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1. a. In allopatric speciation, a physical barrier splits a single ancestral population into two
or more populations that are no longer able to exchange genes. Because gene flow
between the populations is prevented, each population acts as an independent
evolutionary lineage. Different mutations will arise in each population and different
substitutions will also occur due to random effects of genetic drift and local differences in
natural selection. Thus, given a sufficient time period, genetic differences will
accumulate between the two physically separated populations. Presumably, this genetic
divergence is accompanied by the evolution of reproductive isolation. When the nascent
species come back into physical contact (i.e. the barrier is removed), reproductive
isolating mechanisms prevent gene exchange and thus, preserve species differences.
b. The Dobzhansky-Muller model proposes that postzygotic isolation evolves when
novel, deleterious allelic combinations arise in hybrids. To illustrate the model, consider
an ancestral population with the genotype AABB. This ancestral population splits into
two allopatric populations that fix alternate alleles at the two loci (Population1: AAbb,
Population 2: aaBB). Each new species is perfectly fit with its own particular
combination of alleles. However, if the physical barrier is removed and the nascent
species are able to mate, hybrid progeny will have a novel genotype: AaBb. Before these
hybrids, the a allele has never been in the same genome as the b allele. Because novel
allele combinations like a+b have not been tested by natural selection, some deleterious
combinations may arise and result in hybrid inviability or sterility.
Exam 2. Question 2.
a. Neutralists: Most mutations are deleterious and will be eliminated by selection as soon
as they occur. Some mutations will have little effect on fitness and are effectively neutral.
A small fraction of these will be fixed by drift and cause evolutionary change in protein
sequence. This fixation accounts for most protein evolution. Advantageous mutations are
very rare.
Selectionists: Most mutations are deleterious and will be eliminated by selection as soon
as they occur. Few mutations have negligible effects on fitness and are governed by drift.
A substantial number are selectively advantageous and are fixed by selection when they
b. A molecular clock assumes that DNA or protein sequences diverge at a fairly constant
rate (i.e. – there is a linear relationship between divergence time and number of
substitutions). As long as the mutation rate is constant over time, the molecular clock
follows directly from the properties of genetic drift and neutral evolution.
c. Neutral theory predicts that rate of protein evolution should be proportional to the
mutation rate, but mutation rate is measured in terms of mutations/generation. The
molecular clock is usually calibrated in terms of substitutions/year. So,
No. subs/year = (No. subs/generation)/(No. years/generation)
= (No. mutations/generation)(No. years/generation)
The number of substitutions per generation should be constant if we assume that the
mutation rate is more or less constant. Assuming that mutation rate is comparable for
most organisms, then the above relationship says that the number of substitutions/year
should be proportional to (No. years/generation). Another way of saying this is that the
substitution rate/year should be smaller for organisms with longer generation times. The
existence of a generation time effect is consistent with the neutralist theory, whereas its
absence is inconsistent and thus favors the selectionist theory.
d. i) Amino acid substitutions may be largely neutral. However, there is also the
possibility that positive selection just cancels purifying selection, so that some amino acid
substitutions were driven by selection. This situation is thus ambiguous.
ii) Selection has caused some amino acid substitutions. Some substitutions may also have
been caused by drift. Purifying selection also likely operates, but is not strong enough to
overcome the effects of positive selection.
Exam 2. Question 3.
a. Male and female breeding pairs are often joined by another young jay who is active in
helping raise the young and forgoes reproduction that breeding season. Woolfenden’s
study showed that the assistance provided by the helper increases the reproductive
success of the helped pair – helped pairs produce more surviving young in a season.
Woolfenden marked young birds and followed them over a period of years so that he
could determine the degree of relatedness of helpers to the individuals they helped. He
found that most altruists assisted close kin (their parents or a sibling), indicating that
altruism was not randomly directed and could have evolved by kin selection.
b. Dodd set up two types of Drosophila populations – one was reared on starch-based
media and one on maltose-based media. Neither media is “normal” for flies in the wild.
Dodd selected for adaptation to these new lab conditions and reasoned that this situation
would be similar to two physically separated populations evolving in different directions.
If in nature this is accompanied by the development of reproductive isolation, this should
also occur in the lab. Flies from starch-adapted populations were paired with flies from
maltose-adapted populations. Dodd observed that homogametic (within pop.) matings
were more common than heterogamic (between pop.) matings, indicating that pre-zygotic
isolating mechanisms had evolved.
c. When the physical barrier responsible for allopatric lineage splitting breaks down and
the two daughter lineages’ ranges overlap, coexistence is possible only if the two lineages
are not too ecologically similar. So, we expect in areas of sympatry that characters
indicative of ecological niche should be more different than in areas of allopatry. Huey et
al. found that where the two species of lizard co-exist, snout-vent length of T. lineatus is
much greater than snout-vent length of T. gariepensis, while in regions where T. lineatus
does not overlap with T. gariepensis, snout-vent length is not much greater. Since snoutvent length was found to be a good indicator of the animals’ diets, it appears that
character displacement has occurred in areas of sympatry as expected.
4. a. Altrusim is illustrated in sterile castes of social insects. This image shows
different castes of termites, including a very large reproductive queen, a
reproductive male, and several sterile workers.
b. Allopatric speciation and adaptive radiation. Many different species of Hawaiian
honeycreepers have evolved. Most species inhabit a single island and those that
inhabit more than one island have different subspecies on different islands,
indicating that population divergence is ongoing.
c. Signature of balancing selection with recombination. Variability at silent sites in
the region of the D. melanogaster Adh locus using the sliding window technique.
The peak is centered on the site of amino acid substitution between Fast and Slow
alleles of the Adh locus. Moving away from the site of balancing selection, the
effects of recombination become more dominant, and the amount of silent-site
variation decreases towards an equilibrium level.
d. Star phylogeny depicting the radiation of mammals. The time since the common
ancestor is the same for all lineages in a star phylogeny. By calculating the
number of amino acid substitutions, it is possible to determine whether variation
in substitution rates among lineages is consistent with a Poisson process, which is
predicted if genetic drift is the primary force shaping protein evolution. Kimura
found deviations from a Poisson clock for all five proteins he examined for the
star phylogeny shown.
5. The results of a MacDonald-Kreitman test suggest that positive selection may have
contributed to the evolution of Ipmyb1. If genetic drift is the primary force
influencing Ipmyb1 evolution, we expect that the ratio of non-synonymous to
synonymous polymorphisms within species will not differ from the ratio of
synonymous to non-synonymous fixed differences between species. However, as we
can see from the table below, these ratios are not equal. Instead, there is an excess of
non-synonymous differences between species, which might be the result of natural
selection acting to fix advantageous alleles within species (thereby removing genetic
On the other hand, it is not clear that 9/6 is statistically significantly different
from 19/9. If the ratios are not significantly different, we cannot rule out genetic drift
as the primary force shaping Ipmyb1 evolution.
within species
between species