eLife Assessment: Still waters run deep: Large scale genome rearrangements in the evolution of morphologically conservative Polyplacophora
Bibliographic record
Abstract
The phylum Mollusca is bifurcated into the hyperdiverse Conchifera (Gastropoda, Bivalvia, Cephalopoda, et al.) and the spiny Aculifera (Polyplacophora and Aplacophora). High quality genomic data for the deeply divergent, morphologically constrained chitons, would be expected to offer an opportunity to explore ancient genetic traits and evolutionary mechanisms preserved across the long span of animal evolution. We present a comparative analysis of five reference quality genomes, including four de novo assemblies, covering all major chiton clades: Lepidopleurida (Deshayesiella sirenkoi), Callochitonida (Callochiton septemvalvis) and Chitonida (Acanthochitona discrepans and A. rubrolineata), and an updated phylogeny for the phylum. Comparison with conchiferan genomes recovers 20 ancient molluscan linkage groups (MLGs) that are relatively conserved in bivalve karyotypes, but subject to re-ordering, rearrangement, fusion, and early occurring duplication (or fission) in chitons and conchiferan genomes. Two congeners each have 8 haploid chromosomes, results of two independent fusion events from the karyotype of their most recent common ancestor. The largest number of novel fusions is in the supposedly most plesiomorphic clade Lepidopleurida, and the chitonid Liolophura japonica has a partial genome duplication, extending the known occurrence of large-scale gene duplication within Mollusca. The extreme and dynamic genome rearrangements in this class stands in contrast to most other animals and is not explained by accumulated change since the deep divergence time of this clade. The apparently conservative phenome of chitons is not reflected in a conservative genome.
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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 | 0.006 |
| Meta-epidemiology (narrow) | 0.001 | 0.002 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.003 | 0.003 |
| Science and technology studies | 0.002 | 0.001 |
| Scholarly communication | 0.005 | 0.003 |
| Open science | 0.003 | 0.006 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.093 | 0.037 |
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".