Phenotype shift scores reveal the scale and phylogenetic structure of phenotypic differentiation in primates.

Continuous traits evolve unevenly across phylogenies, producing patterns of phenotypic differentiation shaped by both shared ancestry and lineage-specific change. Identifying exceptionally differentiated species pairs may therefore improve genome-phenome comparisons, but existing approaches rarely rank such contrasts across entire trees. Here we introduce the Phenotype Shift Score (PSS), a phylogenetic comparative framework integrating model-based trait divergence, observed trait range and patristic distance. Applying PSS to 153 continuous primate traits reveals trait-specific distributions of extreme differentiation across evolutionary depth. Body and brain mass show deeper-than-expected extremes under fitted Brownian motion or Ornstein-Uhlenbeck nulls, whereas body-size-adjusted brain mass localizes recent differentiation within cercopithecid lineages, complementing published branchwise reconstructions. PSS-informed groups produce more selective and more strongly enriched comparative-genomic signals than groups based on absolute phenotypic extremes. PSS is implemented in the open-source R package phyloPSS, with pairwise results available through the Primate Genome-Phenome Archive.