Transcriptome sequencing reveals the evolutionary histories and gene expression evolution in two related Pagurus species
Bibliographic record
Abstract
Pagurus lanuginosus (De Haan, 1833-1850) and Pagurus maculosus (Komai and Imafuku, 1996) are two closely related species of the genus Pagurus, generally referred to as "right-handed hermit crabs". Previously thought to be color morphs of the same species, recent studies have itemized their unique features. To investigate the molecular and gene expression evolution that have followed the divergence of these two species, we performed transcriptome sequencing and de novo transcriptome assembly using cephalothorax (head) and pereopod (leg) of the two species. Synonymous and nonsynonymous divergence between the two species was estimated to be 0.0246 and 0.0066, respectively. About 5% of the protein-coding transcripts had signatures of positive selection. The phylogenetic analyses showed that the two species are indeed closely related and diverged about 6.24 million years ago. Comparison of tissue expression showed that head expressions were more conserved, and that more genes were upregulated in the legs of P. maculosus leg; while more pigmentation genes were found to be upregulated in the legs of P. lanuginosus. Genes associated with the extracellular matrix and space, chitin binding and chitin-based larval cuticles were found to have higher expression in the legs of P. maculosus, suggesting the roles in morphological differences. This study sheds light on the evolutionary history of the two species at the molecular level.
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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 | 0.000 |
| 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".