Biology Reference
In-Depth Information
4
CHAPTER
Input
One can use NEWGARDEN to analyze the effect of changing initial input
conditions for a set of user-specifi ed founders on population growth rates,
loss of unique alleles, changes in observed and expected heterozygosity,
and F in a population that develops from those founders under the specifi ed
conditions (the output statistics are discussed in more detail below).
Examples of input fi les, or sections of input fi les, with options for different
initial conditions (e.g., number of founders, position of founders, number
of alleles specifi ed for a specifi ed number of loci) and different continuing
conditions (e.g., rates of selfi ng, age-specifi c mortality, distance of male
gamete dispersal) are given below in the text and in appendices. It is
recommended that readers print one of the sample input trials provided in
the appendices so that they can compare the printed fi le to the description
of fi le sections given below. To become familiar with using the program and
interpreting output, users can clip out portions of these appendix fi les and
paste chosen input specifi cations into the input fi les they are constructing.
In the following sections, the conditions that can be changed in the input
fi le for an initial founding population are reviewed.
General Input Concepts
Before embarking on a detailed review of user-specifi ed, initial founder
population and subsequent population development conditions, we
will defi ne some basic terms and concepts as used in NEWGARDEN
analyses.
Entities and Terms Involved in Reproduction
The development of populations through generations involves the
alternation of generations (haploid alternating with diploid phases). Terms
for the entities involved in this alternation differ for different groups of
organisms. To simplify and standardize NEWGARDEN to make it more
usable across taxonomic groups, we will use the following terms and
defi nitions:
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