Luikart, Gordon, Jean-Marie Cornuet, and Fred W. Allendorf. 1999. Temporal changes in allele frequencies provide estimates of population bottleneck size. Conservation Biology 13: p.523-30.

(Amy Pedersen)


The authors utilized the temporal method to estimate Ne (effective population size). They then examined the biases associated with this method, as well as the causes of these biases, and attempted to correct for these biases.

Some basic assumptions were made before evaluations were made using Monte Carlo computer simulations: the examined loci were selectively neutral, new mutations were not incorporated (because any effect of mutations was considered negligible due to the small population size and brevity of the study), and to acquire a suitable sample size (30 individuals or 60 gametes), it was assumed that 30 offspring would result from four individuals (Ne=4).

The authors analyzed the results of the Monte Carlo simulations and determined the biases. They found that bias (specifically overestimation of Ne) increased with the severity of the bottleneck, i.e. smaller Ne yielded greater overestimation. However, when Ne=4 (a severe bottleneck), bias did not get "large enough to cause bottlenecks to go undetected". Bias was found to be negligible for larger estimates of Ne unless the bottleneck lasted for more than five generations.

It was uncovered that three factors brought about bias, namely the loss of variation (alleles), "the assumption that the increase in variance in allele frequencies with time is additive (instead of multiplicative), and the assumption that selfing can occur when it cannot".

The authors found that the precision and power of the temporal method could be altered when different parameters of the simulation were changed. They discovered that the main limitation of the temporal method was that the upper confidence limits were often too high when estimating Ne. However, suggestions (below) were made to remedy this situation.

The authors made some recommendations to help alleviate the overestimation of Ne. They derived a new equation for estimating Ne which assumed that selfing did not occur and the increase in variance in allele frequencies was additive. This equation significantly reduced the overestimation of Ne. A suggestion that corrected for the overestimation of Ne caused by loss of alleles was to only monitor alleles that were found to be above a certain frequency. This minimized the possibility that the studied alleles would be lost in the first few generations of a bottleneck. They also suggested frequent sampling (one-generation sampling interval) and increasing the number of individuals or alleles sampled to increase precision of the estimation of Ne. Other suggestions included development of the temporal method into a "more formal statistical test" and further study of statistical analysis including bootstrapping.