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in the simulation data than in the West Salem stand (Pierson et al. 2007).
This convention was used so that the simulations are a more stringent and
statistically meaningful test of low-frequency allele loss though drift. All
told, among the nine founders in the simulations, there should be about
18 unique alleles per locus multiplied by 30 loci, giving a total of at most
540 unique alleles among the founding trees establishing these simulated
trials.
Figure 16.3
depicts the number of the founding unique alleles in each
cohort across the 100 rounds of mating (generations) for chestnut trials a,
b, e, and f (graph A). At generation 0, the average number of unique alleles
in the nine founders was 496-497, meaning that for each locus, duplicate
copies of some unique alleles were drawn in the 18 draws, from the pool
of 100 unique alleles for each locus, approximately 40 times over all of
the draws. In the early individual cohorts, trials a, b, and f retain only
about 300 of the founding unique alleles, but by generation 40, most of the
founding unique alleles will be passed to each new cohort. Trial e, with
its much lower rate of growth, loses all but approximately 110 founding
unique alleles in early generation cohorts, and even after 100 generations,
each new cohort possesses only about 90% of the unique alleles present at
the founding event.
Another way of considering this data is to ask, “As new generations
develop, how many randomly generated offspring in a new cohort are
needed to ensure that most or all of the founders' mostly unique alleles
are present in that new cohort?” Figure 16.3B shows the number of unique
founder alleles passed to successive cohorts based on the size of the cohort.
500
a
500
b
b
bb
b
b
b
b
bb
b
b
b
b
b
b
b
b
b
b
bb
bbbb
bbbb
b
b
bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbb
b
bbbbb
b
bbbbbbb
b
bbbb
b
f, b, a
a
b
e
f
f
f
f
f
f
f
f
f
f
f
f
f
f
f
f
ff
f
f f
f
fff
f
f ff
ff f
f
f
ff
b
b
b
b
b
b
b
b
b
b
b
bb
b
bbb
b bb
bb
a
a
a
aa
aa
aa
a
aa
aaaa
aa
aa
f, b, a
e
f
f
f
f
ff
f
f
f
f
ff
f
f
ff
f
fff
ff
f
f
f
fff
ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
a
a
a
a
aa
a
a
a
a
a
a
a
aa
a
a
aa
a
a
a
aaaaa
aaaa
a
a
a
a
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa
e
ee
e e
e
e
e
e
ee
e
ee
e
eee
e
ee
e
e
ee
ee
e
ee
e
e
ee
e
ee
e
e
e
e
e
e
e
400
400
ff
f
f
e
e
e
e
e
b
b
b
a
a
a
a
a
a
e
e
e
e
ee
e
e
a
a
b
b
b
b
bb
bb
b
b
bb
b
b
e
e
e
e
e
a
a
f
f
f
f
f
e
e
e
e
a
a
a
a
e
e
e
e
e
eee
e
f
e
e
e
e
ff
f
b
b
bb
b
b
300
300
a
a
a
a
e
e
e
f
e
e
a
a
a
a
aa
a
b
a
e
e
eee
e
e
e
e
e
e
ee
e
e
e
e
e
e
e
e
e
e
e
e
e
ee
ee
e
e
200
e
e
ee
e
e
200
e
e
e
e
e
e
e
e
e
e
e
e
e
e
e
e
e
ee
e
e
e
e
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e
e
e
e
e
e
100
B
A
100
e
e
0
0
0
20
40
60
80
100
1
10
100
GENERATION
COHORT POPULATION SIZE
Fig. 16.3
Founding unique alleles retained in successive cohorts across generations (A), and
in cohorts of different sizes (B) for NEWGARDEN virtual populations with input conditions
designed to refl ect the development of the West Salem American chestnut population. See
text for details of the basic trial a, and associated trials.
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