Coalescent Effective Size
According to the neutral theory of molecular evolution, a neutral allele remains in a population for Ne generations, where Ne is the effective population size. An idealised diploid population with have a pairwise nucleotide diversity equal to 4Ne, where is the mutation rate. The sojourn effective population size can therefore be estimated empirically by dividing the nucleotide diversity by the mutation rate.
The coalescent effective size may have little relationship to the number of individuals physically present in a population. Measured coalescent effective population sizes vary between genes in the same population, being low in genome areas of low recombination and high in genome areas of high recombination. Sojourn times are proportional to N in neutral theory, but for alleles under selection, sojourn times are proportional to log(N). Genetic hitchhiking can cause neutral mutations to have sojourn times proportional to log(N): this may explain the relationship between measured effective population size and the local recombination rate.
Read more about this topic: Effective Population Size
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