Barcoding Gaps and Sequencing Prioritisation in a Global Biodiversity Stronghold

Barcoding Gaps and Sequencing Prioritisation in a Global Biodiversity Stronghold | 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 Article Barcoding Gaps and Sequencing Prioritisation in a Global Biodiversity Stronghold Thomas Luypaert, Izeni Farias, Tomas Hrbek, Carlos Peres, Torbjørn Haugaasen This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-9096952/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Effective ecological monitoring increasingly depends on eDNA metabarcoding, yet the accuracy of these approaches hinges on the completeness and quality of reference databases. In tropical biodiversity strongholds, where conservation urgency is greatest, systematic gaps and biases in these databases remain poorly characterised. Here, we develop an integrated framework to quantify, explain, and prioritise barcode reference gaps for mammals from Brazil – the world’s largest tropical forest country. Evaluating barcode presence for 731 species across ten primer combinations spanning four mitochondrial loci, we find that fewer than half of species are represented in any single primer database, with interspecific barcode sharing reducing effective taxonomic resolution by up to 50% in recently radiated clades. Database gaps are strongly phylogenetically structured: coverage is highest in charismatic, species-poor lineages and lowest in species-rich clades dominated by small-bodied taxa. Critically, conservation status does not predict barcode inclusion, revealing a fundamental misalignment between molecular infrastructure and conservation need. Using hierarchical Bayesian models, we show that range size and time since scientific description are the strongest predictors of inclusion, and that gaps are driven primarily by clade-level research traditions rather than individual species traits - implying that closing them requires targeted investment across entire neglected lineages. We integrate these drivers with evolutionary distinctiveness and extinction risk into a Barcoding Priority Score that identifies sequencing priorities at global and national scales, and map these priorities across Brazilian biomes. Our transferable framework provides a scalable roadmap for guiding sequencing investments in hyperdiverse regions where biodiversity loss is outpacing molecular documentation. Earth and environmental sciences/Ecology/Ecological genetics Earth and environmental sciences/Ecology/Biodiversity Earth and environmental sciences/Ecology/Tropical ecology eDNA metabarcoding DNA barcoding gaps reference database completeness sequencing prioritisation evolutionary distinctiveness Barcoding Priority Score tropical biodiversity monitoring conservation genomics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files Luypaertetal2026SupplementaryMaterials.pdf Luypaert_et_al_2026_Supplementary_Materials Cite Share Download PDF Status: Under Review Version 1 posted 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-9096952","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":609595931,"identity":"475cd36c-2b02-4b9c-b465-0b8caa51cb99","order_by":0,"name":"Thomas 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