Integrated Molecular Evolution

LIFE AND EVOLUTION Definitions of Life Introduction RNA and Life Defining Life Imagining Cellular and Molecular Dimensions Key Points Additional Readings Earth and Evolution Introduction What Is Evolution? Earth History A Short History of the Study of Evolution Earth History as One Year Key Points Additional Readings BIOMOLECULES DNA, RNA, and Proteins Introduction Nucleic Acids Translation Amino Acids and Polypeptides Lipids Carbohydrates Key Points Additional Readings The Central Dogma and Beyond Introduction Ribosomal RNA Transfer RNA (tRNA) Messenger RNA Other Small Noncoding RNA Beyond the Central Dogma Key Points Additional Readings Ribosomes and Ribosomal RNA Introduction Ribosomes as Ribozymes Origin of the Ribosome Translation How Many rDNA Copies Are Needed? Mechanisms for Increasing rRNA Gene Copy Number Complexity of Ribosomes Key Points Additional Readings Structure of the Genetic Code Introduction Evolution of the Genetic Code Why a Triplet Codon? The First Genetic Code Life Before Translation Key Points Additional Readings DNA Replication Introduction Fidelity of Replication Variations of Replication Topology During Replication Replication of Chromosomes Key Points Additional Readings DNA Segregation Introduction Variations on DNA Segregation in Bacteria and Archaea Mitosis Variations in Mitosis and the Cell Cycle Variations in Chromosome Number Changes in DNA Amount through the Cell Cycle Meiosis Sexual Reproduction Key Points Additional Readings GENETICS Mendelian and Non-Mendelian Characters Introduction Alleles The Basics of Mendelian Inheritance Codominance, Incomplete Dominance, Overdominance, and Underdominance Epistasis Quantitative Trait Loci Recombination and Linkage Non-Mendelian Traits Key Points Additional Readings Population Genetics Introduction Hardy-Weinberg Equilibrium Population Size Life Histories Modes of Reproduction Key Points Additional Readings Alleles through Time Introduction Natural Selection Levels of Selection Random Genetic Drift Mating and Dispersal Gene Flow Other Factors Affecting Allelic Proportions Key Points Additional Readings Changes to DNA Introduction Classes of Mutations Causes of Mutations Mutation During Replication DNA Repair Genetic Recombination Key Points Additional Readings Infectious Changes to DNA: Viruses, Plasmids, Transposons, and Introns Introduction Integration Into Chromosomes Viruses Introns Transposable Elements Plasmids Key Points Additional Readings MULTICELLULARITY Multigene Families Introduction Ribosomal RNA Gene Family Globin Gene Family Bacterial Flagella Gene Family Laccase Gene Family Orthologs and Paralogs Polyploidization and Multigene Family Evolution Key Points Additional Readings Horizontal Gene Transfer Introduction Plasmids Viruses Symbionts and Organelles Parasites and Pathogens Origin of Gram Negative Bacteria Signs of HGT Introns Key Points Additional Readings Development: Part I-Cooperation among Cells Introduction Quorum Sensing Development in Animals Nematode Development Homeotic Genes and Proteins Arthropod Development Development in Vertebrates Hierarchy and Evolution of Homeotic Genes Key Points Additional Readings Development: Part II-Plants Introduction Plant Morphology Development in Plants Gene Expression during Development Formation of Leaves and Floral Organs Plants versus Animals Key Points Additional Readings Cancer Introduction Progression of Cancer Genes Involved in Cancer Types of Cancer Causes of Mutations in Carcinogenesis Hormones Key Points Additional Readings MOLECULAR BIOLOGY AND BIOINFORMATIC METHODS Extraction and Quantification of Biological Molecules Introduction Extraction of Nucleic Acids Using CTAB Purification of Organellar DNA Extraction of RNA Quantification of Nucleic Acids Agarose Gel Electrophoresis Extraction of Proteins Quantification of Proteins Polyacrylamide Gel Electrophoresis Key Points Additional Readings Recombinant DNA and Characterization of Biological Molecules Introduction Polymerase Chain Reaction Recombinant DNA Methods Southern Hybridization Determination of Gene Copy Number Microscopy Protein Analysis Key Points Additional Readings Sequencing and Alignment Methods Introduction Development of DNA Sequencing Methods High-Throughput Technologies Next-Generation Sequencing Protein Sequencing Sequence Homology Searches Aligning Sequences Key Points Additional Readings OMICS: Part I Introduction Genomics Transcriptomics Metagenomics/Metatranscriptomics Microbiomics Key Points Additional Readings OMICS: Part II Introduction Proteomics Structural Genomics RNAomics Epigenomics Metabolomics Functional Genomics Key Points Additional Readings Species Concepts and Phylogenetics Introduction What Is a Species? Classification of Life Reconstruction of Evolutionary History Phylogenetics Tree Terminology Choosing a Genomic Region for Phylogenetics Other Considerations When Performing Phylogenetic Analyses Models of Mutation Analyzing Aligned Sequences Unweighted Pair Group Method with Arithmetic Mean Neighbor Joining Maximum Parsimony Maximum Likelihood Bayesian Phylogenetic Analysis Bootstrapping Vertical versus Horizontal Evolutionary Events Key Points Additional Readings Phylogenetic Networks and Reticulate Evolution Introduction Phylogenetic Analyses of Reticulate Events Advantages of Phylogenetic Networks Horizontal Gene Transfers Species Hybridization Recombination Transposition Reassortment Examples of Reticulate Evolution Events Key Points Additional Readings Phylogenomics and Comparative Genomics Introduction Improvements in Sequencing and Phylogenomics What to Compare Single-Nucleotide Polymorphisms Microsatellites and Minisatellites How to Compare Testing for Selection Incongruent Trees Comparative Genomics Synteny Key Points Additional Readings GENOMES RNA Viruses Introduction C-Value Paradox Genomes and Genomics RNA Virus Genomes Human Immunodeficiency Virus Influenza A Virus Ebola Virus Key Points Additional Readings DNA Viruses Introduction Bacteriophage X174 Bacteriophage Lambda ( ) Bacteriophage T4 Mimivirus Key Points Additional Readings Bacteria and Archaea Introduction Escherichia coli Photosynthetic Bacteria Aquifex Euryarchaeota Crenarchaeota Key Points Additional Readings Mutualists and Pathogens Introduction Termite Gut Microbes Smallest Bacterial Genome Coresident Symbionts Animal Parasite Genome Mixing and Sorting Key Points Additional Readings Endosymbionts and Organelles Introduction Intracellular Endosymbionts Mitochondria How Many Genes Make a Functional Mitochondrion? Chloroplasts How Many Genes Make a Functional Chloroplast? Differential Development and Function Chimeric Pathways Endosymbioses Leading to Other Organelles Key Points Additional Readings Protein Trafficking Introduction Signal Peptides in Bacteria Signal Peptide Systems in Eukarya Protein Trafficking in Mitochondria Protein Trafficking in Chloroplasts Evolution of Protein Trafficking Systems Key Points Additional Readings Eukaryotic Genomes Introduction Origin of the Nucleus and Mitochondrion Multicellularity Chromalveolata Opisthokonta Archaeplastida Key Points Additional Reading Human Genome Introduction The Human Genome Medical Genetics Single Nucleotide Polymorphisms Forensics Human Migration Key Points Additional Readings