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FIGURE 4.1 Two populations share a common boundary where hybridization occurs. Shown are two metacentric chromosomes that differ by an inversion (box) and incompatible alleles at two loci (*). Gene flow can readily occur along regions not linked to the inverted region (solid arrows) but is severely inhibited in regions linked to the inversion (dotted arrows). Natural selection favors the evolution of reproductive isolation between the populations by accumulation of incompatible alleles along the chromosome regions protected from recombination by the inversions. Figure was modified from Hey (2003).

rearrangements, allelic differences that might arise would not readily accumulate, because genetic recombination would tend to diffuse them between the populations (Fig. 4.1). This hypothesis can be tested, according to Navarro and Barton (2003b), by comparing genic differentiation between humans and chimps for different chromosome regions.

According to evolutionary theory, the rate of nonsynonymous nucleotide substitution per nonsynonymous site (KA) is generally expected to be much lower than the rate of synonymous substitution per synonymous site (KS), because random amino acid changes are usually deleterious, whereas synonymous changes are likely to be neutral or nearly so (Kimura, 1983). Thus, the expectation is KAKS, except when positive selection is involved favoring particular amino acid replacements, in which case KA will increase and may even become larger than KS. KA/KS ratios close to or >1 indicate positive selection.

Navarro and Barton (2003b) have investigated nucleotide sequences that exhibit nucleotide differences between chimps and humans in 115 genes, about evenly distributed between rearranged chromosomes (59 genes) and colinear chromosomes (56 genes) (Table 4.1). Of the 26 genes with KA/KS ratios ≤1, 20 (76.9%) are located on rearranged chromosomes,

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