Identification of three new Alu Yb subfamilies by source tracking of recently integrated Alu Yb elements
Bibliographic record
Abstract
BACKGROUND: Alu elements are the most abundant mobile elements in the human genome, with over 1 million copies and constituting more than 10% of the genome. The majority of these Alu elements were inserted into the primate genome 35 to 60 million years ago, but certain subfamilies of Alu elements are relatively very new and suspected to be still evolving. We attempted to trace the source/master copies of all human-specific members of the Alu Yb lineage using a computational approach by clustering similar Yb elements and constructing an evolutionary relation among the members of a cluster. RESULTS: We discovered that one copy of Yb8 at 10p14 is the source of several active Yb8 copies, which retrotransposed to generate 712 copies or 54% of all human-specific Yb8 elements. We detected eight other Yb8 elements that had generated ten or more copies, potentially acting as 'stealth drivers'. One Yb8 element at 14q32.31 seemed to act as the source copy for all Yb9 elements tested, having producing 13 active Yb9 elements, and subsequently generated a total of 131 full-length copies. We identified and characterized three new subclasses of Yb elements: Yb8a1, Yb10 and Yb11. Their copy numbers in the reference genome are 75, 8 and 16. We analysed personal genome data from the 1000 Genome Project and detected an additional 6 Yb8a1, 3 Yb10 and 15 Yb11 copies outside the reference genome. Our analysis indicates that the Yb8a1 subfamily has a similar age to Yb9 (1.93 million years and 2.15 million years, respectively), while Yb10 and Yb11 evolved only 1.4 and 0.71 million years ago, suggesting a linear evolutionary path from Yb8a1 to Yb10 and then to Yb11. Our preliminary data indicate that members in Yb10 and Yb11 are mostly polymorphic, indicating their young age. CONCLUSIONS: Our findings suggest that the Yb lineage is still evolving with new subfamilies being formed. Due to their very young age and the high rate of being polymorphic, insertions from these young subfamilies are very useful genetic markers for studying human population genetics and migration patterns, and the trend for mobile element insertions in the human 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 | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.001 | 0.001 |
| 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 | 0.001 |
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".