**In-Class
Population Genetics Exercise (note that this exercise will take more than one
class to complete: at the end of 1**^{st} class, remind students to hold
onto their cards).

To perform this exercise, you will need: *i)* a class of students; *ii)* sufficient playing cards so that
each student can obtain 2 cards each (remove joker & instruction cards); *iii)* one distinct set of playing cards
(that will be distributed among the sets); *iv)*
everyone has a personal response system (PRS), *i.e.* an iClicker.

When cards are initially handed out to the
students, DO NOT shuffle them, as we want initial population be in a state of *non*-H-W-equilibrium.

These cards represent (initially) a one gene,
two-allele system. Hearts & Diamonds represent the red allele (r), while
spades & clubs represent the black (B) allele. We initially treat B as
dominant over r. (A real-life equivalent is the B & r alleles at the
K-locus for coat colour in Cocker Spaniels). Each student represents a diploid
individual, who is hermaphroditic (capable of mating with anyone else in the
population).

Initial census of the class:

Total starting population size of 270, most of
which will be BB or rr.

Use clicker to 1^{st} count phenotypes
(Black or red) in population

Use clicker to then count genotypes.

Ask students to calculate p & q in starting
population (should be p~0.5, q~0.5).

Simulation of Random Mating:

In this exercise, the point is to establish a
population which is stable, and in which Hardy-Weinberg equilibrium becomes
established

A new organism will replace each individual
organism.

Ask students to turn to someone nearby, and to
randomly exchange one of their two playing cards. This represents a
reproductive event.

Using clicker, ask students what they think has
happened to the frequencies of p & q (same as before, increase in
p/decrease in q, increase in q/decrease in p, decrease in p/decrease in q,
increase in p, increase in q).

Explain why p & q don’t change (no loss or
gain of cards)

Ask students what they think will happen to
phenotypes (same as before, increase in BLACK/decrease in RED, increase in
RED/decrease in BLACK). Assuming that there will be more heterozygotes, we
should see increase in Black phenotypes, and a decrease in Red phenotypes.

Poll students using iClicker to determine the
distribution of RED & BLACK phenotypes in the population. Compare to
initial distribution.

Ask students what they think will happen to
genotypes (same as before, increase in BB & Br decrease in rr; decrease in
BB increase in Br decrease in rr; decrease in BB, increase in Br decrease in
rr, increase in BB decrease in Br increase in rr). Assuming that there will be
more heterozygotes (due to random mating), we should see increase in Br
phenotypes, and a decrease in BB & rr genotypes.

Poll students using iClicker to determine the
distribution of BB, Br & rr phenotypes in the population.

At this point, discuss concept of H-W
equilibrium: what is a model, why is it useful, what are its limitations (i.e.
assumptions: sexually reproducing organism, reasonable large population, mating
is random, no migration into or out of the population, no mutations, no
selection

Use H-W formula to calculate predicted
genotypes & phenotypes in the population. Compare these values to
observations made in class.

Discuss why values may not match (mating was
not fully random, finite population means no fractional individuals possible).

Get class to repeat random mating exercise as
above. Use clicker to poll for phenotypes & genotypes. Discuss why or why
not these frequencies have changed, and if they are getting closer to H-W equilibrium
(hopefully they are).

Get class to repeat random mating exercise one
additional time above. Use clicker to poll for phenotypes & genotypes.
Discuss why or why not these frequencies have changed, and if they are getting
closer to H-W equilibrium (hopefully they have). Use this data to indicate that
as long as the assumptions are not violated, and that p and q remain constant,
the genotype frequencies will hold constant at the Hardy-Weinberg equilibrium
values, generation after generation.

Now, we want to see what happens if we start to
violate the assumptions, starting with random mating.

Ask students to “mate” with others of the same *phenotype*
(RED with RED; BLACK with BLACK). This is assortative mating.

Ask students what they think will happen to
phenotypes/genotypes (same as before;

Increase in BLACK (more BB) decrease in RED;
Increase in BLACK (more Br) decrease in RED, Decrease in BLACK (but more Br)
increase in RED, Decrease in BLACK (but more BB) increase in RED.

Poll students using iClicker to determine the
distribution of RED & BLACK phenotypes in the population. Were the results
(hopefully Decrease in BLACK (but more BB) increase in RED) what people
predicted?

Discuss how while mating in the whole
population was non-random (assortative mating), that within the subset of BLACK
phenotypes mating was random (because mating was based on phenotypes, not
genotypes.

Assuming that there were (before the
assortative mating) 135 Br individuals in the class & 67 BB individuals
(H-W predicts 67.5), then for the 202 individuals (and 404 alleles in the
population), there should be 269 B alleles (p=0.665) and 135r alleles
(q=0.335). From these p & q values, we can predict how many BB, Br & rr
individuals would be produced. BB: p^{2}=0.44 (~89 individuals), Br:
2pq=0.44 (~89 individuals), rr: q^{2}=0.11 (~23 individuals).

Ask students what would happen if we continued
to have assortative mating? Changes in phenotypes/genotypes?

Now, get students to undergo dissortative
mating (BLACK with RED, whenever possible).

Ask students what will happen to
phenotypes/genotypes (same as before;

Increase in BLACK (more BB) decrease in RED;
Increase in BLACK (more Br) decrease in RED, Decrease in BLACK (but more Br)
increase in RED, Decrease in BLACK (but more BB) increase in RED. This should
show how we get an increase in the amount of heterozygotes.

To show how random mating will restore
population to H-W equilibrium, get students to undergo one round of random
mating. Use iClicker to examine genotypes.

Next, we shall consider why a violation of the
assumption of large population might affect our estimate of H-W equilibrium. Pick
a row of ~10 students at random from the class, and get them to input (via
iClicker, their genotypes). How close are their values to the p & q of the
whole population and the predicted H-W values? Repeat with another row (this is
to increase your odds of getting some atypical p & q values). This will
show how small samples may not provide accurate representations.

Using a shuffled spare deck of cards, get 5-10
students to select 2 cards each at random from the deck. While p & q
are=0.5, the observed frequencies of BB, Br & rr should (hopefully) not be
in H-W equilibrium.

Next we shall consider effect of selection.
Start by imagining that people don’t like RED Cocker Spaniels, and start only
breeding BLACK dogs with BLACK dogs. This means that RED dogs don’t contribute
to the next generation. Ask all students with 2 red cards to sit out the next
mating round. Quickly survey the students on their genotypes before and after 2
rounds of mating (with any RED phenotypes) getting dropped from the population.
Ask the students if they think that the r allele will be lost from the population
selection against RED continues?

Demonstrate (using the rare (q=0.038)
green-backed cards that have been mixed in with the regular black-backed cards
q=0.962) how that even there is strong selection, that rate recessive
deleterious genes will be retained in low frequencies (mostly as heterozygotic
state). In a class of 270, there should be ~20 green cards in total, H-W
predicts that there will be 0.38 individuals that are greenback/greenback
(i.e.~0), 19.7 individuals that greenback/blackback are and 250 that are
blackback/blackback. This means that >98% of green cards will be in
heterozygous state (and hidden from selection).

Ask how the efficiency of selection would be
affected if r or greenback alleles were dominant or co-dominant?

Next, let us consider selection acting on a
quantitative trait (ask students to define quantitative vs. quantitative:
perhaps asking them to write a list of 4 quantitative and 4 qualitative
traits). Using the values on the face of the cards as allelic value (A=1,
2,3,4,5,6,7,8,9,10,J=11,Q=12, &K=13), get students to indicate phenotypic
values (in clicker group into sets of 5: (2-6, 7-11, 12-16, 17-21, 22-26).
Discuss the bell-shaped nature of the data: all value cards are in same
proportions in the gene pool, but few outliers.

Perform directional selection (all those with
values less than 7 must sit out) in two successive rounds of mating. Note how
mean and distribution of population phenotypes changes.

Next, start stabilizing selection (all those
with values less than 7 or more than 18 must sit out). Note how mean and
distribution of population phenotypes changes.

If time permits, do several rounds of
assortative mating and divergent selection: Selection for high values of BLACK,
and low values of RED. Examine phenotypes over time.