The Eukaryote Genome in Development and Evolution

1 General Molecular Organization of Genomes.- 1.1 Dissecting genomes.- 1.1.1 Microdissection and microcloning.- 1.1.2 Chromosome walking and jumping.- 1.1.3 Transposon mutagenesis and transformation.- 1.1.4 Synthetic DNA probes.- 1.1.4.1 From protein to gene using monoclonal antibodies.- 1.1.4.2 From gene to protein.- 1.2 DNA components of genomes.- 1.2.1 Non-functional DNA.- 1.2.2 Conserved DNA elements.- 1.2.3 Genomic flux.- 1.2.3.1 Transposition.- 1.2.3.2 DNA replication quirks.- 1.2.3.3 Unequal exchange.- 1.2.3.4 Conversion.- 1.2.3.5 Sequence amplification.- 2 Developmental Activities of Genomes.- 2.1 From egg to adult.- 2.2 The genetic control of development in Drosophila melanogaster.- 2.2.1 Embryonic development.- 2.2.2 Pupal development.- 2.2.3 Genetic control of spatial organization in the Drosophila melanogaster embryo.- 2.2.3.1 The antero-postero gradient.- 2.2.3.2 The dorso-ventral gradient.- 2.2.3.3 Body segmentation.- 2.2.3.4 Homeotic genes.- 2.2.4 Sexual development.- 2.2.5 Neurogenesis.- 2.2.6 General conclusions.- 2.3 General principles of development.- 2.3.1 Polarity.- 2.3.2 Cell lineages.- 2.4 Genome alterations during development.- 2.4.1 Nucleotide sequence alterations.- 2.4.1.1 The transposable mating type loci of yeast.- 2.4.1.2 Immunoglobulin class switching.- 2.4.2 Presomatic diminution.- 2.4.3 Macronuclear development in unicellular ciliates.- 2.4.4 Antigenic switching in trypanosomes.- 2.4.5 The molecular bases of genomic alterations.- 3 Coding Capacities of Genomes.- 3.1 Gene regulation in eukaryotes.- 3.1.1 Transcriptional controls.- 3.1.1.1 Polymerase II systems.- 3.1.1.2 Polymerase I systems.- 3.1.1.3 Polymerase III systems.- 3.1.1.4 DNA methylation and gene activity.- 3.1.2 Post-transcriptional controls.- 3.2 Drosophila genomes.- 3.2.1 The general molecular organization of Drosophila genomes.- 3.2.2 Heterochromatic DNA.- 3.2.2.1 Functional studies.- 3.2.2.2 Distribution of highly repetitive sequences within the heterochromatin.- 3.2.2.3 Satellite DNA binding proteins.- 3.2.3 Euchromatic DNA.- 3.3 Comparative genome organization.- 3.3.1 Size variation between genomes.- 3.3.1.1 Chordates.- 3.3.1.2 Insects.- 3.3.1.3 Plethodontid salamanders.- 3.3.2 Interspersion pattern differences.- 3.3.3 'Short' dispersed repetitive sequences.- 3.3.4 Message complexities in eukaryotes.- 3.3.4.1 Ciliate protozoans.- 3.3.4.2 Fungi.- 3.3.4.3 The sea urchin, Strongylocentrotus purpuratus page.- 3.3.4.4 Vertebrates.- 3.3.4.5 Developmental capacities of eukaryote genomes.- 3.3.5 Differences in heterochromatin content.- 3.3.6 Differences in coding DNA.- 3.3.6.1 Multigene families.- 3.3.6.2 Structural gene systems.- 3.3.6.3 Genome structure and function.- 3.4 Gene dosage relationships.- 3.4.1 Compensation and magnification.- 3.4.2 Selective gene amplification.- 3.4.2.1 The chorion genes of Drosophila melanogaster.- 3.4.2.2 The DNA puffs of Rhynchosciara americana.- 3.4.2.3 rDNA amplification.- 3.4.2.4 Somatic endoploidy.- 3.4.3 Dosage compensation.- 3.4.3.1 Female X-inactivation.- 3.4.3.2 Male X-compensation.- 3.4.4 Default transcription.- 3.4.5 Genetic balance and development.- 3.5 The developmental dilemma.- 4 Genome Change and Evolutionary Change.- 4.1 The basis of evolutionary change.- 4.2 Stability and change in the genome.- 4.2.1 The spread and fixation of genome change.- 4.2.1.1 Natural selection.- 4.2.1.2 Neutral drift.- 4.2.1.3 Molecular drive.- 4.2.2 Genome turnover.- 4.3 Nucleotype and genotype.- 4.3.1 Genome size and cell size.- 4.3.2 Genome size and metabolic rate.- 4.3.3 Genome size and division cycle time.- 4.3.4 Genome size and developmental time.- 4.4 Genome change and speciation.- 4.4.1 Species differences in mammals.- 4.4.1.1 Muntjacs.- 4.4.1.2 Equids.- 4.4.1.3 Mice.- 4.4.1.4 Rats.- 4.4.2 Structural changes in the Drosophila genome.- 4.4.3 Speciation and morphological change.- 4.4.4 Hybrid dysgenesis in Drosophila melanogaster.- 4.5 Changes in genome size.- 4.5.1 Modes of change.- 4.5.1.1 Polyploidy.- 4.5.1.2 Duplication.- 4.5.1.3 Amplification.- 4.5.2 Genome size, specialization and speciation.- 4.5.3 Supernumerary chromatin.- 4.6 Summary statement.- 5 The Unsolved Problem - The Origin of Morphological Novelty.- 5.1 Timing adjustments.- 5.2 Binary switch mechanisms.- 5.3 Cell interactions.- 5.4 Cell position.- 5.5 The evolutionary dilemma.- 6 Coda.- 6.1 Facts and conclusions.- 6.2 Future prospects.- 6.3 Final statement.- References.