Phylogenomics: 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.

Previous edition: 2013.

<P><EM>P</EM><EM>reface </EM></P><P><EM>Acknowledgements </EM></P><B><P>Section I. Foundations of Phylogenomics</P></B><P>1. What is Phylogenomics? </P><P>2. The Biology and Sequencing of Genetic Information: DNA, RNA, and Proteins </P><P>3. Evolutionary Principles: Populations and Trees </P><B><P>Section II. Data</P></B><P>4. Data Storage-The Basics </P><P>5. Sequence Alignment and Searching Sequence Databases </P><P>6. Multiple Alignments </P><P>7. Genome Sequencing and Annotation </P><P>8. Genomics Databases: Genomes and Transcriptomes </P><P>9. Amplicon Databases: BoLD and Bacterial 16S rDNA Databases </P><B><P>Section III. Phylogenetic/Phylogenomic Analysis</P></B><P>10. Introduction to Tree Building </P><P>11. Distance and Clustering </P><P>12. Maximum Likelihood </P><P>13. Search Strategies and Robustness </P><P>14. Rate Heterogeneity, Long Branch Attraction, and Likelihood Models </P><P>15. Bayesian Approaches in Phylogenetics </P><P>16. Incongruence of Gene Trees </P><P>17. Phylogenetic Programs and Websites </P><B><P>Section IV. Population Genomics</P></B><P>18. Population Genetics and Genomes </P><P>19. Population Genomics Approaches </P><P>20. Detecting Natural Selection: The Basics </P><P>21. Refining the Approach to Natural Selection at the Molecular Level </P><B><P>Section V. Phylogenomics in Action</P></B><P>22. Constructing Phylogenomic Matrices </P><P>23. Phylogenomics and the Tree of Life </P><P>24. Comparative Genomics </P><P>25. Environmental DNA (eDNA) </P><P>26. Phylogenomic Approaches to Understanding Gene Function and Evolution </P><I><P>Index </P></I><P></P>

Cover -- Half Title -- Title Page -- Copyright Page -- Dedication -- Table of Contents -- Detailed Contents -- Preface -- Acknowledgements -- Section I Foundations of Phylogenomics -- Chapter 1 What is Phylogenomics? -- Phylogenomics and Bioinformatics -- Bioinformatics Tools for Finding Patterns in Biological Experiments -- The rise of phylogenomics -- Sub-Branches of Phylogenomics -- The Phylogenomic Toolbox -- Basic Computational Tools in Phylogenomics -- Statistics Help Compare Genetic Sequences and Generate Phylogenetic Trees -- Parametric Statistics Are Derived from Distributions

Nonparametric Statistical Analyses Are Useful in Many Situations -- Maximum Likelihood and Bayesian Analysis Are Standard Statistical Methods Used in Phylogenomics -- Key Attributes of Phylogenomicists -- Summary -- Recommendations for Students -- Discussion Questions -- Further Reading -- Chapter 2 The Biology and Sequencing of Genetic Information: DNA, RNA, and Proteins -- Nucleic Acids -- DNA molecules efficiently transmit information -- DNA is synthesized by specific pairing -- DNA can mutate and lead to descent with modification -- Polymerase chain reaction (PCR) is a milestone development

Pr…