Fitness costs, and genotype inter-conversion by deposition and expression

In the transition from the zygotic to the embryonic state, the model takes into account deposition and fitness effects. Through deposition, each individual zygotic genotype (z_i) can give rise to multiple embryonic genotypes (e). Genotype conversion is mediated by matrix K, which converts genotypes according to the deposition cut and repair rates. Furthermore, based on the fitness parameters (Fig 1c), we can, for each genotype, define a particular fitness cost (0–1) in the vector θ. The fitness cost vector has a female (θ) and male (θ) specific version because for some simulations sex-specific fitness costs are applied. The fitness of a particular genotype (θ_i) is determined by multiplying the fitness costs of individual alleles. The dominant fitness cost imposed by a particular allele is applied only once, even if two copies are present. Some simulations impose an additional recessive fitness cost on the A locus, which only occurs if two loss of function alleles are present at A (e.g., _AEE, _AE2, _A22). As the multiple genotypes produced by deposition are within the same mosaic organism, the fitness cost contribution of individual genotypes is summed and applied uniformly over all genotypes arising from the same zygotic genotype. The deposition conversion outcomes and fitness costs of any one genotype do not vary throughout a simulation, only the relative frequency of the input genotypes in the form of z. As such, conversion matrix D/D can be constructed that mediates both deposition conversion (K), and fitness costs (θ_i and θ_i). Matrix D is the product of the row-wise multiplication of matrix K_i,* by θ and normalisation. When z is then subjected to conversion matrix D it produces the embryonic frequency vector e (Eq 3). Vector e represents the genotype frequency at the end of the embryonic stage, after deposition and fitness costs have been applied. Vector e/e is subsequently multiplied by the expression-based gene conversion matrix C/C to produce the gamete frequency vector g/g (Eq 4). The construction of matrices C and K is discussed after gamete production.