University of Puerto Rico Rio Piedras Department of Biology Evolution Biol 4345 Spring 2012 Professor: Office: e-mail:

l: Office Hours: Lectures: Quizzes: Textbook: Sunderland, MA. Lectures: Midterms: Final: Tugrul Giray/Richard Thomas JGD 202/FB230 tgiray2@yahoo.com /jprthomas32@yahoo.com Monday and Wednesday 9:00-12:00 (RT) or by appointment Monday, Tuesday, Wednesday 10-12 (TG) or by appointment Monday and Wednesday, 2:00-3:20, CNL-A-231 in class Futuyma, D. J. 2009. Evolution, Second Edition. Sinauer Associates, Available on Blackboard 1st Midterm: Wednesday, Feb 15 2nd Midterm: Wednesday, Mar 28 Finals week TBA

Course overview: Biol 4345 is an in-depth introduction to evolution. Evolution is a heritable change over time that has given rise to lifes rich diversity. Evolution itself is the result of many different processes at the micro- and macro-evolutionary level. Understanding these evolutionary processes is fundamental to understanding all aspects of biology. In the course of the semester we will study the mechanisms of the evolutionary process, and resultant patterns of biological diversity. Throughout the course we will discuss major questions in evolutionary biology and how scientists ask and answer those questions. We will also focus on the impact of evolutionary biology on modern issues of health, agriculture, and conservation. A central aspect of the course is working through details of evolutionary theory and quantitative modeling. Of all the biological sciences, evolution is inherently the most integrative and comprehensive. It is the unifying theory of biology. By the end of the course we hope you will fully appreciate the famous statement by Theodosius Dobzhansky Nothing in biology makes sense, except in the light of evolution. By the end of this course you will be able to: 1 Learn to apply rigorous evolutionary thinking to any question in biology. 2 Understand how to ask and answer questions in evolutionary biology. 3 Understand how different mechanisms of evolution (natural selection, drift, mutation and gene flow), individually and combined, affect changes in allele frequencies in populations. 4 Appreciate how evolution has, and is, influencing issues in social sciences, medicine, conservation and agriculture. 5 Understand how new species originate and the factors that influence species diversity. Reading: Each week there will be chapters or parts of chapters to read from the textbook. You are expected to have read these before coming to class. A class may start with a brief quiz regarding the subject of the class, and such quizzes count towards your final grade. Some weeks there will also be additional material to read. About eight quizzes are expected to be given during the semester, and the best five of these quizzes will be used toward your final grade.

Exercises/assignments: There will a few assignments (quantitative problem sets/reading) that will give you opportunities to spend quality time thinking about concepts learned in lecture. We encourage students to work together on exercise problems. However, written responses need to be composed individually, and will be evaluated in the midterm and final tests. Exams: There are two exams in the class, one midterm and one final. The exams will cover material from lectures, discussion readings and assigned readings, and quantitative problems. The final exam will concentrate on material from the last third of the semester, but will include some cumulative general questions. Exams will be curved. Quizzes: 20% of total Assignments: 10% of total Midterm Exams: 40% of total Final Exam: 30% of total Course participation/prof. evaluation 5% additional. Final Grades will be as follows: A: 90 100 B: 80 89 C: 70 79 D: 60 69 F: below 60 Receiving or making phone calls during class will not be tolerated. You will be asked to leave the class, and you will get a zero (0) for that weeks quiz. Receiving or making phone calls during exams or quizzes will result in an immediate dismissal from the exam room and a score of zero (0) for that test. The university strictly follows the policies of the Ley 51. If your case qualifies under the provisions of this law, please come and talk to me as soon as possible so that we can make appropriate accommodations.

Week 1 TG/RT 2 TG TG 3 RT RT 4 RT TG 5 TG RT/TG 6 TG 7 TG TG

Date Jan 18 Jan 23 Jan 25 Jan 30 Feb 1 Feb 6 Feb 8 Feb 13 Feb 15 Feb 20 Feb 22 Feb 27 Feb 29

Theme Introduction What is evolution? and what is it not? Adaptation and natural selection, Classification, phylogeny and the tree of life, Evidence for evolution; Evolution in our lifetime Evidence for Evolution; Darwins Finches Fossil record History of life on Earth Evolution of Biodiversity Macroevolution, trends, progress and evolutionary dead ends Genetic variation, phenotypic variation Hardy-Weinberg equilibrium; Natural Selection Population genetics models Midterm I No Class: Presidents day Natural Selection: Long term effects of Selection; Maintenance of genetic variation Genetic Drift 2-locus population genetics : Linkage Disequilibrium; Quantitative genetics; Molecular Evolution: neutral theory, molecular clock, detecting selection Speciation: genetics & rates Species & Speciation: Modes of speciation Species & Speciation: Modes of speciation (cont.) Shared evolutionary histories: Biogeography Molecular Evolution: Genome evolution, origin of new genes Shared evolutionary histories: coevolution

Chapter Futuyma 1 Futuyma 1, 2,11 Futuyma 2, 3,11 Futuyma 4, 5 Futuyma 7 Futuyma 22 Futuyma 8-9 Futuyma 9

Futuyma 9-10 Futuyma 10 Futuyma 12

8 RT RT 9 RT RT 10TG RT 11 TG RT/TG 12 RT RT

Mar 5 Mar 7 Mar 12 Mar 14 Mar 19 Mar 21 Mar 26 Mar 28 Apr 2 Apr 4

Futuyma 17 Futuyma 18 Futuyma 18 Futuyma 6 Futuyma 20 Futuyma 19 Futuyma 21 Futuyma 15 Futuyma 14 Futuyma 16 Futuyma 13 Futuyma 13 (11) Futuyma 23 Dobzhansky 1973

Evolution and development MidtermII Why sex? Sex and sexual selection Life History Evolution (mating systems, parental care, and group living) 13 TG Apr 9 Evolution of cooperation and Kin recognition TG Apr 11 Evolution of Sociality & Multilevel selection 14 Apr 16 No Class (Jose De Diego) TG Apr 18 Phenotypic Evolution 15 RT Apr 23 Phylogenetic applications, testing adaptation, phylogeny and conservation RT Apr 25 Evolution & Human Health/ Darwinian Medicine 16TG/RT Apr 30 Discussion about the role of evolution in our lives RT/TG May 2 Evolution, society and religion 17RT/TG May 7 Review FINALS Final Exam Note: This schedule is subject to change