Tests of Evolutionary Mechanisms for the Maintenance and Origin of Chromosomal Rearrangements in Drosophila pseudoobscura. Gwilym D. Haynes^1*, Zachary L. Fuller¹, Ian S. Leopold¹, Atousa Janshahil¹, Shannon Duggan², Dianhuiz Zhu^2,3, Stephen Richards², Stephen W. Schaeffer¹. 1) Biology, The Pennsylvania State University, University Park, PA; 2) Human Genome Sequencing Center, Baylor College of Medicine, One Baylor Plaza, Houston TX 77030; 3) Chevron, 1500 Louisiana St, Houston, Texas, 77002.

   Drosophila pseudoobscura has over 30 different gene arrangements on the third chromosome that were generated by a series of overlapping inversions. Four classes of hypotheses can be used to explain how inversions are established in populations including direct effects of the mutation, indirect effects of recombination suppression, selective sweeps of an adaptive mutation, and genetic drift. Next generation sequences of 50 isochromosomal strains for seven inversion types within D. pseudoobscura were used to test these hypotheses about the origin and maintenance of the third chromosome gene arrangements. The third chromosome is segregating for over 1.3 million SNPs. SNP phylogenies from segments across the chromosome are consistent with the cytological phylogeny except for the central region, which departs from the accepted cytological phylogeny because two arrangements clustered with unexpected chromosomes, despite monophyly of the arrangements. Nucleotide and amino acid polymorphism for the 2831 annotated genes on the third chromosome found that 2662 genes had segregating amino acid variation. Premature stop codons or reading frame extending mutations were found to be segregating in 240 genes. Significant linkage disequilibrium of amino acid variation with chromosomal arrangement was found in 89 to 475 genes with amino acid LD being distributed across the chromosome. These results suggest that indirect effects of recombination suppression is the likely mechanism for the establishment and maintenance of the chromosomal polymorphism in D. pseudoobscura. We are testing genes in LD for evidence of positive selection with analyses of synonymous and nonsynonymous variation and of extended homozygosity.