DNA barcoding of Neotropical black flies (Diptera: Simuliidae): Species identification and discovery of cryptic diversity in Mesoamerica
Bibliographic record
Abstract
Although correct taxonomy is paramount for disease control programs and epidemiological studies, morphology-based taxonomy of black flies is extremely difficult. In the present study, the utility of a partial sequence of the COI gene, the DNA barcoding region, for the identification of species of black flies from Mesoamerica was assessed. A total of 32 morphospecies were analyzed, one belonging to the genus Gigantodax and 31 species to the genus Simulium and six of its subgenera (Aspathia, Eusimulium, Notolepria, Psaroniocompsa, Psilopelmia, Trichodagmia). The Neighbour Joining tree (NJ) derived from the DNA barcodes grouped most specimens according to species or species groups recognized by morphotaxonomic studies. Intraspecific sequence divergences within morphologically distinct species ranged from 0.07% to 1.65%, while higher divergences (2.05%-6.13%) in species complexes suggested the presence of cryptic diversity. The existence of well-defined groups within S. callidum (Dyar & Shannon), S. quadrivittatum Loew, and S. samboni Jennings revealed the likely inclusion of cryptic species within these taxa. In addition, the suspected presence of sibling species within S. paynei Vargas and S. tarsatum Macquart was supported. DNA barcodes also showed that specimens of species that are difficult to delimit morphologically such as S. callidum, S. pseudocallidum Díaz Nájera, S. travisi Vargas, Vargas & Ramírez-Pérez, relatives of the species complexes such as S. metallicum Bellardi s.l. (e.g., S. horacioi Okazawa & Onishi, S. jobbinsi Vargas, Martínez Palacios, Díaz Nájera, and S. puigi Vargas, Martínez Palacios & Díaz Nájera), and S. virgatum Coquillett complex (e.g., S. paynei and S. tarsatum) grouped together in the NJ analysis, suggesting they represent valid species. DNA barcoding combined with a sound morphotaxonomic framework provided an effective approach for the identification of medically important black flies species in Mesoamerica and for the discovery of hidden diversity within this group.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".