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This chapter considers methods for quantifying the importance of bees in pollinating a crop and in producing field-to-field cross-pollination and gene flow. Simple theoretical models are presented whose parameters identify key governing influences on bee pollination. The values of some parameters are known, particularly in systems involving honey bees and bumble bees, and their implications for the confinement of genetically-modified crops are discussed. Specific parameters whose values are unknown are identified as targets for future work.

This chapter looks at empirical methods for quantifying gene flow and inferring its role in adaptive divergence. An important point made therein is that gene flow can sometimes aid adaptation, such as when it enhances the genetic variation on which selection acts. The key questions addressed with empirical data are divided into the potential negative versus positive effects. On the negative side, questions include to what extent gene flow constrains adaptive divergence among environments, and how the resulting maladaptation might cause population declines and limit species' ranges. On the positive side, questions include whether gene flow has a special benefit in the case of antagonistic coevolution, and whether it can save (rescue) populations that would otherwise go extinct.

Landscape genetics explores how the microevolutionary processes of gene flow, genetic drift, and natural selection interact with environmental heterogeneity to shape population genetic structure. This chapter begins with a review of the various types of genetic data used in population and landscape genetics and discusses how these data are used to estimate genetic variation (heterozygosity) and gene flow among populations. From there, the chapter considers how population genetic structure can be assayed, which then segues into an analysis of the landscape correlates of population genetic structure, the identification of movement corridors and barriers to gene flow, and the relative effects of current versus historical landscape factors on population genetic structure. The chapter concludes with an overview of evolutionary landscape genetics, by considering the adaptive potential of populations in response to future landscape and climatic changes.

This chapter reports data, mainly from comparative genomics, which confirm a long-suspected high rate of interspecies gene flow due to hybridisation. It also reports the present interest in hybrids because of the recently documented hybrid origin of many species. However, sex is not the only mechanism to exchange genetic material among species. This chapter describes how horizontal gene transfer is a major mechanism that shapes the prokaryote genome, and a common mechanism in the eukaryotic world. Since reproductive isolation cannot often constitute an efficient barrier to preserve species identity, other mechanisms must be at work. This chapter argues that natural selection and genetic drift, acting at times in concert with reproductive isolation, are main factors that define the species borders in face of gene exchange among species. The chapter concludes that the ubiquity of gene flow and horizontal transfer may allow us to talk of the ‘web of life’.

In 2001, a group of researchers at the University of California-Berkeley published a report claiming that transgenes had moved from commercial corn to landrace corn in Oaxaca, Mexico. Transgenic corn had never been planted — at least legally — in Mexico, and so the researchers thought that it was an important scientific result with political implications. Mexican landrace corn had been propagated by indigenous farmers for centuries, and transgenes could be disruptive to the plant and the culture. The finding that transgenes were in landrace corn and parts of transgenes were hopping around the genome was hotly contested because of the flawed methodology used in the original study. Furthermore, the findings were never confirmed by any other researchers. In an unprecedented move, the journal editor announced that the paper should have never been published in the first place. This is one example of exaggerated claims that have encouraged the unnecessary controversy in agricultural biotechnology.

This chapter reviews the genetic consequences of environmental change. These changes are often so rapid that contemporary populations are often not found in genetic equilibrium. Furthermore, human-induced habitat fragmentation often results in a complex mosaic of remaining populations that differ in size and connectivity. A number of tools have been developed to detect population structure, gene flow, and evolution in such complex situations. The chapter provides evidence of rapid evolutionary responses in many organisms to changes in the environment. Such changes may be induced by a multitude of factors, including habitat loss and fragmentation, hindrances to dispersal and hence gene flow, climatic changes, and introduction of invasive species.

This chapter focuses on the geographic component of ecological speciation. It begins by giving different definitions of the geography of speciation and then studies the effects of geography on the sources of divergent selection. It considers how geographic contact between populations might constrain or promote ecological speciation, and how speciation can involve multiple geographic modes of divergence. It also assesses the empirical problem of detecting gene flow, through consideration of comparative geographic, coalescent-based, and genomic approaches. It concludes with a consideration of speciation along continuous environmental gradients versus between discrete patches and the unresolved issue of the spatial scale of speciation.

Current models of speciation assume that species arise when nuclear genotypes diverge following the disruption of gene flow between populations. This chapter explores the idea that speciation is specifically the result of divergence in coadapted mitonuclear gene complexes with divergence of most nuclear genes playing little or no role in speciation. To maintain mitonuclear coadaptation, nuclear genes must coevolve with rapidly changing mitochondrial genes. According to the mitonuclear compatibility concept of species, mitonuclear coevolution in isolated populations leads to speciation because population-specific mitonuclear coadaptations create between-population mitonuclear incompatibilities and hence barriers to gene flow between populations. In addition, selection for adaptive divergence of products of mitochondrial genes can lead to rapid fixation of novel mitochondrial genotypes between populations and consequently to disruption in gene flow between populations as the initiating step in animal speciation. The chapter considers the evidence for the involvement of mitonuclear compatibility in the process of speciation and the implications for this new concept of speciation and species.

This chapter examines competition in the context of pollination ecology. Competition is typically treated from the perspective of the plants, but it is also likely to occur among and between the pollinators. Furthermore, competition can occur at various levels—as a structuring factor in communities, as a selective force on an individual plant’s phenology, morphology, or rewards, and at a genetic level structuring competition for pollens between males, and female choice between possible mates. The chapter first considers several types of of competition in pollination ecology, potential outcomes of competition, and competition between pollinators before discussing how selection reduces intraspecific competition among plants and competition among pollinators. It also explores paternity, maternity, and gene flow in coflowering communities, focusing in particular on male competition and female choice, along with gene flow via pollen dispersal and seed dispersal.

Ant colony structure is a colony's caste, demographic, genealogical, and spatial make‐up. Characters of colony structure include the number and identity of reproductives, worker task allocation, and the nest number and architecture. A diversity of factors affect character states: genetics and gene flow, morphology, signal chemistry, nutrition, habitat, pathogen and parasite load, cooperation and conflict in the colony, colony age, and chance. Colony structure, in turn, has consequences for the colony, the population, the ant community, other organisms, and the abiotic environment. The formation of supercolonies represents a paradox in colony structure; reproductive altruism among unrelated individuals is not explicable by evolutionary theory that involves relatedness. Future work requires a more holistic approach to draw more universal conclusions on colony structure.

How close were the Neanderthals to modern humans? Are Neanderthal genes in our gene pool? This chapter explores recent studies analyzing the DNA from Neanderthal fossils to provide a framework to address these and related questions. Based on these fossil DNA studies, it appears that little if any gene flow occurred between Neanderthals despite many centuries of these groups living in proximity. For this reason, Neanderthals and modern humans are likely separate species.

This chapter reviews findings relating to the effect of genetic exchange on the evolution of the human lineage and lineages of organisms with which we interact (e.g. disease vectors, food sources). It considers fossil and genetic data that suggest gene flow between various archaic taxa, and between archaic taxa and anatomically modern Homo. It shows that the disastrous effects of natural hybridization and lateral gene transfer in disease and disease-vector evolution. The chapter also considers the highly beneficial results from the same processes in producing food products, drugs, and even clothing. It concludes with a discussion demonstrating that Homo sapiens has played an active role in producing new strands of the web of life.

Cities are home to a continuum of species that range from those specially adapted to exploit urban habitats, to others passing through as transient dispersers. Urbanization often has a profound impact on the movement and gene flow of these species. Compared to natural landscapes, urban environments are complex matrices of roads, buildings, bare soil, slopes, green space, and subterranean infrastructure. Urban neighbourhoods also vary greatly in their socioeconomic and cultural characteristics. This heterogeneity can lead to complex movement patterns in wildlife that are difficult or impossible to characterize using direct tracking methods. Population genetic analyses provide powerful approaches to evaluate spatial patterns of genetic variation and even signatures of adaptive evolution across the genome. When analysed with landscape, environmental, and socioeconomic data, genetic approaches may also identify which features of urban habitats impede or facilitate gene flow. These landscape genetic approaches, when paired with high-resolution sampling and replicated studies across multiple cities, identify dynamic processes that underpin wildlife movement in cities. This chapter reviews the use of spatially explicit genetic approaches in understanding urban wildlife movement, and highlights the many insights gained from rodents in particular as models for urban landscape genetics.

Populations are seldom uniform; they tend to be subdivided, with gene frequencies unevenly distributed across landscapes. In this chapter, determinants of population structure in parasites are first reviewed. Lice turn out to be excellent models for studies of population structure. Population genetic structure arises largely because of limitations to dispersal and gene flow. Population variation in parasites is influenced by the rate of parasite dispersal at three scales: dispersal among host individuals, among host populations, and among host species. If most dispersal consists of vertical transmission from parent hosts to their offspring, then parasites living on individual hosts and their progeny will accumulate genetic differences, contributing to population genetic structure. If horizontal transmission is common, however, it will tend to erode population genetic structure among host individuals. It is essential to have information regarding the dispersal ecology of parasites in order to interpret parasite population structure.

Migration and its consequence, gene flow, have been a major force affecting the frequency, spatial pattern, and spread of genes in human populations. Methodologies to document or infer local and regional movement include such ethnographic techniques as migration histories and genealogies, and ethnohistory. Anthropological geneticists also attempt to infer larger scale movement in past times by using both “classical” and molecular gene distributions. Inference based on genetic markers, however, often is contentious since alternative explanations are hard to exclude. This chapter employs an extended case study of a population, the Semai Senoi of Peninsular Malaysia, to examine and evaluate migration from the recent and local to the long-term in the Southeast Asian region.

This chapter begins by reflecting upon the major theme of this book: that genetic exchange is pervasive across all biological lineages. It discusses the implications of this regarding the tree-of-life and web-of-life concepts. Research directions that will benefit our understanding of the role of genetic exchange in evolution are also discussed. Some of these, including the use of genomic information to discern web processes, are gaining momentum with the appearance of many new data-sets. Others, such as studies that investigate the role of ecological setting on the outcome of genetic exchange, are rare, yet they represent another Golden Fleece because of their potential to yield new insights of major importance.

When the decision is made to augment gene flow into an isolated population, managers must decide how to augment gene flow, when to start, from where to take the individuals or gametes to be added, how many, which individuals, how often and when to cease. Even without detailed genetic data, sound genetic management strategies for augmenting gene flow can be instituted by considering population genetics theory, and/or computer simulations. When detailed data are lacking, moving (translocating) some individuals into isolated inbred population fragments is better than moving none, as long as the risk of outbreeding depression is low.