Evolutionary Biology Spring 2015 Study Questions
The following study questions are designed to help you think about the lecture material. They are not comprehensive questions. Exam material is NOT limited to the topics in study questions and will not follow this format.
- 1 Lecture 1 - Jan 20th 2015
- 2 Lecture 2 - Jan 22nd 2015
- 3 Lecture 3 - Jan 29th 2015
- 4 Lecture 4 - Feb 3rd 2015
- 5 Lecture 5 - Feb 5th 2015
- 6 Lectures 6 & 7 - Feb 10th and 12th 2015
- 7 Lecture 8 - Feb 17th 2015
- 8 Lecture 9 - Feb 19th 2015
- 9 Lecture 10 - Feb 24th 2015
- 10 Lecture 11 - Feb 26th 2015
- 11 Lecture 12 - Mar 03rd 2015
- 12 Lecture 13 - Mar 10th 2015
- 13 Lecture 14 - Mar 12th 2015
- 14 Lecture 15 - Mar 24th 2015
- 15 Lecture 16 - Mar 26th 2015
- 16 Lecture 17 - Mar 31st 2015
- 17 Lecture 18 - Apr 02nd 2015
- 18 Lecture 19 - Apr 07th 2015
- 19 Lecture 20 - Apr 09th 2015
- 20 Lecture 21 - Apr 14th 2015
- 21 Lecture 22 - Apr 16th 2015
- 22 Lecture 23 - Apr 21st 2015
Lecture 1 - Jan 20th 2015
1) What type of adaptation would you expect to see in an organism trying to survive in an environment with visual predators?
2) What’s one possible explanation for powered flight appearing only once in invertebrates and at least three times in vertebrates?
3) Why would it be advantageous for an organism to resemble something else; i.e. a caterpillar that looks like bird droppings or an orchid that smells like carrion?
4) What’s convergence? Can you think of an example we saw in lecture?
5) Do similar traits always evolve to solve the same challenges? For instance, are all brightly colored organisms just trying to get a mate?
6) In what ways can humans be a source of selection to other organisms?
7) What’s the difference between evolutionary change and phenotypic plasticity?
Lecture 2 - Jan 22nd 2015
1) Suppose you observe that the average weight of squirrels on campus is greater than their average weight on Horsebarn Hill. Describe how you would use a reciprocal translocation experiment to test the hypothesis that the difference in weight of squirrels on campus and on Hosebarn Hill is the result of an evolutionary change. Explain what outcome(s) would support this hypothesis. What outcome(s) would not support the hypothesis?
2) In class, we focused on figuring out how to tell if a phenotypic difference was caused by an evolutionary change. What if there's no phenotypic difference between two populations you observe in the wild--could there still have been an evolutionary change? Why or why not?
3) Why do we focus on genetic differences in studying evolutionary change?
4) What is the relationship between Mendelian genetics and population genetics?
5) What are the variables used to describe the genetic composition of a population?
6) In general terms, what genotype frequencies are expected under the Hardy-Weinberg equilibrium with 2 alleles? What do you think the proportions are going to be if we’re studying a locus with 3 alleles? Trying drawing one of those box diagrams we saw in class to support your answer.
7) What happens to genotype frequencies in a population under Hardy-Weinberg equilibrium in subsequent generations? What happens to allele frequencies?
8) Hardy-Weinberg practice: try the problems here to get practice with describing the genetic composition of a population and determining Hardy-Weinberg proportions.
9) Challenge Problem: What’s the highest frequency of heterozygotes that is expected under HWE for a locus with 2 alleles?
Don’t forget to finish Activity 2 – It should be handed in at the beginning of lecture on Thursday Jan. 29th.
Lecture 3 - Jan 29th 2015
1) Why do we use allele and genotypes frequencies instead of the number of gametes or individuals in a population?
2) How many generations does it take for a population to establish genotype frequencies in HWE (Hardy-Weinberg equilibrium) given all the assumptions are met?
3) In what situation do we need to assume Hardy-Weinberg equilibrium instead of testing for it? What information do we need in order to test for HWE?
4) HWE assumes that there is no new genetic mutations. However, all new genetic variation occurs through mutation. Why do we mostly ignore this assumption violation?
5) You observe the genotype frequencies of a cow population for 2 generations. The allele frequencies and genotype frequencies do not change. Is this population in HWE? Why or why not.
6) What happens to genetic variation, allele frequencies, and genotype frequencies as a result of inbreeding?
7) What are the different types of non-random mating?
8) How can you tell the difference between inbreeding and assortative mating?
9) What is the most extreme form of inbreeding?
10) What do you expect the effects of inbreeding would generally be on fitness? Why?
11) Why are inbred lines of model organisms (e.g. Drosophila, mice, C. elegans) often used in biomedical research?
12) Under what conditions would assortative mating cause evolution? Under what conditions would it not result in evolution?
13) Given what you know about the different types of non-random mating and their effects on genotype and allele frequencies, what would you expect to be the result of disassortative mating?
There are very good practice questions at the end of each chapter of the textbook. Try doing questions 1 through 5 at the end of Chapter 9 - page 255
Lecture 4 - Feb 3rd 2015
1) Give an example of assortative mating in which mates are NOT chosen by the way they look. What other types of phenotypic characteristics can also be used to choose mates?
2) Assortative mating by size is very common in nature. Can you think of any explanation for why this type of preference arises so frequently?
3) What’s the Wahlund effect? How does it affect the genetic diversity of a population?
4) Is the pattern produced by the Wahlund effect more similar to that observed for inbreeding or assortative mating? How does it differ from that pattern?
5) Why does population size matter when studying population genetics?
6) What effect does genetic drift have on: (a) genetic variation (b) genotype frequencies (are they in Hardy-Weinberg proportions or not? Do they change from generation to generation?)
7) What does it mean when an allele has ‘been fixed’ or ‘gone to fixation’ in a population?
8) If an A allele has a frequency of 0.95 in a population, will this always fixed through drift? What is the probability the A allele will be fixed?
9) One of the consequences of small population size is a tendency to mate with close relatives. What other evolutionary change have we studied that also affects small populations more than large ones? How are these processes similar and how do the two differ on how they affect genotype frequencies in the population?
10) What’s the effect of genetic drift in the genetic diversity of individuals belonging to the same population? How about on individuals belonging to different populations?
11) Given what you know about genetic drift, what’s most likely to happen to a new mutation in a small population? How about in a large (infinite) population?
Lecture 5 - Feb 5th 2015
1) Which assumption of the HWE do both mutation and migration violate and why?
2) What is migration in an evolutionary sense and why is it important for understanding evolution in populations? Give an example of migration and explain its effects on allele frequencies.
3) Why is it important to consider the effects of migration and drift together?
4) How many migrants does it take to keep populations from diverging? Why is this the same for small and large populations?
5) What factor(s) affects the rate of homogenization of allele frequencies when populations are connected by migration?
6) How does inbreeding depression affect populations? Can you think of a real example of inbreeding depression?
7) What level of genetic diversity do we expect to see in a population that has been through a bottleneck? What evolutionary forces are at play in this case? If nothing changes, what’s the ultimate fate of this population?
8) Imagine you are hired by the US government to take part in a conservation effort as a consultant. What aspects of a population’s structure do you have to consider in order to maximize maintenance of genetic diversity? How would you explain to government representatives why it is crucial to maintain genetic diversity?
9) What’s the impact of habitat fragmentation on genetic diversity? What are the evolutionary processes that contribute to that scenario?
Lectures 6 & 7 - Feb 10th and 12th 2015
1) What are the premises of the theory of evolution by natural selection?
2) What is the difference between natural selection and evolution by natural selection?
3) What is artificial selection? Give examples of organisms that have been artificially selected.
4) What do evolutionary biologists mean when they talk about the fitness of an individual?
5) What HWE assumption does natural selection violate?
6) How do natural selection and genetic drift affect phenotypes? Give an example of when genetic drift and natural selection could be acting on a population.
7) Imagine one of your family members is really curious about what you are learning in this class. How would you explain to him/her how natural selection increases the frequency of an advantageous trait in a population?
8) Can natural selection act on a population with very little genetic diversity (most loci have one fixed allele)?
Lecture 8 - Feb 17th 2015
1) Thinking about the examples of natural selection in action we saw in lecture, what’s the source of selection pressure for the guppies? How about for the Darwin finches in the Galapagos?
2) How do we know the increase in bill depth in the Darwin finches example is a result of evolution by natural selection instead of genetic drift?
3) Can evolution happen from one generation to the next? In order words, can evolution happen in a short period of time?
4) Why do organisms have to be constantly changing in order to increase (or maintain) their fitness? How come different phenotypes can be the fittest in different geographical areas or at different points in time?
5) What are the three modes of natural selection? What’s the evolutionary consequence of each of them and how are they affected by initial allele frequency?
6) What is Fisher’s Fundamental Theorem and why is it important?
7) What does w symbolize and how is it calculated?
8) If the most fit genotype is the heterozygote, why does natural selection lead to the decrease of heterozygotes in the entire population?
Lecture 9 - Feb 19th 2015
1) What are the three types of selection covered in lecture and what is the relative fitness of heterozygotes for each type?
2) Which genotype is most important for predicting a population’s future?
3) What is the evolutionary consequence of directional selection?
4) What is the effect of the starting allele frequency on its fate under directional selection?
5) How does a trait’s dominance influence its fate in a population?
6) What do you predict is the evolutionary consequence of disruptive selection?
7) Why do we say natural selection is short-sighted? Explain.
8) What is a fitness landscape? What are the axis labels?
9) Which type of selection has an outcome that is dependant on the starting frequency of allele A?
10) In a population experiencing evolution as a result of disruptive selection, how would you expect observed genotype frequencies to compare to those expected under Hardy-Weinberg equilibrium in zygotes? What about in adults?
11) What are the differences between quantitative and Mendelian traits?
12) What are the four consequences of traits being determined by multiple loci?
13) Suppose a population has a normal distribution of some trait, the trait is heritable, and only members with above average trait values were allowed to reproduce. What would the trait distribution look like in the following generation?
Lecture 10 - Feb 24th 2015
1) What is the phenotype of an organism dependent on?
2) How is heritability defined? What are two different ways you could measure it?
3) In a scenario which a phenotype has a normal distribution and only individuals with above average traits reproduce. The trait is heritable and after one generation the average of the trait is larger than in the original population. What would the graph of number of individuals vs. phenotype value look like before and after reproduction?
4) What do R and S stand for and how do you calculate them?
5) If h2 = 0 then what is variation in the phenotype a result of? What if h2 = 1?
6) A selection event occurs in a population allowing only some of the individuals to survive. The average trait value of the survivors is different than the original population. You know the heritability of the trait and calculate S and R. What happens to the mean trait value in the next generation relative to the original population's mean trait value when R is positive? negative?
7) Even though natural selection leads to an increase in the mean fitness of populations, it does not always result in a population that has maximum fitness. Explain why not.
8) How is sexual selection different from non-random mating?
9) What are intrasexual and intersexual selection? Give an example of each.
10) What is the common consequence of sexual selection in a population?
11) What is sexual dimorphism? Give a real life example not covered in class.
12) What could be a direct benefit of female choice? What could be an indirect benefit of female choice?
Lecture 11 - Feb 26th 2015
1) So far we have focused on selection on individuals and how it impacts the frequency of advantageous traits in a population. What other levels can selection act on, besides individuals?
2) What are the arguments in favor of selection at the gene level?
3) What is an example of conflict for selection at the gene level?
4) In the example of selection at the organelle level presented in class, what was the organelle in question? What mechanism allowed flowers to produce functional anthers again?
5) Can selection act at the cell level? What’s a good example of conflict between selection at the cell level and selection at the individual level?
6) What are the arguments in favor of group selection? What are the arguments against it?
7) According to Hamilton’s Rule, would an individual be more likely to share its resources with full-siblings or cousins? Why is that so?
8) Why is it advantageous for a female lion to help raise her sister’s offspring?
9) What is an explanation for how eusociality arose in certain insects?
10) Does eusociality have a single origin or has it arisen multiple times?
11) During activity 12, you were asked to choose between two strategies: sharer or monopolizer. Which one had better individual mean fitness? How about the group’s overall mean fitness? In the second part of the game, sharers slightly changed their strategy to what we call tit-for-tat. How did that change both individual mean fitness and the group’s overall mean fitness? What is an example of tit-for-tat occurring in nature?
12) Can selection act at the level of species/lineages? What is the difference between differential speciation and differential extinction? What do they have in common (think about it in terms of number of extant lineages as a result)?
13) Evidence suggests that lineages comprised of asexual organism tend to be younger than lineages of sexual organisms. What is an explanation for this observation? How can sexual reproduction allow a lineage to persist longer in time?
Lecture 12 - Mar 03rd 2015
1) What are the three explanations for the evolution of female preference?
2) In the Runaway Sexual Selection explanation how does the female preference become more common in the population?
3) What is the “Good Genes Model” of sexual selection? Does it rely on the role of direct or indirect benefits to the female?
4) Could the Bird of Paradise courtship display that we watched in class a few weeks ago (watch it again here) be a result of the direct phenotypic benefit explanation to female preference? Could it be a result of the other two explanations of female preference? (This link on female choice might be helpful)
5) What are the four assumptions of Hardy-Weinberg Equilibrium ? What evolutionary forces violate each of them and how?
6) What factors have likely been responsible for divergence in Ensatina? In general, what factors tend to promote divergence of populations? What factors tend to prevent divergence? What evidence is there that color pattern is adaptive in Ensatina?
7) Why is Ensatina treated as a single species even though the southern forms are reproductively isolated from each other?
8) How could gene flow occur from the southernmost inland population to the southernmost coastal population if there is no reproduction between these two populations? (Hint: what other populations are they exchanging genes with?)
Lecture 13 - Mar 10th 2015
1) Why is it important to study reproductive isolation?
2) What is the definition of the term speciation?
3) Is reproductive success easy to achieve? What are some of the obstacles to successful mating?
4) What are the two types of barriers to reproductive success? How do they relate to the obstacles you talked about in the previous question?
5) What are some of the ways two populations can be reproductively isolated from one another other than geographically? Think about time and space!
6) How important is courtship in animals? What is the main function of courtship?
7) What aspects of an organism could result in mechanical barriers to reproduction?
8) How is species recognition done in plants? What role can pollinators play in reproductive isolation of plants?
9) How about animals that release their gametes in the environment? How can species recognition happen at the gamete level?
10) What are some of the issues that could hinder proper zygote development?
11) Two populations of individuals belonging to different species produce viable hybrids. In general, what would you expect the fitness of the hybrids to be, relative to the parental individuals? What type of reproductive isolation is this?
12) Does reproductive isolation happen quickly in one step or is it a gradual process?
13) What is the minimum number of incompatible genes required for the establishment of reproductive isolation? (Dobzhansky-Müller incompatibility – check textbook)
Lecture 14 - Mar 12th 2015
Special web-based question for the next exam: Search the web for the term "agressive mimicry". Find two examples where a pre-mating reproductive signal of one species is co-opted by a predator of another species. How does the predator use this signal to increase its own fitness and decrease the fitness of the prey? The predator may be a closely related species or a more distantly related species.
You might want to check these links below:
Bolas spiders I
1) What is a species? Is the concept of species an easy one to determine? What makes it so complex?
2) What are some fo the reasons why it is a good idea to give species names? What do species represent in nature?
3) What are some of the most important species concepts we talked about in class? How do they differ from one another? What are the issues associated with each of them?
4) What do we have to know about a group of organisms in order to apply Templeton’s Cohesion Species Concept?
5) What kind of information do we use to recognize species? Is it only about what organisms look like?
6) Do different species mate with one another? Do they produce hybrids? If so, does it mean they are not “good” species? What do the Kikihia cicadas tell us about hybridization in nature?
7) What does the Barcode of Life project do? What kind of data do they use to identify/recognize species? What problems are associated with barcoding?
8) Is describing a species a simple procedure? Why or why not?
9) In practice what is the most common species concept to be applied in a large biodiversity study?
10) Remember that: Although in practice the biological and cohesion species concepts are not easily used, they are useful in theory for understanding the biological basis for speciation.
Lecture 15 - Mar 24th 2015
1) Spatial speciation mechanisms can be divided into what three categories?
2) In allopatric speciation, how does the vicariance model differ from the founder model?
3) How does the founder effect work to encourage speciation?
4) What conditions are necessary for parapatric speciation to occur?
5) How does reinforcement work in parapatric speciation?
6) Define sympatric speciation. What conditions does it require?
7) Define host-race speciation and give an example.
8) How did gradual allochronic change evolve in true fruit flies of the genus Rhagoletis?
9) Why do chromosomal mutations like inversions reduce fertility of the individuals carrying them?
10) Why is chromosomal speciation (other than polyploidy) expected only in organisms that exist in small populations?
Lecture 16 - Mar 26th 2015
1) The tree frog Hyla versicolor is believed to have evolved from Hyla chrysoscelis by what mechanism?
2) What is very unusual about the species H. versicolor and how do the “species as lineages” and “species as a reproductive community” speciation concepts apply to this case? In other words, how would you classify Hyla versicolor and Hyla chrysoscelis under the biological concept? Under the phylogenetic species concept? Under each concept would H. versicolor be one species, three species, or not a species?
3) Hybrid species are often not very fit at first but over generations individuals become more fit. What is the explanation for this?
4) In the case of the hybrid sunflower, H. anomalus, when Rieseberg et al. created three artificial lines in the laboratory by hybridizing the parents and then breeding the hybrid offspring, how did these lines compare to the wild hybrids? Why was this interesting?
5) What happened when Higgie et al crossed undisplaced Drosophila birchii with D. serrata? Why was this important?
6) Explain how allochronic speciation works to create new species in periodical cicadas. Use the following words in your answer: plasticity, predator satiation, reproductive character displacement.
7) At a hybrid zone between two species, what do you predict would be the fate of an allele that was …
a) selectively advantageous? B) selectively neutral?; c) selectively disadvantageous?
8) Define Systematics.
9) Define the following terms:
Lecture 17 - Mar 31st 2015
1) Define Systematics.
2) Define the following terms:
- Symplesiomorphic character state
- Synapomorphic character state
The most parsimonious solution
Homologous character states
3) Know that Linnaeus published Systema Naturae in the early 1700’s (as a reference point for the age of modern taxonomy).
4) Are the sucking mouthparts in cicada and mosquito homologous? What is the evidence?
5) How is the phenomenon of convergence good evidence for the existence of the process of evolution? Use real examples in your answer.
6) When studying evolutionary relationships among taxa, what special problems might be associated with discovering the relatedness of parasitic organisms to other species?
7) How might developmental or DNA studies solve the above problem?
8) How can a phylogenetic tree help to recognize homoplasy?
9) Explain how a synapomorphy at one node can be a symplesiomorphy for descendant taxa at shallower nodes of the tree.
10) Give two synonyms of “phylogenetic tree.”
11) What number of possible rooted trees exist for three taxa? For 10 taxa?
12) Draw a tree that has a polytomy. Draw a tree that is fully resolved. Draw a reticulated tree.
13) Know that a phylogenetic tree can be swiveled at any node. How does this fact relate to the concept of sister group? Be able to recognize trees by their sister groups.
14) Why is it misleading to call a living group “primitive”?
15) What are the two components of a phylogenetic tree?
16) Why is it wrong to claim that humans are descended from chimps?
17) A branch of a phylogenetic tree can be longer than another branch for two reasons what are they?
18) How do population and species trees look different?
19) Why are reptiles considered to be an "artificial" or "unnatural" grouping?
20) Why are computer algorithms necessary for examining relationships among more than five taxa?
Lecture 18 - Apr 02nd 2015
1) A branch of a phylogenetic tree can be longer than another branch for two reasons: what are they?
2) What is an outgroup and what is it used for?
3) Be able to map character state changes onto a phylogenetic tree and know how to count steps. See Tree building practice exercise below.
4) There are the two basic Categories of methods for constructing evolutionary trees from DNA data, the first is “Distance-Based Methods”. What is the second category?
5) In the second category, we discussed three different ways of constructing trees. What are these?
6) Know how to take a tree and translate it into parenthetical notation and vice versa.
Lecture 19 - Apr 07th 2015
1) List the advantages of molecular data for phylogenetic analysis.
2) Does DNA data guarantee the correct phylogenetic tree? Why or why not?
3) Do substitutions occur at random along the length of a gene? Why or why not?
4) What is a pseudogene and how fast does it evolve compared to synonymous and non-synonymous sites in non-pseudogenes?
5) Who first proposed the molecular clock idea and when?
6) What is the main assumption behind the "molecular clock"?
7) How are molecular clocks calibrated (name two different types of data that can be used for calibration?
Lecture 20 - Apr 09th 2015
1) What problems are associated with attempting to use molecular clocks?
2) How does the rate of evolution of mitochondrial DNA sequences vary between endotherms and ectotherms (hint- this is related to metabolic rate)?
3) How does the rate of DNA substitution vary within genes, among genes, and among taxa?
4) If different lineages evolve at different rates (clearly violate the clock assumption) does that prevent the use of the molecular clock? Explain.
5) Where would you expect to see substitutions in each of the following types of genes: rRNA, tRNA, mRNA?
Lecture 21 - Apr 14th 2015
1) What are the three major divisions (domains) of life?
2) Looking at the Balduf et al. 2003, Keeling et al. 2005, and Lane & Archibald 2008. tree of Eukaryotes: how are plants, animals, various types of algae and fungi related to the various protist lineages?
3) What characteristics do all animals share?
4) Explain the importance of choanoflagellates.
5) Cnidaria possess two basic body plans what are these?
6) Which phyla are not bilaterally symmetrical?
7) If given the simplified evolutionary tree of animal phyla, be able to pinpoint the following major events in evolution: the origin of two embryonic tissue layers, the origin of three embryonic tissue layers, the origin of the mouth and digestive cavity, the origin of an bilateral symmetry, the two origins of the anus, the two origins of the coelom, the protostome versus deuterostome lineage. 8) List five ways in which the development of protostomes differs from the development of deuterostomes.
9) What are the ecdysozoa?
10) What controversy surrounded the relationships between Arthropods, Mollusks and Annelids? How was it resolved?
11) Match the organisms (common names) to the correct Phyla:
A) Porifera, B) Cnidaria; C) Ctenophora; D) Platyhelminthes, E) Bryozoa; F) Brachiopoda; G) Mollusca; H) Annelida; I) Nematoda; J) Arthropoda; K) Echinodermata; L) Chordata
“Moss animals” _____, beetles _____, sharks ____, sea cucumbers _____, sea anemones _____, harvestmen (daddy long legs) _____, tunicates _____, lamp shells _____; planaria _____; leeches _____, flukes _____, clams, ______, starfish _____, Portuguese man-o-war _____, fish _____, snails _____, tapeworms _____, comb jellies _____, hydra _____, corals _____, cicadas _____, salamanders _____, Sponge Bob _____, Cassiopea _____, flies _______, lancelets ____, centipedes _____, horseshoe crabs _____, sea urchins _____, birds _____, crinoids _____, octopus _____, earth worms ____, marine segmented worms __, barnacles _____, shrimp ____, damselflies _____, lobsters ____, snakes _____, chimps_____, scorpions _____, lamprey _____, cuttlefish _____.
12) What are the shared derived characteristics (synapomorphies) of Chordata?
13) From what structures in agnathans are jaws hypothesized to originate?
14) How do lobe-finned fishes differ from other fishes?
15) Know the synapomorphies of amphibians; reptiles; birds; and mammals.