Environmental DNA-based biomonitoring of Cuban Crocodylus and their accompanying vertebrate fauna from Zapata Swamp, Cuba

• Published in: Scientific reports Vol. 13; no. 1; p. 20438
• Main Authors: Pérez-Fleitas, Etiam, Milián-García, Yoamel, Sosa-Rodríguez, Gustavo, Amato, George, Rossi, Natalia, Shirley, Matthew H., Hanner, Robert H.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 22-11-2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/1647/514/1948; 631/1647/514/2254; Alligators and Crocodiles - genetics; Animals; Aquatic reptiles; Biodiversity; Bioinformatics; Biological Monitoring; Biomonitoring; Crocodylus; Crocodylus acutus; Crocodylus rhombifer; Cuba; DNA barcoding; DNA Barcoding, Taxonomic; DNA, Environmental - genetics; Economic importance; Ecosystem; Endangered Species; Environmental DNA; Environmental Monitoring - methods; Geographical distribution; Habitats; Humanities and Social Sciences; Humans; Introduced species; Mice; multidisciplinary; Phylogeny; Population decline; Population genetics; Predators; Science; Science (multidisciplinary); Threatened species; Vertebrates; Vertebrates - genetics; Wetlands; Cuba; Zapata Swamp
• ISSN: 2045-2322; 2045-2322
• DOI: 10.1038/s41598-023-47675-8

Crocodylians globally face considerable challenges, including population decline and extensive habitat modification. Close monitoring of crocodylian populations and their habitats is imperative for the timely detection of population trends, especially in response to management interventions. Here we use eDNA metabarcoding to identify the Critically Endangered
Crocodylus rhombifer
and the Vulnerable
C. acutus
, as well as vertebrate community diversity, in Cuba’s Zapata Swamp. We tested four different primer sets, including those used previously in
Crocodylus
population genetic and phylogenetic research, for their efficiency at detecting crocodylian eDNA. We detected
C. rhombifer
eDNA in 11 out of 15 sampled locations within its historical geographic distribution. We found that data analyses using the VertCOI primers and the mBRAVE bioinformatics pipeline were the most effective molecular marker and pipeline combination for identifying this species from environmental samples. We also identified 55 vertebrate species in environmental samples across the four bioinformatics pipelines— ~ 85% known to be present in the Zapata ecosystem. Among them were eight species previously undetected in the area and eight alien species, including known predators of hatchling crocodiles (e.g.,
Clarias
sp.) and egg predators (e.g.,
Mus musculus
). This study highlights eDNA metabarcoding as a powerful tool for crocodylian biomonitoring within fragile and diverse ecosystems, particularly where fast, non-invasive methods permit detection in economically important areas and will lead to a better understanding of complex human-crocodile interactions and evaluate habitat suitability for potential reintroductions or recovery programs for threatened crocodylian species.