Testing for correlation between marker’s amplicon size and DNA degradation
Since the primer set producing the larger amplicon (MarVer3, 216bp) was found to perform less efficiently than the other two (see Results), we tested whether the drop of signal between a high-quality DNA sample and a degraded DNA sample (as eDNA) was the same for all three loci (whose sizes are multiple of ca 70bp) regardless the dimension of the fragment they amplify. This was possible thanks to the availability of two exceptional samples in our data set: 1) a high molecular weight DNA sample, such as MmoT01, freshly extracted from a tissue collected in the immediate post-mortem and 2) the best possible eDNA sample, such as MmoM+01, collected in a site at high monk seal eDNA concentration. This sample was collected in a site characterized by two peculiar conditions: a) proximity to a cave contextually inhabited by many seals and b) limited mixing with surrounding waters (thus little signal dispersal) due to a counter-current flux pushing the water against the opening of the cave (see Discussion). All three loci produced a strong signal in both samples and all replicas thus allowing to test for correlation between amplicon size and DNA quality. We applied a Kruskal-Wallis test, as not requiring data being normally distributed and having similar levels of variance.