Optimizing Marine eDNA Protocols for Rare Megafauna: A Case Study on Dugongs in the Western Indian Ocean

Optimizing Marine eDNA Protocols for Rare Megafauna: A Case Study on Dugongs in the Western Indian Ocean | Authorea try { document.documentElement.classList.add('js'); } catch (e) { } var _gaq = _gaq || []; _gaq.push(['_setAccount', 'G-8VDV14Y67G']); _gaq.push(['_trackPageview']); (function() { var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true; ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js'; var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s); })(); Skip to main content Preprints Collections Wiley Open Research IET Open Research Ecological Society of Japan All Collections About About Authorea FAQs Contact Us Quick Search anywhere Search for preprint articles, keywords, etc. Search Search ADVANCED SEARCH SCROLL Ecology and Evolution This is a preprint and has not been peer reviewed. Data may be preliminary. 12 May 2026 V1 Latest version Share on Optimizing Marine eDNA Protocols for Rare Megafauna: A Case Study on Dugongs in the Western Indian Ocean Authors : Léa Bernagou [email protected] , Auriane Serval [email protected] , François Beudard [email protected] , Jerôme Mathey [email protected] , Yann Mercky [email protected] , Charles Le Bozec [email protected] , Evan Trotzuk [email protected] , Keila Paunde [email protected] , Marielle Garcia [email protected] , Eva Bellemain [email protected] , and Emmanuel Corse 0000-0003-0992-726X [email protected] Authors Info & Affiliations https://doi.org/10.22541/authorea.15003154/v1 15 views 7 downloads Contents Abstract Supplementary Material Information & Authors Metrics & Citations View Options References Figures Tables Media Share Abstract Assessing habitat use, spatial distribution, and site fidelity is critical for the conservation of threatened marine species, yet monitoring rare and elusive species in such complex environment remains difficult. This limitation is particularly critical for dugong (Dugong dugon) populations in the Western Indian Ocean, which are extremely small, fragmented, and difficult to monitor, posing a major conservation challenge. This pilot study presents a field experiment aimed at developing a cost-effective and field-optimized eDNA workflow based on species-specific qPCR for large-scale monitoring of this threatened sirenian in shallow tropical coastal ecosystems. Field experiments were conducted in Mozambique, which hosts the only remaining large dugong population in the region. A species-specific qPCR assay was first developed and validated. Sampling was then conducted along survey tracks using different sampling and DNA extraction strategies, to evaluate three key variables of the detection protocol— (i) vertical sampling position (surface, near-bottom, and sediment), (ii) filtration volume (1.5–30–60 L), and (iii) field versus laboratory DNA extraction—resulting in a total of eleven sampling–extraction strategies. At every visually confirmed location, at least one of the eleven sampling–extraction strategies resulted in a positive detection, including more than two hours after dugong passage. All strategies detected dugong DNA except those based on sediment sampling. Positive rates of qPCR increased markedly with filtration volume and was higher in near-bottom samples, consistent with limited vertical dispersion of eDNA. Laboratory extractions outperformed field extractions, likely due to reduced centrifugation efficiency and reagent limitations under field conditions. Ultimately, the best-performing combination—filtering a large volume of near-bottom water followed by laboratory-based sample processing—enabled detection in all cases where a visual sighting had occurred. The proposed workflow provides a robust and cost-efficient framework for eDNA-based dugong monitoring, supporting scalable and long-term surveillance efforts in tropical coastal ecosystems. Supplementary Material File (si i alignment of vertebrate 16s gene sequences from genbank used for the design of dugong-specific qpcr primers.fas) si i alignment of vertebrate 16s gene sequences from genbank used for the design of dugong-specific qpcr primers Download 627.56 KB File (sii sampling metadata and edna detection results.xlsx) sii sampling metadata and edna detection results Download 20.54 KB Information & Authors Information Version history V1 Version 1 12 May 2026 Collection Ecology and Evolution Authors Affiliations Léa Bernagou [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author Auriane Serval [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author François Beudard [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author Jerôme Mathey [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author Yann Mercky [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author Charles Le Bozec [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author Evan Trotzuk [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author Keila Paunde [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author Marielle Garcia [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author Eva Bellemain [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author Emmanuel Corse 0000-0003-0992-726X [email protected] Association des Naturalistes Environnement et Patrimoine de Mayotte, Dembeni, Mayotte, 97660 View all articles by this author Metrics & Citations Metrics Article Usage 15 views 7 downloads .FvxKWukQNSOunydq8rnd { width: 100px; } Citations Download citation Léa Bernagou, Auriane Serval, François Beudard, et al. Optimizing Marine eDNA Protocols for Rare Megafauna: A Case Study on Dugongs in the Western Indian Ocean. Authorea . 12 May 2026. DOI: https://doi.org/10.22541/authorea.15003154/v1 If you have the appropriate software installed, you can download article citation data to the citation manager of your choice. Simply select your manager software from the list below and click Download. For more information or tips please see 'Downloading to a citation manager' in the Help menu . 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