I. Introduction and History of Evolution
8/26: 1 – Evolution, science, and anti-science: the current threat to rationality.
No discussion section today.
8/29: 2 -- What is evolution? – The major questions in evolutionary biology.
8/31: 3 -- How the idea of evolution evolved. – What Darwin said and didn’t say.
9/2: 4 -- Evolution since Darwin: Modern Synthesis and … “post-modern” synthesis?
First discussion section today.
II. The structure of evolution in time and space: homology, systematics, biogeography
9/5: LABOR DAY -- NO CLASS
9/7: 5 -- Homology as the central concept in comparative biology.
9/9: 6 -- Systematics: how evolutionary relationships are constructed.
9/12: 7 -- How phylogenetic trees test evolutionary hypotheses.
9/14: 8 – Using phylogenies to test evolutionary questions
9/16: 9 -- Origin & evolution of the solar system & Earth – establishing the conditions for life
III. Macroevolution: explanations of the great patterns in the history of life.
9/19: 10 –- Historical biogeography: one half of knowing why organisms live where they do.
9/21: 11 –- Ecological biogeography: the other half of why organisms live where they do.
9/23: 12 -- Speciation rates as the motor of evolution.
9/26: 13 -- How change occurs during speciation: Punctuated equilibrium vs. gradualism.
9/28: 14 -- Diversity through time. Patterns of change in Phanerozoic animals and plants.
9/30: 15 -- Extinction. -- Background and mass extinction. Are we still in a mass extinction?
10/3: 16 -- Adaptation: its hierarchical study from populations to clades.
10/5: 17 -- Adaptation and exaptation. Heterochrony, development, and macroevolution.
Evening Q&A session 7-9 pm (location to be announced).
Thursday, October 6: FIRST MIDTERM EXAM (to be held 7-9 pm, location TBA)
IV. Population processes important in evolution
10/7: 18 -- Genotypes and phenotypes: molecular basis of adaptation.
10/10: 19 -- Genetic models of evolutionary change in populations.
10/12: 20 – Interaction of selection with mutation, migration and drift; Term paper topics due in
class (or emailed beforehand).
10/14: 21 – Islands, finches and the relationship between adaptation and divergence.
10/17: 22 -- Selection on multiple traits. Tradeoffs and limits to selection response.
10/19: 23 – The evolutionary significance of sex (recombination).
10/21: 24 -- Sex and selection.
V. Speciation
10/24: 25 – Species concepts and their difficulties.

10/26: 26 -- Modes of speciation. Geographic models of speciation. Extended term paper topics
due in class (or emailed beforehand).
10/28: 27 -- Ecology as a driver of speciation.
10/31: 28 -- Genetic basis for speciation. – The connection between speciation and adaptation.
11/2: 29 -- Genomics and speciation: the basis for reproductive isolation; Evening Q&A session.
Thursday, November 3: SECOND MIDTERM EXAM (7-9 pm, location TBA)
VI. Evolutionary genomics
11/4: 30 – Sequencing genes and genomes. Using molecular sequences for reconstructing phylogeny. Phylogeny using genome-level characters. Using evolutionary principles to inform genomics.
11/7: 31 – Comparing prokaryote genomes – What have we learned about evolution?
Horizontal gene transfers. Coevolution.
11/9: 32 – Comparing eukaryotic genomes – What have we learned about evolution? Genome size changes. Evolution of multigene families. Whole genome duplications. Rough drafts (optional) due
11/11: 33 – Comparing organelle genomes – What have we learned about evolution? Patterns of endosymbiosis. Comparing gene arrangements for phylogeny.
VII. Development and evolution
11/14: 34 – Relationship between developmental and evolutionary biology. Comparing embryos for phylogenetic reconstruction.
11/16: 35 – Developmental mechanisms that mediate evolutionary change. Evo-Devo concepts, e.g. atavisms, heterochrony, neoteny, and allometry. Gene expression and homology.
Term papers due IN CLASS.
VIII. Evolution of behavior
11/18: 36 – Evolution of behavior – Basic concepts
11/21: 37 – Evolution of social behavior. Altruism, kin selection, and group selection.
IX. Human evolution
11/23: 38 – The fossil record of human evolution
11/25: Thanksgiving break (no class)
11/28: 39 – Genetic structure and history of human populations.
11/30: 40 – Evolution’s impact on health and human affairs
12/2: 41 – Evolution – What are the next big questions? (Padian, Simms, Boore)
12/5: Informal Q&A in preparation for final
FINAL EXAM: TO BE ANNOUNCED
Term paper: 7-10 pages (no more) on a question of importance to evolutionary theory and understanding. The subject should not be simply a report on an evolutionary phenomenon but an exploration of what questions it raises, how it is understood, evidence for and against its importance, and what more needs to be known in order to assess remaining questions. A list of

example topics and a selection of past term papers will be available, and we will spend time in discussion sections talking about researching and writing term papers. The paper is due in class on the date indicated (November 16) and late papers will be penalized 10% per day (after class counts as one day). A grading rubric will be provided so that you can see how your papers will be graded. See dates in the syllabus for when your paper topic, expanded topic, and rough draft
(if desired) must be turned in. It is imperative that you consult instructors and GSIs in this class, as well as others that they may suggest. Plagiarism, which includes turning in papers from other classes, will be penalized accordingly and referred to the Student Judicial Office.
Information on plagiarism and correct citation of the work of others can also be found on the course and university websites.
Discussion sections: These are mandatory and will comprise part of your grade. They are offered Fridays 11-12, 12-1, 1-2, or 2-3. Your GSI will explain the organization of discussion sections with you.
Grading structure: There are three midterms (including the final exam), all of which count 25%.
The term paper counts another 25%, but this score is multiplied by your section grade; so, for example, if you get an 80 on your paper and a 90 in section, your grade for that 25% of the course is 72. This course is never graded on a curve.
Text: Evolution, by Douglas Futuyma. We will key readings to most lectures as far as possible.
Readings for lectures will be posted on the course bSpace site, as will those for discussion sections.