Data from: Optimizing detectability of the endangered fan mussel using eDNA and ddPCR

Spatial and temporal monitoring of species threatened with extinction is
of critical importance for conservation and ecosystem management. On the
Mediterranean coast, the fan mussel (Pinna nobilis) is listed as
critically endangered after suffering from a mass mortality event since
2016, leading to 100% mortality in most marine populations. Conventional
monitoring for this macroinvertebrate is done using scuba, which is
challenging in dense meadows or with low visibility. Here we developed an
environmental DNA assay targeting the fan mussel and assessed the
influence of several environmental parameters on the species detectability
in situ. We developed and tested an eDNA molecular marker and collected 48
water samples in two sites at the Thau lagoon (France) with distinct fan
mussel density, depths, and during two seasons (summer and autumn). Our
marker can amplify fan mussel DNA but lacks specificity since it also
amplifies a conspecific species (Pinna rudis). We successfully amplified
fan mussel DNA from in situ samples with 46 positive samples (out of 48)
using ddPCR, although the DNA concentrations measured were low over almost
all samples. Deeper sampling depth slightly increased DNA concentrations,
but no seasonal effect was found. We highlight a putative spawning event
on a single summer day with much higher DNA concentration compared to all
other samples. We present an eDNA molecular assay able to detect the
endangered fan mussel and provide guidelines to optimize the sampling
protocol to maximize detectability. Effective and non-invasive monitoring
tools for endangered species are promising to monitor remaining
populations and have the potential for ecological restoration or habitat
recolonisation following a mass mortality event.