Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

So far in this course we have dealt entirely with the evolution of characters that are controlled by simple Mendelian inheritance at a single locus. There are notes on the course website about gametic disequilibrium and how allele frequencies change at two loci simultaneously, but we didn’t discuss them. In every example we’ve considered we’ve imagined that we could understand something about evolution by examining the evolution of a single gene. That’s the domain of classical population genetics. For the next few weeks we’re going to be exploring a field that’s actually older than classical population genetics, although the approach we’ll be taking to it involves the use of population genetic machinery. If you know a little about the history of evolutionary biology, you may know that after the rediscovery of Mendel’s work in 1900 there was a heated debate between the “biometricians” (e.g., Galton and Pearson) and the “Mendelians” (e.g., de Vries, Correns, Bateson, and Morgan). Biometricians asserted that the really important variation in evolution didn’t follow Mendelian rules. Height, weight, skin color, and similar traits seemed to

Human biochemical genetics

Genetics and analysis of quantitative traits

▪ Abstract Many uses of gene trees implicitly assume that nominal species are monophyletic in their alleles at the study locus. However, in well-sampled gene trees, certain alleles in one species may appear more closely related to alleles from different species than to other conspecific alleles. Such deviations from species-level monophyly have a variety of causes and may lead to erroneous evolutionary interpretations if undetected. The present paper describes the causes and consequences of these paraphyletic and polyphyletic patterns. It also provides a detailed literature survey of mitochondrial DNA studies on low-level animal phylogeny and phylogeography, results from which reveal the frequency of nonmonophyly and patterns of interpretation and sampling. This survey detected species-level paraphyly or polyphyly in 23% of 2319 assayed species, demonstrating this phenomenon to be statistically supported, taxonomically widespread, and far more common than generally recognized. Our findings call for increa...

Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA

The aim of this review is to consider the potential benefits that females may gain from mating more than once in a single reproductive cycle. The relationship between non-genetic and genetic benefits is briefly explored. We suggest that multiple mating for purely non-genetic benefits is unlikely as it invariably leads to the possibility of genetic benefits as well. We begin by briefly reviewing the main models for genetic benefits to mate choice, and the supporting evidence that choice can increase offspring performance and the sexual attractiveness of sons. We then explain how multiple mating can elevate offspring fitness by increasing the number of potential sires that compete, when this occurs in conjunction with mechanisms of paternity biasing that function in copula or post-copulation. We begin by identifying cases where females use pre-copulatory cues to identify mates prior to remating. In the simplest case, females remate because they identify a superior mate and 'trade up' genetically. The main evidence for this process comes from extra-pair copulation in birds. Second, we note other cases where pre-copulatory cues may be less reliable and females mate with several males to promote post-copulatory mechanisms that bias paternity. Although a distinction is drawn between sperm competition and cryptic female choice, we point out that the genetic benefits to polyandry in terms of producing more viable or sexually attractive offspring do not depend on the exact mechanism that leads to biased paternity. Post-copulatory mechanisms of paternity biasing may: (1) reduce genetic incompatibility between male and female genetic contributions to offspring; (2) increase offspring viability if there is a positive correlation between traits favoured post-copulation and those that improve performance under natural selection; (3) increase the ability of sons to gain paternity when they mate with polyandrous females. A third possibility is that genetic diversity among offspring is directly favoured. This can be due to bet-hedging (due to mate assessment errors or temporal fluctuations in the environment), beneficial interactions between less related siblings or the opportunity to preferentially fertilise eggs with sperm of a specific genotype drawn from a range of stored sperm depending on prevailing environmental conditions. We use case studies from the social insects to provide some concrete examples of the role of genetic diversity among progeny in elevating fitness. We conclude that post-copulatory mechanisms provide a more reliable way of selecting a genetically compatible mate than pre-copulatory mate choice. Some of the best evidence for cryptic female choice by sperm selection is due to selection of more compatible sperm. Two future areas of research seem likely to be profitable. First, more experimental evidence is needed demonstrating that multiple mating increases offspring fitness via genetic gains. Second, the role of multiple mating in promoting assortative fertilization and increasing reproductive isolation between populations may help us to understand sympatric speciation.

Why do females mate multiply? A review of the genetic benefits.

1 Gender and Sexual Dimorphism in Flowering Plants: A Review of Terminology, Biogeographic patterns, Ecological Correlates, and Phylogenetic Approaches.- 1.1 Introduction.- 1.2 Terminology.- 1.3 Incidence of Dioecy.- 1.3.1 Overview.- 1.3.2 Ecological Associations.- 1.3.3 Geographic Patterns.- 1.4 Importance of Phylogenetic Approaches.- 1.5 Using Phylogenies to Understand Process and Pattern.- 1.5.1 Phylogenetic Distributions.- 1.5.2 Self-Incompatibility and Dioecy.- 1.5.3 Dioecy and Fleshy Fruits.- 1.5.4 Habitat Shifts, Pollination Biology, and Changes in Outcrossing Rates.- 1.6 Conclusions.- References.- 2 Theories of the Evolution of Dioecy.- 2.1 Introduction.- 2.2 Importance of Theoretical Models.- 2.3 Pathways to Dioecy.- 2.4 Theoretical Relationships Between Allocation of Reproductive Resources and Invasion of Populations by New Sex Morphs.- 2.4.1 Fitness in Outcrossing and Partially Selfing Cosexes and Allocation in Cosexes.- 2.4.2 Invasion of Populations by Females and Males.- 2.4.3 Effect of Cosex Allocations on Invasion by Unisexuals or Partially Sterile Types.- 2.4.4 Effects of Unisexuals on Cosex Allocations.- 2.4.5 Other Possible Routes to Dioecy.- 2.5 Testing the Theory.- 2.5.1 Comparative Tests.- 2.5.2 Gain Curves.- 2.5.3 Intraspecific Data.- 2.5.4 Genetic Data.- 2.6 Conclusions.- 2.7 References.- 3 Empirical Studies: Evolution and Maintenance of Dimorphic Breeding Systems.- 3.1 Introduction.- 3.2 Evolutionary Pathways to Gender Dimorphism.- 3.2.1 Approaches to the Study of Gender.- 3.2.1.1 Quantitative Description of Plant Gender.- 3.2.1.2 Theoretical Modelling.- 3.2.1.3 Phylogenetic Analysis.- 3.2.2 Overview of Pathways.- 3.2.3 From Cosexuality Via Gynodioecy to Dioecy.- 3.2.4 From Monoecy Via Paradioecy to Dioecy.- 3.2.5 From Cosexuality Via Androdioecy to Dioecy.- 3.2.6 From Heterostyly to Dioecy.- 3.2.7 From Duodichogamy or Heterodichogamy to Dioecy.- 3.2.8 The Evolution of Trioecy.- 3.3 Maintenance of Gender Dimorphism in Natural Populations.- 3.3.1 Sex Ratios.- 3.3.2 Evidence for an Outcrossing Advantage: Rates of Selfing and Levels of Inbreeding Depression.- 3.3.3 Relative Seed Fecundity of the Two Sexes.- 3.3.4 Relative Pollen Fecundity of the Two Sexes.- 3.3.5 Case Studies: Tests of Theoretical Models.- 3.3.5.1 Female Frequency and Habitat in Plantago lanceolata.- 3.3.5.2 Plant Vigour, Fruit Production and the Sex Ratio in Hebe strictissima.- 3.3.5.3 Rates of Selfing, Inbreeding Depression and the Sex Ratio.- 3.3.5.4 The Breakdown of Outcrossing Mechanism in Aralia.- 3.4 Directions for Future Research.- 3.4.1 Testable Predictions from Ecological Correlations.- 3.4.2 Other Research Gaps.- 3.5 Conclusions.- References.- 4 Theories of the Evolution of Sexual Dimorphism.- 4.1 Introduction.- 4.2 Models of Sexual Dimorphism.- 4.2.1 Types of Models.- 4.2.2 General Features.- 4.2.3 Sexual Dimorphism in a Dioecious Organism.- 4.2.3.1 Genetic Models.- 4.2.3.2 ESS Models.- 4.2.4 The Evolution of Gender and Sexual Dimorphism.- 4.2.4.1 ESS Models.- 4.2.4.2 Genetic Models.- 4.3 The Biology of Sexual Dimorphism.- 4.3.1 Disruptive Selection on Homologous Characters.- 4.3.1.1 Biological Circumstances.- 4.3.1.2 Theory on Disruptive Selection in Dioecious Organisms.- 4.3.1.3 Theory on the Evolution of Gender and Sexual Dimorphism.- 4.3.1.4 Disruptive Selection and Sexual Dimorphism in Plants.- 4.3.2 Ecological Competition.- 4.3.2.1 Biological Circumstances.- 4.3.2.2 Theory on Character Displacement Due to Intraspecific Competition.- 4.3.2.3 Competitive Character Displacement and SSS in Dioecious Plants.- 4.3.3 Intersexual Selection.- 4.3.3.1 Biological Circumstances.- 4.3.3.2 Theory on Intersexual Selection.- 4.3.3.3 Mate Choice and Sexual Dimorphism in Plants.- 4.4 Conclusions.- References.- 5 Sexual Dimorphism in Flowers and Inflorescences.- 5.1 Introduction.- 5.2 Patterns.- 5.2.1 Perianth Size.- 5.2.2 Perianth Shape.- 5.2.3 Nectar.- 5.2.4 Vestigial Characters.- 5.2.5 Other Flower Characters.- 5.2.6 Multi-Flower Characters.- 5.2.7 Questions.- 5.3 Evolutionary Hypotheses.- 5.3.1 Sexual Selection and Character Exaggeration.- 5.3.2 Specific Tests, Hypotheses, and Uncertainties.- 5.3.2.1 Perianth Size.- 5.3.2.2 Perianth Shape.- 5.3.2.3 Nectar.- 5.3.2.4 Vestigial Character.- 5.3.2.5 Other Flower Characters: Longevity.- 5.3.2.6 Multi-Flower Characters.- 5.4 Conclusions.- 5.4.1 Towards Quantitative Understanding.- 5.4.2 Size-Number Trade-Offs.- 5.4.3 Costs of Exaggeration.- 5.4.4 Variation in Costs and Benefits.- 5.4.5 Macro evolution.- References.- 6 Sexual Dimorphism in Live History.- 6.1 Introduction.- 6.2 Predictions Based on Sex-Differential Reproductive Investment.- 6.3 Patterns of Sexual Dimorphism in Life-History Traits.- 6.3.1 Response to Stress.- 6.3.2 Case Studies of Two Species in which the Cost of Reproduction Is Higher for Females.- 6.4 Factors Offsetting Between-Sex Differences in the Cost of Reproduction.- 6.4.1 Sexual Dimorphism in the Timing of Investment in Reproduction Versus Growth Within a Season.- 6.4.2 Sexual Dimorphism in the Timing of Flowering Within a Season.- 6.4.3 Sexual Dimorphism in the Frequency of Flowering.- 6.4.4 Sexual Dimorphism in Age of Maturation.- 6.4.5 Sexual Dimorphism in Physiological Traits.- 6.4.6 Sex-Differential Herbivory.- 6.5 The Contrary Case of Silene latifolia.- 6.6 Conclusions.- References.- 7 Dimorphism in Physiology and Morphology.- 7.1 Introduction.- 7.1.1 Causes of Sexual Dimorphism in Physiology and Vegetative Morphology.- 7.1.2 Physiological and Morphological Responses to Natural Selection.- 7.1.3 Physiological and Morphological Responses to Sexual Selection.- 7.1.4 Functional Significance of Dimorphism in Physiology and Morphology.- 7.2 History of Studies on Sexual Dimorphism in Plants.- 7.3 Sexual Dimorphism in Plant Form and Function in Species with SSS.- 7.3.1 Salix (Willow Salicaceae).- 7.3.2 Acer negundo (Boxelder Aceraceae).- 7.3.3 Simmondsia chinensis (Jojoba/Goat Nut Buxaceae).- 7.3.4 Phoradendron juniperinum (Mistletoe Viscaceae).- 7.3.5 Other Species.- 7.4 Sexual Dimorphism in Plant Form and Function in Species Without SSS.- 7.4.1 Silene latifolia (White Campion Caryophyllaceae).- 7.4.2 Leucadendron (Proteaceae).- 7.4.3 Other Species.- 7.4.3.1 Agricultural and Weedy Species.- 7.4.3.2 Populus (Aspen Salicaceae).- 7.5 Conclusions and Future Directions.- References.- 8 Sexual Dimorphism and Biotic Interactions.- 8.1 Introduction.- 8.1.1 Reproductive Allocation and Biotic Interactions.- 8.2 Sexual Differences in Competitive Ability.- 8.3 Sexual Differences in Herbivory.- 8.3.1 Herbivore Preference.- 8.3.2 Correlates of Sexual Differences in Herbivore Damage.- 8.3.3 Herbivore Performance on Male and Female Hosts.- 8.3.4 Sexual Differences in Response to Herbivory.- 8.4 Sexual Differences in Parasitism.- 8.4.1 Foliar Pathogens.- 8.4.2 Flower-Infecting Pathogens.- 8.4.3 Nonfungal Parasites.- 8.5 General Discussion.- 8.5.1 Biotic Interactions and Biased Sex Ratios.- 8.5.2 Evolution of Sexual Differences in Herbivory.- 8.5.3 Future Studies.- References.- 9 Genetics of Gender Dimorphism in Higher Plants.- 9.1 Introduction.- 9.2 Monoecious Plants.- 9.2.1 Gender Dimorphism in Cucumber.- 9.2.2 Molecular Biology of Gender Dimorphism in Maize.- 9.2.2.1 Tasselseed2.- 9.2.2.2 Gibberellin and gender dimorphism in maize.- 9.2.2.3 The Anther ear1 gene.- 9.3 Multigenic gender determination systems in dioecious plants.- 9.3.1 Mercurialis annua.- 9.3.2 A single gender determination locus.- 9.3.3 Sex chromosomes.- 9.3.3.1 Morphologically distinct sex chromosomes.- 9.3.3.2 Structure of sex chromosomes in plants.- 9.3.3.3 X/autosome balance can regulate gender dimorphism.- 9.3.3.4 X/autosome balance in Drosophila melanogaster.- 9.3.4 Comparison of Active Y Sex Chromosomes in Plants and Animals.- 9.3.4.1 The active-Y gender determination of white campion.- 9.3.4.2 The mammalian active-Y gender determination mechanism.- 9.3.4.3 Does dosage compensation occur in white campion?.- 9.3.5 Evolution of the active-Y chromosome: Male sterility.- 9.3.5.1 Cytoplasmic male sterility.- 9.3.5.2 Suppression of carpel or pistil development.- 9.4 Expression of MADS-box genes in unisexual flowers.- 9.5 Conclusions.- References.- 10 Quantitative Genetics of Sexual Dimorphism.- 10.1 Introduction.- 10.2 Quantitative Genetic Models of Sexual Dimorphism.- 10.3 Integration of Quantitative Genetics with Sexual Selection.- 10.4 Correlated Evolution and Divergence of Male and Female Traits in Dioecious Plants.- 10.5 Correlated Evolution and Divergence of Male and Female Function in Hermaphroditic Plants.- 10.6 Conclusions.- 10.7 References.- Taxonomic Index.

Gender and sexual dimorphism in flowering plants

A hypothesis is presented which states that flower production in hermaphroditic flow- ering plants is primarily controlled by male function. The male function hypothesis predicts a lower fruit-to-flower ratio for hermaphrodites as compared to monoecious or dioecious plants. The hy- pothesis also predicts that self-compatible hermaphrodites should exhibit a higher percent fruit-set than self-incompatible hermaphrodites. These predictions are supported by fruit-set data compiled from the literature. An alternative hypothesis relating fruit-set to the probability of self-fertilization also predicts low fruit-set for hermaphrodites as compared to monoecious or dioecious plants. The self-incompatibility hypothesis is tested and rejected on the basis of fruit-set patterns in self-incom- patible andromonoecious, self-incompatible monoecious, and self-compatible monoecious species. The effect of the male function hypothesis on current ideas concerning low fruit-set in hermaphrodites is then examined.

On the Importance of Male Fitness in Plants: Patterns of Fruit-Set

Life-history theory revolves around the idea that various activities, such as growth, maintenance, and reproduction, compete for limited resources. Hence, current reproduction may lead to a reduction in growth and survival, and consequently a reduction in future reproduction. Gadgil and Bossert (1970) termed this a “cost function” and the phenomenon is now called the “cost of reproduction.” They interpreted life-history differences among species (e.g. age at first reproduction) as being adaptive, in that the particular life history selected for would be the one that maximizes fitness (Gadgil and Bossert 1970). Trivers (1972) and Bell (1980) extended this to comparisons between the sexes of animals, rather than between species, and noted that sex-specific differences in the cost of reproduction would lead to sexual dimorphism in timing of death and age at first reproduction, respectively.

Sexual Dimorphism in Life History

Vegetative growth and sexual reproduction were compared (under natural conditions and following defoliation) for the two sexual morphs of the subdioecious ev- ergreen shrub Hebe subalpina. Under natural conditions, both morphs produced the same number of flowers, but because the flowers of the polleniferous morph (here called "males") are larger males allocated almost twice as much biomass to flower production as did females. Females, by contrast, produced larger fruit as well as more fruit than males. In terms of biomass, females allocated 4.7 times as much as males on fruit production. Overall, females allocated almost twice the biomass to flowers and fruit. The morphs also differed in the timing of their growth, with each morph growing less during the phase in which its repro- ductive costs were highest. In spite of the greater allocation by females to reproduction, the two morphs grew the same amount over the entire reproductive cycle. This may be a result of the fact that females produced more leaves earlier in the season, which enabled them to accumulate more resources than males. The defoliation experiment substantiated the morph-differential allocation patterns. Defoliated shoots on females fruited, but did not grow relative to controls, and defoliated shoots on males grew, but did not fruit. These differences suggest that divergent selection has been operating on the morphs since the evolution of subdioecy (via gynodioecy) from cosexuality in Hebe, and may be related to differences in the relative fitness gains to the morphs through pollen vs. seeds.

Sex-Differential Resource Allocation Patterns in the Subdioecious Shrub Hebe Subalpina

It has long been known that rates of synonymous substitutions are unusually low in mitochondrial genes of flowering and other land plants. Although two dramatic exceptions to this pattern have recently been reported, it is unclear how often major increases in substitution rates occur during plant mitochondrial evolution and what the overall magnitude of substitution rate variation is across plants. A broad survey was undertaken to evaluate synonymous substitution rates in mitochondrial genes of angiosperms and gymnosperms. Although most taxa conform to the generality that plant mitochondrial sequences evolve slowly, additional cases of highly accelerated rates were found. We explore in detail one of these new cases, within the genus Silene. A roughly 100-fold increase in synonymous substitution rate is estimated to have taken place within the last 5 million years and involves only one of ten species of Silene sampled in this study. Examples of unusually slow sequence evolution were also identified. Comparison of the fastest and slowest lineages shows that synonymous substitution rates vary by four orders of magnitude across seed plants. In other words, some plant mitochondrial lineages accumulate more synonymous change in 10,000 years than do others in 100 million years. Several perplexing cases of gene-to-gene variation in sequence divergence within a plant were uncovered. Some of these probably reflect interesting biological phenomena, such as horizontal gene transfer, mitochondrial-to-nucleus transfer, and intragenomic variation in mitochondrial substitution rates, whereas others are likely the result of various kinds of errors. The extremes of synonymous substitution rates measured here constitute by far the largest known range of rate variation for any group of organisms. These results highlight the utility of examining absolute substitution rates in a phylogenetic context rather than by traditional pairwise methods. Why substitution rates are generally so low in plant mitochondrial genomes yet occasionally increase dramatically remains mysterious.

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Lynda F. Delph

Papers

Gender and sexual dimorphism in flowering plants

On the Importance of Male Fitness in Plants: Patterns of Fruit-Set

Sexual Dimorphism in Life History

Sex-Differential Resource Allocation Patterns in the Subdioecious Shrub Hebe Subalpina

Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants