Phylogenomic analysis of Cervidae provides insights into antler origin and evolution

Antlers represent the only known example of complete annual organ regeneration in mammals. Despite this unique regenerative capacity, the genetic mechanisms driving antler origin and morphological diversification across Cervidae remain poorly understood. This study assembled six high-quality chromosome-level genomes of cervids spanning four distinct tribes, including the first genomic reference for the tufted deer ( Elaphodus cephalophus). Comparative analyses across the Cervidae lineage identified signatures of positive selection on gene networks governing stem cell differentiation and bone metabolism, with elevated expression of these genes detected in antler developmental and regenerative tissues. Tribe-specific selective pressures in Cervini and Odocoileini further revealed convergent evolution targeting core developmental pathways, notably the RAS/MAPK pathway, implicating these pathways in both the emergence and enhancement of antler traits. In contrast, relaxed selective constraints in the antlerless Chinese water deer ( Hydropotes inermis) revealed disruptions in gene modules associated with tumor suppression and skeletal homeostasis, suggesting a rewiring of regulatory homeostasis. These findings highlight how antler evolution reshaped physiological trade-offs, including reduced oncogenic susceptibility and enhanced tissue regeneration and cyclic bone remodeling. This study advances current understanding of antler evolution and diversification, while providing genomic resources for mammalian regenerative biology.