Terms to know: neutral (with respect to selection), silent substitution, morphology, DNA, convergent evolution, chance convergence, homology, saturation, alignment, the fossil record, radiometric dating, molecular clock hypothesis, the relative rates test.

Questions: phylogenetic analysis

1. Suppose you want to study phylogeny based on traits that are neutral with respect to natural selection.  (a) Why would you want to study neutral traits to study phylogeny?  (b)  What parts of a DNA sequence would you want to study? Why?
2. Consider two reconstructed phylogenetic trees of a group of closely related fish.  One is based on silent base-pair substitutions.  The other is based on mouth position and aspects of jaw structure and head shape that are important functionally in how the fish eats.  The two phylogenies disagree with respect to the relationships among some of the fish species.  Which should be more reliable? Why?
3. Give advantages of using molecules such as DNA rather than morphological characters for studying phylogenetic relationships.  Give advantages of using morphological characters rather than molecules for studying phylogenetic relationships.
4. What is the significance of convergent evolution with respect to studying phylogenetic relationships?  Under what circumstances do you expect morphological characteristics to show convergent evolution?  Why? Under what circumstances do you expect DNA sequence data to show convergent evolution?  Why? What form of DNA data have we discussed that is expected to be phylogenetically informative and to have very little convergent evolution?  Why?
5. It has been argued that, in order to develop a well supported phylogeny, one should study both morphological and molecular characters (not just

morphological or just molecular.)  Explain why this is by explaining one way in which studying morphological characters may result in a more reliable phylogeny than studying molecular characters, and one way in which studying molecular characters may result in a more reliable phylogeny than studying morphological characters.
6. One major difficulty in the study of phylogeny is the existence of convergent evolution.  Explain what convergent evolution is and why it makes it difficult to study phylogeny.  Explain why convergent evolution occurs in morphological data (data on the structure of organisms) and explain or give examples of kinds of structures especially likely to show convergent evolution.  Explain why convergent evolution occurs in DNA sequences, state where in the DNA sequence we are most likely to see convergence, and explain why.  Finally, explain why convergent evolution is expected to be much lower in SINE/LINE data than either morphological data or DNA sequence data.
7. When people first started using DNA data for phylogenetic analysis, they expected that it would avoid a variety of problems observed in morphological (structural) data.  What are the problems DNA data was expected to overcome.  Does it really overcome these problems or does it still have some or all of them?  Explain.
8. What is alignment?  Why is it important for DNA sequence based phylogenetic analyses -- what error(s) might you make if you do not use it, and why?
9. Suppose that the following graph represents differences in DNA sequence of a gene coding for the protein cytochrome-b between species whose speciation dates have been determined from the fossil record.

 

 
 
 
 
 
 
 



10.  What type of DNA would you use to study each of the following groups?  Explain why different types of DNA are more appropriate for different phylogenetic studies in general, and why you choose the type you do for each specific case.  (a) Different subspecies of honeybee.  (b) Relationships among the three subphyla of the Chordata (tunicates, amphioxus, and vertebrates). (c) Relationships within the fish family Salmonidae (includes trout and salmon).  (d)  Relationships among the different phyla of worm (flatworms, roundworms, segmented worms).  (e)  Species within the bird genus Icterus (orioles)
11. DNA that evolves slowly is least likely to show chance convergence.  (a) Explain why this is likely to make variation in slowly evolving DNA a particularly good indicator of phylogeny.  (b)  Given what you discussed in (a), why would we ever want to use rapidly evolving DNA to study phylogeny?
12. Why should the rate of neutral DNA evolution (per generation) be equal to the mutation rate -- since it's neutral, and evolves through genetic drift, and drift depends on the population size, why doesn't the rate of neutral DNA evolution also depend on population size?  (You need to give an algebraic answer to this question).
13. Explain what is meant by the molecular clock, how it is calibrated, and how it is used in phylogenetic reconstruction.  Upon what assumption is the molecular clock hypothesis based?  How would you test to determine whether this assumption is met?
14. You want to test a hypothesis that speciation between two species of ground squirrel occurred as a result of the Pleistocene ice ages, about 1 million years ago.  You have a good fossil record that indicates that speciation between a ground squirrel and a prairie dog occurred 5 million years ago.  You are studying a gene that has  70 DNA differences between the ground squirrel and the prairie dog.   Assuming the molecular clock hypothesis applies to this gene, how many differences should there be between the two ground squirrel species you're studying if your hypothesis about the Pleistocene is correct?  Show how you get your answer.
15. Assume that the following trees represent the true phylogenetic relationships among the species.  Each "tick" marks on the trees represents a molecular change.  Which one supports the molecular clock hypothesis?  Which does not?  Why?
16. On the following phylogeny, if the molecular clock hypothesis is true, which pairs of species should have the same number of DNA differences between them?
17. What is the relative rates test?  Draw a plausible phylogeny of three species of your favorite group of organism, and state how you would apply the relative rates test to this phylogeny.
18. Suppose you have developed a molecular phylogeny for a group of species of clam.  You would like to use the molecular clock to estimate the times of speciation of the clam species, and you have a date of speciation for two species from the fossil record.  (a) explain how you would use this information to determine the speciation dates of all the other species.  (b) explain how to use the relative rates test to determine whether rates of evolution were constant, as is required for the molecular clock hypothesis.
19. Discuss whether you would expect each of the following kinds of molecule to evolve rapidly or slowly, and whether you would expect them to evolve at a constant rate.  Explain why you predict what you do. What is the relevance of this information to the study of phylogeny?  (a) the sequence of amino acids in a peptide (protein) hormone.  (b) the base pairs in the third codon positions of a gene coding for a peptide (protein) hormone.  (c) the base pairs in the first codon positions of a gene coding for a peptide (protein) hormone.  (d) a region of non-coding mitochondrial DNA.  (e) DNA that codes for ribosomal RNA. (f) DNA in an intron (a region in a gene whose information is ultimately "spliced out" so it does not code for any amino acids) in a gene coding for an important glycolytic enzyme.  (g) DNA in an exon (a region of a gene whose information does ultimately code for amino acids) in a gene coding for an important glycolytic enzyme. (h) insertions of SINES and LINES into specific genes
20. Describe one benefit and one problem for phylogenetic analysis with the fact that mtDNA in vertebrates is non-recombining.
21. Suppose you want to study relationships among populations in a species to test whether speciation is occurring.  What form of DNA should you use?  Why?

1. What are two possible kinds of mutations that could lead to the origin of very different traits from those present in the ancestral species (more different than expected for alternate alleles for a typical gene)
2. Explain how to distinguish between positive and negative selection on DNA traits.
3. You are studying a group of deep sea animals that produce mating displays by flashing bioluminescent (that is, biological pigments that produce light so they can be seen in the darkness) colors.  You have identified the gene that codes for the enzyme needed for production of the main bioluminscent pigment.  You suspect that the active site of this enzyme has been subject to positive selection to lead to the differences among species in pigment that allow for species recognition.  How would you test this hypothesis?  This enzyme is apparently a new trait, not present in other related forms.   How would such a new enzyme evolve, and how could you test this hypothesis?
4. Based on a phylogenetic analysis, blue coloration in a group of butterflies has evolved independently five times.  Give two different possible genetic bases for convergent evolution and explain how you would test between them.
5. Explain how gene duplication can lead to each of the following, and explain how you would test to see if it had occurred: (a) a new adaptive trait, (b) a key innovation
6. What are three main features of Hox genes? Relate these main features to: (a) the evolutionary origin of new Hox genes, and (b) the function of Hox genes (c) the significance for further evolution of the evolution of new Hox genes
7. What evidence suggests that Hox gene duplication and elaboration was a key innovation?
8. Hypotheses of heterochrony were developed before people knew much about the actual developmental mutations that might have occurred.  How does the more recent information on the genetics of development of the tetrapod limb relate to these older hypotheses of heterochrony?  What kinds of mutation could cause heterochrony?  In what kinds of genes would they occur?
9. The initial pattern of development of lobe-finned fish lobes and tetrapod limbs is dependent on the timing of expression of the same genes (including Hox genes).  Late in development, expression of Hox genes in lobe-finned fish stops.  In contrast, Hox genes are expressed late in development in tetrapods; they regulate the development of the hand.  The tetrapod condition is apparently the derived condition.  Relate this description of the genetic regulation of development to hypotheses of heterochrony.  Does this suggest terminal addition or paedomorphosis? Why?
10. What is "deep homology"?  Use the Dll (distal-less) gene described in Chapter 17 of Freeman and Herron (2001) as an example to explain what this means.