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

Rob DeSalle is a curator at the Sackler Institute of Comparative Genomics in the Division of Invertebrate Zoology at the American Museum of Natural History. DeSalle works in molecular systematics, microbial evolution, and genomics. His current research concerns the development of bioinformatics tools to handle large-scale genomics problems using phylogenetic systematic approaches. Dr DeSalle has worked closely with colleagues from Cold Spring Harbor Labs, New York University, and the New York Botanical Garden on seed plant genomics and development of tools to establish gene family membership on a genome-wide scale. His group also focuses on microbial genomics, taxonomy, and systematics. In particular, they approach tree-of-life questions concerning microbial life using whole genome information.

Jeffrey Rosenfeld is Assistant Professor for Pathology and Laboratory Medicine and the Manager of the Biomedical Informatics Shared Resource at the Rutgers Cancer Institute. His research focuses on the use of new genomics technologies to investigate previously unsolvable problems. He is currently working with long-read and single-cell sequencing. Dr Rosenfeld also has an appointment as a Research Associate at the American Museum of Natural History where he works on whole-genome phylogenetics. With collaborators at the Museum, he has sequenced and assembled the genomes of non-model insects.

Michael Tessler is Adjunct Faculty in Ecology at Sterling College. He received his PhD from the Richard Gilder Graduate School, American Museum of Natural History. His research explores the evolution and ecology of overlooked organisms and includes phylogenetic research on terrestrial leeches, combining his collections from China and Cambodia with AMNH’s legacy collections to produce a phylogenetic revision of all terrestrial leech groups. His dissertation focused on the evolution of leech anticoagulants and on how leeches process difficult to digest blood such as urea-packed shark blood, and the ways anticoagulants evolved in leech lineages that no longer drink blood and instead eat invertebrates.