Input - Genetic Diversity in Establishing Plant Populations: Founder Number and Geometry - page 56

an already established stand (e.g., Cochrane et al. 2007) or the effects of
seed dormancy and a seed bank with seeds germinating variably over
generations to assess how these factors can alter genetic diversity. As noted
above, barriers to establishment can be placed on the grid by setting the age
of some individuals very high and also setting offspring and microgamete
contributions of such aged individuals, as well as their mortality, to 0.
Source Population Level of Inbreeding
As noted earlier, the founders are drawn at random from virtual source
population. However, not all natural source populations are at Hardy-
Weinberg equilibrium; some may deviate in the balance of homozygous loci
relative to heterozygous loci because of apparent inbreeding, for example.
The input fi le FoundersF value statement controls the process of selecting
the genotypes of the founding population from source populations with
user-designated levels of F (inbreeding coeffi cient). Genotypes of founders
are selected at random so that, on average, the inbreeding coeffi cient of the
founders is the user-specifi ed value of F. For example, for a locus with two
alleles with frequencies specifi ed as p and q, we pick the genotypes of a
founder at this locus according to the following probabilities:
P(00) = (1-F)p^2 + Fp
P(01) = (1-F)2pq
P(11) = (1-F)q^2 + Fq
The level of inbreeding for the source population and thus theoretically for
the founders (small founder populations are likely to deviate) is specifi ed
by the user in the input statement
<FoundersF value=“F”/>
where F = the coeffi cient value. The F value can range from 0 (no inbreeding,
random mating) to 1 (complete inbreeding). Under the assumption that the
source and founding populations are at Hardy-Weinberg equilibrium, the
user would input the following statement value:
<FoundersF value=“0”/>