Two's company, three's a crowd: new insights on spruce budworm species boundaries using genotyping‐by‐sequencing in an integrative species assessment (Lepidoptera: Tortricidae)
Bibliographic record
Abstract
Abstract Species delimitation requires an assessment of varied traits that can contribute to reproductive isolation, as well as of the permanence of evolutionary differentiation among closely related lineages. Integrative taxonomy, including the combination of genome‐wide molecular data with ecological data, offers an effective approach to this issue. We use genotyping‐by‐sequencing together with a review of ecological divergence to assess the traditionally recognized species status of three closely related members of the spruce budworm species complex, Choristoneura fumiferana (Clemens), C. occidentalis Freeman (= C. freemani Razowski) and C. biennis Freeman, each of which is a major defoliator of conifer forests. We sampled a broad region of overlap between these three taxa in Alberta and British Columbia (Canada) where potential for gene flow provides a strong test of the durability of divergence among lineages. A total of 2218 single nucleotide polymorphisms ( SNPs ) were assayed, and patterns of differentiation were evaluated under the biological, ecological, genotypic cluster and phylogenetic species concepts. Choristoneura fumiferana was genetically distinct with substantial barriers to genetic exchange with C. occidentalis and C. biennis . Conversely, divergence between C. occidentalis and C. biennis was limited to a small subset of outlier loci and was within the range observed within any one of the taxa. Considering both population genetic and ecological patterns of divergence, C. fumiferana should continue to be recognized as a distinct species, and C. biennis ( syn.n. ) should be treated as a subspecies ( C. occidentalis biennis Freeman, 1967) of C. occidentalis, thereby automatically establishing the nominate name C. occidentalis occidentalis Freeman, 1967 for univoltine populations of this species.
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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 | 0.002 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| 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".