Genes in conflict: the biology of selfish genetic elements

Preface 1. SELFISH GENETIC ELEMENTS Genetic Cooperation and Conflict Three Ways to Achieve Within-Individual Kinship Conflicts Rates of Spread Effects on the Host Population The Study of Selfish Genetic Elements Design of This Book 2. AUTOSOMAL KILLERS The t Haplotype Discovery Structure of the t Haplotype History and Distribution Genetics of Drive Importance of Mating System and Gamete Competition Fate of Resistant Alleles Selection for Inversions Recessive Lethals in t Complexes Enhancers and Suppressors t and the Major Histocompatability Complex Heterozygous (+/t) Fitness Effects: Sex Antagonistic? Accounting for t Frequencies in Nature Other Gamete Killers Segregation Distorter in Drosophila Spore Killers in Fungi Incidence of Gamete Killers Maternal-Effect Killers Medea in Flour Beetles HSR, scat+, and OmDDK in Mice The Evolution of Maternal-Effect Killers Gestational Drive? Gametophyte Factors in Plants 3. SELFISH SEX CHROMOSOMES Sex Chromosome Drive in the Diptera Killer X Chromosomes Killer Y Chromosomes Taxonomic Distribution of Killer Sex Chromosomes Evolutionary Cycles of Sex Determination Feminizing X (and Y) Chromosomes in Rodents The Varying Lemming The Wood Lemming Other Murids Other Conflicts: Sex Ratios and Mate Choice 4. GENOMIC IMPRINTING Imprinting and Parental Investment in Mammals Igf2 and Igf2r: Oppositely Imprinted, Oppositely Acting Growth Factors in Mice Growth Effects of Imprinted Genes in Mice and Humans Evolution of the Imprinting Apparatus The Mechanisms of Imprinting Involve Methylation and Are Complex Conflict Between Different Components of the Imprinting Machinery History of Conflict Reflected in the Imprinting Apparatus Evolutionary Turnover of the Imprinting Apparatus Intralocus Interactions, Polar Overdominance, and Paramutation Transmission Ratio Distortion at Imprinted Loci Biparental Imprinting and Other Possibilities Other Traits: Social Interactions after the Period of Parental Investment Maternal Behavior in Mice Inbreeding and Dispersal Kin Recognition Functional Interpretation of Tissue Effects in Chimeric Mice Deceit and Selves-Deception Imprinting and the Sex Chromosomes Genomic Imprinting in Other Taxa Flowering Plants Other Taxa Predicted to Have Imprinting 5. SELFISH MITOCHONDRIAL DNA Mitochondrial Genomics: A Primer Mitochondrial Selection within the Individual Petite Mutations in Yeast Within-Individual Selection and the Evolution of Uniparental Inheritance Within-Individual Selection under Uniparental Inheritance DUI: Mother-to-Daughter and Father-to-Son mtDNA Inheritance in Mussels Cytoplasmic Male Sterility Uniparental Inheritance Implies Unisexual Selection Disproportionate Role of mtDNA in Plant Male Sterility Mechanisms of Mitochondrial Action and Nuclear Reaction CMS and Restorers in Natural Populations CMS, Masculinization, and the Evolution of Separate Sexes Pollen Limitation, Frequency Dependence, and Local Extinction Resource Reallocation Versus Inbreeding Avoidance Importance of Mutational Variation CMS and Paternal Transmission Other Traces of Mito-Nuclear Conflict Mitochondria and Apoptosis Mitochondria and Germ Cell Determination Mitochondria and RNA Editing 6. GENE CONVERSION AND HOMING Biased Gene Conversion Molecular Mechanisms Effective Selection Coefficients Due to BGC in Fungi BGC and Genome Evolution BGC and Evolution of the Meiotic Machinery Homing and Retrohoming How HEGs Home HEGs Usually Associated with Self-Splicing Introns or Inteins HEGs and Host Mating System Evolutionary Cycle of Horizontal Transmission, Degeneration, and Loss HEG Domestication and Mating-Type Switching in Yeast Group II Introns Artificial HEGs As Tools for Population Genetic Engineering The Basic Construct Increasing the Load Preventing Natural Resistance and Horizontal Transmission Population Genetic Engineering Other Uses 7. TRANSPOSABLE ELEMENTS Molecular Structure and Mechanisms DNA Transposons LINEs and SINEs LTR Retroelements Population Biology and Natural Selection Transposition Rates Low But Greater Than Excision Rates Natural Selection on the Host Slows the Spread of Transposable Elements Rapid Spread of P Elements in D. melanogaster Net Reproductive Rate a Function of Transposition Rate and Effect on Host Fitness Reducing Harm to the Host Transposition Rate and Copy Number Regulation Selection for Self-Recognition Defective and Repressor Elements Extinction of Active Elements in Host Species Horizontal Transmission and Long-Term Persistence Transposable Elements in Inbred and Outcrossed Populations Beneficial Inserts Rates of Fixation Transposable Elements and Host Evolution Transposable Elements and Chromosomal Rearrangements Transposable Elements and Genome Size Co-Option of Transposable Element Functions and Host Defenses Transposable Elements As Parasites, Not Host Adaptations or Mutualists Origins Ancient, Chimeric, and Polyphyletic Origins 8. FEMALE DRIVE Selfish Centromeres and Female Meiosis Abnormal Chromosome 10 of Maize Other Knobs in Maize Deleterious Effects of Knobs in Maize Knobs, Supernumerary Segments, and Neocentromeres in Other Species Meiosis-Specific Centromeres and Holocentric Chromosomes Selfish Centromeres and Meiosis I The Importance of Centromere Number: Robertsonian Translocations in Mammals Sperm-Dependent Female Drive? Female Drive and Karyotype Evolution Polar Bodies Rejoining the Germline 9. B CHROMOSOMES Drive Types of Drive Genetics of A and B Factors Affecting B Drive Transmission Rates inWell-Studied Species Absence of Drive Degree of Outcrossing and Drive Effects on the Phenotype Effects on Genome Size, Cell Size, and Cell Cycle Effects on the External Phenotype Disappearance from Somatic Tissue B Number and the Odd-Even Effect Negative Effects of Bs More Pronounced under Harsher Conditions Is the Sex of Drive Associated with the Sex of Phenotypic Effect? B Effects on Recombination Among the As Pairing of A Chromosomes in Hybrids Neutral and Beneficial Bs Beneficial B Chromosomes B Chromosomes in Eyprepocnemis plorans: A Case of Continuous Neutralization? Structure and Content Size Polymorphism Heterochromatin Genes Tandem Repeats The Origin of Bs A Factors Associated with B Presence Genome Size Chromosome Number Ploidy Shape of A Chromosomes Bs and the Sex Ratio Paternal Sex Ratio (PSR) in Nasonia X-B Associations in Orthoptera Has the Drosophila Y Evolved from a B? Other Effects of Bs on the Sex Ratio Male Sterility in Plantago 10. GENOMIC EXCLUSION Paternal Genome Loss in Males, or Parahaplodiploidy PGL in Mites PGL in Scale Insects PGL in the Coffee Borer Beetle PGL in Springtails? Evolution of PGL PGL and Haplodiploidy Sciarid Chromosome System Notable Features of the Sciarid System An Evolutionary Hypothesis Mechanisms PGL in Gall Midges Hybridogenesis, or Hemiclonal Reproduction The Topminnow Poeciliopsis The Water Frog Rana esculenta The Stick Insect Bacillus rossius-grandii Evolution of Hybridogenesis Androgenesis, or Maternal Genome Loss The Conifer Cupressus dupreziana The Clam Corbicula The Stick Insect Bacillus rossius-grandii 11. SELFISH CELL LINEAGES Mosaics Somatic Cell Lineage Selection: Cancer and the Adaptive Immune System Cell Lineage Selection in the Germline Evolution of the Germline Selfish Genes and Germline-Limited DNA Chimeras Taxonomic Survey of Chimerism Somatic Chimerism and Polar Bodies 12. SUMMARY AND FUTURE DIRECTIONS Logic of Selfish Genetic Elements Molecular Genetics Selfish Genes and Sex Fate of a Selfish Gene within a Species Movement between Species Distribution among Species Role in Host Evolution The HiddenWorld of Selfish Genetic Elements References Glossary Index