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THIS
KEY WAS PRODUCED USING THE ANSWERS PROVIDED BY SEVERAL STUDENTS.
1.
Provide definitions for the following 13 terms. (2 pts each)
·
Bounded
hybrid superiority model: Hybrids have low fitness in either parental
environment, but there will be an area, usually intermediate between the
parental environments, in the hybrid zone where the hybrid will do better than
either parental type can.
·
Cenancestor:
the ancestor of all organisms alive today (term can also be used to refer to
the ancestor of any particular extant clade)
·
Cytonuclear
discordance: when the nuclear DNA and cytoplasmic DNA tell a different heritage
story. This can occur, for example, if
males of one species (C) mate with females of another (Z), but not vice versa. If the males swamp the other species in one
geographic area, the nuclear DNA may show that an individual belongs to C, but
the mitochondrial DNA will place the individual in species Z.
·
Gynodioecy:
when individual plants come in two types: male and hermaphrodite.
·
Monoecy:
when both sexes are found on all individual plants (usually in the form of
hermaphrodite flowers)
·
Neofunctionalization:
when a duplicated gene takes on a new function
·
Peripatric
speciation: separation of species when a small groups
is separated allopatrically from the larger group. In this form of speciation drift can separate
species because the group is rather small and vulnerable to drift.
·
Progenote:
the ancestor of all organisms that have ever lived. This is not the same thing as the
cenancestor, because it takes into account all the species that have gone
extinct, and so goes back further.
·
Pseudogene:
a genetic section that either does not have function (because it lacks a start
codon, etc.) or because it has not been under selection and has had mutations
in it that lead to loss of function.
Sometimes, on rare occasions, these pseudogenes can be reactivated
(possibly via mutations that make them functional) and become genes again.
·
Subfunctionalization:
when each daughter gene in a duplicated gene pair takes on part of the function
of the original gene. This is shown in
monkeys with and RNase 1a and 1b, where one copy of the gene works incredibly
well in the acidic stomach, while the other functions in the rest of the body
and in zebrafish where the genes are expressed in different parts of the
body.
·
Tension
zone model: there should be low hybrid fitness because the hybrid is not the
highest fitness for either of the parental zones, and will have to compete
(unsuccessfully) for resources with the parental types. In this model hybridization is maintained
passively by meeting and mating between parental types, but the hybrids
themselves never take off.
·
Transgressive
segregation: When a hybrid exhibits novel features that are not intermediates
of either of the parent species. This
can allow them to fill new niches and allow for hybrid-based adaptive
radiations.
2.
How do each of the following potentially influence the
transfer of genetic material from organelles to nuclei? (6 pts)
a.
Muller’s rachet: because organelles reproduce asexually, they are susceptible
to accumulation of deleterious mutations (and the loss of the most fit class via drift).
Transfer of genes to the nucleus can thwart this.
b.
Organelle replication rate: It is an advantage for an organelle to replicate
quickly, particularly if there are other organelles in the same cell with
different genomes (heteroplasmy.)
Therefore, there is selection for the organelle genome to become smaller
(and thus able to more rapidly divide.)
c.
Free radical damage: some organelles undergo processes that lead to the
creation of free radicals (like respiration in mitochondria). These free radicals will cause mutations in
the genome, leading, again, to selection favoring a nuclear gene if there are
two copies.
3.
The fact that non-coding regions are targeted for deletion supports which of
the above hypotheses and why? (2 pts)
The
fact that non-coding regions are targeted for deletion supports the
organelle-replication rate hypothesis, because it shows that it is not just
that genes with functions are becoming defunctionalized, but even that neutral
genes (or pseudogenes) are being targeted for removal—which wouldn’t matter if
it were only a matter of Muller’s ratchet or damage due to free radicals.
4.
What is a sexually antagonistic cytoplasmic nuclear interaction? (3 pts)
One
example would be mutations in mitochondrial DNA, which can cause very low
fertility in males, but which will not be selected against because mtDNA is
only passed through the female line (and female gametes, with more mitochondria
and fewer energy demands can continue to reproduce even with a mutational load
that might knock out a male mitochondria.)
The nuclear DNA wants to reproduce itself, even if it’s in a male
gamete, but the mitochondrial selection won’t go against the mutation because
it doesn’t harm the females who are passing on the mitochondria.
5.
Sperm size in black field crickets and yellow dung flies (both of which have
heterogametic males) responded to selection on females but not on males. A similar result was found for sperm motility
in chickens (which have heterogametic females).
Which taxa provides better support for the hypothesis that male fitness
traits can be located in the mitochondrial genome? Why? (2 pts)
The
chicken example provides better support for the hypothesis that male fitness
traits can be located in the mitochondrial genome. This is because, in the crickets and dung
flies, the male fitness traits could be linked to either mitochondria or the
X-chromosome (both of which the male will inherit from his mother.) In the chicken example, the male could
inherit either chromosome from his mother, so the fitness trait is almost
certainly linked to the mitochondria.
6.
The size of the olfactory receptor gene family is similar in humans and mice,
but the percentage of pseudogenes is >60% in humans and only 20% in mice. Explain. (2 pts)
When
a gene becomes a pseudogene, it usually indicates a relaxation of selection. This would seem to suggest that the selection
for olfactory genes has been more relaxed in humans than in the mice, leading
to our genes accumulating mutations and eventually losing functionality to the
extent that they are pseudogenes now.
This would indicate, probably, that humans no longer need as strong a
sense of smell as we once did in our genetic past so the loss of the olfactory genes was not
selected against.
7.
Describe the stages through which the most “successful” adaptive radiations
pass. (4 pts)
Successful
adaptive radiations tend to pass through the stages of: habitat division, when
a progenitor species divides by habitat (for example, when the cichlid
progenitor divided between sand and rock); trophic morphology changes, when the
species subdivides to fill niches (for example, when the cichlids took over the
many small-scale niches in Lake Victoria and their morphology changed to fill
these niches); and communicative barriers, when species further divide based on
assortative mating for communication traits (such as color in cichlids). These
stages can all be occuring at the same time, although one should be dominant at
any given time, and may not happen in the order that is laid out here. If the environment does not allow for
dividing and subdividing into niches or if the species does not have requisite
genetic variation to allow for specializing into trophically morphological
niches, or for communication differences to arise, the radiation will halt in
one of these stages, and not go on to create further species.
8.
How does one measure the success of an adaptive radiation? (2 pts)
One
could measure the success of an adaptive radiation in the number of new species
it generates, but there are questions there about whether it is really
successful if it generates a lot of new species, but they die out quickly, or
if the species generated are really only separated by communication differences,
so sometimes the success of an adaptive radiation is measured by the number of
new niches it manages to fill.
9.
How does multiple mating influence the likelihood of observing the evolution of
reinforcement in species with strong CGP? (while you’re at it, define/explain
CGP) (2 pts)
Conspecific
gamete precedence, or the reproductive preference for your own species’ sperm
can be found sometimes among allopatrically separated species that are then
brought back together. A female may mate
with males of another species, but she tends to only produce offspring from
matings with males of her own species.
If CGP is strong low-quality hybrid offspring are not produced, which
would cause the evolution of other reinforcement strategies to be favored if
the species were monogamous (since the heterospecific matings would produce few
offspring). However, if there is
multiple mating the selection for other methods of reinforcement are not as
strong, since the likelihood is the male will mate with someone of his own
species (as well as some heterospecifics) and the female will mate with a male
of her species, and preferentially produce those children, keeping the costs of
heterospecific mating down.
10.
What is the effect of nuptial gifts on the evolution of reinforcement in
species with multiple mating and strong CGP? (2 pts)
The
female will mate with males of either species (she’s going to be likely to get
some good sperm, she won’t have children with lower hybrid fitness because of
CGP, and she’ll get a nice gift for her small expenditure of mating
energy.) In these instances, though, it
would be incumbent upon the male of the other species to recognize and not mate
with females that are not of his species because he’ll not have a chance of
passing on his genes through her, and he’s expending all the energy in giving
her a nuptial gift. But, unless
selection on the males to do this is strong enough, there will be no
reinforcement because the female sees no reason to be choosy.
11.
What’s the difference between reinforcement and reproductive character
displacement? (5 pts)
Reproductive
character displacement just has to do with waste of time—species don’t want to
waste time and energy mating with other species, so they assortatively mate
with their own. Reinforcement has to do
with prezygotic barriers to reproduction being developed because of costs of
low-fitness hybrids. Mutations that keep
the species from wasting reproductive energy on producing low fitness hybrids
are selected for, especially if their affect on mating is pre-zygotic (which
makes the energy costs even lower).
Reinforcement is a way to keep species separate when they come back
together in sympatry. But some see
reproductive character displacement’s waste of time as part of the cost of low-hybrid
fitness, and so would lump it under reinforcement. It all depends on your perception.
12.
Briefly explain the three constituents of sensory drive. (6 pts):
Habitat
transmission, perceptual tuning, and signal matching are the three constituents
of sensory drive. In habitat transmission, the signal that females choose for
must not be degraded as it passes through a habitat. If the signal does not transmit well in a new
environment, selection favors those females who select for another quality-telling
signal that does transmit well—this can cause groups who have gone into new
environments to change or shift signals.
Perceptual tuning is the tuning of signals to match the perception of
the opposite sex, if the opposite sex cannot pick up on the signal sent, you
will not reproduce. However, perceptual
tuning also favors signals that work well in the environment (if a slight shift
in frequency of call attracts predators, that shift will not be favored.) Signal matching describes the necessity
of the male to use signals that fall
within the female’s range of response and liking (which may shift); a male who
comes close to the female preference will have more reproductive success. Sensory drive may not create new species in
and of itself, but it can help speciation via creating communication signal
barriers.
13.
T or F: Hybrid taxa will be intermediate overall to the parent species but
identical to one or the other parent at each individual AFLP (amplified
fragment length polymorphism) locus. (1 pt) TRUE
14.
Describe the “hybrid origins of adaptive radiations” hypothesis. (4 pts)
When
two species have diverged sufficiently that they can mate without causing the
overmixing and collapse of their own species, it can be advantageous for them
to mate and create hybrid species. These
hybrid species may not be intermediates of their parents, but novel phenotypes
(due to transgressive segregation) and can fill new niches. They, in turn, can speciate again and again
into new novel phenotypes that fill new niches, creating an adaptive
radiation. This only works if you
believe in the bounded hybrid superiority model, and if there are many niches
unfilled in an environment. Under this
theory, most adaptive radiations came about after the creation of such hybrid
swarms.
16.
Many of the genes that differentiate races of flies that feed on either apple
or hawthorn are located in chromosomal rearrangements. Explain (mechanistically) how such
rearrangements facilitate disruptive selection (2 pts).
Chromosomal
rearrangements are not subject to recombination, and so can stay together and
form coadapted gene complexes, not taking part in directional selection to one
end of the spectrum.
Then
explain how it can be that most of these genetic differences between the
hawthorn and the apple races actually preceded the introduction of apples to
North America. (2 pts)
We
know that these levels of chromosomal rearrangements are very unlikely to have
occurred since apples were brought to North America, meaning that this
variation almost certainly existed in the population before the apples
came. Moreover, it has been shown that
these rearrangements have existed for millennia and have spread from southern
portions of the species range. These
genes code for diapause traits… that fit well with the apples that were only
recently introduced.
Then
explain how it is that the apple race has evolved an attraction to apple
volatiles if most of the genetic differences between the races evolved before
the introduction of apples. (2 pts)
Even
though the major diapause difference, which is what the chromosomal
rearrangements account for, evolved in the flies earlier than the apple trees
arrived, the flies are still currently evolving sympatrically. The attraction to apple volatiles is a prime
example of this, as maggot flies who were attracted to apple volatiles (which
neither the Northern nor the Southern maggot flies are) were probably favored
because it increased host fidelity.
And
finally, explain how selection could produce an attraction for apple volatiles
when apple race larvae grow more poorly when fed apple than they do when fed
hawthorn. (1 pts)
Apples
may be a less nutritional food source than hawthorn, but they were an
unexploited niche. As such, the
competition for food would have been smaller for any larvae that happened to
grow on, there would also be less competition for places to lay eggs, and the
possibility for fewer predators (since the apples were a new introduced
species.) Since there were advantages to
staying with the apples, it isn’t unlikely that it would be advantageous to
develop an attraction for apple volatiles, as a way of reinforcing host
fidelity.
17.
Why do the authors use the term “adaptive speciation” instead of “sympatric
speciation”? (3 pts)
They
want to put across the suggestion that talking about sympatric and allopatric
speciation can get messy and confusing (especially since two species can have
developed in allopatry then returned to sympatry and evolved further apart,
leading one to question how exactly they evolved.) Instead, they suggest, one should think about
whether a species speciated via adaptation and selection, or simply by
drift. This would give a new way to
think about speciation and a new way of dividing speciation up (since sometimes
allopatric speciation is a result of adaptation and sometimes the result of
drift, and the same holds true for sympatric speciation.) It would get rid of
one conflict, but it may be that it would simply open up a new discussion since
drift and selection can play roles in the speciation of the same species.
18.
There are >750 species of figs in the world, making the genus Ficus one of the largest genera of land
plants. As it happens, these figs are
pollinated by species of wasps within the Family Agaonidae. Ficus
contains four subgenera and 18 sections; the Agaonidae contains 20 genera. What does this say about taxonomic categories
above the level of species? (2 pts)
The
taxonomic categories above the level of species clearly diverge among different
groups. For example, the wasps are
linked on the family level, while the fig trees are linked on the genus level.
It
would seem that the taxonomic categories above the species level are relatively
arbitrary (one could question whether the wasps have really subdivided so much
more dramatically than the figs, or if
the figs shouldn’t just be a family with
the sections being referred to as genera.)
19.
Why do fig wasps tend to have female-biased sex ratios? (2 pts)
The female fig wasps are the ones who will
compete to get into figs and lay eggs, so you want more of them to increase the
chance that your line will be carried on.
If you are the only wasp in a syconium, especially, you will prefer to
have more daughters (since the sons you produce can mate with more than one
female.)
Why
is the degree of bias so variable from one fig to the next? (2 pts).
If
only one wasp reproduces in a syconium, the female:male ratio should be
extremely high. If, however, another
wasp gets in after the first wasp has laid her eggs, it would behoove her to
lay more male eggs because then her sons would have a chance of reproducing
with the females already in the syconium as well as with the daughters you
produce, carrying on the genes in two ways.
The wasps can do this because they are hymenopterans and can bias sex
ratio fairly quickly.
20.
What is the main proximate determinant of whether a fig wasp egg galls the
ovule and becomes a wasp or whether that ovule develops into a seed? (2 pts)
The
main proximate determinate of whether an ovule is galled or becomes a seed is
the length of the style that leads to the ovule. If the style is longer than the wasp’s
ovipositor, the ovule will become a seed, if the style is short enough, though,
the wasp will lay an egg in the ovule and it will gall and become a wasp. In female flowers in dioecious figs all the
styles are too long for the wasp to lay an egg in the ovule, while in male
flowers the ovules have shorter styles that
21.
Who has the larger anther:ovule ratio – an actively or passively pollinated
fig? Explain your answer. (2 pts)
The
passively pollinated fig has a larger anther:ovule ratio because it must
produce more pollen in order to ensure pollination occurs, since the wasps
pollinating passively aren’t collecting pollen, so the chances they’ll get
pollen on them are increased significantly when they have more anthers.
22.
Why hasn’t selection produced fig wasps that can avoid seed synconia? (2 pts)
If
all the fig wasps avoided seed syconia, the figs would not produce seeds, and
therefore would eventually die out. If
the figs die out, the wasps die out.
There is generally more selective pressure on a fig to have their female
syconia mimic male syconia behavior than there is on a fig wasp to worry about
telling the difference between the two, especially since fig wasps are evolved
to rush to the nearest syconium after they emerge (so they have some chance of
reproducing before the ostioles close).
23.
How is it that mitochondrial Eve lived 200,000 years ago and Y-chromosome Adam
lived only 50,000 years ago? (and who
are they?) (4 pts)
Mitochondrial
Eve is the name given to the “lucky ancestor” (or maybe “lucky village”) in
Ethiopia whose mitochondria is the cenancestor of all the mitochondria in the
world today. Y-Chromosome Adam is the
“lucky ancestor” whose Y-chromosome is the cenancestor to all the Y-chromosomes
in the male population today. These are
both molecular cenancestors, and are probably not organismal cenancestors. The mitochondria passes through the female
line since males don’t (usually) pass on mitochondrial DNA and the Y-chromosome
passes through the male line. Males in
polygamous societies (which humans were for most of our early pre-history) tend
to have greater competition for mates, so some males will not get to mate and
some males will mate an incredibly high amount, decreasing the effective
population size and making it possible for the male cenancestor to be later
than the female cenancestress, since almost all females tend to reproduce in
polygamous societies, meaning we have to go back further to find the common
cenancestress.
24.
What are two ways that organisms can transfer genes that would mess up a tree?
(2 pts)
Horizontal
gene transfer, which occurred early on (and still occurs today among
archaebacteria and eubacteria) can cause a molecular cenancestor (the
cenancestor for one gene or molecule) to be in another species from the
organismal cenancestor. Endosymbiosis is another means of getting “foreign”
genes into an organism (especially if there is subsequent transfer of genes
from the organelle to the nucleus).
Hybridization could also be considered a problem.
25.
Discuss the advantages and disadvantages of using “DNA barcoding” to assign
individuals to species. (6 pts)
DNA
barcoding could be a relatively quick way to identify which species an
individual belonged to, and could allow for the assignment of larval-stage
individuals to species, as well as allowing for the possible identification of
cryptic species, which are morphologically indistinct but genetically different
species and for furthering our taxonomic knowledge of species that are not
often studied such as nematodes.
However, the question of which gene to use as identification comes up,
and many question what variation threshold should be established for
determining if an individual belongs to a species or not, as well as whether
the barcoding would work if species had hybridized (and thus might have the
genes that identified them as belonging to one parental type when they really
do not) or if the barcoding would be able to distinguish between species that
had recently diverged sympatrically (and thus may not be terribly different
genetically.) If mtDNA is used, the
question of whether mtDNA really accurately reflects nuclear divergence also
comes into play.
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