Input - Genetic Diversity in Establishing Plant Populations: Founder Number and Geometry - page 22

that locus from the source population in accordance with the frequencies
(probabilities) assigned by the user in the input fi le to each unique allele
at that locus in the source population. Similarly, the alleles assigned to
each locus in each individual founder are drawn across all loci described
for the source population. In an infi nite population of founders, the allele
frequencies among the founders would exactly refl ect the frequencies in the
source population. However, since NEWGARDEN is designed to examine
the effects of small founding populations, alleles selected for the founding
population will vary from run to run of a trial. The reported mean alleles
and level of heterozygosity for a founding population in the output fi le
are averages calculated from the unique alleles “captured” in the founding
population from the user-designated source population, averaged across
runs for a trial (the number of replicate runs for a trial can be user-specifi ed;
see below), with a standard deviation provided. Thus, the founders in one
run will usually not have exactly the specifi ed allele frequencies, nor will
frequencies be equal from run to run; if averaged across runs, however, the
mean will tend towards the specifi ed source population frequencies as the
number of runs specifi ed for a given trial increases.
After the allelic composition of each locus in each founder of the
founding population for a run of a trial is established, in creating each new
derived generation, NEWGARDEN then chooses at random, for a particular
locus of a particular mating individual, one or the other allele for that locus
to be included in a particular gamete to be used in a given mating. Either of
these alleles has a 0.5 probability of being chosen in any one gamete drawn
from that individual. Since NEWGARDEN keeps track of the allelic status of
all individuals for each new cohort and total population, users can compare
rates of change of the total number of unique alleles, heterozygosity, and
F relative to changes in input conditions.
Loci: Some Theoretical Considerations
Users may be interested only in the gain or loss of unique alleles or
heterozygosity in founding and developing populations for loci with
particular allelic diversities. For example, one may want to investigate
species with very low genetic variation at each of numerous loci (e.g.,
introduction of closely related individuals or multiple clones), while another
study might involve numerous loci, each of which has a high diversity of
unique alleles in the source population from which founders are drawn,
and yet others may be interested in organisms with a complex mixture of
these loci types.
Some users may be interested in how single nucleotide polymorphisms
(SNPs) are affected by contrasting founding conditions. SNP loci most
frequently involve two alleles, and in some cases, possession of one or the