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Why you should care about allele frequency:

Allele frequencies are one way to measure evolution in natural populations.  Measuring allele frequencies is an important component in understand how populations are changing, and has significance for conservation biology (i.e. not carrying all your genetic eggs in one allele basket).

1. Let's start from the bottom up.  What's an allele?

Most of us have a basic understanding of what a gene is: a piece of our DNA that, in essence, does a thing (or in the case of certain genetic disease, perhaps fails to do the thing). An allele is a particular version or variant of a gene.  So for example, there are genes that affect hair color, and there alleles that specify brown hair, black hair, blond hair, or red hair.  The brown hair allele has different DNA than the blond hair allele, and all the others.  There may be several DNA differences, or there may be only one.  Sometimes, despite the differences in DNA, two different alleles may act the exact same way!

[Additional Reading: Genes are pieces of DNA that encode for proteins.  Different alleles code for different final protein products, which may be different at only one amino acid, or which may vary greatly in size.  The amount of DNA differences between the alleles isn't really related to how different the proteins they produce are; a single changed letter in the DNA early in the gene may create an early "stop" signal for when the protein is being put together instead of the amino acid that should have gone there to continue the chain.  Several diseases are caused by the often nonfunctional proteins that result, such as cystic fibrosis; some white pigmentations in plants and animals are also caused by proteins that wind up "unfinished" in this way.]

2. For the most part, we have two copies of each gene, one from each of our parents (represented below by two very stereotypically-colored chromosomes).  You may have the same allele from both parents (you are homozygous) or you may have two different alleles (heterozygous).

We often represent different alleles with capital versus small letters.  You can see that the alleles are in the same place on both chromosomes; the gene is always located in the same place on a chromosome, and that place is called a locus.  The DNA may be different, giving you different alleles, but the gene itself isn't going anywhere.  This individual is heterozygous, because they have two different alleles.

[Additional Reading: Some people may actually have more or less than two copies of particular genes.  In Down's Syndrome, a third copy of the 21st chromosome is present, so people with this syndrome have an extra copy of each gene.]

3. Of course, each gene doesn't have its own chromosome.  There can be anywhere from about 50 to over 2,000 genes on any given human chromosome (chromosome 1 has the most, while the Y chromosome has the fewest.  Sorry, Y-chromosome folks) and any of those genes can have a variation of alleles.

So when we use the terms homozygous or heterozygous, we can really only talk about one gene at a time.  No one gets the exact same chromosome from both parents (unless you are from a species of hermaphroditic time-travelers). Zygosity describes particular genes, not entire organisms.  You can be homozygous for the hair color gene, you can't be a homozygous person.

4. So, for any given gene, there are two copies for each individual in a population.  If you have a population of 200 people, there are 400 copies of Gene A.  The allele frequency is the portion of those 400 gene copies that are allele A versus the portion that are allele a. 

In the above (small) population of flowers, we have one homozygous red flower (two A alleles); two homozygous white flowers (two a alleles); and two heterozygous red flowers (one A allele and one a allele).  To find the allele frequency for any particular allele, we just divide the number of copies of that allele by the total number of copies of the gene.

Total number of copies of this gene: (5 flowers) x (2 copies) = 10

Total number of A: (2 x 1 homozygous A) + (1 x 2 heterozygous)

                                               (2)               +            (2)              = 4 A

Total number of a: (2 x 2 homozygous a) + (1 x 2 heterozygous)

                                               (4)               +            (2)              = 6 a

Frequency of A in population: (4 A) / (10 total copies) = 0.4

Frequency of a in population: (6 a) / (10 total copies) = 0.6

If you know the frequency of either in allele in any situation where there are only two possible alleles, you can easily calculate the other by subtracting from 1.

Why you should care about allele frequency (redux):

Change in allele frequencies over time means a population is evolving.  If allele A has always had a higher frequency than allele a, but suddenly starts to drop off and fall behind, allele a might have become advantageous due to a change in environment.  Or - more likely - the change in frequency may be due to random chance; even randomly, though, important and useful alleles can be wiped out of a population, and new ones can spread.

Allele frequencies also have an impact for conservation.  For species like cheetahs that have dropped dangerously low in numbers at some point, the allele frequency of certain genes may equal 1, or close to it - this lack of diversity means the population has fewer options on the table should an environmental change occur.  Having a more moderate frequency spread across a few different alleles is better for an endangered species.

Useful Greek and Latin terms

hetero- : different

homo- : same

-zygous : state of allele pairings for a gene; from the word for 'yoke', as in oxen

locus (pl. loci) : place

Simplifications and Common Misconceptions

A single gene can have more than two alleles (alleles for brown, red, black, and blond hair, for example).

Two different alleles can behave the exact same way, if the DNA changes between them aren't enough to create any real difference in the proteins they produce.

A person may have more or fewer than two copies of each gene if they have conditions such as Down's or Turner's Syndrome.

While humans have two copies of each chromosome and therefore each gene, this isn't true of all species.  Male bees have only one copy of each, and some species of strawberry have as many as 10 copies!

When calculating allele frequency, don't forget to count BOTH copies of the allele in homozygous individuals.  A common mistake is to just count the individuals themselves, which will give you too low of an end result.

Questions for Practice (answers below the cut)

1. Some species of wheat get four chromosomes from each parent, instead of one apiece like we do.  How many copies of each gene does a wheat plant have?

2. Imagine gene D.  A population of people has 20 people who are homozygous for allele D, 13 people who are homozygous for allele d, and 47 people who are heterozygous. 

a. How many copies of allele D are in the population?

b. How many copies of the gene are in the population?

c. What is the allele frequency of D?

3. A population of people has an allele frequency of 0.1 for the version of a gene that causes cystic fibrosis.  What is the allele frequency of the normal version of that gene?

Up next time: Hardy-Weinberg

Answers to Practice Questions