Why Trees Are Important

The Tree of Life is the result of the interplay of changes in information and speciation. Almost 100 years after publication of Darwin’s Origin, the inception of Phylogenetic Systematics has resulted in a revolution in data inference. I briefly trace the development of this revolution and show examples of how data are interpreted relative to phylogenetic trees. I then provide brief discussions of how to read tree diagrams and the need to access the quality of phylogenetic inference.     

Driving forces for data exchange

The subgroup ‘Driving Forces for Data Exchange’ as part of the SETAC LCA Workgroup on Data Availability and Quality is finishing its final report with recommendations and guidelines to stimulate availability and exchange of LCI data. Activities in the past three years involved a literature review, interviews with LCI data publishers and stakeholder discussions. The final report will be part of a SETAC ‘Code of Life Cycle Inventory Practice’, dealing with LCI data availability and quality aspects in a broader sense.     

Yale Peabody Museum of Natural History’s “Travels in the Great Tree of Life”

The Yale Peabody Museum of Natural History developed a 1,000-square-foot exhibition to help the general public understand the concept of phylogenetic relationships and their depiction on scientific Trees, or cladograms. In addition, exhibition planners hoped visitors would understand that research on the Tree of Life is a massive, complex undertaking requiring powerful computers and that Tree research has many potential practical applications. Museum exhibits designed to convey scientific information must use “stealth” to accomplish their cognitive goals: Unlike students in formal science education classes, visitors are not obliged to learn—they do not learn because they must pass a final examination. Informal educators must engage visitors’ interest so that they willingly take in new information and perhaps even learn new skills, change attitudes, and behaviors. “Travels in the Great Tree of Life” succeeded in engaging visitors who came away with awareness and understanding of scientific Trees, the immensity of the construct, and to a lesser extent, potential practical applications.     

Communicating Phylogeny: Evolutionary Tree Diagrams in Museums

Tree of life diagrams are graphic representations of phylogeny—the evolutionary history and relationships of lineages—and as such these graphics have the potential to convey key evolutionary ideas and principles to a variety of audiences. Museums play a significant role in teaching about evolution to the public, and tree graphics form a common element in many exhibits even though little is known about their impact on visitor understanding. How phylogenies are depicted and used in informal science settings impacts their accessibility and effectiveness in communicating about evolution to visitors. In this paper, we summarize the analysis of 185 tree of life graphics collected from museum exhibits at 52 institutions and highlight some potential implications of how trees are presented that may support or hinder visitors’ understanding about evolution. While further work is needed, existing learning research suggests that common elements among the diversity of museum trees such as the inclusion of anagenesis and absence of time and shared characters might represent potential barriers to visitor understanding.     

The series,the network,and the tree: changing metaphors of order in nature

The history of biological systematics documents a continuing tension between classifications in terms of nested hierarchies congruent with branching diagrams (the ‘Tree of Life’) versus reticulated relations. The recognition of conflicting character distribution led to the dissolution of the scala naturae into reticulated systems, which were then transformed into phylogenetic trees by the addition of a vertical axis. The cladistic revolution in systematics resulted in a representation of phylogeny as a strictly bifurcating pattern (cladogram). Due to the ubiquity of character conflict—at the genetic or morphological level, or at any level in between—some characters will necessarily have to be discarded (qua noise) in favor of others in support of a strictly bifurcating phylogenetic tree. Pattern analysts will seek maximal congruence in the distribution of characters (ultimately of any kind) relative to a branching tree-topology; process explainers will call such tree-topologies into question by reference to incompatible evolutionary processes. Pattern analysts will argue that process explanations must not be brought to bear on pattern reconstruction; process explainers will insist that the reconstructed pattern requires a process explanation to become scientifically relevant, i.e., relevant to evolutionary theory. The core question driving the current debate about the adequacy of the ‘Tree of Life’ metaphor seems to be whether the systematic dichotomization of the living world is an adequate representation of the complex evolutionary history of global biodiversity. In ‘Questioning the Tree of Life’, it seems beneficial to draw at least four conceptual distinctions: pattern reconstruction versus process explanation as different epistemological approaches to the study of phylogeny; open versus closed systems as expressions of different kinds of population (species) structures; phylogenetic trees versus cladograms as representations of evolutionary processes versus patterns of relationships; and genes versus species as expressions of different levels of causal integration and evolutionary transformation.     

The attempt on the life of the Tree of Life: science,philosophy and politics

Lateral gene transfer (LGT), the exchange of genetic information between (primarily prokaryotic) lineages, not only makes construction of a universal Tree of Life (TOL) difficult to achieve, but calls into question the utility and meaning of any result. Here I review the science of prokaryotic LGT, the philosophy of the TOL as it figured in Darwin’s formulation of the Theory of Evolution, and the politics of the current debate within the discipline over how threats to the TOL should be represented outside it. We could encourage a more realistic and supportive public understanding of evolution by admitting that what we believe in is not a unified meta-theory but a versatile and well-stocked explanatory toolkit.     

John Maynard Smith and the natural philosophy of␣adaptation

One of the most remarkable aspects of John Maynard Smith’s work was the fact that he devoted time both to doing science and to reflecting philosophically upon its methods and concepts. In this paper I offer a philosophical analysis of Maynard Smith’s approach to modelling phenotypic evolution in relation to three main themes. The first concerns the type of scientific understanding that ESS and optimality models give us. The second concerns the causal–historical aspect of stability analyses of adaptation. The third concerns the concept of evolutionary stability itself. Taken together, these three themes comprise what I call the natural philosophy of adaptation.     

Does the 'Ring of Life' ring true?

In a recent stimulating paper, Rivera and Lake applied a new phylogenetic method to study the evolution of genomes, which challenges the classical representation of the Tree of Life. Acknowledging the evolutionary importance of lateral gene transfer, they used the conditioned genome approach to reconstruct the Tree of Life, and in the end proposed a Ring of Life. They explained that the Ring of Life structure is a result of a single fusion event between two prokaryotic genomes at the base of the eukaryotic tree, probably between the ancestors of a photosynthetic bacterium and an archaeon. Because this constitutes an important conclusion with regards to the evolutionary process and origin of the eukaryotic cell, their work deserves further attention before these conclusions can be accepted. Here we question the reconstruction and the meaning of the Ring of Life. In addition to general problems associated with gene-content-based phylogenetic analyses, we discuss some implicit premises and potential weaknesses of the conditioned genome method and conclude that, although Rivera and Lake's conclusions might be right, they have not been established by their current approach.     

God Versus the Human Genome Inside the Human Genome: A Case for Non-Intelligent Design, by John C. Avise. Oxford: Oxford University Press, 2010. Pp. xi + 222. H/b $19.95.

The University of Arizona’s Tree of Life Web Project organizes information about the biological taxa on the model of the tree of life itself. This creates intuitive and informative pathways for browsing. The Project has a well-articulated protocol for checking on the quality of information published on the site, which is evaluated a number of times as it is added to the site. This paper is intended to be an entreé to the site for teachers at all levels and the general public.     

113 Toward Resolution of the Fuzzy Nodes in Green Plant Phylogeny

We are funded to resolve the primary pattern of evolutionary diversification among green plants, and to establish a model for doing so that will be applicable to other groups of organisms with long evolutionary histories. To achieve this goal we will 1) complete a matrix of whole genome sequences for chloroplast and mitochondria and develop either nuclear or organellar bacterial artificial chromosome, BAC, libraries for about 50 representatives of the critical deep-branching lineages of green plants; 2) produce a comprehensive set of comparable morphological and ultrastructural data for these same taxa; 3) incorporate inferences from across the phylogenetic hierarchy in green plants using methods designed to permit scaling across studies. We shall indicate how this work will link to other research being conducted on green plants and various scales, especially the concatenation of our data sets with theirs. We will present the fuzzy nodes we have chosen to resolve and discuss our choices of taxa in this preliminary report. Funded by NSF's Tree of Life Program, 2002–2006, DEB #0228655 (lead institution), #228432, #0228679, #0228729, #0228660, #0228576.     

Universal scaling in the branching of the tree of life

Understanding the patterns and processes of diversification of life in the planet is a key challenge of science. The Tree of Life represents such diversification processes through the evolutionary relationships among the different taxa, and can be extended down to intra-specific relationships. Here we examine the topological properties of a large set of interspecific and intraspecific phylogenies and show that the branching patterns follow allometric rules conserved across the different levels in the Tree of Life, all significantly departing from those expected from the standard null models. The finding of non-random universal patterns of phylogenetic differentiation suggests that similar evolutionary forces drive diversification across the broad range of scales, from macro-evolutionary to micro-evolutionary processes, shaping the diversity of life on the planet.     

Characters Are Key: The Effect of Synapomorphies on Cladogram Comprehension

Cladograms, phylogenetic trees that depict evolutionary relationships among a set of taxa, are one of the most powerful predictive tools in modern biology. They are usually depicted in one of two formats—tree or ladder. Previous research (Novick and Catley 2007) has found that college students have much greater difficulty understanding a cladogram’s hierarchical structure when it is depicted in the ladder format. Such understanding would seem to be a prerequisite for successful tree thinking. The present research examined the effect of a theoretically guided manipulation—adding a synapomorphy on each branch that supports two or more taxa—on students’ understanding of the hierarchical structure of ladder cladograms. Synapomorphies are characters shared by a group of taxa due to inheritance from a common ancestor. Thus, their depiction on a cladogram may facilitate the understanding of evolutionary relationships. Students’ comprehension was assessed in terms of success at translating relationships depicted in the ladder format to the tree format. The results indicated that adding synapomorphies provided powerful conceptual scaffolding that improved comprehension for students with both weaker and stronger backgrounds in biology. For stronger background students, the benefit of adding synapomorphies to the ladders was comparable to that of approximately two hours of instruction in phylogenetics that emphasized the ladder format.     

Universal common ancestry,LUCA, and the Tree of Life: three distinct hypotheses about the evolution of life

Common ancestry is a central feature of the theory of evolution, yet it is not clear what “common ancestry” actually means; nor is it clear how it is related to other terms such as “the Tree of Life” and “the last universal common ancestor”. I argue these terms describe three distinct hypotheses ordered in a logical way: that there is a Tree of Life is a claim about the pattern of evolutionary history, that there is a last universal common ancestor is an ontological claim about the existence of an entity of a specific kind, and that there is universal common ancestry is a claim about a causal pattern in the history of life. With these generalizations in mind, I argue that the existence of a Tree of Life entails a last universal common ancestor, which would entail universal common ancestry, but neither of the converse entailments hold. This allows us to make sense of the debates surrounding the Tree, as well as our lack of knowledge about the last universal common ancestor, while still maintaining the uncontroversial truth of universal common ancestry.     

Do orthologous gene phylogenies really support tree-thinking?

Background  

Since Darwin's Origin of Species, reconstructing the Tree of Life has been a goal of evolutionists, and tree-thinking has become a major concept of evolutionary biology. Practically, building the Tree of Life has proven to be tedious. Too few morphological characters are useful for conducting conclusive phylogenetic analyses at the highest taxonomic level. Consequently, molecular sequences (genes, proteins, and genomes) likely constitute the only useful characters for constructing a phylogeny of all life. For this reason, tree-makers expect a lot from gene comparisons. The simultaneous study of the largest number of molecular markers possible is sometimes considered to be one of the best solutions in reconstructing the genealogy of organisms. This conclusion is a direct consequence of tree-thinking: if gene inheritance conforms to a tree-like model of evolution, sampling more of these molecules will provide enough phylogenetic signal to build the Tree of Life. The selection of congruent markers is thus a fundamental step in simultaneous analysis of many genes.     

The Origins of Species: The Debate between August Weismann and Moritz Wagner

Weismann’s ideas on species transmutation were first expressed in his famous debate with Moritz Wagner on the mechanism of speciation. Wagner suggested that the isolation of a colony from its original source is a preliminary and necessary factor for speciation. Weismann accepted a secondary, facilitating role for isolation, but argued that natural and sexual selection are the primary driving forces of species transmutation, and are always necessary and often sufficient causes for its occurrence. The debate with Wagner, which occurred between 1868 and 1872 within the framework of Darwin’s discussions of geographical distribution, was Weismann’s first public battle over the mechanism of evolution. This paper, which offers the first comprehensive analysis of this debate, extends previous analyses and throws light on the underlying beliefs and motivations of these early evolutionists, focusing mainly on Weismann’s views and showing his commitment to what he later called “the all sufficiency of Natural Selection.” It led to the crystallization of his ideas on the central and essential role of selection, both natural and sexual, in all processes of evolution, and, already at this early stage in his theoretical thinking, was coupled with sophisticated and nuanced approach to biological organization. The paper also discusses Ernst Mayr’s analysis of the debate and highlights aspects of Weismann’s views that were overlooked by Mayr and were peripheral to the discussions of other historians of biology.     

Using Tinbergen��s Four Questions (Plus One) to Facilitate Evolution Education for Human-Oriented Disciplines

Nikolaas Tinbergen provided an elegantly comprehensive guide to behavioral research with his Four Questions. Unsurprisingly, these questions summarize the different aspects that are vital to an evolutionary perspective. In this article, the authors describe how they use these Four Questions (plus one they have added regarding the role of culture) to facilitate evolution education in the human-oriented disciplines. The use of evolutionary theory in these fields is young, and educating new members of these fields in evolutionary theory is an even newer idea. Tinbergen’s Four Questions (Plus One) make the goals of an evolutionary perspective clear and the application of the mechanisms of evolution apparent. It can effectively dispel myths that surround evolutionary theory, like genetic determinism and hyperadaptationism, and can help ameliorate other ideological concerns. Finally, it is suggested that it is a heuristic that encourages students to make the transition from understanding the mechanisms of evolution in biology to applying this knowledge in cross-disciplinary research.     

Ontogeny, anatomy, and the problem of homology: Carl Gegenbaur and the American tradition of cell lineage studies

Summary In this paper we analyze Carl Gegenbaur’s conception of the relationship between embryology (“Ontogenie”) and comparative anatomy and his related ideas about homology. We argue that Gegenbaur’s conviction of the primacy of comparative anatomy and his careful consideration of caenogenesis led him to a more balanced view about the relationship between ontogeny and phylogeny than his good friend Ernst Haeckel. We also argue that Gegenbaur’s ideas about the centrality of comparative anatomy and his definitions of homology actually laid the conceptual foundations for Hans Spemann’s (1915) later analysis of homology. We also analyze Gegenbaur’s reception in the United States and how the discussions between E.B. Wilson and Edwin Conklin about the role of the “embryological criterion of homology” and the latter’s argument for an even earlier concept of cellular homology reflect the recurring theme of preformism in ontogeny, a theme that finds its modern equivalent in various genetic definitions of homology, only recently challenged by the emerging synthesis of evolutionary developmental biology. Finally, we conclude that Gegenbaur’s own careful methodological principles can serve as an important model for proponents of present day “evo-devo”, especially with respect to the integration of ontogeny with phylogeny embedded in comparative anatomy.     

Modelling the valuesphere and the ecosphere: Integrating the decision makers’ perspectives into LCA

Methods for Life Cycle Impact Assessment have to cope with two critical aspects, the uncertainty in values and the (unknown) system behaviour. LCA methodology should cope explicitly with these subjective elements. A structured aggregation procedure is proposed that differentiates between the technosphere and the ecosphere and embeds them in the valuesphere. LCA thus becomes a decision support system that models and combines these three spheres. We introduce three structurally identical types of LCA, each based on one coherent but different set of values. These sets of values can be derived from the Cultural Theory and are labeled as ‘egalitarian’, ‘individualistic’, and ‘hierarchic’. Within Life Cycle Impact Assessment, a damage oriented assessment model is complemented with both a newly developed precautionary indicator designed to address unknown damage and an indicator for the manageability of environmental damages. The indicators for unknown damage and for manageability complete the set of indicators judged to be relevant by decision makers. The weights given to these indicators are also value-dependent. The framework proposed here answers the criticisms that present LCA methodology does not strictly enough separate subjective from objective elements and that it fails to accurately model environmental impacts.     

Modelling the Valuesphere and the Ecosphere: Integrating the Decision Makers' Perspectives into LCA

Methods for Life Cycle Impact Assessment have to cope with two critical aspects, the uncertainty in values and the (unknown) system behaviour. LCA methodology should cope explicitly with these subjective elements. A structured aggregation procedure is proposed that differentiates between the technosphere and the ecosphere and embeds them in the valuesphere. LCA thus becomes a decision support system that models and combines these three spheres. We introduce three structurally identical types of LCA, each based on one coherent but different set of values. These sets of values can be derived from the Cultural Theory and are labeled as ‘egalitarian’, ‘individualistic’, and ‘hierarchic’. Within Life Cycle Impact Assessment, a damage oriented assessment model is complemented with both a newly developed precautionary indicator designed to address unknown damage and an indicator for the manageability of environmental damages. The indicators for unknown damage and for manageability complete the set of indicators judged to be relevant by decision makers. The weights given to these indicators are also value-dependent. The framework proposed here answers the criticisms that present LCA methodology does not strictly enough separate subjective from objective elements and that it fails to accurately model environmental impacts.     

Individuals at the Center of Biology: Rudolf Leuckart’s <Emphasis Type="Italic">Polymorphismus der Individuen</Emphasis> and the Ongoing Narrative of Parts and Wholes. With an Annotated Translation

Rudolf Leuckart’s 1851 pamphlet Ueber den Polymorphismus der Individuen (On the polymorphism of individuals) stood at the heart of naturalists’ discussions on biological individuals, parts and wholes in mid-nineteenth-century Britain and Europe. Our analysis, which accompanies the first translation of this pamphlet into English, situates Leuckart’s contribution to these discussions in two ways. First, we present it as part of a complex conceptual knot involving not only individuality and the understanding of compound organisms, but also the alternation of generations, the division of labor in nature, and the possibility of finding general laws of the organic world. Leuckart’s pamphlet is important as a novel attempt to give order to the strands of this knot. It also solved a set of key biological problems in a way that avoided some of the drawbacks of an earlier teleological tradition. Second, we situate the pamphlet within a longer trajectory of inquiry into part-whole relations in biology from the mid-eighteenth century to the present. We argue that biological individuality, along with the problem-complexes with which it engaged, was as central a problem to naturalists before 1859 as evolution, and that Leuckart’s contributions to it left a long legacy that persisted well into the twentieth century. As biologists’ interests in part-whole relations are once again on the upswing, the longue durée of this problem merits renewed consideration.