Liver zonation—the spatial compartmentalization of hepatocyte functions along the lobule—originated in the mammalian ancestor approximately 180-320 million years ago through the emergence of WNT and R-spondin signaling from central vein endothelial cells that activate TCF7L2-mediated central gene expression, yet despite this conserved architecture and signaling mechanism, zonated genes exhibit rapid evolutionary turnover driven by reduced functional constraints in hepatocytes, enabling adaptive metabolic innovations including human-specific shifts in lipid metabolism.

The liver is a central organ with essential roles in processes such as nutritional metabolism, detoxification, and immune defense. It has been instrumental in the adaptation of mammalian species to diverse environments, as reflected by its rapid molecular evolution. However, the origins and evolutionary dynamics of liver cell types and their structural organization remain largely unexplored. Here we report evolutionary analyses of transcriptome and chromatin accessibility data for liver cells from 17 species, spanning all major feeding strategies (herbivory, omnivory, carnivory, insectivory), great apes (including humans), placental clades (Afrotheria, Xenarthra, Laurasiatheria, Euarchontoglires), major mammalian lineages (placentals, marsupials, monotremes), and a bird as outgroup. Integrated with spatial transcriptomics, our data reveal that liver zonation—the compartmentalization of hepatocyte functions along the lobule, the liver’s fundamental anatomical and functional unit—is conserved across mammals but absent in other vertebrates. We find that zonation originated in the mammalian ancestor, driven by the emergence of WNT and R-spondin signaling from central vein endothelial cells, which activate central hepatocyte gene expression via the transcription factor TCF7L2. Despite this conserved architecture and signaling, genes with zonated expression exhibit rapid evolutionary turnover. Consistently, hepatocytes evolve fast, likely due to reduced selective constraints, enabling adaptive changes under positive selection. Alongside immune cells, hepatocytes are therefore key drivers of the liver’s rapid evolution and functional innovations. In great apes, we identify human-specific shifts in zonation and cell-type-specific expression linked to recent cis-regulatory changes, particularly in genes involved in lipid metabolism, likely contributing to human-specific metabolic traits. Our study uncovers the origins of a mammal-specific liver cell architecture, within which reduced constraints facilitated molecular changes underlying ecological adaptations.