Supporting the assessment of extinction risk for terrestrial vertebrates: Metabarcoding as a tool for decision-making

• Grant number: 25/02034-7
• Support Opportunities: Regular Research Grants
• Start date: July 01, 2025
• End date: June 30, 2027
• Field of knowledge: Biological Sciences - Ecology - Applied Ecology
• Principal Investigator: Marcio Roberto Costa Martins
• Grantee: Marcio Roberto Costa Martins
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated researchers: Ana Paula Carmignotto ; Carla Martins Lopes ; Joyce Rodrigues Do Prado

Abstract

Brazil is committed to assessing the extinction risk of approximately 10,000 vertebrate species, using IUCN guidelines to analyze population status and trends. Based on this assessment, the National List of Threatened Species is developed. Additionally, species for which information is insufficient for an accurate evaluation are identified, becoming priorities for biodiversity research. However, monitoring these species using traditional methods is challenging, especially for those that are small, rare, or difficult to detect.In this context, environmental DNA (eDNA) metabarcoding emerges as an innovative approach, enabling the non-invasive detection of rare and threatened species. Although the use of eDNA in terrestrial and open environments, such as the cerrado, is still underexplored, this technique shows great potential. Furthermore, existing DNA sequence databases currently have low representativeness of Neotropical species, limiting their application.This project aims to enhance the use of eDNA metabarcoding to record rare, elusive, threatened, or data-deficient terrestrial vertebrates from the cerrado of the Central Plateau. Its main objectives are: (1) to increase the representativeness of mitochondrial genomes (mtDNA) of Brazilian mammals in public databases, and (2) to compare the effectiveness of eDNA metabarcoding with traditional methods for surveying herpetofauna and small mammals in savanna environments.The project is supported by the Brazilian Biodiversity Genomics Program (GBB), a partnership between the Chico Mendes Institute for Biodiversity Conservation (ICMBio) and the Vale Technological Institute (ITV), which will be responsible for sequencing mitochondrial genomes of species whose tissues are deposited in Brazilian collections. However, some species still lack available tissue samples, and for these, sequencing will be performed using specimens from zoological collections, with support from the project "Old Samples Tell Great Stories," led by Joyce do Prado. This initiative will assist with fieldwork and the extraction of historical DNA (hDNA) from bones, teeth, or skin fragments.This will be the first study to compare the detectability of eDNA metabarcoding with traditional methods for studying vertebrate fauna in the cerrado, creating a valuable opportunity for documenting rare and threatened species in this biome. In this study, 90 samples will be collected from soil and water in the Chapada dos Veadeiros National Park, located in the state of Goiás, alongside a 30-day collection using pitfall traps and box or cage traps (Sherman and Tomahawk).We expect that eDNA will recover a greater number of species, with better representation of threatened and data-deficient species, compared to traditional methods for reptiles, amphibians, and mammals. (AU)