{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,20]],"date-time":"2025-11-20T06:53:15Z","timestamp":1763621595404,"version":"3.37.3"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2024,6,1]],"date-time":"2024-06-01T00:00:00Z","timestamp":1717200000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","award":["854248"],"award-info":[{"award-number":["854248"]}],"id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001871","name":"FCT","doi-asserted-by":"publisher","award":["2020.03608","2020.03526"],"award-info":[{"award-number":["2020.03608","2020.03526"]}],"id":[{"id":"10.13039\/501100001871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The Corubal (Guinea-Bissau) is a wild but underexplored river in West Africa. This study underscores the potential of environmental DNA (eDNA) surveys to fill biodiversity knowledge gaps in the region. We filtered large water volumes at 11 sites along the watershed, amplified multiple molecular markers, and performed high PCR (polymerase chain reaction) replication and in-depth sequencing. We recorded 2589 amplicon sequence variants, with accumulation curves indicating the need for additional sampling to achieve a thorough survey. The taxonomic assignments were constrained by the scarcity of genomic resources. We recorded 125 species of aquatic and terrestrial vertebrates, including 21 new to the country, predominantly fish (61.9%). Surprisingly, crocodiles were not detected, despite their known presence. There were 11 imperiled species, two of which are Critically Endangered (Western chimpanzee and the mussel Pleiodon ovatus). Our findings support the conservation importance of the Corubal, provide a baseline for future monitoring, and highlight the challenges and opportunities of eDNA surveys in remote tropical rivers.<\/jats:p>","DOI":"10.1093\/biosci\/biae036","type":"journal-article","created":{"date-parts":[[2024,6,27]],"date-time":"2024-06-27T09:43:15Z","timestamp":1719481395000},"page":"405-412","source":"Crossref","is-referenced-by-count":10,"title":["Rapid eDNA survey reveals a unique biodiversity hotspot: The Corubal River, West Africa"],"prefix":"10.1093","volume":"74","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2761-7962","authenticated-orcid":false,"given":"Manuel","family":"Lopes-Lima","sequence":"first","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity, Land Planning, CIBIO Vair\u00e3o , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6261-3270","authenticated-orcid":false,"given":"Vincent","family":"Pri\u00e9","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity, Land Planning, CIBIO Vair\u00e3o , Portugal"},{"name":"SPYGEN, Savoie Technolac , Le Bourget du Lac Cedex , France"}]},{"given":"Mutaro","family":"Camar\u00e1","sequence":"additional","affiliation":[{"name":"Universidade Lus\u00f3fona da Guin\u00e9 , Bissau , Guin\u00e9-Bissau"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0591-9978","authenticated-orcid":false,"given":"Luis M P","family":"Cer\u00edaco","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity, Land Planning, CIBIO Vair\u00e3o , Portugal"},{"name":"Departamento de Vertebrados, Museu Nacional, Universidade Federal do Rio de Janeiro , Rio de Janeiro , Brazil"},{"name":"Section of Amphibians and Reptiles Carnegie Museum of Natural History , Pittsburgh, Pennsylvania , United States"}]},{"given":"Vasco","family":"Fernandes","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity, Land Planning, CIBIO Vair\u00e3o , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6884-3966","authenticated-orcid":false,"given":"S\u00f3nia","family":"Ferreira","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4299-0375","authenticated-orcid":false,"given":"Duarte V","family":"Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity, Land Planning, CIBIO Vair\u00e3o , Portugal"},{"name":"Interdisciplinary Centre of Marine and Environmental Research, University of Porto , Matosinhos , Portugal"}]},{"given":"Miguel","family":"Lecoq","sequence":"additional","affiliation":[{"name":"Lisbon , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4191-5031","authenticated-orcid":false,"given":"Filipa M S","family":"Martins","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity, Land Planning, CIBIO Vair\u00e3o , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1302-025X","authenticated-orcid":false,"given":"Diogo","family":"Parrinha","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity, Land Planning, CIBIO Vair\u00e3o , Portugal"}]},{"given":"Aissa Regalla","family":"de Barros","sequence":"additional","affiliation":[{"name":"Instituto da Biodiversidade e das \u00c1reas Protegidas , Bissau , Guin\u00e9-Bissau"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5829-5479","authenticated-orcid":false,"given":"Alice","family":"Valentini","sequence":"additional","affiliation":[{"name":"SPYGEN, Savoie Technolac , Le Bourget du Lac Cedex , France"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8721-9376","authenticated-orcid":false,"given":"Joana","family":"Ver\u00edssimo","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity, Land Planning, CIBIO Vair\u00e3o , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2899-9269","authenticated-orcid":false,"given":"Lu\u00eds","family":"Palma","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity, Land Planning, CIBIO Vair\u00e3o , Portugal"},{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Laborat\u00f3rio Associado, Instituto Superior de Agronomia, Universidade de Lisboa , Lisbon , Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8164-0760","authenticated-orcid":false,"given":"Pedro","family":"Beja","sequence":"additional","affiliation":[{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos (CIBIO), InBIO Laborat\u00f3rio Associado, Universidade do Porto , Vair\u00e3o , Portugal"},{"name":"BIOPOLIS Program in Genomics, Biodiversity, Land Planning, CIBIO Vair\u00e3o , Portugal"},{"name":"Centro de Investiga\u00e7\u00e3o em Biodiversidade e Recursos Gen\u00e9ticos, InBIO Laborat\u00f3rio Associado, Instituto Superior de Agronomia, Universidade de Lisboa , Lisbon , Portugal"}]}],"member":"286","published-online":{"date-parts":[[2024,6,27]]},"reference":[{"key":"2024072408011855800_bib1","doi-asserted-by":"crossref","first-page":"14341","DOI":"10.1002\/ece3.5871","article-title":"Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding","volume":"9","author":"Bakker","year":"2019","journal-title":"Ecology and Evolution"},{"key":"2024072408011855800_bib2","doi-asserted-by":"crossref","first-page":"2089","DOI":"10.1007\/s10531-020-01980-0","article-title":"Applications of environmental DNA (eDNA) in ecology and conservation: Opportunities, challenges and prospects","volume":"29","author":"Beng","year":"2020","journal-title":"Biodiversity and Conservation"},{"key":"2024072408011855800_bib3","doi-asserted-by":"crossref","first-page":"e4847","DOI":"10.7717\/peerj.4847","article-title":"Primate occurrence across a human-impacted landscape in Guinea-Bissau and neighbouring regions in West Africa: Using a systematic literature review to highlight the next conservation steps","volume":"6","author":"Bersacola","year":"2018","journal-title":"PeerJ"},{"key":"2024072408011855800_bib4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/jmammal\/gyx147","article-title":"How many species of mammals are there?","volume":"99","author":"Burgin","year":"2018","journal-title":"Journal of Mammalogy"},{"key":"2024072408011855800_bib5","doi-asserted-by":"crossref","first-page":"3085","DOI":"10.1038\/s41598-019-39399-5","article-title":"Optimizing environmental DNA sampling effort for fish inventories in tropical streams and rivers","volume":"9","author":"Cantera","year":"2019","journal-title":"Scientific Reports"},{"key":"2024072408011855800_bib6","first-page":"27","article-title":"Results from an avifaunal survey along the Corubal and Fefine rivers","volume":"26","author":"Catry","year":"2019","journal-title":"Guinea-Bissau Airo"},{"key":"2024072408011855800_bib7","first-page":"265","article-title":"Nonparametric estimation of the number of classes in a population","volume":"11","author":"Chao","year":"1984","journal-title":"Scandinavian Journal of Statistics"},{"key":"2024072408011855800_bib8","doi-asserted-by":"crossref","first-page":"783","DOI":"10.2307\/2531532","article-title":"Estimating the population size for capture-recapture data with unequal catchability","volume":"43","author":"Chao","year":"1987","journal-title":"Biometrics"},{"key":"2024072408011855800_bib9","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1890\/13-0133.1","article-title":"Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies","volume":"84","author":"Chao","year":"2014","journal-title":"Ecological Monographs"},{"key":"2024072408011855800_bib10","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1111\/1755-0998.12900","article-title":"Unlocking biodiversity and conservation studies in high-diversity environments using environmental DNA (eDNA): A test with Guianese freshwater fishes","volume":"19","author":"Cilleros","year":"2019","journal-title":"Molecular Ecology Resources"},{"key":"2024072408011855800_bib11","doi-asserted-by":"crossref","first-page":"1875","DOI":"10.1111\/1755-0998.13393","article-title":"Amazonian mammal monitoring using aquatic environmental DNA","volume":"21","author":"Coutant","year":"2021","journal-title":"Molecular Ecology Resources"},{"key":"2024072408011855800_bib12","first-page":"265","article-title":"Trabalhos da miss\u00e3o zool\u00f3gica da Guin\u00e9 I\u2013IV: Relat\u00f3rio da miss\u00e3o zool\u00f3gica e contribui\u00e7\u00f5es para o conhecimento da fauna da Guin\u00e9 Portuguesa","volume":"2","author":"Frade","year":"1946","journal-title":"Anais da Junta de Investiga\u00e7\u00f5es Coloniais"},{"article-title":"FishBase, vers. 02\/2024. FishBase","year":"2024","author":"Froese","key":"2024072408011855800_bib13"},{"volume-title":"Amphibian Species of the World: An Online Reference, vers. 6.2","year":"2023","author":"Frost","key":"2024072408011855800_bib14"},{"key":"2024072408011855800_bib15","doi-asserted-by":"crossref","first-page":"e0139633","DOI":"10.1371\/journal.pone.0139633","article-title":"Deep-sea, deep-sequencing: Metabarcoding extracellular DNA from sediments of marine canyons","volume":"10","author":"Guardiola","year":"2015","journal-title":"PLOS ONE"},{"key":"2024072408011855800_bib16","doi-asserted-by":"crossref","first-page":"e0121655","DOI":"10.1371\/journal.pone.0121655","article-title":"Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive Burmese pythons","volume":"10","author":"Hunter","year":"2015","journal-title":"PLOS ONE"},{"key":"2024072408011855800_bib17","doi-asserted-by":"crossref","first-page":"837","DOI":"10.1002\/edn3.191","article-title":"eDNA in a bottleneck: Obstacles to fish metabarcoding studies in megadiverse freshwater systems","volume":"3","author":"Jackman","year":"2021","journal-title":"Environmental DNA"},{"key":"2024072408011855800_bib18","doi-asserted-by":"crossref","first-page":"742","DOI":"10.1111\/1755-0998.13746","article-title":"Navigating the seven challenges of taxonomic reference databases in metabarcoding analyses","volume":"23","author":"Keck","year":"2023","journal-title":"Molecular Ecology Resources"},{"key":"2024072408011855800_bib19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12864-017-4428-5","article-title":"Unique, dual-indexed sequencing adapters with UMIs effectively eliminate index cross-talk and significantly improve sensitivity of massively parallel sequencing","volume":"19","author":"MacConaill","year":"2018","journal-title":"BMC Genomics"},{"key":"2024072408011855800_bib20","doi-asserted-by":"crossref","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"Phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data","volume":"8","author":"McMurdie","year":"2013","journal-title":"PLOS ONE"},{"key":"2024072408011855800_bib21","doi-asserted-by":"crossref","first-page":"e02335","DOI":"10.1002\/eap.2335","article-title":"Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests","volume":"31","author":"Mena","year":"2021","journal-title":"Ecological Applications"},{"year":"1938","author":"Monard","key":"2024072408011855800_bib22"},{"key":"2024072408011855800_bib23","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1471-2105-12-385","article-title":"Interactive metagenomic visualization in a web browser","volume":"12","author":"Ondov","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2024072408011855800_bib24","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1017\/S0030605323000674","article-title":"African forest elephants persist in Guinea-Bissau but require an emergency conservation plan","volume":"58","author":"Palma","year":"2023","journal-title":"Oryx"},{"key":"2024072408011855800_bib25","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1002\/edn3.443","article-title":"Multi-species occupancy modeling reveals methodological and environmental effects on eDNA detection of amphibians in temporary ponds","volume":"5","author":"Peixoto","year":"2023","journal-title":"Environmental DNA"},{"key":"2024072408011855800_bib26","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1002\/edn3.140","article-title":"Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes","volume":"3","author":"Polanco Fern\u00e1ndez","year":"2021","journal-title":"Environmental DNA"},{"key":"2024072408011855800_bib27","doi-asserted-by":"crossref","first-page":"10361","DOI":"10.1038\/s41598-018-28424-8","article-title":"Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation","volume":"8","author":"Pont","year":"2018","journal-title":"Scientific Reports"},{"key":"2024072408011855800_bib28","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1126\/science.adf9994","article-title":"EU deforestation law overlooks emerging crops","volume":"379","author":"Powell","year":"2023","journal-title":"Science"},{"key":"2024072408011855800_bib29","doi-asserted-by":"crossref","first-page":"2931","DOI":"10.1007\/s10750-020-04260-8","article-title":"Environmental DNA metabarcoding for freshwater bivalves biodiversity assessment: Methods and results for the Western Palearctic (European sub-region)","volume":"848","author":"Pri\u00e9","year":"2021","journal-title":"Hydrobiologia"},{"key":"2024072408011855800_bib30","doi-asserted-by":"crossref","first-page":"e145","DOI":"10.1093\/nar\/gkr732","article-title":"ecoPrimers: Inference of new DNA barcode markers from whole genome sequence analysis","volume":"39","author":"Riaz","year":"2011","journal-title":"Nucleic Acids Research"},{"key":"2024072408011855800_bib31","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1126\/science.344.6186.814","article-title":"Specimen collection: An essential tool","volume":"344","author":"Rocha","year":"2014","journal-title":"Science"},{"key":"2024072408011855800_bib32","doi-asserted-by":"crossref","first-page":"171","DOI":"10.5194\/piahs-383-171-2020","article-title":"Hydropluviometric variability in non-Sahelian West Africa: Case of the Koliba\/Corubal River Basin (Guinea and Guinea-Bissau)","volume":"383","author":"Sambou","year":"2020","journal-title":"Proceedings of the International Association of Hydrological Sciences"},{"key":"2024072408011855800_bib33","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1111\/1755-0998.12402","article-title":"Tag jumps illuminated: Reducing sequence-to-sample misidentifications in metabarcoding studies","volume":"15","author":"Schnell","year":"2015","journal-title":"Molecular Ecology Resources"},{"key":"2024072408011855800_bib34","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.cosust.2020.08.005","article-title":"Technological advances in biodiversity monitoring: Applicability, opportunities and challenges","volume":"45","author":"Stephenson","year":"2020","journal-title":"Current Opinion in Environmental Sustainability"},{"key":"2024072408011855800_bib35","doi-asserted-by":"crossref","first-page":"2282","DOI":"10.1016\/j.biocon.2009.05.006","article-title":"eBird: A citizen-based bird observation network in the biological sciences","volume":"142","author":"Sullivan","year":"2009","journal-title":"Biological Conservation"},{"key":"2024072408011855800_bib36","doi-asserted-by":"crossref","DOI":"10.1093\/oso\/9780198767220.001.0001","volume-title":"Environmental DNA: for Biodiversity Research and Monitoring","author":"Taberlet","year":"2018"},{"article-title":"The Reptile Database","year":"2023","author":"Uetz","key":"2024072408011855800_bib37"},{"key":"2024072408011855800_bib38","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1111\/mec.13428","article-title":"Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding","volume":"25","author":"Valentini","year":"2016","journal-title":"Molecular Ecology"},{"key":"2024072408011855800_bib39","first-page":"e.T147658723A147658788","article-title":"Pleiodon ovatus","volume":"2020","author":"Van Damme","year":"2020","journal-title":"The IUCN Red List of Threatened Species"}],"container-title":["BioScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioscience\/article-pdf\/74\/6\/405\/58626257\/biae036.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioscience\/article-pdf\/74\/6\/405\/58626257\/biae036.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T02:08:22Z","timestamp":1721873302000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioscience\/article\/74\/6\/405\/7700002"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,6]]},"references-count":39,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2024,6,27]]},"published-print":{"date-parts":[[2024,7,24]]}},"URL":"https:\/\/doi.org\/10.1093\/biosci\/biae036","relation":{},"ISSN":["0006-3568","1525-3244"],"issn-type":[{"type":"print","value":"0006-3568"},{"type":"electronic","value":"1525-3244"}],"subject":[],"published-other":{"date-parts":[[2024,6]]},"published":{"date-parts":[[2024,6]]}}}