DNA barcoding is currently unreliable for species identification in Crayfish

DNA barcoding is commonly used for species identification. Despite this,
there has not been a comprehensive assessment of the utility of DNA
barcoding in crayfishes (Decapoda: Astacidea). Here we examined the extent
to which local barcoding gaps (used for species identification) and global
barcoding gaps (used for species discovery) exist among crayfishes, and
whether global gaps, if present, met a previously suggested 10 ×
threshold. Using publicly available mitochondrial COI sequence data from
the National Center for Biotechnology Information’s nucleotide database,
we created two versions of the COI datasets used for downstream analyses:
one focused on the number of unique haplotypes (NH) per species, and
another that focused on total number of sequences (NS; i.e., including
redundant haplotypes) per species. Ultimately, a total of 81 species were
included, with 58 species and five genera from family Cambaridae and 23
species from three genera from family Parastacidae. We found that local
barcoding gaps were present in only 30 species (20 members of Cambaridae
and 10 Parastacidae). Global barcoding gaps were detected in only four
genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), and they were
all well below the previously suggested 10× threshold. We propose that a
~5x threshold could act as a more appropriate working hypothesis for
species discovery. While the NH and NS datasets yielded largely similar
results, there were some discrepant inferences. Currently, the utility of
DNA barcoding for species identification and discovery in crayfish is
quite limited, and caution should be exercised when molecular approaches
are used in place of taxonomic expertise. Assessment of the evidence for
local and global barcoding gaps is important for understanding the
reliability of molecular species identification and discovery, but
outcomes are dependent on the current state of taxonomy. As this improves
(e.g., via resolving species complexes, possibly elevating some subspecies
to the species-level status, and redressing specimen misidentifications in
natural history and other collections), so too will the utility of DNA
barcoding.