Evolution Through Genetic Exchange
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Even before the publication of Darwin's Origin of Species, the perception of evolutionary change has been a tree-like pattern of diversification - with divergent branches spreading further and further from the trunk. In the only illustration of Darwin's treatise, branches large and small never reconnect. However, it is now evident that this view does not adequately encompass the richness of evolutionary pattern and process. Instead, the evolution of species from microbes to mammals builds like a web that crosses and re-crosses through genetic exchange, even as it grows outward from a point of origin. Some of the avenues for genetic exchange, for example introgression through sexual recombination versus lateral gene transfer mediated by transposable elements, are based on definably different molecular mechanisms. However, even such widely different genetic processes may result in similar effects on adaptations (either new or transferred), genome evolution, population genetics, and the evolutionary/ecological trajectory of organisms. For example, the evolution of novel adaptations (resulting from lateral gene transfer) leading to the flea-borne, deadly, causative agent of plague from a rarely-fatal, orally-transmitted, bacterial species is quite similar to the adaptations accrued from natural hybridization between annual sunflower species resulting in the formation of several new species. Thus, more and more data indicate that evolution has resulted in lineages consisting of mosaics of genes derived from different ancestors. It is therefore becoming increasingly clear that the tree is an inadequate metaphor of evolutionary change. In this book, Arnold promotes the 'web-of-life' metaphor as a more appropriate representation of evolutionary change in all lifeforms.
History of investigations 1Pre-Darwin, Darwin, the Modern Synthesis and genetic exchange: development of a paradigm 1Post-Modern Synthesis: case studies of genetic exchange 5Louisiana irises 5Plague 11Darwin's finches 13Influenza 18Summary and conclusions 21The role of species concepts 23Species concepts and understanding genetic exchange 23Genetic exchange considered through four species concepts 24Biological species concept 24Phylogenetic species concept 28Cohesion species concept 30Prokaryotic species concept 31Summary and conclusions 33Testing the hypothesis 34Genetic exchange as a testable hypothesis 34Controversy over genetic exchange: examples from oaks 35North American oaks 35European oaks 37Methods to test for genetic exchange 38Concordance across data sets: hybrid zone analyses 38Phylogenetic discordance 47Gene genealogies and models of speciation 55Intragenomicdivergence 57Nested clade analysis 59Summary and conclusions 61Barriers to gene flow 62Barriers to exchange form a multi-stage process 62Genetic exchange: Louisiana irises and reproductive barriers 63Ecological setting as a barrier 63Gamete competition as a barrier 65Hybrid viability as a barrier 66Hybrid fertility as a barrier 67Genetic exchange: five stages of reproductive isolation 67Ecological setting 67Behavioral characteristics 72Gamete competition 76Hybrid viability 77Hybrid fertility 79Summary and conclusions 81Hybrid fitness 82Components of hybrid fitness 82Genetic exchange and fitness: microorganisms 84Mycobacterium tuberculosis 84Legionella pneumophila 85Brazilian purpuric fever 86Entamoeba histolytica 87Bacterial viruses 90Yeast 91Salmonella 92Genetic exchange and fitness: plants 93Ipomopsis 93Louisiana irises 94Helianthus 96Artemisia 97Populus 98Hawaiian Silversword complex 101Salix 101Genetic exchange and fitness: animals 102Bombina 102Rana 103Cichlids 104Whitefish, redfish, and charr 105Flycatchers 106Manakins 107Summary and conclusions 108Gene duplication 109Gene duplication and evolution 109Genetic exchange: genomewide evolution following duplication 110Genomewide effects-epigenetic changes through methylation 110Genomewide effects-activation of transposable elements 112Genomewide effects-genome downsizing 114Genomewide effects-chromosome rearrangements 115Genetic exchange: gene and gene family evolution following duplication 116Genes and gene families: concerted evolution 116Genes and gene families: changes in gene expression patterns and function 119Genes and gene families: evolution of adaptations 120Genetic exchange: genome duplication and adaptive radiations 121Duplication and adaptive radiation: the vertebrate lineage 121Duplication and adaptive radiation: the fish clade 122Summary and conclusions 122Origin of new evolutionary lineages 123Viral recombination, lateral transfer, natural hybridization, and evolutionary diversification 123Natural hybridization, allopolyploidy, and evolutionary diversification in non-flowering plants 125Ferns 125Bryophytes 127Natural hybridization, allopolyploidy, and evolutionary diversification in flowering plants 128Draba 128Paeonia 129Glycine 131Spartina 132Natural hybridization, allopolyploidy, and evolutionary diversification in animals 133Parthenogenesis 133Gynogenesis 137Sexually reproducing, allopolyploid animals 139Natural hybridization, homoploidy, and evolutionary diversification 141Evolution by homoploid hybrid lineage formation in plants 141Evolution by homoploid hybrid lineage formation in animals-parthenogenetic and hybridogenetic taxa 144Evolution by homoploid hybrid lineage formation in animals-sexually reproducing taxa 145Viral recombination, lateral exchange, introgressive hybridization, and evolutionary diversification in microorganisms 147Viral recombination, lateral exchange, and the evolution of bacteriophages 147Lateral exchange and the evolution of bacterial lineages 148Introgressive hybridization and the evolution of the protozoan genus Trypanosoma 149Summary and conclusions 150Implications for endangered taxa 151Introgressive hybridization and the conservation and restoration of endangered taxa 151Introgressive hybridization involving endangered plant taxa 152Eucalyptus 152Carpobrotus 154Taraxacum 156Introgressive hybridization involving endangered animal taxa 157Felidae 157African elephants 159Aves 160Summary and conclusions 163Humans and associated lineages 164The role of genetic exchange in the evolutionary history of humans and their food, drugs, clothing, and diseases 164Introgressive hybridization and the evolution of Homo sapiens 165Hominoids 165Introgressive hybridization, hybrid speciation, and the evolution of human food sources 169Animals 169Plants 171Introgressive hybridization, hybrid speciation, and the evolution of human drugs 174Coffee 174Chocolate 175Tobacco 176Introgressive hybridization, hybrid speciation, and the evolution of pathogens of plants utilized by humans 176Phytophthora 176Dutch elm disease 177Erwinia carotovora 178Introgressive hybridization, hybrid speciation, and the evolution of human clothing materials 179Leather 179Deer skin 180Cotton 181Introgressive hybridization, hybrid speciation, and the evolution of human disease vectors 182Anopheles funestus 182Culex pipiens 183Lateral transfer and the evolution of human diseases 183Propionibacterium acnes 183Burkholderia pseudomallei 183Human-mediated genetic exchange 185Summary and conclusions 186Emergent properties 187Genetic exchange is pervasive 187Genetic exchange: research directions 189Glossary 191Reference 194Index 235
