BIO605: Molecular Evolution
Fall 2010
Instructor: J. Craig Bailey, PhD
Office: 2339 Center for Marine Science (910-962-2371)
Lab: 2304 Center for Marine Science (910-962-2372)
Email: baileyc@uncw.edu
Required text: Grauer D and Li W-H (2000) Fundamentals of Molecular
Evolution, 2nd Ed. Sinauer Associates, Sunderland, MA.
Grading and attendance policies: Your grade will be based on equally weighted
scores on weekly quizzes. A total of 11 quizzes will be given during the course
and the lowest quiz score will be omitted from calculation of your final grade.
Grades will be awarded on the basis of a strict 10 point scale using the +/system. Attendance is mandatory.
Lecture Topics and Reading Assignments:
Lecture Topic
Date
Course Introduction
24 August
Chapter 8: Genome Evolution
31 August
C Values
Evolution of Genome Size in Prokaryotes
The Minimal Genome
Genome Miniaturization
Genome Size in Eukaryotes and the C Value Paradox
Mechanisms for Global Increases in Genome Size
Maintenance of Nongenic DNA
The Repetitive Structure of the Eukaryotic Genome
Mechanisms for Regional Increases in Genome Size
Gene Distribution
Chromosomal Evolution
Mechanisms for Changes in Gene Order and Gene Distribution among Chromosomes
GC Content in Bacteria
Chirochores
Compositional Organization of the Vertebrate Genome
The Distribution of Genes and Other Genetic Elements among Isochores
Emergence of Nonuniversal Genetic Codes
Chapter 1: Genes, Genetic Codes, and Mutation
Nucleotide Sequences
Genomes and DNA Replication
Genes and Gene Structure
Amino Acids
Proteins
Genetic Codes and Translation
Mutation
07 September
Chapter 2: Dynamics of Genes in Populations
Changes in Allele Frequencies
Natural Selection
Random Genetic Drift
Effective Population Size
Gene Substitution
Genetic Polymorphism
The Driving Forces in Evolution
14 September
Chapter 3: Evolutionary Change in Nucleotide Sequences
Nucleotide Substitution in a DNA Sequence
Number of Nucleotide Substitutions between Two DNA Sequences
Number of Amino Acid Replacements between Two Proteins
Alignment of Nucleotide and Amino Acid Sequences
21 September
Chapter 4: Rates and Patterns of Nucleotide Substitution
Rates of Nucleotide Substitution
Causes of Variation in Substitution Rates
Positive Selection
Patterns of Substitution and Replacement
Nonrandom Usage of Synonymous Codons
28 September
Molecular Clocks
Relative-Rate Tests
Local Clocks
Evaluation of the Molecular Clock Hypothesis
Rates of Substitution in Organelle DNA
RNA Viruses
12 October
Chapter 5: Molecular Phylogenetics
The Impact of Molecular Data on Phylogenetic Studies
The Advantages of Molecular Data in Phylogenetic Studies
Terminology of Phylogenetic Trees
Types of Data
19 October
Methods of Tree Reconstruction
Distance Matrix Methods
Maximum Parsimony Methods
Maximum Likelihood Methods
Rooting Unrooted Trees
Estimation of Branch Lengths
Estimation of Species Divergence Times
26 October
Topological Comparisons
Assessing Tree Reliability
Problems Associated with Phylogenetic Reconstructions
Molecular Phylogenetic Examples
Molecular Phylogenetic Archeology
The Universal Phylogeny
02 November
Chapter 6: Gene Duplication, Exon Shuffling,
and Concerted Evolution
Types of Gene Duplication
Domains and Exons
Domain Duplication and Gene Elongation
09 November
Formation of Gene Families and the Acquisition of New Functions
Dating Gene Duplications
Gene Loss
The Globin Superfamily of Genes
Prevalence of Gene Duplication, Gene Loss, and Functional Divergence
Exon Shuffling
The “Introns-Early” Versus the “Introns-Late” Hypotheses
Alternative Pathways for Producing New Functions
Molecular Tinkering
Concerted Evolution
Mechanisms of Concerted Evolution
Detection and Examples of Concerted Evolution
Evolutionary Implications of Concerted Evolution
Chapter 7: Evolution by Transposition
Transposition and Retroposition
Transposable Elements
Retroelements
Retrosequences
LINEs and SINEs
Genetic and Evolutionary Effects of Transposition
Horizontal Gene Transfer
16 November