I am a bit confused and would be grateful for some advice. I know that the effective population size can be calculated using the following relation (for diploid organisms, under neutrality): Ne = pi / (4 * mu)
By copying the work of someone else, I mistakenly used Ne = 4 * (pi / mu) This, however, resulted in much more realistic estimates, despite being larger by a factor of 16. Estimates obtained from the first equation do not make sense, especially when compared to the results of another estimation method of Ne (extended Bayesian skyline plots), which are very close to the estimates obtained from the second equation. Because I only found the first equation in published work, am I (and my colleague) wrong to use the second equation, or is the latter one indeed valid?