Sexual reproduction
Each individual’s genotype consists of a number of diploid, biallelic
loci. A subset of these loci, np contributes to
an individual’s phenotype; nc are involved in
incompatibility; nn are neutral and used to track
the recipient genome; and nh are used to score
the heterozygosity of each locus through time. We differentiate between
loci used to track the recipient genome and those used to track
heterozygosity in order to compare two contrasting management
objectives. Each offspring’s genotype is a result of the fusion of
gametes from a ‘male’ and ‘female’ parent. Genetic recombination is
based on an algorithm described by Kelly et al. (2018) in which
the genome wide recombination rate is calculated as the average
proportion of pairwise crossover events between loci.