It is a popularly held view that Darwin was the first author to draw a phylogenetic tree diagram. However, as is the case with most popular beliefs, this one also does not hold true. Firstly, Darwin never called his diagram of common descent a tree. Secondly, even before Darwin, tree diagrams were used by a variety of philosophical, religious, and secular scholars to depict phenomena such as "logical relationships," "affiliations," "genealogical descent," "affinity," and "historical relatedness" between the elements portrayed on the tree. Moreover, historically, tree diagrams themselves can be grouped into a larger class of diagrams that were drawn to depict natural and/or divine order in the world. In this paper, we trace the historical roots and cultural meanings of these tree diagrams. It will be demonstrated that tree diagrams as we know them are the outgrowth of ancient philosophical attempts to find the "true order" of the world, and to map the world "as it is" (ontologically), according to its true essence. This philosophical idea would begin a fascinating journey throughout Western European history. It lies at the foundation of the famous "scala naturae," as well as religious and secular genealogical thinking, especially in regard to divine, familial (kinship), and linguistic pedigrees that were often depicted by tree images. These scala naturae would fuse with genealogical, pedigree thinking, and the trees that were the result of this blend would, from the nineteenth century onward, also include the element of time. The recognition of time would eventually lead to the recognition of evolution as a fact of nature, and subsequently, tree iconographies would come to represent exclusively the evolutionary descent of species.

Applied Evolutionary Epistemology is a scientific-philosophical theory that defines evolution as the set of phenomena whereby units evolve at levels of ontological hierarchies by mechanisms and processes. This theory also provides a methodology to study evolution, namely, studying evolution involves identifying the units that evolve, the levels at which they evolve, and the mechanisms and processes whereby they evolve. Identifying units and levels of evolution in turn requires the development of ontological hierarchy theories, and examining mechanisms and processes necessitates theorizing about causality. Together, hierarchy and causality theories explain how biorealities form and diversify with time. This paper analyzes how Applied EE redefines both hierarchy and causality theories in the light of the recent explosion of network approaches to causal reasoning associated with studies on reticulate and macroevolution. Causality theories have often been framed from within a rigid, ladder-like hierarchy theory where the rungs of the ladder represent the different levels, and the elements on the rungs represent the evolving units. Causality then is either defined reductionistically as an upward movement along the strands of a singular hierarchy, or holistically as a downward movement along that same hierarchy. Upward causation theories thereby analyze causal processes in time, i.e. over the course of natural history or phylogenetically, as Darwin and the founders of the Modern Synthesis intended. Downward causation theories analyze causal processes in space, ontogenetically or ecologically, as the current eco-evo-devo schools are evidencing. This work demonstrates how macroevolution and reticulate evolution theories add to the complexity by examining reticulate causal processes in space-time, and the interactional hierarchies that such studies bring forth introduce a new form of causation that is here called reticulate causation. Reticulate causation occurs between units and levels belonging to different as well as to the same ontological hierarchies. This article concludes that beyond recognizing the existence of multiple units, levels, and mechanisms or processes of evolution, also the existence of multiple kinds of evolutionary causation as well as the existence of multiple evolutionary hierarchies needs to be acknowledged. This furthermore implies that evolution is a pluralistic process divisible into different kinds.

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Symbiogenesis is a form of horizontal evolution that occurred 2 billion years ago, with the evolution of eukaryotic cells. It will be argued that, just as we can develop universal selection theories based upon a general account of natural selection, we can also develop a universal symbiogenetic principle that can serve as a general framework to study the origin and evolution of language. (1) Horizontal evolution will be compared with and distinguished from vertical evolution. ( 2) Different examples of intra-and interspecific horizontal evolution will be given to show that horizontal evolution is quantitatively and qualitatively the most commonly occurring form of evolution throughout the history of life. (3) Finally, three examples are given of how a universal symbiogenesis principle can be implemented in the study of language origins and evolution, more specifically within: (a) the study of language variation, (b) language genes and (c) conceptual blending.

Reticulation is a recurring evolutionary pattern found in phylogenetic reconstructions of life. The pattern results from how species interact and evolve by mechanisms and processes including symbiosis; symbiogenesis; lateral gene transfer (that occurs via bacterial conjugation, transformation, transduction, Gene Transfer Agents, or the movements of transposons, retrotransposons, and other mobile genetic elements); hybridization or divergence with gene flow; and infectious heredity (induced either directly by bacteria, bacteriophages, viruses, prions, protozoa and fungi, or via vectors that transmit these pathogens). Research on reticulate evolution today takes on inter-and transdisciplinary proportions and is able to unite distinct research fields ranging from microbiology and molecular genetics to evolutionary biology and the biomedical sciences. This chapter summarizes the main principles of the diverse reticulate evolutionary mechanisms and situates them into the chapters that make up this volume.

Evolutionary epistemology can provide a unified scientific methodology that enables scholars to study the evolution of life as well as the evolution of cognition, science, culture and any other phenomenon displayed by living organisms. In this article, three heuristics are provided that allow for a thorough search for the units, levels and mechanisms of evolution. Contrary to previous approaches, units, levels and mechanisms are not identified by pointing out essential features, but rather ostensive definitions are preferred. That is, units are considered as such if a level of evolution and a mechanism of evolution is identifiable. Levels are levels if one can point out units that evolve at that level according to evolutionary mechanisms, and mechanisms are considered as such if one can point out units and levels where the mechanism is active.

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We distinguish between four cosmological transitions in the history of Western intellectual thought, and focus on how these cosmologies differentially define matter, space and time. We demonstrate that how time is conceptualized significantly impacts a cosmology's notion on causality, and hone in on how time is conceptualized differentially in modern physics and evolutionary biology. The former conflates time with space into a single spacetime continuum and focuses instead on the movement of matter, while the evolutionary sciences have a tradition to understand time as a given when they cartography how organisms change across generations over or in time, thereby proving the phenomenon of evolution. The gap becomes more fundamental when we take into account that phenomena studied by chrono-biologists demonstrate that numerous organisms, including humans, have evolved a "sense" of time. And micro-evolutionary/genetic, mesoevolutionary/developmental and macro-evolutionary phenomena including speciation and extinction not only occur by different evolutionary modes and at different rates, they are also timely phenomena that follow different periodicities. This article focusses on delineating the problem by finding its historical roots. We conclude that though time might be an obsolete concept for the physical sciences, it is crucial for the evolutionary sciences where evolution is defined as the change that biological individuals undergo in/over or through time.