Phylogenomics
A Primer

Phylogenomics: A Primer is for advanced undergraduate and graduate biology students studying molecular biology, comparative biology, evolution, genomics, and biodiversity. It
explores the origins of organic life on the planet, examines the use of scientific databases to understand the function of proteins within organisms, and provides insight into the interpretation of linear sequence information in the context of organismal change. 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. Online exercises are also available to assist students in working with the programs and databases used to analyze phylogenomic data.

1. Why Phylogenomics Matters
2. The Biology of Linear Molecules: DNA and Proteins
3. Evolutionary Principles: Populations and Trees
4. Databases
5. Homology and Pairwise Alignment
6. Multiple Alignments and Constructing Phylogenomic Matrices
7. Genome Sequencing and Annotation
8. Tree Building
9. Robustness and Rate Heterogeneity in Phylogenomics
10. A Beginner's Guide to Bayesian Approaches in Evolution 11. Incongruence
12. Adapting Population Genetics to Genomics
13. Detecting Natural Selection in Genomes – Part 1
14. Detecting Natural Selection in Genomes – Part 2
15. Advanced Population Genetics Topics
16. Genome Content Analysis
17. A Phylogenomic Perspective of Biological Diversity: Tree of Life, DNA Barcoding and Metagenomics
18. Microarrays in Evolutionary Studies and Functional Phylogenomics