Output: What NEWGARDEN Tallies, Calculates, and Reports - Genetic Diversity in Establishing Plant Populations: Founder Number and Geometry - page 60

population of 106 diploid individuals there is a total of 212 alleles present.
However, all of the 212 alleles may be identical (by descent or by state),
in which case all 212 alleles would constitute only one unique allele. As
another example, considering one locus, 20 founders will have a total of 40
alleles among them, but if only 13 of the 40 are different from one another
(non-identical) and thus unique, the remaining 27 alleles are copies of one
or another of the 13 unique alleles. If in the next generations 106 individuals
are generated from these isolated founders, they can have at most (barring
mutation, which is not considered in the current version of NEWGARDEN)
13 unique alleles among them. If fewer than 13 unique alleles are reported
for the 106 offspring, those alleles have been permanently lost from the
population as it develops further, and this value is thus one measure of
maintenance or loss of genetic diversity.
Sd(alleles)
Sd(alleles) is the s.d. of the mean unique alleles calculated for the runs of
a given trial. It is reported for each cohort and for the entire population at
each age of population development for a trial.
Mean(H observed)
Mean(H observed) is the mean observed heterozygosity reported for each
cohort and the total population at each age of the population for a trial. It
is calculated not from a subsampling of individuals or loci taken from each
generation, but across the actual status of each locus for all individuals in the
population. Thus, the reported observed heterozygosity is based on actual
counts of the status of each locus in all individuals of a generation, and is
not based on Hardy-Weinberg estimation. Since NEWGARDEN population
genetics develop according to matings subject to the user-designated
input constraints, mean observed heterozygosity can change because of
the interaction of several factors, including loss of unique alleles from the
population or subpopulations, inbreeding or outbreeding in subdivided
populations, or with increased rates of inbreeding brought on by increased
selfi ng rates as designated by the user, among other considerations.
Sd(H observed)
Sd(H observed) is the standard deviation in mean observed heterozygosity
values at each population age reported for each cohort and total population
as calculated across runs of a given trial.