DQ5.1: Explain what it means for a trait to be vertically inherited.

DQ5.2: Darwin's phrase for evolution was "descent with modification." Explain what he meant.

DQ5.3: (Box 5.1) Contrast mono-, para-, and polyphyletic groupings on a branching tree.

DQ5.4: (Box 5.1) How would you distinguish between cladogram, additive, and ultrametric trees?

DQ5.5: (Box 5.1) Contrast two alternative interpretations of a polytomy within a tree.

DQ5.6: (Box 5.1) How do phylogeneticists test for the robustness of a particular node within a tree?

DQ5.7: Distinguish convergence and parallel evolution.

DQ5.8: What are some problems that might result in an inference of an incorrect phylogeny?

DQ5.9: Summarize homologous traits for all living organisms (i.e., inherited from LUCA).

DQ5.10: When is evolutionary character state reconstruction likely to be unambiguous, or not?

DQ5.11: Use a tree diagram to distinguish ancestral ("primitive") vs. derived character states?

DQ5.12: Contrast Whittaker's five-kingdom tree with the current division of life into three domains.

DQ5.13: Given the data in Fig. 5.16 (p. 122) how would you determine which are derived similarities?

DQ5.14: Briefly explain approaches that have been used to root the three-domain tree of life.

DQ5.15: Distinguish between gene orthologs and paralogs.

DQ5.16: What advantage is gained by determining the root of the tree of life? What good is it?

DQ5.17: Characterize the confounding problem of "long branch attraction" in phylogenetic inference.

DQ5.18: How can lateral gene transfer (LGT) confound a phylogenetic estimate? How is it detected?

DQ5.19: Where do viruses sit on the tree of life? Contrast two alternative theories presented in the text.