic and morphological diversity. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02080-z.
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Affiliation(s)
- Lara Baptista
- grid.5808.50000 0001 1503 7226Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, 9501-801 Pólo dos Açores, Ponta Delgada, Açores, Portugal ,grid.5808.50000 0001 1503 7226BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal ,grid.7338.f0000 0001 2096 9474MPB-Marine Palaeontology and Biogeography Lab, Universidade dos Açores, 9501-801 Ponta Delgada, Açores, Portugal ,grid.5808.50000 0001 1503 7226Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal ,grid.5173.00000 0001 2298 5320University of Natural Resources and Life Sciences (BOKU), Department of Integrative Biology and Biodiversity Research, Institute for Integrative Nature Conservation Research, Vienna, Austria
| | - Björn Berning
- grid.5808.50000 0001 1503 7226Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, 9501-801 Pólo dos Açores, Ponta Delgada, Açores, Portugal ,grid.7338.f0000 0001 2096 9474MPB-Marine Palaeontology and Biogeography Lab, Universidade dos Açores, 9501-801 Ponta Delgada, Açores, Portugal ,Oberösterreichische Landes-Kultur GmbH, Geowissenschaftliche Sammlungen, 4060 Leonding, Austria
| | - Manuel Curto
- grid.5173.00000 0001 2298 5320University of Natural Resources and Life Sciences (BOKU), Department of Integrative Biology and Biodiversity Research, Institute for Integrative Nature Conservation Research, Vienna, Austria ,grid.9983.b0000 0001 2181 4263MARE, Marine and Environmental Sciences Centre, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Harald Meimberg
- grid.5173.00000 0001 2298 5320University of Natural Resources and Life Sciences (BOKU), Department of Integrative Biology and Biodiversity Research, Institute for Integrative Nature Conservation Research, Vienna, Austria
| | - António M. Santos
- grid.5808.50000 0001 1503 7226Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal ,grid.5808.50000 0001 1503 7226Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, Universidade do Porto, Campus de Vairão, 4485-661 Vairão, Portugal
| | - Sérgio P. Ávila
- grid.5808.50000 0001 1503 7226Centro de Investigação em Biodiversidade e Recursos Genéticos, CIBIO, InBIO Laboratório Associado, 9501-801 Pólo dos Açores, Ponta Delgada, Açores, Portugal ,grid.5808.50000 0001 1503 7226BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal ,grid.7338.f0000 0001 2096 9474MPB-Marine Palaeontology and Biogeography Lab, Universidade dos Açores, 9501-801 Ponta Delgada, Açores, Portugal ,grid.5808.50000 0001 1503 7226Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 1021/1055, 4169-007 Porto, Portugal ,grid.7338.f0000 0001 2096 9474Departamento de Biologia, Faculdade de Ciências e Tecnologia, Universidade dos Açores, 9501-801 Ponta Delgada, Açores, Portugal
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DNA Barcode Gap Analysis for Multiple Marker Genes for Phytoplankton Species Biodiversity in Mediterranean Aquatic Ecosystems. BIOLOGY 2022; 11:biology11091277. [PMID: 36138756 PMCID: PMC9495960 DOI: 10.3390/biology11091277] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Environmental DNA metabarcoding (eDNA) has strong potential in the assessment of biodiversity in aquatic ecosystems. The incompleteness of DNA barcode reference libraries represents a current limit to unveiling the whole biodiversity of an aquatic ecosystem. Therefore, barcode gap analyses at species level are of great significance, in particular at local/regional level, for the advancement of eDNA metabarcoding application to aquatic ecosystems surveillance and future biodiversity assessment. Abstract The implementation of DNA metabarcoding and environmental DNA (eDNA) to the biodiversity assessment and biomonitoring of aquatic ecosystems has great potential worldwide. However, DNA metabarcoding and eDNA are highly reliant on the coverage of the DNA barcode reference libraries that are currently hindered by the substantial lack of reference sequences. The main objective of this study was to analyze the current coverage of DNA barcode reference libraries for phytoplankton species of the aquatic Mediterranean ecoregion in the southeast of Italy (Apulia Region) in order to assess the applicability of DNA metabarcoding and eDNA in this area. To do so, we investigated three main DNA barcode reference libraries, BOLD Systems, GenBank and SILVA, for the availability of DNA barcodes of the examined phytoplankton species. The gap analysis was conducted for three molecular gene markers, 18S, 16S and COI. The results showed a considerable lack of barcodes for all three markers. However, among the three markers, 18S had a greater coverage in the reference libraries. For the 18S gene marker, the barcode coverage gap across the three types of ecosystems examined was 32.21–39.68%, 60.12–65.19% for the 16S marker gene, and 72.44–80.61 for the COI marker gene. Afterwards, the interspecific genetic distance examined on the most represented molecular marker, 18S, was able to distinguish 80% of the species mined for lakes and 70% for both marine and transitional waters. Conclusively, this work highlights the importance of filling the gaps in the reference libraries, and constitutes the basis towards the advancement of DNA metabarcoding and eDNA application for biodiversity assessment and biomonitoring.
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Leite BR, Vieira PE, Troncoso JS, Costa FO. Comparing species detection success between molecular markers in DNA metabarcoding of coastal macroinvertebrates. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.70063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
DNA metabarcoding has great potential to improve marine biomonitoring programs by providing a rapid and accurate assessment of species composition in zoobenthic communities. However, some methodological improvements are still required, especially regarding failed detections, primers efficiency and incompleteness of databases. Here we assessed the efficiency of two different marker loci (COI and 18S) and three primer pairs in marine species detection through DNA metabarcoding of the macrozoobenthic communities colonizing three types of artificial substrates (slate, PVC and granite), sampled between 3 and 15 months of deployment. To accurately compare detection success between markers, we also compared the representativeness of the detected species in public databases and revised the reliability of the taxonomic assignments. Globally, we recorded extensive complementarity in the species detected by each marker, with 69% of the species exclusively detected by either 18S or COI. Individually, each of the three primer pairs recovered, at most, 52% of all species detected on the samples, showing also different abilities to amplify specific taxonomic groups. Most of the detected species have reliable reference sequences in their respective databases (82% for COI and 72% for 18S), meaning that when a species was detected by one marker and not by the other, it was most likely due to faulty amplification, and not by lack of matching sequences in the database. Overall, results showed the impact of marker and primer applied on species detection ability and indicated that, currently, if only a single marker or primer pair is employed in marine zoobenthos metabarcoding, a fair portion of the diversity may be overlooked.
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Radulovici AE, Vieira PE, Duarte S, Teixeira MAL, Borges LMS, Deagle BE, Majaneva S, Redmond N, Schultz JA, Costa FO. Revision and annotation of DNA barcode records for marine invertebrates: report of the 8th iBOL conference hackathon. METABARCODING AND METAGENOMICS 2021. [DOI: 10.3897/mbmg.5.67862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The accuracy of specimen identification through DNA barcoding and metabarcoding relies on reference libraries containing records with reliable taxonomy and sequence quality. The considerable growth in barcode data requires stringent data curation, especially in taxonomically difficult groups such as marine invertebrates. A major effort in curating marine barcode data in the Barcode of Life Data Systems (BOLD) was undertaken during the 8th International Barcode of Life Conference (Trondheim, Norway, 2019). Major taxonomic groups (crustaceans, echinoderms, molluscs, and polychaetes) were reviewed to identify those which had disagreement between Linnaean names and Barcode Index Numbers (BINs). The records with disagreement were annotated with four tags: a) MIS-ID (misidentified, mislabeled, or contaminated records), b) AMBIG (ambiguous records unresolved with the existing data), c) COMPLEX (species names occurring in multiple BINs), and d) SHARE (barcodes shared between species). A total of 83,712 specimen records corresponding to 7,576 species were reviewed and 39% of the species were tagged (7% MIS-ID, 17% AMBIG, 14% COMPLEX, and 1% SHARE). High percentages (>50%) of AMBIG tags were recorded in gastropods, whereas COMPLEX tags dominated in crustaceans and polychaetes. The high proportion of tagged species reflects either flaws in the barcoding workflow (e.g., misidentification, cross-contamination) or taxonomic difficulties (e.g., synonyms, undescribed species). Although data curation is essential for barcode applications, such manual attempts to examine large datasets are unsustainable and automated solutions are extremely desirable.
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Jażdżewska AM, Tandberg AHS, Horton T, Brix S. Global gap-analysis of amphipod barcode library. PeerJ 2021; 9:e12352. [PMID: 34760373 PMCID: PMC8572522 DOI: 10.7717/peerj.12352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/29/2021] [Indexed: 12/02/2022] Open
Abstract
In the age of global climate change and biodiversity loss there is an urgent need to provide effective and robust tools for diversity monitoring. One of the promising techniques for species identification is the use of DNA barcoding, that in Metazoa utilizes the so called 'gold-standard' gene of cytochrome c oxidase (COI). However, the success of this method relies on the existence of trustworthy barcode libraries of the species. The Barcode of Life Data System (BOLD) aims to provide barcodes for all existing organisms, and is complemented by the Barcode Index Number (BIN) system serving as a tool for potential species recognition. Here we provide an analysis of all public COI sequences available in BOLD of the diverse and ubiquitous crustacean order Amphipoda, to identify the barcode library gaps and provide recommendations for future barcoding studies. Our gap analysis of 25,702 records has shown that although 3,835 BINs (indicating putative species) were recognised by BOLD, only 10% of known amphipod species are represented by barcodes. We have identified almost equal contribution of both records (sequences) and BINs associated with freshwater and with marine realms. Three quarters of records have a complete species-level identification provided, while BINs have just 50%. Large disproportions between identification levels of BINs coming from freshwaters and the marine environment were observed, with three quarters of the former possessing a species name, and less than 40% for the latter. Moreover, the majority of BINs are represented by a very low number of sequences rendering them unreliable according to the quality control system. The geographical coverage is poor with vast areas of Africa, South America and the open ocean acting as "white gaps". Several, of the most species rich and highly abundant families of Amphipoda (e.g., Phoxocephalidae, Ampeliscidae, Caprellidae), have very poor representation in the BOLD barcode library. As a result of our study we recommend stronger effort in identification of already recognised BINs, prioritising the studies of families that are known to be important and abundant components of particular communities, and targeted sampling programs for taxa coming from geographical regions with the least knowledge.
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Affiliation(s)
- Anna Maria Jażdżewska
- Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | | | - Tammy Horton
- National Oceanography Centre, Southampton, United Kingdom
| | - Saskia Brix
- Department for Marine Biodiversity Research (DZMB), Senckenberg am Meer, Hamburg, Germany
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Yang J, Zhang X, Jin X, Seymour M, Richter C, Logares R, Khim JS, Klymus K. Recent advances in environmental DNA‐based biodiversity assessment and conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13415] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Jun Yang
- Aquatic EcoHealth Group Fujian Key Laboratory of Watershed Ecology Key Laboratory of Urban Environment and Health Institute of Urban Environment Chinese Academy of Sciences Xiamen China
| | - Xiaowei Zhang
- School of the Environment State Key Laboratory of Pollution Control & Resource Reuse Nanjing University Nanjing China
| | - Xiaowei Jin
- China National Environmental Monitoring CentreMinistry of Ecology and Environment of the People's Republic of China Beijing China
| | - Mathew Seymour
- Department of Ecology Swedish University of Agricultural Sciences Uppsala Sweden
| | - Catherine Richter
- Columbia Environmental Research CenterU.S. Geological Survey Columbia MO USA
| | - Ramiro Logares
- Institute of Marine Sciences CSICPasseig Marítim de la Barceloneta Barcelona Spain
| | - Jong Seong Khim
- School of Earth & Environmental Sciences College of Natural Sciences Seoul National University Seoul Republic of Korea
| | - Katy Klymus
- Columbia Environmental Research CenterU.S. Geological Survey Columbia MO USA
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