The allelic variants that underlie heritable phenotypic variation are distributed along chromosomes. Their distribution is shaped by the machinery of meiosis within individuals and by mutation, selection, and drift among them. To discover the genetic basis of complex traits, and to understand the evolutionary dynamics that shape this genetic architecture, we must characterize empirical patterns of linkage and linkage disequilibrium. We have undertaken this task in the nematode C. elegans.
Mapping of thousands of mutants to the genome and molecular studies of meiotic machinery have provided a view of the large-scale landscape of the C. elegans
recombination map. The chromosomes exhibit nearly complete crossover interference 
, such that each chromosome experiences one crossover per meiosis and has a genetic length of 50 cM 
. Accumulated data from thousands of two- and three-point mapping crosses and small-scale SNP-based analyses have demonstrated a general pattern of large, nearly constant-rate domains on the autosomes, with high recombination in chromosome arms and low recombination in chromosome centers. Despite strong global regulation of crossover number, many details remain unclear, including the locations of the domain boundaries, the occurrence of fine-scale variation within domains, and the existence of domain structure on the X chromosome. Moreover, evidence for the genetic control of crossover number and position 
leaves open the possibility that segregating variants may influence recombination patterns in experimental crosses of natural isolates. Because recombination patterns have been studied only on broad scales in individual crosses, involving fewer than two dozen markers per chromosome, dense characterization of a massive cross promises to clarify the recombinational landscape.
is one of the most exhaustively studied of all species with respect to developmental, behavioral, and physiological genomics, but studies of its population biology have lagged. Although natural genetic variation has been a source of alleles for genetic analysis in C. elegans
since long before the system became a model 
, the widely accepted notion that worms exhibit little variation has discouraged investigations of their diversity. The difficulty of collecting C. elegans
from the wild has compounded the problem. Nevertheless, recent work has revealed abundant heritable phenotypic variation among wild C. elegans
and has begun to reveal the ecological context for this species 
. C. elegans
geneticists have exploited this variation to map quantitative trait loci 
, and in a handful of cases to identify the causal mutations underlying phenotypic variation (in genes npr-1
, and scd-2 
In parallel, studies of variation at molecular markers have begun to provide an account of the distribution of genetic variation within and among localities and across genomic regions 
. These studies have shown that the species exhibits substantially lower levels of polymorphism and higher levels of linkage disequilibrium than other model systems, even those, like Arabidopsis thaliana
, that share with C. elegans
a primarily selfing mating system. The empirical pattern of linkage disequilibrium may result as much from selection against recombinant genotypes as from attributes of population biology such as population size and outcrossing rate 
. A genome-wide assessment of linkage disequilibrium is required to determine whether natural isolates of C. elegans
will be useful for mapping loci by association.
We generated and genetically characterized a recombinant inbred advanced intercross population to gain insights into the recombination map in C. elegans, and we characterized a large panel of wild strains to characterize linkage disequilibrium. The data on recombination in the lab and in the wild reveal the role of population genomic processes in shaping genotypic diversity in C. elegans, and they lay the groundwork for rapid discovery of the genes underlying phenotypic variation.