Understanding Evolutionary Trees

Charles Darwin sketched his first evolutionary tree in 1837, and trees have remained a central metaphor in evolutionary biology up to the present. Today, phylogenetics—the science of constructing and evaluating hypotheses about historical patterns of descent in the form of evolutionary trees—has become pervasive within and increasingly outside evolutionary biology. Fostering skills in “tree thinking” is therefore a critical component of biological education. Conversely, misconceptions about evolutionary trees can be very detrimental to one’s understanding of the patterns and processes that have occurred in the history of life. This paper provides a basic introduction to evolutionary trees, including some guidelines for how and how not to read them. Ten of the most common misconceptions about evolutionary trees and their implications for understanding evolution are addressed.

Evolutionary Trends

The occurrence, generality, and causes of large-scale evolutionary trends—directional changes over long periods of time—have been the subject of intensive study and debate in evolutionary science. Large-scale patterns in the history of life have also been of considerable interest to nonspecialists, although misinterpretations and misunderstandings of this important issue are common and can have significant implications for an overall understanding of evolution. This paper provides an overview of how trends are identified, categorized, and explained in evolutionary biology. Rather than reviewing any particular trend in detail, the intent is to provide a framework for understanding large-scale evolutionary patterns in general and to highlight the fact that both the patterns and their underlying causes are usually quite complex.

Hierarchies and the Sloshing Bucket: Toward the Unification of Evolutionary Biology

Evolutionary biology presents a bewildering array of phenomena to scientists and students alike—ranging from molecules to species and ecosystems; and embracing 3.8 billion years of life’s history on earth. Biological systems are arranged hierarchically, with smaller units forming the components of larger systems. The evolutionary hierarchy, based on replication of genetic information and reproduction, is a complex of genes/organisms/demes/species and higher taxa. The ecological hierarchy, based on patterns of matter–energy transfer, is a complex of proteins/organisms/avatars/local ecosystems/regional ecosystems. All organisms are simultaneously parts of both hierarchical systems. Darwin’s original formulation of natural selection maps smoothly onto a diagram where the two hierarchical systems are placed side-by-side. The “sloshing bucket” theory of evolution emerges from empirical cases in biological history mapped onto this dual hierarchy scheme: little phenotypically discernible evolution occurs with minor ecological disturbance; conversely, greatest concentrations of change in evolutionary history follow mass extinctions, themselves based on physical perturbations of global extent. Most evolution occurs in intermediate-level regional “turnovers,” when species extinction leads to rapid evolution of new species. Hierarchy theory provides a way of integrating all fields of evolutionary biology into an easily understood—and taught—rubric.

Carl Gegenbaur versus Anton Dohrn

Summary Both Carl Gegenbaur and Ernst Haeckel feuded with Anton Dohrn with respect to vertebrate origins and how one should study phylogeny. Although they argued about methodology, and also had serious differences with respect to philosophical issues, their different personal agendas with respect to research and institution-building may have been equally significant.     

Biological Levers and Extended Adaptationism

Two critiques of simple adaptationism are distinguished: anti-adaptationism and extended adaptationism. Adaptationists and anti-adaptationists share the presumption that an evolutionary explanation should identify the dominant simple cause of the evolutionary outcome to be explained. A consideration of extended-adaptationist models such as coevolution, niche construction and extended phenotypes reveals the inappropriateness of this presumption in explaining the evolution of certain important kinds of features—those that play particular roles in the regulation of organic processes, especially behavior. These biological or behavioral ‘levers’ are distinctively available for adaptation and exaptation by their possessors and for co-optation by other organisms. As a result they are likely to result from a distinctive and complex type of evolutionary process that conforms neither to simple adaptationist nor to anti-adaptationist styles of explanation. Many of the human features whose evolutionary explanation is most controversial belong to this category, including the female orgasm.

The paradox of the clumps mathematically explained

The lumpy distribution of species along a continuous one-dimensional niche axis recently found by Scheffer and van Nes (Scheffer and van Ness 2006) is explained mathematically. We show that it emerges simply from the eigenvalue and eigenvectors of the community matrix. Both the transient patterns—lumps and gaps between them—as well as the asymptotic equilibrium are explained. If the species are evenly distributed along the niche axis, the emergence of these patterns can be demonstrated analytically. The more general case, of randomly distributed species, shows only slight deviations and is illustrated by numerical simulation. This is a robust result whenever the finiteness of the niche is taken into account: it can be extended to different analytic dependence of the interaction coefficients with the distance on the niche axis (i.e., different kernel interactions), different boundary conditions, etc. We also found that there is a critical value both for the width of the species distribution σ and the number of species n below which the clusterization disappears.

Seven types of adaptationism

Godfrey-Smith (2001) has distinguished three types of adaptationism. This article builds on his analysis, and revises it in places, by distinguishing seven varieties of adaptationism. This taxonomy allows us to clarify what is at stake in debates over adaptationism, and it also helps to cement the importance of Gould and Lewontin’s ‘Spandrels’ essay. Some adaptationists have suggested that their essay does not offer any coherent alternative to the adaptationist programme: it consists only in an exhortation to test adaptationist hypotheses more thoroughly than was usual in the 1970s. Here it is argued that the ‘Spandrels’ paper points towards a genuinely non-adaptationist methodology implicit in much evolutionary developmental biology. This conclusion helps to expose the links between older debates over adaptationism and more recent questions about the property of evolvability.

The end of the adaptive landscape metaphor?

The concepts of adaptive/fitness landscapes and adaptive peaks are a central part of much of contemporary evolutionary biology; the concepts are introduced in introductory texts, developed in more detail in graduate-level treatments, and are used extensively in papers published in the major journals in the field. The appeal of visualizing the process of evolution in terms of the movement of populations on such landscapes is very strong; as one becomes familiar with the metaphor, one often develops the feeling that it is possible to gain deep insights into evolution by thinking about the movement of populations on landscapes consisting of adaptive valleys and peaks. But, since Wright first introduced the metaphor in 1932, the metaphor has been the subject of persistent confusion, from equivocation over just what the features of the landscape are meant to represent to how we ought to expect the landscapes to look. Recent advances—conceptual, empirical, and computational—have pointed towards the inadequacy and indeed incoherence of the landscapes as usually pictured. I argue that attempts to reform the metaphor are misguided; it is time to give up the pictorial metaphor of the landscape entirely and rely instead on the results of formal modeling, however difficult such results are to understand in ‘intuitive’ terms.

Assessing the fitness landscape revolution

According to Pigliucci and Kaplan, there is a revolution underway in how we understand fitness landscapes. Recent models suggest that a perennial problem in these landscapes—how to get from one peak across a fitness valley to another peak—is, in fact, non-existent. In this paper I assess the structure and the extent of Pigliucci and Kaplan’s proposed revolution and argue for two points. First, I provide an alternative interpretation of what underwrites this revolution, motivated by some recent work on model-based science. Second, I show that the implications of this revolution need to carefully assessed depending on question being asked, for peak-shifting is not central to all evolutionary questions that fitness landscapes have been used to explore.

Experimenting with Transmutation: Darwin, the Beagle, and Evolution

Detailed analysis of Darwin’s scientific notes and other writings from the Beagle voyage reveals a focus on endemism and replacement of allied taxa in time and in space that began early in the journey. Though it is impossible to determine exactly when Darwin became a transmutationist, the evidence suggests that he was conversant with the transmutational ideas of Lamarck and others and testing (“experimenting” with) them—before he received a copy of Lyell’s Principles of Geology, vol. 2, in November 1832, in which Lyell describes and disputes Lamarck’s theory. To the two rhea species of Patagonia and the four mockingbird species of the Galapagos, we can now add the living Patagonian cavy (rodent) species, and its extinct putatively related species that Darwin collected at Monte Hermoso (Bahia Blanca) in the Fall of 1832, as a replacement pattern absolutely critical to the development of Darwin’s transmutational thinking. Darwin developed his first transmutational theory by adopting “Brocchi’s analogy” (Rudwick 2008)—i.e. that births and deaths of species are analogous to the births and deaths of individuals. Births and deaths of species, as of individuals, are thus explicable in terms of natural causes. Darwin explored these themes and the replacement of the extinct cavy by the modern species explicitly in his February 1835 essay (Darwin 1835a).

Sexual selection and mate choice in evolutionary psychology

The importance of mate choice and sexual selection has been emphasized by the majority of evolutionary psychologists. This paper assesses three cases of work on mate choice and sexual selection in evolutionary psychology: David Buss on cross-cultural human mate preferences, Randy Thornhill and Steve Gangestad on the link between mate preferences and fluctuating asymmetry, and Geoffrey Miller on the role of Fisher’s runaway process in human evolution. A mixture of conceptual and empirical problems in each case highlights the general weakness of work in evolutionary psychology on these issues.

Teaching Evolution with Historical Narratives

This paper focuses on evolution as a unifying theme in biology education. Our aim is to argue that the different topics taught in secondary school biology classes should be enriched with and linked together by means of accounts of the history of life. We named this approach a “natural history perspective” on biology education. An essential aspect of the natural history perspective is the claim that evolutionary history forms the context for the development of an understanding of evolutionary processes. While there are some indications that a natural history perspective can function as a context for understanding micro-evolutionary processes, more research is called for.

Anthropocentricisms in cladograms

Both written and graphic accounts of history can be biased by the perspective of the historian. O’Hara (Biol Philos 7:135–160, 1992) has demonstrated that this also applies to evolutionary history and its historians, and identified four narrative devices that introduce anthropocentricisms into accounts of phylogeny. In the current paper, I identify a fifth such narrative device, viz. the left–right ordering of the taxa at the tips of cladograms. I define two measures that make it possible to quantify the degree of anthropocentricism of cladograms, the human attention score and human rightness score. I then carry out an analysis of the presence of the different distorting mechanisms in phylogenetic textbooks. I deliberately chose two textbooks that adopted a cladistic perspective, since their authors can be assumed to be more conscious about the aim of avoiding anthropocentricisms. Three of the narrative devices are thus absent from cladistic works. However, there is a weak tendency that the resolution of cladogram branches is biased in favour of Homo sapiens. Furthermore, the human perspective is clear and highly significant in the positioning of taxa along the left–right axis of cladograms. I discuss the reasons for and implications of these biased presentations.

Blogging Evolution

A weblog (“blog”) is an publication on the WorldWideWeb in which brief entries are displayed in date order, much like a diary or journal. I describe the general characteristics of blogs, contrasting blogs with other of WWW formats for self-publishing. I describe four categories for blogs about evolutionary biology: “professional,” “amateur,” “apostolic,” and “imaginative.” I also discuss blog networks. I identify paradigms of each category. Throughout, I aim to illuminate blogs about evolutionary biology from the point of view of a user looking for information about the topic. I conclude that blogs are not the best type of source for systematic and authoritative information about evolution, and that they are best used by the information-seeker as a way of identifying what issues are of interest in the community of evolutionists and for generating research leads or fresh insights on one’s own work.

Five Misunderstandings About Cultural Evolution

Recent debates about memetics have revealed some widespread misunderstandings about Darwinian approaches to cultural evolution. Drawing from these debates, this paper disputes five common claims: (1) mental representations are rarely discrete, and therefore models that assume discrete, gene-like particles (i.e., replicators) are useless; (2) replicators are necessary for cumulative, adaptive evolution; (3) content-dependent psychological biases are the only important processes that affect the spread of cultural representations; (4) the “cultural fitness” of a mental representation can be inferred from its successful transmission; and (5) selective forces only matter if the sources of variation are random. We close by sketching the outlines of a unified evolutionary science of culture.

Membrane microdomains from early gastrula embryos of medaka, <Emphasis Type="Italic">Oryzias latipes</Emphasis>, are a platform of E-cadherin- and carbohydrate-mediated cell–cell interactions during epiboly

Formation of membrane microdomain is critical for cell migration (epiboly) during gastrulation of medaka fish [Adachi et al. (Biochem. Biophys. Res. Commun. 358:848–853, 2007)]. In this study, we characterized membrane microdomain from gastrula embryos to understand its roles in epiboly. A cell adhesion molecule (E-cadherin), its associated protein (β-catenin), transducer proteins (PLCγ, cSrc), and a cytoskeleton protein (β-actin) were enriched in the membrane microdomain. Le^X-containing glycolipids and glycoproteins (Le^X-gp) were exclusively enriched in the membrane microdomain. Interestingly, the isolated membrane microdomain had the ability to bind to each other in the presence of Ca²⁺. This membrane microdomain binding was achieved through the E-cadherin homophilic and the Le^X-glycan-mediated interactions. E-cadherin and Le^X-gp were co-localized on the same membrane microdomain, suggesting that these two interactions are operative at the same time. Thus, the membrane microdomain functions as a platform of the E-cadherin- and Le^X-glycan-mediated cell adhesion and signal transduction.

The Evolution of Complex Organs

The origin of complex biological structures has long been a subject of interest and debate. Two centuries ago, natural explanations for their occurrence were considered inconceivable. However, 150 years of scientific investigation have yielded a conceptual framework, abundant data, and a range of analytical tools capable of addressing this question. This article reviews the various direct and indirect evolutionary processes that contribute to the origins of complex organs. The evolution of eyes is used as a case study to illustrate these concepts, and several of the most common misconceptions about complex organ evolution are discussed.

Do Students See the “Selection” in Organic Evolution? A Critical Review of the Causal Structure of Student Explanations

This paper critically reviews and characterizes the student's causal-explanatory understanding; this is done as a step toward explicating the problematic of evolution education as it concerns the cognitive difficulties in understanding Darwin's theory of natural selection. The review concludes that the student's understanding is fundamentally different from Darwin's, for the student understands evolutionary change as necessary individual transformation caused by the transformative action of various physical and behavioral factors. This is in complete contrast to Darwin's (and even the Darwinian's, for that matter) understanding of evolutionary change as a change caused by accumulative selection. Hence, to understand natural selection, the student has to learn to “see” how the accumulative selection causes evolutionary change.

Amazon Forestry Tranformed: Integrating Knowledge for Smallholder Timber Managemet in Eastern Brazil

Recent discussions of local knowledge emphasize its dynamic nature invoking local peoples’ ability to effectively integrate traditional or local with science-based or “modern” knowledges. The smallholder timber industry of the Amazon’s estuarine floodplain provides an outstanding example of local patterns of resource management and economic activities transformed from within by smallholder farmers who participated in the industrial timber boom of the 1970s and 1980s. These farmers of eastern Amazonia have developed a vertically integrated local industry based on expertise reflecting profound locally developed knowledge of specific forests and management of ecological processes, individual observation and experimentation, as well as concepts and practices derived from temporary employment by large-scale industrial timber firms. At each stage of the smallholder forestry process—from managing natural regeneration to running small sawmills and marketing lumber—local managers apply an innovative set of practices reflecting their diverse experiences. This combination of technical, market, and ecological knowledge results in forests, timber markets, and economic patterns that do not correspond to many of the widely-held generalizations concerning either local or industrial tropical timber exploitation. This article uses data from 7 years of research in the Amazon floodplain.

An all-conquering ecological journey: from the sea,calanoid copepods mastered brackish,fresh, and athalassic saline waters

Although it is commonly acknowledged that calanoid copepods inhabiting fresh water evolved from marine ancestors via the brackish water of estuaries, it is less well appreciated that a restricted number of species with freshwater affinities have conquered athalassic saline waters. The global importance of the latter habitat has been under-estimated and, with climate change and human population growth, it is expanding at the expense of fresh waters. Considering Australia, South America and the Holarctic, at least seven halobiontic calanoid species occur in athalassic saline waters (the situation in Africa is not visited). In Australian inland-water Centropagidae, there is a high degree of congruence between the ecological trend in habitat occupancy (marine through brackish and fresh to athalassic saline waters) and the assumed evolutionary trend towards reduction in the setation and segmentation of swimming legs. The validity of the inference by Adamowicz et al. (Biological Journal of the Linnean Society of London 90: 279–292, 2007a) that a hypothesis of oligomerization was not supported as the mode of evolution of South American non-marine Centropagidae is criticized for reasons of inadequate character sampling. The phylogeny, biogeography and osmo-regulatory physiology of Southern Hemisphere inland-water centropagids are reviewed in some detail. Calanoids have mastered a significant portion of the total salinity range for athalassic saline waters (3 to 300+ g l⁻¹) but, unlike brine shrimps, they have not evolved a mechanism for hypo-osmotic regulation and do not tolerate saturated or near-saturated brines.