Y-haplogroup diversity, non-paternity estimates, and Y chromosome mutation rates in Quebec
Bibliographic record
Abstract
The male-specific region of the Y chromosome (MSY) is extensively used to assess relatedness between male individuals. Single-nucleotide polymorphisms in the MSY enable this assessment, as they are mostly identical by descent in individuals due to the MSY’s lack of recombination and slow mutation rate. Specific bi-allelic sets of mutations in the MSY (haplogroups) are also utilized to analyze population diversity and migration events. In addition, when genealogical data is available, markers in the MSY can help confirm genealogical relationships. Conversely, genealogical relationships can help us address questions on the biology of the MSY, specifically mutation rates.In this study, we utilized a large-scale cohort of present-day male individuals from metropolitan areas in Quebec and a deep-rooted genealogy to examine the interplay between the MSY and paternal lineages. We aimed to characterize the haplogroup composition of men in Quebec to uncover patterns of diversity and migration. We sought to estimate the rate of non-paternity events within the genealogy. Finally, leveraging genealogical paternal lineages, we aimed to estimate the MSY point mutation rate and evaluate the effect of paternal age on mutation rates.The top five more common haplogroups in our cohort were R1b1a1 (62.4%), E1b1b1 (6.4%), R1a1a1 (3.13%), J2a1a1 (2.7%) and E1b1a1 (2.58%). The observed haplogroup diversity reflects multiple waves of migration to Quebec dating back to the 17th century. We identified a non-paternity rate of 0.73% per generation, consistent with previous findings in Quebec and other European populations. Finally, in the MSY, we observed a rate of 2.398 × 10−8 mutations per base pair per generation and 6.47 × 10−10 per base pair per year
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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 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.002 | 0.002 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.003 | 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".