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.