Whole genome expression profiling identifies speciation genes in Drosophila. K.L. Harmon ¹, S.V. Nuzhdin ¹, L. McIntyre ², M.L. Wayne ³. 1) Evolution & Ecology, Univ California, Davis, CA; 2) Computational Genomics, Purdue University, West Lafayette, IN 47905; 3) Department of Zoology, University of Florida, Gainesville, FL 32611-8525.

   The sequence divergence between species scaled by variation within species, has been a source of inferences on selection acting on genes. The genes with disproportionally small divergence are under selection preserving sequences unchanged, but the genes diverging fast are under selection for sequence changes. Similar logic should be applicable to gene expression - if RNA levels are strongly divergent between species, while genetic variation within species is not, the expression level was the target of divergent selection. We compared whole genome RNA levels in ten Drosophila simulans lines - each F1 heterozygote from a cross of stocks isogenized by 30 generations of full-sib mating; and in D. melanogaster. Three replicated measurements per genotype were made using Affymetrix whole genome arrays. We have found abundant variation in the rate of expression evolution, and identified genes whose expression have evolved the fastest when scaled by within species variation. Among them, there were Acp26Aa and Acp63f - genes sequences of which have been known to evolve fast, as well as genes of function unknown [CG15306, CG9975, CG7045, and CG4716]. To test whether divergent selection affects both coding sequences and expression level, we have correlated those. We also compared the rates of expression divergence between genes with different degrees of sequence similarity, and by gene functions.