Biol375 2014

Molecular Evolution (BIOL 375.00/790.64/793.03, Fall 2014) Instructor: Dr Weigang Qiu, Associate Professor, Department of Biological Sciences Room:926 HN (Seminar Room, North Building Hours: Mon. & Thur 2:45-4:00 pm Office Hours: Room 839 HN; Wed 5-7 pm or by appointment

---

Course Description

Molecular evolution is the study of the change of DNA and protein sequences through time. Theories and techniques of molecular evolution are widely used in species classification, biodiversity studies, comparative genomics, and molecular epidemiology. Contents of the course include:

1. Population genetics, which is a framework of understanding mechanisms of sequence evolution through mutation, recombination, gene duplication, genetic drift, and natural selection.
2. Molecular systematics, which introduces statistical models of sequence evolution and methods of reconstructing species phylogeny.
3. Bioinformatics, which provides hands-on training on data acquisition and the use of software tools for phylogenetic analyses.

This 3-credit course is designed for upper-level biology-major undergraduates. Hunter pre-requisites are BIOL203, and MATH150 or STAT113.

Textbooks

(Required) Roderic M. Page and Edward C. Holmes,1998, Molecular Evolution: A phylogenetic Approach, Blackwell Science Ltd. [Book Cover Image] (Reference) E.Paradis, 2012, Analysis of Phylogenetics and Evolution with R. 2nd Edition. Springer LLC.

Learning Goals

1. Understand mechanisms of DNA sequence evolution
2. Be able to describe evolutionary relationships using phylogenetic trees
3. Understand the computational algorithms for building phylogenetic trees
4. Be able to use web-based as well as stand-alone software to infer phylogenetic trees

Links for phylogenetic tools

1. NCBI sequence databases: http://www.ncbi.nlm.nih.gov/
2. R Package: http://r-project.org/ & R Studio: http://rstudio.org
3. CLUSTALW web server at EBI: http://www.ebi.ac.uk/Tools/clustalw2/
4. A Molecular Phylogeny Web Server: http://phylogeny.fr/
5. MEGA webpage: http://www.megasoftware.net/index.html

Exams & Grading

A total of 200 points breaking down to:

1. Assignments (100): 5 exercises. All assignments should be handed in as hard copies only. Email submission will not be accepted. Late submissions will receive 10% deduction (of the total grade) per day.
2. Mid-term Exam (50)
3. Comprehensive Final Exam (50)

Bonus for active participation in classroom discussions (10): Read the text & bring questions!

Academic Honesty

While students may work in groups and help each other for assignments, duplicated answers in assignments will be flagged and investigated as possible acts of academic dishonesty. To avoid being investigated as such, do NOT copy anyone else's work, or let others copy your work. At the least, rephrase using your own words. Note that the same rule applies regarding the use of textbook and online resources: copied sentences are not acceptable and will be considered plagiarism. Hunter College regards acts of academic dishonesty (e.g., plagiarism, cheating on examinations, obtaining unfair advantage, and falsification of records and official documents) as serious offenses against the values of intellectual honesty. The College is committed to enforcing the CUNY Policy on Academic Integrity and will pursue cases of academic dishonesty according to the Hunter College Academic Integrity Procedures.

Course Schedule

Week 1

8/27 (M). 1.1. Introduction: What is Evolution? [Intro Slides] 8/30 (TH). 1.1. Introduction (Continued) [Assignment 1]

Week 2

9/3 (M). Labor Day. No Class 9/6 (TH). 2.1. Introduction to Trees [Chapter 2 Slides] & Basic R [R Tutorial: Plotting Trees] [Assignment 1 Due]

Week 3

9/10 (M). 2.2 & 2.3. Reconstruction and Distance & Tree-plotting with R [Assignment 2] 9/13 (TH). Instructor travels to meeting. Class Canceled.

Week 4

9/17 (M). Holiday Recess. No Class 9/20 (TH). 2.4 & 2.5. Species Tree [Chapter 2 Slides] [Assignment 2 Due]

Week 5

9/24 (M). 3.1. Genome and Gene Structure. [Chapter 3 Slides] 9/27 (TH). 3.2 & 3.3. Genome Evolution [Assignment 3]

Week 6

10/1 (M). 5.1. Homology and Alignment [Chapter 5 Slides] 10/4 (TH). 5.2. Genetic Distance [Assignment 3 Due]

Week 7

10/8 (M). Columbus Day. No Class 10/10 (Wed, Monday Schedule). 5.2. Genetic Distance (Continued) [Assignment 4] 10/11 (TH). 5.3. Character Reconstruction

Week 8

10/15 (M). Midterm Review [Assignment 4 Due] 10/18 (TH). Midterm Exam

Week 9

10/22 (M). Instructor travels to meeting. Class Canceled. 10/25 (TH). Midterm: answers and analysis

Week 10

10/29 (M). School closed due to Sandy 11/1 (TH). School closed due to Sandy

Week 11

11/5 (M). 6.1. Introduction to Phylogenetic Inference [Chapter 6 Slides] 11/8 (TH). 6.2 Distance Methods [Assignment 5]

Week 12

11/12 (M). 6.4. Maximum Parsimony 11/15 (TH). 6.5. Maximum Likelihood

Week 13

11/19 (M). 6.7. Tree Testing: Accuracy & Precision [Assignment 5 Due] [Assignment 6] 11/22 (TH). Thanksgiving week. No Class.

Week 14

11/26 (M). 4.1 Intro to Population Genetics [Chapter 4 Slides] 11/29 (TH). 4.2. Mechanisms of Evolution: Genetic Drift [Assignment 6 Due]

Week 15

12/3 (M). 4.4. Genetics and Speciation; Selected Topics in Chapter 7: Molecular Clock [Assignment 7] 12/6 (TH). Selected topics in Chapter 7: Neutral Theory and molecular tests of natural selection [Chapter 7 Slides]

Week 16

12/10 (M). Last class: Review [Assignment 7 Due]

12/17 (M)

Final (Regular class hours & Room) 12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)