Preface

1. SELFISH GENETIC ELEMENTS

Genetic Cooperation and Conflict

Three Ways to Achieve "Drive"

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