Neanderthal-derived variants increase <i>SOX9</i> enhancer activity in craniofacial progenitors that shape jaw development
Bibliographic record
Abstract
Human facial appearance is a highly variable morphological trait, with both rare and common genetic variants shaping craniofacial morphology between individuals and in disease. Deletions encompassing an enhancer cluster 1.45 megabases upstream of SOX9 (EC1.45) cause Pierre Robin sequence, a craniofacial disorder characterised by underdevelopment of the lower jaw and associated with cleft palate. We hypothesised therefore that single nucleotide variants within EC1.45 may cause more subtle alterations in facial form. Leveraging recent human evolution, and the distinct jaw morphology of Neanderthals, we investigated the impact of three Neanderthal-derived variants on EC1.45 function. Using zebrafish dual enhancer-reporters, we observed higher activity of Neanderthal EC1.45 in neural crest-derived progenitor cells during a specific developmental window. These EC1.45-active cells reside proximal to and are transcriptionally related to precartilaginous condensations that contribute to craniofacial skeletal development. Mimicking the observed increase in enhancer activity, we overexpressed human SOX9 in EC1.45-active cells and detected an expanded volume of developing cartilaginous precursors. Our work implicates Neanderthal-derived variants in increasing regulatory activity for a disease-associated enhancer, with the potential to impact craniofacial morphology across recent hominin evolution.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 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) | 0.000 | 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 teacher head, 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".