This module illustrates the evolution of a quantitative trait depending on the specific nature of the genetic architecture of the trait. Users can alter parameters that make up the genetic architecture - numbers of loci, initial allele frequencies, mutation rates - and then track allele frequencies at the individual quantitative trait loci (QTL). Users can also see the consequences of genetic architecture in terms of phenotypic mean and variance along with the heritability.
User entered parameters are the genetic effective population size (Ne), the number of loci or QTL that influence the trait, the mutation rate for all QTL (m), the number of generations to simulate, the strength of directional natural selection, the amount of environmental variation in trait values, the initial allele frequency at all QTL and the maximum genotypic value of an individual.
There are two general types of genetic architecture tat can be modeled and these are set using the radio buttons on the top right. One possibility is all QTL having equal effects on the genotypic variance in the trait. The other possibility is that some QTL have large effects on the genotypic variance in the trait. If the latter option is chosen, the number of “large” effect QTL can be specified and the effect of each of these loci (as a percentage of the total genotypic variation) can be specified. For example, clicking on the bottom radio button and setting Number of large effect loci equal to 2 and the VG explained by each large QTL to 0.2 would simulate a situation where two QTL explain 40% of genotypic variance while the remaining nQTL-2 loci (their number is set in the Number of QTL field) would explain equal amounts of the remaining 60% of genotypic variance in the trait.
Natural selection is modeled as truncation selection. The parameter given in “Nat. selxn. truncation point” specifies the proportion of individuals in the upper end of the distribution of phenotypic values that breed to form the next generation. A value of 1.0 means that all individuals can breed and there is no natural selection. A value of 0.8, for example, means that the 80% of the population with the largest phenotypic values breeds while those with the lowest 20% of phenotypic values do not breed. Parameters less than one but greater than zero produce directional natural selection for larger phenotypic values. Natural selection is stronger as the parameter value entered approaches zero.
For more background, see chapter 9 in Hamilton, 2009.