Research article

Selection dramatically reduces effective population size in HIV-1 infection

Yi Liu and John E Mittler

Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, 98195, USA

author email corresponding author email

BMC Evolutionary Biology 2008, 8:133doi:10.1186/1471-2148-8-133

Published:	3 May 2008

Abstract

Background

In HIV-1 evolution, a 100–100,000 fold discrepancy between census size and effective population size (N_e) has been noted. Although it is well known that selection can reduce N_e, high in vivo mutation and recombination rates complicate attempts to quantify the effects of selection on HIV-1 effective size.

Results

We use the inbreeding coefficient and the variance in allele frequency at a linked neutral locus to estimate the reduction in N_e due to selection in the presence of mutation and recombination. With biologically realistic mutation rates, the reduction in N_e due to selection is determined by the strength of selection, i.e., the stronger the selection, the greater the reduction. However, the dependence of N_e on selection can break down if recombination rates are very high (e.g., r ≥ 0.1). With biologically likely recombination rates, our model suggests that recurrent selective sweeps similar to those observed in vivo can reduce within-host HIV-1 effective population sizes by a factor of 300 or more.

Conclusion

Although other factors, such as unequal viral reproduction rates and limited migration between tissue compartments contribute to reductions in N_e, our model suggests that recurrent selection plays a significant role in reducing HIV-1 effective population sizes in vivo.