There is NO required book for this course. Any required reading (journal articles or other files) will be provided to you via Canvas.
The Phylogenetic Handbook: A practical approach to phylogenetic analysis and hypothesis testing, Edited by Phillippe Lemey, Marco Salemi and Anne-Mieke Vandamme, 2nd Edition, Cambridge University Press 2009.
This course will cover both the theoretical and practical aspects of performing phylogenetic analyses, with particular emphasis on understanding the differences and applications of the most commonly used methods. Topics to be covered will include: finding the appropriate data and getting it into the right format; using distance-based and probability-based methods to construct phylogenetic trees; understanding and calibrating the molecular clock to calculate divergence times; incorporating “big data” into phylogenetics, and estimating population parameters such as population size, growth, and migration rates.
Pre/Co-requisites: BINF 6201: Molecular Sequence Analysis; BINF 6200: Statistics for Bioinformatics
Learning Objectives:
Each class period will consist of a combination of lecture and in-class computer exercises. Each week, students will be expected to complete all parts of the assigned exercises; anything not finished in class must be completed at home and submitted by 6:00PM on the due date. Students are permitted to work together on the exercises, but must turn in completed assignments individually. Some weeks may also include assigned reading to supplement the lecture material. The final project will require students to analyze a real data set and submit a written report.
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Section I: Sequence Data for Phylogenetics |
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Date |
Topic |
Quizzes |
Exercises Due |
Week 1 |
8/20 |
Introduction & Course Overview |
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8/26 |
8/22 |
Multiple Sequence Alignment |
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Week2 |
8/27 |
Identifying Homologous Genes |
Quiz 1 |
9/2 |
8/29 |
Orthology vs Paralogy (continued) |
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Section II: Constructing Trees |
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Week 3 |
9/3 |
Genetic Distance and Substitution Models |
Quiz 2 |
9/9 |
9/5 |
Distance-based Methods (UPGMA, NJ) |
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Week4 |
9/10 |
Distance-based Methods continued; bootstrapping and jackknifing |
Quiz 3 |
9/16 |
9/12 |
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Week 5 |
9/17 |
Maximum Likelihood (RAxML) |
Quiz 4 |
9/23 |
9/19 |
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Section III: Testing and Interpreting Trees |
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Week 6 |
9/24 |
ML continued; intro to Bayesian methods |
Quiz 5 |
9/30 |
9/26 |
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Week 7 |
10/1 |
Bayesian methods continued; mid-term review |
Quiz 6 |
10/14 |
10/3 |
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Week 8 |
10/8 |
FALL BREAK (No Class) |
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10/10 |
MidTerm Exam |
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Section IV: Using Trees to Test Evolutionary Models |
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Week 9 |
10/15 |
Go over midterm solutions; Ancestral State Reconstruction |
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10/21 |
10/17 |
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Week 10 |
10/22 |
Comparing Trees & assessing tree estimation methods |
Quiz 7 |
10/28 |
10/24 |
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Week 11 |
10/29 |
Multi-gene trees & data partitioning; next-gen data and phylogenetic methods |
Quiz 8 |
11/4 |
10/31 |
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Week 12 |
11/5 |
Gene Genealogies & Intro to Coalescent Theory; effects of selection on gene trees |
Quiz 9 |
11/11 |
11/7 |
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Week 13 |
11/12 |
Calibrating the Molecular Clock to estimate divergence times |
Quiz 10 |
11/18 |
11/14 |
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Week 14 |
11/19 |
Gene Flow and non-tree like evolution
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11/20 |
11/21 |
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Week 15 |
11/26 |
Review session and discuss final projects |
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11/28 |
THANKSGIVING BREAK (No Class) |
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Week 16 |
12/3 |
Work on Projects |
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12/5 |
READING DAY (No Class) |
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Exam Week |
12/6-12/12 |
No Exam; Final Projects Due |
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All students are required to read and abide by the Code of Student Academic Integrity. Violations of the Code of Student Academic Integrity, including plagiarism, will result in disciplinary action as provided in the Code. Definitions and examples of plagiarism are set forth in the Code. The Code is available from the Dean of Students Office or online at: https://legal.uncc.edu/policies/up-407. A set of links to various resources on plagiarism and how to avoid it is available here: https://wts.indiana.edu/writing-guides/plagiarism.html.
Attendance at lecture is required, although exceptions will be made for reasons such as illness or family emergency. Missed quizzes CANNOT be made up, but can be administered in advance or electronically if you notify Dr. Cooper by 7:00PM before the day of the scheduled quiz. Excessive absences will result in a reduced classroom participation score and will negatively impact the overall course grade.
Students in this course seeking accommodations for disabilities should first consult with the Office of Disability Services and follow the instructions of that office for obtaining accommodations.