This book describes the dynamics of evolutionary change at the molecular level, the driving forces behind the
evolutionary process, the effects of the various molecular mechanisms on the structure of genes, proteins, and
genomes, the methodology involved in dealing with molecular data from an evolutionary perspective, and the logic
of molecular hypothesis testing. The Second Edition incorporates newly acquired evolutionary insight from genome
projects involving bacteria, plants, and animals, as well as analytical tools that have been developed and perfected
in the last decade, and has been brought up to date in line with the many advances in genomics, protein engineering,
computational biology, and bioinformatics.
The authors explain evolutionary phenomena at the molecular level in a way that can be understood without much
prerequisite knowledge of molecular biology, evolution, or mathematics. Both mathematical and intuitive explanations
are provided, and examples that support and clarify the many theoretical arguments and methodological discussions
are included.
Table of Contents
Introduction
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.
Further Readings
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.
Further Readings
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.
Further Readings
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.
Molecular Clocks.
Relative-Rate Tests.
Local Clocks.
Evaluation of the Molecular Clock Hypothesis.
Rates of Substitution in Organelle DNA.
RNA Viruses
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
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.
Topological Comparisons.
Assessing Tree Reliability.
Problems Associated with Phylogenetic Reconstructions.
Molecular Phylogenetic Examples.
Molecular Phylogenetic Archeology.
The Universal Phylogeny.
Further Readings
Chapter 6: Gene Duplication, Exon Shuffling, 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.
Further Readings
Chapter 7: Evolution by Transposition Transposition and Retroposition
Transposable Elements.
Retroelements.
Retrosequences.
LINEs and SINEs.
Genetic and Evolutionary Effects of Transposition.
Horizontal Gene Transfer.
Further Readings
Chapter 8: Genome Evolution 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.
Further Readings
Appendix I. Timetables of Evolution
Appendix II. Basics of Probability
