Spatial and temporal occurrence of stream frogs in the Atlantic forest and their detection through environmental DNA

Brazil ranks as the country with one of the highest amphibian species diversity. Streams in the Atlantic forest of southeastern Brazil have an important availability of microenvironments and harbors a particular richness in amphibian species. Monitoring herpetofauna and knowledge on their spatial and temporal dynamics provide primary information for ecological studies, and are essential to the development of other areas such as conservation biology. In this work we gather information on the occurrence and abundance of three torrent frogs, Cycloramphus boraceiensis, Hylodes asper and Hylodes phyllodes and examine the reliability of eDNA analysis to detect anuran communities. Samplings occurred within a 95 to 115 m transect in four streams in Núcleo Picinguaba, at the Parque Estadual da Serra do Mar, São Paulo, Brazil. Individual encounter number and their habitat were monthly recorded from January 2007 to December 2010 and every two months in 2011. We searched for post-metamorphic individuals while walking upstream for 30-60 min, checking all visually accessible spots in the streambed. The location of each active and inactive individual was mapped and its habitat use was characterized in relation to five ecological parameters. We collected eDNA samples at 16 sites on April, 2015. We used eDNA metabarcoding approach with a universal amphibian primer of a mitochondrial marker (12S) to detect amphibian communities. We recorded a total of 6335 visual observations. The three species abundance varied along and between streams and only Hylodes phyllodes were found in the stream 2. Abundance of C. boraceiensis and H. asper was significantly higher in the wet seasons. The three species were found active mainly in wet rocks, without moss and without cover. Inactive individuals of Hylodes asper and H. phyllodes were found mainly in dry leaves, without moss or cover. Through eDNA metabarcoding, we detected nine species, which were consistent with traditional survey results. DNA of riparian species and species with higher constancy in traditional surveys were detected in higher proportions. Our study showed that traditional survey and DNA metabarcoding results can be complementary and both methodologies can be combined in future ecology studies (AU)