Rediscovering the lost: eDNA detection of freshwater decapods on Réunion Island | Knowledge and Management of Aquatic Ecosystems

Biological conservation, ecosystems restoration and ecological engineering

Open Access

Issue		Knowl. Manag. Aquat. Ecosyst. Number 427, 2026 Biological conservation, ecosystems restoration and ecological engineering


Article Number		2
Number of page(s)		13
DOI		https://doi.org/10.1051/kmae/2025035
Published online		30 January 2026

Allison MJ, Round JM, Bergman LC, Mirabzadeh A, Allen H, Weir A, Helbing C. 2020. The effect of silica desiccation under different storage conditions on filter-immobilized environmental DNA [Preprint]. In Review. https://doi.org/10.21203/rs.3.rs-117231/v1 [Google Scholar]
Barnes MA, Turner CR. 2016. The ecology of environmental DNA and implications for conservation genetics. Conserv Genet 17: 1–17. [CrossRef] [Google Scholar]
Barua A, Afrin T, Akhand AA, Ahmed Md. S. 2021. Molecular characterization and phylogenetic analysis of crabs (Crustacea: Decapoda: Brachyura) based on mitochondrial COI and 16S rRNA genes. Conserv Genet Resour 13: 291–301. [Google Scholar]
Baselga A. 2010. Partitioning the turnover and nestedness components of beta diversity: partitioning beta diversity. Glob Ecol Biogeogr 19: 134–143. [Google Scholar]
Bauer RT. 2013. Amphidromy in shrimps: a life cycle between rivers and the sea. Latin Am J Aquat Res 41: 633–650. [Google Scholar]
Beng KC, Corlett RT. 2020. Applications of environmental DNA (eDNA) in ecology and conservation: Opportunities, challenges and prospects. Biodivers Conserv 29: 2089–2121. [CrossRef] [Google Scholar]
Bernardes SC, Pepato AR, Von Rintelen T, Von Rintelen K, Page TJ, Freitag H, De Bruyn M. 2017. The complex evolutionary history and phylogeography of Caridina typus (Crustacea: Decapoda): Long-distance dispersal and cryptic allopatric species. Sci Rep 7: 9044. [Google Scholar]
Calo-Mata P, Pascoal A, Fernández-No I, Böhme K, Gallardo JM, Barros-Velázquez J. 2009. Evaluation of a novel 16 S rRNA/tRNAVal mitochondrial marker for the identification and phylogenetic analysis of shrimp species belonging to the superfamily Penaeoidea. Anal Biochem 391: 127–134. [Google Scholar]
Chao A, Gotelli NJ, Hsieh TC, Sander EL, Ma KH, Colwell RK, Ellison AM. 2014. Rarefaction and extrapolation with Hill numbers: a framework for sampling and estimation in species diversity studies. Ecol Monogr 84: 45–67. [CrossRef] [Google Scholar]
Chevallier L, Vatin-Perignon N. 1982. Volcano-structural evolution of Piton des Neiges, Reunion Island, Indian Ocean. Bull Volcanol 45: 285–298. [Google Scholar]
Closek CJ, Santora JA, Starks HA, Schroeder ID, Andruszkiewicz EA, Sakuma KM, Bograd SJ, Hazen EL, Field JC, Boehm AB. 2019. Marine vertebrate biodiversity and distribution within the central California current using environmental DNA (eDNA) metabarcoding and ecosystem surveys. Front Mar Sci 6:732. [Google Scholar]
Comité de l’eau et de la biodiversité de La Réunion. 2022. Le Schéma Directeur d’Aménagement et de Gestion des Eaux (SDAGE)—2022–2027. [Google Scholar]
Cook BD, Bernays S, Pringle CM, Hughes JM. 2009. Marine dispersal determines the genetic population structure of migratory stream fauna of Puerto Rico: Evidence for island-scale population recovery processes. J North Am Benthol Soc 28: 709–718. [Google Scholar]
De Grave S. 2013. Macrobrachium hirtimanus : De Grave, S.: The IUCN Red List of Threatened Species 2013: E.T197879A2503622 [Jeu de données]. https://doi.org/10.2305/IUCN.UK.2013-1.RLTS.T197879A2503622.en [Google Scholar]
De Mazancourt V, Mennesson M, Marquet G, Keith P. 2025. Revision of the species of Caridina (Decapoda : Atyidae) from the Western Indian Ocean islands with description of a new species. Eur J Taxon 1007. https://doi.org/10.5852/ejt.2025. 1007.2995 [Google Scholar]
de Mazancourt V, Abdou A, Castelin M, Ellien C, Lord C, Mennesson M, Renneville C, Marquet G, Keith P. 2023. Molecular ecology of the freshwater shrimp Caridina natalensis and comparative analysis with other amphidromous species (Decapoda, Teleostei, and Gastropoda). Hydrobiologia 850: 3997–4014. [Google Scholar]
de Mazancourt V, Klotz W, Marquet G, Mos B, Rogers DC, Keith P. 2021. New insights on biodiversity and conservation of amphidromous shrimps of the Indo-Pacific islands (Decapoda : Atyidae : Caridina). In: Recent Advances in Freshwater Crustacean Biodiversity and Conservation, 1st ed. Taylor & Francis, p. 24. [Google Scholar]
de Mazancourt V, Mennesson M, Marquet G, Valade P, Keith P. in press. NGS data from historical museum collections helps clarifying the status of endangered or supposedly extinct species: The case of the Mascarene endemic freshwater shrimp Macrobrachium hirtimanus (Olivier, 1811). [Google Scholar]
Dunn N, Priestley V, Herraiz A, Arnold R, Savolainen V. 2017. Behavior and season affect crayfish detection and density inference using environmental DNA. Ecol Evol 7: 7777–7785. [Google Scholar]
Elbrecht V, Vamos EE, Meissner K, Aroviita J, Leese F. 2017. Assessing strengths and weaknesses of DNA metabarcoding-based macroinvertebrate identification for routine stream monitoring. Methods Ecol Evol 11. [Google Scholar]
Edgar RC, Haas BJ, Clemente JC, Quince C, Knight R. 2011. UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27: 2194–2200. [Google Scholar]
Escudié F, Auer L, Bernard M, Mariadassou M, Cauquil L, Vidal K, Maman S, Hernandez-Raquet G, Combes S, Pascal G. 2018. FROGS : find, rapidly, OTUs with galaxy solution. Bioinformatics 34: 1287–1294. [Google Scholar]
Falkland a. 2002. Tropical island hydrology and water resources current knowledge and future needs. 237. [Google Scholar]
FDAAPPMA La Réunion. 2021. Plan Départemental de Protection du milieu aquatique et de Gestion des ressources piscicoles de la Réunion 2021–2026, p. 294. [Google Scholar]
Gibson JF, Shokralla S, Curry C, Baird DJ, Monk WA, King I, Hajibabaei M. 2015. Large-scale biomonitoring of remote and threatened ecosystems via high-throughput sequencing. PLOS ONE 10: e0138432. [Google Scholar]
Hoarau PE, Courtecuisse E, Treilhes CR, Lagarde R, Teichert N, Valade PB. 2019. Reproductive biology of a small amphidromous shrimp Atyoida serrata on Reunion Island, south-west Indian Ocean. Limnologica 76: 41–47. [Google Scholar]
Hsieh TC, Ma KH, Chao A. 2016. iNEXT : An R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods Ecol Evol 7: 1451–1456. [CrossRef] [Google Scholar]
Ip JC, Loke H, Yiu SKF, Zhao M, Li Y, Lin Y, How C, Mo J, Yan M, Cheng J, Lai VC, Chan LL, Leung KMY, Qiu J. 2024. Bottom trawling and multi-marker metabarcoding surveys reveal highly diverse vertebrate and crustacean communities : a case study in an urbanized subtropical estuary. Environmental DNA 6: e70031. [Google Scholar]
Jaisankar I. 2018. Chapter 19-Biodiversity conservation : Issues and strategies for the tropical islands. In: Biodiversity Conservation. [Google Scholar]
Jannel L-A, Valade P, Chabanet P, Jourand P. 2024. Aquatic biodiversity on Reunion Island : responses of biological communities to environmental and anthropogenic pressures using environmental DNA. Aquat Ecol. https://doi.org/10.1007/s10452-024-10168-5. [Google Scholar]
Jarvis MG, Closs GP. 2019. Water infrastructure and the migrations of amphidromous species: Impacts and research requirements. J Ecohydraulics 4: 4–13. [Google Scholar]
Keith P. 2002. Freshwater fish and decapod crustacean populations on Réunion island, with an assessment of species introductions. Bulletin Français de la Pêche et de la Pisciculture, 364: 97–107. [Google Scholar]
Keith P. 2003. Biology and ecology of amphidromous Gobiidae of the Indo-Pacific and the Caribbean regions. J Fish Biol 63: 831–847. [Google Scholar]
Keith and Vigneux. 2000. First capture of Macrobrachium lepidactylus (Hilgendorf, 1879) (Palaemonidae) on Réunion Island, followed by a commentary on Macrobrachium hirtimanus (Olivier, 1811). Crustaceana 73: 215–222. [Google Scholar]
Kiener A. 1981. Etude des problèmes piscicoles des eaux intérieures de la réunion (Rapport d’étude No. 25; Etudes du CEMAGREF, série Qualités des eaux-Pêche et pisciculture, CEMAGREF, p. 140. [Google Scholar]
Kobayashi S, Hamasaki K, Dan S. 2024. Upper temperature and salinity tolerance of six freshwater shrimp species in the genera Caridina and Paratya (Decapoda: Caridea: Atyidae). [Google Scholar]
Lal MM, Seeto J, Pickering TD. 2014. Complete larval development of the Monkey River Prawn Macrobrachium lar (Palaemonidae) using a novel greenwater technique. SpringerPlus 3: 568. [Google Scholar]
Legendre P. 2014. Interpreting the replacement and richness difference components of beta diversity. Glob Ecol Biogeogr 23: 1324–1334. [Google Scholar]
Lord C, Lorion J, Dettai A, Watanabe S, Tsukamoto K, Cruaud C, Keith P. 2012. From endemism to widespread distribution: Phylogeography of three amphidromous Sicyopterus species (Teleostei: Gobioidei: Sicydiinae). Mar Ecol Prog Ser 455: 269–285. [Google Scholar]
Mahé F, Rognes T, Quince C, De Vargas C, Dunthorn M. 2014. Swarm: Robust and fast clustering method for amplicon-based studies. PeerJ 2: e593. [Google Scholar]
Majaneva M, Diserud OH, Eagle SHC, Boström E, Hajibabaei M, Ekrem T. 2018. Environmental DNA filtration techniques affect recovered biodiversity. Sci Rep 8: 4682. [Google Scholar]
McDowall RM. 2010. Why be amphidromous : expatrial dispersal and the place of source and sink population dynamics? Rev Fish Biol Fish 20: 87–100. [Google Scholar]
McMurdie PJ, Holmes S. 2012. phyloseq : A bioconductor package for handling and analysis of High-Throughput phylogenetic sequence data. Biocomputing 2012: 235–246. [Google Scholar]
McMurdie PJ, Holmes S. 2013. phyloseq: An R package for reproducible interactive analysis and graphics of Microbiome Census Data. PLoS ONE 8: e61217. [CrossRef] [PubMed] [Google Scholar]
Meyer A. 1994. DNA technology and phylogeny of fish. In: Genetics and Evolution of Aquatic Organisms, Chapman & Hall, p. 220–290. [Google Scholar]
Myers N, Mittermeier RA, Mittermeier CG, Da Fonseca GAB, Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature 403: 853–858. [CrossRef] [PubMed] [Google Scholar]
OCEA Consult’, OFB, Fédération de pêche Réunion, & Office de l’Eau Réunion. 2023. Suivi des éléments biologiques «Poissons et Macro-crustacés» des rivières du bassin Réunion-Campagne 2023. Suivi des réseaux de contrôle de surveillance de la qualité des masses d’eau de surface de La Réunion. Volet Poissons et macro-crustacés. https://www.documentation.eauetbiodiversite.fr/notice/suivi-des-elements-biologiques-poissons-et-macro-crustaces-des-rivieres-du-bassin-reunion-campagne-20 [Google Scholar]
Oksanen J, Simpson G, Blanchet F, Kindt R, Legendre P, Minchin P, O’Hara RB, Solymos P, Stevens M, Szoecs E, Wagner H, Barbour M, Bedward M, Bolker B, Borcard D, Carvalho G, Chirico M, De Caceres M, Durand S, Weedon J. 2022. vegan: Community Ecology Package. https://CRAN.R-project.org/package=vegan [Google Scholar]
Palumbi. 1996. Nucleic acids II: the polymerase chain reaction. In: Hillis DM, Mable BK, Moritz C, eds. Sunderland, MA: Sinauer Associates, p. 205–247. [Google Scholar]
Pawlowski J, Apothéloz-Perret-Gentil L, Mächler E, Altermatt F. 2020. Environmental DNA applications for biomonitoring and bioassessment in aquatic ecosystems. https://doi.org/10.5167/UZH-187800 [Google Scholar]
Peixoto S, Chaves C, Velo-Antón G, Beja P, Egeter B. 2021. Species detection from aquatic eDNA: assessing the importance of capture methods. Environmental DNA 3: 435–448. [Google Scholar]
Poupin J. 2010. Crustacés de la Réunion : Décapodes et stomatopodes. IRD/Réserve naturelle marine de la Réunion. [Google Scholar]
Prati S, Faivre L, De Mazancourt V, Sures B, Valade P. 2024. Paradise under threat: The successful invasion of the freshwater shrimp Neocaridina davidi and its parasites on La Réunion Island. https://doi.org/10.1101/2024.08.23.609356 [Google Scholar]
R Core Team. 2024. R: A language and environment for statistical computing [Logiciel], R Foundation for Statistical Computing. https://www.R-project.org [Google Scholar]
Reynolds J, Souty-Grosset C, Richardson A. 2013. Ecological roles of crayfish in freshwater and terrestrial habitats. Freshw Crayfish 19(2). [Google Scholar]
Rognes T, Flouri T, Nichols B, Quince C, Mahé F. 2016. VSEARCH: A versatile open source tool for metagenomics. Peer J 4: e2584. [Google Scholar]
Sahu A, Singh M, Amin A, Malik MM, Qadri SN, Abubakr A, Teja SS, Dar SA, Ahmad I. 2025. A systematic review on environmental DNA (eDNA) Science: An eco-friendly survey method for conservation and restoration of fragile ecosystems. Ecol Indic 173:113441. [Google Scholar]
Siriwut W, Jeratthitikul E, Panha S, Chanabun R, Ngor PB, Sutcharit C. 2021. Evidence of cryptic diversity in freshwater Macrobrachium prawns from Indochinese riverine systems revealed by DNA barcode, species delimitation and phylogenetic approaches. PLOS ONE, 16: e0252546. [Google Scholar]
Song JW, Small MJ, Casman EA. 2017. Making sense of the noise: the effect of hydrology on silver carp eDNA detection in the Chicago area waterway system. Sci Total Environ 605–606: 713–720. [Google Scholar]
Szaniawska A. 2018. Function and Importance of Crustaceans. In: Szaniawska A ed. Baltic Crustaceans, Springer International Publishing, p. 185–188. https://doi.org/10.1007/978-3-319-56354-1_11 [Google Scholar]
Teichert N, Lagarde R, Faivre L, Valade P, Grondin H, Labeille M, Keith P, Feunteun E. 2025. Fish and macro-crustacean assemblages are relevant ecological indicators for monitoring rivers of tropical islands. Ecol Indic 175:113585. [Google Scholar]
Thébaud C, Strasberg D, Warren BH, Cheke A. 2009. Mascarene Islands, Biology. In: Gillespie R, Clague D, eds. Encyclopedia of Islands, University of California Press, p. 612–619. https://doi.org/10.1525/9780520943728-146 [Google Scholar]
Torres MV, Giri F, Collins PA. 2018. Temporal and spatial patterns of freshwater decapods associated with aquatic vegetation from floodplain rivers. Hydrobiologia 823: 169–189. [Google Scholar]
UICN France. 2016. Rapport BEST. Profil d’écosystème–Ocean Indien–La Réunion. [Google Scholar]
UICN France, MNHN, SEOR, ARDA, Insectarium de La Réunion, GLOBICE, Kélonia. 2013. La Liste rouge des espèces menacées en France–Faune de La Réunion. [Google Scholar]
Veilleux HD, Misutka MD, Glover CN. 2021. Environmental DNA and environmental RNA: Current and prospective applications for biological monitoring. Sci Total Environ 782:146891. [Google Scholar]
von Rintelen K, Page TJ, Cai Y, Roe K, Stelbrink B, Kuhajda BR, Iliffe TM, Hughes J, von Rintelen T. 2012. Drawn to the dark side: a molecular phylogeny of freshwater shrimps (Crustacea: Decapoda: Caridea: Atyidae) reveals frequent cave invasions and challenges current taxonomic hypotheses. Mol Phylogenet Evol 63: 82–96. [Google Scholar]
Williams-Subiza EA, Epele LB. 2021. Drivers of biodiversity loss in freshwater environments: A bibliometric analysis of the recent literature. Aquat Conserv: Mar Freshw Ecosyst 31: 2469–2480. [Google Scholar]

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