... | ... | @@ -8,4 +8,15 @@ See [genes map code](https://github.com/Ibasam/IBASAM/blob/master/IBASAM/src/Gen |
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IBASAM included a bi-allelic (favourable-unfavourable) multilocus system for each individual trait that was considered to be genetically coded and transmissible (e.g. Gavrilets and Vose, 2006; Kopp and Gavrilets, 2006; Gavrilets et al., 2007). Thus, for each trait, 2 branches (branch1 and branch2) representing 2 chromosomes were attributed with a given number of loci (nloci). Each locus carried 0 (unfavourable) or 1 (favourable). A genetic value (gValTrait) could be computed as:
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$$ gValTrait = $$ |
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\ No newline at end of file |
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$$ gValTrait = $$
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where branchn(r) was returning the locus r value (0 or 1) of the branch n, MTrait was the initialization mean value (at population level) and RTrait was the range of genetic values the trait could take. For a trait with heritability (h2) higher than zero, this range was computed by:
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where VarTrait was the phenotypic variance of the trait. A pheno- typic value (pValTrait) of the trait was set at the initialization of the individuals following a normal distribution around the mean gValTrait and with an environmental variance (VarEnv) computed as:
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This genetic structure ensured that if h2 tended towards 0, pValTrait and gValTrait were equal and normally distributed around MTrait with variance VarTrait. On the contrary, if h2 was 1, the environmen- tal variance was 0 and pValTrait was always gValTrait. To describe a trait with this structure it was only necessary to give a population mean and variance of the phenotypic value (MTrait and VarTrait) and a heritability value (h2) at start. The number of loci (nloci) was set arbitrarily to 20 for the present version of IBASAM to avoid the potential of rapid genetic drift by random fixation of alleles in the population. The genetic material of a newly born individ- ual was thus determined from that of its respective parents (see Section 2.1.7.2). For a given trait, one of the two alleles (from the two branches) at each locus was randomly chosen to make up a unique branch of code per parent. The two branches from the two parents were then transferred to the new individual to constitute its traitMap. Due to the high number of loci and the few number of generations simulated (generally <100) we considered that muta- tion was unimportant and did not implement it. However, natural selection and genetic drift were two potential evolution forces on these genetically coded traits.
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In the current version of IBASAM, only threshold values for maturation were considered genetically coded and heritable (see Section 2.1.7.7). Four respective set of genetically coded traits were implemented. Four genetic values: gFmida , gFmidb , gFmidc and gFmidd ; corresponded to male parr, female parr, anadromous males and anadromous females genetic maturation thresholds. These val- ues were transformed respectively to pFmida, pFmidb, pFmidc and pFmidd as phenotypic expression of the genetic maturation thresh- olds. All these traits had respective initial population values of phenotypic mean (Fmidma→d) and standard deviation (Fmidsda→d) (Table 2). A common heritability value (h2) was used for all these parameters (Table 2). |