Enviromental DNA datasets of the Colombian Amazon and Orinoco basins

The massive loss of biodiversity in recent years has driven the development of rapid, cost-effective, non-invasive, and efficient sampling alternatives, such as environmental DNA. With this method, a water sample can be used to evaluate a community's diversity, in addition with low abundance, cryptic and threatened species detection. Therefore, in this study, environmental DNA was used to determine the diversity of aquatic, semi-aquatic and terrestrial vertebrates in the Colombian Amazon and Orinoco basins, which included four main subregions: Bojonawi Natural Reserve and adjacent areas (Vichada Department), Sierra de la Macarena National Park and Tillavá (Meta Department), Puerto Nariño and adjacent areas (Amazonas Department) and the Municipality of Solano (Caquetá Department). A total of 709 OTUs were identified for all locations. The Orinoco river showed the highest number of fish genera (68) and the Guayabero river, the largest number of genera for tetrapods (13). New taxonomic records were found on all locations, mianly in Bita, Orinoco and Tillavá rivers, which portrayed the highest record of unknown fish diversity compared with traditional surveys. Likewise, two vulnerable fish species and three vulnerable mammal species were identified, as well as four threatened mammal species, including the giant otter (Pteronura brasiliensis), the giant anteater (Myrmecophaga tridactyla), the two subspecies of the Amazon river dolphin (Inia geoffrensis geoffrensis and Inia geoffrensis humboldtiana) and the tucuxi (Sotalia fluviatilis). It is essential to improve current DNA sequence databases for the neotropics and standardize the methodology according to the animal of interest in order to develop future studies that maximize environmental DNA analyses efficiency.