EEB2245W S2009 Review Questions

Review Questions for 30 April 2009 (Human Impacts on Evolution)

What are some of the major ways that humans impact the evolution of other lineages?

Describe the major changes that have occurred in the fauna of New Zealand since the arrival of humans. What evidence suggests that humans are a primary cause of these changes?

What is coextinction? What groups are most threatened by coextinction?

What effects, beyond loss of particular taxa, did the extinction of the Pleistocene megafauna have?

Human predation can act as a strong selective factor. What evidence suggests that this pressure has led to evolutionary changes? What are the conservation consequences of such changes? What are some examples of evolutionary change that have occurred as a result of human predation?

What sorts of changes in habitat may be changing selection pressures on native populations at present? What sorts of evolutionary change do we expect to result from this changing selection pressure?

What are two ways in which the domestication of animals has impacted the evolution of humans?

Review Questions for 28 April 2009 (Human Evolution)

What are the two interpretations of the Cambrian Explosion?

What explanations have been offered to explain the sudden burst of diversification in the Cambrian?

Among living taxa, who are humans most closely related to? When did the most recent common ancestor of humans and their sister group live? What are the relationships among ape species? What is the sister group to apes?

What major evolutionary changes occurred along the branch leading to extant humans? What evidence supports the conclusion that these are derived features of humans?

What evidence from living taxa supports the conclusion that humans evolved in Africa? What evidence from fossil taxa supports this conclusion?

Which three lineages migrated out of Africa? Which close relative of humans has never been found in Africa?

Know the names, general geographical range, and order in time of the fossil groups that are more closely related to living humans than to chimps. Also know in what significant ways each species differed from species that are found earlier and later in the fossil record.

What are the relationships among the fossil groups we have been discussing? In particular, what features do the various proposed trees have in common?

Though question: Using the fossil data, reconstruct the order of evolutionary changes in the evolution of modern humans. What traits changed earliest in human evolution? What traits evolved only recently? What traits show evidence of gradual change from the ancestral state to the state found in modern humans? What traits show a more rapid transformation?

Review Questions for 23 April 2009 (Cambrian Explosion)

What are the three interpretations of the Ediacaran fauna?

In what ways are the Ediacaran, Small Shelly, and Cambrian Explosion faunas similar? In what ways are they different? Given a fossil from one of these faunas, what characteristics would you use to identify which it most likely belongs to?

How does the Cambrian Explosion fauna (and related faunas from this time period) differ from the animal fauna alive today? How is it similar?

Describe two morphological clues found in the Cambrian Explosion fossils that give us an indication of the how the organisms of this time lived and interacted with one another.
How does this compare to what we infer about organismal interactions in the Ediacaran?

Why do we know that some phyla that aren't represented in the Cambrian fossil record must have already originated?

What evidence is there that the major animal phyla arose in a short period of time in the mid-Cambrian?

Dates to remember: 
       

  Age of Earth
  Earliest fossils
  Dramatic increase in atmospheric oxygen
  Earliest eukaryotes 
        
  Earliest multicellular organisms 
        
  Ediacaran fauna 
        
  Small Shelly fauna 
        
  Cambrian Explosion fauna

Taxa to remember: Who are they? When did they live? What is their evolutionary significance?

  Grypania
  Dickinsonia
  Eoandromeda
  Parapandorina

  Halkieria       
  Archaeocyathids 
        
  Pikaia
  Odontogriphus

  Hallucigenia       
  Olenoides
  Anomalocaris
  Opabinia
  Wiwaxia

Review Questions for 21 April 2009 (Phylogenetic Perspective on the History of Life)

What two major groups of organisms were recognized based on cell structure? What did molecular sequence data show about these two major groups? What three major groups are now recognized? What other evidence supports the existence of three major groups?

Why do we need a new method for rooting the tree of life? Why does the placement of the root matter?

What method was used to root the tree of life? How does it work? Where did this method place the root?

What evidence did Lynn Margulis use to support her hypothesis that mitochondria (and chloroplasts) originated as endosymbiotic bacteria? What additional data have provided strong support for her hypothesis?

What role did the primary endosymbiosis and secondary endosymbiosis play in the evolution of chloroplasts?

Why would you be surprised to discover an organism with chloroplasts but without mitochondria?

What, in general, can phylogenetic trees reveal about the history of life?

What are stromatolites? What is their evolutionary significance?

Review Questions for 16 April 2009 (Molecular Clocks and Positive Selection)

Why does the neutral theory predict that taxa that have been diverging for twice as long a time will have twice as much sequence divergence? How was the molecular clock prediction tested?

What is the dn/ds ratio? Why does the neutral theory predict that dn/ds > 1 indicates that a protein is under positive selection?

Why is the dn/ds ratio test not a very sensitive indicator of positive selection? Describe a scenario in which dn/ds < 1, but the divergence between two proteins still resulted from positive selection.

What explanations are possible when a large number of replacement substitutions occur in a gene? (We identified four different possible explanations in lecture.)

What is the evidence for positive selection in each of the following examples:

  antigen recognition site of the MHC proteins
  microcephalin in the most recent common ancestor of great apes
  FOXP2 in humans
  codon usage in E. coli

Thought question: Molecular clock estimates (calibrated using the bird-mammal divergence) for the age of major groups of placental mammals suggests that these groups radiated more than 100 million years ago. This conflicts with the fossil evidence that major lineages of mammals diverged from each other after the non-avian dinosaurs went extinct 65 million years ago. Assuming that the molecular clock dates are correct, describe two ways you could explain the gap in the fossil record. Assuming that the current understanding of the fossil record is correct, give a specific explanation of what could have changed at the molecular level to cause the inflated estimates of divergence times.

Review Questions for 14 April 2009 (The Neutral Theory of Molecular Evolution)

What are some of the commonly observed patterns of DNA sequence variation that a theory of molecular evolution needs to explain?

According to the neutral theory, how frequent are each of the following kinds of mutations? What fate do they have? What determines their fate?

   mutations with a negative effect on fitness 
   neutral mutations 
   mutations with a positive effect on fitness

What are the equations for the following:

   Rate of fixation of neutral mutations 
   Rate of production of neutral mutations 
   Probability of fixation of a neutral mutation

Perhaps surprisingly, population size has no effect on the rate of fixation of neutral mutations. Why is this?

Why is the fraction of mutations that are neutral important in predicting how much sequence divergence is expected?

In which of the following do you generally expect more sequence divergence? In each case, explain why:

   silent substitutions or replacement substitutions in a gene 
   3rd codon positions or 1st codon positions of a gene 
   a functionally constrained gene and a gene under less functional constraint 
   silent substitutions of a functionally constrained gene and a gene under less functional constraint 

Thought question: Suppose that the neutral mutation rate is measured to be 3 x 10-9 in a gene encoding a milk protein and as 1 x 10-9 in a gene encoding a DNA binding protein. Give two biological explanations for why the neutral mutation rate could be higher in the milk gene. How could you distinguish between these two explanations using only the DNA sequences?

Review Questions for 7 April 2009 (Inferring Phylogenies 2)

What is the difference between characters and character states?

How can homology of proposed characters be evaluated? How can homology of proposed character states be evaluated?

What evidence would convince you that the feather-like structures of Tianyulong are homologous to feathers? What evidence would convince you that they are not homologous to feathers?

For DNA sequence data, explain why some As may not be homologous while an A and a T in different taxa can be homologues.

If given a small data set and trees, be able to do the following:

   indicate how many evolutionary steps there are in each character 
   figure out which tree is best by the criterion of maximum parsimony 
 

What does the tree resulting from a phylogenetic analysis represent? How can you evaluate support for it?

What is an outgroup? Why are outgroups used in phylogenetic analysis?

Review Questions for 2 April 2009 (Inferring Phylogenies)

In the angiosperm-feeding beetle example, why was it important to compare the number of species in sister groups?

If angiosperm-feeding beetles had formed a monophyletic group, how much confidence would you have had in the conclusion that angiosperm-feeding beetles have an increased speciation rate?

Why is it generally reasonable to conclude that taxa that share an evolutionarily derived trait are more closely related to each other than they are to taxa that lack that trait?

Why do ancestral similarities not tell us anything about closeness of relationships?

What are synapomorphies? What is the evolutionary significance of synapomorphies? Given a tree, how can you identify synapomorphies for a particular clade?

What kinds of evolutionary change can mislead us about the closeness of relationships?

How can homology of proposed characters be evaluated? How can homology of proposed character states be evaluated?

Why is similarity in function not used as evidence of homology?

Why would it be incorrect to have a character called 'malleus' with two states, present and absent, and to code the malleus as present in mammals but absent in reptiles?

Thought questions: A centipede expert observes that the number of body segments and leg length are negatively correlated in centipedes (i.e. centipedes with only a few body segments usually have long legs; those with a lot of body segments usually have short legs), and proposes that this relationship between segment number and leg length is an adaptation for efficient locomotion (perhaps because a lot of long legs would be more likely to get tangled up). You look up the phylogeny of centipedes and discover that the short-legged centipedes form a clade and the long-legged centipedes form a clade.

       Why would this phylogeny NOT provide much support for the centipede expert's hypothesis? 
       What alternate explanation could account for the association between number of body segments and leg length? 
       Why would a phylogeny in which multiple independent long-legged short-bodied clades evolved from short-legged, long-bodied ancestors provide stronger support for the expert's hypothesis? 
       Draw a tree that would show this pattern of character transformation.

Review Questions for 31 March 2009 (Using Trees to Study Trait Evolution)

Why was the hypothesis that spider webs evolved from less complex to more complex rejected? What did the phylogeny of spiders suggest was the evolutionary history of webs?

What accounts for most similarity among taxa? How does this justify use of the principle of parsimony when choosing among different evolutionary scenarios?

What is the difference between homology and homoplasy?

What are the two kinds of homoplasy? How can they be distinguished?

If a trait evolves homoplastically, what is the minimum number of evolutionary changes that must occur on the tree? Why?

Given a tree and the traits of terminal taxa, be able to:

     identify the ancestral state
     identify the derived state(s)
     find the most parsimonious reconstruction of trait history (in simple cases)
     choose among difference scenarios of trait evolution

How was a phylogeny used to show that the preference for swords arose before swords did in swordtail fish?

How was a phylogeny used to show that the ancestral function of feathers was not flight?

Why do some scientists think that feathers were present in the common ancestor of all dinosaurs, even though this is not the most parsimonious scenario for the evolution of feathers?

Review Questions for 26 March 2009 (Using Trees)

Given a tree, be able to identify all of the following:

       monophyletic groups (=clades) 
       paraphyletic groups 
       polyphyletic groups

Why must the sister group of a taxon be either a species or a monophyletic group? Why can't it be a paraphyletic group?

How were phylogenies used to show the following:

     that multiple transmissions of SIV from chimps to humans occurred?  
     What would the phylogeny of HIV and chimp SIV have looked like had only a single transmission occurred?
     that two of these transmissions likely occurred in Camaroon?
     that the globally pandemic strain of HIV originated in Haiti?
     that the Maryland patient was infected with HIV from the blood donor rather than the surgeon?  
     What would the phylogeny of HIV from the patient, donor and surgeon have looked like if the patient had instead been infected by the surgeon?

What evidence supports the conclusion that Galapagos Tortoises originated from mainland South America?

What is the difference between an ancestral and a derived trait?

Thought question: What kind of group (mono-, para- or polyphyletic?) would you expect to be defined by the possession of a particular ancestral trait (e.g. fins)? What kind of group would you expect to be defined by the possession of a particular derived trait? Why?

Review Questions for 24 March 2009 (Sympatric Speciation, Phylogenetic Trees)

What evidence suggests that cichlids in Lake Apoyo speciated in sympatry?

What is the usual evolutionary outcome under conditions of disruptive selection? What else must occur for a single population to evolve sympatrically into divergent populations on both fitness peaks?

Why is assortative mating essential in models of sympatric speciation?

What do phylogenetic trees represent?

What are the three general features that characterize phylogenetic trees?

How is speciation represented on a tree?

What is the significance of the root of a tree?

Given a tree, be able to identify all of the following:

       sister groups 
       most recent common ancestors 
       relative closeness of relationships (e.g. is A more closely related to B or C?)

How can you determine whether two trees show the same pattern of relationships? Given two trees, be able to tell whether or not they show the same relationships.

Why, if A is the sister group to B, must B be the sister group to A?

Review Questions for 19 March 2009 (Mechanisms of Speciation)

What argument would you give for the existence of 4 species of Plestiodon in California? How about 2 species? And 1 species? Which of these is arguments do you think is strongest? Why?

Define and give examples of prezygotic and postzygotic reproductive isolation.

What is the first step in allopatric speciation?

Why do the genetic models of the evolution of postzygotic reproductive isolation involve at least two genetic changes?

What is epistasis? What is its role in speciation?

What role does natural selection play in speciation according to the Dobzhansky-Muller model?

Why do we expect reproductive isolation to evolve if populations are isolated for long enough?

Give examples of genes known to contribute to low fitness in hybrids. Do these examples suggest that there is a special class of "speciation genes" that are responsible for the evolution of reproductive isolation?

Thought question: We looked at the 3D fitness landscape for a model of speciation by natural selection. A very similar model in which genetic changes are due to drift can also lead to speciation. How would the fitness landscape be similar if the changes in each of the populations were caused by drift? How would it be different?

Review Questions for 17 March 2009 (Geographic Variation and Speciation)

What is speciation? Why is speciation said to be a bridge between microevolution and macroevolution?

What evolutionary processes have likely been responsible for divergence in Ensatina? What evidence shows that these have been important?

In general, what factors tend to promote divergence of populations? What factors tend to prevent divergence?

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

How did reproductive isolation evolve in Ensatina?

What is the significance of the three evolutionary experiments in Ensatina?

       experiment 1 = closing of the ring in southern California 
       experiment 2 = Spread of solid forms across the Central Valley and into contact with the blotched forms in the Sierra Nevada 
       experiment 3 = extinction experiment--what would be the effect of extinction of the northern California populations?

Compare the role of natural selection in generating geographic variants in Ensatina and Plestiodon. What is the role of natural selection in the evolution of reproductive isolation in each of these examples?

Thought question: Why can't natural selection act directly to produce postzygotic isolation between populations?