Ch. 6 RQs
Part One (pp. 231-247)
Skim these pages.
Part Two (pp. 248-277)
1. (Table 6.3) What ecological or life history factors are likely to lead to high population genetic structure?
2. If FST values can range from 0.0 to 1.0, what do values at these extremes imply?
3. Try your best to describe what the three allelic correlations of Sewall Wright's "F statistics" represent: FIT, FIS, and FST. If you have ever been exposed to ANOVA statistics, think of them as parallel to the way one partitions the variance in an ANOVA into different components. "AMOVA is like an hierarchical analysis of variance in that it separates and tests tiers of genetic diversity:
a) diversity among groups of populations; b) diversity among the populations within groups;
c) diversity among the individuals within a population" (quoted from here). The important paper referred to by Cockerham and Weir (1993) is here. I also recommend reading what Palumbi (2003) has to say about problems in interpreting F statistics here. If you would like to have a more practical idea of how to calculate F statistics, see the help files associated with the program Arlequin here. Some other links are here: 1 - 2 - 3 - 4.
4. (Box 6.3) If the amount of gene flow between populations is of fundamental interest, expressed as a migration rate m, why do most statistical procedures estimate the product "Nm" instead, where N is the size of islands or demes?
5. (p. 255) What is autogamy? Briefly explain it using the example of the snail Rumina decollata (p. 256-257).
6. (p. 258) Explain why Fig. 6.3 (A) is different from Fig. 6.3 (B). In other words, how are tropical trees different from marine fishes in their relationship between gene flow and natural history dispersal potential?
7. (p. 259) For marine animals with planktonic larvae, do species with greater potential for gene flow via the dispersal of gametes or larvae have less population structure than species with more limited dispersal, such as those with "crawl away" larvae? What is the evidence for which ever answer you gave? Can you give a specific example?
8. (p. 262) Give an example of a species with planktonic larvae that has pronounced genetic structure, despite an apparent opportunity for dispersal. Can you explain why such structure might exist with more than one alternative possible explanations?
9. (p. 264) Can you give an example of a species that appears to have much gene flow with one set of genetic markers and very little with another?
10. (p. 266) How did Rick Grosberg (UC Davis) make direct measurements of how far sperm effectively disperse from a sea squirt? What are some general limitations with this sort of direct measurement of gamete dispersal?
11. Explain how Fig. 6.5 addresses the question of whether female turtles return to nest at the same place they were born. How does natal homing behavior complicate the estimation of gene flow?
12. (p. 273) How does gender-dependent behavior lead to a problem if only mtDNA is used as a molecular marker?
Part Three (pp. 277-320)
1. Sometimes one class of molecular markers shows either more or less population structure than other sampled markers. What possible explanations for each of these situations involves selection acting on those markers?
2. Why do population geneticists normally use equilibrium theory models even though it is appreciated that most natural populations are not strictly conforming to equilibrium conditions?
3. What is the potential advantage of treating each individual organism sequenced as the fundamental units in population structure analysis, as is common to do in mtDNA-based phylogeographic analysis? Why not just group them by the locality collected?
4. Define phylogeography. Briefly explain how it is related to other similar fields of study as in Figure 6.7. Why is mtDNA so popular for phylogeographic studies?
5. What is the difference between a species and an "evolutionary significant unit" or "ESU"?
6. Choose any two of the case studies between pp. 289-298: (a) green turtles; (b) Amazonia small mammals; (c) brown bears; (d) red-winged blackbirds; (e) high latitude fishes; (f) lacertid lizards; (g) mimic butterflies; (h) European trees; (i); free-living microbes. How did phylogeography studies reveal some details that were revolutionary in terms of the understanding of populations of whichever case studies you chose?
7. Give two general conclusions that have arisen from the extensive phylogeographic studies on humans.
8. Give one example each of a phylogeography study that has used "genealogical concordance" by Aspects I, II, III, or IV (Fig. 6.13). Describe the example in sufficient detail so that it is clear what the relationships is between the study and the corresponding tree on p. 302.
9. Why is "genealogical discordance" considered the flip side of genealogical concordance? Give an example and briefly explain it.
10. What is meant by "microtemporal phylogeny"? Explain the example illustrated in Fig. 6.19.