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Originally published as Genetics Published Articles Ahead of Print on October 8, 2006.
Genetics, Vol. 174, 2045-2059, December 2006, Copyright © 2006
doi:10.1534/genetics.106.062760
Selection, Recombination and Demographic History in Drosophila miranda
Doris Bachtrog1 and Peter Andolfatto
Division of Biological Sciences, University of California, San Diego, California 92093
1 Corresponding author: Division of Biological Sciences, University of California, 9500 Gilman Dr., MC 0116, San Diego, CA 92093.
E-mail: dbachtrog{at}ucsd.edu
Selection, recombination, and the demographic history of a species can all have profound effects on genomewide patterns of variability. To assess the impact of these forces in the genome of Drosophila miranda, we examine polymorphism and divergence patterns at 62 loci scattered across the genome. In accordance with recent findings in D. melanogaster, we find that noncoding DNA generally evolves more slowly than synonymous sites, that the distribution of polymorphism frequencies in noncoding DNA is significantly skewed toward rare variants relative to synonymous sites, and that long introns evolve significantly slower than short introns or synonymous sites. These observations suggest that most noncoding DNA is functionally constrained and evolving under purifying selection. However, in contrast to findings in the D. melanogaster species group, we find little evidence of adaptive evolution acting on either coding or noncoding sequences in D. miranda. Levels of linkage disequilibrium (LD) in D. miranda are comparable to those observed in D. melanogaster, but vary considerably among chromosomes. These patterns suggest a significantly lower rate of recombination on autosomes, possibly due to the presence of polymorphic autosomal inversions and/or differences in chromosome sizes. All chromosomes show significant departures from the standard neutral model, including too much heterogeneity in synonymous site polymorphism relative to divergence among loci and a general excess of rare synonymous polymorphisms. These departures from neutral equilibrium expectations are discussed in the context of nonequilibrium models of demography and selection.
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