Phylogenomics (2^nd Ed.) A Primer

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.

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.

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 Assistant Professor of Pathology and Laboratory Medicine at the Robert Wood Johnson Medical School of Rutgers, The State University of New Jersey. He has extensive experience in the analysis of next-generation sequencing data. His doctoral research resulted in one of the earliest papers on ChIP-seq utilizing Illumina sequencing. He also performed an extensive analysis of the function of the H3K9me3 histone modification. After completing his doctorate, Dr. Rosenfeld began working as a research scientist in the laboratory of Dr. Todd Lencz at Zucker Hillside Hospital. He was in charge of all nextgeneration sequencing analysis at the hospital including family-based exome sequencing and RNA-seq of cerebrospinal fluid (CSF). He has studied the occurrence of multiple nucleotide polymorphisms (MNP) in the human genome and is supervising the study of non-traditional human variants such as MNPs and polymorphic SNPs for the 1000 Genomes Project. Recently, Dr. Rosenfeld joined the High Performance and Research Computing group at UMDNJ and he is playing a key role in assistin