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difference in average heterozygosity values between runs can be as great
as approximately 8%, even though both alleles are present (see Fig. 7.1).
Figure 7.4 shows that variance in heterozygosity approaches 0 as the number
of founders increases to about 900.
0.6
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0.5
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0.4
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0.3
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0.2
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0.1
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1
10 100
FOUNDERS
Fig. 7.4
Variation in standard deviation for average observed heterozygosity values of founding
populations of different sizes (these results from the same trials described for Fig. 7.1). In the
source population from which founders are randomly drawn, there is only one locus with
two alleles of equal frequency (both 0.5). Each letter represents the standard deviation value
for one trial (25 replicate runs per trial) with a particular number of founders. Overlapping
values are shown as one letter. As the number of founders increases, standard deviation for
average heterozygosity values converges on 0.
The above results are derived from a very simple and special case that
is not usually of much concern to conservation biologists, whose goal is to
save as much diversity as possible, especially at loci with numerous unique
alleles at lower frequencies. However, as noted earlier, SNPs generally
occur with only two alleles, and NEWGARDEN can be used to model
their behavior at founding and in population development. Further, there
may be certain other types of genes in which two alleles predominate, or
populations started from very few (one or two?) individuals or clones or
highly homozygous experimental lines, where such considerations are of
interest. NEWGARDEN can be used to explore the population genetics
of such situations when various population development parameters are
varied.
To move on to a more complex case, consider one locus with 10
unique alleles, all of equal frequency (0.1). This case can be studied with
NEWGARDEN by replacing the code above, which describes the two-allele
locus, with the following code:
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