BIO 770 – Fall 2015
Dr. Pangloss reborn? Natural selection in evolution
Course information
| Instructor | Jeremy Van Cleve |
| Webpage | http://vancleve.theoretical.bio/teaching/bio-770-fall-2015/ |
| Office hours | By appointment via e-mail |
| Time | Tue 1pm-1:50pm |
| Location | THM 109 |
| Credits | 1 |
Course description
The aim of this course will be to review some of the past and current issues with the role and significance of natural selection in evolutionary change. Although natural selection was the main focus in Darwin’s On the Origin of Species by Means of Natural Selection, evolutionary forces such as mutation, recombination, migration, and genetic drift are integral to a complete understanding of evolutionary change. The relative importance of these nonselective forces in shaping organisms have long been a topic of substantial study and debate both using both theoretical and empirical tools. Beginning with the rival viewpoints of Sewall Wright and Ronald Fisher who helped establish the “modern evolutionary synthesis”, the course will involve reading and discussion of classic and recent scientific papers that investigate selective and nonselective forces. Attention will be paid to the conceptual and mathematical theory that provides a framework for understanding evolutionary change. Surveys of the signature of selection in population genomic data will also be discussed.
Student learning outcomes
Through reading primary articles on the natural selection and other evolutionary forces, students should be able to:
- Summarize the major strains of thought concerning the important of natural selection in shaping biological traits
- Connect current controversies regarding natural selection and evolution with their antecedents in the formation of the “modern synthesis” in the 1930s.
- Relate current issues regarding the detection of selection from genetic data and the assembly of genealogies and phylogenies to Kimura’s “neutral theory of molecular evolution” and the “modern synthesis”.
- Map the concepts of natural selection and adaptation to mathematical formalisms including “selection gradients”, “evolutionary equilibria”, and “evolutionarily stable strategies”.
Course materials
The course will focus on readings from the primary literature with augmentation by other sources as needed.
Reading schedule
| Week | Date | Topic | Readings |
| 1 | Sep 1 | Fisher’s fundamental theorem | Frank 2012 |
| 2 | Sep 8 | Fisher’s fundamental theorem | Ewens 2011 |
| 3 | Sep 15 | Wright’s shifting balance | Wright 1932, 1988, Lande 1985 |
| 4 | Sep 22 | Critique of the shifting balance | Coyne et al. 1997 |
| 5 | Sep 29 | A new slice of the shifting balance | Kryazhimskiy 2012, Nahum et al. 2015, Van Cleve & Weissman 2015 |
| 6 | Oct 6 | Lewontin and adaptationism | Gould & Lewontin 1979, Lewontin 2015 |
| 7 | Oct 13 | When fitness is not “maximized” | Frean & Abraham 2001, Kerr et al. 2002 |
| 8 | Oct 20 | The Price equation, kin selection, and group selection | Hamilton 1975 |
| 9 | Oct 27 | “Design” and fitness optimization | West & Gardner 2013 |
| 10 | Nov 3 | Phylogeny and ecology | Kamilar & Cooper 2013 |
| 11 | Nov 10 | Molecular evolution: the Neutral Theory | Kimura 1968 Kimura & Ohta 1971 |
| 12 | Nov 17 | Molecular evolution: detecting selection with intra/interspecific data | McDonald & Kreitman 1991 Smith & Eyre-Walker 2002 |
| 13 | Nov 24 | Molecular evolution: linkage and selection: Drosophila | Begun & Aquadro 1992 Cutter & Payseur 2013 |
| 14 | Dec 1 | Molecular evolution: linkage and selection: Humans | Enard et al. 2014 |
| 15 | Dec 8 | Molecular evolution: Adaptation vs Drift in organismal complexity | Lynch 2007 |
Assignments
Before each class meeting, students should submit two questions about the reading to the Canvas course website under “Assignments”
Grading
- 25%: questions submitted before each meeting
- 75%: participation in class discussion
Course policies
Attendance Policy
Two excused or unexcused absences are permitted in the course. Please talk me if you have questions about this policy.
Excused Absences
Students need to notify the professor of absences prior to class when possible. Senate Rule 5.2.4.2 defines the following as acceptable reasons for excused absences: (a) serious illness, (b) illness or death of family member, (c) University-related trips, (d) major religious holidays, and (e) other circumstances found to fit “reasonable cause for nonattendance” by the professor. Students anticipating an absence for a major religious holiday are responsible for notifying the instructor in writing of anticipated absences due to their observance of such holidays no later than the last day in the semester to add a class. Information regarding dates of major religious holidays may be obtained through the religious liaison, Mr. Jake Karnes (859-257-2754). Students are expected to withdraw from the class if more than 20% of the classes scheduled for the semester are missed (excused or unexcused) per university policy.
Verification of Absences
Students may be asked to verify their absences in order for them to be considered excused. Senate Rule 5.2.4.2 states that faculty have the right to request “appropriate verification” when students claim an excused absence because of illness or death in the family. Appropriate notification of absences due to university-related trips is required prior to the absence.
Academic Integrity
Per university policy, students shall not plagiarize, cheat, or falsify or misuse academic records. Students are expected to adhere to University policy on cheating and plagiarism in all courses. The minimum penalty for a first offense is a zero on the assignment on which the offense occurred. If the offense is considered severe or the student has other academic offenses on their record, more serious penalties, up to suspension from the university may be imposed.
Plagiarism and cheating are serious breaches of academic conduct. Each student is advised to become familiar with the various forms of academic dishonesty as explained in the Code of Student Rights and Responsibilities. Complete information can be found at the following website: http://www.uky.edu/Ombud. A plea of ignorance is not acceptable as a defense against the charge of academic dishonesty. It is important that you review this information as all ideas borrowed from others need to be properly credited.
Please see Section 6.3 “Academic Offenses and Procedures” of the University Senate Rules for UK’s policy on academic integrity
Accommodations due to disability
If you have a documented disability that requires academic accommodations, please see me as soon as possible during scheduled office hours. In order to receive accommodations in this course, you must provide me with a Letter of Accommodation from the Disability Resource Center (Room 2, Alumni Gym, 257-2754, email address: