Fixed Differences Polymorphic Sites
Gene1
Replacement 2
10
Silent
20
100
% of fixed differences that involve replacement changes = 9.1%
% of polymorphic sites that involve replacement changes = 9.1%
Form of selection (Circle all that apply):
a) None (neutral)
b) Positive selection (= amino acid changes are advantageous)
c) Purifying selection (= amino acid changes are deleterious)
d) Balancing selection (e.g., heterozygote advantage)
Explanation: Replacement mutations within the species occurred at the same rate as they
are fixed between the species, therefore we cannot reject the null hypothesis that
replacement mutations have been neutral.
Fixed Differences Polymorphic Sites
Gene2
Replacement 10
0
Silent
50
100
% of fixed differences that involve replacement changes = 16.7%
% of polymorphic sites that involve replacement changes = 0%
Form of selection (Circle all that apply):
a) None (neutral)
b) Positive selection (= amino acid changes are advantageous)
c) Purifying selection (= amino acid changes are deleterious)
d) Balancing selection (e.g., heterozygote advantage)
Explanation: A large number of replacement mutations occurred between the species, but
none were polymorphic. Thus, replacement mutations must have been beneficial and fixed
rapidly at this gene.
Fixed Differences Polymorphic Sites
Gene3
Replacement 0
100
Silent
40
10
% of fixed differences that involve replacement changes = 0%
% of polymorphic sites that involve replacement changes = 90.1%
Form of selection (Circle all that apply):
a) None (neutral)
b) Positive selection (= amino acid changes are advantageous)
c) Purifying selection (= amino acid changes are deleterious)
d) Balancing selection (e.g., heterozygote advantage)
Explanation: Replacement mutations occurred within the species but are not being fixed
between the species, therefore replacement mutations have been deleterious (and don’t fix)
or are subject to heterozygote advantage (and remain polymorphic). On the basis of the
McDonald-Kreitman test alone, it is not possible to distinguish these two alternative
hypotheses (purifying selection or balancing selection).
Fixed Differences Polymorphic Sites
Gene4
Replacement 10
40
Silent
2
60
% of fixed differences that involve replacement changes = 83.3%
% of polymorphic sites that involve replacement changes = 40%
Form of selection (Circle all that apply):
a) None (neutral)
b) Positive selection (= amino acid changes are advantageous)
c) Purifying selection (= amino acid changes are deleterious)
d) Balancing selection (e.g., heterozygote advantage)
Explanation: Replacement mutations are fixed more frequently between species than are
found at polymorphic sites within species, therefore replacement mutations must have been
advantageous and rapidly fixed (this might be expected in a new environment at genes
involved in adaptation to the new environment).
Fixed Differences Polymorphic Sites
Gene5
Replacement 2
20
Silent
18
45
% of fixed differences that involve replacement changes = 10%
% of polymorphic sites that involve replacement changes = 30.8%
Form of selection (Circle all that apply):
a) None (neutral)
b) Positive selection (= amino acid changes are advantageous)
c) Purifying selection (= amino acid changes are deleterious)
d) Balancing selection (e.g., heterozygote advantage)
Explanation: Replacement mutations occur more frequently within the species than are
fixed between species, therefore replacement mutations must have been deleterious or
subject to heterozygote advantage.
Fixed Differences Polymorphic Sites
Gene6
Replacement 4
9
Silent
30
60
% of fixed differences that involve replacement changes = 11.8%
% of polymorphic sites that involve replacement changes = 13.0%
Form of selection (Circle all that apply):
a) None (neutral)
b) Positive selection (= amino acid changes are advantageous)
c) Purifying selection (= amino acid changes are deleterious)
d) Balancing selection (e.g., heterozygote advantage)
Explanation: Replacement mutations within the species occurred at nearly the same rate
as they are fixed between the species, therefore we cannot reject the null hypothesis that
replacement mutations have been neutral. (It is possible that there was selection, but by
chance these ratios still worked out to be the similar. For example, there could have been
both deleterious replacement mutations and advantageous ones.)
For each of these 2x2 tables, a chi-squared test (or similar contingency test) can be
performed to ascertain whether there is a statistically significant association between row
(fixed vs polymorphic) and column (replacement vs. silent). In this last example, the
probability of observing this or a more extreme association by chance alone is high
(p=0.854), confirming the notion that there is nothing significant going on (see
http://www.physics.csbsju.edu/stats/contingency_NROW_NCOLUMN_form.html).