EVOLUTION THIRD EDITION MARK RIDLEY. Blackwell Publishing

Transcription

1 EVOLUTION THIRD EDITION MARK RIDLEY Blackwell Publishing

2 Brief Contents Full Contents Preface VII xxii PART1. INTRODUCTION 1. The Rise of Evolutionary Biology 2. Molecular and Mendelian Genetics 3. The Evidence for Evolution 4. Natural Selection and Variation PART 2. EVOLUTIONARY GENETICS The Theory of Natural Selection 6. Random Events in Population Genetics 7. Natural Selection and Random Drift in Molecular Evolution 8.. Two-locus and Multilocus Population Genetics 9. Quantitative Genetics PART 3. ADAPTATION AND NATURAL SELECTION Adaptive Explanation 11. The Units of Selection 12. Adaptations in Sexual Reproduction PART 4. EVOLUTION AND DIVERSITY Species Concepts and Intraspecific Variation 14. Speciation 15. The Reconstruction of Phylogeny 16. Classification and Evolution 17. Evolutionary Biogeography

3 vi Brief Contents PART 5. MACROEVOLUTION The History of Life Evolutionary Genomics Evolutionary Developmental Biology Rates of Evolution Coevolution Extinction and Radiation 643 Glossary 682 Answers to Study and Review Questions 690 References 699 Index 733 Color plate section between pp. 70 and 71

4 Full Contents Preface xxii PART1. INTRODUCTION 1 1. The Rise of Evolutionary Biology Evolution means change in living things by descent with modification Living things show adaptations A short history of evolutionary biology Evolution before Darwin Charles Darwin Darwin's reception The modern synthesis Molecular and Mendelian Genetics Inheritance is caused by DNA molecules, which are physically passed from parent to offspring DNA structurally encodes information used to build the body's proteins Information in DNA is decoded by transcription and translation Large amounts of non-coding DNA exist in some species Mutational errors may occur during DNA replication Rates of mutation can be measured Diploid organisms inherit a double set of genes Genes are inherited in characteristic Mendelian ratios Darwin's theory would probably not work if there was a non-mendelian blending mechanism of heredity The Evidence for Evolution We distinguish three possible theories of the history of life On a small scale, evolution can be observed in action Evolution can also be produced experimentally Interbreeding and phenotypic similarity provide two concepts of species 48

5 viii Full Contents 3.5 Ring "species" show that the variation within a species can be extensive enough to produce a new species New, reproductively distinct species can be produced experimentally Small-scale observations can be extrapolated over the long term Groups of living things have homologous similarities Different homologies are correlated, and can be hierarchically classified Fossil evidence exists for the transformation of species The order of the main groups in the fossil record suggests they have evolutionary relationships Summary of the evidence for evolution Creationism offers no explanation of adaptation Modern "scientific creationism" is scientifically untenable Natural Selection and Variation In nature, there is a struggle for existence Natural selection operates if some conditions are met Natural selection explains both evolution and adaptation Natural selection can be directional, stabilizing, or disruptive Variation in natural populations is widespread Organisms in a population vary in reproductive success New variation is generated by mutation and recombination Variation created by recombination and mutation is random with respect to the direction of adaptation 88 PART 2. EVOLUTIONARY GENETICS The Theory of Natural Selection Population genetics is concerned with genotype and gene frequencies An elementary population genetic model has four main steps Genotype frequencies in the absence of selection go to the Hardy- Weinberg equilibrium We can test, by simple observation, whether genotypes in a population are at the Hardy-Weinberg equilibrium The Hardy-Weinberg theorem is important conceptually, historically, in practical research, and in the workings of theoretical models The simplest model of selection is for one favored allele at one locus The model of selection can be applied to the peppered moth Industrial melanism in moths evolved by natural selection One estimate of the fitnesses is made using the rate of change in gene frequencies 109

6 Full Contents ix A second estimate of thefitnessesis made from the survivorship 1 of the different genotypes in mark-recapture experiments The selective factor at work is controversial, but bird predation was probably influential Pesticide resistance in insects is an example of natural selection Fitnesses are important numbers in evolutionary theory and can be estimated by three main methods Natural selection operating on a favored allele at a single locus is not meant to be a general model of evolution A recurrent disadvantageous mutation will evolve to a calculable equilibrial frequency Heterozygous advantage Selection can maintain a polymorphism when the heterozygote is fitter than either homozygote Sickle cell anemia is a polymorphism with heterozygous advantage The fitness ofa genotype may depend on its frequency Subdivided populations require special population genetic principles A subdivided set of populations have a higher proportion of homozygotes than an equivalent fused population: this is the Wahlund effect Migration acts to unify gene frequencies between populations Convergence of gene frequencies by gene flow is illustrated by the human population of the USA A balance of selection and migration can maintain genetic differences between subpopulations Random Events in Population Genetics The frequency of alleles can change at random through time in a process called genetic drift A small founder population may have a non-representative sample of the ancestral population's genes One gene can be substituted for another by random drift Hardy-Weinberg "equilibrium" assumes the absence of genetic drift Neutral drift over time produces a march to homozygosity A calculable amount of polymorphism will exist in a population because of neutral mutation Population size and effective population size Natural Selection and Random Drift in Molecular Evolution Random drift and natural selection can both hypothetically explain molecular evolution 156

7 x Full Contents 7.2 Rates of molecular evolution and amounts of genetic variation can be measured Rates of molecular evolution are arguably too constant for a process controlled by natural selection The molecular clock shows a generation time effect The nearly neutral theory The "purely" neutral theory faces several empirical problems The nearly neutral theory of molecular evolution posits a class of nearly neutral mutations The nearly neutral theory can explain the observed facts better than the purely neutral theory The nearly neutral theory is conceptually closely related to the original, purely neutral theory Evolutionary rate and functional constraint More functionally constrained parts of proteins evolve at slower rates Both natural selection and neutral drift can explain the trend for proteins, but only drift is plausible for DNA Conclusion and comment: the neutralist paradigm shift Genomic sequences have led to new ways of studying molecular evolution DNA sequences provide strong evidence for natural selection on protein structure A high ratio of non-synonymous to synonymous changes provides evidence of selection Selection can be detected by comparisons of the dn/ds ratio within and between species The gene for lysozyme has evolved convergently in cellulosedigesting mammals Codon usages are biased Positive and negative selection leave their signatures in DNA sequences Conclusion: 35 years of research on molecular evolution Two-locus and Multilocus Population Genetics Mimicry in Papilio is controlled by more than one genetic locus Genotypes at different loci in Papilio memnon axe coadapted Mimicry in Heliconius is controlled by more than one gene, but they are not tightly linked Two-locus genetics is concerned with haplotype frequencies Frequencies ofhaplotypes may or may not be in linkage equilibrium Human HLA genes are a multilocus gene system Linkage disequilibrium can exist for several reasons Two-locus models of natural selection can be built 206

8 Full Contents xi 8.9 Hitch-hiking occurs in two-locus selection models Selective sweeps can provide evidence of selection in DNA sequences Linkage disequilibrium can be advantageous, neutral, or disadvantageous Wright invented the influential concept of an adaptive topography The shifting balance theory of evolution Quantitative Genetics Climatic changes have driven the evolution of beak size in one of Darwin's finches Quantitative genetics is concerned with characters controlled by large numbers of genes Variation isfirstdivided into genetic and environmental effects Variance of a character is divided into genetic and environmental effects Relatives have similar genotypes, producing the correlation between relatives Heritability is the proportion of phenotypic variance that is additive A character's heritability determines its response to artificial selection Strength of selection has been estimated in many studies of natural populations Relations between genotype and phenotype may be non-linear, producing remarkable responses to selection Stabilizing selection reduces the genetic variability of a character Characters in natural populations subject to stabilizing selection show genetic variation Levels of genetic variation in natural populations are imperfectly understood Conclusion 249 PART 3. ADAPTATION AND NATURAL SELECTION Adaptive Explanation Natural selection is the only known explanation for adaptation Pluralism is appropriate in the study of evolution, not of adaptation Natural selection can in principle explain all known adaptations New adaptations evolve in continuous stages from pre-existing adaptations, but the continuity takes various forms In Darwin's theory, no special process produces evolutionary novelties The function of an adaptation may change with little change in its form A new adaptation may evolve by combining unrelated parts 265

9 xii Full Contents 10.5 Genetics of adaptation Fisher proposed a model, and microscope analogy, to explain why the genetic changes in adaptive evolution will be small An expanded theory is needed when an organism is not near an adaptive peak The genetics of adaptation is being studied experimentally Conclusion: the genetics of adaptation Three main methods are used to study adaptation Adaptations in nature are not perfect Adaptations maybe imperfect because of time lags Genetic constraints may cause imperfect adaptation Developmental constraints may cause adaptive imperfection Historic constraints may cause adaptive imperfection An organism's design may be a trade-off between different adaptive needs Conclusion: constraints on adaptation How can we recognize adaptations? The function of an organ should be distinguished from the effects it may have Adaptations can be defined by engineering design or reproductive fitness The Units of Selection What entities benefit from the adaptations produced by selection? Natural selection has produced adaptations that benefit various levels of organization Segregation distortion benefits one gene at the expense of its allele Selection may sometimes favor some cell lines relative to other cell lines in the same body Natural selection has produced many adaptations to benefit organisms Natural selection working on groups of close genetic relatives is called kin selection Whether group selection ever produces adaptations for the benefit of groups has been controversial, though most biologists now think it is only a weak force in evolution Which level in the hierarchy of organization levels will evolve adaptations is controlled by which level shows heritability Another sense of "unit of selection" is the entity whose frequency is adjusted directly by natural selection 306

10 Full Contents xiii 11.4 The two senses of "unit of selection" are compatible: one specifies the entity that generally shows phenotypic adaptations, the other the entity whose frequency is generally adjusted by natural selection Adaptations in Sexual Reproduction The existence of sex is an outstanding, unsolved problem in evolutionary biology Sex has a 50% cost Sex is unlikely to be explained by genetic constraint Sex can accelerate the rate of evolution Is sex maintained by group selection? There are two main theories in which sex may have a short-term advantage Sexual reproduction can enable females to reduce the number of deleterious mutations in their offspring The mutational theory predicts U > Coevolution of parasites and hosts may produce rapid environmental change Conclusion: it is uncertain how sex is adaptive The theory of sexual selection explains many differences between males and females Sexual characters are often apparently deleterious Sexual selection acts by male competition and female choice Females may choose to pair with particular males Females may prefer to pair with handicapped males, because the male's survival indicates his high quality Female choice in most models of Fisher's and Zahavi's theories is open ended, and this condition can be tested Fisher's theory requires heritable variation in the male character, and Zahavi's theory requires heritable variation in fitness Natural selection may work in conflicting ways on males and females Conclusion: the theory of sex differences is well worked out but incompletely tested The sex ratio is a well understood adaptation Natural selection usually favors a 50 : 50 sex ratio Sex ratios may be biased when either sons or daughters disproportionately act as "helpers at the nest" Different adaptations are understood in different levels of detail 341

11 xiv Full Contents PART 4. EVOLUTION AND DIVERSITY Species Concepts and Intraspecific Variation In practice species are recognized and defined by phenetic characters Several closely related species concepts exist The biological species concept The ecological species concept The phenetic species concept Isolating barriers Isolating barriers prevent interbreeding between species Sperm or pollen competition can produce subtle prezygotic isolation Closely related African cichlid fish species are prezygotically isolated by their color patterns, but are not postzygotically isolated Geographic variation within a species can be understood in terms of population genetic and ecological processes Geographic variation exists in all species and can be caused by adaptation to local conditions Geographic variation may also be caused by genetic drift Geographic variation may take the form of a cline "Population thinking" and "typological thinking" are two ways of thinking about biological diversity Ecological influences on the form of a species are shown by the phenomenon of character displacement Some controversial issues exist between the phenetic, biological, and ecological species concepts The phenetic species concept suffers from serious theoretical defects Ecological adaptation and gene flow can provide complementary, or in some cases competing, theories of the integrity of species Both selection and genetic incompatibility provide explanations of reduced hybrid fitness Taxonomic concepts may be nominalist or realist The species category Categories below the species level Categories above the species level Conclusion Speciation How can one species split into two reproductively isolated groups oforganisms? 382

12 Full Contents xv 14.2 A newly evolving species could theoretically have an allopatric, parapatric, or sympatric geographic relation with its ancestor Reproductive isolation can evolve as a by-product of divergence in allopatric populations Laboratory experiments illustrate how separately evolving populations of a species tend incidentally to evolve reproductive isolation Prezygotic isolation evolves because it is genetically correlated with the characters undergoing divergence Reproductive isolation is often observed when members of geographically distant populations are crossed Speciation as a by-product of divergence is well documented The Dobzhansky-Muller theory of postzygotic isolation The Dobzhansky-Muller theory is a genetic theory of postzygotic isolation, explaining it by interactions among many gene loci The Dobzhansky-Muller theory is supported by extensive genetic evidence The Dobzhansky-Muller theory has broad biological plausibility The Dobzhansky-Muller theory solves a general problem of "valley crossing" during speciation Postzygotic isolation may have ecological as well as genetic causes Postzygotic isolation usually follows Haldane's rule An interim conclusion: two solid generalizations about speciation Reinforcement Reproductive isolation may be reinforced by natural selection Preconditions for reinforcement maybe short lived Empirical tests of reinforcement are inconclusive or fail to support the theory Some plant species have originated by hybridization Speciation may occur in non-allopatric populations, either parapatrically or sympatrically Parapatric speciation Parapatric speciation begins with the evolution of a stepped cline Evidence for the theory of parapatric speciation is relatively weak Sympatric speciation Sympatric speciation is theoretically possible Phytophagous insects may split sympatrically by host shifts Phylogenies can be used to test whether speciation has been sympatric or allopatric The influence of sexual selection in speciation is one current trend in research 413

13 xvi Full Contents Identification of genes that cause reproductive isolation is another current trend in research Conclusion The Reconstruction of Phylogeny Phylogenies express the ancestral relations between species Phylogenies are inferred from morphological characters using cladistic techniques Homologies provide reliable evidence for phylogenetic inference, and homoplasies provide unreliable evidence Homologies can be distinguished from homoplasies by several criteria Derived homologies are more reliable indicators of phylogenetic relations than are ancestral homologies The polarity of character states can be inferred by several techniques Outgroup comparison The fossil record Other methods Some character conflict may remain after cladistic character analysis is complete Molecular sequences are becoming increasingly important in phylogenetic inference, and they have distinct properties Several statistical techniques exist to infer phylogenies from molecular sequences An unrooted tree is a phylogeny in which the common ancestor is unspecified One class of molecular phylogenetic techniques uses molecular distances Molecular evidence may need to be adjusted for the problem of multiple hits A second class of phylogenetic techniques uses the principle of parsimony A third class of phylogenetic techniques uses the principle ofmaximumlikelihood Distance, parsimony, and maximum likelihood methods are all used, but their popularity has changed over time Molecular phylogenetics in action Different molecules evolve at different rates and molecular evidence can be tuned to solve particular phylogenetic problems Molecular phylogenies can now be produced rapidly, and are used in medical research Several problems have been encountered in molecular phylogenetics Molecular sequences can be difficult to align 452

14 Full Contents xvii The number of possible trees may be too large for them all to be analyzed Species in a phylogeny may have diverged too little or too much Different lineages may evolve at different rates Paralogous genes may be confused with orthologous genes Conclusion: problems in molecular phylogenetics Paralogous genes can be used to root unrooted trees Molecular evidence successfully challenged paleontological evidence in the analysis of human phylogenetic relations Unrooted trees can be inferred from other kinds of evidence, such as chromosomal inversions in Hawaiian fruitflies Conclusion Classification and Evolution Biologists classify species into a hierarchy of groups There are phenetic and phylogenetic principles of classification There are phenetic, cladistic, and evolutionary schools of classification A method is needed to judge the merit of a school of classification Phenetic classification uses distance measures and cluster statistics Phylogenetic classification uses inferred phylogenetic relations Hennig's cladism classifies species by their phylogenetic branching relations Cladists distinguish monophyletic, paraphyletic, and polyphyletic groups A knowledge of phylogeny does not simply tell us the rank levels in Linnaean classification Evolutionary classification is a synthesis of phenetic and phylogenetic principles The principle of divergence explains why phylogeny is hierarchical Conclusion Evolutionary Biogeography Species have defined geographic distributions Ecological characteristics of a species limit its geographic distribution Geographic distributions are influenced by dispersal Geographic distributions are influenced by climate, such as in the ice ages Local adaptive radiations occur on island archipelagos Species of large geographic areas tend to be more closely related to other local species than to ecologically similar species elsewhere in the globe 503

15 xviii Full Contents 17.7 Geographic distributions are influenced by vicariance events, some of which are caused by plate tectonic movements The Great American Interchange Conclusion 517 PART 5. MACROEVOLUTION The History of Life Fossils are remains of organisms from the past and are preserved in sedimentary rocks Geological time is conventionally divided into a series of eras, periods, and epochs Successive geological ages were first recognized by characteristic fossil faunas Geological time is measured in both absolute and relative terms The history of life: the Precambrian The origin of life The origin of cells The origin of multicellular life The Cambrian explosion Evolution of land plants Vertebrate evolution Colonization of the land Mammals evolved from the reptiles in a long series of small changes Human evolution Four main classes of change occurred during hominin evolution Fossil records show something of our ancestors for the past 4 million years Macroevolution may or may not be an extrapolated form of microevolution Evolutionary Genomics Our expanding knowledge of genome sequences is making it possible to ask, and answer, questions about the evolution ofgenomes The human genome documents the history of the human gene set since early life The history of duplications can be inferred in a genomic sequence Genome size can shrink by gene loss 561

16 Full Contents xix 19.5 Symbiotic mergers, and horizontal gene transfer, between species influence genome evolution The X/Y sex chromosomes provide an example of evolutionary genomic research at the chromosomal level Genome sequences can be used to study the history of non-coding DNA Conclusion Evolutionary Developmental Biology Changes in development, and the genes controlling development, underlie morphological evolution The theory of recapitulation is a classic idea (largely discredited) about the relation between development and evolution Humans may have evolved from ancestral apes by changes in regulatory genes Many genes that regulate development have been identified recently Modern developmental genetic discoveries have challenged and clarified the meaning of homology The Hox gene complex has expanded at two points in the evolution ofanimals Changes in the embryonic expression of genes are associated with evolutionary changes in morphology Evolution of genetic switches enables evolutionary innovation, making the system more "evolvable" Conclusion Rates of Evolution Rates of evolution can be expressed in "darwins," as illustrated by a study of horse evolution How do population genetic, and fossil, evolutionary rates compare? Rates of evolution observed in the short term can explain speciation over longer time periods in Darwin's finches Why do evolutionary rates vary? The theory of punctuated equilibrium applies the theory of allopatric speciation to predict the pattern of change in the fossil record What is the evidence for punctuated equilibrium and for phyletic gradualism? A satisfactory test requires a complete stratigraphic record and biometrical evidence Caribbean bryozoans from the Upper Miocene and Lower Pliocene show a punctuated equilibrial pattern of evolution 603

17 xx Full Contents Ordovician trilobites show gradual evolutionary change Conclusion Evolutionary rates can be measured for non-continuous character changes, as illustrated by a study of "living fossil" lungfish Taxonomic data can be used to describe the rate of evolution of higher taxonomic groups Conclusion Coevolution Coevolution can give rise to coadaptations between species Coadaptation suggests, but is not conclusive evidence of, coevolution Insect-plant coevolution Coevolution between insects and plants may have driven the diversification of both taxa Two taxa may show mirror-image phylogenies, but coevolution is only one of several explanations for this pattern Cophylogenies are not found when phytophagous insects undergo host shifts to exploit phylogenetically unrelated but chemically similar plants Coevolution between plants and insects may explain the grand pattern of diversification in the two taxa Coevolutionary relations will often be diffuse Parasite-host coevolution Evolution of parasitic virulence Parasites and their hosts may have cophylogenies Coevolution can proceed in an "arms race" Coevolutionary arms races can result in evolutionary escalation The probability that a species will go extinct is approximately independent of how long it has existed Antagonistic coevolution can have various forms, including the Red Queen mode Both biological and physical hypotheses should be tested on macroevolutionary observations Extinction and Radiation The number of species in a taxon increases during phases of adaptive radiation Causes and consequences of extinctions can be studied in the fossil record Mass extinctions The fossil record of extinction rates shows recurrent rounds of mass extinctions 648

18 Full Contents xxi The best studied mass extinction occurred at the Cretaceous-Tertiary boundary Several factors can contribute to mass extinctions Distributions of extinction rates may fit a power law Changes in the quality of the sedimentary record through time are associated with changes in the observed extinction rate Species selection Characters that evolve within taxa may influence extinction and speciation rates, as is illustrated by snails with planktonic and direct development Differences in the persistence of ecological niches will influence macroevolutionary patterns When species selection operates, the factors that control macroevolution differ from the factors that control microevolution Forms of species selection may change during mass extinctions One higher taxon may replace another, because of chance, environmental change, or competitive replacement Taxonomic patters through time can provide evidence about the cause of replacements Two bryozoan groups are a possible example of a competitive replacement Mammals and dinosaurs are a classic example of independent replacement, but recent molecular evidence has complicated the interpretation Species diversity may have increased logistically or exponentially since the Cambrian, or it may have increased little at all Conclusion: biologists and paleontologists have held a range of views about the importance of mass extinctions in the history of life 677 Glossary 682 Answers to Study and Review Questions 690 References 699 Index 733 Color plate section between pp. 70 and 71