Phylogenomics is a rapidly growing field of study concerned with using genome-wide data—usually in the form of DNA sequence loci—to infer the evolution of genes, genomes, and the Tree of Life. Accordingly, this discipline connects many areas in biology including molecular and genomic evolution, systems biology, molecular systematics, phylogeography, conservation genetics, DNA barcoding, and others. With the advent of Next Generation Sequencing in addition to advances in computer hardware and software over the past decade, researchers can now generate unparalleled phylogenomic datasets that are helping to illuminate many areas in the life sciences. This book is an introduction to the principles and practices of gathering these data. Phylogenomic Data Acquisition: Principles and Practice is intended for a broad cross-section of biologists and anyone else interested in learning how to obtain phylogenomic data using the latest methods.
Table of Contents
Introduction. PHYLOGENOMIC DATA CHARACTERISTICS AND ACQUISITION. Genomes, Molecular Evolution, and Molecular Markers. DNA Extraction. PCR Theory and Methodology. Loci Acquisition. Sanger and Next Generation DNA Sequencing. UNDERSTANDING AND MAKING GENE TREES: THE UNITS OF PHYLOGENOMIC ANALYSIS. Gene Tree Inference. Advanced Gene Tree Inference. PHYLOGENOMIC ANALYSIS: USING GENE TREES TO ANSWER EVOLUTIONARY QUESTIONS. Gene and Genome Evolution. Primer of Coalescent Theory. Species Tree Inference. Phylogeography I. Phylogeography II. DNA Barcoding and Forensics. Future Prospects. References. Glossary. Answers to End-of-chapter Questions.
W. Bryan Jennings is professor and coordinator for the Molecular Laboratory of Biodiversity Research at Universidade Federal do Rio de Janeiro.
"There is definitely a need for this book written in the language of the phylogeneticist. The general organization of the book is good. This book addresses a broad range of topics in a way that makes them comprehensible to people who are not experts in bioinformatics and will be extremely influential. Jennings has been in on the ground floor of the multilocus coalescent revolution in phylogenetics."
Jim McGuire, University of California Berkeley
"Genome sequencing technologies and data collection techniques are changing rapidly, and this book is a great resource for getting up to speed in this exciting field. Jennings outlines the essential data collection strategies that all students entering the field of molecular systematics need to know. "
Adam Leaché, University of Washington, Seattle
"This new book by evolutionary biologist Bryan Jennings brings together a wealth of useful information allowing researchers to move from start to finish in the rapidly changing field of phylogenomics. It details step-by-step protocols and provides masterful summaries of best practices for the modern phylogeneticist. Graduate students, postdoctoral fellows and principal investigators will find this book extremely useful. Jennings cuts through the jungle of sometimes conflicting information and provides cogent reviews of important topics and guidelines for avoiding common pitfalls."
Scott Edwards, Harvard University
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