BIOL 4366/6366 Genes and Genomes: Fundamentals of Molecular Evolution
(formerly, Molecular Evolution) - Spring 2012
The class is suitable for upper-division undergraduates and graduate students in Biology
(BIOL), Biochemistry (BCHS), and Biomedical Engineering (BIOE). Other students are
advised to discuss suitability with the Instructor before registration. Honors credits are
available.
Lecture times: TTh: 8:30-10:00 AM
Classroom: SEC 202
Instructor: Dr. Dan Graur
Office: Science & Research Building 2, 3rd Floor, Room 352
e-mail: dgraur@uh.edu
Website: http://nsm.uh.edu/~dgraur/
Office hours: 10:30-12:00 AM Tuesday or by e-mail appointment
Textbook: A draft textbook will be posted on the website and provided to registered
students free of charge.
Catalog description: The evolution of genes, gene-products, genomes, and intergenomic relationships. Methodology of molecular evolutionary analysis. Identification of
the evolutionary forces operating at the molecular level.
Prerequisties: No official prerequisite.
Course structure: Frontal lectures, discussions, compulsory reading, optional reading,
writing assignments
Course objectives: The objectives of this class are to provide advanced, upper division
undergraduates and graduate students with a basic introduction to the main areas of
molecular evolutionary research. In particular, the class will emphasize the methodology
of molecular evolutionary analysis, the identification of the evolutionary forces operating
on genes, gene products, and genomes, and the use of molecular evolutionary data to
solve problems in taxonomy, functional genomics, and medicine. This is a survey class;
some topics will only be covered very briefly.
General course information and policies
Attendance in class is strongly encouraged, past experience indicates a strong correlation
between attendance, comprehension of course material, and good grades.
No textbook is required. A draft textbook will be posted on the website free of charge.
Please do not distribute the material. All exam material will come from the lectures,
however the text and figures from the draft manuscript will be referred to regularly.
Lecture presentations, as well as additional material, will be posted on the website of Dr.
Graur.
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Requirements and expectations
There will be two midterms and a final exam for all students.
Students wishing to receive honors credit should obtain the proper form from the Honors
College to be signed by the Instructor of Record (Dan Graur). The additional
requirements that the student must fulfill to receive Honors Credit for the course will be
determined in consultations between the student and the instructor.
Honors students and Graduate students will be assigned the task of writing or improving
selected molecular evolution and genome evolution entries. Each student will have a
separate Wikipedia account. Each student will write a new article and/or significantly
expand and update upon existing articles. Individual requirements will be determined in
consultations between the student and the instructor. Undergraduate students may also
participate in this project for bonus points.
Evaluation and Grading
Undergraduates: The final grade will be composed of the following components:
Midterm I = 15 points, midterm II = 20 points, final exam = 65 points, optional bonus =
15 points.
Graduates: The final grade will be composed of the following components: Midterm I =
10 points, midterm II = 15 points, final exam = 55 points, research and writing
assignment = 20 points.
Policy on I (incomplete) grades: The I-grade option will be used only very rarely in
extraordinary circumstances. Students with an I grade will be given a very strict deadline
by which to complete the missing assignments. The student will have to acknowledge the
deadline in writing. Unfinished assignments past the deadline will be given a grade of 0
(zero) to be factored into the final grade.
Course content and dates*
Jan 17 Administrative matters and logistics. Overview of syllabus. Intellectual
foundations of molecular evolution. Temporal, spatial, and taxonomic constraints of the
evolutionary process. A short history of DNA.
Jan 19 A short overview of molecular biology (DNA, RNA, proteins, replication,
transcription, and translation). Mutation (point mutations and segmental mutations). Is
mutation random?
Jan 24 Dynamics of genes in population. Changes in allele and genotype frequencies.
What is evolution? The weak driving forces of evolution (deviation from random mating,
migration, mutational input).
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Jan 26 Selection. Directional selection (dominant, recessive, and codominant selection).
Balancing selection (overdominant, and underdominant selection).
Jan 31 A short introduction to probability. Random genetic drift.
Feb 2 Gene substitution. Fixation probability. Fixation time.
Feb 7 Genetic variability.
Feb 9 Evolutionary change in nucleotide sequences, number of substitutions between two
protein-coding genes. Corrections for multiple hits.
Feb 14 Data in molecular evolution. Positional homology, Alignment of amino-acid and
nucleotide sequences. Exhaustive and heuristic approaches to the problem of alignment.
Dynamic programming.
Feb 16 Molecular evolutionary analysis. Rates of mutation. Rates of substitution.
Functional constraint
Feb 21 Midterm I
Feb 23 Adaptive evolution. Positive Darwinian selection. The “male driven evolution”
concept.
Feb 28 Patterns of nucleotide substitution. Codon usage. Selection related to translation
accuracy. Selection related to mRNA stability.
Mar 1 Molecular clocks. Generation time effects on rate of substitution. Metabolic
effects on rate of substitution. Gradual evolution versus punctuated equilibria. Is
evolution progressive?
Mar 6 Introduction to phylogenetics and phylogenetic terminology.
Mar 8 Methods of phylogenetic reconstruction. Processing and testing phylogenetic
trees.
Spring Break
Mar 20 Phylogenetic examples: human phylogeny, cetacean phylogeny, molecular
archeology, early divergence events.
Mar 22 Phylogenetic networks. Origin of eukaryotes. Endosymbiotic processes.
Evolution of prokaryotes.
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Mar 27 Segmental and contextual changes. Internal gene duplication. Gene death
(unitary pseudogenes). Gene duplication. Genome duplication. Post-duplication
evolutionary processes: nonfunctionalization, neofunctionalzation, subfunctionalization.
Mar 29 Concerted evolution. Gene birth-and-death processes.
Apr 3 Midterm II
Apr 5 Molecular tinkering. Exon shuffling. Alternative spicing. Exonization and
pseudoexonization. De novo origin of genes. Chimerical coding genes. Overlapping
genes. Functional convergence. RNA editing. Gene sharing. Origin of introns.
Apr 10 Transposable and retrotransposable elements, SINEs and LINEs.
Apr 12 Mobile nontransposable elements. Promiscuous DNA. Horizontal gene transfer
Apr 17 Evolution of genome size in prokaryotes and eukaryotes. The C-value paradox
Apr 19 Evolution of gene content. Repetitive DNA. Gene geography.
Apr 24 Evolution of genome composition
Apr 26 Evolution of genetic codes. The difference between predictive and postdictive
sciences. Experimental molecular evolution
May 8 Final Exam (8:00-11:00)
*Both content and dates may change if necessary.
Assistance
Whenever possible, and in accordance with 504/ADA guidelines, the University of
Houston will attempt to provide reasonable academic accommodations to students who
request and require them. Please call 713-743-5400 for more assistance.
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