Molecular species delimitation reveals hidden specific diversity within a freshwater burrowing crayfish (Decapoda: Parastacidae) from southern Chile

Amador, Luís; Victoriano, Pedro; D’Elı́a, Guillermo

doi:10.1080/14772000.2020.1865471

Cited by 8 publications

(5 citation statements)

References 84 publications

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“…Nonetheless, DNA barcoding assessments in these families relies on the continued generation of geo‐referenced COI sequence data tied to accessible voucher specimens. This highlights the importance of recent taxonomic updates (e.g., Loughman & Williams, 2021 ; Perkins et al., 2023 ; Thoma et al., 2023 ), investigations into the taxonomic status of crayfishes (e.g., Amador et al., 2021 ; Bláha et al., 2023 ; Hildreth et al., 2023 ), and population genetics studies (e.g., Clay et al., 2020 ; Hurt et al., 2022 ) from the Astacology community.…”

Section: Discussionmentioning

confidence: 94%

“…virilis complex clade 2; Table S3 , Figure S10 ). Notwithstanding the limitations of single locus species delimitation analyses, we suggest that these approaches may nonetheless be a useful initial step in evaluating the taxonomic status of crayfishes (e.g., Amador et al., 2021 ; Larson et al., 2016 ).…”

Section: Discussionmentioning

confidence: 99%

“…Notably, outcomes of our species delimitation analyses indicate that a simple taxonomic change (e.g., naming a new species) will not reconcile the discrepancy, given high numbers of undersplit taxa were classified as Oversplitting is another concern, as species that share one or more COI haplotypes (and thus, lack local barcoding gaps) may actually be a single species (e.g., F. virilis, and F. virilis complex clade 2; Table S3, Figure S10). Notwithstanding the limitations of single locus species delimitation analyses, we suggest that these approaches may nonetheless be a useful initial step in evaluating the taxonomic status of crayfishes (e.g., Amador et al, 2021;Larson et al, 2016).…”

Section: Species Delimitation Analysesmentioning

confidence: 99%

“…Phenotypically unusual specimens have also been identified through DNA barcoding, such as blue‐colored exotic species (Maciaszek et al., 2020 ). Crayfish species descriptions and delimitation analyses have also used COI barcodes (e.g., Amador et al., 2021 ; Perkins et al., 2023 ). Targeted assessments using eDNA for both rare (e.g., Boyd et al., 2020 ; Quebedeaux et al., 2023 ) and invasive (e.g., Dougherty et al., 2016 ; Geerts et al., 2018 ) species have been successful applications of DNA barcoding, and in the context of crayfish, as have metabarcoding studies (e.g., Drake et al., 2023 ; Kataoka et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

“…Phenotypically unusual specimens have also been identified through DNA barcoding, such as blue-colored exotic species (Maciaszek et al, 2020). Crayfish species descriptions and delimitation analyses have also used COI barcodes (e.g., Amador et al, 2021;Perkins et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

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DNA barcoding is currently unreliable for species identification in most crayfishes

Allison,

Pickich,

Barnett

et al. 2024

Ecology and Evolution

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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 met a previously suggested 10× threshold (mean interspecific difference being 10× larger than mean intra specific difference). We examined barcoding gaps 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. A total of 81 species were included, with 58 species and five genera from the family Cambaridae and 23 species from three genera from the family Parastacidae. Local barcoding gaps were present in only 30 species (20 Cambaridae and 10 Parastacidae species). We detected global barcoding gaps in only four genera (Cambarus, Cherax, Euastacus, and Tenuibranchiurus), which were all below (4.2× to 5.2×) the previously suggested 10× threshold. We propose that a ~5× threshold would be a more appropriate working hypothesis for species discovery. While the NH and NS datasets yielded largely similar results, there were some discrepant inferences. To understand why some species lacked a local barcoding gap, we performed species delimitation analyses for each genus using the NH dataset. These results suggest that current taxonomy in crayfishes may be inadequate for the majority of examined species, and that even species with local barcoding gaps present may be in need of taxonomic revisions. Currently, the utility of DNA barcoding for species identification and discovery in crayfish is quite limited, and caution should be exercised when mitochondrial‐based 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.

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