Ideating iDNA: Lessons and limitations from leeches in legacy collections

• Published in: PloS one Vol. 14; no. 2; p. e0212226
• Main Authors: Siddall, Mark E, Barkdull, Megan, Tessler, Michael, Brugler, Mercer R, Borda, Elizabeth, Hekkala, Evon
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 22.02.2019; Public Library of Science (PLoS)
• Subjects: Analysis; Animal defenses; Animals; Antibiotics; Bar codes; Beef cattle; Biodiversity; Biodiversity conservation; Biology and Life Sciences; Cameras; Chelonia mydas; Cytochrome; Databases, Nucleic Acid; Deoxyribonucleic acid; DNA; DNA - genetics; DNA - isolation & purification; DNA Barcoding, Taxonomic; Ecology and Environmental Sciences; Environmental DNA; Inventories; Inventory management; Invertebrates; Leeches; Medicine and Health Sciences; Microbial activity; Microbiota; Microorganisms; Mitochondrial DNA; Monitoring; Museums; Protected areas; Reptiles & amphibians; Research and Analysis Methods; Surveying; Terrestrial environments; Vertebrates; Vertebrates - classification; Vertebrates - genetics; Virology; Zoology; China; New York; United States > US; Texas
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0212226

Indirect methods for conducting faunal inventories present great promise, and genomic inventories derived from environmental sources (eDNA) are improving. Invertebrate ingested DNA (iDNA) from terrestrial leeches in the family Haemadipsidae has shown potential for surveying vertebrates and biodiversity monitoring in protected areas. Here we present an initial, and critical, evaluation of the limitations and biases of current iDNA protocols for biodiversity monitoring using both standard and NGS barcoding approaches. Key findings include the need for taxon relevant multi-locus markers and reference databases. In particular, the limitations of available reference databases have profound potential to mislead and bias eDNA and iDNA results if not critically interpreted. Nevertheless, there is great potential for recovery of amplifiable DNA from gut contents of invertebrate museum specimens which may reveal both temporal patterns and cryptic diversity in protected areas with increased efficiency. Our analyses of ingested DNA (iDNA) from both freshly stored and previously collected (legacy) samples of terrestrial leeches successfully identified vertebrates from Myanmar, Australia and Madagascar and indicate the potential to characterize microbial communities, pathogen diversity and interactions at low cost.