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Published on November 19, 2008; 10.1104/pp.108.127787

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Received August 8, 2008
Accepted November 12, 2008

Analysis of site frequency spectra from Arabidopsis thaliana with context-dependent corrections for ancestral misinference

Brian R. Morton *, Vaqaar-un-Nisa Dar , and Stephen I. Wright

Department of Biological Science, Barnard College, Columbia University, 3009 Broadway, New York NY USA; Department of Biology, York University, 4700 Keele St. Toronto Ont Canada M3J 1P3

* Corresponding author; email: bmorton{at}barnard.edu.

Previous studies have shown that the pattern of single nucleotide polymorphism (SNP) in Arabidopsis thaliana deviates from the distribution expected under a neutral model. Here we test whether or not ancestral misinference could explain this deviation. We start by showing that there are significant and complex influences of context on mutation dynamics, as inferred from SNP frequency, in Arabidopsis, and compare the results to observations about context-dependency that have been made on a previous analysis of a maize SNP dataset. The data concerning heterogeneity across sites are then used to make corrections for ancestral misinference in a context-dependent manner. Using A. lyrata to infer the ancestral state for SNPs we show that the resulting unfolded site frequency spectrum (SFS) in A. thaliana is skewed towards sites with high frequency derived nucleotides. Sites are also partitioned into two general functional classes, second codon position and four-fold degenerate sites. These two classes show different site frequency spectra; although both show an over-representation of high frequency derived sites, low frequency derived sites are vastly over-represented at the second codon position but significantly under-represented at four-fold degenerate sites. We find that these results are robust to corrections for ancestral misinference, even when context-dependent variation in mutation properties is taken into consideration. The data suggest that in addition to purifying selection, complex demographic events and/or linked positive selection need to be invoked to explain the SFS, and they highlight the importance of sequence context in analyses of variation genome-wide.






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