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A goal shared by this chapter with all the other parts of this book is to emphasize the ubiquity of reticulate evolution as an agent of genetic and evolutionary change. Another goal, unique to the topic in this chapter, is to address the hypothesis that genetic exchange events have impacted greatly the evolutionary trajectory of organisms that parasitize and kill humans. The first of these goals is accomplished as this chapter is considered in the context of the previous seven. The second objective is obvious from the examples given. The organisms that make up the lion-share of the pathogens that maim and kill humans are represented in the examples discussed.

This chapter investigates the fit of genetic, phenotypic, and linguistic data to two well-known models of population history. The first of these models, termed the population fissions model, emphasizes population splitting, isolation, and independent evolution. It predicts that genetic and linguistic data will be perfectly tree-like. The second model, termed isolation by distance, emphasizes genetic exchange among geographically proximate populations. It predicts a monotonic decline in genetic similarity with increasing geographic distance. While these models are overly simplistic, deviations from them were expected to provide important insights into the population history of northern Island Melanesia. The chapter finds scant support for either model because the prehistory of the region has been so complex. Nonetheless, the genetic and linguistic data are consistent with an early radiation of proto-Papuan speakers into the region followed by a much later migration of Austronesian speaking peoples. While these groups subsequently experienced substantial genetic and cultural exchange, this exchange has been insufficient to erase this history of separate migrations.

This chapter discusses methodologies to test the hypothesis of genetic exchange. The goal is to indicate the diversity of approaches that facilitate such tests. It begins by examining conflicting conclusions, drawn by different investigators, concerning the importance of gene flow in the genus Quercus. This is used to indicate the importance of utilizing a comparative approach when investigating possible instances of genetic exchange. Five methodologies to test for such exchange are discussed: (i) trans-generational hybrid zone analyses; (ii) estimates of phylogenetic discordance; (iii) analyses involving gene genealogies and models of speciation; (iv) estimations of intragenomic divergence; and (v) the application of nested clade analysis. Examples that highlight the specific utility of each of these approaches are reviewed.

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.

This chapter begins with a brief history of pre-Darwinian, evolutionary studies concerning genetic exchange. It then discusses various organismal systems to exemplify some ways in which post-Modern Synthesis research has been pursued to test the evolutionary role of genetic exchange. It considers examples of well-developed evolutionary model systems including plants, animals, bacteria, and viruses. These were chosen because they reflect broadly based, in-depth studies of the possible evolutionary consequences from natural hybridization and/or lateral gene transfer. Some cases (e.g. viral lineages) also afford the opportunity to point to the uncertainty in categorizing them as either natural hybridization or lateral gene transfer.

This chapter considers the barriers that limit genetic exchange. The conceptual framework for this chapter assumes that specific barriers are part of a multi-tiered process. In sexually reproducing organisms, these barriers can be easily placed into the categories of pre- and postzygotic. However, even for those organisms thought to spend most of their life history reproducing asexually (e.g. bacterial species) limits to genetic exchange can be typified with this concept. Various ecological, behavioral, gametic, viability, and fertility barriers can thus isolate both ‘asexual’ and ‘sexual’ species. The chapter adopts a model in which multiple, life-history-stage-specific characteristics must be overcome for gene exchange to occur.

This chapter examines the effects of gene exchange on the formation of new evolutionary lineages. In some cases this can be viewed as the origin of new species, in others the organisms formed from genetic exchange are given subspecific classifications. In some instances, the genetic exchange event is seen to be the basal event for entire evolutionary assemblages. Regardless of the evolutionary timing of such events and the taxonomic identity of the products, the importance remains in the outcome: that is, novelty has been produced, both in terms of new organisms and new adaptations. The chapter presents examples from a wide range of microorganismic and multicellular lineages. It highlights cases of diversification that can be placed into the categories of polyploid, homoploid, ecological, and recombinational speciation.

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.

This chapter introduces the topic of species concepts and the study of genetic exchange. It uses only four (biological, phylogenetic, cohesion, and prokaryotic) of the many definitions to illustrate how our concept of (i) what a species is and (ii) how it originates influences what evolutionary importance (or lack there of) we ascribe to genetic exchange. The chapter concludes by suggesting how we might use species concepts — often the bane of evolutionists interested in gene exchange — to afford a clearer understanding of the importance of natural hybridization and lateral gene transfer.

This chapter illustrates the fact that hybrid genotypes, like any other set of genotypes, demonstrate a range of fitness estimates. It demonstrates this point with examples involving natural hybridization, viral recombination, and lateral gene transfer. For all classes the conclusion is the same, some hybrid/recombinant genotypes have lower, some the same, and others higher fitness estimates relative to their progenitors.

This chapter focuses on the positive and negative effects of genetic exchange on the fate of endangered flora and fauna. In particular, it considers the role that such gene flow may have (i) in replenishing populations with limited genetic variability; or (ii) in causing genetic assimilation of rare forms by more numerous, related taxa. It argues that if evolutionary diversification is indeed a web-like process, then we should not give weight to whether members of one evolutionary lineage exchange genes with another when attempting to determine a value for conservation. Instead, we should ask the question of whether genetic exchange can help or hinder the conservation of manageable units (i.e. taxa). The chapter also examines the hypothesis that invasive species sometimes originate through introgressive hybridization.

Much debate has been generated as to how one can go about testing for the presence of past and contemporary genetic exchange. In this chapter, a number of analytical approaches (e.g. phylogenetic analysis and ABBA/BABA) are discussed including some of the most recent and most frequently applied theoretical methodologies. Each of these protocols is discussed in terms of their ability to test the alternative hypotheses of genetic exchange versus the retention of ancestral polymorphisms (i.e., incomplete lineage sorting). Furthermore, several classes of data, from hybrid zones, fossil assemblages, experimental populations, etc. are also highlighted. To illustrate the various concepts and methods, examples from plants, fungi, and animals are discussed.

This chapter considers instances where the genetic exchange, in this case resulting in genomic duplications, has derived from sexual reproduction as well as other forms of recombination. It looks at how genetic-exchange-induced duplications are seen as affecting genome evolution, gene function, adaptations and radiations of entire clades. In keeping with the tenor of the entire book, the chapter emphasizes evolutionarily creative outcomes that derive from the duplication of the genomic components of microorganisms, plants, and animals.

This chapter illustrates evolutionary outcomes from natural hybridization within plant and animal assemblages. Included in the discussions are examples of adaptive evolutionary change resulting in single evolutionary lineages and also entire clades. Likewise, the range of possible effects from allopolyploidy, in terms of the evolution of whole genomes, genes, gene families, and species complexes is examined. Included in the illustrations are plant and animal complexes that reflect homoploid and polyploid speciation, asexual and sexual hybrid lineage formation, and adaptive radiations. In everything from asexual gekkos and grasshoppers to New World butterflies, African cichlids, and Hawaiian silverswords genetic exchange has been a catalyst of adaptive evolutionary change.

One of the main messages of this text is that genetic exchange occurs throughout viral, prokaryotic and eukaryotic complexes, and that these exchange events can lead to evolutionary novelty via the production of genotypes/phenotypes possessing increased fitness (in certain environments) relative to their progenitors. Processes that prevent or promote viral recombination, horizontal gene transfer, and natural hybridization (i.e. reticulate evolution) are thus of primary importance in determining the evolutionary potential of admixture. In this chapter, processes that affect pre- or post-exchange reproductive isolation (e.g., prezygotic or postzygotic reproductive barriers in eukaryotes) are discussed in light of data from viruses, prokaryotes, plants, and animals. Each illustration shows that in spite of often-severe limitations to genetic exchange, admixture occurs leading to adaptive evolution and biological diversification and mosaic genomes.

This chapter begins with information from analyses of genomic and phenotypic traits resulting in tests of alternative models of human evolution. The remaining sections illustrate how genetic exchange has also affected organisms upon which humans depend for food, companionship, and entertainment. The discussion of human evolutionary history begins with analogous cases of reticulate evolution in a limited set of nonhominine taxa. It then proceeds to data for the clade containing Gorilla, Pan, and Homo. The data sets for the hominin primates derive from numerous genomic studies and a more limited set of morphological analyses. However, the diverse types of data lead to the same inference—all hominine lineages analyzed to date, including Homo, likely possess genomes consisting of segments of DNA derived from multiple, divergent lineages. Likewise, animals and plants on which we depend for protein, mobility, and stimulation illustrate the various outcomes from natural hybridization, including adaptive evolutionary change.

Some outcomes of genetic exchange between divergent lineages reflect risks to biodiversity. These include cases in which reticulate evolution produces highly virulent pathogens that decimate native populations. Likewise, introgressive hybridization between numerically or reproductively superior species and rare congeners can lead to the genetic assimilation and extinction of the endangered form. Examples reflecting such dire consequences are reviewed in this chapter. However, some of the potential outcomes from genetic exchange are less clearly negative. Examples of such outcomes include the relaxing of inbreeding depression in rare forms from the introgression of genetic material from a congener. Furthermore, many of the organismic clades suggested as illustrative of the need for preventing genetic exchange (e.g. rare canids) also are models of ancient reticulate evolution. Thus, many lineages involved in conservation programs belong to clades typified by introgressive hybridization and hybrid lineage formation not catalyzed by human interference.

The history of investigations into genetic exchange—resulting from natural hybridization, horizontal gene transfer, and viral recombination—between both closely- and distantly-related organisms has been marked by volatility between those holding different conceptual frameworks. Those applying “species purity” have voiced considerable chagrin concerning anything other than a marginal role for non-allopatric divergence (i.e. leading to gene transfer between different lineages). In contrast, an increasing number of evolutionary biologists are recognizing the growing data indicating just such non-allopatric diversification across many lineages and all corners of biological diversity. This chapter provides the conceptual framework, termed the web of life, and illustrations of organisms from all domains of life that reflect a reticulate evolutionary history. The development of this paradigm from Darwin’s time through the present is discussed in light of the debate over whether or not taxa are more or less likely to exchange genomic information along their evolutionary trajectories.