## Description

This track displays results of a variation of the standard McDonald-Kreitman (1) test to examine intra-species (human, HapMap phase II or dbSNP126) polymorphism and inter-species (human-chimp and human-rhesus) divergence in non-coding DNA in non-overlapping 10 kb windows tiled across the genome. The MKAR test uses repeats ancestral to human-macaque (AR) as the neutral proxy. These are defined as LTR, SINE, LINE, and DNA elements excluding AluY, L1PA1-L1PA7, L1HS, and others shown to violate neutral expectations (2).

## Methods

Non-overlapping 10 kb windows were tiled across the genome. A 2X2 contingency table was generated for each window by apportioning SNP counts and divergence counts within a window into AR and non-AR categories. A SNP count is registered when a SNP is present in an aligned position. A divergence count is registered when aligned bases differ. An AR count is registered when either a SNP or diverged base fall in an ancestral repeat site within a window. A non-AR site is registered when either a SNP or a diverged base fall outside an AR site within a window. Gaps or regions that do not align in either species pair (human-chimp or human-macaque), or windows with a zero count in any member of the 2X2 contingency table were not counted. The significance of the table.s deviation from neutrality was determined by the Fisher.s exact as implemented in R (3). The FDR multiple tests correction procedure was applied to the empirical distribution of p-values as implemented in R, using the qvalue library and the bootstrap method of estimating the proportion of true null hypotheses (4).

## Credits

This work is a collaborative effort among researchers in Anthropology, Biology and the Center for Comparative Genomics and Bioinformatics at the Pennsylvania State University.

## References

1. McDonald J.H.,Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 1991 Jun 20;351(6328):652-4.
2. Kamal M., Xie X., Lander E.S. A large family of ancient repeat elements in the human genome is under strong selection. Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2740-5.
3. Team R.D.C. (R Foundation for Statistical Computing, Vienna, 2005).
4. Storey J.D. Journal of the Royal Statistical Society Series B-Statistical Methodology. 64, 479 (2002).