ABSTRACT

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.

part Section I|46 pages

Foundations of Phylogenomics

chapter Chapter 1|12 pages

What is Phylogenomics?

chapter Chapter 3|14 pages

Evolutionary Principles: Populations and Trees

part Section II|84 pages

Data

chapter Chapter 4|11 pages

Data Storage—The Basics

chapter Chapter 5|18 pages

Sequence Alignment and Searching Sequence Databases

chapter Chapter 6|10 pages

Multiple Alignments

chapter Chapter 7|9 pages

Genome Sequencing and Annotation

chapter Chapter 8|14 pages

Genomics Databases: Genomes and Transcriptomes

part Section III|92 pages

Phylogenetic/Phylogenomic Analysis

chapter Chapter 10|14 pages

Introduction to Tree Building

chapter Chapter 11|10 pages

Distance and Clustering

chapter Chapter 12|9 pages

Maximum Likelihood

chapter Chapter 13|10 pages

Search Strategies and Robustness

chapter Chapter 15|12 pages

Bayesian Approaches in Phylogenetics

chapter Chapter 16|13 pages

Incongruence of Gene Trees

chapter Chapter 17|10 pages

Phylogenetic Programs and Websites

part Section IV|70 pages

Population Genomics

chapter Chapter 18|20 pages

Population Genetics and Genomes

chapter Chapter 19|16 pages

Population Genomics Approaches

chapter Chapter 20|14 pages

Detecting Natural Selection: The Basics

part Section V|80 pages

Phylogenomics in Action

chapter Chapter 22|13 pages

Constructing Phylogenomic Matrices

chapter Chapter 23|19 pages

Phylogenomics and the Tree of Life

chapter Chapter 24|14 pages

Comparative Genomics

chapter Chapter 25|11 pages

Environmental DNA (eDNA)