Evolution: The Origins and Mechanisms of Diversity

Description

Evolution is the single unifying principle of biology and core to everything in the life sciences. More than a century of work by scientists from across the biological spectrum has produced a detailed history of life across the phyla and explained the mechanisms by which new species form. This textbook covers both this history and the mechanisms of speciation; it also aims to provide students with the background needed to read the research literature on evolution. Students will therefore learn about cladistics, molecular phylogenies, the molecular-genetical basis of evolutionary change including the important role of protein networks, symbionts and holobionts, together with the core principles of developmental biology. The book also includes introductory appendices that provide background knowledge on, for example, the diversity of life today, fossils, the geology of Earth and the history of evolutionary thought. Key Features Summarizes the origins of life and the evolution of the eukaryotic cell and of Urbilateria, the last common ancestor of invertebrates and vertebrates.Reviews the history of life across the phyla based on the fossil record and computational phylogenetics.Explains evo-devo and the generation of anatomical novelties.Illustrates the roles of small populations, genetic drift, mutation and selection in speciation.Documents human evolution using the fossil record and evidence of dispersal across the world leading to the emergence of modern humans. Cover Half Title Title Page Copyright Page Dedication Contents Preface Website Support Materials Acknowledgements About the Author SECTION ONE: AN INTRODUCTION TO EVOLUTION 1. Approaching Evolution Perspectives Evolutionary research today Systems biology Further readings Websites 2. A Potted History of Evolutionary Science The pre-Darwinian Era The Darwinian Era The era of evolutionary genetics The molecular era Further readings Website 3. The Ancient World The evolving earth Extinctions Four billion years of life Prokaryotes Unicellular eukaryotes Early large eukaryotes Further readings Websites 4. Life Today: Species, Diversity, and Classification The diversity of life today Defining a species Variation within a species The numbers of species today Taxonomies: Organising diversity Phylogenies and evolutionary history Key points Further readings Websites SECTION TWO: THE EVIDENCE FOR EVOLUTION 5. Analysing Evolutionary Change Descent with modification is the identifier for evolution Cladistic links organisms by anatomical inheritance Linnaean and cladistic taxonomies are different Apparent anomalies Homoplasies Lost plesiomorphies Exaptations The broader importance of Darwin’s ideas Key points Further reading Websites 6. The Anatomical Evidence for Evolutionary Change The evolution of the pentadactyl limb The evolution of the mammalian skull The evolution of middle-ear bones and the reorganization of the jaw The evolution of the zygomatic arch The evolution of the secondary palate The evolution of mammalian teeth The evolution of the equidae Key points Further readings Website 7. The Genomic Evidence Phylograms and cladograms are subtly different Constructing sequence-based phylogenetic trees Ancestral sequences Choosing sequences for phylogenetic analysis Three examples of molecular phylogenies The evolutionary status of the AmphilLim 1/5 Gene Phylogenetic relationships among a group of anemone fish Phylogenetic relationships across the family of hox genes Gene trees, species trees, and phylogenomics Adding timings to phylograms Molecular phylogenetics today Key points Further readings Websites 8. The Evo-Devo Evidence The molecular basis of evo-devo homologies Signal and receptor homologies Transcription factor homologies Protein network homologies Implications of protein homologies Key points Further readings Websites SECTION THREE: THE HISTORY OF LIFE 9. The First Two Billion Years The origin of life FUCA, the first universal common ancestor LUCA, the last universal common ancestor The prokaryotic seas: Eubacteria and Archaebacteria Eubacteria Archaebacteria FECA, the first eukaryote common ancestor LECA, the last eukaryote common ancestor Mitochondria Membranes and cytoskeleton Timings Key points Further readings Websites 10 The Roots of the Eukaryotic Tree of Life The diversification of the leca Flagella, centrioles, and basal bodies Cell walls Sexual reproduction and diploidy Plastids Protist systematics The origins of social behaviour The acquisition of multicellularity Fungal evolution Key points Further readings Websites Fungi 11. The Evolution of Algae and Plants Algae Algal fossil record Evolution of algae Plants Plant evolution Plant systematics Key points Further readings Websites 12. The Ediacaran Period and the Early Evolution of the Metazoa The Ediacaran biota The evolution of diploblastic and triploblastic embryos Protostomes Deuterostomes The evolution of Urbilateria Key points Further readings Website 13. The Cambrian Explosion and the Evolution of Protostomes The Cambrian fossil record The protostome world Porifera Coelenterata The Bilateria and protostome diversity Protostome systematics The major protostome phyla Molluscs Arthropods Key points Further readings Websites 14. Deuterostome Evolution: From the Beginnings to the Amphibians Modern deuterostome anamniotes Ambulacraria The minor chordate clades Craniata The early deuterostome fossil record The fish fossil record From water to land Limb evolution Girdle evolution Breathing Metamorphosis Amphibians Key points Further readings Websites 15. Vertebrate Evolution: Stem Mammals, Reptiles, and Birds Anatomical innovations in stem amniotes The evolution of the amniote egg The evolution of the early amniote skeleton The fossil record of mesozoic reptiles The Palaeozoic Era The Mesozoic Era (252–66 Mya) The K-T extinction and the beginnings of the Cenozoic Era (66 Mya) The origin of flight Pterosaurs Birds Key points Further readings Websites 16. Vertebrate Evolution: Mammals The mammalian fossil record from the Mesozoic The evolution of some key mammalian features Changes to the skull Changes to soft tissues The evolution of the Cetacea Defensive adaptations Probosces with a second function Flight Back to the sea and the evolution of whales Key points Further readings Websites SECTION FOUR: THE MECHANISMS OF EVOLUTION 17. Variation 1: Mutations and Phenotypes Phenotypic variation Unusual variation: Sports and anomalies Variation leading to human disease Secondary variation Genotypic variation Mutation The effects of mutation on the genotype The effect of mutation on individual genes Larger-scale genomic changes Horizontal gene transfer The role of the environment in generating variation Transgenerational epigenetic inheritance (TEI) The wider context Key points Further readings Websites 18. Variation 2: Evolutionary Change Some origins of anatomical change Organism size Timing changes Limb variation Other evolutionary variants The effect of mutation on signaling and network systems Signals, receptors, and transcription factors Networks Developmental constraints on variation The mutational basis of trait change—The broader view Key points Further readings Websites 19. Adaptation, Symbionts, and Holobionts Types of adaptation Camouflage and mimicry Exaptation Niche construction Parasites Facilitating reproduction Increasing offspring numbers Symbiosis Holobiosis Developmental plasticity and adaptive change Key points Further readings Websites 20. Selection Natural selection The evolution of the camera eye under selection Sexual selection The advantages and disadvantages of sexual reproduction The sexual phenotype The sex ratio Kin selection and altruism The speed of change under selection Controlling selection Selective breeding Generating anatomical novelties Selection pressures imposed by humans Key points Further readings Websites 21. Evolutionary Population Genetics Classical population genetics Linkage Nonrandom breeding Migration Genetic drift The effects of selection Practical considerations Neutral theory versus selection Small populations and founder groups Quantitative and complex traits Gene identification Selfish genes Coalescence approaches Conclusion Key points Further readings Websites 22. Speciation Defining a species The breeding criterion The morphological criterion The habitat criterion The molecular criterion The timing criterion How new species form Modes of reproductive isolation Allopatric separation Peripatric speciation Parapatric speciation Sympatric separation The rate of speciation Hybrids Speciation speeds under allopatric conditions Species flocks Experimental speciation The genetics of speciation The key role of chromosomes Key points Further readings Websites SECTION FIVE: HUMAN EVOLUTION 23. Human Evolution 1: The Fossil Evidence Human fossil material The major hominin groups Possible early hominins (7–4.5 Mya) Archaic hominins (4.5–2.5 Mya) Megadont archaic hominins (2.5–1 Mya) Transitional hominins (~2.5–1.4 Mya) Pre-modern Homo (1.9 Mya–30 Kya) Anatomically modern Homo (from 0.2 Mya onwards) Selection and speciation Key points Further readings Websites 24. Human Evolution 2: Genes and Migrations Information from chimpanzee genomes Ancient Homo DNA Contemporary human genomes Mitochondrial DNA Migrations within Africa Migrations out of Africa The wider picture Key points Further readings Websites 25. Human Evolution 3: The Origins of Modern Humans The rise of H. sapiens Cultural inheritance Tool-making Social living Speech Art The modern brain The origins of human differences Skin pigmentation Eye colour Genetic disorders Body differences Are humans still evolving? Key points Further readings Websites 26. Conclusions The achievements of evolutionary science Contemporary challenges The history of life The mechanisms of speciation Is anything missing? The speed of evolutionary change and noncanonical heritability The origins of novel phenotypes Neurobiology and behaviour Origin of life The evolutionary future of Homo sapiens Is the human species still evolving The effect of humans on the planet Finally Websites APPENDICES Appendix 1: Systems Biology The narrow view The broader view Events within each level are complex There are interactions between levels Causality is distributed A note on systems terminology Further readings Websites Appendix 2: A History of Evolutionary Thought The early days The move to evolutionary thinking The early 19th century Lamarck: The first evolutionary scientist The era of Darwin The 19th century after Darwin The early 20th century Taxonomy The molecular era DNA sequence analysis Evo-devo Systems biology Further readings Websites Appendix 3: A Brief History of the World Appendix 4: Rocks, Dates, and Fossils Rock types Ageing rocks (geochronology) Paleoclimatology How fossils form Dating ancient organisms Further readings Websites Appendix 5: Constructing Molecular Phylogenies Phylogenies based on shared/absent sequences Phylogenies based on distance matrices Phylogenies based on tree-searching methods Maximum parsimony Maximum likelihood Bayesian methods Phylogeny choices Further readings Websites Appendix 6: Three Key Model Organisms: Mouse, Drosophila, and H. sapiens Drosophila development Mouse development Similarities and differences Homo sapiens Further readings Websites Appendix 7: Some Principles of Animal Developmental Biology Driving developmental change How tissues form Tissue modules The origins of anatomical differences The role of the genome in development Key points Further readings Websites Appendix 8: Evolution and Creationism Creationism The claim Evolutionary criticisms of creationism Evolution The claims The creationists’ criticisms of evolution Conclusions Websites Glossary References Index