Evolution, 4th Edition

176 CHAPTER 7

beneficial mutation eliminates variation in the surrounding region of chromosome

(see Fig ure 5.15). In a similar way, when selection eliminates a deleterious muta-

tion, polymorphism is reduced nearby on the chromosome (FIGURE 7.10). T his

effect is called background selection. Both selective sweeps and background selec-

tion affect larger pieces of a chromosome in regions where recombination rates are

low, producing the pattern seen in Figure 7.9. Selective sweeps and background

selection reduce the amount of polymorphism at neutral sites of the genome below

what Equation 7.1 predicts.

Estimating population size

The relation between heterozygosity and popu-

lation size suggests a strategy for estimating the

effective population size of a species. The idea is

to estimate π by sequencing several individuals

at sites in the genome that are evolving neutrally.

(Introns are often used for this purpose.) We can

also estimate the total mutation rate (μ) using the

methods discussed in Chapter 4. Because we are

focusing on sites that are selectively neutral, the

total mutation rate is equal to the neutral muta-

tion rate (μn). We find the value of Ne that solves

Equation 7.1 for each DNA site, then average those

values.

Estimates of the effective population sizes have

been made this way for several species (FIGURE

7. 11). The lowest estimate shown comes from
   humans: Ne for our species is roughly 10,000.
   While there are now more than 7 billion people on
   Earth, our numbers were much smaller just a few
   thousand generations ago.
   This approach can be pushed further to do
   something even more impressive: we can estimate
   a species’ effective population size from just a
   single individual [19]. The approach is to sequence
   its DNA to find the average heterozygosity at a
   large number of selectively neutral sites, then use
   the logic just described to estimate Ne. Another
   remarkable use of DNA polymorphism is to esti-
   mate population sizes in the past. The zebra finch
   discussed earlier now has an effective population

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(A)

1 2 3 4 5

(B)

1 2 3 4 5

(C)

1 2 3 4 5

FIGURE 7.10 Background selection

decreases neutral genetic polymorphism.

(A) A population of chromosomes is poly-

morphic for neutral mutations at five sites

(yellow bands). (B) Deleterious mutations

appear on two chromosomes (red bands).

(C) Selection eliminates chromosomes car-

rying deleterious mutations. A side effect

is that neutral polymorphism is reduced

nearby on the chromosome (at sites 2 and

5): the population is now polymorphic at

only three sites.

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Gray whale

Gorilla

Human

Chimpanzee

C. remanei

C. elegans

E. coli

0 10,000 100,000 1,000,000 10,000,000

Effective population size, Ne

D. melanogaster

FIGURE 7.11 Effective population sizes (Ne), estimated from levels of DNA

polymorphism. The species are ordered by body size; notice that large or-

ganisms tend to have smaller effective population sizes. The horizontal scale

is logarithmic, so that each vertical line shows a change of Ne by a factor of

10. Humans have a very small Ne: although there are now more than 7 billion
    people, we descended from only about 10,000 individuals living 100,000
    years ago. Two nematode worms are shown. The effective population size of
    Caenorhabditis remanei, which does not self-fertilize, is 20 times larger than
    that of C. elegans, which does self-fertilize. The gut bacterium Escherichia
    coli has an effective population size much larger than that of any of the ani-
    mals or plants. (Data from [7].)

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