Biology Reference
In-Depth Information
NEWGARDEN can be used to explore whether, all other input
conditions held equal, introduction of founders in different geometric
patterns leads to different degrees of population subdivision and, further,
whether degree of subdivision changes over time.
Effective Population Size
For one reason or another, NEWGARDEN populations will be seen to
change in population genetics parameter values through time, unlike an
ideal population of infi nite size with no mutation, selection, immigration, or
emigration. If the last four factors are ignored (as they are in NEWGARDEN
analyses unless explicitly stated), populations will increasingly deviate
from ideal expectations as they become smaller. The (variance) effective
population size of an observed population is the size of an ideal population
that would change population genetics characteristics through time in the
same way (Falconer and Mackay 1996). For example, a large NEWGARDEN
population (say, 1000 individuals) may lose heterozygosity at a rate
equivalent to a population that is behaving ideally except that it has been
reduced in size to 45 individuals. In other words, that NEWGARDEN
population has an effective population size of 45.
Cohorts, Generations, Age, Years
Development of populations across “generations” is also a complex topic.
In NEWGARDEN analyses, we use the concept of a cohort: groups of
individuals that germinate, establish, or are otherwise recruited into a
population effectively at the same time. A cohort generally consists of
all the surviving offspring generated from a given episode of mating. In
some analyses described below, cohorts may include such offspring plus
individuals drawn from the original source population programmed to enter
the NEWGARDEN population contemporaneously with those offspring.
The defi nitions for age or generations of a cohort are also complex.
Since individuals of different cohorts, some separated by a large number of
“years” (i.e., bouts of reproduction), can intermate in iteroparous species, the
defi nition of exactly what a generation is can be diffi cult. To make matters
more complex, many species may have several rounds of mating, or may
mate diffusely for long periods, over one year or supra-annually, and these
mating bouts may vary in different ways across years.
In using NEWGARDEN, we defi ne populations as developing from
serial bouts of mating. We usually use the term “age”, not in the sense of time
(e.g., years), but to refer to the number of mating bouts from founding, with
the founders being of age 0. Thus, the cohort labeled age 1 is the offspring
produced from the fi rst round of mating among the founders. Note that the
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