A novel environmental DNA (eDNA) sampling method for aye-ayes from their feeding traces

Non-invasive sampling is an important development in population genetic monitoring of wild animals. Particularly, the collection of environmental DNA (eDNA) which can be collected without needing to encounter the target animal, facilitates the genetic analysis of cryptic and threatened species. One method that has been applied to these types of sample is target capture and enrichment which overcomes the issue of high proportions of exogenous (non-host) DNA from these lower quality samples. We tested whether target capture of mitochondrial DNA from sampled feeding traces of wild aye-ayes would yield mitochondrial DNA sequences for population genetic monitoring. We sampled gnawed wood from feeding traces where aye-ayes excavate wood-boring insect larvae from trees. We designed RNA probes complementary to the aye-aye’s mitochondrial genome and used these to isolate aye-aye DNA from other non-target DNA in these samples. We successfully retrieved six near-complete mitochondrial genomes from two sites within the aye-aye’s geographic range that had not been sampled previously. This method can likely be applied to alternative foraged remains to sample species other than aye-ayes. Our method demonstrates the application to next-generation molecular techniques to species of conservation concern.