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.
Contents: فهرست فصول
CoverHalf-TitleTitleCopyrightDedicationContentsDetailed ContentsPrefaceAcknowledgementsSection I Foundations of Phylogenomics1 What is Phylogenomics?2 The Biology and Sequencing of Genetic Information: DNA, RNA, and Proteins3 Evolutionary Principles: Populations and TreesSection II Data4 Data Storage—The Basics5 Sequence Alignment and Searching Sequence Databases6 Multiple Alignments7 Genome Sequencing and Annotation8 Genomics Databases: Genomes and Transcriptomes9 Amplicon Databases: BoLD and Bacterial 16S rDNA DatabasesSection III Phylogenetic/Phylogenomic Analysis10 Introduction to Tree Building11 Distance and Clustering12 Maximum Likelihood13 Search Strategies and Robustness14 Rate Heterogeneity, Long Branch Attraction, and Likelihood Models15 Bayesian Approaches in Phylogenetics16 Incongruence of Gene Trees17 Phylogenetic Programs and WebsitesSection IV Population Genomics18 Population Genetics and Genomes19 Population Genomics Approaches20 Detecting Natural Selection: The Basics21 Refining the Approach to Natural Selection at the Molecular LevelSection V Phylogenomics in Action22 Constructing Phylogenomic Matrices23 Phylogenomics and the Tree of Life24 Comparative Genomics25 Environmental DNA (eDNA)26 Phylogenomic Approaches to Understanding Gene Function and EvolutionIndex