Targeted Next Generation Sequencing data for European Green Crab

In the northeast Pacific Ocean there is high interest in developing
eDNA-based survey methods to aid management of invasive populations of
European green crab (Carcinus maenas). Expected benefits are improved
sensitivity for early detection of secondary spread and to assess the
outcome of eradication efforts. A new eDNA-based approach we term
‘Targeted Next Generation Sequencing (tNGS)’ is introduced here and shown
to improve detection relative to qPCR at sites with lower green crab CPUE
values measured by trapping. DNA standards (gBlock) with starting molecule
copies that were 10- to 100- times lower than the qPCR limit of detection
returned significant numbers of sequencing reads, which in our field
assessments translated to a 7% - 10% increase in detection probability
from tNGS relative to qPCR at sites with lower CPUE. We also found the
number of sequencing reads from tNGS was significantly correlated with
green crab CPUE whereas Ct values from qPCR were not. When sources of
variation were partitioned for each assay, we found the difference between
mean within-site and mean between-site variation was much larger and had
non-overlapping confidence intervals for tNGS relative to qPCR, suggesting
the former may offer more power for detecting spatial variation in eDNA
availability. Results presented here indicate this approach is suitable
for species of known low abundances where a positive detection has high
economic or environmental consequences. Any species with an existing qPCR
assay can be easily tested with a tNGS assay. We conclude with a
discussion on the fit for purpose applications of tNGS vs. qPCR on how to
best apply molecular surveys in management programs.