Previous edition: 2013.

Preface

Acknowledgements

Section I. Foundations of Phylogenomics

1. What is Phylogenomics?

2. The Biology and Sequencing of Genetic Information: DNA, RNA, and Proteins

3. Evolutionary Principles: Populations and Trees

Section II. Data

4. Data Storage-The Basics

5. Sequence Alignment and Searching Sequence Databases

6. Multiple Alignments

7. Genome Sequencing and Annotation

8. Genomics Databases: Genomes and Transcriptomes

9. Amplicon Databases: BoLD and Bacterial 16S rDNA Databases

Section III. Phylogenetic/Phylogenomic Analysis

10. Introduction to Tree Building

11. Distance and Clustering

12. Maximum Likelihood

13. Search Strategies and Robustness

14. Rate Heterogeneity, Long Branch Attraction, and Likelihood Models

15. Bayesian Approaches in Phylogenetics

16. Incongruence of Gene Trees

17. Phylogenetic Programs and Websites

Section IV. Population Genomics

18. Population Genetics and Genomes

19. Population Genomics Approaches

20. Detecting Natural Selection: The Basics

21. Refining the Approach to Natural Selection at the Molecular Level

Section V. Phylogenomics in Action

22. Constructing Phylogenomic Matrices

23. Phylogenomics and the Tree of Life

24. Comparative Genomics

25. Environmental DNA (eDNA)

26. Phylogenomic Approaches to Understanding Gene Function and Evolution

Index

Cover --
Half Title --
Title Page --
Copyright Page --
Dedication --
Table of Contents --
Detailed Contents --
Preface --
Acknowledgements --
Section I Foundations of Phylogenomics --
Chapter 1 What is Phylogenomics? --
Phylogenomics and Bioinformatics --
Bioinformatics Tools for Finding Patterns in Biological Experiments --
The rise of phylogenomics --
Sub-Branches of Phylogenomics --
The Phylogenomic Toolbox --
Basic Computational Tools in Phylogenomics --
Statistics Help Compare Genetic Sequences and Generate Phylogenetic Trees --
Parametric Statistics Are Derived from Distributions Nonparametric Statistical Analyses Are Useful in Many Situations --
Maximum Likelihood and Bayesian Analysis Are Standard Statistical Methods Used in Phylogenomics --
Key Attributes of Phylogenomicists --
Summary --
Recommendations for Students --
Discussion Questions --
Further Reading --
Chapter 2 The Biology and Sequencing of Genetic Information: DNA, RNA, and Proteins --
Nucleic Acids --
DNA molecules efficiently transmit information --
DNA is synthesized by specific pairing --
DNA can mutate and lead to descent with modification --
Polymerase chain reaction (PCR) is a milestone development Proteins --
Proteins are linear polymers of amino acids --
Proteins have multiple levels of structure --
Translation of DNA to amino acids is accomplished by the genetic code --
Reading frame in nucleic acid sequences --
The DNA Data Explosion --
Nucleic acid sequencing methods are increasingly powerful --
Next-generation sequencing allows for rapid analysis of genomes --
Other applications of next-generation sequencing --
Alternatives to Whole Genome Sequencing --
Single-nucleotide polymorphisms (SNPs) differ at one position in a designated DNA sequence --
Microarrays --
Genome reduction methods Analyzing Gene Expression --
RNA-Seq is a method for obtaining transcriptomic data --
Summary --
Recommendations for Students --
Discussion Questions --
Further Reading --
Chapter 3 Evolutionary Principles: Populations and Trees --
Darwin, Wallace, and Evolutionary Theory --
Four early contributions --
Darwin's ideas lacked a valid genetic mechanism --
The study of evolution can be divided into microevolution and macroevolution --
Microevolution --
Population genetics focuses on microevolution --
Advances in molecular techniques led to new thinking in evolutionary biology Codon changes and usage can provide insights into natural selection --
Microevolutionary studies often rely on computational modeling --
Macroevolution --
Macroevolution studies rely heavily on systematics and phylogenetics --
Relationships and systematics --
There are several approaches to tree building --
Tree thinking --
Phylogenetics can help establish homology --
Species --
The definition of species is heavily debated --
Defining species phylogenetically --
Updates on Darwinian Evolution --
Punctuated equilibrium suggests that not all evolution is gradual

Phylogenomics: A Primer, Second Edition is for advanced undergraduate and graduate biology students studying molecular biology, comparative biology, evolution, genomics, and biodiversity. This book explains the essential concepts underlying the storage and manipulation of genomics level data, construction of phylogenetic trees, population genetics, natural selection, the tree of life, DNA barcoding, and metagenomics. The inclusion of problem-solving exercises in each chapter provides students with a solid grasp of the important molecular and evolutionary questions facing modern biologists as well as the tools needed to answer them.