Biol375 2014

Molecular Evolution (BIOL 375.00/790.64/793.03, Fall 2014) Instructor: Dr Weigang Qiu, Associate Professor, Department of Biological Sciences Teaching Assistant: Ms Saymon Akther <saymon.akther@gmail.com> 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

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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:

• Population genetics, which is a framework of understanding mechanisms of sequence evolution through mutation, recombination, gene duplication, genetic drift, and natural selection.
• Molecular systematics, which introduces statistical models of sequence evolution and methods of reconstructing species phylogeny.
• 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.

Learning Goals

• Understand mechanisms of DNA sequence evolution
• Be able to describe evolutionary relationships using phylogenetic trees
• Understand the computational algorithms for building phylogenetic trees
• 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
6. FigTree
7. EvolView: An online tree viwer/editor. http://www.evolgenius.info/evolview/

Exams & Grading

• Assignments. 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.
• Three Mid-term Exams (50 pts each)
• Comprehensive Final Exam (50 pts)

Bonus for active participation in classroom discussions

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

Part 1. Tree-Thinking Skills

• 8/28 (TH). 1.1. Introduction: Misconceptions about Evolution
• 9/1 (M). 1.1. Introduction: Tree-thinking (Continued) [Assignment 1]
• 9/4 (TH). Introduction to Trees [Chapter 2 Slides]
• 9/8 (M). 2.1. Intro to trees
• 9/11 (TH). 2.2 & 2.3. Reconstruction and Distance & Tree-plotting with R [Assignment 2]
• 9/15 (M). 2.4 & 2.5. Species Tree [Chapter 2 Slides] [Assignment 2 Due]
• 9/18 (TH). 3.1. Genome and Gene Structure. [Chapter 3 Slides]
• 9/22 (M). Midterm Exam I

Part 2. Trait Evolution

• 9/25 (TH). Holiday Recess. No Class
• 9/29 (M). TBD
• 10/2 (TH). 5.1. Homology and Alignment [Chapter 5 Slides]
• 10/6 (M). 5.2. Genetic Distance [Assignment 3 Due]
• 10/9 (TH). 5.2. Genetic Distance (Continued) [Assignment 4]
• 10/13 (M). 5.3. Character Reconstruction
• 10/16 (TH). TBD [Assignment 4 Due]
• 10/20 (M). Midterm Exam 2

Part 3. Alignment and Tree Algorithms

• 10/23 (TH). TBD
• 10/27 (M). TBD
• 10/30 (TH). TBD
• 11/3 (M). TBD
• 11/6 (TH). TBD
• 11/10 (M). TBD
• 11/13 (TH). TBD
• 11/17 (M). Midterm Exam 3

Part 4. Mechanisms of Molecular Evolution

• 11/20 (TH). Instructor traveling. No class
• 11/24 (M). 6.7. Tree Testing: Accuracy & Precision [Assignment 5 Due] [Assignment 6]
• 12/1 (M). Instructor traveling. No class
• 12/4 (TH). 4.2. Intro to Population Genetics [Chapter 4 Slides] 4.1. Mechanisms of Evolution: Genetic Drift [Assignment 6 Due]
• 12/8 (M). 4.4. Genetics and Speciation; Selected Topics in Chapter 7: Molecular Clock [Assignment 7]
• 12/11 (TH). Selected topics in Chapter 7: Neutral Theory and molecular tests of natural selection [Chapter 7 Slides]
• 12/15 (M). Last class: Review [Assignment 7 Due]
• 12/19 (TH) Comprehensive Final Exam (Regular class hours & Room)
• 12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)