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BBio466 Study Guide Exam2
Jensen, Spring 2016
I’m a bit behind so the meeting numbers don’t always match up with the syllabus. The content is
the same, though. Some of the specific examples may change.
Meeting 9: Finish up single locus; Evolution at multiple loci: Linkage, linkage disequilibrium, sex
Short narrative:
So far we have considered single locus models – we had HWE as a null model, and we introduced
wxx to incorporate in predict the effects of selection. We continued single locus models to consider
substitution rates and to contrast (again) neutral and selection models. We considered the
relative effects of population size, generation time, and selection on rates of substitution. The
nearly neutral model addresses the roughly constant rate of substitution (in absolute time)
regardless of generation time by suggesting that selection on slightly deleterious alleles reduced
substitution rates in large populations (with short generation times) but that drift is more
important in small populations (with longer generation times). These effects balance each other
out in absolute time. We also introduced multilocus models of evolution and, in particular, the
idea of linkage disequilibrium. This will be relevant to us as we discuss the evolution of sex.
Some key terms:
Mutation
Substitution
Neutral mutations
Neutral Theory
Nearly neutral theory
Synonymous vs. nonsynonymous substitutions
Linkage
Fixation
Hitch hiking
Haplotype
Linkage equilibrium/disequilibrium
Inbreeding depression
D = gABgab - gaBgAb
Concepts/examples:
Relative rates of beneficial, neutral, deleterious mutations
Substitutions versus mutations
Red Queen Hypothesis
Relationship between population size and the relative strengths of selection and drift
How populations are moved out of linkage equilibrium, and why we care to know
Skills:
Can you explain the difference between mutations and substitutions?
What does substitution rate depend on?
Can you explain why large and small populations have similar rates of substitution even when
variation is neutral? Shouldn’t substitution rates be higher in small populations?
Can you explain why are deleterious and neutral mutations more common than beneficial
mutations?
Can you explain the difference between synonymous and non-synonymous substitutions?
Why would you expect rates of divergence to generally be lower for nonsynonymous substitutions
than for synonymous substitutions?
Why would you expect rates of substitution to be dependent on generation time? Can you explain
why rates of divergence are roughly independent of generation time?
What is the nearly neutral theory, and why did neutralists modify their neutral theory to include
some selection?
1
Can you explain the significance of this equation? 𝑠 ≤ (2𝑁 )
𝑒
Can you explain how it is possible for selection to be effective at some population sizes but not
others?
Can you explain why the rate of synonymous substitutions serves as a good baseline for detecting
selection?
What does it mean if (dN/dS) = 1? (dN/dS) < 1? (dN/dS) > 1?
Is it possible for selection to affect rates of substitution for a synonymous mutation? If so, how?
Can you explain what inbreeding does to heterozygosity, and why?
What is linkage equilibrium? Can you explain how populations can be out of equilibrium, and why
populations tend to return to equilibrium?
Do you know how to calculate D for a population? Do you understand why values for D range
from -0.25 to +0.25? What does is mean when D = 0?
Why would finding neutral alleles at linkage disequilibrium suggest positive selection on adjacent
alleles?
Meeting 10 was Exam1
Meeting 11: Review of Disequilibrium, Sex, and Introduction to Quantitative Genetics
Short narrative:
We reviewed linkage disequilibrium, and the “paradox of sex.” Sex is costly in terms of
reproduction and yet predominates in eukaryotes. There are organisms that are obligately sexual,
facultatively sexual or asexual, and obligately asexual. Asexuality does not appear to be difficult to
evolve, and facultatively sexual organisms often reproduce sexually despite the obvious cost. This
suggests that sex must have an advantage, at least under some circumstances. We considered
several ways in which sex could be advantageous, including breaking Muller’s ratchet and
promoting offspring survival in varied or variable environments. The beetle example illustrated
conditions under which asexual or sexual reproduction would be favored.
Some key terms:
Sexual vs. asexual
Obligate vs. facultative
Sexual reproduction
Muller’s Ratchet
Genetic Load
Continuous variation
Blending inheritance
Multiple loci
Segregation and independent assortment
QTL mapping
Genetic markers
Concepts/examples:
When two populations of beetles were placed in competition, but one was manipulated to mimic
asexual reproduction and the other was allowed to reproduce sexually, asexual beetles won under
standard conditions but sexual beetles won in the presence of malathion. Explain these different
outcomes.
What happens to variation in small populations? How does sex help?
Why is sex advantageous in variable environments? How does this relate to the Red Queen
Hypothesis?
Can you explain how genetic markers are used to find quantitative trait loci? What does this have
to do with linkage disequilibrium?
Skills:
Can you explain several ways in which sex is costly? Why are males disadvantageous in terms of
producing offspring? How might males be advantageous in viability of offspring?
Is asexuality difficult to evolve?
Can you explain Muller’s ratchet, and how sex can break it?
Can you explain the linkage (har har) between sex and linkage equilibrium? What does sex do to
linkage disequilibrium? How?
Meeting 12: More with Quantitative Traits (haven’t gotten to all of this yet)
Short narrative:
We illustrated the difference between complete linkage (fully dependent assortment) and no
linkage (independent assortment). If we look at offspring of crosses (e.g. of double heterozygous
for a trait and a marker), we can see whether and how our offspring deviate from the null model of
no linkage. Fully linked traits would obviously be very different from unlinked traits; traits that
are linked but are far apart will not look like unlinked traits, but will also not look like fully linked
traits. Some intermediate level linkage will best describe the distribution of genotypes in
offspring. The LOD score describes how well a particular linkage model explains the distribution
of offspring (relative to a no linkage model). We can use outcomes of matings and look for traits
and markers that have a high LOD scores – these will be close to our marker in the genome. We
also revisited the idea of heritability, and broke down genetic variance into additive and
dominance components – we used this to distinguish between broad sense and narrow sense
heritability (we are concerned with the latter). We reviewed strategies for estimating heritability,
including an example of cross fostering. Once we have estimated heritability, we can use this
information to predict the response of the population to a given level of selection (or,
alternatively, estimate S if we know R and h2, or estimate h2 if we know S and R). We used the
Bugsville simulation to estimate h2, set up selection, and estimate R.
Some key terms
Independent assortment
Dependent assortment
LOD score (know what this means and how it’s used, not how to calculate)
How LOD scores are used to identify quantitative trait loci
VG, VA, VD, VE
𝑉𝐴
𝑉𝐴
=
𝑉𝑃
𝑉𝐴 + 𝑉𝐷 + 𝑉𝐸
𝑉𝐴
𝑉𝐴
ℎ2 =
=
𝑉𝑃
𝑉𝐴 + 𝑉𝐷 + 𝑉𝐸
Cross fostering
Response to selection
Selection differential = 𝑆 = 𝑡 ∗ − 𝑡̅
Concepts/examples
Broad sense vs. Narrow sense heritability – Don’t worry about the distinction.
Review the example of cross fostering (song sparrows). Do you understand what cross fostering
accomplishes?
How to estimate h2 from matings and twin studies
The meaning and application of LOD scores
The relationship among R, S, and h2.
Skills
Can you describe high vs. low heritability graphically? Verbally?
What is the relationship between heritability and selection?
Can you describe and explain expected similarities between monozygotic and dizygotic twins if
heritability is high vs. low?
Can you explain what crossfostering studies are, and how they reveal the relative influence of
genes and environment on phenotypic variation?
Can you verbally and graphically describe the relationship between h2, R, and S?
What is the difference between h2 and r2 in a regression of mid offspring against mid parent?
Remember, the response to selection is R, not r.
Can you describe how R will differ if h2 is large vs. small?
Can you describe how R will differ if S is large vs. small?
Given phenotypes for a group of parents and values for their offspring, can you calculate h2?
If you know S and R, can you estimate h2?
If you know S and h2, can you predict R?
Meeting 13: Adaptation
Short narrative:
It’s easy to look at structures/behaviors that are useful to organisms and assume that natural
selection has molded them for that “purpose.” In reality, the relationship between phenotype and
selection is much more complicated than that. Evolutionary biologists have been rightly criticized
for telling “Just-so stories” – plausible but untestable narratives for how natural selection has
molded lineages into their current form. In this meeting we considered how we could make a
stronger and testable case for features being adaptations. We considered approaches ranging
from verifying how a feature is actually used in nature to how it may affect current fitness to the
circumstances under which the feature actually evolved. We marshaled observational,
experimental, and comparative information in this endeavor. Finally, we considered phenotypic
plasticity as a potential complication in studies of adaptation, and as an adaptive feature in itself.
Some key terms:
Adaptation
Just-so stories
Exaptation
The comparative method
Phylogenetically independent contrasts
Norm of reaction
Phenotypic plasticity
Concepts/examples:
Oxpeckers and oxen – Do oxpeckers eat ticks? Do they actually help oxen?
Shaving the hooks off pigeon bills – what did this demonstrate? What did it not demonstrate?
Rock choice in garter snakes – what did this demonstrate? What did it not demonstrate?
Fly wings (and moth wings) and jumping spiders – what did this demonstrate? What did it not
demonstrate?
Anolis limb proportions and habitat
Bat testes vs. social structure
Daphnia behavior in the presence and absence of visual predators
Skills:
Can you define adaptation?
Give structure or behavior X, how would you construct at strong argument that it is an adaptation
for Y? What kinds of evidence would you use in your argument? How would you acquire it?
Can you explain how phylogenies were used in assessing adaptation of limb proportions in Anolis
lizards?
Can you explain why simply drawing a regression line between two traits is not sufficient to
determine whether they evolve together? How do phylogenies help?
Can you explain why phenotypic plasticity may confound us in assessing adaptation?
Can plasticity itself evolve?
Meeting 14: Sexual Selection
Short narrative:
We begin with observation that many species are sexually dimorphic, and that it is usually the
males that are most brightly colored, larger, etc. This raises two questions: 1) how does sexual
dimorphism arise? and 2) why is it males that are usually brighter, larger, etc.? We framed this in
terms of different levels of investment in offspring and different strengths of sexual selection (i.e.
variation in reproductive success) in males and females. Males often show extreme variation in
mating success, but invest relatively little in offspring – what limits their reproductive success is
mating opportunities, not the costs of producing/rearing offspring. Females are typically the
reverse. This means males will generally be competitive for mating opportunities (intra or
intersexual selection) and females will tend to be more selective. We reviewed examples of
intrasexual and intersexual selection, and considered why females should even care about the
sometimes comical displays and ornaments of males. Finally, we considered a case where females
are competing for mating opportunities, and males have a great investment in producing
offspring.
Some key terms:
Sexual dimorphism
Fundamental asymmetry of sex
Sexual selection
Intra- vs. intersexual selection
Combat, sperm competition, infanticide
Mate guarding, copulatory plug, nuptial gift
Sexy Son hypothesis
Runaway sexual selection
Good genes hypotheses – Handicap, parasite, developmental stability
Direct benefits
Pre-existing biases
Concepts/examples:
Elephant seals, rough skin newts – male vs. female mating success
Intrasexual selection – Elephant seals, iguanas
Infanticide – Gorillas and lions
Parental investment
Intersexual selection
Female choice
Widowbirds – costs/benefits of long tails
Gray tree frogs – female preferences and quality of offspring
Seahorses and pipefishes
Skills:
Can you explain why, as Darwin noted, it is usually the males that the brighter, larger, more
ornamented, etc. when species are sexually dimorphic?
Can you generalize this phenomenon? I.e. is it a feature of males, or is there a more general
explanation that might apply to cases in which the females are the brighter, larger, more
ornamented, etc. sex?
Can you explain why mating success is usually less evenly distributed in males than in females?
How is sexual selection different from natural selection? Why would selection on males and
females be different, and how does this lead to sexual dimorphism?
Can sexual selection act in ways that compromise survival?
How might size be advantageous in intrasexual selection? How might it be costly overall? Can you
provide examples?
How can infanticide in lions be good for the species? Is that even a sensible question?
Can you explain why features that have no value in intrasexual selection might still be sexually
selected?
Why would females tend to be more discriminating than males when mating? Can you provide
counterexamples?
Can you explain why females would even care about elaborate displays and ornaments in males?
What are males actually advertising?
What did Alison Welch’s experiment with breeding long-call and short-call male frogs with
females demonstrate? How is this relevant to theories of sexual selection?
Can you explain why the sex subject to strong sexual selection will tend to be competitive, and the
sex subject to weak sexual selection will be choosy?
Can you explain how seahorses and pipefish reverse the usual sex roles, but still uphold the
general pattern of sexual selection?
Meeting 15: Kin Selection and Social Behavior
Short narrative:
Behavior is a phenotype, and like most phenotypes, it has both genetic and environmental
components. Because behavior can satisfy all of the premises of natural selection, behaviors can
represent adaptations. A particularly challenging behavior to think of as being adaptive is
altruism. Nevertheless, apparently altruistic behavior is quite common. There are two main
explanations for the existence of such behavior: 1) inclusive fitness, where one helps others who
share their own alleles, thus indirectly increasing the chance of theirs being passed on. Hamilton’s
rule dictates that the more closely related two organisms are the more likely the other organism is
willing to help. Eusociality is an extreme example of this in which there is an overlap in parent and
offspring generations, specialized castes for reproduction and other tasks, and cooperative care
for offspring; 2) Reciprocal altruism occurs not because the actor and recipient are closely related,
but because individuals help each other under circumstances in which the favor may be repaid in
the future. Reciprocal altruism is more likely when the benefits to the recipient outweigh the cost
to the action; there are stable groups so individuals will see each other multiple times; there are
repeated opportunities for the act to be practiced (and reciprocated); cheaters can be recognized
and punished; and there is a symmetrical relationship, meaning that there is no expectation that
one will always be the donor or the recipient.
Some key terms:
VP = VG + VE
Altruism
Group selection
Inclusive fitness, direct fitness, and indirect fitness
Relatedness (r)
Hamilton’s Rule: Br – C > 0
Kin recognition
Eusociality and its three characteristics: Parent/offspring overlap, cooperate care, specialize
reproductive/nonreporductive casts
Reciprocal altruism
Cheaters
Concepts/examples:
Group selection models – difficult to see how cheating would not be favored.
Benefits, costs, relatedness.
Black-tailed Prairie dogs
White fronted Bee eaters
Eusociality in hymenoptera and naked mole rats.
Altruism in vampire bats
Skills:
Can you explain how altruistic behavior might be favored by natural selection when it occurs
between related individuals? Would it make a difference how closely related the individuals are?
Can you explain how altruistic behavior might be favored by natural selection when it occurs
between unrelated individuals?
Can you explain why behaviors that confer an advantage to the group but not the short term
interests of the individual would be difficult to maintain by selection
Can you explain the logic behind Haldane’s statement that he would gladly give up his life for “two
siblings or eight first cousins”? To which model of the evolution of altruism does this statement
apply?
Can you explain what it means if Br – C > 0? If Br – C < 0?
What would prompt a prairie dog to send a warning signal if a predator is near? Under what
circumstance would a prairie dog “decide” not to call?
Can animals besides humans recognize their kin? Examples? What about plants … can they
recognize kin? How does this relate to Hamilton’s rule.
Can you describe circumstances in which it makes more sense (in terms of fitness) to help your
parents raise offspring than to attempt to raise your own? What kind of fitness is being
maximized here?
Can you explain why haplodiploidy is not considered a strong explanation for the evolution of
eusociality in hymenoptera?
Can you explain why a large r in naked mole rats facilitates the evolution of eusociality?
Can you explain why each of the following help promote the evolution of altruistic behavior even
in unrelated individuals? Stable groups, repeated opportunities to commit altruist acts, memory,
symmetrical interactions? Do any or all of these apply in humans?
Is altruism in vampire bats an example of kin selection, reciprocal altruism, or both? How can you
distinguish reciprocal altruism from altruism based on kin selection?
The cost to a well-fed bat regurgitating blood for a starving bat is less than the benefit received by
the starving bat. Can you explain why this is true? How would this favor the evolution of
altruism?