Selection, recombination and demographic history in Drosophila miranda

¹ University of California, San Diego

^* To whom correspondence should be addressed. E-mail: dbachtrog{at}ucsd.edu.

Submitted on June 28, 2006
Revised on August 11, 2006
Accepted on 14 September 2006

	Abstract

Selection, recombination and the demographic history of a species can all have profound effects on genome wide 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 non-coding DNA generally evolves more slowly than synonymous sites, that the distribution of polymorphism frequencies in non- coding DNA is significantly skewed towards rare variants relative to synonymous sites, and that long introns evolve significantly slower than short introns or synonymous sites. These observations suggest that most non-coding 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 non-coding 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 non-equilibrium models of demography and selection.

Key Words: demography, linkage disequilibrium, selection

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