Fundamentals of Molecular Evolution,9780878932665

Fundamentals of Molecular Evolution

by ;
Edition: 2nd
ISBN13: 9780878932665
ISBN10: 0878932666
Format: Paperback
Pub. Date: 2000-01-15
Publisher(s): Sinauer Associates is an imprint of Oxford University Press
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Summary

Tel Aviv Univ., Israel. Introductory textbook for beginners in molecular evolution. Describes the dynamics of evolutionary change at the molecular level, the driving forces behind this process, and the effects of the various molecular mechanisms on the long-term evolution of genomes, genes, and their products. Previous edition: c1991. Softcover.

Author Biography


Dan Graur is John and Rebecca Moores Professor in the Department of Biology and Biochemistry at the University of Houston and Professor Emeritus of Zoology at Tel Aviv University, Israel.

Wen-Hsiung Li is James D. Watson Professor Emeritus in the Department of Ecology and Evolution at the University of Chicago.

Table of Contents

Preface xiii
Introduction 1(4)
Genes, Genetic Codes, and Mutation
5(34)
Nucleotide Sequences
5(3)
Genomes and DNA Replication
8(1)
Genes and Gene Structure
9(6)
Protein-coding genes
9(3)
RNA-specifying genes
12(1)
Posttranscriptional modifications of RNA
13(1)
Untranscribed genes
13(1)
Pseudogenes
14(1)
Amino Acids
15(5)
Proteins
20(2)
Translation and Genetic Codes
22(3)
Mutation
25(13)
Substitution mutations
26(3)
Recombination
29(3)
Deletions and insertions
32(3)
Inversions
35(1)
Mutation rates
35(2)
Spatial distribution of mutations
37(1)
Patterns of mutation
38(1)
Are mutations random?
38(1)
Further Readings
38(1)
Dynamics of Genes in Populations
39(28)
Changes in Allele Frequencies
40(1)
Natural Selection
41(6)
Codominance
43(1)
Dominance
44(1)
Overdominance and under-dominance
45(2)
Random Genetic Drift
47(5)
Effective Population Size
52(1)
Gene Substitution
53(4)
Fixation probability
54(1)
Fixation time
55(2)
Rate of gene substitution
57(1)
Genetic Polymorphism
57(2)
Gene diversity
57(1)
Nucleotide diversity
58(1)
The Driving Forces in Evolution
59(6)
The neo-Darwinian theory and the neutral mutation hypothesis
61(2)
Testing the neutral mutation hypothesis
63(2)
Further Readings
65(2)
Evolutionary Change in Nucleotide Sequences
67(32)
Nucleotide Substitution in a DNA Sequence
67(7)
Jukes and Cantor's one-parameter model
68(3)
Kimura's two-parameter model
71(3)
Number of Nucleotide Substitutions Between Two DNA Sequences
74(12)
Number of substitutions between two noncoding sequences
75(2)
Substitution schemes with more than two parameters
77(2)
Violation of assumptions
79(1)
Number of substitutions between two protein-coding genes
79(6)
Indirect estimations of the number of nucleotide substitutions
85(1)
Amino Acid Replacements between Two Proteins
86(1)
Alignment of Nucleotide and Amino Acid Sequences
86(12)
Manual alignment by visual inspection
87(1)
The dot matrix method
87(3)
Distance and similarity methods
90(4)
Alignment algorithms
94(3)
Multiple alignments
97(1)
Further Readings
98(1)
Rates and Patterns of Nucleotide Substitution
99(66)
Rates of Nucleotide Substitution
100(8)
Coding regions
101(4)
Noncoding regions
105(2)
Similarity profiles
107(1)
Causes of Variation in Substitution Rates
108(11)
Functional constraints
108(2)
Synonymous versus nonsynonymous rates
110(1)
Variation among different gene regions
111(2)
Variation among genes
113(2)
Acceleration of nucleotide substitution rates following partial loss of function
115(1)
Estimating the intensity of purifying selection
116(1)
Mutational input: Male-driven evolution
117(2)
Positive Selection
119(4)
Detecting positive selection
119(2)
Parallelism and convergence
121(2)
Prevalence of positive selection
123(1)
Patterns of Substitution and Replacement
123(9)
Pattern of spontaneous mutation
124(3)
Pattern of substitution in human mitochondrial DNA
127(1)
Patterns of amino acid replacement
128(2)
What protein properties are conserved in evolution?
130(2)
Nonrandom Usage of Synonymous Codons
132(7)
Measures of codon-usage bias
132(1)
Universal and species-specific patterns of codon usage
133(1)
Codon usage in unicellular organisms
134(3)
Codon usage in multicellular organisms
137(2)
Codon usage and population size
139(1)
Molecular Clocks
139(3)
Relative Rate Tests
142(4)
Margoliash, Sarich, and Wilson's test
142(2)
Tajima's 1D method
144(1)
Tests involving comparisons of duplicate genes
145(1)
Local Clocks
146(4)
Nearly equal rates in mice and rats
146(1)
Lower rates in humans than in African apes and monkeys
147(1)
Higher rates in rodents than in primates
148(2)
Evaluation of the Molecular Clock Hypothesis
150(5)
Causes of variation in substitution rates among evolutionary lineages
151(2)
Are living fossils molecular fossils too?
153(1)
``Primitive'' versus ``advanced'': A question of rates
153(1)
Phyletic gradualism versus punctuated equilibria at the molecular level
154(1)
Rates of Substitution in Organelle DNA
155(5)
Mammalian mitochondrial genes
157(1)
Plant nuclear, mitochondrial, and chloroplast DNAs
157(3)
Substitution and rearrangement rates
160(1)
Rates of Substitution in RNA Viruses
160(3)
Estimation models
161(1)
Human immunodeficiency viruses
162(1)
Further Readings
163(2)
Molecular Phylogenetics
165(84)
Impacts of Molecular Data on Phylogenetic Studies
165(2)
Advantages of Molecular Data in Phylogenetic Studies
167(1)
Terminology of Phylogenetic Trees
167(10)
Rooted and unrooted trees
169(1)
Scaled and unscaled trees
169(1)
The Newick format
170(1)
Number of possible phylogenetic trees
170(3)
True and inferred trees
173(1)
Gene trees and species trees
174(2)
Taxa and clades
176(1)
Types of Data
177(4)
Character data
177(1)
Assumptions about character evolution
178(2)
Polarity and taxonomic distribution of character states
180(1)
Distance data
180(1)
Methods of Tree Reconstruction
181(1)
Distance Matrix Methods
182(7)
Unweighted pair-group method with arithmetic means (UPGMA)
183(2)
Transformed distance method
185(1)
Sattath and Tversky's neighbors-relations method
186(3)
Saitou and Nei's neighbor-joining method
189(1)
Maximum Parsimony Methods
189(9)
Weighted and unweighted parsimony
193(1)
Searching for the maximum parsimony tree
194(4)
Maximum Likelihood Methods
198(2)
Rooting Unrooted Trees
200(2)
Estimating Branch Lengths
202(2)
Estimating Species Divergence Times
204(2)
Topological Comparisons
206(2)
Penny and Hendy's topological distance
206(1)
Consensus trees
206(2)
Assessing Tree Reliability
208(4)
The bootstrap
209(2)
Tests for two competing trees
211(1)
Problems Associated with Phylogenetic Reconstruction
212(5)
Strengths and weaknesses of different methods
214(2)
Minimizing error in phylogenetic analysis
216(1)
Molecular Phylogenetic Examples
217(13)
Phylogeny of humans and apes
217(8)
Cetartiodactyla and SINE phylogeny
225(3)
The origin of angiosperms
228(2)
Molecular Phylogenetic Archeology
230(7)
Phylogeny of the marsupial wolf
232(1)
Is the quagga extinct?
232(2)
The dusky seaside sparrow
234(3)
The Universal Phylogeny
237(10)
The first divergence events
238(5)
The cenancestor
243(2)
Endosymbiotic origin of mitochondria and chloroplasts
245(2)
Further Readings
247(2)
Gene Duplication, Exon Shuffling, and Concerted Evolution
249(74)
Types of Gene Duplication
250(1)
Domains and Exons
250(5)
Domain Duplication and Gene Elongation
255(7)
The ovomucoid gene
258(1)
Enhancement of function in the α2 allele of haptoglobin
258(2)
Origin of an antifreeze glycoprotein gene
260(2)
Prevalence of domain duplication
262(1)
Formation of Gene Families and the Acquisition of New Functions
262(9)
RNA-specifying genes
265(3)
Isozymes
268(1)
Opsins
269(2)
Dating Gene Duplications
271(2)
Gene Loss
273(5)
Unprocessed pseudogenes
274(1)
Unitary pseudogenes
275(1)
Nonfunctionalization time
276(2)
The Globin Superfamily
278(3)
Prevalence of Gene Duplication, Gene Loss, and Functional Divergence
281(2)
Exon Shuffling
283(8)
Mosaic proteins
283(3)
Phase limitations on exon shuffling
286(3)
Exonization and pseudoexonization
289(1)
Different strategies of multidomain gene assembly
290(1)
The ``Introns-Early'' versus ``Introns-Late'' Hypotheses
291(3)
Intron sliding
292(2)
The relative fraction of ``early'' and ``late'' introns
294(1)
Alternative Pathways for Producing New Functions
294(9)
Overlapping genes
294(2)
Alternative splicing
296(3)
Intron-encoded proteins and nested genes
299(1)
Functional convergence
299(2)
RNA editing
301(1)
Gene sharing
302(1)
Molecular Tinkering
303(1)
Concerted Evolution
304(4)
Mechanisms of Concerted Evolution
308(5)
Gene conversion
308(1)
Unequal crossing over
309(3)
Relative roles of gene conversion and unequal crossing over
312(1)
Detection and Examples of Concerted Evolution
313(4)
The Aγ and Gγ-globin genes in the great apes
314(1)
The concerted evolution of genes and pseudogenes
315(2)
Factors affecting the rate of concerted evolution
317(3)
Number of repeats
318(1)
Arrangement of repeats
318(1)
Structure of the repeat unit
318(1)
Functional requirement
319(1)
Populational processes
320(1)
Evolutionary Implications of Concerted Evolution
320(2)
Spread of advantageous mutations
320(1)
Retardation of paralogous gene divergence
321(1)
Generation of genic variation
321(1)
Methodological Pitfalls due to Concerted Evolution
322(1)
Further Readings
322(1)
Evoution by Transposition
323(44)
Transposition and Retroposition
323(2)
Transposable Elements
325(4)
Insertion Sequences
326(1)
Transposons
327(1)
Taxonomic, developmental, and target specificity of transposition
328(1)
Autonomy of transposition
329(1)
Retroelements
329(7)
Retroviruses
330(1)
Retroposons and retrotransposons
330(3)
Retrons
333(1)
Pararetroviruses
333(1)
Evolutionary origin of retroelements
334(2)
Retrosequences
336(7)
Retrogenes
336(2)
Semiprocessed retrogenes
338(1)
Retropseudogenes
338(3)
Sequence evolution of retropseudo-genes
341(2)
LINEs and SINEs
343(6)
SINEs derived from 7SL RNA
344(2)
SINEs derived from tRNAs
346(1)
Where there's a Sine, there's a Line
347(2)
DNA-mediated transposable elements and transposable fossils
349(1)
Rate of Sine evolution
349(1)
Genetic and Evolutionary Effects of Transposition
349(10)
Hybrid dysgenesis
354(3)
Transposition and speciation
357(1)
Evolutionary dynamics of transposable element copy number
358(1)
Horizontal Gene Transfer
359(7)
Horizontal transfer of virogenes from baboons to cats
361(2)
Horizontal transfer of P elements between Drosophila species
363(2)
Promiscuous DNA
365(1)
Further Readings
366(1)
Genome Evolution
367(62)
C Values
368(1)
The Evolution of Genome Size in Prokaryotes
368(3)
The Minimal Genome
371(3)
The analytical approach
371(2)
The experimental approach
373(1)
Genome Miniaturization
374(1)
Genome size reduction following endosymbiosis
374(1)
Genome size reduction in parasites
375(1)
Genome Size in Eukaryotes and the C Value Paradox
375(5)
Mechanisms for Global Increases in Genome Size
380(4)
Polyploidization
380(2)
Polysomy
382(1)
The yeast genome
382(2)
Polyploidy of the vertebrate genome
384(1)
Maintenance of Nongenic DNA
384(5)
The hypotheses
386(1)
The evidence
387(1)
Why do similar species have different genome sizes?
388(1)
The Repetitive Structure of the Eukaryotic Genome
389(6)
Localized repeated sequences
390(2)
Dispersed repeated sequences
392(2)
Repetitive sequences as a cause of variation in genome size
394(1)
Mechanisms for Regional Increases in Genome Size
395(2)
Gene Distribution
397(5)
How many genes are there, where are they, and do we need them?
397(3)
Gene number evolution
400(2)
Chromosomal Evolution
402(2)
Chromosomes, plasmids, and episomes
402(1)
Evolution of chromosome number in prokaryotes
402(1)
Chromosome number variation in eukaryotes
403(1)
Mechanisms for Changes in Gene Order and Gene Distribution among Chromosomes
404(8)
Counting gene order rearrangement events
406(2)
Gene order rearrangements in bacteria
408(2)
Gene order rearrangements in eukaryotes
410(1)
Gene order as a phylogenetic character
411(1)
GC Content in Bacteria
412(3)
Chirochores
415(2)
Compositional Organization of the Vertebrate Genome
417(8)
The distribution of genes and other genetic elements among isochores
420(2)
Origin of isochores
422(3)
Emergence of Nonuniversal Genetic Codes
425(2)
Further Readings
427(2)
Appendix I Spatial and Temporal Frameworks of the Evolutionary Process 429(8)
Appendix II Basics of Probability 437(4)
Literature Cited 441(26)
Index 467(12)
Taxonomic Index 479

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