BINF 6205/8205: Computational Molecular Evolution

Instructor: Liz Cooper

Contact Info: Office: Bioinformatics 271, Phone: 704-687-2402, Email: lizcooper@uncc.edu

Time and Place: Tuesdays and Thursdays, 11:30am – 12:45am, Bioinformatics 301

Textbooks:

There is NO required book for this course.  Any required reading (journal articles or other files) will be provided to you via Canvas.

Optional Book:

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.

Course Description:

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:

  1. Understand the basic concept of a phylogeny: what it represents and how to interpret it.
  2. Know where to find and how to generate data sets that are appropriate for phylogenetic analyses, and understand how to construct a data set for answering a particular evolutionary question.
  3. Gain a solid understanding of the algorithms underlying different methods and know the strengths and weaknesses of each.
  4. Be able to use several of the most commonly used phylogenetic software packages, including BEAST, RAxML, MrBayes, and the R APE package.
  5. Know how to interpret trees and how to use them to test evolutionary models.

Homework and Grading

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.

Grading

Grades will be assigned on the following scale:

   A=90-100%

   B=80-89%

   C=70-79%

   D=60-69%

 

 

   Class/Home Work: 25%

   Quizzes: 20%

   Midterm: 20%

   Final Project: 30%

   Class Participation: 5%

 

Schedule of Topics:

Section I: Sequence Data for Phylogenetics        

 

Date

Topic

Quizzes

Exercises Due

Week 1

8/20

Introduction & Course Overview

 

8/26

8/22

Multiple Sequence Alignment

 

Week2

8/27

Identifying Homologous Genes

Quiz 1

9/2

8/29

Orthology vs Paralogy (continued)

 

Section II: Constructing Trees

Week 3

9/3

Genetic Distance and Substitution Models

Quiz 2

9/9

9/5

Distance-based Methods (UPGMA, NJ)

 

Week4

9/10

Distance-based Methods continued; bootstrapping and jackknifing

Quiz 3

9/16

9/12

 

Week 5

9/17

Maximum Likelihood (RAxML)

Quiz 4

9/23

9/19

 

Section III: Testing and Interpreting Trees

Week 6

9/24

ML continued; intro to Bayesian methods

Quiz 5

9/30

9/26

 

Week 7

10/1

Bayesian methods continued; mid-term review

Quiz 6

10/14

10/3

 

Week 8

10/8

FALL BREAK (No Class)

 

 

10/10

MidTerm Exam

 

 

Section IV: Using Trees to Test Evolutionary Models

Week 9

10/15

Go over midterm solutions;

Ancestral State Reconstruction

 

10/21

10/17

 

 

Week 10

10/22

Comparing Trees & assessing tree estimation methods

Quiz 7

10/28

10/24

 

 

Week 11

10/29

Multi-gene trees & data partitioning; next-gen data and phylogenetic methods

Quiz 8

11/4

10/31

 

 

Week 12

11/5

Gene Genealogies & Intro to Coalescent Theory; effects of selection on gene trees

Quiz 9

11/11

11/7

 

 

Week 13

11/12

Calibrating the Molecular Clock to estimate divergence times

Quiz 10

11/18

11/14

 

 

Week 14

11/19

Gene Flow and non-tree like evolution

 

 

11/20

11/21

 

 

Week 15

11/26

Review session and discuss final projects

 

 

11/28

THANKSGIVING BREAK (No Class)

 

 

Week 16

12/3

Work on Projects

 

 

12/5

READING DAY (No Class)

 

 

Exam Week

12/6-12/12

No Exam; Final Projects Due

 

 

Policies and Procedures:

  1. Academic Integrity

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.

 

  1. Attendance

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.

 

  1. Disability Accommodations

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.