Phylogenomic Data Acquisition: Principles and Practice

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 What Is Phylogenomics? The Early View of Phylogenomics An Expanded View of Phylogenomics Anatomy of Gene Trees Gene Trees vs. Species Trees Phylogenomics and the Tree of Life Sequencing Workflows to Generate Phylogenomic Data Sanger Sequencing Workflow Next Generation Sequencing Workflow Is Sanger Sequencing Still Relevant in Phylogenomics? The Phylogenomics Laboratory PROPERTIES OF DNA SEQUENCE LOCI: PART I Genomic Background Genome Types and Sizes Composition of Eukaryotic Organellar Genomes Composition of Eukaryotic Nuclear Genomes Gene Numbers and Densities among Nuclear Genomes Intergenic DNA DNA Sequence Evolution Patterns and Processes of Base Substitutions Transition Bias Transition Bias and DNA Replication Errors Saturation of DNA Sites Among-Site Substitution Rate Variation Tandemly Repeated DNA Sequences Transposable Elements Processed Pseudogenes Mitochondrial Pseudogenes ("Numts") Numt Abundance in Eukaryotic Genomes Mechanisms of Primary Numt Integration Differences between Numts and Mitochondrial DNA PROPERTIES OF DNA SEQUENCE LOCI: PART II Six Assumptions about DNA Sequence Loci in Phylogenomic Studies Assumption 1: Loci Are Single-Copy in the Genome Assumption 2: Loci Are Selectively Neutral Does "Junk DNA" Exist? The Neutrality Assumption and the Indirect Effects of Natural Selection Assumption 3: Sampled Loci Have Independent Gene Trees How Many Independent Loci Exist in Eukaryotic Genomes? Criteria for Delimiting Loci with Independent Gene Trees Assumption 4: No Historical Recombination within Loci Intra-Locus Recombination and Gene Trees What Is the Optimal Locus Length? Assumption 5: Loci Evolved Like a Molecular Clock Assumption 6: Loci Are Free of Ascertainment Bias DNA Sequence Loci: Terminology and Types On Genes, Alleles, and Related Terms Commonly Used DNA Sequence Loci in Phylogenomic Studies Mitochondrial DNA Loci Nuclear DNA Loci DNA EXTRACTION DNA Extraction Methodology Summary of the DNA Extraction Process A Note about DNA Storage Buffers Extracting DNA from Plants, Fungi, and Invertebrates Extracting DNA from Formalin-fixed Museum Specimens Evaluating the Results of DNA Extractions Agarose Gel Electrophoresis Troubleshooting UV Spectrophotometric Evaluation of DNA Samples UV Spectrophotometry to Determine Concentrations of Nucleic Acid Samples UV Spectrophotometry to Determine the Purity of DNA Samples Fluorometric Quantitation of DNA Samples The High Throughput Workflow High Throughput DNA Extractions Extracting DNA from 96 Tissue Samples High Throughput Agarose Gel Electrophoresis High Throughput UV Spectrophotometry Preparation of Diluted DNA Templates for High Throughput PCR PCR THEORY AND PRACTICE Historical Overview DNA Polymerization in Living Cells vs. PCR Brief Review of DNA Polymerization in Living Cells How the Polymerase Chain Reaction Works PCR Procedures Preparation of PCR Reagents and Reaction Setup PCR Reagents Importance of Making Reagent Aliquots Setting up PCR Reactions Thermocycling Checking PCR Results Using Agarose Gel Electrophoresis PCR Troubleshooting Reducing PCR Contamination Risk High Throughput PCR Setting up PCR Reactions in a 96-sample Microplate Format Other PCR Methods Hot Start PCR Long PCR RT-PCR SANGER SEQUENCING Principles of Sanger Sequencing The Sanger Sequencing Concept Modern Sanger Sequencing Cycle Sequencing Reaction Gel Electrophoresis of Extension Products Sequence Data Quality Sanger Sequencing Procedures Purification of PCR Products Exo-SAP Treatment of PCR Products Spin Column and Vacuum Manifold Kits for PCR Product Purification 20% PEG 8000 Precipitation of PCR Products Solid-Phase Reversible Immobilization (SPRI) Beads Gel Purification of PCR Products Which PCR Product Purification Method Is Best? Setting up Cycle Sequencing Reactions Purification of Extension Products Sequencing in a Capillary Sequencer: Do-it-Yourself or Outsource? High Throughput Sanger Sequencing Sequencing 96 Samples on Microplates Adding Sequencing Primer "Tails" to PCR Primers How an M13-tailed Primer Functions in PCR Cycle Sequencing and M13 Primer Tails On the Importance of Matching Sequencing Primers Benefits of Using M13-Tailed Primers Haplotype Determination from Sanger Sequence Data PCR Amplification and Sanger Sequencing of Diploid or Polyploid Loci Multiple Heterozygous SNP Sites and Haplotype Sequences Methods for Obtaining Nuclear Haplotype Sequences from Sanger Sequence Data Physical Isolation of PCR Haplotypes Prior to Sequencing Statistical Inference of Haplotypes from Sanger Sequence Data ILLUMINA SEQUENCING How Illumina Sequencing Works Construction of Indexed Sequencing Libraries Generation of Clusters on the Flow Cell Sequencing of Clusters Methods for Obtaining Multiplexed Hybrid Selection Libraries Library Preparation Approaches Traditional Illumina Library Approach Meyer and Kircher Library Approach Rohland and Reich Library Approach Nextera Library Approach In-Solution Hybrid Selection Indexing, Pooling, and Hybrid Selection Efficiency Revisited Cost-effective Methods for Obtaining Multiplexed Targeted-Loci Libraries Sequence Capture Using PCR-generated Probes (SCPP) Parallel Tagged Amplicon Sequencing (PTS) DEVELOPING DNA SEQUENCE LOCI Primer Design Theory Rules of Primer Design Final Comments about Primer Design Rules Testing New Primers in the Lab Primer and Probe Design Approaches Single Template Approaches for Developing PCR-based Loci Single Template Methods Using Genomic Cloning Methods Single Template Methods Using Available Genomics Resources Single Template Methods Using NGS Partial Genome Data Single Template Methods Using Whole Genome Sequences Multiple Homologous Template Approaches for Designing PCR-based and Anchor Loci Designing Universal Primers by Comparative Sequence Analysis Multiple Homologous Template Approaches Using Whole Genome Sequences Designing Anchor Loci Probes Using Whole Genome Sequences FUTURE OF PHYLOGENOMIC DATA ACQUISITION The Impending Flood of Genomes In Silico Acquisition of Phylogenomic Datasets

About the Author :
W. Bryan Jennings is professor and coordinator for the Molecular Laboratory of Biodiversity Research at Universidade Federal do Rio de Janeiro.

Review :
"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