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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 provides a manifesto for the importance of taking proper account of microbes, from many perspectives the dominant form of life certainly in the past and arguably even today, in the philosophy of biology. It is argued that this will transform ideas on ontology, evolution, taxonomy, and biodiversity. A number of recent developments in microbiology—including biofilm formation, chemotaxis, quorum sensing, and gene transfer—highlight microbial capacities for cooperation and communication and break down conventional thinking that microbes are solely or primarily single-celled organisms. These insights also bring new perspectives to the levels of selection debate, as well as to discussions of the evolution and nature of multicellularity, and to neo-Darwinian understandings of evolutionary mechanisms.

The idea that all living things arose from their progenitors by descent with modification, and that this history can be depicted as a great tree, goes back to Darwin and beyond. Construction of a universal tree became possible after Carl Woese introduced ribosomal RNA sequences as a molecular chronometer. The tree consists of three great stems, or domains, designated Bacteria, Archaea and Eukarya, and this tripartite division is now generally accepted. But soon a serious complication arose: lateral transfer of genes between species, genera and even domains is common, particularly among prokaryotes. Lateral gene transfer erodes the phylogenetic trace, and has led some to question the very principle of a tree of life, but the division of all living things into three domains has held up. It is not easy to assign absolute dates to their emergence. The prokaryotes, Bacteria and Archaea, clearly go back more than 3 billion years. Modern Eukarya are much more recent, a billion years or so, but the eukaryotic lineage appears to be very ancient, possibly comparable to the prokaryotic ones.

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.

W. Ford Doolittle is well known as an iconoclastic and visionary microbial evolutionist. As well as challenging orthodoxies about the tree of life, he has made major contributions to empirically grounded evolutionary theory. His ideas about selfish DNA, introns, Gaia, and non-adaptive evolution have made a significant impact on how evolutionary biologists think about evolution. But how did these fundamental challenges to orthodoxy come about, and how did they succeed in gaining footing within mainstream biology? This chapter will address all these aspects of Doolittle’s long career, and also his recent more explicitly philosophical turn, in which he brings each of these revolutionary moments together under an emerging advocacy for explanatory and conceptual pluralism.