Tracing sex in deep time: Archaeological and palaeontological applications of amelogenin-based palaeoproteomics

Biological sex represents a fundamental parameter for reconstructing population structure, life histories, and evolutionary dynamics, yet it remains inaccessible in many archaeological and palaeontological contexts due to fragmentation, ontogeny, and biomolecular degradation. Amelogenin-based enamel proteomics has emerged as a molecular approach capable of extending chromosomal sex estimation beyond many of the temporal and preservation constraints affecting morphological and ancient DNA-based approaches. This review synthesizes the molecular foundations, methodological developments, and analytical frameworks underlying amelogenin-based sex estimation and evaluates its applications across archaeological, zooarchaeological, palaeoanthropological, and palaeontological contexts. We examine how this approach can facilitate the inclusion of otherwise unclassifiable individuals and contribute to demographic, ecological, and evolutionary reconstructions, particularly in fragmentary and deep-time assemblages. We also critically assess its current limitations, including incomplete and asymmetric peptide preservation, lineage-specific genomic variation, dependence on appropriate reference sequences, sampling constraints, and the interpretative boundaries of chromosomal sex inference. Rather than replacing osteological or genomic approaches, enamel proteomics provides a complementary molecular framework whose value extends beyond deep-time contexts and whose integration with other lines of evidence can enhance the study of past populations.