Individual

All individuals are considered diploid, thus Individual is matrix of chromosomes with two rows and number of columns set by parameter number of chromosomes (C).

The class Individual has a method which creates a haploid gamete. Number of recombination events per chromosome pair is drawn from the Poisson distribution with λ set by parameter mean number of chiasmata (λ). The distribution of these events is with respect to the probability vector p. The probability of splitting two loci by recombination (recombination rate) can be computed through Haldane's mapping function. Suppose that loci L_m and L_n are on the same chromosome at positions m and n. The probability P_sep of one chiasma to separate these loci is then

and the probability of these two loci to be separated by recombination event is

where λ is the parameter mean number of chismata. The equation for the default probability vector is

,

the fitness of an individual is computed using an epistatic model. The fitness is

,

where parameter β sets the strength of the epistatic effect, s is selection pressure against maximally admixed individuals and x is the hybrid index. The function is symmetrical around proportion 0.5, therefore, which population is labeled by zero and which is labeled by one is irrelevant, when the hybrid index is computed.