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Appendix B

The HardyWeinberg Equilibrium

In Chapter 5, we introduced the HardyWeinberg equilibrium in the context
of our discussion of the forces of evolutionary change. Population genetics
provides the mathematical underpinnings of evolutionary theory, and the
HardyWeinberg equilibrium is at the heart of mathematical and quantitative approaches to understanding evolutionary change in diploid organisms.
In this appendix, we will briefly go over a derivation of the HardyWeinberg
equilibrium and show some applications of the equilibrium in evolutionary
Throughout the discussion, we will use the simplest case to illustrate our
examples: a single gene (or locus) with two alleles, A and a. The frequency of
A in the population is represented by p; the frequency of a is represented by q.
By definition, p + q = 1.

Derivation of the
HardyWeinberg Equilibrium
The HardyWeinberg equilibrium states that, given known
allele frequencies p and q, we can represent the genotype
frequencies by AA = p2, Aa = 2pq, and aa = q2. Furthermore, these allele frequencies remain constant from generation to generation if the following conditions are met:
Large population size (or theoretically infinite population size), which minimizes the influence of genetic
drift on allele frequencies
Random mating (no inbreeding or assortative or disassortative mating)
No mutation
No gene flow
No natural selection
Let us begin by considering a specific example, where
the allele frequency of A is 0.6 (p = 0.6) and that of a
is 0.4 (q = 0.4). To look at this another way, the probability that any given sperm or egg will carry A is 0.6, and
the probability that it will carry a is 0.4. Thus under conditions of totally random mating, with no other evolutionary forces in effect (under equilibrium conditions), the
probability of producing a zygote with a homozygous AA
genotype is (0.6) (0.6) = 0.36. We can represent the
probabilities of all the genotypes occurring in a modified
Punnett square:
freq ( A) = p = 0.6 freq(a) = q = 0.4


freq(A)5p50.6 freq( AA) = p2 =

freq( Aa) = pq =

(0.6)(0.6) = 0.36

(0.6)(0.4) = 0.24

freq(a)5q50.4 freq ( Aa) = pq =

freq( aa) = q 2 =

(0.6)(0.4) = 0.24

(0.4)(0.4) = 0.16

This gives us a population with genotype frequencies

of 0.36 (for AA), 0.48 (for Aa), and 0.16 (for aa). What
are the allele frequencies for this population? For A, it is
0.36 + (0.5)(0.48) = 0.36 + 0.24 = 0.6, which is what
the frequency of A was originally. The allele frequency of a
is 0.16 + (0.5)(0.48) = 0.16 + 0.24 = 0.40, which is the
original frequency of a. This demonstrates that allele frequencies are maintained in equilibrium under conditions
of random mating and in the absence of other evolutionary forces.
The general equation for the distribution of genotypes for a population in HardyWeinberg equilibrium is
given by the equation
p2 + 2pq + q2 = 1
We can derive this equation directly from the modified
Punnett square.
The constancy of allele frequencies over generations
is shown by the following equations. Let p9 equal the allele
frequency of A in the first generation. From the preceding
example we see that
p' = (frequency of AA) + (0.5)(frequency of Aa)
We want to count only half the alleles for A in the heterozygotes. Substituting the allele frequency values from
the HardyWeinberg equation, we get
p' = p2 + (0.5)(2pq)
Because (0.5)(2pq) = pq, we now have
p' = p2 + pq
Which, factoring out p, is the same thing as
p' = p(p + q)
As you recall, p + q = 1; therefore,
p' = p
This demonstrates that allele frequencies remain constant
in a population in HardyWeinberg equilibrium.
One of the main uses of the HardyWeinberg equation is to determine if a population is not in equilibrium.
We do this by comparing observed allele frequencies with




observed genotype frequencies. If the observed genotype

frequencies are significantly different from those expected
based on the allele frequencies (which we usually check
by using a chi-square statistical test), then we can say the
population is not in equilibrium. This result indicates that
one of the assumptions of the HardyWeinberg equilibrium is being violated and that an evolutionary force may
be acting on the population or acted on the population
in the past to produce the non-equilibrium distribution of
Another application of the HardyWeinberg equation
is to estimate the frequency of heterozygotes in a population. As we discussed in Chapter 5, it is particularly useful
for estimating the frequency in a population of carriers of
recessive autosomal illnesses, such as TaySachs disease or
cystic fibrosis. The recessive allele frequency is simply
q = 2frequency of autosomal recessive condition
And the dominant allele frequency is
p = 1 - q
Thus the frequency of heterozygous carriers = 2pq.

HardyWeinberg and Natural Selection

The HardyWeinberg equilibrium can help us mathematically model the effects of any of the forces of evolution
(mutation, genetic drift, gene flow, and natural selection).
Let us consider how to use the HardyWeinberg equation to understand how natural selection may affect the
distribution of allele frequencies in a population. In these
equations, we assume that natural selection is the only
force of evolution acting on the population.
In the simple case of one gene with two alleles, we
have three possible genotypes that are subject to natural
selection. To model the change in allele frequencies, we
need to know not the absolute fitness of each genotype
(which we could measure as its likelihood of survival),
but rather each genotypes fitness relative to each other.
Relative fitness usually is represented by the letter w; thus
we have
wAA = relative fitness of AA
wAa = relative fitness of Aa
waa = relative fitness of aa
Lets say that the homozygous genotype AA has the highest fitness; its relative fitness wAA therefore would be equal
to 1. The relative fitnesses of Aa and aa are lower, such
wAA = 1.0
wAa = 0.8
waa = 0.4
Lets also assume starting allele frequencies of p = 0.7
and q = 0.3.

If the population were in HardyWeinberg equilibrium, the expected genotype frequencies after one generation would be
p2 = (0.7)(0.7) = 0.49 for AA
2pq = 2(0.7)(0.3) = 0.42 for Aa
q2 = (0.3)(0.3) = 0.09 for aa
However, natural selection is working on this population
and affecting the survival of the different genotypes. So
the genotype frequencies after selection are
wAAp2 = 1.0(0.7)(0.7) = 0.49 for AA
wAa2pq = 0.8(2)(0.7)(0.3) = 0.336 for Aa
waaq2 = 0.4(0.3)(0.3) = 0.036 for aa
The frequency of p after natural selection has acted
on the population is
p' = 3 (0.49) + (0.5)(0.336) 4 >(0.49 + 0.336 + 0.036)
= 0.658>0.862
= 0.763
The frequency of q is
q' = 1 - p' = 1 - 0.763 = 0.237
So after only one generation of natural selection
operating at these levels, there is a substantial change in
allele frequencies, with A going from 0.7 to 0.763 and a
decreasing from 0.3 to 0.237. Following this through five
generations, the allele frequencies would be











In the case of a lethal autosomal recessive condition (such

as TaySachs disease), in which the relative fitness of the
recessive homozygote is 0 and for the other two genotypes
it is 1, we can represent the change in allele frequency of
the recessive allele by a simple equation (which is derived
from the HardyWeinberg equation):
qg = q0 > (1 + gq0 )
where g is the number of generations passed, qg is the
frequency of a in generation g, and q0 is the starting
frequency of a. Consider a founding population in
which the allele frequency of a lethal recessive is 0.20.
Over ten generations, the frequency of this allele will
decrease to
q10 = 0.2> 3 1 + (10)(0.2) 4
= 0.2>3
= 0.067
Of course, a small founding population violates one of the
conditions of the HardyWeinberg equilibrium (infinite
population size), but we can ignore that for the sake of
this example.