Founder Number and Allelic Diversity - Genetic Diversity in Establishing Plant Populations: Founder Number and Geometry - page 87

the population genetics of the developing population. When comparing
the effects of differences in other input features (e.g., spatial orientation of
the founders), we must consider whether trials with identical allelic arrays
have been used.
For restoration genetics, these issues raise several questions. How many
functionally important unique alleles are there at most loci? How many
functional alleles are found at the most diverse loci? How many diverse
loci, however defi ned, are there in a given species? In this context, is the
infi nite alleles model realistic for what actually occurs in reintroduction or
new colonization?
For the conservationist, it is the most diverse loci that are of interest
when examining unique allele loss under different introduction scenarios.
Lawrence et al. (1995) have argued that there are very low chances of the
20,000 polymorphic loci discussed above all having at least one allele with
frequency < 0.05, and that such loci may be rather uncommon. Obviously,
some functional genes have such exacting structural requirements for
proper function and are of such great fi tness importance that they often
have very few low-frequency variants in a large population (e.g., some
variants of the genes for human hemoglobin). While SNPs commonly have
only two alleles, surveys of the frequency and functionality of such alleles
in large populations are only beginning. Using a panel of 3,000 Europeans
analyzed for over 500,000 SNP loci, fi ne-scale differentiation of European
populations was detected, suggesting that rare SNP alleles (i.e., rare when
considering the entire species), possibly maintained through mutation and
small population effects, may be involved in such differentiation (Novembre
et al. 2008). Further, there may be types of functional genes where high
functional allelic diversity is present and selected for, such as the MHC
system, self-incompatibility systems, omyb systems, or other anti-pathogen
defense systems. Some highly diverse systems may involve gene families,
and deciphering allelic diversity at a “locus” in such cases may be diffi cult.
Not only do we know very little about the total number of unique alleles
at structural gene loci in large populations, but other potentially variable
“gene” systems, such as loci with variable regulatory alleles, are even less
well characterized. These considerations demonstrate the need for extensive
population surveys of the allelic diversity of the most diverse loci to help
us better understand how founder events of different sizes will affect the
capture of source population unique alleles, and potentially, descendant
population functional diversity. In such studies, past or future strong
phenotypic effects of low-frequency unique alleles remain a possibility,
although alleles rare in current populations are often thought to play a
minor role in current evolutionary trajectories. Obviously, however, future
selection pressures are unpredictable, and the maintenance of even alleles
of very low frequency may eventually become of evolutionary importance.