Input - Genetic Diversity in Establishing Plant Populations: Founder Number and Geometry - page 21

User-specifi ed Initial Conditions for a NEWGARDEN Trial
In the following sections, input conditions that can be specifi ed by the user
in the initial data input fi le that describe (1) the founding population and (2)
the conditions under which it will develop through generations, are briefl y
described in the order that they appear in the input fi le. When useful, the
exact data input statement in the form required for the input fi le is given
for comparison with the sample input fi les given in the appendices.
Loci
The number of loci per individual is specifi ed in the data input fi le. For
each founder, the two alleles for each locus are drawn at random from a
“virtual” ideal source population for which the frequency of alleles at each
locus is designated by the user in the data input fi le. In other words, for each
locus specifi ed, the user specifi es the number of unique alleles available for
that locus in the source population, as well as the frequency of each unique
allele in the source population. For each locus of a founder, two alleles are
drawn at random weighted by their designated frequencies and consequent
distributions in an ideal Hardy-Weinberg population (except when the
inbreeding coeffi cient of the source population is specifi ed by the user, as
described below in the section Source Population Level of Inbreeding).
The frequencies of all the unique alleles for one locus input for the source
population must sum to 1.
For example, a trial may analyze 20 loci per individual, 10 of those
loci having two unique alleles, 5 loci having four unique alleles, and 5 loci
having 100 unique alleles in the virtual source population. Of the 10 loci
each with two unique alleles, 8 might have both alleles at equal frequency,
while 2 might have one allele at a frequency of 0.3 and the other allele at
0.7 in the source population. Of the 5 loci with four unique alleles each, one
locus might have the four alleles in equal frequencies (0.25, 0.25, 0.25, 0.25),
while the other 4 loci might have the four allele frequencies designated
differently (e.g., 0.33, 0.65, 0.01, 0.01 versus 0.5, 0.20, 0.20, 0.10, and so on).
A locus with 100 unique alleles might have all 100 at equal frequency (each
at 0.01), or have different allelic frequencies attributed to different alleles,
as long as the frequencies for all 100 unique alleles sum to 1.
As noted, the frequency specifi ed for a unique allele describes that
allele's frequency in the source population from which the founding
population is drawn, and accordingly affects its probability of being
drawn in determining the allelic status of founders. Consider one locus
of one founder in a founding population totaling 10 individuals, where
each individual is assigned 5 loci. In determining the allelic status of
that one locus in that one founder, two alleles are drawn at random for