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. Generally, class periods will include both lecture and discussion. Commonly, there will be take-home writing exercises that we will discuss the following class period. 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. These discussions will focus primarily on the supplementary (i.e., non-Futuyma) readings.

Grading:

Students will be evaluated based on (1) the writing exercises; (2) participation in discussions; and (3) three exams. The exams will cover material from the lectures, readings, and discussions. The material for later sections of the course will build upon topics covered earlier in the semester. Points will be assigned as follows: (1) writing exercises: 20%; (2) participation in discussions: 20%; Exam 1: 20 %; Exam 2: 20 %; Final Exam: 20%. 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. 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, geology, and paleontology	Ch. 3 (pp. 31–47; Basic genetics) Ch. 6 (pp. 127–132; Geology and the fossil record) Ch. 7 (p. 184; Plate tectonics)
27 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.
3 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.
10 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.
17 Sept.	EXAM 1
24 Sept.	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.	No class
8 Oct.	No class
15 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. 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. 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.
22 Oct.	Historical biogeography and phylogeography	Ch. 8 (pp. 207–209; Historical biogeography) Ch. 11 (pp. 327–333; Gene trees and species trees)	pp. pp. 283–289, 301–314, 418–432 in: Avise, J.C. 2004. Molecular markers, natural history, and Evolution. Sinauer, Sunderland, MA.
29 Oct.	EXAM 2
5 Nov.	Species concepts	Ch. 15 (pp. 447–456; Species concepts)	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.
12 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.
19 Nov.	Development and allometry	Ch. 17 (pp. 523–527; Allometry) Ch. 23 (pp. 651–658; Ontogeny and heterochrony)	Gayon, G. 2000. History of the concept of allometry. American Zoologist, 40:748–758.
26 Nov.	No formal class; self-guided tour of evolutionary exhibits at the American Museum of Natural History
3 Dec.	Macroevolution	Ch. 6 (pp. 137, 155–162; Macroevolutionary patterns, measuring evolutionary rates revisited) Ch. 24 (pp. 677–678, 689–691; Punctuated equilibrium)
10 Dec.	FINAL EXAM

Robert P. Anderson, Ph.D.