Fundamentals of Molecular Evolution
Gene structure and mutation. Protein-coding genes. RNA-specifying genes. Regulatory genes. Nucleotide substitutions. Deletions and insertions. Spatial distribution of mutations. Dynamics of genes in populations. Changes in allele frequencies. Natural selection. Codominance. Overdominance. Random genetic drift. Effective population size. Gene substitution. Fixation probability. Fixation time. Rate of gene substitution. Genetic polymorphism. The neo-darwinian theory and the neutral mutation hypothesis. Evolutionary change in nucleotide sequences. Jukes and cantor's one-parameter model. Kimura's two-parameter model. Number of substitutions between two noncoding sequences. Protein-coding. Alignment of nucleotide and amino acid sequences. The dot-matrix method. The sequence-distance method. Indirect estimation of the number of nucleotide substitutions. Restriction endonuclease fragment patterns and site maps DNA-DNA hybridization. Rates and patterns of nucleotide substitution. Variation among different gene regions. A case of positive selection: lysozyme in cows and langurs. Relative-rate tests. Nearly equal rates in mice and rats. Lower rates in humans than in monkeys. Higher rates in rodents than in primates. Causes of variation in substitution rates among evolutionary lineages. Organelle. Pseudogenes. Nonrandom usage of synonymous codons. Phylogeny. Impact of molecular data on phylogenetic studies. Rooted and unrooted trees. True and inferred trees. Gene trees and species trees. Unweighted pair group method with arithmetic mean (UPGMA). Transformed distance method. Neighbors relation methods. Maximum parsimony methods. Phenetics versus cladistics. Estimation of branch lengths. Rooting unrooted trees. Estimation of species-divergence times clades. Phylogeny of humans and apes. Endosymbiotic origin of mitochondria and chloroplasts. Molecular paleontology. The dusky seaside sparrow: a lesson in conservation biology. Evolution by gene duplication and exon shuffling. Domain duplication and gene elongation. The ovomucoid gene. Formation of gene families and the acquisition of new functions. RNA-specifying genes. Isozymes. Color-sensitive pigment proteins. The globin superfamily of genes. Exon shuffling. Mosaic proteins. Phase limitations on exon shuffling. Alternative pathways for producing new functions. Overlapping genes. Alternative splicing. Gene sharing. Concerted evolution of multigene families. Mechanisms of concerted evolution. Evolution by transposition. Transposable elements. Transposons. Retroelements. Retrosequences. Retrogenes. Processed pseudogenes. Effects of transposition on the host genome. Hybrid dysgenesis. Horizontal transfer of virogenes from baboons to cats. Drosophila. Genome organization and evolution. Genome size of eukaryotes and the C-value paradox. Mechanisms for increasing genome size. Chromosomal duplication. Maintenance of nongenic DNA. Bacteria. Compositional organization of the vertebrate genome. Origins of isochores.
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EFFECTIVE POPULATION SIZE
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allele frequencies Alu sequences amino acid bacteria cell chloroplast chromosome clade coding region codon usage coli concerted evolution contain copies deletion denote divergence DNA sequence domain Drosophila melanogaster encoded enzyme Equation estimate eukaryotes evolutionary example exon Figure fixation GC content gene conversion gene duplication genome genotypes globin homologous human hybrid insertion introns isochores lineages locus mammalian mammals maximum parsimony method million years ago mitochondrial molecular evolution molecule mRNA mutation neutral nongenic DNA nonsynonymous substitution nuclear nucleotide nucleotide substitution number of nucleotide number of substitutions occur organisms outgroup pair phylogenetic tree polymorphism population position probability processed pseudogenes protein protein-coding genes pseudogenes rate of substitution reading frame repeated sequences replication retrosequence reverse transcriptase rRNA rRNA genes selection sequence data species splicing strand structure substitution rates synonymous substitution Table taxa transcribed transcription transposable elements transposition transposons tRNA types unequal crossing-over unrooted trees vertebrates World monkeys