PROJECT SUMMARY Sex-bias exists in the human genome in DNA content and gene expression. The human X and Y chromosomes are useful tools for inferring human demography, and crucial for our understanding of human health. However, despite the genomics era, X and Y chromosomes are still vastly underutilized, especially in a genome-wide context. Most established genomics methods and analyses fail to explicitly incorporate sex chromosomes, missing more than 5% of typical genomic variation, and ignoring regions known to contribute to disease. The study of sex chromosome evolution therefore addresses deficits in conventional approaches with critical implications for human health and biology. My research has focused on the integration of these chromosomes to build comprehensive analyses of human history and utilizing an evolutionary approach to characterize sex-bias in gene expression. This project will utilize multiple approaches for studying sex chromosome variation across human and non-human species. First, we will focus on development and extensive testing of novel methodology for accurately accounting for technical variation that affects alignment and variant calling on the sex chromosomes. Current alignment pipelines do not account for the shared homology between the X and Y chromosome, resulting in mis-mapping of reads between the sex chromosomes and reduced power for variant calling. We will incorporate sex chromosome biology to improve alignment and variant calling on the sex chromosomes. Second, we will study the evolution of sex chromosomes and X-inactivation in non-human animals, focused on our close evolutionary relative, the rhesus macaque. Third, we will study gene expression variation (with an emphasis on X-linked gene expression and X-inactivation) between the sexes, and between human populations in the human placenta. The placenta is the one organ routinely expelled from the body that also provides a crucial interface during development, and is not studied in current large-scale tissue expression projects. In collaboration with a long-term pregnancy outcome study we will generate and comprehensively analyze population-specific sex-bias in the human placenta. Fourth, we will study truly genome-wide patterns of variation (autosomes, X chromosome, Y chromosome, and mtDNA) in African populations. Populations in Africa are the most diverse in the world, and representation of that diversity is conspicuously absent from global population studies. In collaboration with anthropologists, who are studying, cultural variation, we will use patterns of variation across the sex chromosomes and autosomes to infer recent and ancient demography, informed by sex-biased migration and demography. Finally, we will contribute novel training materials for instructors and study student learning and self-efficacy as they learn genomics research skills. This work will improve methodology for studying sex-linked variation, provide estimates of sex-biased human demog...