Phylogenomics: A Primer, 2nd Edition (Paperback) book cover


A Primer, 2nd Edition

By Rob DeSalle, Jeffrey Rosenfeld, Michael Tessler

CRC Press

448 pages | 165 B/W Illus.

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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.

Table of Contents

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.

About the Authors

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 assisting researchers across the university in processing their next-generation sequencing data. Dr. Rosenfeld also has an appointment as a Research Associate at the American Museum of Natural History where he works on whole-genome phylogenetics.

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.

Subject Categories

BISAC Subject Codes/Headings:
COMPUTERS / Computer Science
SCIENCE / Biotechnology
SCIENCE / Life Sciences / Cytology
SCIENCE / Life Sciences / Evolution
SCIENCE / Life Sciences / Genetics & Genomics
SCIENCE / Life Sciences / Biology / Molecular Biology
SCIENCE / Life Sciences / General