Ideating iDNA: Lessons and limitations from leeches in legacy collections

PloS One
Mark E SiddallEvon Hekkala

Abstract

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 character...Continue Reading

References

Nov 26, 2003·Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases·Imna MaleleWendy Gibson
Mar 17, 2004·Molecular Phylogenetics and Evolution·Mark E SiddallSherwin S Desser
Mar 23, 2004·Nucleic Acids Research·Robert C Edgar
Sep 17, 2004·Nature Reviews. Genetics·Rob DeSalle, George Amato
Oct 16, 2004·Science·Simon N StuartRobert W Waller
Nov 4, 2004·Molecular Phylogenetics and Evolution·Nigel P BarkerJohn P Rourke
Mar 22, 2005·International Journal for Parasitology·P B HamiltonW C Gibson
Oct 11, 2005·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Rob DeSalleMark Siddall
Jul 18, 2006·Trends in Microbiology·Joerg GrafRita V M Rio
Jul 18, 2006·International Journal of Legal Medicine·Takashi KitanoMotoki Osawa
Nov 23, 2006·Applied and Environmental Microbiology·Mark E SiddallJoerg Graf
Aug 12, 2008·Applied and Environmental Microbiology·Alison S LauferJoerg Graf
Nov 27, 2009·American Journal of Critical Care : an Official Publication, American Association of Critical-Care Nurses·Steven M LevineJamie P Levine
Oct 6, 2010·Revue Scientifique Et Technique·F Moutou, P P Pastoret
Dec 31, 2010·Trends in Parasitology·Patrick B Hamilton, Jamie R Stevens
May 6, 2011·Proceedings of the National Academy of Sciences of the United States of America·Tina L ChengVance T Vredenburg
Apr 28, 2012·Current Biology : CB·Ida Bærholm SchnellM Thomas P Gilbert
May 11, 2012·Gut Microbes·Michael C Nelson, Joerg Graf
Jan 10, 2013·Molecular Ecology·Sébastien Calvignac-SpencerFabian H Leendertz
Mar 12, 2013·Molecular Ecology·Kristine BohmannM Thomas P Gilbert
Jul 11, 2013·PloS One·Alistair S GlenBruce Warburton
Mar 19, 2016·Journal of Mammalogy·Bryan S McLeanJoseph A Cook
Jun 25, 2016·Conservation Biology : the Journal of the Society for Conservation Biology·John-James WilsonAlison K S Wee
Aug 3, 2016·Annual Review of Microbiology·Joerg Graf
Sep 19, 2017·Molecular Ecology·Kristy DeinerLouis Bernatchez
Sep 20, 2017·Molecular Ecology·Arthur KocherJérôme Murienne

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Citations

Mar 7, 2021·Applied and Environmental Microbiology·Emily Ann McClureJoerg Graf
Aug 18, 2021·Molecular Ecology Resources·Christina LynggaardKristine Bohmann

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Datasets Mentioned

BETA
PRJNA175704

Methods Mentioned

BETA
PCR
electrophoresis

Software Mentioned

Geneious
CodonCode Aligner
PhyML
FASTX Toolkit
sff
native
MUSCLE
454 GS Junior
emPCR Amplification Method Manual ( Lib - L )
extract

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