Supplementary data for the thesis Reconstructing the Demographic History of the Pacific Nudibranch Genus Hermissenda
Bibliographic record
Abstract
The Pacific nudibranch Hermissenda crassicornis (sensu lato) is a well-known model organism in neuroscience. This species was recently split into three pseudocryptic species based on differences in genetics, morphology, and behaviour. We used ddRADSeq data from 33 individuals (2354 loci) and coalescent isolation-with-migration models to estimate the demographic history of the clade. We inferred (1) a novel phylogenetic tree topology, (2) relatively old divergence times (0.55 and 1.29 mya), (3) a much larger population size in the southern species H. opalescens, and (4) no gene flow between the sympatric species H. crassicornis and H. opalescens. We then used forward simulations to investigate the plausibility of these results. Preliminary simulations suggest the inference approach applied to the Hermissenda data may be incorrectly estimating the older split, an observation needing further study. Overall, our results support the need to reassess previous studies that used H. crassicornis (sensu lato) as a model organism.
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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 | 0.010 |
| Meta-epidemiology (narrow) | 0.002 | 0.001 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.004 | 0.008 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.003 | 0.002 |
| Research integrity | 0.002 | 0.002 |
| Insufficient payload (model declined to judge) | 0.279 | 0.141 |
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".