Genetics, Vol. 156, 257-268, September 2000, Copyright © 2000

A Genome-Wide Departure From the Standard Neutral Model in Natural Populations of Drosophila

Peter Andolfattoa and Molly Przeworskib
a Institute for Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
b Committee on Evolutionary Biology, University of Chicago, Chicago, Illinois 60637

Corresponding author: Molly Przeworski, Statistics Department, University of Oxford, 1 South Parks Rd., Oxford OX1 3TG, United Kingdom., molly{at}stats.ox.ac.uk (E-mail)

Communicating editor: A. G. CLARK

We analyze nucleotide polymorphism data for a large number of loci in areas of normal to high recombination in Drosophila melanogaster and D. simulans (24 and 16 loci, respectively). We find a genome-wide, systematic departure from the neutral expectation for a panmictic population at equilibrium in natural populations of both species. The distribution of sequence-based estimates of 2Nc across loci is inconsistent with the assumptions of the standard neutral theory, given the observed levels of nucleotide diversity and accepted values for recombination and mutation rates. Under these assumptions, most estimates of 2Nc are severalfold too low; in other words, both species exhibit greater intralocus linkage disequilibrium than expected. Variation in recombination or mutation rates is not sufficient to account for the excess of linkage disequilibrium. While an equilibrium island model does not seem to account for the data, more complicated forms of population structure may. A proper test of alternative demographic models will require loci to be sampled in a more consistent fashion.




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