Molecular Evolution

HunterCollege of the City University of New York
Instructor: Weigang Qiu, Ph.D., Department of BiologicalSciences
Room 926 HN; Mon. & Thur. 2:45-4:00 pm

OfficeHour: Room 839 HN; Tuesdays 3-5pm
 Phone: 212-772-5296; E-mail: This e-mail address is being protected from spambots. You need JavaScript enabled to view it
Coursewebsite:http//darwin.hunter.cuny.edu/ BIOL375_2009.htm

Course Description 

            Molecularevolution is the study of the diversification of DNA and proteinsequences through time. Theories and techniques of molecular evolutionare widely used in species classification, biodiversity studies,comparative genomics, and molecular epidemiology. Contentsof the course include: 

• Population genetics,which provides a framework of understanding mechanisms of sequenceevolution through mutation, gene duplication, genetic drift, andnatural selection;
•  Molecular systematics,which introduces statistical models of sequenceevolution and methods of phylogenetic inference;  
• Bioinformatics, which  provideshands-on training on data acquisition and the use of softwaretools forphylogenetic analyses;
• Applications of molecular evolutionin biological classification, epidemiology, and comparativegenomics. 

       This 3-credit courseis designedfor upper-level biology-major undergraduates.  Hunterpre-requisites are BIOL300 or BIOL302, and MATH150 orSTAT113.

Textbooks

• (Required) Roderic M. Page andEdward C. Holmes,1998, Molecular Evolution: A phylogeneticApproach, Blackwell Science Ltd.
• (Reference) J.Felsenstein. 2003. Inferring Phylogenies. Sinauer Associates,Inc

Learning Objectives

• Understand thepopulation processes of DNA sequence evolution
• Be able to describeevolutionary relationships using phylogenetic trees
• Understand thecomputational algorithms for building phylogenetic trees
• Be able to useweb-based as well as stand-alone software to infer phylogenetic trees
  

Important links

• NCBI sequencedatabases: http://www.ncbi.nlm.nih.gov/
• CLUSTALW web serverat EBI: http://www.ebi.ac.uk/Tools/clustalw2/
• A Molecular PhylogenyWeb Server: http://mobyle.pasteur.fr/cgi-bin/portal.py
• A Web PhylogenyServer with a Newick Viewer: The T-Rex Server
• MEGA webpage: http://www.megasoftware.net/index.html
  

Exams & Grading

A total of 150 points breaking down to:

Assignments (60): 5 exercises

Mid-term (40)

Final exam (40)

Classroom Q & A (10): Read the chapters before lecture.

Bonus (10). Full attendance: 10; 1-2 absences: 5; Three or more absence: zero

AcademicHonesty

HunterCollege regards acts of academic dishonesty (e.g., plagiarism,cheating on examinations, obtaining unfair advantage, and falsificationof records and official documents) as serious offenses against thevalues of intellectual honesty. The College is committed to enforcingthe CUNY Policy on Academic Integrity and will pursue cases of academicdishonesty according to the Hunter College Academic IntegrityProcedures.

CourseSchedule

8/31(M). 1.1. Introduction & the "Tree-Thinking" Challenge (Part I)

9/3 (TH). 2.1. Introduction to Trees [Assignment 1: Tree-ThinkingQuizes]
9/10 (TH). 2.2 & 2.3. Reconstruction and Distance [Assignment 1 Due]
9/14 (M). 2.4 & 2.5. SpeciesTree [Chapter 2 Slides]
9/17 (TH). 3.1. Genome and Gene Structure. [Assignment 2: NCBI BLAST]
9/21 (M). 3.2& 3.3. Genome Evolution [Chapter 3Slides]
9/24 (TH). 5.1. Homology and Alignment [Assignment 2 Due]
9/29 (Tuesday). 5.2.Genetic Distance

10/1 (TH). 5.3. Changes on a Tree [Assignment 3] [Chapter 5 Slides]
10/5 (M). "Tree-Thinking" Challenge (Part II)
10/8 (TH). 6.1. Introduction to Phylogenetic Inference [Assignment 3 Due]
10/14 (Wed). 6.2.Distance Methods
10/15 (TH). 6.2. Distance Methods
10/19 (M). Midterm Exam
10/22 (TH). 6.4. Maximum Parsimony
10/26 (M). 6.5. Maximum Likelihood
10/29 (TH). 6.5. Tree Testing: Accuracy [Assignment 4]

11/2 (M). 6.7. Class Cancelled
11/5 (TH). 6.7. Tree Testing: Precision [Assignment 4 Due] [Chapter 6Slides]
11/9 (M). p.85-87,Box 3.2. MolecularTechniques;4.1 Intro to Population Genetics
11/12 (TH). 4.2. Mechanisms of Evolution: Genetic Drift
11/16 (M). 4.4.Genetics and Speciation
11/19 (TH). 4.6.Case studies: Human evolution and Lyme Biogeography [Assignment 5][Chapter 4 Slides]
11/23 (M). 7.1& 7.2. Models ofevolutionary processes and Functional constraints
11/30 (M). 7.4,7.5, Molecular clock and Nearly neutral theory; [Assignment 5 Due] [Distributions of Timeto Fixation by simulation: N=10; N=20; N=20 (Cheung) ]

12/3 (TH). Class Cancelled
12/7 (M). 7.6& 7.7. Molecular tests of natural selection
12/10 (TH). 8.2 Gene Trees andSpecies Trees; [Chapter 7 Slides] Review
12/17 (TH). Final
12/31 (W). Grades Submitted to Registrar Office (Hunter andGraduate Center)