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Abstract

Gene expression programs are central to the emergence of phenotypic diversity across species, shaping how cells acquire their identities and functions during development and evolution. In this thesis, I explore two complementary dimensions of how such programs evolve in mammals: (i) the developmental establishment and evolutionary dynamics of sex differences across organs, and (ii) the origin and molecular evolution of the liver’s spatial cell architecture. In the first part, I used comparative transcriptomic datasets from males and females spanning developmental time series of five major organs (brain, cerebellum, heart, kidney, and liver) in five mammals and one bird. Through this analysis, I showed that sex-biased gene expression is widespread but highly variable across organs and species, and often restricted to specific cell types. Its onset is not gradual but occurs abruptly around sexual maturity, coinciding with the increase of circulating sex hormones. While the identity of sex-biased genes evolves rapidly and the underlying mechanisms differ between organs, the cell types that exhibit sexual dimorphism are deeply conserved, indicating that molecular programs evolve fast, but the cellular framework they act within changes slowly. In the second part, I investigated the evolutionary origins and dynamics of liver cell organization using single-nucleus transcriptome and chromatin accessibility data from 17 species—16 mammals and one bird—complemented with spatial transcriptomics data. This analysis demonstrated that liver zonation, the compartmentalization of hepatocyte functions along the porto-central axis, is a mammalian innovation absent in birds and fish. Zonation is 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. Once established, this architecture has been remarkably conserved across mammals for ~180 million years. Yet, beneath this conserved architecture, the genes showing zonation patterns show a fast turnover, reflecting fast molecular evolution operating within a slow-evolving structural framework. Overall, this work advances our understanding of the principles that govern gene expression evolution in mammals, showing that although expression programs can change rapidly, functional outcomes evolve more slowly, constrained by developmental, physiological, and ecological demands.