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Updated: Aug 19, 2026

Precise, High-throughput Analysis of Bacterial Growth
Published on: September 19, 2017
Maximum likelihood estimation of population growth rates based on the coalescent
M K Kuhner1, J Yamato, J Felsenstein
1Department of Genetics, University of Washington, Seattle, Washington 98195, USA. mkkuhner@genetics.washington.edu
Abstract:
We describe a method for co-estimating 4Nemu (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 4Nemu is low; there is also a slight upwards bias in the estimate of 4Nemu 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.
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