Migration drift equilibrium
Mutation drift equilibrium: The equilibrium value of diversity is known as the population mutation parameter (theta).
Recombination drift equilibrium: As a consequence LD can reach an equilibrium value in finite populations. This equilibrium value of LD is determined by the population recombination parameter (rho). This parameter combines information on effective population size and recombination rate (c) using the equation: rho=4Ne*c. The precise relationship between measures of LD and rho is complex, but under certain conditions (r^2=1/1+rho). So that when rho is large, r^2=1/rho.
If we are examining LD over a large genomic region containing many polymorphic markers, it is unclear how best to combination the information from measures LD based on comparisons between individual pairs of markers (i.e., D, |D'| or r^2). Therefore recent attention has focused on estimating rho itself for these kinds of data, as this gives a single measure of LD for the entire region.
Mutation selection equilibrium:
Some deleterious mutational events have sufficiently high mutation rates that within a large population they occur several times within a single generation, and can be considered recurrent mutations.
The rate at which new mutations are generated can be balanced by the eventual elimination of each mutant by selection so that the average number of a given mutation reaches an equilibrium value within the population.
If we consider all deleterious alleles together, a balance between mutation and selection may operate over the genome as a whole, such that at equilibrium each genome contains a certain number of deleterious alleles.
A general rule for diploid loci is that for selection to be operating then the following relationship should hold:
s>1/2Ne
For haploid loci with one quarter the effective population size of diploid loci, the relevant rule is s>2/Ne.
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