This chapter explores the idea that phylogenetic diversity plays a unique role in underpinning conservation endeavour. The conservation of biodiversity is suffering from a rapid, unguided proliferation of metrics. Confusion is caused by the wide variety of contexts in which we make use of the idea of biodiversity. Characterisations of biodiversity range from all-variety-at-all-levels down to variety with respect to single variables relevant to very specific conservation contexts. Accepting biodiversity as the sum of a large number of individual (...) measures results in an empirically intractable framework. However, large-scale decisions cannot be based on biodiversity variables inferred from local conservation imperatives because the variables relevant to the many systems being compared would be incommensurate with one another. We therefore need some general conception of biodiversity that would make tractable such large-scale environmental decision-marking. We categorise the large array of strategies for the measurement of biodiversity into four broad groups for consideration as general measures of biodiversity. We compare common moral justifications for the conservation of biodiversity and conclude that some form of instrumental value is the most plausible justification for biodiversity conservation. Although this is often interpreted as a reliance on option value, we opt for a broadly consequentialist characterisation of biodiversity conservation. We conclude that the best justified general measure of biodiversity will be some form of phylogenetic diversity. (shrink)

The simple systems methodology is a powerful reductionistic research strategy. It has problems as implemented in developmental genetics because the organisms studied are few and unrepresentative. Stronger inferences require independent arguments that key traits are widely distributed phylogenetically. Evolutionary and developmental mechanisms of generative entrenchment and self-organization provide possible support, and are also necessary components of a developmental systems approach.

Some recent conservation proposals – including the Zoological Society of London’s (ZSL) EDGE of Existence programme – have focused on the value of protecting species with high evolutionary distinctiveness, a dimension of biodiversity conservation that’s not been much emphasized in conservation practice. In this paper we critically examine this strategy, investigating whether there are good reasons for prioritizing evolutionarily distinctive species, and the phylogenetic diversity to which they contribute, over other forms of biodiversity. We first discuss evolutionary distinctiveness, (...) its relationship to phylogenetic diversity, how phylogenetic diversity can be measured, and intuitive thoughts about its value. Then we consider five kinds of arguments about the value of phylogenetic diversity that might be made to support prioritizing it, given its current lack of emphasis in conservation practice. These are: arguments based on protecting biodiversity, arguments based on option value, arguments based on ecological resilience, arguments based on historical value, and arguments based on aesthetic value. We maintain that these arguments, taken individually, offer varying degrees of fairly weak support for valuing species with high evolutionary distinctiveness. Taken together, however, these arguments seem sufficiently strong to justify programs such as EDGE, insofar as such programs are framed as correctives to a past lack of emphasis on the protection of phylogenetic diversity. We suggest, however, that these arguments are not sufficiently strong to support an absolute prioritization of phylogenetic diversity over protecting other forms of biodiversity. (shrink)

The concept of individuality as applied to species, an important advance in the philosophy of evolutionary biology, is nevertheless in need of refinement. Four important subparts of this concept must be recognized: spatial boundaries, temporal boundaries, integration, and cohesion. Not all species necessarily meet all of these. Two very different types of pluralism have been advocated with respect to species, only one of which is satisfactory. An often unrecognized distinction between grouping and ranking components of any species concept is necessary. (...) A phylogenetic species concept is advocated that uses a grouping criterion of monophyly in a cladistic sense, and a ranking criterion based on those causal processes that are most important in producing and maintaining lineages in a particular case. Such causal processes can include actual interbreeding, selective constraints, and developmental canalization. The widespread use of the biological species concept is flawed for two reasons: because of a failure to distinguish grouping from ranking criteria and because of an unwarranted emphasis on the importance of interbreeding as a universal causal factor controlling evolutionary diversification. The potential to interbreed is not in itself a process; it is instead a result of a diversity of processes which result in shared selective environments and common developmental programs. These types of processes act in both sexual and asexual organisms, thus the phylogenetic species concept can reflect an underlying unity that the biological species concept can not. (shrink)

Amine acetylation is a diverse topic with importance to the regulation of several physiological processes as well as the metabolism of drugs and environmental chemicals. Arylalkylamine N‐acetyltransferase is widely distributed in several species, where this enzyme plays an important role in the seasonal regulation of reproduction and photoperiodism in vertebrates through the pathway of melatonin formation. In insects, this enzyme is involved in monoamine neurotransmitter inactivation and the formation of catecholamine intermediates necessary for sclerotization of the insect cuticle.

Mutation and lateral transfer are two categories of processes generating genetic diversity in prokaryotic genomes. Their relative importance varies between lineages, yet both are complementary rather than independent, separable evolutionary forces. The replication process inevitably merges together their effects on the genome. We develop the concept of “open lineages” to characterize evolutionary lineages that over time accumulate more changes in their genomes by lateral transfer than by mutation. They contrast with “closed lineages,” in which most of the changes are (...) caused by mutation. Open and closed lineages are interspersed along the branches of any tree of prokaryotes. This patchy distribution conflicts with the basic assumptions of traditional phylogenetic approaches. As a result, a tree representation including both open and closed lineages is a misrepresentation. The evolution of all prokaryotic lineages cannot be studied under a single model unless new phylogenetic approaches that are more pluralistic about lineage evolution are designed. (shrink)

The phylogenetic species concept is applied for the first time to a major radiation of birds, the birds-of-paradise (Paradisaeidae) of Australasia. Using the biological species concept, previous workers have postulated approximately 40–42 species in the family. Of these, approximately 13 are monotypic and 27 are polytypic with about 100 subspecies. Phylogenetic species are irreducible (basal) clusters of organisms (terminal taxa) that are diagnosably distinct from other such clusters. Within the context of this concept, approximately 90 species of paradisaeids (...) are postulated to have diversified within Australasia. The phylogenetic species concept more accurately describes evolutionary diversity within the family and provides a better theoretical and empirical framework for analysing speciation, historical biogeography and patterns of morphological, behavioral and ecological diversification within this group than does the biological species concept. (shrink)

Defining and measuring biodiversity is an important research area in biology, with very interesting theoretical and applied aspects. Numerous definitions have been proposed, and these definitions of biodiversity influence how it is measured. From the still commonly used measure of species diversity, through higher taxon diversity, molecular measures, ecological measures and indicator taxa, these measures have as their fundamental shortcoming the lack of an explicit consideration of the evolutionary context represented by phylogenies. Attempts have been made to incorporate (...) phylogenetic considerations into measuring biodiversity, but more hypothesis‐driven research needs to be done. A specific case study is presented of how this added emphasis on phylogeny‐based biodiversity measurement can influence the way in which research is directed and hypotheses are generated. The elucidation of the relationship of biodiversity to ecosystem functioning is a very timely concern with the unarguable loss of biodiversity this planet is experiencing, whichever way biodiversity is measured. (shrink)

Graphical AbstractUsing the indices δ+ and δ* for assessing phylogenetic diversity may lead to spurious results and interpretations; it can bias recommendations for conservation and lead to inappropriate management decisions. Therefore these indices should be avoided and other indices based on quadratic entropy (Qδ+ and Q) should be used instead.

A concept for a primitive angiospermous branch system is given in order to have a starting point for the derivation of the diverse and highly differentiated branch systems observed in contemporary angiosperms. Hitherto Troll's (1964, 1969) comparative study of the synflorescences in this plant group — developed out predominantly on herbaceous plants — was the most comprehensive and sophisticated treatment dealing with branch systems. Unfortunately, the work on tropical tree architecture by Hallé et al. (1978) has no reference to the (...) classical studies of Troll and his pupils. Thus Müller-Doblies and Weberling (1984) emphasized the high degree of terminological incompatibility between the two works. Angiosperms are seen as a monophyletic plant division. Consequently, the branch system of the first primitive angiosperms must be the starting point in the evolution of the abundant diversity of branch systems and growth forms of modern angiosperms. If it is accepted that primitive angiospermous shoots were terminated by a large flower, one may assume, that the reproductive end of the shoot was enriched by paracladia early in evolution, thereby developing a terminal inflorescence instead of a single flower. Thus the primitive shoot unit was divided into a basal vegetative region — the trophotagma, branching retardively — and the reproductive terminal region, the anthotagma, branching simultaneously. It is demonstrated through a selection of different examples, that the construction of such a system possesses the options for several modifications, enabling the evolution of the abundant diversity of branch systems which characterizes contemporary angiosperms. (shrink)

The importance of evolutionary parallelisms and their differences from evolutionary convergences have been historically underappreciated, as recently noticed in Gould's last book `The structure of evolutionary history'. In that book, Gould make an effort to distinguish and to reinterpret these concepts in the light of the new discoveries of the last decades on developmental biology and genetics, presenting the elegant metaphor of `Pharaonic bricks versus Corinthian columns'. In this paper I will briefly discuss these concepts, and will argue that, despite (...) the advances that have been made to define them in theory, it is rather hard to differentiate them in a practical phylogenetic context. In order to do so, I will provide some few examples from my own empirical studies on the last years of one of the most morphologically and taxonomically diverse groups of Vertebrates, the catfishes. (shrink)

Lately there has been a wave of criticism of the concept of living fossils. First, recent research has challenged the status of paradigmatic living fossil taxa, such as coelacanths, cycads, and tuataras. Critics have also complained that the living fossil concept is vague and/or ambiguous, and that it is responsible for misconceptions about evolution. This paper defends a particular phylogenetic conception of living fossils, or taxa that exhibit deep prehistoric morphological stability; contain few extant species; and make a high (...) contribution to phylogenetic diversity. The paper shows how this conception of living fossils can make sense of recent research on contested cases. The phylogenetic living fossil concept has both theoretical and practical importance: theoretical, because it picks out an important explanatory target for evolutionary theory; and practical, because it picks out taxa that we might wish to prioritize for conservation. The best way to defend the concept of living fossils is to get clearer about the reasons for defending living fossil taxa. (shrink)

This book attempts to advance Donald Griffin's vision of the "final, crowning chapter of the Darwinian revolution" by developing a philosophy for the science of animal consciousness. It advocates a Darwinian bottom-up approach that treats consciousness as a complex, evolved, and multidimensional phenomenon in nature rather than a mysterious all-or-nothing property immune to the tools of science and restricted to a single species. -/- The so-called emergence of a science of consciousness in the 1990s has at best been a science (...) of human consciousness. This book aims to advance a true Darwinian science of consciousness in which its evolutionary origin, function, and phylogenetic diversity are moved from the field’s periphery to its very centre, thus enabling us to integrate consciousness into an evolutionary view of life. Accordingly, this book has two objectives: (i) to argue for the need and possibility of an evolutionary bottom-up approach that addresses the problem of consciousness in terms of the evolutionary origins of a new ecological lifestyle that made consciousness worth having and (ii) to articulate a thesis and beginnings of a theory of the place of consciousness as a complex evolved phenomenon in nature that can help us to answer the question of what it is like to be a bat, an octopus, or a crow. -/- A Philosophy for the Science of Animal Consciousness will appeal to researchers and advanced students interested in advancing our understanding of animal minds as well as anyone with a keen interest in how we can develop a science of animal consciousness. (shrink)

This goal of this thesis in the philosophy of nature is to move us closer towards a true biological science of consciousness in which the evolutionary origin, function, and phylogenetic diversity of consciousness are moved from the field’s periphery of investigations to its very centre. Rather than applying theories of consciousness built top-down on the human case to other animals, I argue that we require an evolutionary bottomup approach that begins with the very origins of subjective experience in (...) order to make sense of the place of mind in nature. To achieve this goal, I introduce and defend the pathological complexity thesis as both a framework for the scientific investigation of consciousness and as a lifemind continuity thesis about the origins and function of consciousness. (shrink)

Bird songs often display musical acoustic features such as tonal pitch selection, rhythmicity, and melodic contouring. We investigated higher-order musical temporal structure in bird song using an experimental method called “music scrambling” with human subjects. Recorded songs from a phylogenetically diverse group of 20 avian taxa were split into constituent elements and recombined in original and random order. Human subjects were asked to evaluate which version sounded more “musical” on a per-species basis. Species identity and stimulus treatment were concealed from (...) subjects, and stimulus presentation order was randomized within and between taxa. Two recordings of human music were included as a control for attentiveness. Participants varied in their assessments of individual species musicality, but overall they were significantly more likely to rate bird songs with original temporal sequence as more musical than those with randomized temporal sequence. We discuss alternative hypotheses for the origins of avian musicality, including honest signaling, perceptual bias, and arbitrary aesthetic coevolution. (shrink)

How biological form is generated remains one of the most fascinating but elusive challenges for science. Moreover, it is widely documented in contemporary literature that development is tightly coordinated. The idea that such development is governed by a coordinating field of force, the morphogenetic field, and its position in embryology research paradigms, is traced in this article. Empirical evidences for field phenomena are described, ranging from bioelectromagnetic effects, morphology, transplantation, regeneration, and other data. Applications of medical potential including treatment of (...) cancer, birth defects, and wound healing are highlighted. The article hypothesizes that distinct morphological forms may have distinct field parameters. Experimentally tractable field parameters may thus provide an exciting research program for probing morphogenesis and phylogenetic diversity. (shrink)

Horseshoe crabs (Limulus polyphemus) have been in decline in Long Island Sound, and recently there has been discussion of whether the state of Connecticut should stop issuing licenses for commercial harvesting. This paper argues that in spite of concerns about the living fossil concept, the fact that the horseshoe crabs are living fossils should count in favor of more stringent protection. The paper distinguishes four different views about the status of the living fossil concept: 1) eliminativism; 2) redefinition; 3) reframing; (...) and 4) conceptual pluralism. Approaches 2–4 all treat the criteria associated with living fossils as picking out distinctive features of evolutionary history. Those distinctive features of evolutionary history link up with conservation values in several ways. More generally, drawing upon relevant work in environmental philosophy, it is argued that evolutionary history is relevant to aesthetic and environmental value. Moreover, eliminativists have trouble rendering intelligible a striking pattern in the recent scientific literature. Researchers undertaking conservation-relevant work frequently highlight the living fossil status of the taxa under study. (shrink)

Many biological investigations are organized around a small group of species, often referred to as ‘model organisms’, such as the fruit fly Drosophila melanogaster. The terms ‘model’ and ‘modelling’ also occur in biology in association with mathematical and mechanistic theorizing, as in the Lotka–Volterra model of predator-prey dynamics. What is the relation between theoretical models and model organisms? Are these models in the same sense? We offer an account on which the two practices are shown to have different epistemic characters. (...) Theoretical modelling is grounded in explicit and known analogies between model and target. By contrast, inferences from model organisms are empirical extrapolations. Often such extrapolation is based on shared ancestry, sometimes in conjunction with other empirical information. One implication is that such inferences are unique to biology, whereas theoretical models are common across many disciplines. We close by discussing the diversity of uses to which model organisms are put, suggesting how these relate to our overall account. 1 Introduction2 Volterra and Theoretical Modelling3 Drosophila as a Model Organism4 Generalizing from Work on Model Organisms5 Phylogenetic Inference and Model Organisms6 Further Roles of Model Organisms6.1 Preparative experimentation6.2 Model organisms as paradigms6.3 Model organisms as theoretical models6.4 Inspiration for engineers6.5 Anchoring a research community7 Conclusion. (shrink)

Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on (...) both the molecular and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are genetically distinct and (ii) morphologically distinct individuals that are genetically the same. We argue that hypotheses about discordance can be tested using the concept of neutral morphologies, or more broadly neutral phenotypes, as a null hypothesis. -/- . (shrink)

Experimental taxonomy was a diverse area of research, and botanists who helped develop it were motivated by a variety of concerns. While experimental taxonomy was never totally a taxonomic enterprise, improvement in classification was certainly one major motivation behind the research. Hall's and Clements' belief that experimental methods added more objectivity to classification was almost universally accepted by experimental taxonomists. Such methods did add a new dimension to taxonomy — a dimension that field and herbarium studies, however rigorous, could not (...) duplicate. Nonetheless, experimental techniques were never completely divorced from traditional taxonomic methods. In practice, all experimental taxonomists employed a combination of descriptive and experimental methods. Most researchers freely acknowledged a debt to traditional taxonomy. Furthermore, the greater rigor of twentieth-century taxonomy was not due entirely to experimentalism. Both the experimental and descriptive aspects of taxonomy were improved by the increased use of quantitative methods, particularly statistics.52From the beginning, a number of experimental taxonomists were interested primarily in classification. But many approached their research from fields other than taxonomy. These botanists were concerned primarily with ecological and genetic problems rather than with classification. There is little indication that they drew a sharp distinction: for example, taxonomic and cytogenetic conclusions were interwoven in Babcock and Stebbins' 1938 study of Crepis 53 (this was even more true of Babcock's final mongraph on the genus, published in 1947). Similarly, the extensive series of monographs, “Experimental Studies on the Nature of Species,” initiated by the Carnegie Institution group in 1940 combined ecological, cytogenetic, and taxonomic conclusions. Indeed, the significance of the major projects completed by experimental taxonomists was largely due to the fact that they were comprehensive studies rather than strictly taxonomic or cytogenetic.In a general sense, the primary motivation behind much of experimental taxonomy was evolutionary. Beginning in the second decade of the century Hall and Clements exhorted taxonomists to take an explicitly evolutionary perspective on research. Hall undoubtedly spoke for the majority of experimental taxonomists when he stated, “If there be anything at all to organic evolution, then taxonomy is dealing with the products of evolution and it is this that gives to taxonomy both its highest mission and its greatest responsibility.”54Aside from a common interest in evolution, however, the theoretical orientations of experimental taxonomists were varied. This diversity is strikingly illustrated by the evolutionary views of members of the Carnegie Institution research group. Experimental taxonomy was initiated by Clements as one aspect of his Lamarckian study of adaptation and speciation. In contrast, Hall's research was inspired by a broad concern for evolutionary problems. Hall rarely referred to specific evolutionary mechanisms; rather, he applied a general conception of evolutionary processes to deduce phylogenetic relationships. His later associates at the Carnegie Institution explicitly dissociated themselves from Clements' theoretical framework. The neo-Darwinian interpretations of adaptation and speciation presented by Clausen, Keck, and Hiesey could hardly have been more different than those of Clements. However, this major shift in theoretical orientation should not obscure significant similarities between the research of Clements and later Carnegie workers. In terms of research problems and methodology, the first volume of “Experimental Studies on the Nature of Species” was an extension of the Clementsian research program. Clausen, Keck, and Hiesey's monograph was the mature discussion of transplant experimentation that Clements had very tentatively initiated during the first decades of the twentieth century. The bond that linked the members of the Carnegie Institution research group to experimental taxonomists in general was one of shared methodology rather than common theoretical orientation. While Clements' evolutionary views were eventually repudiated, his enthusiasm for innovative experimental methods was shared by later workers.The development of experimental taxonomy faced significant problems. During the period 1920–1950 this area of botanical research remained a hybrid discipline. The aims and scope of experimental taxonomy were never articulated in a completely unified manner. Consequently, even among experimental taxonomists, there were disagreements over the relation of their research to other botanical endeavors. Even though experimental taxonomy had close ties with general taxonomy, a number of experimental taxonomists questioned the “taxonomic” nature of their research55. Even to the extent that this hybrid discipline could be identified as a branch of taxonomy, problems arose. Taxonomists, as we have seen, were justifiably skeptical of what appeared to be a rapid influx of untested methods and ideas. Experimental taxonomists were not merely incorporating well-accepted methods from ecology and cytogenetics; during the period 1920–1950 the fields from which experimental taxonomists borrowed were themselves undergoing major theoretical and methodological changes. Despite problems and conflicts, experimental taxonomists did contribute improvements to classification. Furthermore, they made significant contributions to plant ecology and evolutionary genetics.The development of experimental taxonomy indicates that twentieth-century botanists were not necessarily isolated in naturalist and experimentalist camps. The joint session of taxonomists, cytologists, and geneticists at the 1926 International Congress of Plant Sciences indicates communication among specialists fairly early in the century. The papers and commentaries presented during this session do not reveal the hostility and intolerance that supposedly characterized encounters between experimentalists and naturalists. Nor do they suggest incompatible conceptual worlds separating geneticists and taxonomists.Discussions between taxonomists and other specialists were not limited to a single international congress. Particularly during the 1930s discussions among specialists appear to have been fairly widespread. Groups such as the Biosystematists and the Society for the Study of Systematics in Relation to General Biology served as forums for discussion among biologists from a variety of disciplines. The naturalist-experimentalist dichotomy tends to obscure the broad research interests of a number of prominent twentieth-century botanists. Most of the experimental taxonomists cannot be characterized adequately as either naturalists or experimentalists. Traditionally trained taxonomists such as Hall, Keck, and Turrill throughout their careers participated in both experimental and herbarium research. And a number of specialists in fields other than taxonomy took an active interest in taxonomic problems, not necessarily limited to experimental aspects. For example, Anderson suggested a number of innovations to make herbarium collections more amenable to statistical analysis.This historical study of experimental taxonomy indicates a different relationship between experimentalism and taxonomy than that portrayed by the naturalist-versus-experimentalist dichotomy. F. E. Clements originated experimental taxonomy as a revolt against descriptive botany. In retrospect, this revolution was not vigorously waged and was not successfully completed. Experimental taxonomy was never an entirely experimental approach to botanical research. Even the most ardent advocates of experimentalism relied heavily on methods inherited from traditional taxonomy. Moderate exponents of experimental taxonomy stressed the compatibility of experimental methods, field observation, and herbarium techniques. Attempts to fuse cytogenetics, ecology, and taxonomy during the period 1920–1950 resulted in an impressive body of research. However, this fusion constituted neither a repudiation of descriptive botany nor a complete revision of taxonomic theory of practice. (shrink)

Standard microbial evolutionary ontology is organized according to a nested hierarchy of entities at various levels of biological organization. It typically detects and defines these entities in relation to the most stable aspects of evolutionary processes, by identifying lineages evolving by a process of vertical inheritance from an ancestral entity. However, recent advances in microbiology indicate that such an ontology has important limitations. The various dynamics detected within microbiological systems reveal that a focus on the most stable entities (or features (...) of entities) over time inevitably underestimates the extent and nature of microbial diversity. These dynamics are not the outcome of the process of vertical descent alone. Other processes, often involving causal interactions between entities from distinct levels of biological organisation, or operating at different time scales, are responsible not only for the destabilisation of pre-existing entities, but also for the emergence and stabilisation of novel entities in the microbial world. In this article we consider microbial entities as more or less stabilised functional wholes, and sketch a network-based ontology that can represent a diverse set of processes including, for example, as well as phylogenetic relations, interactions that stabilise or destabilise the interacting entities, spatial relations, ecological connections, and genetic exchanges. We use this pluralistic framework for evaluating (i) the existing ontological assumptions in evolution (e.g. whether currently recognized entities are adequate for understanding the causes of change and stabilisation in the microbial world), and (ii) for identifying hidden ontological kinds, essentially invisible from within a more limited perspective. We propose to recognize additional classes of entities that provide new insights into the structure of the microbial world, namely “processually equivalent” entities, “processually versatile” entities, and “stabilized” entities. (shrink)

This book is a unique exploration of the idea of the "second person" in human interaction, the idea that face-to-face interactions involve a distinctive form of reciprocal mental state attributions that mediates their dynamical unfolding. Challenging the view of mental attribution as a sort of "theory of mind", Pérez and Gomila argue that the second person perspective of mental understanding is the conceptually, ontogenetically, and phylogenetically basic way of understanding mentality. Second person interaction provides the opportunity for the acquisition of (...) concepts of mental states of increasing complexity. The book reviews the growing interest in a variety of second person phenomena, both in development and in adulthood, presenting research that shows how participants in human interaction attribute psychological states of a referentially transparent kind to each other. This review documents the spontaneous preference for face-to-face interaction, from eye contact to joint attention, from forms of vitality to communicative intentions, from interaction detection to joint action, and from synchrony to interpersonal coordination. Also looking at the implications and applications of the second person perspective within fields as diverse as art and morality, this book is fascinating reading for students and academics in social and cognitive psychology, cognitive science, neuroscience, and philosophy. (shrink)

Contemporary biology has inherited two key assumptions from the Modern Synthesis about the nature of population lineages: sexual reproduction is the exemplar for how individuals in population lineages inherit traits from their parents, and random mating is the exemplar for reproductive interaction. While these assumptions have been extremely fruitful for a number of fields, such as population genetics and phylogenetics, they are increasingly unviable for studying the full diversity and evolution of life. I introduce the “mixture” account of population (...) lineages that escapes these assumptions by dissolving the Modern Synthesis’s sharp line separating reproduction and development and characterizing reproductive integration in population lineages by the ephemerality of isolated subgroups rather than random mating. The mixture account provides a single criterion for reproductive integration that accommodates both sexual and asexual reproduction, unifying their treatment under Kevin de Queiroz’s generalized lineage concept of species. The account also provides a new basis for empirically assessing the effect of random mating as an idealization on the empirical adequacy of population genetic models. (shrink)

We undeniably live in an information age—as, indeed, did those who lived before us. After all, as the cultural historian Robert Darnton pointed out: ‘every age was an age of information, each in its own way’ (Darnton 2000: 1). Darnton was referring to the news media, but his insight surely also applies to the sciences. The practices of acquiring, storing, labeling, organizing, retrieving, mobilizing, and integrating data about the natural world has always been an enabling aspect of scientific work. Natural (...) history and its descendant discipline of biological taxonomy are prime examples of sciences dedicated to creating and managing systems of ordering data. In some sense, the idea of biological taxonomy as an information science is commonplace. Perhaps it is because of its self-evidence that the information science perspective on taxonomy has not been a major theme in the history and philosophy of science. The botanist Vernon Heywood once pointed out that historians of biology, in their ‘preoccupation with the development of the sciences of botany and zoology… [have] diverted attention from the role of taxonomy as an information science’ (Heywood 1985: 11). More specifically, he argued that historians had failed to appreciate how principles and practices that can be traced to Linnaeus constituted ‘a change in the nature of taxonomy from a local or limited folk communication system and later a codified folk taxonomy to a formal system of information science [that] marked a watershed in the history of biology’ (ibid.). A similar observation could be made about twentieth-century philosophy of biology, which mostly skipped over practical and epistemic questions about information management in taxonomy. The taxonomic themes that featured in the emerging philosophy of biology literature in the second half of the twentieth century were predominantly metaphysical in orientation. This is illustrated by what has become known as the ‘essentialism story’: an account about the essentialist nature of pre- Darwinian taxonomy that used to be accepted by many historians and philosophers, and which stimulated efforts to document and interpret shifts in the metaphysical understanding of species and (natural) classification (Richards 2010; Winsor 2003; Wilkins 2009). Although contemporary debates in the philosophy of taxonomy have moved on, much discussion continues to focus on conceptual and metaphysical issues surrounding the nature of species and the principles of classification. Discussions centring on whether species are individuals, classes, or kinds have sprung up as predictably as perennials. Raucous debates have arisen even with the aim of accommodating the diversity of views: is monism, pluralism, or eliminativism about the species category the best position to take? In addition to these, our disciplines continue to interrogate what is the nature of these different approaches to classification: are they representational or inferential roles of different approaches to classification (evolutionary taxonomy, phenetics, phylogenetic systematics)? While there is still much to learn from these discussions—in which we both actively participate—our aim with this topical collection has been to seek different entrypoints and address underexposed themes in the history and philosophy of taxonomy. We believe that approaching taxonomy as an information science prompts new questions and can open up new philosophical vistas worth exploring. A twenty-first century information science turn in the history and philosophy of taxonomy is already underway. In scientific practice and in daily life it is hard to escape the imaginaries of Big Data and the constant threats of being ‘flooded with data’. In the life sciences, these developments are often associated with the socalled bioinformatics crisis that can hopefully be contained by a new, interdisciplinary breed of bioinformaticians. These new concepts, narratives, and developments surrounding the centrality of data and information systems in the biological and biomedical sciences have raised important philosophical questions about their challenges and implications. But historical perspectives are just as necessary to judge what makes our information age different from those that preceded us. Indeed, as the British zoologist Charles Godfray has often pointed out, the piles of data that are being generated in contemporary systematic biology have led to a second bioinformatics crisis, the first being the one that confronted Linnaeus in the mid-18th century (Godfray 2007). Although our aim is to clear a path for new discussions of taxonomy from an information science-informed point of view, we continue where others in the history, philosophy, and sociology of science have already trod. We believe that an appreciation of biological taxonomy as an information science raises many questions about the philosophical, theoretical, material, and practical aspects of the use and revision of biological nomenclatures in different local and global communities of scientists and citizen scientists. In particular, conceiving of taxonomy as an information science directs attention to the temporalities of managing an accumulating data about classified entities that are themselves subject to revision, to the means by which revision is accomplished, and to the semantic, material, and collaborative contexts that mediate the execution of revisions. (shrink)

Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate (...) the development of integrative phylogenomics for analyzing these genomes and their histories, with tools suited to analyzing the importance of lateral gene transfer (LGT) and of DNA evolution in extra-cellular mobile genetic elements (e.g., viruses, plasmids). These phenomena greatly increase the complexity of relationships among interacting genetic partners, as they exchange functional genetic units. We examine the ontology of functional genetic units, interacting genetic partners, and emergent genetic associations, argue that these three categories of entities are required for a successful integrated phylogenomics. We conclude with arguments to suggest that the proposed new perspective and associated tools are suitable, and perhaps required, as a replacement for the bifurcating trees that have dominated evolutionary thinking for the last 150 years. (shrink)

The placozoan Trichoplax adhaerens is a tiny hairy plate and more simply organized than any other living metazoan. After its original description by F.E. Schulze in 1883, it attracted attention as a potential model for the ancestral state of metazoan organization, the “Urmetazoon”. Trichoplax lacks any kind of symmetry, organs, nerve cells, muscle cells, basal lamina, and extracellular matrix. Furthermore, the placozoan genome is the smallest (not secondarily reduced) genome of all metazoan genomes. It harbors a remarkably rich diversity (...) of genes and has been considered the best living surrogate for a metazoan ancestor genome. The phylum Placozoa presently harbors three formally described species, while several dozen “cryptic” species are yet awaiting their description. The phylogenetic position of placozoans has recently become a contested arena for modern phylogenetic analyses and view‐driven claims. Trichoplax offers unique prospects for understanding the minimal requirements of metazoan animal organization and their corresponding malfunctions. (shrink)

The last decade has seen an explosion of research on the gut microbiota—the trillions of microorganisms that colonize the human gut. It is now clear that interindividual diversity in microbiota composition plays an important role in determining susceptibility to a wide variety of diseases. However, identifying the precise changes in microbiota composition that play causal roles has remained a largely unrealized goal. Here, we propose that functional classifications of microbes based on their interactions with and effects on the host—particularly (...) the host immune system—will illuminate the role of the microbiota in shaping human physiology. We outline the benefits of “functional” classification compared to phylogenetic classifications, and review current efforts at functional classification of the microbiota. Finally, we outline a theoretical framework for classifying host-microbiota interactions. Future advances enabling broader functional classifications of the microbiota promise to revolutionize our understanding of the role of gut microbes in health and disease. Functional classifications of the human microbiota reveal previously hidden patterns and will be key to cracking the microbiota composition code. This figure shows a theoretical comparison between phylogenetic classification and functional classification of a host-associated microbial community. (shrink)

From the point of view of a dynamic morphology, form is not only the result of process(es) — it is process. This process may be analyzed in terms of two pairs of fundamental processes: growth and decay, differentiation and dedifferentiation. Each of these processes can be analyzed in terms of various modalities (parameters) and submodalities. This paper deals with those of growth (see Table 1). For the purpose of systematits and phylogenetic reconstruction the modalities and submodalities can be considered (...) dynamic characters that have states. Each state of such a dynamic character is a more detailed process, hence not static. For example, determinate growth represents a state of the dynamic character (or modality) of growth duration.The processes of Table 1 can be applied to the whole plant kingdom (although in certain cases only some processes of the whole set may be applicable). Thus, the diversity of plant form is seen as a diversity of process combinations. From this point of view, change in form implies change in the process combination(s). Questions that arise are, for example, the following: Which process combinations actually occur? Which of these are the most frequent? How and why have process combinations changed during ontogeny and phylogeny? (shrink)

Molecular methods have revolutionised virtually every area of biology, and metazoan phylogenetics is no exception: molecular phylogenies, molecular clocks, comparative phylogenomics, and developmental genetics have generated a plethora of molecular data spanning numerous taxa and collectively transformed our understanding of the evolutionary history of animals, often corroborating but at times opposing results of more traditional approaches. Moreover, the diversity of methods and models within molecular phylogenetics has resulted in significant disagreement among molecular phylogenies as well as between these and (...) earlier phylogenies. How should this broad and multifaceted problem be tackled? I argue that the answer lies in integrating evidence to infer the best evolutionary scenario. I begin with an overview of recent development in early metazoan phylogenetics, followed by a discussion of key conceptual issues in phylogenetics revolving around phylogenetic evidence, theory, methodology, and interrelations thereof. I then argue that the integration of different kinds of evidence is necessary for arriving at the best evolutionary scenario rather than merely the best-fitting cladogram. Finally, I discuss the prospects of this view in stimulating interdisciplinary cross-talk in early metazoan research and beyond, and challenges that need to be overcome. (shrink)

From the 1960s, mathematical and computational tools have been developed to arrive at human population trees from various kinds of serological and molecular data. Focusing on the work of the Italian-born population geneticist Luigi Luca Cavalli-Sforza, I follow the practices of tree-building and mapping from the early blood-group studies to the current genetic admixture research. I argue that the visual language of the tree is paralleled in the narrative of the human diasporas, and I show how the tree was actually (...) mapped onto the surface of the earth. This visual and textual structure is mirrored in the liberal discourse of unity in diversity that has been criticized as running counter to the socio-political effects of human population genetics. From this perspective, one may ask how far the phylogenetic diagram in its various forms is a manifestation of the physics of power that according to Michel Foucault consists in mechanisms that analyse distributions, movements, series, combinations, and that uses instruments to render visible, to register, to differentiate and to compare. It is one among other disciplinary technologies that ensure the ordering of human diversity. In the case of intra-human phylogenetic trees, population samples and labels are one issue. Another is that the separated branches seem to show groups of people, who have in reality been interacting and converging, as isolated. Often based on so-called isolated peoples, molecular tree diagrams freeze a hierarchical kinship system that is meant to represent a state before the great historical population movements. (shrink)

Considering the enormous diversity of living organisms, representing mostly untapped resources for studying ecological, ontogenetic and phylogenetic patterns and processes, why should evolutionary biologists concern themselves with the remains of animals and plants that died out tens or even hundreds of millions of years ago? The reason is that important new insights into some of the most vexing evolutionary questions are being revealed at the interfaces of palaeontology, developmental biology and molecular biology. Attempts to synthesise information from these (...) disciplines, however, often encounter their greatest hurdles in considerations of the radiation of the Metazoa. Ongoing challenges relate to the origins of body plans, the relationships of the metazoan phyla and the timing of major evolutionary radiations. Palaeontology not only has its own unique contributions to the study of evolutionary processes, but provides a lynchpin for many of the emerging techniques. BioEssays 22:1142–1152, 2000. © 2000 John Wiley & Sons, Inc. (shrink)

Speech sounds are an essential vehicle of information exchange and meaning expression in approximately 7,000 spoken languages in the world. What functional constraints and evolutionary mechanisms lie behind linguistic diversity of sound systems is under ongoing debate; in particular, it remains conflicting whether there exists any universal relationship between these constraints despite of diverse sounds systems cross-linguistically. Here, we conducted cross-linguistic typological and phylogenetic analyses to address the characteristics of constraints on linguistic diversity of vowel systems. First, (...) the typological analysis revealed a power-law based dependence between the global structural dispersion and the local focalization of vowel systems and validated that such dependence was independent of geographic region, language family, and linguistic affiliation. Second, the phylogenetic analysis further illustrated that the observed dependence resulted from correlated evolutions of these two structural properties, which proceeded in an adaptive process. These results provide empirical evidence that self-organization mechanisms helped shape vowel systems and common functional constraints took effect on the evolution of vowel systems in the world’s languages. (shrink)

Paleontological and molecular data suggest quite different patterns for the early evolution of placental mammals. Paleontological evidence indicates a radiation, with most of the extant orders diverging at approximately the same time, close to the Cretaceous-Tertiary boundary, 65 Myr ago. Molecular evidence suggests a branching pattern of evolution that started much earlier. Resolving this discrepancy requires a consideration of the assumptions that underlie both approaches. It is argued here that the pattern indicated by the molecular approach is the most likely (...) to be correct. If it is correct then either: 1) A diversity of placental mammals remains to be sampled from the Cretaceous, or 2) The placental orders diverged phylogenetically long before they diversified morphologically, implying a decoupling of the evolutionary processes associated with speciation and adaptation. The adaptive diversification of placental mammals may have required the demise of the dinosaurs at the end of the Cretaceous, but it occurred in lineages that had a long prior history of independent existence. BioEssays 21: 1052–1058, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

Current phylogenies show that paired fins and limbs are unique to jawed vertebrates and their immediate ancestry. Such fins evolved first as a single pair extending from an anterior location, and later stabilized as two pairs at pectoral and pelvic levels. Fin number, identity, and position are therefore key issues in vertebrate developmental evolution. Localization of the AP levels at which developmental signals initiate outgrowth from the body wall may be determined by Hox gene expression patterns along the lateral plate (...) mesoderm. This regionalization appears to be regulated independently of that in the paraxial mesoderm and axial skeleton. When combined with current hypotheses of Hox gene phylogenetic and functional diversity, these data suggest a new model of fin/limb developmental evolution. This coordinates body wall regions of outgrowth with primitive boundaries established in the gut, as well as the fundamental nonequivalence of pectoral and pelvic structures. BioEssays 20:371–381, 1998. © 1998 John Wiley & Sons Inc. (shrink)

The concept of superorganism has a mixed reputation in biology—for some it is a convenient way of discussing supra-organismal levels of organization, and for others, little more than a poetic metaphor. Here, I show that a considerable step forward in the understanding of superorganisms results from a thorough review of the supra-organismal levels of organization now known to exist among the “unicellular” protists. Limiting the discussion to protists has enormous advantages: their bodies are very well studied and relatively simple, and (...) they exhibit an enormous diversity of anatomies and lifestyles. This allows for unprecedented resolution in describing forms of supra-organismal organization. Here, four criteria are used to differentiate loose, incidental associations of hosts with their microbiota from “actual” superorganisms: obligatory character, specific spatial localization of microbiota, presence of attachment structures and signs of co-evolution in phylogenetic analyses. Three groups—that have never before been described in the philosophical literature—merit special attention: Symbiontida, Oxymonadida and Parabasalia. Specifically, it is argued that in certain cases—for Bihospites bacati and Calkinsia aureus, Streblomastix strix, Joenia annectens and Mixotricha paradoxa and Kentrophoros —it is fully appropriate to describe the whole protist-microbiota assocation as a single organism and its elements as “tissues” or, arguably, even “organs”. To account for this level of biological complexity, I propose the term “structured superorganism”. (shrink)

Although work on computational and robotic modelling of cognition is highly diverse, as an empirical method it can be roughly divided into at least two clearly different, though non-exclusive branches, motivated to evaluate the sufficiency or the necessity of theories when it comes to accounting for data and/or other observations. With the rising profile of theories of situated/embodied cognition, a third non-exclusive avenue for investigation has also gained in popularity, the investigation of agent-environment embedding or more generally, exploration. Still in (...) its infancy, and often confused with sufficiency testing, this relatively new kind of modelling, which is theory- rather than data-driven, investigates the role of the environment in shaping the ontogenetic and/or phylogenetic development of situated agency. Each of these three approaches presents many issues that modellers must be sensitive to, both in the design of experiments, and in the conclusions that can be drawn from them. This paper highlights some of these issues, provides examples, and addresses the contribution of computational/robotic modelling to cognitive science, as well as some of its limitations. (shrink)

In the eukaryotic cell, DNA compaction is achieved through its interaction with histones, constituting a nucleoprotein complex called chromatin. During metazoan evolution, the different structural and functional constraints imposed on the somatic and germinal cell lines led to a unique process of specialization of the sperm nuclear basic proteins (SNBPs) associated with chromatin in male germ cells. SNBPs encompass a heterogeneous group of proteins which, since their discovery in the nineteenth century, have been studied extensively in different organisms. However, the (...) origin and controversial mechanisms driving the evolution of this group of proteins has only recently started to be understood. Here, we analyze in detail the histone hypothesis for the vertical parallel evolution of SNBPs, involving a “vertical” transition from a histone to a protamine‐like and finally protamine types (H → PL → P), the last one of which is present in the sperm of organisms at the uppermost tips of the phylogenetic tree. In particular, the common ancestry shared by the protamine‐like (PL)‐ and protamine (P)‐types with histone H1 is discussed within the context of the diverse structural and functional constraints acting upon these proteins during bilaterian evolution. (shrink)

Have the large-scale evolutionary patterns illustrated by the fossil record been driven by fluctuations in environmental opportunity, by biotic factors, or by changes in the types of phenotypic variants available for evolutionary change? Since the Modern Synthesis most evolutionary biologists have maintained that microevolutionary processes carrying on over sufficient time will generate macroevolutionary patterns, with no need for other pattern-generating mechanisms such as punctuated equilibrium or species selection. This view was challenged by paleontologists in the 1970s with proposals that the (...) differential sorting and selection of species and clades, and the effects of biotic crises such as mass extinctions, were important extensions to traditional evolutionary theory. More recently those interested in macroevolution have debated the relative importance of abiotic and biotic factors in driving macroevolutionary patterns and have introduced comparative phylogenetic methods to analyze the rates of change in taxonomic diversity. Applying Peter Godfrey-Smith’s distinction between distributional explanations and explanations focusing on the origin of variation, most macroevolutionary studies have provided distributional explanations of macroevolutionary patterns. Comparative studies of developmental evolution, however, have implicated the origin of variants as a driving macroevolution force. In particular, the repatterning of gene regulatory networks provides new insights into the origins of developmental novelties. This raises the question of whether macroevolution has been pulled by the generation of environmental opportunity, or pushed by the introduction of new morphologies. The contrast between distributional and origination scenarios has implications for understanding evolutionary novelty and innovation and how macroevolutionary process may have evolved over time. (shrink)

The eukaryotic genome is a mosaic of eubacterial and archaeal genes in addition to those unique to itself. The mosaic may have arisen as the result of two prokaryotes merging their genomes, or from genes acquired from an endosymbiont of eubacterial origin. A third possibility is that the eukaryotic genome arose from successive events of lateral gene transfer over long periods of time. This theory does not exclude the endosymbiont, but questions whether it is necessary to explain the peculiar set (...) of eukaryotic genes. We use phylogenetic studies and reconstructions of ancestral first appearances of genes on the prokaryotic phylogeny to assess evidence for the lateral gene transfer scenario. We find that phylogenies advanced to support fusion can also arise from a succession of lateral gene transfer events. Our reconstructions of ancestral first appearances of genes reveal that the various genes that make up the eukaryotic mosaic arose at different times and in diverse lineages on the prokaryotic tree, and were not available in a single lineage. Successive events of lateral gene transfer can explain the unusual mosaic structure of the eukaryotic genome, with its content linked to the immediate adaptive value of the genes its acquired. Progress in understanding eukaryotes may come from identifying ancestral features such as the eukaryotic splicesome that could explain why this lineage invaded, or created, the eukaryotic niche. BioEssays 28:57–64, 2006. © 2005 Wiley Periodicals, Inc. (shrink)

Human Evolution provides a comprehensive overview of hominid evolution, synthesising data and approaches from fields as diverse as physical anthropology, evolutionary biology, molecular biology, genetics, archaeology, psychology and philosophy. The book starts with chapters on evolution, population genetics, systematics, and the methods for constructing evolutionary trees. These are followed by a comprehensive review of the fossil history of human evolution since our divergence from the apes. Subsequent chapters cover more recent data, both fossil and molecular, relating to the evolution of (...) modern humans. A final section describes the evolution of culture, language, art, and morality.The authors are leading experts in two complementary fields of scholarship, physical anthropology and molecular evolution. Throughout the book they successfully integrate their expertise in evolutionary theory, phylogenetics, genomics, cultural evolution, language, aesthetics and morality to produce a cutting edge textbook, copiously illustrated and with an extensive and up-to-date bibliography. It will be suitable for both senior undergraduate and graduate level students taking courses on human evolution within departments of biology, anthropology, psychology and philosophy. The book will also appeal to a more general audience seeking a readable, up-to-date and inclusive treatment of human origins and evolution. (shrink)

‘‘Adaptive radiation’’ is an evocative metaphor for explosive evolutionary divergence, which for over 100 years has given a powerful heuristic to countless scientists working on all types of organisms at all phylogenetic levels. However, success has come at the price of making ‘‘adaptive radiation’’ so vague that it can no longer reflect the detailed results yielded by powerful new phylogeny-based techniques that quantify continuous adaptive radiation variables such as speciation rate, phylogenetic tree shape, and morphological diversity. Attempts (...) to shoehorn the results of these techniques into categorical ‘‘adaptive radiation: yes/no’’ schemes lead to reification, in which arbitrary quantitative thresholds are regarded as real. Our account of the life cycle of metaphors in science suggests that it is time to exchange the spent metaphor for new concepts that better represent the full range of diversity, disparity, and speciation rate across all of life. (shrink)

Staphylococcus aureus ST45 is a major global MRSA lineage with huge strain diversity and a high clinical impact. It is one of the most prevalent carrier lineages but also frequently causes severe invasive disease, such as bacteremia. Little is known about its evolutionary history. In this study, we used whole-genome sequencing to analyze a large collection of 451 diverse ST45 isolates from 6 continents and 26 countries. De novo-assembled genomes were used to understand genomic plasticity and to perform coalescent (...) analyses. The ST45 population contained two distinct sublineages, which correlated with the isolates’ geographical origins. One sublineage primarily consisted of European/North American isolates, while the second sublineage primarily consisted of African and Australian isolates. Bayesian analysis predicted ST45 originated in northwestern Europe about 500 years ago. Isolation time, host, and clinical symptoms did not correlate with phylogenetic groups. Our phylogenetic analyses suggest multiple acquisitions of the SCCmec element and key virulence factors throughout the evolution of the ST45 lineage. (shrink)

Human Evolution provides a comprehensive overview of hominid evolution, synthesising data and approaches from fields as diverse as physical anthropology, evolutionary biology, molecular biology, genetics, archaeology, psychology and philosophy. The book starts with chapters on evolution, population genetics, systematics, and the methods for constructing evolutionary trees. These are followed by a comprehensive review of the fossil history of human evolution since our divergence from the apes. Subsequent chapters cover more recent data, both fossil and molecular, relating to the evolution of (...) modern humans. A final section describes the evolution of culture, language, art, and morality. The authors are leading experts in two complementary fields of scholarship, physical anthropology and molecular evolution. Throughout the book they successfully integrate their expertise in evolutionary theory, phylogenetics, genomics, cultural evolution, language, aesthetics and morality to produce a cutting edge textbook, copiously illustrated and with an extensive and up-to-date bibliography. It will be suitable for both senior undergraduate and graduate level students taking courses on human evolution within departments of biology, anthropology, psychology and philosophy. The book will also appeal to a more general audience seeking a readable, up-to-date and inclusive treatment of human origins and evolution. (shrink)

How Darwin's “endless forms most beautiful” have evolved remains one of the most exciting questions in biology. The significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. While our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity are largely unknown. The emerging field (...) of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. This relatively novel approach provides hypotheses and insights into cell biological mechanisms, such as morphogenesis, and their evolution that would have been difficult to obtain by studying only model organisms. We discuss the necessary steps, challenges, and impact of integrating “evolutionary thinking” into bacterial cell biology in the genomic era. (shrink)

Current issues concerning the nature of ancestry and homology are discussed with reference to the evolutionary origin of the tetrapod limb. Homologies are argued to be complex conjectural inferences dependant upon a pre-existing phylogenetic analysisand a theoretical model of the evolutionary development of ontogenetic information. Ancestral conditions are inferred primarily from character (synapomorphy/homology) distributions within phylogeny, because of the deficiencies of palaeontological data. Recent analyses of tetrapod limb ontogeny, and the diverse, earliest morphologies known from the fossil record, are (...) inconsistent with typological concepts such as fixed ancestral patterns or bauplans, emphasising the incompatibility of these with evolutionary continuity. The evolutionary origin of the tetrapod limb is also examined in the light of its recent discussion in developmental genetics. While this field promises to reveal more of the fundamental ontogenetic content of homology (identity), at present it is concerned mostly with the abstraction of a new set of types, rather than investigating diversity and change. (shrink)

Cognitive biases can lead to misinterpretations of human and non-human biology and behavior. The concept of the Umwelt describes phylogenetic contrasts in the sensory realms of different species and has important implications for evolutionary studies of cognition (including biases) and social behavior. It has recently been suggested that the microbiome (the diverse network of microorganisms in a given environment, including those within a host organism such as humans) has an influential role in host behavior and health. In this paper, (...) we discuss the host’s microbiome in relation to cognitive biases and the concept of the Umwelt. Failing to consider the role of host–microbiome (collectively termed a “holobiont”) interactions in a given behavior, may underpin a potentially important cognitive bias – which we refer to as the Holobiont Blindspot. We also suggest that microbially mediated behavioral responses could augment our understanding of the Umwelt. For example, the potential role of the microbiome in perception and action could be an important component of the system that gives rise to the Umwelt. We also discuss whether microbial symbionts could be considered in System 1 thinking – that is, decisions driven by perception, intuition and associative memory. Recognizing Holobiont Blindspots and considering the microbiome as a key factor in the Umwelt and System 1 thinking has the potential to advance studies of cognition. Furthermore, investigating Holobiont Blindspots could have important implications for our understanding of social behaviors and mental health. Indeed, the way we think about how we think may need to be revisited. (shrink)

Eusociality is the form of animal social organization with a reproductive division of labor, most prominently known from ants and bees. Here I ask the question why this enormously successful form of social organization is missing in the largest and most diverse group of vertebrates, the teleost fishes. I first briefly review the phylogenetic distribution and likely evolutionary origins of eusociality. Then, after an equally very brief review of the diverse life history strategies of teleosts, I conclude that it (...) is not the lack of evolutionary pre-adaptations which is keeping teleosts from becoming eusocial. Rather, I argue, that the absence of eusocial fish is caused by a number of differences between aquatic (chiefly marine) and terrestrial ecosystems: (1) Greater offspring dispersal in aquatic ecosystems reduces the role of kin-selection. (2) Lesser predictability of the environment at larger timescales in marine ecosystems disfavors eusociality. (3) A briefer impact of resource pulses in aquatic ecosystems will cause less evolutionary pressure towards cooperation, and eventually eusociality. Finally, I conclude by predicting that the most likely places to find eusocial fishes will be the deep-water regions of the ocean and the African rift lakes. (shrink)

Research on early-divergent angiosperms, including Amborella, the putative sister to all other extant angiosperms, is increasingly used as a yardstick to infer the nature of the hypothetical ancestral angiosperm. Some traits are relatively diverse (and hence relatively labile) in this phylogenetic grade, compared with the more derived eudicot clade, in which developmental patterns have become increasingly canalized. One of the many mysteries surrounding the origin of the angiosperms is the evolutionary origin of the Polygonum-type embryo sac (monosporic, eight-nucleate and (...) seven-celled) that occurs in the majority of flowering plants. Observations on the megagametophyte of Amborella are conflicting, but a recent report of a supernumerary synergid in this genus1 raises the question of whether the Polygonum-type embryo sac is derived by duplication of a four-nucleate structure or by reduction from a multicellular structure. BioEssays 28: 1067–1071, 2006. © 2006 Wiley Periodicals, Inc. (shrink)