Difference between revisions of "Evolutionary Biology Spring 2011 Study Questions"

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(Lecture 15 (March 29, 2011))
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===Lecture 15 (March 29, 2011)===
 
===Lecture 15 (March 29, 2011)===
 +
What kind of data/evidence can be used to construct phylogenies?
 +
 +
What number of possible rooted trees exist for three taxa/sequences?
 +
 +
Draw a tree that has a polytomy. Draw a tree that is fully resolved. Draw a reticulated tree.
 +
 +
Define the following terms by drawing them on a phylogenetic tree:
 +
bifurcation
 +
trifurcation
 +
multifurcation
 +
branch
 +
root
 +
terminal node
 +
internal node
 +
monophyletic
 +
 +
Define the following terms in words:
 +
MRCA
 +
taxon
 +
monophyletic
 +
 +
Know that a phylogenetic tree can be swiveled at any node.  How does this fact relate to the concept of sister group?
 +
 +
Why is it misleading to call a living group “primitive”?
 +
 +
Why is it wrong to claim that humans are descended from chimps?
 +
 +
A branch of a phylogenetic tree can be longer than another branch for two reasons what are they? 
 +
 +
How do population and species trees look different?
 +
 +
What are the two components of a phylogenetic tree?
 +
 +
What two general classes of methods are available for building trees from DNA data?
 +
 +
Name the three major character-based methods for constructing phylogenetic trees.
 +
 +
What is an outgroup and what is it used for?
 +
 +
Why are reptiles considered to be an "artificial" or "unnatural" grouping?
 +
 +
Why are computer algorithms necessary for examining relationships among more than five taxa?
 +
 +
How does a clock-like tree differ from a non-clock-like tree? Why?
 +
 +
Be able to map character state changes onto a phylogenetic tree and know how to count steps (see Problem Set 4)..

Revision as of 00:21, 30 March 2011

EEB2245/2245W

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.

Return to Evolutionary Biology Webpage

Lecture 1 (Jan 20, 2011)

What is speciation?

What are three ways relationships among organisms can be depicted or described?

What is homology?

Explain how the Permian Mass Extinction had a large effect on the diversity of life on Earth. How did that extinction influence the diversity of life present on Earth now?

Describe three different patterns in the diversity of life that evolutionary biology seeks to explain.

Lecture 2 (Jan 25, 2011)

Give an example of the fit between an organism and its environment.

Why do we focus on genetic differences in studying evolutionary change?

Suppose you observe that the average weight of squirrels on campus is greater than their average weight on Horsebarn Hill. Give an example in which this difference in weight is the result of an evolutionary change. Given an example in which this difference is not the result of an evolutionary change. Describe an experiment you could do to determine whether the difference is due to an evolutionary change or not.

What is the relationship between Mendelian genetics and population genetics?

What are the variables used to describe the genetic composition of a population?

In general terms, what genotype frequencies are expected under the Hardy-Weinberg equilibrium?

What happens to genotype frequencies in a population under Hardy-Weinberg equilbrium? What happens to allele frequencies?

Hardy-Weinberg practice: try the Pdficon small.gif problems here to get practice with describing the genetic composition of a population and determining Hardy-Weinberg proportions.

Lecture 3 (Feb 3, 2011)

While studying anole lizards you observe that some lizards are more green in color (found mainly on tree leaves) while others are more brown in color (found mainly on tree trunks). In order for this phenotype to be an evolutionary change what must be the source of variation? How could you test to see the source of this phenotype variation?

Why do we use allele and genotypes frequencies instead of the number of gametes or individuals in a population?

How many generations does it take for a population to establish genotype frequencies in HWE (Hardy-Weinberg equilibrium) given all the assumptions are met?

Why does population size matter when studying population genetics?

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?)

What does it mean when an allele has ‘been fixed’ or ‘gone to fixation’ in a population?

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?

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.

Lecture 4 (Feb 8, 2011)

Which assumption of the HWE do both mutation and migration violate and why?

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?

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.

In the Continent to Island Migration model, it is assumed that the frequency of the continent allele, pc, stays the same. Why is this a reasonable assumption?

How can you calculate the allele frequency of an island population after 1 generation of migration?

Why is it important to consider the effects of migration and drift together?

How many migrants does it take to keep populations from diverging? Why is this the same for small and large populations?

What factor(s) affects the rate of homogenization of allele frequencies when populations are connected by migration?

What is the effective population size, Ne, and what is an ideal population?

Lecture 5 (Feb 10, 2011)

What happens to genetic variation, allele frequencies, and genotype frequencies as a result of inbreeding?

What are the different types of non-random mating?

How can you tell the difference between inbreeding and assortative mating?

What is the most extreme form of inbreeding?

How does inbreeding generally decrease fitness?

Inbreeding generally occurs in smaller populations. What other evolutionary change have we studied that also affects small populations more than large ones? How are they similar and how do the two differ on their affect genotype frequencies in the population?

There are many species of plants that are obligate selfers (they can only reproduce with themselves). Why do you think that this is a successful strategy for these plants? (Think about the effects of inbreeding and fitness)

Why are inbred lines of model organisms (e.g. Drosophila, mice, C. elegans) often used in biomedical research?

How does inbreeding depression affect populations? Give an example of a real example of inbreeding depression.

Lecture 6 (Feb 15, 2011)

What are the 3 premises of the theory of evolution by natural selection?

What is the difference between natural selection and evolution by natural selection?

What HWE assumption does natural selection violate?

Why is the relative number of offspring more important when considering an organism’s fitness than the absolute number of offspring?

What is Fisher’s Fundamental Theorem and why is it important?

What does w symbolize and how is it calculated?

Calculate the mean fitness of the population of flies we used in our example, and show that the change in allele frequency results in an increase in the mean fitness of the population. (Hint: you'll need to keep track of quite a few decimal places to see the effect.)

If the most fit genotype is heterozygote in our fly example, why does natural selection lead to the decrease of heterozygotes in the entire population?

How do you calculate genotype frequencies and allele frequencies before and after selection?

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.

Lecture 7 (Feb 17, 2011)

What is a fitness landscape? What are the axis labels?

Which genotype is most important for predicting a population’s future?

What does a fitness landscape look like for genetic drift?

What is the evolutionary consequence of directional selection?

What is the effect of the starting allele frequency on its fate under directional selection?

How does a trait’s dominance influence its fate in a population?

How do drift and directional selection act on a population together? How does this interaction change with population size? How does this interaction depend on the strength of selection?

What is the evolutionary consequence of stabilizing selection? How can you predict the equilibrium allele frequencies?

What do you predict is the evolutionary consequence of disruptive selection?

Lecture 8 (Feb 22, 2011)

What are the three types of selection covered in lecture and what is the relative fitness of heterozygotes for each type?

Which type of selection has an outcome that is dependant on the starting frequency of allele A?

In the example given today for disruptive selection, the minimum fitness occurred when the allele A frequency was 0.35. Why isn’t the fitness minimum always at an allele A frequency of 0.5, since this maximizes the proportion of heterozygotes in the population?

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?

What is the effect of drift on a small population under stabilizing selection? Predict how a plot of Freq of A vs. generation would change with stronger or weaker selection.

What is phenotypic plasticity?

In Endler’s guppies, why doesn’t drift provide a convincing explanation for the patterns of variation observed in nature?

What were the two kinds of selection that were acting on the guppy populations to produce the color/spot patterns observed in nature? How was this determined?

What are the differences between quantitative and Mendelian traits?

What are the three consequences of traits being determined by multiple loci?

Give two different scenarios in which natural selection is happening, but there is no evolutionary response to this selection.

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 9 (Feb 24, 2011)

What is the phenotype of an organism dependent on?

How is heritability defined? What are two different ways you could measure it?

If 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?

What do R and S stand for and how do you calculate them?

If h^2 = 0 then what is variation in the phenotype a result of?

A selection event occurs in a population allowing only some of the individuals to survive. The average trait value of the survivors are 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?

What do the fitness landscapes for directional, stabilizing and disruptive selection look like when multiple loci contribute to a phenotype? How do these fitness landscapes differ from their single-locus counterparts? In the multi-locus case, explain how the same fitness landscape could give rise to directional or stabilizing selection, depending on the initial distribution of phenotypes in the population.

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.

Lecture 10 (March 1, 2011)

Why does a heritability only apply to the environment in which the estimate was made?

How is sexual selection different from non-random mating?

What are intrasexual and intersexual selection? Give an example of each.

What is the common consequence of sexual selection in a population?

What is sexual dimorphism? Give a real life example not covered in class.

What are the three explanations for the evolution of female preference?

Could the Bird of Paradise courtship display that we watched in class 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?

In the Runaway Sexual Selection explanation why does the female preference become more common in the population?

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?

What evidence is there that drift plays a role in evolutionary divergence?

Why is Ensatina treated as a single species even though the southern forms are reproductively isolated from each other?

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?)

Part II: Mar 15-May 5, Dr. Simon

Exam questions will largely be taken from the study guide, hence the large number of questions. The format of the questions may change (e.g., a question that asks you to list criteria might be changed into a matching or multiple choice question, etc.). If you can’t find the answers in your lecture notes, check the text book!

Lecture 11 (March 15, 2011)

Which of the following is false? Populations may be… a) Allopatric, b) parapatric, c) sympatric, d) allochronic. Explain your answer.

Do all characters vary concordantly (in parallel) with latitude? Do they all vary with geography? Explain.

Give an example of a step cline and explain why phenotypes vary among populations.

Give an example of a gradual cline.

List three reasons for clines.

Which of the above reasons does not involve selection on the trait in question?

Explain how secondary contact between two formerly isolated populations could result in a cline that is stable over time.

What is the updated genetic definition of race?

According to Darwin, were subspecies evolutionary dead ends?

During what decades of the 20th Century did the modern synthetic field of evolutionary biology originate?

Do the named subspecies of rat snakes correspond to the definition of genetic race/subspecies that we discussed in class?

Explain the evidence compiled by Lewontin (1972) and Nei and Roychoudhury (1972), Rosenberg et al. (2002) and Li et al. (2008) that suggested that race was an artificial concept in humans.

Define ring species and explain what they illustrate about geographic variation, gene flow, and genetic variation?

Why is the ADH locus in Drosophila a particularly compelling example of selection correlated with an environmental trait?

What four factors determine the success of mating?

What three major categories did we use to describe “factors that reduce gene flow” in natural populations of organisms?

Give two example of pre-mating factors that reduce gene flow in each of the following categories: spatial isolation, temporal isolation, behavioral isolation. What three examples of allochronic isolation did we discuss?

Define: aggressive mimicry. What two examples did we discuss?

What is the lock and key hypothesis?

What are the four stages at which egg and sperm union (zygote formation) can fail?

Lecture 12 (March 17, 2011)

True or False? The more distantly related two species, the less likely they are to produce viable hybrid offspring.

What are three reasons for post-mating genetic incompatibility?

Lee and Vacquier (1992) sequenced the sperm binding protein in seven species of abalone. After comparing the DNA sequences among all species they found more differences among species at second positions in the active sites of proteins than at third positions. What does this result imply? Does selection at this locus verify that this trait evolved in response to selection favoring mating within species (selection against hybridization)? Explain.

Is it usual to find more second than third position codon changes when comparing proteins of closely related species? Why or why not?

Are reproductive proteins in general faster or slower evolving than other proteins? Is it a general rule that in the active site of reproductive proteins evidence of natural selection will nearly always be found?

What is Haldane’s Rule?

What is Wolbachia? How does it influence sterility?

For each major species concept that we discussed in class know the definition, the advantages and the problems.

In practice what is the most common species concept to be applied in a large biodiversity study?

In a detailed study of a specific group of organisms, the most common and useful species concept to apply is the phylogenetic species concept. This is done via a phylogenetic analysis of morphological and/or molecular data. Why would the biological species concept be impractical in this case?

What are the four categories of speciation mechanisms that we used to organize our class discussion?

Define vicariance speciation and give a real or hypothetical example.

Lecture 13 (March 22, 2011)

What are the four categories of speciation mechanisms?

Spatial speciation mechanisms can be divided into what three categories?

In allopatric speciation, how does speciation by vicariance differ from founder effect speciation?

How does the founder effect work to encourage speciation?

Explain what type of speciation led to >50 species of Hawaiian honeycreeper.

What conditions are necessary for parapatric speciation to occur?

Give a possible example of parapatric speciation.

Define sympatric speciation. What conditions does it require?

Define host-race speciation and give an example.

How did gradual allochronic change evolve in true fruit flies of the genus Rhagoletis?

Why do chromosomal mutations reduce fertility of the individuals carrying them?

Explain how translocations reduce the fitness of heterozygotes.

The tree frog Hyla versicolor is believed to have evolved from Hyla chrysoscelis by what mechanism?

What is very unusual about the species H. versicolor and how do the “biological” and “phylogenetic” speciation concepts apply to this case?

Peter and Rosemary Grant studied hybrids two species of Darwin’s finches on the Galapagos Islands. Which species were involved and what happened to the overall fitness of hybrid offspring over many generations?

In periodical cicadas, what trait is involved in reproductive character displacement?

Higgie et al. 2000. were able to experimentally generate reproductive character displacement in two species of Australian Drosophila in the laboratory. What trait was selected for and how many generations did it take to achieve displacement?

Define gene flow:

How could gene flow and recombination in hybrids work against the reproductive character displacement needed to achieve speciation via reinforcement?

What are the four possible consequences of secondary contact?

Lecture 14 (March 24, 2011)

What is introgression?

How is introgression demonstrated in New Zealand cicadas in the genus Kikihia?

Rieseberg studied the hybrid speciation of sunflowers. What experiments did he do to show that there was good evidence for selection for co-adapted allele complexes in the hybrid species Helianthus anomalus?

Define Systematics.

What is a natural classification? A non-natural classification?

How are evolutionary trees similar to hierarchical classification schemes?

What are the major designations of hierarchical classification (in the Linnean system you were shown in class)?

Why can determining relationships among organisms be difficult? Give specific examples for each reason?

Define the following terms

Character-

Character state-

Symplesiomorphic character state-

Synapomorphic character state-

Homoplasy-

Convergence-

Parallelism-

Reversal-

Phylogeny-

Are the sucking mouth parts in cicada and mosquito homologous? What is the evidence?

What type of homoplasy does comparing North American placental animals to Australian marsupials demonstrate?

How can a phylogenetic tree help to recognize homoplasy?

Explain how a synapomorphy at one node can be a symplesiomorphy for descendant taxa at shallower nodes of the tree.

What type of homoplasy do cave animals typically demonstrate?

What is the main difference between parallelism and convergence?

What famous terms did Haeckel coin?

Give two synonyms of “phylogenetic tree.”

In addition to morphological character, what other kinds of characters are used to construct phylogenies?

Lecture 15 (March 29, 2011)

What kind of data/evidence can be used to construct phylogenies?

What number of possible rooted trees exist for three taxa/sequences?

Draw a tree that has a polytomy. Draw a tree that is fully resolved. Draw a reticulated tree.

Define the following terms by drawing them on a phylogenetic tree: bifurcation trifurcation multifurcation branch root terminal node internal node monophyletic

Define the following terms in words: MRCA taxon monophyletic

Know that a phylogenetic tree can be swiveled at any node. How does this fact relate to the concept of sister group?

Why is it misleading to call a living group “primitive”?

Why is it wrong to claim that humans are descended from chimps?

A branch of a phylogenetic tree can be longer than another branch for two reasons what are they?

How do population and species trees look different?

What are the two components of a phylogenetic tree?

What two general classes of methods are available for building trees from DNA data?

Name the three major character-based methods for constructing phylogenetic trees.

What is an outgroup and what is it used for?

Why are reptiles considered to be an "artificial" or "unnatural" grouping?

Why are computer algorithms necessary for examining relationships among more than five taxa?

How does a clock-like tree differ from a non-clock-like tree? Why?

Be able to map character state changes onto a phylogenetic tree and know how to count steps (see Problem Set 4)..