Rapid evolution and differential expression of transcripts associated with sex chromosome meiotic drive in stalk-eyed flies. Josephine A. Reinhardt¹, Richard H. Baker², Gerald S. Wilkinson¹. 1) Biology, University of Maryland College Park, College Park, MD; 2) Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY.

   Sex chromosome meiotic drive causes a distortion of population sex ratios in many dipterans. In the stalk-eyed fly, Teleopsis dalmanni, males carrying the meiotic drive X chromosome parent almost exclusively daughters. The drive haplotype (X^D) is present at a high frequency in natural populations covering a wide geographic, genetic, and temporal distance. The X^D haplotype associates with a large portion of the X chromosome (which is novel in T. dalmanni relative to other dipterans) and is thought to be maintained by a chromosomal rearrangement suppressing recombination with standard X chromosomes. In addition, the drive haplotype is known to cause a variety of pleiotropic effects in males. To understand how drive may be operating genetically, we obtained Illumina transcriptomes from T. dalmanni testes that carried the meiotic drive haplotype (X^D) and standard X chromosomes (X^ST). We identified hundreds of transcripts that were differentially expressed between X^D and X^ST testes. When compared with other transcripts, genes that were differentially expressed in X^D testes were more likely to be X-linked and to show testes-biased expression. The majority of these genes - particularly those that were the most strongly differentiated - had no orthologs in diptera and had low protein-coding potential. These results imply that drive-associated differences in gene expression occur on the novel X chromosome and may be driven by rapid evolution of genes, including putative noncoding RNA genes. Finally, we found that hundreds of X-linked transcripts carry fixed differences between X^D and X^ST samples while only a handful of such differences were found in autosomal genes. This supports the hypothesis that the X^D haplotype long ago ceased recombination with X^ST, revealing a genomic mechanism for the maintenance of the drive phenotype.