Robert P. Anderson, Department of Biology, City College of New York

Course philosophy:

This graduate course is designed to expose students to the fundamental elements of modern evolutionary theory and research. Class periods will generally include a lecture, followed by discussion. At the end of each class period, I will give an overview of the topic for the following week. To complement the textbook, both classic and modern readings from the primary literature and other books will be assigned.

Active participation in discussions (based on completion of readings before coming to class) will be necessary to meet course objectives. Students will take turns co-leading the discussions with the instructor; the discussion leader(s) will be selected randomly during class. These discussions will focus primarily on the supplementary (i.e., non-Futuyma) readings. Discussion will begin with the student(s) giving a brief (ca. 5 minute) oral overview of the readings. Preparing a brief written outline of the readings before class may be useful.

Grading:

Students will be evaluated based on performance on three exams, which will cover material from the lectures, the readings, and the discussions. The material for later sections of the course will build upon topics covered earlier in the semester. Points will be assigned as follows: Exam 1: 30 %; Exam 2: 30 %; Final Exam: 40%. Because scientists must be able to express themselves in written prose, students must use proper spelling, grammar (including punctuation), and composition. Minor errors in spelling and grammar will be marked 10% off, major grammatical errors will lead to a reduction of 30%, and unintelligible sentences will be given no credit. For essay questions, paragraphs must be composed of organized, coherent thoughts and include a lead sentence (proper composition). Plagiarism will be dealt with subject to CCNY/CUNY policies.

Absences:

Students are responsible for the material in the readings, as well as that covered each week in class (lecture and discussion). If you miss class, you are responsible for obtaining the supplementary (non-Futuyma) readings that were assigned on that day. If you know that you will miss an exam, contact me as soon as possible so that you can take the exam in advance. Make-up exams will be allowed only for documented excused absences (e.g., death in the family, extreme sickness, etc.).

Tentative schedule (may be modified if necessary):

Date	Topic	Futuyma readings	Supplementary readings
Review on your own	Necessary principles from genetics and ecology	Ch. 3 (pp. 31–47; Basic genetics), Ch. 6 (pp. 127–132; Geology and the fossil record), Ch. 7 (p. 184; Plate tectonics)
30 Aug.	From Darwin through the Evolutionary Synthesis (Modern Synthesis)	Ch. 1 (pp. 4–9; What is evolutionary biology?), Ch. 4 (pp. 59–65; Biomes and biogeographic regions; contingency vs. determinism), Ch. 2 (pp. 17–29; Lamarck, Darwin, Wallace, population genetics, and the Evolutionary Synthesis)	pp. 375–379 in: Darwin, C. 1891. Journal of researches into the natural history and geology of the countries visited during the voyage of H.M.S. “Beagle” round the world. Ward, Lock, and Co., London.
6 Sept.	No class
13 Sept.	Hardy-Weinberg equilibrium; Fitness and selection	Ch. 9 (pp. 234–239; Hardy-Weinberg equilibrium), Ch. 13 (pp. 365–368, 375–379, 392–395; Fitness and selection), Ch. 14 (pp. 407–409, 418–422; Adaptive landscapes, measuring selection), Ch. 6 (pp. 157–162; Measuring evolutionary rates)	Anderson, R.P. and C.O. Handley, Jr. 2002. Dwarfism in insular sloths: biogeography, selection, and evolutionary rate. Evolution, 56:1045–1058.
20 Sept.	Genetic drift and neutral evolution	Ch. 11 (pp. 297–304, 320–323; Genetic drift and neutral evolution)	pp. 47–57 in: Graur, D. and W.-H. Li. 2000. Fundamentals of molecular evolution, 2nd edition. Sinauer Associates, Sunderland, MA.
27 Sept.	EXAM 1
4 Oct.	Homology, phylogeny reconstruction, and classification	Ch. 23 (pp. 669–670; Homology), Ch. 5 (pp. 87–100; Schools of systematics and taxonomy; phylogeny reconstruction)	pp. 1–24 in: Wiley, E.O., D. Siegel-Causey, D.R. Brooks, and V.A. Funk. 1991. The compleat cladist: a primer of phylogenetic procedures. Special Publication, University of Kansas Museum of Natural History: 19. pp. 132–143 in: Avise, J.C. 2004. Molecular markers, natural history, and evolution, 2nd edition. Sinauer Associates, Sunderland, Massachusetts.
1 Oct.	Comparative biology and character evolution	Ch. 5 (pp. 107–118; Character evolution)	pp. 401–418 in: Avise, J.C. 2004. Molecular markers, natural history, and Evolution. Sinauer, Sunderland, MA. Waters, J.M. and R.M. McDowall. 2005. Phylogenetics of the Australasian mudfishes: evolution of an eel-like body plan. Molecular Phylogenetics and Evolution, 37:417–425.
18 Oct.	Guest lecture, Dr. Amy Berkov: Species interactions	Ch. 18 (pp. 539–542, 551–557; Evolution of species interactions)	pp. 189–204 in: Brooks, D.R. and D.A. McLennan. 1991. Phylogeny, ecology, and behavior: a research program in comparative biology. Univ. Chicago Press, Chicago.
25 Oct.	Interspecific historical biogeography	Ch. 8 (pp. 207–209; Historical biogeography)	pp. 418–432 in: Avise, J.C. 2004. Molecular markers, natural history, and Evolution. Sinauer, Sunderland, MA. Cook, J.A., A.M. Runck, and C.J. Conroy. 2004. Historical biogeography at the crossroads of the northern continents: molecular phylogenetics of red-backed voles (Rodentia: Arvicolinae). Molecular Phylogenetics and Evolution, 30: 767–777.
1 Nov.	EXAM 2
8 Nov.	Phylogeography	Ch. 11 (pp. 327–333; Gene trees and species trees)	pp. 283–289, 301–314 in: Avise, J.C. 2004. Molecular markers, natural history, and Evolution. Sinauer, Sunderland, MA. Pellegrino, K.C.M., M.T. Rodrigues, A.N. Waite, M. Morando, Y.Y. Yassuda, and J.W. Sites, Jr. 2005. Phylogeography and species limits in the Gymnodactylus darwinii complex (Gekkonidae, Squamata): genetic structure coincides with river systems in the Brazilian Atlantic forest. Biological Journal of the Linnean Society, 85:13–26.
15 Nov.	Species concepts	Ch. 15 (pp. 447–456; Species concepts)	Wiley, E.O. 1978. The evolutionary species concept reconsidered. Systematic Zoology, 27:17–26. de Queiroz, K. 1998. The general lineage concept of species, species criteria, and the process of speciation. Pp. 57–75. In: Endless forms: species and speciation (D.J. Howard and S.H. Berlocher, eds.). Oxford University Press, Oxford. Balakrishnan, R. 2005. Species concepts, species boundaries, and species identification: a view from the tropics. Systematic Biology, 54:689–693.
22 Nov.	No class
29 Nov.	Speciation	Ch. 16 (pp. 481–484, 498–501; Speciation)	pp. 88–109 in: Brooks, D.R. and D.A. McLennan. 1991. Phylogeny, ecology, and behavior: a research program in comparative biology. Univ. Chicago Press, Chicago. Wiens, J.J. 2004. What is speciation and how should we study it? American Naturalist, 163:914–923.
6 Dec.	Development and allometry; macroevolutionary patterns	Ch. 17 (pp. 523–527; Allometry), Ch. 23 (pp. 651–658; Ontogeny and heterochrony), Ch. 6 (pp. 137, 155–162; Macroevolutionary patterns, measuring evolutionary rates revisited), Ch. 24 (pp. 677–678, 689–691; Punctuated equilibrium)	Gayon, G. 2000. History of the concept of allometry. American Zoologist, 40:748–758.
13 Dec.	FINAL EXAM

Robert P. Anderson, Ph.D.