Sex-specific embryonic gene expression at different stages of sex chromosome evolution. Susan E. Lott^1,4, Jacqueline E. Villalta², Doris Bachtrog³, Michael B. Eisen^1,2,3. 1) Dept. of Molecular and Cell Biology; 2) Howard Hughes Medical Institute; 3) Dept. of Integrative Biology, University of California, Berkeley, CA; 4) Dept. of Evolution and Ecology, University of California, Davis, CA.

   The most significant form of natural genetic variation in many species is the difference in sex chromosome dose between males and females. In Drosophila, females have two X chromosomes, while males have one X and one Y. However, the composition of these sex chromosomes has shifted dramatically in many lineages. Several fusions of sex chromosomes with autosomes have occurred along the lineage leading to D. miranda - the first ~15 MYA, before the divergence of D. miranda from D. pseudoobscura, and the second after the divergence of these species, ~1.5 MYA. The resulting neo-X chromosomes are gradually acquiring the properties of sex chromosomes, becoming targets for molecular mechanisms that compensate for differences in X chromosome dose between sexes. We have recently shown that D. melanogaster possess at least two dosage compensation mechanisms: the well-characterized MSL-mediated dosage compensation active in most somatic tissues, and a second system active during early embryogenesis. To investigate the evolutionary constraints on sex chromosome expression and evolution, we used single embryo mRNA-seq to characterize gene expression in female and male embryos of D. pseudoobscura and D. miranda, across the first eight hours of embryogenesis. We observe imperfect dosage compensation at the onset of zygotic transcription, which improves through developmental time with establishment of MSL-mediated dosage compensation. Surprisingly, the young neo-X chromosome of D. miranda is better compensated than the ancestral X and older neo-X chromosomes, and is better compensated in the embryo than in the adult. This suggests differences in how early zygotic dosage compensation and MSL-mediated dosage compensation evolve, with the former being a more general, less gene-specific mechanism which can evolve over a short period of evolutionary time.