In population genetics, the concept of effective population size N_{e} was introduced by the American geneticist Sewall Wright, who wrote two landmark papers on it (Wright 1931, 1938). He defined it as "the number of breeding individuals in an idealized population that would show the same amount of dispersion of allele frequencies under random genetic drift or the same amount of inbreeding as the population under consideration". It is a basic parameter in many models in population genetics. The effective population size is usually smaller than the absolute population size (N). See also small population size.
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Effective population size may be defined in two ways, variance effective size and inbreeding effective size. These are closely linked, and derived from Fstatistics.
In the WrightFisher idealized population model, the conditional variance of the allele frequency p', given the allele frequency p in the previous generation, is
Let denote the same, typically larger, variance in the actual population under consideration. The variance effective population size is defined as the size of an idealized population with the same variance. This is found by equating with and solving for N which gives
Alternatively, the effective population size may be defined by noting how the inbreeding coefficient changes from one generation to the next, and then defining N_{e} as the size of the idealized population that has the same change in inbreeding. The presentation follows Kempthorne (1957).
For the idealized population, the inbreeding coefficients follow the recurrence equation
Using Panmictic Index (1 − F) instead of inbreeding coefficient, we get the approximate recurrence equation
The difference per generation is
The inbreeding effective size can be found by solving
This is
although researchers rarely use this equation directly.
Population size varies over time. Suppose there are t nonoverlapping generations, then effective population size is given by the harmonic mean of the population sizes:
For example, say the population size was N = 10, 100, 50, 80, 20, 500 for six generations (t = 6). Then the effective population size is the harmonic mean of these, giving:
= 0.032416667  
N_{e}  = 30.8 
Note this is less than the arithmetic mean of the population size, which in this example is 126.7.
Of particular concern is the effect of a population bottleneck.
With increased variation in family size, Ne is reduced: N_{e} = (4N)/(V_{k} + 2) Where V_{k} is the variance in family size.
If a population is dioecious, i.e. there is no selffertilisation then
or more generally,
where D represents dioeciousness and may take the value 0 (for not dioecious) or 1 for dioecious.
When N is large, N_{e} approximately equals N, so this is usually trivial and often ignored:
When the sex ratio of a population varies from the Fisherian 1:1 ratio, effective population size is given by:
Where N_{m} is the number of males and N_{f} the number of females. For example, with 80 males and 20 females (an absolute population size of 100):
N_{e}  
= 64 
Again, this results in N_{e} being less than N.
If population size is to remain constant, each individual must contribute on average two gametes to the next generation. An idealized population assumes that this follows a Poisson distribution so that the variance of the number of gametes contributed, k is equal to the mean number contributed, i.e. 2:
However, in natural populations the variance is larger than this, i.e.
The effective population size is then given by:
Note that if the variance of k is less than 2, N_{e} is greater than N. Heritable variation in fecundity, usually pushes N_{e} lower.
When organisms live longer than one breeding season, effective population sizes have to take into account the life tables for the species.
Assume a haploid population with discrete age structure. An example might be an organism that can survive several discrete breeding seasons. Further, define the following age structure characteristics:
The generation time is calculated as
Then, the inbreeding effective population size is (Felsenstein 1971)
Similarly, the inbreeding effective number can be calculated for a diploid population with discrete age structure. This was first given by Johnson (1977), but the notation more closely resembles Emigh and Pollak (1979).
Assume the same basic parameters for the life table as given for the haploid case, but distinguishing between male and female, such as N_{0}^{ƒ} and N_{0}^{m} for the number of newborn females and males, respectively (notice lower case ƒ for females, compared to upper case F for inbreeding).
The inbreeding effective number is


