Where Did the Y Chromosome in the Spiny Rat Go, and How Did It Get There?
Bibliographic record
Abstract
The XX/XY sex chromosome system is highly conserved across mammals, with rare exceptions where males lack a Y chromosome. Among these is the genus Tokudaia, a group of spiny rats comprising three species with unique sex chromosome systems deviating from the typical XX/XY pattern. While Tokudaia osimensis and Tokudaia tokunoshimensis have completely lost the Y chromosome, they retain some Y-linked genes on the X chromosome. In contrast, Tokudaia muenninki retains large sex chromosomes where both the X and Y chromosomes have fused with an autosome pair, carrying multi-copied Y-linked genes, including Sry. In this study, we generated chromosome-level genome assemblies for male individuals of all three Tokudaia species. By investigating loci typically associated with rodent Y-linked genes, we characterized sequences derived from the Tokudaia Y-chromosomal most recent common ancestor (Tokudaia Y-MRCA) and traced their evolutionary trajectories. Our analyses revealed that an initial X-to-Y translocation of a sequence containing the boundary-associated segmental duplication in a common ancestor of Tokudaia marked the beginning of their unique sex chromosome evolution. The boundary-associated segmental duplication, uniquely multi-copied in Tokudaia, facilitated further rearrangements through nonallelic homologous recombination and duplications. These processes culminated in subsequent Y-to-X translocations and duplications, leading to the complete loss of the Y chromosome as a distinct entity while preserving Y-linked genes in a multicopy state on the X chromosome. These findings highlight Tokudaia's rapid sex chromosome evolution within 3 million years and provide insights into the mechanisms underlying Y chromosome loss, contributing to a broader understanding of sex chromosome evolution in rodents.
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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 | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.001 | 0.002 |
| Insufficient payload (model declined to judge) | 0.001 | 0.001 |
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".