Evolution__3rd_Edition

212 PART 2 / Evolutionary Genetics
Drosophila melanogaster has a
local reduction of diversity near the
gene Sdic ...
. . . which is almost certainly due to
a selective sweep
mutation rate is low, we expect not only low diversity within a species, but also a low
rate of evolutionary change. The rate of evolution can be found by comparing the gene
in D. melanogaster and the closely related species D. simulans. In fact the rate of evolution
is high, suggesting that the mutation rate has not been lowered near Sdic.
A second alternative is background selection. Deleterious mutations occur in the
DNA (Section 12.2.2, p. 321, looks at the deleterious mutation rate). Natural selection
acts against deleterious mutations, removing them from the population. As selection
clears out deleterious mutations, it also reduces the local genetic diversity because any
variants linked to a deleterious mutation will be removed along with it.
In some regions of the genome, the recombination rate is lower than in other
regions. For example, recombination is less frequent near the centromere of a chromosome.
Also, a whole chromosome may have a low recombination rate. Chromosome 4
in Drosophila is short and has a low recombination rate (Wang et al. 2002). In regions
where the recombination rate is low, the diversity of DNA is known to be reduced:
D. melanogaster’s fourth chromosome, and all chromosomes near their centromeres,
show low genetic diversity. This reduction could be either because of selective sweeps
or background selection. Both processes reduce genetic diversity, and both operate
more powerfully where the recombination rate is low. Now, the Sdic gene is on the
X chromosome and is near the centromere. The low local diversity could be due to
background selection in a region of low recombination, rather than to a selective sweep.
Figure 8.6 shows how Nurminsky et al. argue that the version of Sdic in
D. melanogaster has caused a selective sweep. D. simulans (Figure 8.6a) shows a standard
decrease in genetic diversity towards the centromere. The picture for D. simulans
may well be due to background selection. If background selection caused the low diversity
in D. melanogaster near the Sdic gene, we should expect much the same graph in
both species. (There is no evidence that Sdic has undergone recent evolutionary change
in D. simulans.) But Figure 8.6b shows that DNA diversity near Sdic in D. melanogaster is
reduced relative to D. simulans. The reduced recombination rates near the centromere
are not enough to explain the trough in diversity seen in D. melanogaster. The Sdic gene
really does appear to have been fixed recently in D. melanogaster, and to have swept out
the local diversity.
Selective sweeps, in which the local genetic diversity is reduced, can be added to the
other signatures of selection that we looked at in Section 7.8 (p. 179 a signatures such
as the relative rates of non-synonymous and synonymous evolution). The test has practical
uses, and Box 8.1 describes how it can be used to detect which genes code for drug
resistance in the malaria parasite. The test is most powerful if alternatives can be ruled
out, and provides a further example of how DNA sequence data are allowing some
novel tests of natural selection.
8.11 Linkage disequilibrium can be advantageous, neutral,
or disadvantageous
Although linkage disequilibrium may be rare when we consider all the genes in a
species, some examples still exist. We can distinguish between cases that are beneficial,
..