Phylogenomics

Rob DeSalle is 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 bioinformatic 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.

Preface. Acknowledgements. Foundations of Phylogenomics. What is Phylogenomics?. The Biology and Sequencing of Genetic Information: DNA, RNA, and Proteins. Evolutionary Principles: Populations and Trees. Data. Data Storage—The Basics. Sequence Alignment and Searching Sequence. Databases. Multiple Alignments. Genome Sequencing and Annotation. Genomics Databases: Genomes and Transcriptomes. Amplicon Databases: BoLD and Bacterial 16S rDNA Databases. Phylogenetic/Phylogenomic Analysis. Introduction to Tree Building. Distance and Clustering. Maximum Likelihood. Search Strategies and Robustness. Rate Heterogeneity, Long Branch Attraction, and Likelihood Models. Bayesian Approaches in Phylogenetics. Incongruence of Gene Trees. Phylogenetic Programs and Websites. Population Genomics. Population Genetics and Genomes. Population Genomics Approaches. Detecting Natural Selection: The Basics. Refining the Approach to Natural Selection at the Molecular Level. Phylogenomics in Action. Constructing Phylogenomic Matrices. Phylogenomics and the Tree of Life. Comparative Genomics. Environmental DNA (eDNA). Phylogenomic Approaches to Understanding Gene Function and Evolution. Index.