DNA barcoding is currently unreliable for species identification in most crayfishes
Abstract 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...
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Wiley
2024-07-01
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| Series: | Ecology and Evolution |
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| Online Access: | https://doi.org/10.1002/ece3.70050 |
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| author | Patrick F. Allison Jr Emily T. Pickich Zanethia C. Barnett Ryan C. Garrick |
| author_facet | Patrick F. Allison Jr Emily T. Pickich Zanethia C. Barnett Ryan C. Garrick |
| author_sort | Patrick F. Allison Jr |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-9b53e3c157ef46c8b7e99c23dba2c65c |
| institution | Matheson Library |
| issn | 2045-7758 |
| language | English |
| publishDate | 2024-07-01 |
| publisher | Wiley |
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| series | Ecology and Evolution |
| spelling | doaj-art-9b53e3c157ef46c8b7e99c23dba2c65c2025-07-24T00:21:19ZengWileyEcology and Evolution2045-77582024-07-01147n/an/a10.1002/ece3.70050DNA barcoding is currently unreliable for species identification in most crayfishesPatrick F. Allison Jr0Emily T. Pickich1Zanethia C. Barnett2Ryan C. Garrick3Department of Biology University of Mississippi University Mississippi USADepartment of Biology University of Mississippi University Mississippi USASouthern Research Station USDA Forest Service, Center for Bottomland Hardwoods Research Clemson South Carolina USADepartment of Biology University of Mississippi University Mississippi USAAbstract 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.https://doi.org/10.1002/ece3.70050cryptic speciesdecapodglobal barcoding gaplocal barcoding gapspecies delimitationspecies identification |
| spellingShingle | Patrick F. Allison Jr Emily T. Pickich Zanethia C. Barnett Ryan C. Garrick DNA barcoding is currently unreliable for species identification in most crayfishes Ecology and Evolution cryptic species decapod global barcoding gap local barcoding gap species delimitation species identification |
| title | DNA barcoding is currently unreliable for species identification in most crayfishes |
| title_full | DNA barcoding is currently unreliable for species identification in most crayfishes |
| title_fullStr | DNA barcoding is currently unreliable for species identification in most crayfishes |
| title_full_unstemmed | DNA barcoding is currently unreliable for species identification in most crayfishes |
| title_short | DNA barcoding is currently unreliable for species identification in most crayfishes |
| title_sort | dna barcoding is currently unreliable for species identification in most crayfishes |
| topic | cryptic species decapod global barcoding gap local barcoding gap species delimitation species identification |
| url | https://doi.org/10.1002/ece3.70050 |
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