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E-raamat: Phylogenomic Data Acquisition: Principles and Practice

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(Universidade Federal do Rio de Janeiro, Brazil)
  • Formaat: 244 pages
  • Ilmumisaeg: 12-Dec-2016
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781482235357
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Phylogenomic Data Acquisition: Principles and PracticeSuurem pilt
  • Formaat: 244 pages
  • Ilmumisaeg: 12-Dec-2016
  • Kirjastus: CRC Press Inc
  • Keel: eng
  • ISBN-13: 9781482235357
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Phylogenomics is a rapidly growing field of study concerned with using genome-wide datausually in the form of DNA sequence locito 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.

Arvustused

"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

Preface ix
Author xi
1 Introduction
1(12)
1.1 What Is Phylogenomics?
1(1)
1.1.1 The Early View of Phylogenomics
1(1)
1.1.2 An Expanded View of Phylogenomics
2(1)
1.2 Anatomy of Gene Trees
2(1)
1.3 Gene Trees versus Species Trees
3(1)
1.4 Phylogenomics and the Tree of Life
4(2)
1.5 Sequencing Workflows to Generate Phylogenomic Data
6(2)
1.5.1 Sanger Sequencing Workflow
6(1)
1.5.2 NGS Workflow
6(1)
1.5.3 Is Sanger Sequencing Still Relevant in Phylogenomics?
7(1)
1.6 The Phylogenomics Laboratory
8(5)
References
10(3)
2 Properties Of Dna Sequence Loci: Part I
13(24)
2.1 Genomic Background
13(8)
2.1.1 Genome Types and Sizes
13(2)
2.1.2 Composition of Eukaryotic Organellar Genomes
15(3)
2.1.3 Composition of Eukaryotic Nuclear Genomes
18(1)
2.1.3.1 Gene Numbers and Densities among Nuclear Genomes
18(1)
2.1.3.2 Intergenic DNA
18(3)
2.2 DNA Sequence Evolution
21(16)
2.2.1 Patterns and Processes of Base Substitutions
21(1)
2.2.1.1 Transition Bias
21(2)
2.2.1.2 Transition Bias and DNA Replication Errors
23(1)
2.2.1.3 Saturation of DNA Sites
24(2)
2.2.1.4 Among-Site Substitution Rate Variation
26(1)
2.2.2 Tandemly Repeated DNA Sequences
26(1)
2.2.3 Transposable Elements
27(3)
2.2.4 Processed Pseudogenes
30(1)
2.2.5 Mitochondrial Pseudogenes ("Numts")
30(1)
2.2.5.1 Numt Abundance in Eukaryotic Genomes
30(1)
2.2.5.2 Mechanisms of Primary Numt Integration
31(1)
2.2.5.3 Differences between Numts and Mitochondrial DNA
32(1)
References
33(4)
3 Properties Of Dnasequenceloci: Part II
37(30)
3.1 Six Assumptions about DNA Sequence Loci in Phylogenomic Studies
37(15)
3.1.1 Assumption 1: Loci Are Single-Copy in the Genome
37(2)
3.1.2 Assumption 2: Loci Are Selectively Neutral
39(1)
3.1.2.1 Does "Junk DNA" Exist?
39(1)
3.1.2.2 The Neutrality Assumption and the Indirect Effects of Natural Selection
40(3)
3.1.3 Assumption 3: Sampled Loci Have Independent Gene Trees
43(1)
3.1.3.1 How Many Independent Loci Exist in Eukaryotic Genomes?
44(1)
3.1.3.2 Criteria for Delimiting Loci with Independent Gene Trees
45(2)
3.1.4 Assumption 4: No Historical Recombination within Loci
47(1)
3.1.4.1 Intralocus Recombination and Gene Trees
47(1)
3.1.4.2 What Is the Optimal Locus Length?
48(3)
3.1.5 Assumption 5: Loci Evolved Like a Molecular Clock
51(1)
3.1.6 Assumption 6: Loci Are Free of Ascertainment Bias
52(1)
3.2 DNA Sequence Loci: Terminology and Types
52(15)
3.2.1 On Genes, Alleles, and Related Terms
52(1)
3.2.2 Commonly Used DNA Sequence Loci in Phylogenomic Studies
53(1)
3.2.2.1 Mitochondrial DNA Loci
53(1)
3.2.2.2 Nuclear DNA Loci
54(6)
References
60(7)
4 Dna Extraction
67(14)
4.1 DNA Extraction Methodology
67(4)
4.1.1 Summary of the DNA Extraction Process
67(2)
4.1.2 A Note about DNA Storage Buffers
69(1)
4.1.3 Extracting DNA from Plants, Fungi, and Invertebrates
70(1)
4.1.4 Extracting DNA from Formalin-Fixed Museum Specimens
70(1)
4.2 Evaluating the Results of DNA Extractions
71(5)
4.2.1 Agarose Gel Electrophoresis
72(2)
4.2.1.1 Troubleshooting
74(1)
4.2.2 UV Spectrophotometric Evaluation of DNA Samples
75(1)
4.2.2.1 UV Spectrophotometry to Determine Concentrations of Nucleic Acid Samples
75(1)
4.2.2.2 UV Spectrophotometry to Determine the Purity of DNA Samples
76(1)
4.2.3 Fluorometric Quantitation of DNA Samples
76(1)
4.3 The High-Throughput Workflow
76(5)
4.3.1 High-Throughput DNA Extractions
77(1)
4.3.1.1 Extracting DNA from 96 Tissue Samples
77(1)
4.3.1.2 High-Throughput Agarose Gel Electrophoresis
78(1)
4.3.1.3 High-Throughput UV Spectrophotometry
78(1)
4.3.1.4 Preparation of Diluted DNA Templates for High-Throughput PCR
78(1)
References
79(2)
5 Pcr Theory And Pr Actice
81(24)
5.1 Historical Overview
81(2)
5.2 DNA Polymerization in Living Cells versus PCR
83(6)
5.2.1 Brief Review of DNA Polymerization in Living Cells
83(2)
5.2.2 How the PCR Works
85(4)
5.3 PCR Procedures
89(5)
5.3.1 Preparation of PCR Reagents and Reaction Setup
90(1)
5.3.1.1 PCR Reagents
90(1)
5.3.1.2 Importance of Making Reagent Aliquots
91(1)
5.3.1.3 Setting Up PCRs
92(1)
5.3.2 Thermocycling
93(1)
5.3.3 Checking PCR Results Using Agarose Gel Electrophoresis
94(1)
5.4 PCR Troubleshooting
94(3)
5.5 Reducing PCR Contamination Risk
97(1)
5.6 High-Throughput PCR
98(1)
5.6.1 Setting Up PCRs in a 96-Sample Microplate Format
98(1)
5.7 Other PCR Methods
98(7)
5.7.1 Hot Start PCR
99(1)
5.7.2 Long PCR
100(1)
5.7.3 Reverse Transcriptase-PCR
101(1)
References
102(3)
6 Sanger Sequencing
105(26)
6.1 Principles of Sanger Sequencing
105(7)
6.1.1 The Sanger Sequencing Concept
105(2)
6.1.2 Modern Sanger Sequencing
107(1)
6.1.2.1 Cycle Sequencing Reaction
107(1)
6.1.2.2 Gel Electrophoresis of Extension Products
108(1)
6.1.2.3 Sequence Data Quality
109(3)
6.2 Sanger Sequencing Procedures
112(4)
6.2.1 Purification of PCR Products
112(1)
6.2.1.1 Exo-SAP Treatment of PCR Products
112(1)
6.2.1.2 Spin Column and Vacuum Manifold Kits for PCR Product Purification
112(1)
6.2.1.3 20% PEG 8000 Precipitation of PCR Products
113(1)
6.2.1.4 Solid-Phase Reversible Immobilization Beads
113(1)
6.2.1.5 Gel Purification of PCR Products
114(1)
6.2.1.6 Which PCR Product Purification Method Is Best?
115(1)
6.2.2 Setting Up Cycle Sequencing Reactions
115(1)
6.2.3 Purification of Extension Products
115(1)
6.2.4 Sequencing in a Capillary Sequencer: Do-It-Yourself or Outsource?
116(1)
6.3 High-Throughput Sanger Sequencing
116(7)
6.3.1 Sequencing 96 Samples on Microplates
116(1)
6.3.2 Adding Sequencing Primer "Tails" to PCR Primers
117(1)
6.3.2.1 How an M13-Tailed Primer Functions in PCR
118(1)
6.3.2.2 Cycle Sequencing and M13 Primer Tails
118(3)
6.3.2.3 On the Importance of Matching Sequencing Primers
121(2)
6.3.2.4 Benefits of Using M13-Tailed Primers
123(1)
6.4 Haplotype Determination from Sanger Sequence Data
123(8)
6.4.1 PCR Amplification and Sanger Sequencing of Diploid or Polyploid Loci
123(3)
6.4.2 Multiple Heterozygous SNP Sites and Haplotype Sequences
126(1)
6.4.3 Methods for Obtaining Nuclear Haplotype Sequences from Sanger Sequence Data
127(1)
6.4.3.1 Physical Isolation of PCR Haplotypes prior to Sequencing
128(1)
6.4.3.2 Statistical Inference of Haplotypes from Sanger Sequence Data
128(1)
References
129(2)
7 Illumina Sequencing
131(64)
7.1 How Illumina Sequencing Works
131(12)
7.1.1 Construction of Indexed Sequencing Libraries
133(1)
7.1.2 Generation of Clusters on a Flow Cell
133(2)
7.1.3 Sequencing of Clusters
135(8)
7.2 Methods for Obtaining Multiplexed Hybrid Selection Libraries
143(44)
7.2.1 Library Preparation Approaches
145(1)
7.2.1.1 Traditional Illumina Library Approach
145(11)
7.2.1.2 Meyer and Kircher Library Approach
156(7)
7.2.1.3 Rohland and Reich Library Approach
163(2)
7.2.1.4 Nextera Library Approach
165(10)
7.2.2 In-Solution Hybrid Selection
175(10)
7.2.3 Indexing, Pooling, and Hybrid Selection Efficiency Revisited
185(2)
7.3 Cost-Effective Methods for Obtaining Multiplexed Targeted-Loci Libraries
187(8)
7.3.1 Sequence Capture Using PCR-Generated Probes (SCPP)
187(3)
7.3.2 Parallel Tagged Amplicon Sequencing
190(1)
References
191(4)
8 Developing Dna Sequence Loci
195(26)
8.1 Primer Design Theory
196(9)
8.1.1 Rules of Primer Design
196(8)
8.1.2 Final Comments about Primer Design Rules
204(1)
8.1.3 Testing New Primers in the Lab
205(1)
8.2 Primer and Probe Design Approaches
205(16)
8.2.1 Single Template Approaches for Developing PCR-Based Loci
206(1)
8.2.1.1 Single Template Methods Using Genomic Cloning Methods
206(4)
8.2.1.2 Single Template Methods Using Available Genomics Resources
210(1)
8.2.1.3 Single Template Methods Using NGS Partial Genome Data
210(1)
8.2.1.4 Single Template Methods Using Whole Genome Sequences
211(1)
8.2.2 Multiple Homologous Template Approaches for Designing PCR-Based and Anchor Loci
211(1)
8.2.2.1 Designing Universal Primers by Comparative Sequence Analysis
212(3)
8.2.2.2 Multiple Homologous Template Approaches Using Whole Genome Sequences
215(1)
8.2.2.3 Designing Anchor Loci Probes Using Whole Genome Sequences
216(1)
References
217(4)
9 Future Of Phylogenomic Data Acquisition
221(4)
9.1 The Impending Flood of Genomes
221(1)
9.2 In Silico Acquisition of Phylogenomic Datasets
222(3)
References
224(1)
Index 225
W. Bryan Jennings is professor and coordinator for the Molecular Laboratory of Biodiversity Research at Universidade Federal do Rio de Janeiro.
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