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 1: The Basics of Phylogenomics. 1. Why Phylogenomics Matters. 2. The Biology of Linear Molecules: DNA and Proteins. 3. Evolutionary Principles: Populations and Trees. Part 2: Phylogenomics in Practice. 4. Genome Sequencing and Annotation. 5. Databases. 6. Pairwise Alignment, Multiple Alignments and Orthology. 7. Phylogenetics. 8. Adopting Population Genetics to Genomics. 9. Genome Content Analysis. Part 3. Advanced Phylogenomics. 10. Advanced Population Genetics. 11. A Phylogenomic Perspective of Biological Diversity: Tree of Life, DNA Barcoding and Metagenomics. 12. Functional Phylogenomics.