Molecular Evolution and Bioinformatics (ALWAYS UNDER CONSTRUCTION)

BIOL 4550--01 Spring 2024


Learning Objectives

Upon completion of this course, students will be able to:

1. Integrate sub-disciplines of Molecular Biology into the unifying theme of Molecular Evolution.

2. Recall the major scientists and ideas that contributed to the history of evolutionary thought.

3. Explain the mechanisms of evolution: natural selection, migration, genetic drift, mutation,
and nonrandom mating.

4. Define the basic terminology and principles of the bioinformatic omics
- such as genomics, transcriptomics, proteomics, etc.

5. Contrast the different methodologies of DNA sequencing.

6. Effectively use databases, websites, and computational methods for studying biological data
in relation to the evolution of genes, proteins, and whole genomes.

7. Interpret reconstructed evolutionary trees derived from sequence data.

8. Apply the broader impacts of molecular evolutionary change as they relate to topics such as
the tree of life, coevolution, biodiversity, evolutionary development, cultural issues, social issues, etc.

9. Compose a variety of disciplinary-appropriate texts, for example:
scientific essays evaluating various evolutionary topics, scientific posters, scientific manuscripts, mock grant proposals, etc.

Schedule (Subject to Change)

Week Dates Topic Readings Due Dates
1 Jan. 9

Jan. 11
Intro. & Syllabus

Scientific Thought and Intro to Evolution
- Syllabus quiz-
due Jan. 12
2 Jan. 16

Jan. 18
Video on History of Evolution

Mendel and the Modern Synthesis
For Class:
Mendelism, Darwinism, and Evolutionism--Dobzhansky
Reading Quiz
Due Jan. 18
3 Jan. 23

Jan. 25
Introduction to Pop. Gen and Hardy-Weinberg

Mechanisms: Mutation and Non-Random Mating
For Class:
Crow 1999
Crow and Dove 1988
Reading Quiz
Due Jan. 23
Modern Synthesis Scientist Essay
Due Jan. 26
4 Jan. 30

Feb. 1
Mechanisms: Selection

Mechanisms: Selection
For Class:
Final Project Topic Selection Due Feb. 1
5 Feb. 6

Feb. 8
Selection on H-W

Mechanisms: Genetic drift and Gene Flow
For Class:
Dobzhansky and Spassky 1962
Reading Quiz
Due Feb. 8
6 Feb. 13

Feb. 15
H-W Work Day

H-W Work Day
- Darwin Day Feb 12!

H-W Assignment due Feb. 15
7 Feb. 20

Feb. 22
Neutral Theory vs. Selection

Neutral Theory Vs. Selection
For Class:
Kern & Hahn 2018
Jensen et al. 2018
Kretiman 1996
Reading Quiz
Due Feb. 20

Exam 1 Due Feb. 23
8 Feb. 27

Feb. 29
Genome Structure, Duplications, And Gene Families

Sequencing and Next Gen. Methods
For Class:
Demuth and Hahn 2009

Reading Quiz
Due. Feb 27

Take a stance on the neutral theory essay
Due Mar. 1
9 Mar. 5

Mar. 7
Finding Sequence data

Genome Sequencing Debate
- Sequencing Debate
March 7

Annotated Bibliography and
Outline for Background of Proposal
Due Mar. 8
- Mar. 12

Mar. 14
10 Mar. 19

Mar. 21
Genotyping and GWAS

Molecular Pop. Gen
- Meet with Dr. Hjelmen by Mar. 22
11 Mar. 26

Mar. 28
Molecular Pop. Gen

Phylogenetics and Tree Thinking
For Class
Schlebusch and Jakobsson 2018
Reading Quiz
Due Mar. 26

Should you have to get approval for DNA kits-Essay
Due Mar. 29
12 Apr. 2

Apr. 4
Substitution Models and Alignments

Making your own Phylogenies
- Submit Draft of Proposal
due Apr. 2

Submit Peer Review
by Apr. 5
13 Apr. 9

Apr. 11
Work on Project

Work on Project
- Exam 2
Due Apr. 12
14 Apr. 16

Apr. 18
Work on Project

- -
15 Apr. 23 Presentations - FInal Proposal
Due Apr. 26 by 5pm

Group Evaluation
Due Apr. 26 by 11:59pm