Biased clustered substitutions in the human genome: The footprints of male-driven biased gene conversion

With the sequencing of the chimpanzee genome (Chimpanzee Sequencing and Analysis Consortium 2005), detailed analysis of the genetic determinants of our humanity has begun. In pursuit of the fastest evolving regions of the human genome, it has been observed that single-base substitutions in the top scoring regions were dramatically biased in favor of changes from AT to GC base pairs (Pollard et al. 2006a, b). In the top four fastest evolving regions, there were 33 cases of an AT pair being replaced by a GC pair, but only one case of a GC being replaced by an AT. Thus, bases that pair with two hydrogen bonds (“weak”) were replaced by bases that pair with three (“strong”). This substitution bias is particularly surprising given that overall numbers of strong-to-weak and weak-to-strong mutations are roughly equal in the human genome (Eyre-Walker 1999; Maki 2002; Lipatov et al. 2006). The force that has biased substitutions in recent human evolution may be related to the pressures that have shaped isochores, areas of warm-blooded vertebrate genomes as large as ∼300 kb with strikingly greater or lesser proportions of G+C than surrounding areas (Bernardi et al. 1985; Bernardi 2000). Three main theories have been proposed to explain the existence of isochores (Eyre-Walker and Hurst 2001). The first involves variation in mutation rates (Sueoka 1988; Wolfe et al. 1989; Fryxell and Zuckerkandl 2000) in different areas of a genome. Under this model, initial mutations vary in the proportion of G+C at different locations, and this imbalance is carried forward as a substitution bias by neutral evolution. The second theory is that natural selection (Bernardi and Bernardi 1986; Eyre-Walker 1999) for GC alleles has driven the formation and maintenance of isochores. Variability in G+C content might be evolutionarily advantageous, since G+C% is known to be correlated with (Lercher et al. 2003) and positively affect (Kudla et al. 2006) gene expression. G+C% may also be related to thermal stability. A third model that could lead to widespread variation in G+C content involves biased gene conversion (BGC) (Eyre-Walker 1993). BGC is a recombination-driven process that results in the biased fixation of GC alleles due to a biochemical bias in the DNA repair mechanism (Brown and Jiricny 1988; Webster and Smith 2004) acting on short stretches of hetero-duplexed DNA during crossing-over. BGC acts much like a selection pressure (Nagylaki 1983), providing a general mechanism for increased G+C, although it remains to be demonstrated (theoretically or experimentally) how BGC could lead to very large increases in substitution rate. Correlation between recombination rates and G+C content in a number of species supports the BGC hypothesis (Brown and Jiricny 1988; Birdsell 2002; Meunier and Duret 2004). The three models to explain bias in G+C give rise to different predictions regarding patterns of bias in polymorphisms and fixed substitutions (Eyre-Walker and Hurst 2001). If mutation bias is at work, then single nucleotide polymorphisms (SNPs) should show a similar pattern of bias as substitutions (Eyre-Walker and Hurst 2001; Lercher et al. 2003). But if higher G+C is the result of a selection pressure, there should be a more pronounced bias in substitutions than in SNPs (Lercher et al. 2002; Schmegner et al. 2007). Distinguishing between natural selection and BGC-mediated increases in G+C can be more difficult (Duret 2002; Meunier and Duret 2004). If natural selection is the source, then substitution bias may be different between areas of low and high conservation. However, if BGC is the cause of bias, then genomic G+C would be correlated with historical recombination rates or hot spots (Kong et al. 2002). To the extent that regional recombination rates remain constant (Myers et al. 2005), biased substitutions might be correlated with measures of current recombination. This study has been undertaken to document the characteristics of biased substitution patterns across the human and chimp genomes. We examine nucleotide bias in human SNPs and fixed chimp–human differences in an effort to characterize the roles of mutation bias, natural selection, and BGC in the observed patterns of substitution bias in the last 6 million years of human evolution.