The craniofacial shape of modern humans embodies genomic signatures of evolution, diversity, and clinical conditions

Human craniofacial morphology is a hallmark of our species' diversity and evolutionary history, shaped by adaptation, introgression, and global dispersal. Cranial globularization and chin emergence are well-documented morphological transformations whose genetic basis remains poorly understood, whereas Neandertal introgression is primarily documented through genomic evidence. How these evolutionary phenomena relate to craniofacial variation in present-day humans remains largely unresolved. Here, we leverage 3D craniofacial data from over 50,000 UK Biobank participants and employ a multivariate, multiscale genome-wide association approach to define axes of variation aligned with interpopulation allele frequency shifts, evolutionary processes, and clinical conditions. We identify continuous craniofacial trends within our cohort that mirror global patterns of genetic diversity, indicating that facial differences between human populations arise at the phenotypic axes already present within a single population. We further demonstrate that modern human-derived alleles underlie the origins of the human chin by reducing midfacial projection relative to other hominins and reveal the persistent effects of Neandertal introgression on craniofacial diversity today. We also model genetically informed endophenotypes for orofacial clefts, obstructive sleep apnoea, and myopia. These findings provide insights into our species' evolutionary history and endophenotypes of clinical conditions and establish a framework for contextualizing craniofacial diversity into biologically meaningful axes of variation relevant to diverse scientific disciplines.

Authors

Institutions

Publication Details

Journal
bioRxiv (Cold Spring Harbor Laboratory)
Published
2025-12-31
DOI
https://doi.org/10.64898/2025.12.29.696848
Primary Topic
Forensic Anthropology and Bioarchaeology Studies
Type
article
Field-Weighted Citation Impact
0.00

Funders

Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

The craniofacial shape of modern humans embodies genomic signatures of evolution, diversity, and clinical conditions

Jaaved Mohammed, Ullrich Bartsch, A Mounier, Joanna Wysocka et al.
bioRxiv (Cold Spring Harbor Laboratory)
Forensic Anthropology and Bioarchaeology Studies
article

The craniofacial shape of modern humans embodies genomic signatures of evolution, diversity, and clinical conditions

Jaaved Mohammed, Ullrich Bartsch, A Mounier, Joanna Wysocka, Jay Devine, Stephen Richmond, Seppe Goovaerts, John R. Shaffer, Hannah K. Long, Sameer Gabbita, Sarah Jayne Lewis, Mark D. Shriver, T. Sofer, Noah Herrick, Susan Walsh, Toomas Kivisild, P. G. CLAES, Sahin Naqvi, Nina Claessens, Benedikt Hallgrimsson, Kaat Pauwels, Sarah Baumeister, Seth M. Weinberg, Jolien Deprest
article en

Abstract

Human craniofacial morphology is a hallmark of our species' diversity and evolutionary history, shaped by adaptation, introgression, and global dispersal. Cranial globularization and chin emergence are well-documented morphological transformations whose genetic basis remains poorly understood, whereas Neandertal introgression is primarily documented through genomic evidence. How these evolutionary phenomena relate to craniofacial variation in present-day humans remains largely unresolved. Here, we leverage 3D craniofacial data from over 50,000 UK Biobank participants and employ a multivariate, multiscale genome-wide association approach to define axes of variation aligned with interpopulation allele frequency shifts, evolutionary processes, and clinical conditions. We identify continuous craniofacial trends within our cohort that mirror global patterns of genetic diversity, indicating that facial differences between human populations arise at the phenotypic axes already present within a single population. We further demonstrate that modern human-derived alleles underlie the origins of the human chin by reducing midfacial projection relative to other hominins and reveal the persistent effects of Neandertal introgression on craniofacial diversity today. We also model genetically informed endophenotypes for orofacial clefts, obstructive sleep apnoea, and myopia. These findings provide insights into our species' evolutionary history and endophenotypes of clinical conditions and establish a framework for contextualizing craniofacial diversity into biologically meaningful axes of variation relevant to diverse scientific disciplines.

bioRxiv (Cold Spring Harbor Laboratory)
University of North Carolina at Chapel Hill (US), Boston Children's Hospital (US), Pennsylvania State University (US), Howard Hughes Medical Institute (US), Harvard University (US), University of Pittsburgh (US), Alberta Children's Hospital (CA), University of Surrey (GB), University of Bristol (GB), University of Oxford (GB), Histoire Naturelle des Humanités Préhistoriques (FR), UK Dementia Research Institute (GB), Murdoch Children's Research Institute (AU), Institute of Genetics and Cancer (GB), Musée de l'Homme (FR), Indiana University Indianapolis (US), Indiana University – Purdue University Indianapolis (US), Cardiff University (GB), Stanford University (US), University of Edinburgh (GB), KU Leuven (BE)
Vlaams Supercomputer Centrum, Fonds Wetenschappelijk Onderzoek, KU Leuven, Vlaamse regering, Canadian Institutes of Health Research
Openalex Percentile: Top 21%
Forensic Anthropology and Bioarchaeology Studies
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.