Biology Reference
In-Depth Information
Using NEWGARDEN to Explore Loci Arrays and Founder
Effects
NEWGARDEN provides an exploratory tool for examining the issues of
founder effect loss of unique alleles and effects on heterozygosity. The
following trials demonstrate how NEWGARDEN can be used to examine
the intensity of the founder effect in different situations. Recall that the
user can specify, in the input fi le, the number of loci and, for each locus, the
number and frequencies of unique alleles in the idealized source population
from which the founding individuals are drawn. For every individual
designated by the user as existing in the initial founding population, each
will have the same number of loci. For each locus of each individual, two
locus-specifi c alleles available in the source population will be randomly
drawn by NEWGARDEN subject to the frequency-weighting of each allele
as designated by the user in the creation of the source population loci array
specifi cations (loci input commands).
In the following initial trials, we assume that the source population
from which founders are drawn is at Hardy-Weinberg equilibrium and
is composed of an infi nite number of individuals. We begin with a very
simple example to demonstrate how to use NEWGARDEN and how
NEWGARDEN can provide information regarding founder effects.
Consider the case of one locus with two alleles, each with equal frequency
of 0.5 in the source population. How does the number of founders drawn
affect the variation in achieving the goal of bringing both alleles into the
founding population? In this example, the loci confi guration input is:
<LOCI
number_loci=“0” auto_alleles_per_locus=“2”
number_automatic_loci=“1”>
</LOCI>
The number of generations is 1, the number of replicate runs is 25, and
these conditions are run in separate trials, each with a different number of
founders (1, 2, 3, 10, 20, 40, 100, 400, or 900).
As long as one is drawing a small number of founders from this source
population, there is some chance that both alleles will not be passed into
the founding population. This probability becomes increasingly small
as the number of founders drawn gets larger. But, if one could draw 50
founders and be relatively assured of including both alleles in the founding
population, that would be more effi cient and economical than drawing 900
founders. Beginning with the fi rst trial for drawing one individual (details
of the input fi le given above), each successive trial involves the drawing
of an increasing number of founders (trial 2 has 2 founders, trial 6 has
40 founders, etc., as noted above). For each individual founder drawn,
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