Evolution__3rd_Edition

..
(proportion of polymorphic sites)
S
(a) Drosophila simulans
0.06
0.05
0.04
0.03
Zw
tty
slgA
0.02
Cdic
run
0.01
shakB su(f)
0
(b) Drosophila melanogaster
0.07
0.06
Zw
0.05
0.04
0.03
0.02
0.01
0
AnnX Pp4-19C
Bap
Bap
AnnX
Cdic
run
tty
slgA
Sdic
Pp4-19C shakB
18E 19A 19E 20A
su(f)
20D
Chromosomal position
Local reductions in genetic diversity
are a signature of selection
CHAPTER 8 / Two-locus and Multilocus Population Genetics 211
Figure 8.6
Selective sweep caused by recent substituion of the Sdic gene in
Drosophila melanogaster. The y-axis gives the amount of genetic
diversity. The x-axis is the position on the X chromosome.
Diversity decreases toward the centromere (off to the right
of the figure) where the recombination rate is decreased.
The diversity near the Sdic gene in D. melanogaster is lower
than we should expect from its position on the X chromosome.
If there had not been a selective sweep of Sdic, the graph for D.
melanogaster (b) would have looked much like the graph for D.
simulans (a). The points are for various genetic loci, and the line
around each point is the approximate 50% confidence interval.
From Nurminsky et al. (2001)
but in decreasing amounts the further we go away from the selected locus. Recombination
is more likely to have separated the favored mutation from its initially linked
nucleotides at sites further away in the DNA. The homogenization (that is, reduction in
diversity) of neighboring DNA when natural selection fixes a favorable new gene is
called a selective sweep. As a mutation increases in frequency, it sweeps diversity out of
the surrounding DNA.
Local reductions in genetic diversity can be used as a “signature” of natural selection
in DNA sequences. We can look down the DNA, and if we find a region of locally
reduced diversity, one explanation is that natural selection has recently fixed a new
gene somewhere in the region. Nurminsky et al.’s (2001) research on the gene called
Sdic in Drosophila melanogaster is an example (Figure 8.6). The gene Sdic codes for a
structure in the sperm. Figure 8.6b shows a trough in genetic diversity near Sdic, and
this trough is part of Nurminsky et al.’s case that the version of Sdic in D. melanogaster
has recently been fixed by natural selection.
A reduction in genetic diversity near a gene such as Sdic is not by itself strong
evidence that selection has recently fixed a new version of the gene. Two alternative
explanations need to be ruled out. One is that the mutation rate is locally depressed.
This can be tested by McDonald & Kreitman’s (1991) test (Section 7.8.3, p. 184). If the