Reassessment of mammalian species believed to be locally extinct at the Pernambuco endemism center (CEP) from mixed sample DNA and metabarcoding

• Grant number: 19/26436-6
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: February 01, 2020
• End date: February 28, 2021
• Field of knowledge: Biological Sciences - Genetics
• Principal Investigator: Pedro Manoel Galetti Junior
• Grantee: Carolina da Silva Carvalho
• Host Institution: Centro de Ciências Biológicas e da Saúde (CCBS). Universidade Federal de São Carlos (UFSCAR). São Carlos , SP, Brazil
• Associated research grant: 17/23548-2 - Evaluation, recovering and conservation of endangered animal species from the Pernambuco Centre of Endemism, AP.BTA.TEM

Abstract

The Pernambuco Endemism Center (CEP) is one of the five Atlantic Forest endemism centers and currently consists of forest remnants with a high degree of degradation. As a consequence, several endemic species in this region are in imminent danger of extinction, and therefore CEP is one of the most urgent conservation hotspots. Studying mammal composition is the first step in understanding CEP's biodiversity and endemism and extinction rates and, therefore, designing effective conservation policies, as these animals occupy a wide range of ecological niches, are responsible for several key ecosystem functions and contain sensitive species to anthropic disorder. Although taxonomic identification for mammals is not a major challenge, its low abundance and nocturnal and elusive habits make field detection difficult with traditional sampling tools. Fortunately, the advancement of next-generation sequencing techniques and metabarcoding tools has helped to overcome most of these limitations, and has established itself as a fast and efficient tool for monitoring biodiversity. eDNA and iDNA are two metabarcoding techniques based on environmental DNA sampling and invertebrate derived DNA, respectively. Although eDNA has been successfully used for monitoring aquatic ecosystems (water samples), its effectiveness in monitoring terrestrial vertebrates is still limited. On the other hand, hematophagous mosquitoes are particularly suited for vertebrate monitoring studies because they are easy to capture and contain better DNA quality compared to DNA obtained from soil samples. Within this context, this project aims to reevaluate the presence or absence of mammals considered locally extinct in the Pernambuco Endemism Center (CEP), using DNA samples obtained from blood of hematophagous mosquitoes and metabarcoding analysis. Specifically, this project aims to evaluate the occurrence of small, medium and large mammal species in the area; develop an unprecedented protocol in Brazil for metabarcoding analysis to identify the vertebrate community based on mixed DNA samples from blood of hematophagous mosquitoes; contribute to the survey of mammal species that occur in the CEP; generate a genetic barcode database of mammal species that occur in the CEP. Hematophagous mosquitoes will be actively harvested using dip net and gravid trap, which are traps that attract female mosquitoes that are about to lay eggs, as oviposition requires the energy of blood ingestion. All hematophagous mosquitoes will be preserved in 95% alcohol. After screening, females with full stomach will be separated and have their abdomen removed for DNA extraction. For the analysis of metabarcoding will be initially used primers 12S and 16S already used in previous work for mammal identification. Large scale sequencing will be performed on the Illumina platform. The sequences obtained will be compared with sequences previously obtained by the research group and with sequences available in different databases, and analyzed with modern bioinformatics programs. With data obtained in this work we intend to contribute to the management and conservation of mammal species found in the CEP area. All results will be presented at congresses and submitted for publication in scientific articles. (AU)

Scientific publications

(6)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

CARVALHO, CAROLINA DA SILVA; LUCAS, MARILIA SOUZA; CORTES, MARINA CORREA. Rescuing intraspecific variation in human-impacted environments. JOURNAL OF APPLIED ECOLOGY, v. 58, n. 2, p. 350-359, FEB 2021. (19/26436-6, 16/22843-8, 14/01029-5)

CARVALHO, CAROLINA DA SILVA; MARTELLO, FELIPE; GALETTI, MAURO; PINTO, FERNANDO; FRANCISCO, MERCIVAL ROBERTO; SILVEIRA, LUIS FABIO; GALETTI JR, PEDRO MANOEL. nvironmental heterogeneity and sampling relevance areas in an Atlantic forest endemism regio. PERSPECTIVES IN ECOLOGY AND CONSERVATION, v. 19, n. 3, p. 311-318, JUL-SEP 2021. (19/26436-6)

SARANHOLI, BRUNO H.; RODRIGUEZ-CASTRO, KAREN G.; CARVALHO, CAROLINA S.; CHAHAD-EHLERS, SAMIRA; GESTICH, CARLA C.; ANDRADE, SONIA C. S.; FREITAS, PATRICIA D.; GALETTI, PEDRO M.. Comparing iDNA from mosquitoes and flies to survey mammals in a semi-controlled Neotropical area. MOLECULAR ECOLOGY RESOURCES, v. 23, n. 8, p. 10-pg., 2023-08-03. (15/20139-9, 22/01741-3, 19/26436-6, 17/23548-2)

CARVALHO, CAROLINA DA SILVA; GARCIA, CRISTINA; LUCAS, MARILIA SOUZA; JORDANO, PEDRO; CORTES, MARINA CORREA. Extant fruit-eating birds promote genetically diverse seed rain, but disperse to fewer sites in defaunated tropical forests. JOURNAL OF ECOLOGY, v. 109, n. 2, p. 1055-1067, FEB 2021. (16/22843-8, 19/03005-0, 14/01029-5, 19/26436-6)

SARANHOLI, BRUNO H.; SANCHES, ALEXANDRA; MOREIRA-RAMIREZ, JOSE F.; CARVALHO, CAROLINA DA SILVA; GALETTI, MAURO; GALETTI JR, PEDRO M.. Long-term persistence of the large mammal lowland tapir is at risk in the largest Atlantic forest corridor. PERSPECTIVES IN ECOLOGY AND CONSERVATION, v. 20, n. 3, p. 9-pg., 2022-07-01. (07/03392-6, 13/24453-4, 13/19377-7, 07/04073-1, 19/26436-6)

CARVALHO, CAROLINA S.; DE OLIVEIRA, MARINA ELISA; RODRIGUEZ-CASTRO, KAREN GISELLE; SARANHOLI, BRUNO H.; GALETTI JR, PEDRO M. JR. Efficiency of eDNA and iDNA in assessing vertebrate diversity and its abundance. MOLECULAR ECOLOGY RESOURCES, NOV 2021. (19/26436-6)