Genomic signatures of tooth simplification and tooth-number expansion in cetaceans

Cetaceans display an unusual combination of tooth simplification and frequent tooth-number expansion: baleen whales (Mysticeti) lost functional teeth, whereas many toothed whales (Odontoceti) have evolved elongated, homodont tooth rows. The genomic underpinnings of these divergent trends remain incompletely resolved. We quantified dental complexity using literature-curated orientation patch count (OPC) and found a pronounced decline from archaeocetes to crown taxa, consistent with the abandonment of mastication. Comparative genomics corroborates recurrent pseudogenisation of enamel-matrix genes (notably ODAM) in lineages with reduced enamel, indicating relaxed selective constraint. In contrast, analyses of tooth-number regulators reveal lineage-specific accelerations in EDA/EDAR and Wnt/FGF modulators (e.g. APC, SPRY2). A branch-site test detects episodic positive selection on EDA along the odontocete stem (2 ΔlnL = 9.82, q = 0.006), with three high-confidence sites (Bayes Empirical Bayes (BEB) ≥ 0.95: 287, 301, 315) in the TNF homology domain, consistent with tuning of EDAR signalling. Phylogenetically controlled regressions link tooth number with EDA evolutionary rate. Our results support a two-track macroevolutionary model in whales: 1) relaxed constraint on enamel-matrix genes accompanying tooth simplification, and 2) adaptive tuning of EDA/EDAR and associated pathways contributing to tooth-number expansion.