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 l..., We searched the NCBI nucleotide database for crayfish COI sequences using the following search terms and Boolean operators: “genus name\" AND “cytochrome” OR “COI” OR “COX1”. All searches were conducted, and sequences downloaded, between March and December 2022. We aligned sequences from each genus separately using MUSCLE (Edgar, 2004), implemented in MEGA v.7.026 (Kumar, Stecher, & Tamura, 2016)., , # Mitochondrial DNA (COI gene) sequences downloaded from NCBI's nucloetide database, aligned, trimmed, and analyzed by Allison et al.

One folder contains seqeunce alignments for crayfish genera that were used for analyses focused on the numbner of unique haplotypes (ie., the NH Datasets), and other other folder contains sequence alignments for crayfish genera that were used for analyses focused on the numbner sequences (i.e., the NS Datasets). All sequence alignments are in FASTA (.fas) file format.

Folder: NH_Dataset
This contains COI sequence alignments for each of seven genera. Haplotype names are arbitrary.

-Cambarus_NH.fas: This alignment is 654-bp long and contains 266 unique haplotypes for members of the genus Cambarus.
-Cherax_NH.fas: This alignment is 594-bp long and contains 208 unique haplotypes for the genus Cherax.
-Creaserinus_NH.fas: This alignment is 579-bp long and contains 105 unique haplotypes for the genus Creaserinus.
-Euastacus_NH.fas: This alignment is 654-bp l...