Nucleotide Polymorphism and Linkage Disequilibrium in Wild Populations of the Partial Selfer Caenorhabditis Elegans
Cutter, Asher D., Genetics
An understanding of the relative contributions of different evolutionary forces on an organism's genome requires an accurate description of the patterns of genetic variation within and between natural populations. To this end, I report a survey of nucleotide polymorphism in six loci from 118 strains of the nematode Caenorhabditis elegans. These strains derive from wild populations of several regions within France, Germany, and new localities in Scotland, in addition to stock center isolates. Overall levels of silent-site diversity are low within and between populations of this self-fertile species, averaging 0.2% in European samples and 0.3% worldwide. Population structure is present despite a lack of association of sequences with geography, and migration appears to occur at all geographic scales. Linkage disequilibrium is extensive in the C. elegans genome, extending even between chromosomes. Nevertheless, recombination is clearly present in the pattern of polymorphisms, indicating that outcrossing is an infrequent, but important, feature in this species ancestry. The range of outcrossing rates consistent with the data is inferred from linkage disequilibrium, using "scattered" samples representing the collecting phase of the coalescent process in a subdivided population. I propose that genetic variation in this species is shaped largely by population subdivision due to self-fertilization coupled with long- and short-range migration between subpopulations.
UNDERSTANDING the genetic basis of evolution \~J requires an accurate description of the patterns of genetic variation in natural populations. The landscape of genetic diversity is molded by the effects of mutation, selection (positive, negative, and balancing), recombination, stochasticity (i.e., genetic drift), and demography. We can attempt to infer how each of these general processes actually contributes to observed natural patterns of diversity by applying the extensive population genetics theory that has developed around the notion of neutral molecular markers and their nonneutral linked loci. Among the factors that can influence patterns of genetic variation in Caenorhabdiiis elegans, its partially selfing breeding system seems likely to play a prominent role. The effect of self-fertilization on diversity is threefold: reduced effective population size and reduced genomewide effective recombination rates, both due to increased homozygosity, and elevated isolation among individuals and subpopulations induced by inbreeding (CHARLESWORTH 2003). Consequently, a predominantly selfing mode of reproduction may be expected to lead to low polymorphism, extensive linkage disequilibrium, and high population subdivision, although migration and metapopulation processes can lead to other patterns (NoRDBORG 2000; INGVARSSON 2002). Here, I test these predictions by quantifying levels of nucleotide diversity, linkage disequilibrium, and population structure from loci across two chromosomes of 118 individuals in population samples of wild C. elegans.
Since the first natural survey of nucleotide variation (KREITMAN 1983), most such studies have focused on obligately outcrossing species, such as humans and species of Drosophila (ZHAO et al. 2000; Yu et al. 2001). However, recent large-scale resequencing efforts in plants (Arabidopsis thaliana and Zea mays) have augmented previous surveys aimed at describing the processes that affect polymorphism throughout the genome of selffertilizing species (MITCHELL-ULDS 2001; NORDBORG et al. 2005; SCHMID et al. 2005; WRIGHT et al. 2005). The patterns of diversity across sequence space and geographic space frequently deviate from neutral predictions, so that population genetic models that include both selection and demographic history are necessary to account for the observed patterns. Like A. thaliana, C. elegansis capable of close inbreeding by selfing: C. elegans reproduce either by hermaphrodite self-fertilization or by hermaphrodite outcrossing with males. …