Ch. 8 RQs: Species Phylogenies and Macroevolution
Part One (pp. 401-421)
1. What is phylogenetic character mapping? (PCM) Explain the normal goal of this procedure.
2. Explain what at least two different phylogenetic hypotheses for the relationship between micro- and macrobats imply about the origin of flight in mammals.
3. Why is the king crab an odd crab? Explain what PCM analysis of recent phylogenies of king crabs and their relatives would imply.
4. Why has the method of independent contrasts been developed? Why don't normal statistical methods work well in the case where one is comparing taxa that might be closely related?
5. What does PCM analysis of recent phylogenies of whales suggest about the evolution of "toothed whale" traits such as echolocation?
6. What do alternative hypotheses for the phylogenetic root of tetrapods imply about the last common ancestor of tetrapods? (see here or here for a update and here for a morphological data matrix)
7. What does PCM analysis and recent phylogenies imply about the giant panda and its evolution?
8. Figure 8.7 uses PCM analysisto map nesting behaviors onto a DNA-based phylogeny of sweat bees. Briefly describe some conclusions resulting from this study.
9. Figure 8.8 uses coarse- and fine-focus PCM analysis to map nesting habits in birds. Briefly describe some conclusions resulting from this study.
Part Two (pp. 422-443)
1. Give an example of how phylogenetic analysis can be used to distinguish between vicariance vs. dispersal explanations.
2. Avise states (p. 423): "Thus, one important advantage of molecular approaches is that the temporal [i.e., timing] issues (based on molecular clock considerations) can be examined in addition to cladistic assessments per se." Explain by way of the hypothesis of the West Indian fauna of the Greater Antilles being formed by an ancient (80+ MYBP) vicariance hypothesis, when the Greater Antilles split from N. and S. America, using this example Gand the data in Fig. 8.11 to illustrate what he means.
3. Give an example of why it is probably unwise to dichotomize dispersal and vicariance too sharply.
4. Some similarities between geographically separated taxa might plausibly be explained either common ancestry or as a result of convergent adaptations. Give at least one example of how scientists have used molecular approaches to address these alternative possibilities.
5. What is the notion of an "Afrotheria" clade of placental mammals? How did this become the leading hypothesis, effectively displacing the earlier classifications?
6. Is the colonization of the Hawaiian Islands, the fly family, Drosophilidae, an example of dispersal from island to island or did the flies split by vicariance as the islands? Be ready to defend your response. Also, compare your response to the case of iguanas in the Galapagos.
7. How did our view of our own ancestry change with the availability of molecular data?
8. What is "The Tapestry" and why was it significant in the history of molecular systematics? What are some proposals about avian relationships that first arose from it?
9. Contrast the use of mtDNA gene arrangements with mtDNA genome sequencing. Give three examples of how the discovery of mtDNA gene arrangements have been used as informative high-level phylogenetic markers to "mark" clades that have the particular rearrangement?
10. In a similar manner, how have the following been used as phylogenetic markers? a. circular vs. linear condition of the mtDNA genome; b. modifications of the genetic code used in animal mtDNA (see Fig. 8.15).
11. In contrast to animal mtDNA, the chloroplast genomes of plants often carry numerous introns. Give an example of how the presence or absence of these have been used as phylogenetically informative markers.
Part Three (pp. 443-452)
Please note: Skim the above pages in the text to get a very brief history of the use of rDNA sequences to construct phylogenies across life. I changed my mind that this is what I want you to read for Thursday after I read it myself. Instead, please download and read the recent article by Peterson et al., 2005, on animal diversification and phylogeny. I think it is a very interesting example of the combined analysis of multiple gene loci, including molecular clock estimates, integrated with information derived from the fossil record. The following review questions are based on this article.
1. The Cambrian Explosion involves the geologically sudden appearance of nearly every modern phylum of large-bodied "triploblast" (ecto-, meso-, and endoderm) animals with or without skeletons. Why is the Cambrian Explosion considered to be so important?
2. Peterson et al. argue on the first page that it matters quite a bit whether all the separate phyla of bilaterian animals evolved from a common ancestor shortly before the observed Cambrian Explosion or else were already separate but still tiny for hundreds of millions of years before. Why?
3. The following animals are listed in semi-random order:
SN = snail (mollusk)
SU = sea urchin (echinoderm)
EW = earthworm (annelid)
CS = calcareous sponge (calcareous spicules)
AC = acoel flatworm
SA = sea anemone (cnidarian)
BF = butterfly (arthropod)
PD = priapulid
PL = flatworm (platyhelminth)
CJ = comb jelly (ctenophore)
AW = acorn worm (hemichordate)
FU = fungus
DS = demosponge (glass spicules)
outgroup = PL = plant
Use the "total evidence" tree in Fig. 1 based on 8 nuclear gene loci and morphological characters to draw a tree including only the above taxa, arranged to match the corresponding relationships shown in the Fig. 1 tree. Use PL for an outgroup. You can use the two-letter abbreviations. Also label these internal nodes: ME = all metazoans or multicellular animals; BI = bilaterian animals (includes cnidarians!); TR = triploblasts; DE = deuterostomes (also includes us); PR = protostomes; SP = spiralians; EC = ecdysozoans. Are any of these supported relationships surprising to you?
4. What does this tree imply about the likely last common ancestor of: 1) all multicellular animals (metazoans)?; 2) all tripoblasts?
5. If fossils of microbial life date back to over 3,500 million (or 3.5 billion) years ago, how old are the oldest know small metazoan fossils? How about the oldest large (macroscopic) metazoan fossils? When did the Cambrian Period start? (see Fig. 2)
6. How do the dates based on molecular clock estimates in Fig. 2 differ from earlier estimates? How do they agree with fossil evidence and what do they imply about the issues in questions 1 and 2 above?
7. What do the blue and yellow histogram bars in Fig. 2 indicate about the pattern of first appearances of higher animal taxa?
8. According to Peterson et al., how many triploblastic "worms" "crawled" across the Ediacaran/Cambrian boundary? What does this imply about the Cambrian Explosion?
9. According to Stephan Jay Gould (1979) and Peterson et al., why was the explosion "inevitable"? Hint: Point to the node on your tree (question 3) for the earliest of our ancestors that had a mouth.
The rest of the article is very interesting but is more than I expect you to read.