4 Molecular Evolution
4.1
The Determination of Homology Between
Protein or DNA Sequences
4.2
The Mechanisms of Molecular Evolution
4.2.1 Nucleotide Substitution
4.2.2 Deletion, Insertion and Duplication of DNA
Sequences
4.2.3 Gene Fusion and Exon Shuffling
4.2.4 Transposition of DNA Sequences
4.2.5 The Evolution of Multi-Gene Families
4.2.6 Polyploidization
4.2.7 Gene Transfer Between Species and "Molecular
Lamarckism"
4.2.8 Adaptive and Innovative Protein Evolution
4.2.9 Molecular Mechanisms in the Evolution
of Complex Characters
4.3
Protein and Nucleic Acid Polymorphism
4.3.1 Definitions and Concepts
4.3.2 Methodological Problems in the Determination
of Protein Polymorphism
4.3.3 Dependence of Protein Polymorphism on Protein
Type
4.3.4 Differences in Protein Polymorphism Between
Different Animal Groups and Habitats
4.3.5 Dependence of Protein Polymorphism on the Size
and History of a Population
4.3.6 Quantitative Genetic Variability
4.3.7 DNA Polymorphism
4.4
The Causes of Genetic Polymorphism
4.4.1 Neutral Theories of Molecular Evolution
Ideas about the process and the laws of evolution
are mainly based upon the comparison of characters of living organisms. Whilst classical research
into evolution indirectly draws conclusions about
evolutionary changes in the genotype by the
observation of phenotypic differences, especially
morphological characters, the molecular
approach to evolution deals directly with the
genome through sequence comparisons of nucleic
acids and proteins. The amount of data now available at this level is enormous and increases continuously. DNA-sequence analysis, which has
been available for only a few years, has already
produced more information than the previous
three decades of protein sequencing [377]. These
days amino acid sequences are mostly determined
4.4.2 Selection Theories of Polymorphism
4.4.3 The Controversy Between Neutralism
and Selectionism
4.5
Methods and Problems in the Molecular
Approach to Evolutionary Relationships
4.5.1 The Evolutionary Distance Between Amino Acid
or Nucleotide Sequences
4.5.2 Determination of Evolutionary Distance from the
Amino Acid Composition of Proteins
4.5.3 Immunological Distance Between Proteins
4.5.4 Genetic Distance Given by Electrophoretic Data
4.5.5 Comparison of DNA Sequences
from the Thermostability of Heteroduplices
4.5.6 DNA Restriction Analysis
4.5.7 Construction of Phylogenetic Trees
from Molecular Data
4.6
The Rate of Molecular Evolution
4.6.1 The Rate of Protein Evolution
4.6.2 The Rate of Evolution of the Nucleic Acids
4.6.3 Is There a Molecular Clock?
4.7
Some Results of Molecular Research
into Evolutionary Relationships
4.7.1 Molecular Phylogenetic Trees
4.7.2 Species Systematics
4.7.3 Molecular Taxonomy Above the Species Level
4.7.4 Molecular Data and the Large-Scale Classification
of Organisms
4.8
Palaeobiochemistry
References
from the coding nucleotide sequences rather than
by direct analysis.
Molecular characters, such as nucleotide or
amino acid sequences, and their directly correlated molecular properties are particularly useful
for studies of evolution on several grounds: (1)
they are unambiguous and there are no gradual
transitions; (2) they are quantifiable and suitable
for genetic analysis; (3) they always relate to distinct genomic sites (loci); (4) they are easily identifiable even when they are not mutated; (5) they
are independent of internal and external conditions and are recognizable in heterozygotes,
where there is no dominance or epistatic interaction between the genes; (6) they have an extraordinary capacity for coding information, and each
4.1
The Determination of Homology Between
Protein or DNA Sequences
4.2
The Mechanisms of Molecular Evolution
4.2.1 Nucleotide Substitution
4.2.2 Deletion, Insertion and Duplication of DNA
Sequences
4.2.3 Gene Fusion and Exon Shuffling
4.2.4 Transposition of DNA Sequences
4.2.5 The Evolution of Multi-Gene Families
4.2.6 Polyploidization
4.2.7 Gene Transfer Between Species and "Molecular
Lamarckism"
4.2.8 Adaptive and Innovative Protein Evolution
4.2.9 Molecular Mechanisms in the Evolution
of Complex Characters
4.3
Protein and Nucleic Acid Polymorphism
4.3.1 Definitions and Concepts
4.3.2 Methodological Problems in the Determination
of Protein Polymorphism
4.3.3 Dependence of Protein Polymorphism on Protein
Type
4.3.4 Differences in Protein Polymorphism Between
Different Animal Groups and Habitats
4.3.5 Dependence of Protein Polymorphism on the Size
and History of a Population
4.3.6 Quantitative Genetic Variability
4.3.7 DNA Polymorphism
4.4
The Causes of Genetic Polymorphism
4.4.1 Neutral Theories of Molecular Evolution
Ideas about the process and the laws of evolution
are mainly based upon the comparison of characters of living organisms. Whilst classical research
into evolution indirectly draws conclusions about
evolutionary changes in the genotype by the
observation of phenotypic differences, especially
morphological characters, the molecular
approach to evolution deals directly with the
genome through sequence comparisons of nucleic
acids and proteins. The amount of data now available at this level is enormous and increases continuously. DNA-sequence analysis, which has
been available for only a few years, has already
produced more information than the previous
three decades of protein sequencing [377]. These
days amino acid sequences are mostly determined
4.4.2 Selection Theories of Polymorphism
4.4.3 The Controversy Between Neutralism
and Selectionism
4.5
Methods and Problems in the Molecular
Approach to Evolutionary Relationships
4.5.1 The Evolutionary Distance Between Amino Acid
or Nucleotide Sequences
4.5.2 Determination of Evolutionary Distance from the
Amino Acid Composition of Proteins
4.5.3 Immunological Distance Between Proteins
4.5.4 Genetic Distance Given by Electrophoretic Data
4.5.5 Comparison of DNA Sequences
from the Thermostability of Heteroduplices
4.5.6 DNA Restriction Analysis
4.5.7 Construction of Phylogenetic Trees
from Molecular Data
4.6
The Rate of Molecular Evolution
4.6.1 The Rate of Protein Evolution
4.6.2 The Rate of Evolution of the Nucleic Acids
4.6.3 Is There a Molecular Clock?
4.7
Some Results of Molecular Research
into Evolutionary Relationships
4.7.1 Molecular Phylogenetic Trees
4.7.2 Species Systematics
4.7.3 Molecular Taxonomy Above the Species Level
4.7.4 Molecular Data and the Large-Scale Classification
of Organisms
4.8
Palaeobiochemistry
References
from the coding nucleotide sequences rather than
by direct analysis.
Molecular characters, such as nucleotide or
amino acid sequences, and their directly correlated molecular properties are particularly useful
for studies of evolution on several grounds: (1)
they are unambiguous and there are no gradual
transitions; (2) they are quantifiable and suitable
for genetic analysis; (3) they always relate to distinct genomic sites (loci); (4) they are easily identifiable even when they are not mutated; (5) they
are independent of internal and external conditions and are recognizable in heterozygotes,
where there is no dominance or epistatic interaction between the genes; (6) they have an extraordinary capacity for coding information, and each