Biol375 2014
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.
- (Recommended) Baum & Smith, 2013. Tree Thinking: an Introduction to Phylogenetic Biology, Roberts & Company Publishers, Inc.
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
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 (30 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). Overview & Introduction
- 9/1 (M). Labor Day. No class
- 9/4 (TH). 1.1. Introduction (Continued)
- 9/8 (M). 2.1. Intro to trees
- 9/11 (TH). 2.2 & 2.3. Reconstruction and Distance
- 9/15 (M). 2.4 & 2.5. Species Tree
- 9/18 (TH). 3.1. Genome and Gene Structure
- 9/22 (M). Midterm Exam I
Part 2. Trait Evolution
- 9/25 (TH). Holiday Recess. No Class
- 9/29 (M). TBD
- 10/2 (TH). TBD
- 10/6 (M). TBD
- 10/9 (TH). TBD
- 10/13 (M). No Class
- 10/16 (TH). TBD
- 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). TBD
- 12/1 (M). Instructor traveling. No class
- 12/4 (TH). TBD
- 12/8 (M). TBD
- 12/11 (TH). TBD
- 12/15 (M). Review
- 12/19 (TH) Comprehensive Final Exam (Regular class hours & Room)
- 12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)