What Is Molecular Phylogenetics?

Molecular evolution and phylogeny. This book starts with research methods and techniques. It explores hot issues in molecular evolutionary biology, and systematically introduces statistical methods for the study of protein and DNA evolution.

Molecular evolution and phylogeny

Category : Education / Technology

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Chapter 1 The Molecular Basis of Evolution.

1.1 The evolutionary tree of life

1.2 Evolutionary mechanism

1.3 Structure and function of genes

1.4 DNA sequence mutations

1.5 Codon usage frequency

Chapter 2 Evolution of amino acid sequences

2.1 Amino acid differences and ratios of different amino acids

2.2 Poisson correction (PC) and plant distance

2.3 Variance and covariance of the self-expanding method

2.4 Amino acid substitution matrix

2.5 Mutation rate and replacement rate

Chapter 3 Evolution of DNA Sequences

3.1 Nucleotide differences between two sequences

3.2 Estimation of the number of nucleotide substitutions

3.3 Factory distance

3.4 Numerical estimation of evolutionary distance

3.5 Paraposition of nucleotide sequences

3.6 Treatment of sequence interval in evolutionary distance estimation

Chapter 4 Synonymous and Nonsynonymous Nucleotide Substitutions

.4.1 Evolutionary Path Approach

4.2 Method based on Kimura two-parameter model

4.3 Nucleotide substitution at three different positions of the codon

4.4 Likelihood method for codon substitution model

Chapter 5 Phylogenetic Tree

5.1 Types of phylogenetic trees

5.2 Topological differences

5.3 Tree-building methods

Chapter 6 Phylogenetic Inference: Distance Method

6.1 UPGMA

6.2 Least squares (LS) method

6.3 Minimal Evolution (ME) method

6.4 Adjacent (NJ) method

6.5 Distance measures for phylogenetic reconstruction

Chapter 7 Phylogenetic Inference: Maximum Parsimony

7.1 Finding the largest minimal (MP) phylogenetic tree

7.2 MP tree search strategy

7.3 Consistent Tree

7.4 Branch length estimation

7.5 Likou right parsimony

7.6 MP method for protein data

7.7 Shared genetic characteristics

Chapter 8 Phylogenetic Inference: Maximum Likelihood ..

8.1 Calculation process of ML method

8.2 Nucleotide substitution model

8.3 Protein Likelihood

0.4 Theoretical basis of ML method

8.5 Parameter estimation for a given topology

Chapter 9 Precision and Statistical Tests of Phylogenetic Trees

9.1 Optimal principle and topology error

9.2 Internal branch inspection

9.3 Self-examination inspection

9.4 Test for differences in topological structure

9.5 Pros and cons of different tree methods

Chapter 10 Molecular Clocks and Linear Trees

10.1 The molecular clock hypothesis

10.2 Relative rate test

10.3 Phylogenetic test

10.4 Linear Construction

Chapter 11 Ancestor Nucleotides and Amino Acid Sequences

11.1 Ancestry Sequence Inference: Parsimony

11.2 Ancestry Sequence Inference: Bayesian Method

11.3 Synonymous and non-synonymous substitutions in ancestral branches

11.4 Tendency and Parallel Evolution

Chapter 12 Genetic Polymorphism and Evolution

12.1 Evolutionary Significance of Genetic Polymorphisms

12.2 Analysis of allele frequency data

12.3 Genetic variation in subdivided populations

12.4 Genetic variation at multiple loci

12.5 DNA Polymorphism

12.6 Statistical tests to detect natural selection

Chapter 13 Building Population Trees with Genetic Markers

13.1 Genetic distance of allele frequency data

13.2 DNA sequence analysis of restriction enzymes

13.3 RAPD Data Analysis

Chapter XIV Outlook

14.1 Statistical methods

14.2 The Genome Project

14.3 Molecular Biology and Evolution

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