BIO605: Molecular Evolution



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 07 September

Nucleotide Sequences

Genomes and DNA Replication

Genes and Gene Structure

Amino Acids

Proteins

Genetic Codes and Translation

Mutation

Chapter 2: Dynamics of Genes in Populations 14 September

Changes in Allele Frequencies

Natural Selection

Random Genetic Drift

Effective Population Size

Gene Substitution

Genetic Polymorphism

The Driving Forces in Evolution

Chapter 3: Evolutionary Change in Nucleotide Sequences 21 September

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

Chapter 4: Rates and Patterns of Nucleotide Substitution 28 September

Rates of Nucleotide Substitution

Causes of Variation in Substitution Rates

Positive Selection

Patterns of Substitution and Replacement

Nonrandom Usage of Synonymous Codons

Molecular Clocks 12 October

Relative-Rate Tests

Local Clocks

Evaluation of the Molecular Clock Hypothesis

Rates of Substitution in Organelle DNA

RNA Viruses

Chapter 5: Molecular Phylogenetics 19 October

The Impact of Molecular Data on Phylogenetic Studies

The Advantages of Molecular Data in Phylogenetic Studies

Terminology of Phylogenetic Trees

Types of Data

Methods of Tree Reconstruction 26 October

Distance Matrix Methods

Maximum Parsimony Methods

Maximum Likelihood Methods

Rooting Unrooted Trees

Estimation of Branch Lengths

Estimation of Species Divergence Times

Topological Comparisons 02 November

Assessing Tree Reliability

Problems Associated with Phylogenetic Reconstructions

Molecular Phylogenetic Examples

Molecular Phylogenetic Archeology

The Universal Phylogeny

Chapter 6: Gene Duplication, Exon Shuffling, 09 November

and Concerted Evolution

Types of Gene Duplication

Domains and Exons

Domain Duplication and Gene Elongation

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 16 November

Transposition and Retroposition

Transposable Elements

Retroelements

Retrosequences

LINEs and SINEs

Genetic and Evolutionary Effects of Transposition

Horizontal Gene Transfer

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