BISC 495-010, Evolution, Spring 2008

Mondays, Wednesdays and Fridays, 11:15 a.m. to 12:05 p.m.
116 Gore Hall

Instructor: John McDonald
322 Wolf Hall (office)
026B Wolf Hall (lab)
Phone: 831-2007
E-mail: mcdonald@udel.edu
Web page: http://udel.edu/~mcdonald

Goals: In this course, I hope that you:

Note that learning facts is last on the list. I will place very little emphasis on memorizing, say, which animal phyla evolved in the Cambrian, the evolutionary relationships of vascular plants, or the assumptions of the Hardy-Weinberg relationship. Instead, I will emphasize evolutionary biology as a "way of knowing," a set of approaches to answering questions that is of broad importance to all kinds of biologists. I will present many examples of evolutionary research, some of which may seem trivial or irrelevant (we'll spend a whole lecture on the evolution of the hippopotamus!), but they will all illustrate how evolutionary biologists make our discoveries. I realize that very few of you will become professional evolutionary biologists, but whether you become a medical professional, a biomedical researcher, a teacher, a forensic detective, or a zookeeper, I hope that when you think about biology, you will think like an evolutionary biologist.

Exams: There will be three exams, on Friday, March 9; Wednesday, April 18; and during finals week. The exams will be cumulative. Study guides, with lists of topics to be covered and some example questions, are linked below (at this point, these are the study guides from 2007; I'll let you know when I update them). The first exam will be worth 15 percent, the second exam 25 percent, and the third exam 35 percent of the total grade. The grades will not be curved, and there will be no extra credit assignments.

Term paper: You will write a paper on an evolutionary topic. It must be at least 15 pages long, and it must cite at least 25 references. This will count for 25 percent of your grade, broken down as follows: topic choice, 2 percent; initial reference list, 3 percent; finished paper, 20 percent. You must choose a topic by March 7, turn in the initial reference list by March 21, and turn in the paper on May 2. If you get more than 4 points deducted on the paper, you must revise it and turn in the revised version on May 11.

Integrity: If you copy another student's work or cheat in some other way on an exam, you will receive an F for the course. See the term paper instructions for the policy on plagiarism.

Grade scale: A 93-100; A- 90-92.9; B+ 87-89.9; B 83-86.9; B- 80-82.9; C+ 77-79.9; C 73-76.9; C- 70-72.9; D+ 67-69.9; D 63-66.9; D- 60-62.9; F 0-59.9.

Students who are less than 3 points below the minimum grade needed for their program (such as an undergraduate biology major with 67 to 69.9 points) will be given the opportunity to take an incomplete grade and complete an extra credit project. This project will be a lot of work, such as writing a 15-page term paper on a topic of my choice. Upon satisfactory completion of the project, you'll get the minimum grade needed for your program (such as C- for undergraduate biology majors). There will be no other extra credit.

Attendance: You are not required to attend the lectures, and your class participation will not affect your grade. It would be a bad idea to skip lots of lectures, however, since you won't be able to learn many of the skills needed for the exams from the reading assignments. If you have a valid reason to miss one of the exams, let me know as soon as possible so that we can schedule a makeup exam. Note that I do not consider having other exams on the same day to be a valid excuse.

Reading assignments: There is no textbook. Instead, there will be reading assignments from the primary scientific literature (papers from scientific journals). Each lecture will have one or two focal papers on the general topic of the lecture. I'll talk about them, and other related papers, in class. Hopefully the lectures will help you understand the papers, and vice versa. I don't expect you to understand every technical detail or bit of specialized jargon in the papers; learning how to get the gist of a paper, even though you don't understand all of it, is an important skill.

I'll put a link for each paper on the class schedule. It's up to you whether you read the papers before or after the lecture, but you definitely should read them; the exams will include questions that you'll only be able to answer if you've read the papers.

Office hours: I will not have formal office hours; if you'd like to talk to me, feel free to call me, e-mail me, or drop by. I'm generally at my office or lab from 9 a.m. to 5 p.m. on Mondays, Wednesdays and Fridays. On other days I'm working at home and can be reached by e-mail.

Tentative schedule: This is a tentative schedule of lecture topics; check back here for updates as the semester progresses.

Day Date Topic Reading Other
Wednesday Feb. 13 Introduction; why study evolution? passage from Darwin, E. 1796. Zoonomia, Or, the laws of organic life. Vol. I. 2nd ed. J. Johnson, London.
[Goal: see if you can figure out the point he's trying to make, and see if you can express it in a few sentences of modern-day English.]
Conybeare, W.D. 1824. On the discovery of an almost perfect skeleton of the Plesiosaurus. Trans. Geol. Soc. Lond., 2nd series, 1: 381-389.
[Goal: By 1824, a number of authors had published rudimentary notions of evolution as an explanation for fossils of extinct organisms. Can you tell from this paper what Conybeare thought of these ideas as a possible explanation for the plesiosaur fossil? Also, who actually found the fossil that Conybeare describes?]
 
Friday Feb. 15 Darwin passage from Darwin, C. 1872. The origin of species by means of natural selection; or, the preservation of favoured races in the struggle for life. 6th ed. John Murray, London.
[Goal: Compare this to the passage you read from Zoonomia by Charles Darwin's grandfather, Erasmus Darwin. How are the points they make, and the way that they make them, similar or different? Can you summarize what Charles Darwin is trying to say in a couple of sentences?]
 
Monday Feb. 18 Web of Science; taxonomy Miyamoto, M.M., J.L. Slightom, and M. Goodman. 1987. Phylogenetic relations of humans and African apes from DNA sequences in the ψη-globin region. Science 238: 369-373.
[Goal: In 1987, what were the competing hypotheses for the phylogeny of humans, chimps, gorillas, and orangutans? What are the data in this paper that support the grouping of humans and chimps?]
 
Wednesday Feb. 20 Systematics Ursing, B.M., and U. Arnason. 1998. Analyses of mitochondrial genomes strongly support a hippopotamus-whale clade. Proc. Roy. Soc. B. 265: 2251-2255.
[Goal: In 1998, what were the competing hypotheses for the phylogeny of hippos, other artiodactyls, and whales? How many different statistical techniques did the authors use to estimate the phylogeny from their data? Why do you think they used so many?]
 
Friday Feb. 22 Problems in inferring relationships--homoplasy, hybridization, horizontal transfer Lerat, E., V. Daubin, H. Ochman, and N.A. Moran. 2005. Evolutionary origins of genomic repertoires in bacteria. PLoS Biology 3: e130.
[Goal: This paper is taking one side in a debate about whether it's meaningful to talk about a single "tree of life." Can you tell from this paper what the other side is? Do you think this paper summarizes the other side fairly?]
 
Monday Feb. 25 Fossil record--kinds of fossils Wilby, P.R., J.D. Hudson, R.G. Clements, and N.T.J. Hollingsworth. 2004. Taphonomy and origin of an accumulate of soft-bodied cephalopods in the Oxford clay formation (Jurassic, England). Paleontology 47: 1159-1180.
[Goal: Belemnites are the state fossil of Delaware. This paper describes fossil belemnites from England that are found in pairs. What hypotheses does the paper suggest for the pairing? Which hypothesis do the authors think the evidence supports? What is their evidence?]
 
Wednesday Feb. 27 History of life--origins Bartel, D.P., and J.W. Szostak. 1993. Isolation of new ribozymes from a large pool of random sequences. Science 261: 1411-1418.
[Goal: What does this tell us about the origin of life on Earth?]
 
Friday Feb. 29 History of life--animal phyla Irimia, M., I. Maeso, D. Penny, J. Garcia-Fernandez, and S.W. Roy. 2007. Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata. Mol. Biol. Evol. 24: 1604-1607.
Rogozin, I.B., Y.I. Wolf, L. Carmel, and E.V. Koonin. 2007. Analysis of rare amino acid replacements supports the Coelomata clade. Mol. Biol. Evol. 24: 2594-2597.
[Goal: What are these two papers arguing about? What kind of evidence do they have? How would you settle the argument?]
 
Monday March 3 History of life--plants Hu, S., D.L. Dilcher, D.M. Jarzen, and D.W. Taylor. 2008. Early steps of angiosperm-pollinator coevolution. Proc. Natl. Acad. Sci. USA 105: 240-245.
[Goal: What is the main question this paper is trying to answer? What are the two kinds of evidence it uses? Do the two kinds of evidence give the same answer?]
 
Wednesday March 5 History of life--vertebrates Shubin, N.H., E.B. Daeschler, and F.A. Jenkins. 2006. The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature 440: 764-771.
[Goal: Neil Shubin, the first author of this paper, has referred to Tiktaalik as a "great-great-great-great cousin" of humans. Why didn't he say "great-great-great-great grandparent"? Would you expect to find fossils of our direct ancestors? If Tiktaalik isn't one of our direct ancestors, what can it tell us?]
 
Friday March 7 Gradual vs. abrupt change in the fossil record Theriot, E.C., S.C. Fritz, C. Whitlock, and D.J. Conley. 2006. Late Quaternary rapid morphological evolution of an endemic diatom in Yellowstone Lake, Wyoming. Paleobiology 23: 38-54.
[Goal: In what way do the results in this paper support the punctuated equilibrium model? In what way are the results inconsistent with that model?]
Topic choice due for paper
Monday March 10 Human evolution Tocheri, M.W., C.M. Orr, S.G. Larson, T. Sutikna, Jatmiko, E. Wahyu Saptomo, R.A. Due, T. Djubiantono, M.J. Morwood, and W.L. Jungers. 2007. The primitive wrist of Homo floresiensis and its implications for hominin evolution. Science 317: 1743-1745.
[Goal: This paper claims that the Homo floresiensis (the "hobbit") lineage split from the Homo sapiens lineage over 800,000 years ago. How can they say that, based on just three little wrist bones?
 
Wednesday March 12 Evolution of biodiversity and mass extinctions McElwain, J.C., D.J. Beerling, and F.I. Woodward. 1999. Fossil plants and global warming at the Triassic-Jurassic boundary. Science 285: 1386-1390.
[Goal: What evidence does this paper have for an increase in atmospheric CO2? What evidence does it have for an increase in temperature?]
 
Friday March 14     First exam (see the study guide)
Monday March 17 Go over first exam No reading assignment  
Wednesday March 19 Mutation and recombination Luria, S.E., and M. Delbrück. 1943. Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28: 491-511.
[Goal: What results of this experiment would have led to a different conclusion? How would that have changed evolutionary theory?]
 
Friday March 21 Chromosomal rearrangements Yunis, J.J., and O. Prakash. 1982. The origin of man: a chromosomal pictorial legacy. Science 215: 1525-1530.
[Goal: What happened during the evolution of chromosome 2? What about chromosome 10?]
Initial reference list due for paper
Monday March 24 Variation in natural populations--DNA Kreitman, M. 1983. Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304: 412-417.
[Goal: This paper contains a lot of descriptive information. What is the main conclusion from the results? What aspect of the result supports this conclusion?]
 
Wednesday March 26 Variation in natural populations--Mendelian characters Lalueza-Fox, C., H. Römpler, D. Caramelli et al. [17 co-authors]. 2007. A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science 318: 1453-1455.
[Goal: Is Dr. McDonald more closely related to Neanderthals than you are?]
 
Friday March 28 Variation in natural populations--quantitative characters and heritability Rose, R.J., J.A. Boughman, L.A. Corey, W.E. Nance., J.C. Christian, and K.W. Kang. 1980. Data from kinships of monozygotic twins indicate maternal effects on verbal intelligence. Nature 283: 375-377.
[Goal: This article has one sentence that ends in an exclamation mark, which is not something you see very often in scientific writing. What is so remarkable about the result described in that sentence? What are the implications of it?]
 
Monday March 31     Spring break
Wednesday April 2     Spring break
Friday April 4     Spring break
Monday April 7 Random drift Rozen, R., M.D.E. Keleer, J. Daigneault, L. Ferreira-Rarajabi, M. Gerdes, L. Lamoureux, G. Aubin, F. Simard, T.M. Fujiwara, and K. Morgan. 1992. Cystic fibrosis mutations in French-Canadians: Three CFTR mutations are relatively frequent in a Quebec population with an elevated incidence of cystic fibrosis. Am. J. Med. Genet. 42: 360-364.
[Goal: What are two possible explanations for the high frequency of cystic fibrosis in this area of Canada? What experiment could you do to test these hypotheses?]
 
Wednesday April 9 Natural selection Etges, W.J., K.L. Arbuckle, and M. Levitan. 2006. Long-term frequency shifts in the chromosomal polymorphisms of Drosophila robusta in the Great Smoky Mountains. Biol. J. Linn.Soc. 88: 131-141.
[Goal: What is the evidence that these polymorphisms are affected by natural selection? What experiment would you do to test this hypothesis?]
 
Friday April 11 Lab selection--Mendelian examples Hickey, D.A. 1977. Selection for amylase allozymes in Drosophila melanogaster. Evolution 31: 800-804.
[Goal: Could you do this kind of experiment on the organism you're writing your term paper about (or its closest living relative, if it's a fossil)? Why or why not?]
 
Monday April 14 Natural selection--Mendelian examples Melin, A.D., L.M. Fedigan, C. Hiramatsu, C.L. Sendall, and S. Kawamura. 2007. Effects of colour vision phenotype on insect capture by a free-ranging population of white-faced capuchins, Cebus capucinus. Anim. Behav. 73: 205-214.
[Goal: What are some lab experiments you could do to follow up on the results in this paper?]
 
Wednesday April 16 Lab selection--quantitative characters Weber, K.E. 1996. Large genetic change at small fitness cost in large populations of Drosophila melanogaster selected for wind tunnel flight: rethinking fitness surfaces. Genetics 144: 205-214.
[Goal: If it's so easy to select for faster flight in the lab, why don't wild Drosophila fly faster? How could you test your speculation?] 
 
Friday April 18 Natural selection--quantitative characters Carroll, S.P., J.E. Loye, H. Dingle, M. Mathieson, t.R. Famula, and M.P. Zalucki. 2005. And the beak shall inherit: evolution in response to invasion. Ecol. Lett. 8: 944-951.
[Goal: The mouthparts of these bugs are 5 to 10% longer after a few decades. What might you do to make them evolve faster, so they'd be more effective at controlling the weeds?]
 
Monday April 21 Sexual selection Ryan, M.J. 1983. Sexual selection and communication in a Neotropical frog, Physalaemus pustulosus. Evolution 37: 261-272.
[Goal: Read the two sentences starting at the bottom of p. 263 ("Males tended to grasp..."). Why are the males so much less choosy than the females? How would you test your speculation?]
 
Wednesday April 23     Second exam; see the study guide
Friday April 25 Go over second exam No reading  
Monday April 28 Natural selection--molecular level McDonald, J.H. and M. Kreitman. 1991. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351: 652-654.
[Goal: The authors interpret the results as an excess of fixed replacement differences between species due to positive selection (the number "7" in Table 2 is bigger than expected). The greater replacement-to-synonymous ratio for fixed differences could also have been due to fewer synonymous fixed differences than expected (the number "17" in Table 2 being smaller than expected). Can you think of a possible reason why there would be fewer synonymous fixed differences than expected, given the number of synonymous polymorphisms?
 
Wednesday April 30 Species Daugherty, C.H., A. Cree, J.M. Hay and M.B. Thompson. 1990. Neglected taxonomy and continuing extinctions of tuatara (Sphenodon). Nature 347: 177-179.
[Goal: What evidence does this paper provide that Sphenodon punctatus and S. guntheri are different species? What kind of further experiments would you want to do to test this hypothesis?]
 
Friday May 2 Speciation Pasterniani, E. 1969. Selection for reproductive isolation between two populations of maize, Zea mays L. Evolution. 23:534-547.
[Goal: Can you imagine a situation in nature that this experiment would be a good model of? If you wanted to do this kind of experiment with an animal, which animal would you use, and how would you do the experiment?
Term paper due
Monday May 5 More on speciation Olafsdottir, G.A., S.S. Snorrason, and M.G. Ritchie. 2007. Postglacial intra-lacustrine divergence of Icelandic threespine stickleback morphs in three neovolcanic lakes. J. Evol. Biol. 20: 1870-1881.
[Goal: The authors conclude that speciation is happening sympatrically within each lake. If it had been allopatric speciation, what result would you have expected from their experiments?
 
Wednesday May 7 Evolution of eyes Nilsson, D.E., and S. Pelger. 1994. A pessimistic estimate of the time required for an eye to evolve. Proc. Roy. Soc. Lond. B 256: 53-58.
[Goal: This paper consists of speculation about what might be possible, not experiments with results. What purpose, if any, does this kind of paper serve?
 
Friday May 9 Applications of evolution--conservation Roman, J., and S.R. Palumbi. 2003. Whales before whaling in the North Atlantic. Science 301: 508-510.
[Goal: What assumptions about evolutionary processes does this paper make? How reasonable do these assumptions seem to you? How would you test them?]
 
Monday May 12 Applications of evolution--agriculture Onstad, D.W., J.L. Spencer, C.A. Guse, E. Levine, and S.A. Isard. 2001.Modeling evolution of behavioral resistance by an insect to crop rotation. Entomol. Exper. Appl. 100: 195-201.
[Goal: Crop rotation is a good way to control some insect pests. In this case, growing corn and soybeans in alternate years used to be a good way to control the western corn rootworm, Diabrotica virgifera virgifera, because eggs laid in a corn field one fall would hatch in a soybean field the next spring. Why doesn't that work any more? What are other possible ways the corn rootworms could have adapted to crop rotation?]
 
Wednesday May 14 Applications of evolution--medicine de Groot, N.G., C.M.C. Heijmans, N. de Groot, N. Otting, A.J.M. de Vos-Rouweler, E. J. Remarque, M. Bonhomme, G.G. M. Doxiadis, B. Crouau-Roy, and R.E. Bontrop. 2008. Pinpointing a selective sweep to the chimpanzee MHC class I region by comparative genomics. Mol. Ecol. 17: 2074-2088.
[Goal: How might the results in this paper someday help humans?]
 
Friday May 16 Creationism Isaak, M., editor. 2006. An index to creationist claims. http://talkorigins.org/indexcc/list.html.
[Goal: Pick five creationist claims, one from each of five main sections on this web page. For each claim, decide whether the creationists are committing some kind of logical fallacy, or are just lying.]
Revised term paper due, if necessary
Monday May 19 Creationism Pallen, M.J., and N.J. Matzke. 2006. From The Origin of Species to the origin of bacterial flagella. Nat. Rev. Micro. 4: 784-790.
[Goal: Look at Table 1. What is the relevance of the "Indispensible?" and "Homologies" columns to the argument this paper is making?]
 
Wednesday May 21 Mysteries of evolution--mammalian body temperature and the evolution of the scrotum Malaivijitnond, S., Y. Hamada, B. Suryobroto, and O. Takenaka. 2007. Female long-tailed macaques with scrotum-like structures. Am. J. Primatol. 69: 721-735.
[Goal: Come up with an adaptive hypothesis that might explain this structure, then design an experiment to test your hypothesis.]
 
Friday May 23 10:30 a.m. to 12:30 p.m.   Final exam; see the study guide

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This page was last revised May 10, 2008. Its URL is http://udel.edu/~mcdonald/495syllabus.html