Recovering host DNA from their invertebrate parasites: a minimally invasive genetic sampling tool for the critically endangered flapper skate

Obtaining host DNA from the blood meals of their invertebrate parasites (invertebrate-derived DNA, iDNA) has proven to be a powerful tool in terrestrial ecology for detecting vertebrates to answer questions relating to host community diversity. However, the use of iDNA in the marine environment is limited. Here, we assessed the efficacy of sampling parasites from the critically endangered flapper skate (Dipturus intermedius) to determine whether iDNA could (i) identify the host species and (ii) obtain host haplotype sequences. In total, 34 copepods (Trebius caudatus specimens, n = 30; Caligus elongatus specimens, n = 4) were processed from 20 flapper skates. Fin-clips were also taken from each flapper for comparison. iDNA identified the host species with 91% success. The host haplotype sequenced from multiple T. caudatus specimens sampled from the same host matched in all cases. A bias-reduced logistic regression found a positive but non-significant association between copepod gut length (z-score) and host-copepod haplotype match success (β = 0.67, p = 0.34). These findings demonstrate the utility of iDNA for confirming the identity and the haplotype of a cryptic conservation-listed batoid and its potential to transform community-led genetic sampling.