A multilocus sequence survey in Arabidopsis thaliana reveals a genome-wide departure from the standard neutral model of DNA sequence polymorphism

The simultaneous analysis of multiple genomic loci is a powerful approach to study the effects of population history and natural selection on patterns of genetic variation of a species. By surveying nucleotide sequence polymorphism at 334 randomly distributed genomic regions in 12 accessions of Arabidopsis thaliana, we examined whether a standard neutral model of nucleotide sequence polymorphism is consistent with observed data. The average nucleotide diversity was 0.0071 for total sites and 0.0083 for silent sites. Although levels of diversity are variable among loci, no correlation with local recombination rate was observed, but polymorphism levels were correlated for physically linked loci (250 kb). We found that observed distributions of Tajima's D, D/D_min, Fu and Li's D, D* F, F* statistics differed significantly from the expected distributions under a standard neutral model due to an excess of rare polymorphisms and high variances. Observed and expected distributions of Fay and Wu's F were not different suggesting that demographic processes and not selection at multiple loci are responsible for the deviation from a neutral model. Maximum likelihood comparisons of alternative demographic models like logistic population growth, glacial refugia or past bottlenecks did not produce parameter estimates that were more consistent with observed patterns. However, exclusion of highly polymorphic 'outlier loci' resulted in a fit to the logistic growth model. Various tests of neutrality revealed a set of candidate loci that may evolve under selection.

Key Words: Arabidopsis thaliana, Coalescent simulations, Maximum likelihood, Neutral evolution, Population genomics

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