Molecular Ecology & Evolution Syllabus Page 1 of 4
Biol6301: Molecular Ecology and Evolution
Prerequisites: BIOL 4305 Organic Evolution and BIOL 3416 Genetics. A
grounding in statistics will also be helpful.
Meeting times: Biol 405 M 10-10:50
W 9-10:50
Instructors:
Matt Olson: office
ESB 217
phone
742-3722 ext 258
email
matt.olson@ttu.edu
Office hours: M 1:30-2:30
Course Description: This course is an introduction to theory and computational
techniques used in to analyze and interpret information contained in among-population
DNA sequence variation. This vibrant and fast-developing discipline has implications for
sciences ranging from global change biology to anthropology and forensics. The course
will have a lecture and a hands-on computer lab. The lecture will cover many of the
major topics in molecular ecology and evolution including generation and maintenance
of nucleotide diversity, theory and application of the coalescent process, estimation of
divergence and migration, and genome-level signatures of selection. The laboratory will
be a hands-on introduction to computational techniques in molecular evolution. We’ll
use a mish-mash of different programs to introduce techniques for large-scale data
manipulation and analysis. Analyses will be conducted on various platforms including
windows and linux.
Course goals: By the end of this course students will have a general knowledge of the
issues facing the field of molecular ecology and evolution. For undergraduates, this will
be a capstone experience that will allow students to draw from their diverse academic
backgrounds and experience the creative side of biological research. The computer lab is
will provide undergraduates hands-on experience and an opportunity to develop an
original scientific project. For graduate students, this course is meant to be a beginning.
It will offer an opportunity to integrate an aspect of molecular evolution into your
current research and will give you perspective for future forays in the field.
Molecular Ecology & Evolution Syllabus Page 2 of 4
Course format and student assessment
The course will consist of lectures and discussions on Tuesdays, and discussions and
computer labs on Thursdays. Students will be expected to prepare for each discussion
by reading and analyzing assigned literature. Literature will be drawn from textbooks
and the primary literature. Questions will be assigned for you to think about while
reading and that will serve as a starting point for discussions. Class time will be spent on
analysis and discussion of the readings, so sufficient preparation is essential for mastery
of the subject.
Grading:
Participation
Problem sets, Think pieces, Labs
Exams
Project
15%
40%
30%
15%
Participation: This is a small class, so participation means engaging in the material,
asking relevant questions, and providing insights that others do not see. Class sessions
will vary from lectures, to discussions to computer labs.
Problem sets/ Think pieces: To help you synthesize and learn to apply the issues covered
in lecture and lab, problem sets will be assigned some weeks. These will be due the
following week. You may work on the homework problem sets independently or in
groups, but if you work in a group you should contribute equally and write up and turn
in your answers separately. Late problem sets will be marked down 10% for each week
they are late.
For some of the readings you will be asked to write a “think piece.” This is a type
of article in journalism that contains discussion, analysis, opinion, etc. and is not a
simple factual summary. The purpose is to engage your creativity and summarize your
thoughts, responses and questions in preparation for or after a class discussion.
Think pieces should be no more than 2 pages typed and carefully proofread.
Grading will be based on demonstration that you are engaging in the material and are
thinking beyond and integrating ideas from the readings. You should also try, when
possible to tie in and make connections with other portions of the course.
Lab Assignments: There will be a few short lab assignments due the week following the
lab
Analysis Project: We will be conducting a class project. More details later.
Overall Course Grades will be determined as follows:
Numerical Score Grade
90.0-100%
A
80.0-89.9
B
70.0-79.9
C
60.0-69.9
D
Below 60.0
F
Plus/minus designations will be based on overall student performance in the class and
may not be awarded in every category, depending on the range of scores.
Molecular Ecology & Evolution Syllabus Page 3 of 4
Students with Disabilities:
Needs of students with disabilities will be accommodates following University policies.
Any student needing accommodation of a disability should provide me with a letter
from the Office of Disability Services (http://www.depts.ttu.edu/students/sds/). The
Office of Disability Services also requires students contact them at least 3 days in
advance of any exam for which they need special arrangements. Please talk to
instructor privately if you have questions or require assistance. The TTU Student
Counseling Center also provides disability services (http://www.depts.ttu.edu/scc/).
Student Absence for Observation of Religious Holy Days: Any student who intends to
observe a religious holy day should make that intention known to the instructor prior to
the absence. A student who is absent from class for the observance of a religious holy
day shall be allowed to take an examination or complete an assignment scheduled for
that day within a reasonable time after the absence.
Important Course Policies:
Plagarism and fabrication of data are unacceptable practices in this course, science, and
your creative life in general. All of your work should be your own and only your own
unless it is explicitly assigned and completed as a group. Plagiarism, data fabrication, or
cheating will result in immediate removal from the course, delivery to the Dean of
Student Affairs and the University Disciplinary and Honor Code Committee, and a course
grade of “F”. See the 2014-2015 TTU Student Handbook for additional details regarding
Academic Integrity and the Code of Student Conduct.
Week
1 Aug 25, 27
2 Sept 3
3 Sept 8, 10
4 Sept 15, 17
5 Sept 22, 24
6 Sept 29 Oct 1
7 Oct 6, 8
8 Oct 13, 15
9 Oct 20,22
10 Oct 27, 29
11 Nov 3, 5
12 Nov 10, 12
13 Nov 17, 19
14 Nov 24
15 Dec 1, 3
Topic
introduction and molecular markers for ecological genetics
homology, alignment, assembly (Bryan Carstens seminar)
homology, alignment, assembly
modeling nucleotide evolution
Phylogeny 1 (Jonathan Wendel Seminar)
Exam 1
Phylogeny 2
Measuring molecular variation
Genetic drift and coalescent process
Site frequency spectra
Linkage Disequilibrium
Exam 2, Demographic inference
Population structure
Detecting Selection
Detecting Selection
Molecular Ecology & Evolution Syllabus Page 4 of 4