1. Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892, USA
2. Center for Evolutionary Functional Genomics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
3. These authors contributed equally to this work.
4. Present address: Department of Biology, University of Pennsylvania, Pennsylvania 19104, USA.

Correspondence to: Yu Zhang^1,3Brian Oliver¹ Correspondence and requests for materials should be addressed to Y.Z. (Email: yuzhang@mail.nih.gov) and B.O. (Email: oliver@helix.nih.gov).

Both genome content and deployment contribute to phenotypic differences between species^{1, 2, 3, 4, 5}. Sex is the most important difference between individuals in a species and has long been posited to be rapidly evolving. Indeed, in the Drosophila genus, traits such as sperm length, genitalia, and gonad size are the most obvious differences between species⁶. Comparative analysis of sex-biased expression should deepen our understanding of the relationship between genome content and deployment during evolution. Using existing^{7, 8} and newly assembled genomes⁹, we designed species-specific microarrays to examine sex-biased expression of orthologues and species-restricted genes in D. melanogaster, D. simulans, D. yakuba, D. ananassae, D. pseudoobscura, D. virilis and D. mojavensis. We show that averaged sex-biased expression changes accumulate monotonically over time within the genus. However, different genes contribute to expression variance within species groups compared to between groups. We observed greater turnover of species-restricted genes with male-biased expression, indicating that gene formation and extinction may play a significant part in species differences. Genes with male-biased expression also show the greatest expression and DNA sequence divergence. This higher divergence and turnover of genes with male-biased expression may be due to high transcription rates in the male germline, greater functional pleiotropy of genes expressed in females, and/or sexual competition.

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