Vertebrate diversity in cave systems of Colombia: an approach based on environmental DNA metabarcoding analysis

Authors

• Rita Daniela Martinelli Marín, Universidad El Bosque, ColombiaFollow
• Carlos Andres Lasso, Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, ColombiaFollow
• Francesco Sauro, Università degli studi di Padova, ItalyFollow
• Susana Josefina Caballero, Nova South Eastern University, USAFollow

Highlights

• eDNA revealed 110 vertebrate species across 21 Colombian cave systems
• Fish diversity: 49 species, mainly Siluriformes and Characiformes
• Tetrapods: 61 species, with Anura, Rodentia, and Chiroptera most common
• El Cóndor, Sara’s, and Cascada del Hayal caves showed highest diversity
• eDNA proved effective for detecting hard-to-sample cave vertebrates

Abstract

There is currently limited knowledge of the biological communities inhabiting cave ecosystems in South America. This study examines the vertebrate community composition of 21 caves across diverse subterranean ecosystems in Colombia using environmental DNA (eDNA) analysis. Water was collected from water bodies inside caves and subterranean systems in six of the eight speleological regions of Colombia in eight departments. Water was filtered manually through a 0.8 m pore size filter and preserved with Longmire solution. A 170-base pair (bp) fragment of the 12s mitochondrial gene specific for vertebrate identification was amplified by PCR and sequenced by Illumina (metabarcoding). Data corresponding to 208 OTUs were obtained from 21 caves or subterranean ecosystems. In total, 33 orders, 56 families, 81 genera, and 110 species were detected. Thirteen orders, 22 families, 31 genera, and 51 species of fish were identified, with Trichomycterus being the most representative genus. For tetrapods, 20 orders, 34 families, 50 genera, and 59 species were identified, where the bird genus Steatornis was the most commonly detected. For fish, the predominant orders were Siluriformes and Characiformes, with Loricariidae being the family with the highest detection. In the case of tetrapods, the most prevalent orders were Anura, Rodentia, and Chiroptera and among these taxa, the most numerous families corresponded to Leptodactylidae, Cricetidae, and Phyllostomidae, respectively. Environmental DNA proved to be an effective tool to quickly obtain information on diversity in areas that are difficult to access and sample, such as underground systems, allowing identification of difficult to detect species by traditional observation methods in these systems.

DOI

https://doi.org/10.5038/1827-806X.ijs2576

Creative Commons License

This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 4.0 License.

Recommended Citation

Martinelli-Marín, D., Lasso, C.A., Sauro, F., Caballero-Gaitán, S., 2026. Vertebrate diversity in cave systems of Colombia: an approach based on environmental DNA metabarcoding analysis. International Journal of Speleology, 55(2), ijs2576 https://doi.org/10.5038/1827-806X.ijs2576