Effective population size is related to genetic variability and is a basic parameter in many models of population genetics. A number of methods for inferring current and past population sizes from genetic data have been developed since the introduction of coalescent theory in 1982 by JFC Kingman. Joseph Heled and I have recently developed a non-parametric method that extends on the Bayesian Skyline Plot in several ways, including the ability to analyze multiple loci.
We have employed extensive simulations to show the accuracy and limitations of recovery of population dynamics such as bottlenecks and this has enabled us to give an indication of the amount of data required for recovering past population dynamics, including recovering information about evolutionary bottlenecks.
Figure 1 above shows that even 480 sequences sampled from a single locus are unable to accurately reconstruct a complex population history involving two bottlenecks in quick succession. The blue line represents the true population history, whereas the dotted line represents the reconstruction. See how the most recent period of growth is very accurately reconstructed but the population history before the time of the first bottleneck is poorly reconstructed. However notice that the uncertainty in the estimate still mostly encloses the truth.
On the contrary, when the same total number of sequences are sampled from 32 independent loci (16 sequences per locus), the reconstruction becomes much more accurate as can be seen from this second figure.
These results demonstrate the essential role of multi-locus data in recovering complex population dynamics. Multi-locus data from a small number of individuals can precisely recover past bottlenecks in population size which can not be characterized with a single locus. However typical data sets used today are probably too small for obtaining precise estimates of population history and providing information on past bottlenecks.
I will keep you posted when the paper comes out.
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1 Inferring Demographic History Using Multiple Loci [evolgen] - Biology // Mar 3, 2008 at 5:11 am
[...] Skyline Plot, which allows you to infer historical changes in population sizes. On his blog, Drummond describes an extension to the Bayesian Skyline Plot which takes advantage of data from mult…. Here's what they found: These results demonstrate the essential role of multi-locus data in [...]
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