Relative influences of crossing over and gene conversion on the pattern of linkage disequilibrium in Arabidopsis thaliana

Abstract

In this article we infer the rates of gene conversion and crossing over in Arabidopsis thaliana from population genetic data. Our data set is a genomewide survey consisting of 1347 fragments of length 600 bp sequenced in 96 accessions. It has several orders of magnitude more markers than any previous nonhuman study. This allows for more accurate inference as well as a detailed comparison between theoretical expectations and observations. Our methodology is specifically set to account for deviations such as recurrent mutations or a skewed frequency spectrum. We found that even if some components of the model clearly do not fit, the pattern of LD conforms to theoretical expectations quite well. The ratio of gene conversion to crossing over is estimated to be around one. We also find evidence for fine-scale variations of the crossing-over rate.

Figure 1.

The observed frequency spectrum in exons and noncoding regions, compared to coalescent expectations with and without growth.

Figure 2.

Difference between expected and observed decay of D′ as a function of the crossing-over rate ρ. The solid line indicates the least-squares distance and the dashed line indicates Hudson's composite likelihood. The minimum of the squared distance and maximum of the composite likelihood (which both estimate the average ρ) are ∼0.3/kb.

Figure 3.

Decay of D′, observed (dashed line) and expected (solid line) for ρ = 0.3/kb, which minimizes distance between expectation and data.

Figure 4.

Five percent and 95% quantiles of the distribution of the number of incompatible fragments for different values of f. The horizontal line shows the number observed in the data (227). The dashed line indicates the value of Hudson's pseudo-likelihood.