Evolutionary Analysis

Chapter 14: Reconstructing Evolutionary Trees

Study and Review

These essay/discussion questions provide a comprehensive review of the facts and concepts presented in each chapter, with special attention to connections among scientific facts, individual case studies, and broader principles.

1. What is a phylogeny? What is a phylogenetic tree? From what general kinds of data can phylogenies be inferred, and what general issues must researchers address when estimating phylogenies? [Hint]

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2. What is a synapomorphy, and why are these characters uniquely valuable for phylogeny inference? What is the name of the methods that use these principles for phylogeny inference? [Hint]

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3. What is outgroup analysis, and what is its significance for phylogeny inference? Briefly describe how this kind of analysis is performed, using the evolution of birds to illustrate your answer. [Hint]

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4. What is homoplasy? What processes give rise to it, and what specific, problematic pattern does each produce? What qualities do researchers look for in characters in hopes of reducing homoplasy? [Hint]

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5. What is the general logical criterion of parsimony? What is the rationale for invoking parsimony in phylogeny inference (i.e., what underlying evolutionary principles justify its use)? [Hint]

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6. Outline the two competing hypotheses for the evolutionary relationships between whales and artiodactyls. With what types of data is each hypothesis associated? What are the relative advantages and disadvantages of these types of data? [Hint]

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7. Use the example of the structure of the astragalus in ungulates to illustrate how the principle of parsimony is applied to the inference of phylogeny based on morphological data. Does the morphology of this specific structure support one of the two whale hypotheses unambiguously? Defend your answer. [Hint]

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8. Using the molecular sequence data provided in Figure 14.6, explain the general process by which molecular data are used to construct phylogenetic trees, and by which parsimony is applied to evaluate those trees. Do all the data provided support a whale-hippo clade unambiguously? How strongly do the molecular data assessed to date support the whale-hippo clade? Explain. [Hint]

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9. What is an "exact method" for evaluating the possible phylogenetic relationships among a group of organisms? What are the advantages and disadvantages of this method? Describe how bootstrapping can be used to evaluate the most parsimonious tree inferred from a dataset. Why is this important? [Hint]

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10. Discuss maximum likelihood and genetic distance methods as alternatives to parsimony. How, in general, do these methods differ? Why is it useful to use all three approaches? [Hint]

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11. What options are available to scientists when datasets produce conflicting hypotheses about phylogenetic relationships? Discuss the usefulness of SINEs and LINEs in the resolution of this problem for whale phylogeny. [Hint]

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12. Define the term systematics and compare and contrast phenetic with cladistic approaches to classification. How would phylogenetic naming schemes change our existing classifications? Use examples to illustrate your answer. [Hint]

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13. Using the example of compound eyes in ostracods, discuss how phylogenies can be used to determine homology. For what general kinds of questions can this method be used? [Hint]

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14. Describe the rationale for expecting that at least some types of DNA sequences change in a clock-like fashion. What caveats must scientists take into account when using molecular clocks to date evolutionary events? Describe in general terms how molecular clocks are "calibrated." [Hint]

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15. Define the terms biogeography and phylogeography. Use the example of the diversification of chameleons to illustrate how phylogenetic approaches can help answer biogeographic questions. [Hint]

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16. Define the term coevolution and illustrate, using the example of aphids and their endosymbionts, how phylogenetic analyses can shed light on this phenomenon. [Hint]

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17. Describe how Achtman and colleagues used phylogenetic analysis to explore the origin of Yersinia pestis populations. Where did today's strains originate? How did the investigators infer the relative ages of the strains? What new questions arose as a consequence of this study? [Hint]

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