DNA barcodes reveal cryptic genetic diversity within the blackfly subgenus Trichodagmia Enderlein (Diptera: Simuliidae: Simulium) and related taxa in the New World
Bibliographic record
Abstract
In this paper we investigate the utility of the COI DNA barcoding region for species identification and for revealing hidden diversity within the subgenus Trichodagmia and related taxa in the New World. In total, 24 morphospecies within the current expanded taxonomic concept of Trichodagmia were analyzed. Three species in the subgenus Aspathia and 10 species in the subgenus Simulium s.str. were also included in the analysis because of their putative phylogenetic relationship with Trichodagmia. In the Neighbour Joining analysis tree (NJ) derived from the DNA barcodes most of the specimens grouped together according to species or species groups as recognized by other morphotaxonomic studies. The interspecific genetic divergence averaged 11.2% (range 2.8–19.5%), whereas intraspecific genetic divergence within morphologically distinct species averaged 0.5% (range 0–1.2%). Higher values of genetic divergence (3.2–3.7%) in species complexes suggest the presence of cryptic diversity. The existence of well defined groups within S. piperi, S. duodenicornium, S. canadense and S. rostratum indicate the possible presence of cryptic species within these taxa. Also, the suspected presence of a sibling species in S. tarsatum and S. paynei is supported. DNA barcodes also showed that specimens from species that were taxonomically difficult to delimit such as S. hippovorum, S. rubrithorax, S. paynei, and other related taxa (S. solarii), grouped together in the NJ analysis, confirming the validity of their species status. The recovery of partial barcodes from specimens in collections was time consuming and PCR success was low from specimens more than 10 years old. However, when a sequence was obtained, it provided good resolution for species identification. Larvae preserved in ‘weak’ Carnoy’s solution (9:1 ethanol:acetic acid) provided full DNA barcodes. Adding legs directly to the PCR mix from recently collected and preserved adults was an inexpensive, fast methodology to obtain full barcodes. In summary, DNA barcoding combined with a sound morphotaxonomic framework provides an effective approach for the delineation of species and for the discovery of hidden diversity in the subgenus Trichodagmia.
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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 | 0.000 |
| 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) | 0.001 | 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".