One prediction of the neutral theory is that silent (synonymous) sites in protein coding regions will evolve faster than replacement (nonsynonymous) sites(due to different functional constraints). This provides a null hypothesis about DNA evolution. Most sequences fit this neutral model; however, the histocompatibility loci appear to deviate from a neutral model in that there are morenonsynonymous substitutions than synonymous substitutions. This holds only for the antigen binding region; the rest of the molecule is consistent with neutral expectations. (see figure 7.10, pg. 185). Another prediction of the neutral theory is that amount of sequence divergence will be correlated with the level of heterozygosity; heterozygosity is measured as 2pq for a two allele situation or (2pq+2pr+2qr) for a three allele situation, or 1-xi2for i alleles; see figure 5.2 pg. 96 for a two allele view). Loci with high heterozygosity should evolve at a faster rate under the assumption that these loci have a higher rate of neutral mutation (thus more variation within species and more substitution between
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