This dialog box allows you to change initial population general parameters, such as the initial number of individuals, the number of locus in their genome, the number of alleles per locus (this number is constant across loci), and the carrying capacity.
population size: Initial number of individuals
carrying capacity: The carrying capacity influences the survival of individuals, but keep in mind that other factors control for this survival (such as the amount of resource invested in reproduction) and therefore, the population size equilibrium can be lower or greater than the carrying capacity.
locus number: The number of loci will influence the genetic values of traits which is the sum of allelic values over loci.
chromosome number: The number of chromosome will condition the distances between loci and thus probabilities of recombination. For instance, with 2 chromosomes half of the loci will be on each of the chromosomes. Loci on different chromosomes are segregated independently during meiosis (and have a recombination probability of 0.5), whereas loci on the same chromosome are linked and have a recombination probability define hereafter.
intra-chromosomal recombination probability: probability of recombination between adjacent loci.
allele number per locus: number of different alleles existing for each loci. The number of alleles defines the total potential for evolution: mutations are drawn randomly in that alleles pool. If you pick a small value here (say 10), then the possible genetic combinations to build phenotype will be reduced. If you pick a high value (say 1000), the model dynamics will begin to approach quantitative genetics behaviour. Finally, while the initial individuals genomes will be built by randomly drawing alleles in this pool, the mutation/drift equilibrium will quickly converge depending on various factors among which population size and mutation rate.