Data from: Effect of mutation mechanisms on variant composition and distribution in Caenorhabditis elegans

Genetic diversity is maintained by continuing generation and removal of
variants. While examining over 800,000 DNA variants in wild isolates of
Caenorhabditis elegans, we made a discovery that the proportions of
variant types are not constant across the C. elegans genome. The variant
proportion is defined as the fraction of a specific variant type (e.g.
single nucleotide polymorphism (SNP) or indel) within a broader set of
variants (e.g. all variants or all non-SNPs). The proportions of most
variant types show a correlation with the recombination rate. These
correlations can be explained as a result of a concerted action of two
mutation mechanisms, which we named Morgan and Sanger mechanisms. The two
proposed mechanisms act according to the distinct components of
recombination rate, specifically the genetic and physical distance.
Regression analysis was used to explore the characteristics and
contributions of the two mutation mechanisms. According to our model,
~20–40% of all mutations in C. elegans wild populations are derived from
programmed meiotic double strand breaks, which precede chromosomal
crossovers and thus may be the point of origin for the Morgan mechanism. A
substantial part of the known correlation between the recombination rate
and variant distribution appears to be caused by the mutations generated
by the Morgan mechanism. Mathematically integrating the mutation model
with background selection model gives a more complete depiction of how the
variant landscape is shaped in C. elegans. Similar analysis should be
possible in other species by examining the correlation between the
recombination rate and variant landscape within the context of our
mutation model.