Data from: Environmental DNA surveillance for invertebrate species: advantages and technical limitations to detect invasive crayfish Procambarus clarkii in freshwater ponds

The introduction of non-native species is a major threat to
biodiversity. While eradication programs of well-established invaders
are costly and hazardous for non-target species, the early detection
of a non-native species at low density is critical for preventing
biological invasions in recipient ecosystems. Recent studies reveal
that environmental DNA (eDNA) is a powerful tool for detecting target
species in aquatic ecosystems, but these studies focus mostly on fish
and amphibians. We examine the reliability of using eDNA to detect the presence of an
invasive freshwater crustacean species, the red swamp crayfish
Procambarus clarkii. Species-specific primers and probes were
designed; their specificity was tested using in silico PCR simulations
and against tissues of other crayfish species. Limits of detection and
quantification were specified for the target DNA sequence by means of
quantitative PCR amplifications on dilution series of known amount of
P. clarkii DNA. The method was applied to water samples collected in 158 ponds in a
French Nature Park, and results were compared to a traditional method
using food-baited funnel traps. Environmental DNA had a better
detection efficiency but predominantly led to divergent results
compared with the trapping method. While habitat features partly
explained the failure of crayfish detection by trapping, detection by
eDNA was problematic at low crayfish abundances. When P. clarkii was
detected, the estimated concentrations of crayfish DNA in water
samples were always below the limit of quantification for the target
DNA sequence. Synthesis and applications. The combination of environmental DNA
(eDNA) and conventional trapping methods is recommended to monitor the
invasion by P. clarkii in small water-bodies such as ponds. However,
the risk of mortality for non-target species, notably amphibians, has
to be carefully evaluated before large-scale deployment of traps.
Contrary to fish and amphibians, a low amount of extracellular DNA in
water is suspected to be the major limitation for crayfish detection
by molecular approaches. Current advancements in PCR technology,
together with optimization of the water sampling method, promise
upcoming developments of eDNA detection for aquatic invertebrate
species.