Maximum likelihood estimation of population growth rates based on the coalescent

Abstract

We describe a method for co-estimating 4N(e)μ (four times the product of effective population size and neutral mutation rate) and population growth rate from sequence samples using Metropolis-Hastings sampling. Population growth (or decline) is assumed to be exponential. The estimates of growth rate are biased upwards, especially when 4N(e)μ is low; there is also a slight upwards bias in the estimate of 4N(e)μ itself due to correlation between the parameters. This bias cannot be attributed solely to Metropolis- Hastings sampling but appears to be an inherent property of the estimator and is expected to appear in any approach which estimates growth rate from genealogy structure. Sampling additional unlinked loci is much more effective in reducing the bias than increasing the number or length of sequences from the same locus.