Conclusions and Discussion - Genetic Diversity in Establishing Plant Populations: Founder Number and Geometry - page 325

upon intense investigation exhibited high levels of variation, and thus
alleles of low frequency, include antipathogen system genes (Hamilton
1982; Trachtenberg et al. 2003), self-incompatibility alleles (e.g., Finkeldey
and Hattemer 2007), cholesterol quality (Cohen et al. 2004), and some types
of copy number variants (Springer et al. 2009).
It is generally thought that most mutations are neutral or deleterious.
The loss of such alleles due to founding processes reviewed here thus is of
little concern or may actually be of benefi t to populations.
While most adaptive evolution in establishing populations may be
derived from standing genetic variation rather than new mutations (e.g.,
Prentis et al. 2008), examples of conserved recent mutations that can increase
fi tness in populations have been noted (and see Draghi et al. 2010). For
example, in some cases, high rates of mutation have been found to provide
competitive advantages to populations (Haas et al. 2009; Springman et al.
2009). Variation in tandem DNA repeats arising at specifi c loci has been
found to have genetic functional signifi cance in numerous cases (e.g.,
Hammock and Young 2005). Studies with maize indicate that numerous
traits (such as fl owering time) are affected by many alleles of small effect.
This suggests that strong selection has not been active on most of these
alleles. The complex of loci and alleles involved in this maize example can
potentially accommodate the accumulation of some forms of mutant alleles
at a given fl owering time locus. Surveying across different maize lines, 30%
of the polymorphisms were found to be unique to one line “...which indicates
that rare sequence variants are common in diverse maize” (Buckler et al.
2009: 716). While Buckler et al. found that numerous loci affect fl owering
time, there “...were many functionally distinct alleles at each locus, each
occurring at low frequency” (p. 717). When low-frequency alleles (including
SNPs) were shared across founder lines, allelic effects differed in different
genetic contexts across those lines. To cite another example, multiple gene
interactions involving a number of modifi ers have also been found to affect
the expression of the same mutation in different genetic backgrounds of
yeast, suggesting that differences in numerous genes of relatively small
effect can bring about strain-specifi c phenotypic variation (Dowell et al.
2010). In fact, increasing theory and evidence indicate that mutations of
small effect commonly persist in populations and are responsible for a
signifi cant portion of the additive genetic variation present in many traits
involved in fi tness (e.g., see Tomkins et al. 2010 and references).
Above we give just a few examples of phenomena by which low-
frequency unique alleles can arise or be maintained in populations, and
how they might play a role in genotypic and phenotypic variation. Loss
via drift of such low-frequency alleles in some populations versus others
due to differing spationumeric effects of establishment may thus affect the
accumulation of new alleles in such contrasting populations.