Biol375 2014: Difference between revisions

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==Course Schedule==
==Course Schedule==
===Week 1===
===Week 1===
8/27 (M). 1.1. Introduction: What is Evolution? [Intro Slides]
# 8/28 (TH). 1.1. Introduction: What is Evolution? [Intro Slides]
8/30 (TH). 1.1. Introduction (Continued) [Assignment 1]
# 9/1 (M). 1.1. Introduction (Continued) [Assignment 1]


===Week 2===
===Week 2===
9/3 (M). Labor Day. No Class
# 9/4 (TH). Labor Day. No Class
9/6 (TH). 2.1. Introduction to Trees [Chapter 2 Slides] & Basic R [R Tutorial: Plotting Trees] [Assignment 1 Due]
# 9/8 (M). 2.1. Introduction to Trees [Chapter 2 Slides] & Basic R [R Tutorial: Plotting Trees] [Assignment 1 Due]


===Week 3===
===Week 3===
9/10 (M).  2.2 & 2.3. Reconstruction and Distance & Tree-plotting with R [Assignment 2]
# 9/11 (TH).  2.2 & 2.3. Reconstruction and Distance & Tree-plotting with R [Assignment 2]
9/13 (TH). Instructor travels to meeting. Class Canceled.  
# 9/15 (M). Instructor travels to meeting. Class Canceled.  


===Week 4===
===Week 4===
9/17 (M). Holiday Recess. No Class
# 9/18 (TH). 2.4 & 2.5. Species Tree [Chapter 2 Slides] [Assignment 2 Due]
9/20 (TH). 2.4 & 2.5. Species Tree [Chapter 2 Slides] [Assignment 2 Due]
# 9/22 (M). Genome and Gene Structure. [Chapter 3 Slides]


===Week 5===
===Week 5===
9/24 (M). 3.1. Genome and Gene Structure. [Chapter 3 Slides]
# 9/25 (TH). 3.1. Holiday Recess. No Class
9/27 (TH). 3.2 & 3.3. Genome Evolution [Assignment 3]  
# 9/29 (M). 3.2 & 3.3. Genome Evolution [Assignment 3]  


===Week 6===
===Week 6===
10/1 (M). 5.1. Homology and Alignment  [Chapter 5 Slides]
# 10/2 (TH). 5.1. Homology and Alignment  [Chapter 5 Slides]
10/4 (TH). 5.2. Genetic Distance [Assignment 3 Due]
# 10/6 (M). 5.2. Genetic Distance [Assignment 3 Due]


===Week 7===
===Week 7===
10/8 (M). Columbus Day. No Class
# 10/9 (TH). 5.2. Genetic Distance (Continued) [Assignment 4]
10/10 (Wed, Monday Schedule). 5.2. Genetic Distance (Continued) [Assignment 4]
# 10/13 (M). 5.3. Character Reconstruction
10/11 (TH). 5.3. Character Reconstruction


===Week 8===
===Week 8===
10/15 (M). Midterm Review [Assignment 4 Due]
# 10/16 (TH). Midterm Review [Assignment 4 Due]
10/18 (TH). Midterm Exam
# 10/20 (M). Midterm Exam


===Week 9===
===Week 9===
10/22 (M). Instructor travels to meeting. Class Canceled.
10/23 (TH). Instructor travels to meeting. Class Canceled.
10/25 (TH). Midterm: answers and analysis
10/27 (M). Midterm: answers and analysis


===Week 10===
===Week 10===
10/29 (M). School closed due to Sandy
10/30 (TH). School closed due to Sandy
11/1 (TH). School closed due to Sandy
11/3 (M). School closed due to Sandy


===Week 11===
===Week 11===
11/5 (M). 6.1. Introduction to Phylogenetic Inference [Chapter 6 Slides]  
11/6 (TH). 6.1. Introduction to Phylogenetic Inference [Chapter 6 Slides]  
11/8 (TH). 6.2 Distance Methods [Assignment 5]  
11/10 (M). 6.2 Distance Methods [Assignment 5]  


===Week 12===
===Week 12===
11/12 (M). 6.4. Maximum Parsimony  
11/13 (TH). 6.4. Maximum Parsimony  
11/15 (TH). 6.5.  Maximum Likelihood   
11/17 (M). 6.5.  Maximum Likelihood   


===Week 13===
===Week 13===
11/19 (M). 6.7. Tree Testing: Accuracy & Precision [Assignment 5 Due] [Assignment 6]  
11/20 (TH). 6.7. Tree Testing: Accuracy & Precision [Assignment 5 Due] [Assignment 6]  
11/22 (TH). Thanksgiving week. No Class.
11/24 (M). Thanksgiving week. No Class.


===Week 14===
===Week 14===
11/26 (M). 4.1 Intro to Population Genetics [Chapter 4 Slides]  
12/1 (M). 4.1 Intro to Population Genetics [Chapter 4 Slides]  
11/29 (TH). 4.2. Mechanisms of Evolution: Genetic Drift [Assignment 6 Due]
12/4 (TH). 4.2. Mechanisms of Evolution: Genetic Drift [Assignment 6 Due]


===Week 15===
===Week 15===
12/3 (M). 4.4. Genetics and Speciation; Selected Topics in Chapter 7: Molecular Clock [Assignment 7]
12/8 (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]
12/11 (TH). Selected topics in Chapter 7:  Neutral Theory and molecular tests of natural selection [Chapter 7 Slides]


===Week 16===
===Week 16===
12/10 (M). Last class: Review [Assignment 7 Due]
12/15 (M). Last class: Review [Assignment 7 Due]
 
12/19 (TH) Final (Regular class hours & Room)
===12/17 (M)===
Final (Regular class hours & Room)
12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)
12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)

Revision as of 04:13, 25 August 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

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

  • Weekly 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.
  • Mid-term Exam (50)
  • 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

  1. 8/28 (TH). 1.1. Introduction: What is Evolution? [Intro Slides]
  2. 9/1 (M). 1.1. Introduction (Continued) [Assignment 1]

Week 2

  1. 9/4 (TH). Labor Day. No Class
  2. 9/8 (M). 2.1. Introduction to Trees [Chapter 2 Slides] & Basic R [R Tutorial: Plotting Trees] [Assignment 1 Due]

Week 3

  1. 9/11 (TH). 2.2 & 2.3. Reconstruction and Distance & Tree-plotting with R [Assignment 2]
  2. 9/15 (M). Instructor travels to meeting. Class Canceled.

Week 4

  1. 9/18 (TH). 2.4 & 2.5. Species Tree [Chapter 2 Slides] [Assignment 2 Due]
  2. 9/22 (M). Genome and Gene Structure. [Chapter 3 Slides]

Week 5

  1. 9/25 (TH). 3.1. Holiday Recess. No Class
  2. 9/29 (M). 3.2 & 3.3. Genome Evolution [Assignment 3]

Week 6

  1. 10/2 (TH). 5.1. Homology and Alignment [Chapter 5 Slides]
  2. 10/6 (M). 5.2. Genetic Distance [Assignment 3 Due]

Week 7

  1. 10/9 (TH). 5.2. Genetic Distance (Continued) [Assignment 4]
  2. 10/13 (M). 5.3. Character Reconstruction

Week 8

  1. 10/16 (TH). Midterm Review [Assignment 4 Due]
  2. 10/20 (M). Midterm Exam

Week 9

10/23 (TH). Instructor travels to meeting. Class Canceled. 10/27 (M). Midterm: answers and analysis

Week 10

10/30 (TH). School closed due to Sandy 11/3 (M). School closed due to Sandy

Week 11

11/6 (TH). 6.1. Introduction to Phylogenetic Inference [Chapter 6 Slides] 11/10 (M). 6.2 Distance Methods [Assignment 5]

Week 12

11/13 (TH). 6.4. Maximum Parsimony 11/17 (M). 6.5. Maximum Likelihood

Week 13

11/20 (TH). 6.7. Tree Testing: Accuracy & Precision [Assignment 5 Due] [Assignment 6] 11/24 (M). Thanksgiving week. No Class.

Week 14

12/1 (M). 4.1 Intro to Population Genetics [Chapter 4 Slides] 12/4 (TH). 4.2. Mechanisms of Evolution: Genetic Drift [Assignment 6 Due]

Week 15

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]

Week 16

12/15 (M). Last class: Review [Assignment 7 Due] 12/19 (TH) Final (Regular class hours & Room) 12/31 (Wed). Grades Submitted to Registrar Offices (Hunter and Graduate Center)

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