Andean Fish inventories using an eDNA metabarcoding approach

Andean Fish inventories using an eDNA metabarcoding approach | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Andean Fish inventories using an eDNA metabarcoding approach Martín Holguín Osorio, Tatiana Arias, Luz Fernanda Jiménez Segura, and 1 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-7342325/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted 11 You are reading this latest preprint version Abstract Fish diversity inventories often rely on capture-based methods, which are typically lethal and may have long-term impacts on fish populations. A promising alternative is environmental DNA (eDNA) metabarcoding —a non-invasive technique that uses molecular DNA barcodes to identify fish species. Implementing eDNA methods for fish inventories in the Andean region offers a sustainable solution for long-term monitoring programs. In this study, eDNA analyses were conducted using water samples collected from dammed rivers, where continuous monitoring of impacted areas is essential. The objectives were to compare the effectiveness of eDNA metabarcoding and traditional sampling methods for tracking fish communities in a reservoir of the Porce River, located in northwestern Colombia, and to develop a standardized, replicable protocol for long-term monitoring of Andean fish diversity. A range of sampling, molecular, and bioinformatic techniques were tested across different ecosystems, including rivers, reservoirs, and streams. Novel primer pairs targeting the mitochondrial COX1 and 12S genes were designed and evaluated through in silico simulations. Among the markers tested, the 12S gene showed the highest performance in our field-cllected samples, detecting 23 taxa —compared to only 6 taxa identified by COX1 and 14 species recorded through traditional fishing methods. When COX1 and 12S were combined, eDNA metabarcoding demonstrated greater sensitivity and cost-effectiveness than traditional approaches. This research establishes a foundational protocol for enhancing the detection of fish species in Andean aquatic ecosystems. Critical factors—including primer selection, the quality and taxonomic coverage of reference databases, and bioinformatic parameters—substantially influence the results and should be carefully considered in future studies. cytochrome oxidase c subunit 1 non-invasive DNA ichthyofauna mitochondria Neotropics molecular taxonomy South America 12S ribosomal Full Text Additional Declarations No competing interests reported. Supplementary Files SupplementaryMaterial.docx Cite Share Download PDF Status: Under Review Version 1 posted Editorial decision: Revision requested 24 Oct, 2025 Reviews received at journal 17 Oct, 2025 Reviewers agreed at journal 03 Oct, 2025 Reviews received at journal 30 Sep, 2025 Reviews received at journal 27 Sep, 2025 Reviewers agreed at journal 20 Sep, 2025 Reviewers agreed at journal 19 Sep, 2025 Reviewers invited by journal 18 Sep, 2025 Editor assigned by journal 01 Sep, 2025 Submission checks completed at journal 31 Aug, 2025 First submitted to journal 31 Aug, 2025 You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-7342325","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":521529649,"identity":"44c3c1eb-d3dc-49ac-bf50-77ed4784b66e","order_by":0,"name":"Martín Holguín 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approach","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"discover-conservation","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"Learn more about [Discover Conservation](https://link.springer.com/journal/44353)","snPcode":"44353","submissionUrl":"https://submission.springernature.com/new-submission/44353/3","title":"Discover Conservation","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Discover Series","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"cytochrome oxidase c subunit 1, non-invasive DNA, ichthyofauna, mitochondria, Neotropics, molecular taxonomy, South America, 12S ribosomal","lastPublishedDoi":"10.21203/rs.3.rs-7342325/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-7342325/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eFish diversity inventories often rely on capture-based methods, which are typically lethal and may have long-term impacts on fish populations. A promising alternative is environmental DNA (eDNA) metabarcoding \u0026mdash;a non-invasive technique that uses molecular DNA barcodes to identify fish species. Implementing eDNA methods for fish inventories in the Andean region offers a sustainable solution for long-term monitoring programs. In this study, eDNA analyses were conducted using water samples collected from dammed rivers, where continuous monitoring of impacted areas is essential. The objectives were to compare the effectiveness of eDNA metabarcoding and traditional sampling methods for tracking fish communities in a reservoir of the Porce River, located in northwestern Colombia, and to develop a standardized, replicable protocol for long-term monitoring of Andean fish diversity. A range of sampling, molecular, and bioinformatic techniques were tested across different ecosystems, including rivers, reservoirs, and streams. Novel primer pairs targeting the mitochondrial COX1 and 12S genes were designed and evaluated through in silico simulations. Among the markers tested, the 12S gene showed the highest performance in our field-cllected samples, detecting 23 taxa \u0026mdash;compared to only 6 taxa identified by COX1 and 14 species recorded through traditional fishing methods. When COX1 and 12S were combined, eDNA metabarcoding demonstrated greater sensitivity and cost-effectiveness than traditional approaches. This research establishes a foundational protocol for enhancing the detection of fish species in Andean aquatic ecosystems. Critical factors\u0026mdash;including primer selection, the quality and taxonomic coverage of reference databases, and bioinformatic parameters\u0026mdash;substantially influence the results and should be carefully considered in future studies.\u003c/p\u003e","manuscriptTitle":"Andean Fish inventories using an eDNA metabarcoding approach","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2025-09-29 19:38:35","doi":"10.21203/rs.3.rs-7342325/v1","editorialEvents":[{"type":"communityComments","content":0},{"type":"decision","content":"Revision requested","date":"2025-10-24T11:21:59+00:00","index":"","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-10-17T18:01:22+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"84582534528477979086204903558040177437","date":"2025-10-03T10:20:43+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-30T17:04:14+00:00","index":"hide","fulltext":""},{"type":"editorInvitedReview","content":"","date":"2025-09-27T14:30:46+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"36436621002123227063252215625743051240","date":"2025-09-20T04:07:55+00:00","index":"hide","fulltext":""},{"type":"reviewerAgreed","content":"189664058498701266319127648442338208291","date":"2025-09-19T10:21:00+00:00","index":"hide","fulltext":""},{"type":"reviewersInvited","content":"","date":"2025-09-18T13:16:50+00:00","index":"","fulltext":""},{"type":"editorAssigned","content":"","date":"2025-09-01T10:05:47+00:00","index":"","fulltext":""},{"type":"checksComplete","content":"","date":"2025-09-01T02:04:00+00:00","index":"","fulltext":""},{"type":"submitted","content":"Discover Conservation","date":"2025-09-01T02:00:59+00:00","index":"","fulltext":""}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"discover-conservation","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"Learn more about [Discover Conservation](https://link.springer.com/journal/44353)","snPcode":"44353","submissionUrl":"https://submission.springernature.com/new-submission/44353/3","title":"Discover Conservation","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"stoa","reportingPortfolio":"Discover Series","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"f9f4a410-990e-4e94-a93d-eff938485e4c","owner":[],"postedDate":"September 29th, 2025","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[],"tags":[],"updatedAt":"2026-02-16T17:39:04+00:00","versionOfRecord":[],"versionCreatedAt":"2025-09-29 19:38:35","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-7342325","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-7342325","identity":"rs-7342325","version":["v1"]},"buildId":"8U1c8b4HqxoKbykW_rLl7","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}