Topics 7.4 -7.

5, Part 1: Understanding Allele Frequencies

1. A Population Genetics Case Study: The Cheetah

When chasing down prey, cheetahs have a top sprinting speed

of up to 60 miles (100 kilometers) per hour. It’s hard to imagine a better-adapted animal.

But even apart from human-caused problems related to hunting and the destruction of their habitat,
cheetahs are in trouble. For one thing, cheetahs have extremely low fertility. Studies of cheetah
sperm (collected by investigators who were trying to figure out why it was so hard to breed captive
cheetahs in zoos and wildlife parks) have shown that

1.​ Up to 79% of the sperm cells in any cheetah sperm sample are abnormal.
2.​ Cheetah sperm count is low (only 25 million per ejaculate, much lower than in other
species of cats).

The underlying problem is that cheetahs have extremely low genetic variability. It’s almost as if all
cheetahs were members of the same family. They have much less genetic variation than other wild
cats (source: The Cheetah in Genetic Peril, Scientific American, O’Brien, Wildt, and Bush). As we’ll
see, this genetic uniformity could put the cheetah at risk of extinction. With very little variation, their
ability to adapt to environmental change is limited.

To understand the cheetah’s genetic situation, we need to look at how genes are distributed and how
genes change in populations. This field is known as population genetics. Let’s start.

2. Population Genetics Interactive Reading: Gene Pools,

Fixed Alleles, Variable AllelesA gene pool
Move each item to its correct place

●​ 20,000
●​ alleles
●​ inherited
●​ parents
●​ same

The first population genetics concept to understand is the gene pool. The gene
pool is the total of all the ________

alleles

for all of the genes in a population.

To understand this concept, start by thinking of yourself. It took about 20,000

genes to spell out how to make your body, and to tell your body’s cells how to
behave. You inherited these 20,000 genes from your ___________

parents

, receiving one copy from your mother, and a second from your father.

Now, you’re not the only person who has these ___________

20,000

genes. You ____________

inherited
 your genes from your parents, so they have them. If you have siblings, they have
these genes, too. So do your cousins. Every human being has the ______

same

set of genes.

Move each item to its correct place

●​ alternative
●​ bases
●​ copies
●​ identical
●​ recipe
●​ sequence

Two homologous chromosomes, one from the

mother, and one from the father. At the locus for gene “A,” both alleles are the
same. At the locus for gene “B,” the two alleles are different (“b” and “B”)

Put together, all of these genes can be thought of as a cookbook. In this analogy,
each of our 20,000 genes is a different _________
recipe

: one recipe may be for a muscle protein. A second one may be for a digestive
enzyme. To develop from a zygote, and for your body to properly function, you
need to have two ________

copies

of each of these 20,000 recipes. But those recipes aren’t ____________

identical

. In the same way as your recipe for tomato sauce might be slightly different from
mine, it’s also possible that your mother’s genetic recipe for making a particular
enzyme might be slightly different from your father’s. In genetics, these
______________

alternative

versions of a gene are known as alleles.

You can also think of this in terms of where genes are on chromosomes. A gene’s
physical location on a chromosome is called its locus. At any locus, the DNA is
going to code for the protein that this gene is responsible for. But the specific
___________

sequence

of DNA _________

bases

might be different.

Move each item to its correct place

●​ alleles
●​ blood
 ●​ fixed
●​ homozygous
●​ population

Now, zoom out from thinking about your genes to thinking about the genes of an entire
population. Every member of that ___________

population

will have the same genes. But there will be a variety of _______

alleles

. On a very small scale, in a population with only five individuals and five genes, you
can think about it like this.

gene locus 1 gene locus 2 gene locus 3 gene locus 4 gene locus 5

Individual 1 allele 1a only allele 2a only allele 3b only allele 4a only allele 5a only

Individual 2 alleles 1a and allele 2a only allele 3c only allele 4a only allele 5b only
1b

Individual 3 allele 1b only allele 2a only allele 3a only allele 4a only alleles 5a and
5b

Individual 4 allele 1a only allele 2a only allele 3b and allele 4a only alleles 5a and
3c 5b
 Individual 5 alleles 1a and allele 2a only allele 3b only allele 4a only allele 5b only
1b

Focus first on gene locus 1. If you follow the column downward, you can see that it has
two alleles, allele 1a and allele 1b. By contrast, gene 2 has only one allele. Genes that
have only one allele in an entire population are known as fixed alleles. Gene 3 has three
alleles, the kind of situation that you’d find with the alleles for the ABO _______

blood

type system, which also has three alleles (A, B, and o). Gene 4 is also a _fixed allele.

Now, look at the individuals. Individual 1 happens to be ______________

Homozygous for all five of the genes. But individual two is heterozygous for gene 1
and homozygous for the other genes.

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3. Key Population Genetics Terms: Checking

Understanding
 A gene pool

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4. Allele Frequency

Allele frequency is another key concept in population genetics. Allele frequency is how common an
allele is in a gene pool. It’s usually stated as a decimal or a percentage.

4.a. Counting Alleles

Here’s an example. The table below represents the alleles for one gene in a population of 20 mice.
In this population, we’re going to look at two phenotypes: albino (white, with no pigmentation), and
normal (pigmented). Two alleles control this phenotype: “A” codes for normal color, and “a” codes for
albino coloration.

Albino

Normal (pigmented)
 aa Aa AA AA aa

AA aa Aa Aa AA

AA aa AA AA aa

Aa Aa aa Aa aa

To find the frequency of the “a” allele, start by counting each “a” allele within this gene pool. If an
individual’s genotype is “aa” then count two “a” alleles. If the individual is “Aa,” then count one “a”
allele. In other words, in the first row, you’d count a total of five “a” alleles.

Calculate allele

●​
▼

Albino
Normal (pigmented)

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5. Misconception Alert! “Dominant Allele” does not

mean “Most Common Allele”

The case of the Peppered moth allows us to demolish a misconception about genes and
populations: the false idea that dominant alleles, because they’re dominant, must be common.
Intuitively, it makes sense: if these alleles are dominant, why don’t they come to dominate? However,
this intuition is wrong. What we’ll see is that the frequency of an allele has nothing to do with whether
it is dominant or recessive.
 Start quiz

6. Allele frequencies and fixed alleles in dogs

Rhodesian Ridgeback: Dogs with pedigrees are homozygous for many genes.Source: Wikipedia

German Shepherd Golden Retriever Mutt: Mixed breed dogs are heterozygous for many
genes.Source, Wikipedia

For another angle on allele frequencies, let’s think about dogs. If you buy a dog with a pedigree (a
dog of a known breed), then you’re buying a certain look and disposition. You can count on this
because dog breeds are controlled populations where the gene pool is closely guarded by dog
owners who care about the breed. In other words, if you buy a Rhodesian Ridgeback, you can be
assured that your new puppy had two parents who were both Rhodesian Ridgebacks. For all the
traits that define the breed, these dogs are completely homozygous. Most of the defining alleles, in
other words, are fixed and would have an allele frequency of 1.0 (or 100%) in these very artificial
gene pools.
If your preference is for mutts, then your dog is probably heterozygous for many genes. As a result,
when you breed two mutts, the offspring’s appearance is much less predictable.