Observational and experimental discoveries of new factual entities such as objects, systems, or processes, are major contributors to some advances in the life sciences. Yet, whereas discovery of theories was extensively deliberated by philosophers of science, very little philosophical attention was paid to the discovery of factual entities. This paper examines historical and philosophical aspects of the experimental discovery by Carl Woese of archaea, prokaryotes that comprise one of the three principal domains of the phylogenetic tree. Borrowing Kuhn’s (...) terminology, this discovery of a major biological entity was made during a ‘normal science’ project of building molecular taxonomy for prokaryotes. Unexpectedly, however, an observed anomaly instigated the discovery of archaea. Substantiation of the existence of the new archaeal entity and consequent reconstruction of the phylogenetic tree prompted replacement of a long-held model of a prokarya and eukarya bipartite tree of life by a new model of a tripartite tree comprising of bacteria, archaea, and eukarya. This paper explores the history and philosophical implications of the progression of Woese’s project from normal science to anomaly-instigated model-changing discovery. It is also shown that the consequential discoveries of RNA splicing and of ribozymes were similarly prompted by unexpected irregularities during normal science activities. It is thus submitted that some discoveries of factual biological entities are triggered by unforeseen observational or experimental anomalies. (shrink)

Deep‐level arthropod phylogeny has been in a state of upheaval ever since the emergence of molecular tree reconstruction approaches. While a consensus has settled in that hexapods are more closely related to crustaceans than to myriapods, the phylogenetic position of the latter has remained a matter of debate. Mitochondrial, nuclear, and genome‐scale studies have proposed rejecting the long‐standing superclade Mandibulata, which unites myriapods with insects and crustaceans, in favor of a clade that unites myriapods with chelicerates (...) and has become known as Paradoxapoda or Myriochelata. Here we discuss the progress, problems, and prospects of arriving at the final arthropod tree. (shrink)

Tree diagrams are the prevailing form of visualization in biological classification and phylogenetics. Already during the time of the so-called Systematist Wars from the mid-1960s until the 1980s most journal articles and textbooks published by systematists contained tree diagrams. Although this episode of systematics is well studied by historians and philosophers of biology, most analyses prioritize scientific theories over practices and tend to emphasize conflicting theoretical assumptions. In this article, I offer an alternative perspective by viewing the conflict (...) through the lens of representational practices with a case study on tree diagrams that were used by numerical taxonomists (phenograms) and cladists (cladograms). I argue that the current state of molecular phylogenetics should not be interpreted as the result of a competition of views within systematics. Instead, molecular phylogenetics arose independently of systematics and elements of cladistics and phenetics were integrated into the framework of molecular phylogenetics, facilitated by the compatibility of phenetic and cladistic practices with the quantitative approach of molecular phylogenetics. My study suggests that this episode of scientific change is more complex than common narratives of battles and winners or conflicts and compromises. Today, cladograms are still used and interpreted as specific types of molecular phylogenetic trees. While phenograms and cladograms represented different forms of knowledge during the time of the Systematist Wars, today they are both used to represent evolutionary relationships. This indicates that diagrams are versatile elements of scientific practice that can change their meaning, depending on the context of use within theoretical frameworks. (shrink)

Reconstructing the genetic traits of the Last Common Ancestor and the Tree of Life are two examples of the reaches of contemporary molecular phylogenetics. Nevertheless, the whole enterprise has led to paradoxical results. The presence of Lateral Gene Transfer poses epistemic and empirical challenges to meet these goals; the discussion around this subject has been enriched by arguments from philosophers and historians of science. At the same time, a few but influential research groups have aimed to reconstruct the (...) LCA with rich-in-detail hypotheses and high-resolution gene catalogs and metabolic traits. We argue that LGT poses insurmountable challenges for detailed and rich in details reconstructions and propose, instead, a middle-ground position with the reconstruction of a slim LCA based on traits under strong pressures of Negative Natural Selection, and for the need of consilience with evidence from organismal biology and geochemistry. We defend a cautionary perspective that goes beyond the statistical analysis of gene similarities and assumes the broader consequences of evolving empirical data and epistemic pluralism in the reconstruction of early life. (shrink)

The reconstruction of bacterial evolutionary relationships has proven to be a daunting task because variable mutation rates and horizontal gene transfer (HGT) among species can cause grave incongruities between phylogenetic trees based on single genes. Recently, a highly robust phylogenetic tree was constructed for 13 γ‐proteobacteria using the combined alignments of 205 conserved orthologous proteins.1 Only two proteins had incongruent tree topologies, which were attributed to HGT between Pseudomonas species and Vibrio cholerae or enterics. While (...) the evolutionary relationships among these species appears to be resolved, further analysis suggests that HGT events with other bacterial partners likely occurred; this alters the implicit assumption of γ‐proteobacteria monophyly. Thus, any thorough reconstruction of bacterial evolution must not only choose a suitable set of molecular markers but also strive to reduce potential bias in the selection of species. BioEssays 26:463–468, 2004. © 2004 Wiley Periodicals, Inc. (shrink)

The long-awaited revision of the industry standard on phylogenetics Since the publication of the first edition of this landmark volume more than twenty-five years ago, phylogenetic systematics has taken its place as the dominant paradigm of systematic biology. It has profoundly influenced the way scientists study evolution, and has seen many theoretical and technical advances as the field has continued to grow. It goes almost without saying that the next twenty-five years of phylogenetic research will prove as fascinating (...) as the first, with many exciting developments yet to come. This new edition of Phylogenetics captures the very essence of this rapidly evolving discipline. Written for the practicing systematist and phylogeneticist, it addresses both the philosophical and technical issues of the field, as well as surveys general practices in taxonomy. Major sections of the book deal with the nature of species and higher taxa, homology and characters, trees and tree graphs, and biogeography—the purpose being to develop biologically relevant species, character, tree, and biogeographic concepts that can be applied fruitfully to phylogenetics. The book then turns its focus to phylogenetic trees, including an in-depth guide to tree-building algorithms. Additional coverage includes: Parsimony and parsimony analysis Parametric phylogenetics including maximum likelihood and Bayesian approaches Phylogenetic classification Critiques of evolutionary taxonomy, phenetics, and transformed cladistics Specimen selection, field collecting, and curating Systematic publication and the rules of nomenclature Providing a thorough synthesis of the field, this important update to Phylogenetics is essential for students and researchers in the areas of evolutionary biology, molecular evolution, genetics and evolutionary genetics, paleontology, physical anthropology, and zoology. (shrink)

We discuss the impact of horizontal gene transfer (HGT) on phylogenetic reconstruction and taxonomy. We review the power of HGT as a creative force in assembling new metabolic pathways, and we discuss the impact that HGT has on phylogenetic reconstruction. On one hand, shared derived characters are created through transferred genes that persist in the recipient lineage, either because they were adaptive in the recipient lineage or because they resulted in a functional replacement. On the other (...) hand, taxonomic patterns in microbial phylogenies might also be created through biased gene transfer. The agreement between different molecular phylogenies has encouraged interpretation of the consensus signal as reflecting organismal history or as the tree of cell divisions; however, to date the extent to which the consensus reflects shared organismal ancestry and to which it reflects highways of gene sharing and biased gene transfer remains an open question. Preferential patterns of gene exchange act as a homogenizing force in creating and maintaining microbial groups, generating taxonomic patterns that are indistinguishable to those created by shared ancestry. To understand the evolution of higher bacterial taxonomic units, concepts usually applied in population genetics need to be applied. (shrink)

The discoveries, advancements and continuing controversies in the field of molecular evolution are reviewed. Topics summarized are (1) the evolution of the genetic code, (2) gene evolution including the demonstration of homology, estimation of sequence divergence, phylogenetic trees, the molecular clock and the origin of genes and gene families by various genetic mechanisms, and (3) eukaryotic genome evolution, including the highly repeated satellite sequences, the interspersed and potentially mobile repeated sequences and the unique sequence fraction of the (...) genome. (shrink)

When phylogenetic trees constructed from morphological and molecular evidence disagree (i.e. are incongruent) it has been suggested that the differences are spurious or that the molecular results should be preferred a priori. Comparing trees can increase confidence (congruence), or demonstrate that at least one tree is incorrect (incongruence). Statistical analyses of 181 molecular and 49 morphological trees shows that incongruence is greater between than within the morphological and molecular partitions, and this difference is significant (...) for the molecular partition. Because the level of incongruence between a pair of trees gives a minimum bound on how much error is present in the two trees, our results indicate that the level of error may be underestimated by congruence within partitions. Thus comparisons between morphological and molecular trees are particularly useful for detecting this incongruence (spurious or otherwise). Molecular trees have higher average congruence than morphological trees, but the difference is not significant, and both within- and between-partition incongruence is much lower than expected by chance alone. Our results suggest that both molecular and morphological trees are, in general, useful approximations of a common underlying phylogeny and thus, when molecules and morphology clash, molecular phylogenies should not be considered more reliable a priori. (shrink)

A strong case has been made for the role and value of mechanistic explanation in neuroscience and molecular biology. A similar demonstration in other domains of scientific investigation, however, remains an important challenge of scope for the new mechanists. This article helps answer that challenge by demonstrating one valuable role mechanisms play in phylogenetics. Using the transition/transversion rate parameter as a case example, this article argues that models embedded with mechanisms produce stronger phylogenetic tree hypotheses, as measured (...) by maximum likelihood logL values. Two important implications for the new mechanistic account of explanation are considered. (shrink)

In this paper, I study the application of phylogenetic analysis in evolutionary archaeology. I show how transfer of this apparently general analytic tool is affected by salient differences in disciplinary context. One is that archaeologists, unlike many biologists, do not regard cladistics as a tool for classification, but are primarily interested in explanation. The other is that explanation is traditionally sought in terms of individual-level rather than population-level mechanisms. The latter disciplinary difference creates an ambiguity in the application and (...) interpretation of phylogenetic analyses. Moreover, I argue that, while archaeologists have claimed that “cladistics is useful for reconstructing artefact phylogenies”, these reconstructions only contribute minimally to the explanatory research agenda of evolutionary archaeology. (shrink)

The relation between method, concept and theory in science is complicated. I seek to shed light on that relation by considering an instance of it in systematics: The additional challenges phylogeneticists face when reconstructing phylogeny not at a single level, but simultaneously at multiple levels of the hierarchy. How does this complicate the task of phylogenetic inference, and how might it inform and shape the conceptual foundations of phylogenetics? This offers a lens through which the interplay of method, theory (...) and concepts may be understood in systematics, which, in turn, provides data for a more general account. (shrink)

Abstract: Biology continues to use the Tree of Life image to show the temporal continuity and discontinuity of the living beings. Moreover, the development of genetic, molecular biology and paleontology has originated phylogenetics. This discipline studies evolutionary relatedness among various groups of organisms through molecular sequencing data and morphological data matrices. The Tree offers interesting points for semiotic perspectives and for theological approaches too. The symbolic reading of the Tree of Life, on the one hand, (...) and the analogies with the Biblical genealogies and some Christian images, on the other hand, will be explored. -/- . (shrink)

Although the justification for using cladistic parsimony to infer phylogenetic trees has been extensively discussed, much less attention has been paid to the use of cladistic parsimony to reconstruct the character states of the ancestral species postulated by an inferred phylogenetic tree. These two problems differ in terms of both their inputs and their outputs, as shown in the following table. In the former, one begins with data on the character states of extant species and tries to (...) find the best supported phylogenetic tree. In the latter, one begins with the tree that is most firmly supported by characteristics C1, C2,... Cn-1; one then takes some new characteristic Cn and records the character states of Cn that attach to the tree’s interior nodes, which represent common ancestors. In both cases, cladistic parsimony solves the problem by finding the hypothesis that requires the fewest changes in character state that are needed to explain the observations. (shrink)

Phylogenetic trees are a crucial backbone for a wide breadth of biological research spanning systematics, organismal biology, ecology, and medicine. In 2015, the Open Tree of Life project published a first draft of a comprehensive tree of life, summarizing digitally available taxonomic and phylogenetic knowledge. This paper reviews, investigates, and addresses the following questions as a follow-up to that paper, from the perspective of researchers involved in building this summary of the tree of life: Is (...) there a tree of life and should we reconstruct it? Is available data sufficient to reconstruct the tree of life? Do we have access to phylogenetic inferences in usable form? Can we combine different phylogenetic estimates across the tree of life? And finally, what is the future of understanding the tree of life? A schematic of the process of building a unified tree of life. Inputs are published phylogenetic estimates and a unified taxonomy. These inputs are combined into a summary supertree containing ≈2 million taxa. The relationships among any subset of taxa may easily be accessed and used in downstream analyses. (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)

138 titles across a wide range of scholarly publications illustrate the conceptual affinities that connect the palaetiological sciences of biological systematics, historical linguistics, and stemmatics. These three fields all have as their central objective the reconstruction of evolutionary "trees of history" that depict phylogenetic patterns of descent with modification among species, languages, and manuscripts. All three fields flourished in the nineteenth century, underwent parallel periods of quiescence in the early twentieth century, and in recent decades have seen widespread (...) parallel revivals. "Tree thinking" (O'Hara, 1988) is now standard within evolutionary biology, and the unity of what William Whewell called palaetiology is being once again appreciated by scholars and scientists in many fields. (shrink)

The canonical view of a 3‐domain (3D) tree of life was recently challenged by the discovery of Asgardarchaeota encoding eukaryote signature proteins (ESPs), which were treated as missing links of a 2‐domain (2D) tree. Here we revisit the debate. We discuss methodological limitations of building trees with alignment‐dependent approaches, which often fail to satisfactorily address the problem of ‘‘gaps.’’ In addition, most phylogenies are reconstructed unrooted, neglecting the power of direct rooting methods. Alignment‐free methodologies lift most difficulties but (...) require employing realistic evolutionary models. We argue that the discoveries of Asgards and ESPs, by themselves, do not rule out the 3D tree, which is strongly supported by comparative and evolutionary genomic analyses and vast genomic and biochemical superkingdom distinctions. Given uncertainties of retrodiction and interpretation difficulties, we conclude that the 3D view has not been falsified but instead has been strengthened by genomic analyses. In turn, the objections to the 2D model have not been lifted. The debate remains open. Also see the video abstract here:https://youtu.be/-6TBN0bubI8. (shrink)

Although molecular systematists may use the terminology of cladism, claiming that the reconstruction of phylogenetic relationships is based on shared derived states , the latter is not the case. Rather, molecular systematics is based on the assumption, first clearly articulated by Zuckerkandl and Pauling , that degree of overall similarity reflects degree of relatedness. This assumption derives from interpreting molecular similarity between taxa in the context of a Darwinian model of continual and gradual change. Review (...) of the history of molecular systematics and its claims in the context of molecular biology reveals that there is no basis for the “molecular assumption.”. (shrink)

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

Despite the promises made by molecular evolutionists since the early 1960s that phylogenies would be readily reconstructed using molecular data, the construction of molecular phylogenies has both retained many methodological problems of the past and brought up new ones of considerable epistemic relevance. The field is driven not only by changes in knowledge about the processes of molecular evolution, but also by an ever-present methodological anxiety manifested in the constant search for an increased objectivity—or in its (...) converse, the avoidance of subjectivity.This paper offers an exhaustive account of the methodological and conceptual difficulties embedded in each of the steps required to elaborate molecular phytogenies. The authors adopt a historical perspective on the field in order to follow the development of practices that seek to increase the objectivity of their methods and representations. These include the adoption and development of explicit criteria for evaluation of evidence, and of procedures associated with methods of statistical inference, quantification and automation. All these are linked to an increasing use of computers in research since the mid 1960s. We will show that the practices of objectivity described are highly dependent on the problems and tools of molecular phylogenetics. (shrink)

"The Natural System" is the name given to the underlying arrangement present in the diversity of life. Unlike a classification, which is made up of classes and members, a system or arrangement is an integrated whole made up of connected parts. In the pre-evolutionary period a variety of forms were proposed for the Natural System, including maps, circles, stars, and abstract multidimensional objects. The trees sketched by Darwin in the 1830s should probably be considered the first genuine evolutionary diagrams of (...) the Natural System—the first genuine evolutionary trees. Darwin refined his image of the Natural System in the well-known evolutionary tree published in the Origin of Species, where he also carefully distinguished between arrangements and classifications. Following the publication of the Origin, there was a great burst of evolutionary tree building, but interest in trees declined substantially after 1900, only to be revived in recent years with the development of cladistic analysis. ¶ While evolutionary trees are modern diagrams of the Natural System, they are at the same time instances of another broad class of diagrams that may be called "trees of history": branching diagrams of genealogical descent and change. During the same years that Darwin was sketching his first evolutionary trees, the earliest examples of two other trees of history also appeared: the first trees of language evolution and of manuscript genealogy. Though these were apparently independent of evolutionary trees in their origin, the similarities among all these trees of history, and among the historical processes that underlie them, were soon recognized. Darwin compared biological evolution and language evolution several times in the Origin of Species, and both Ernst Haeckel and the linguist August Schleicher made similar comparisons. Both linguists and stemmaticists (students of manuscript descent) understood the principle of apomorphy—the principle that only shared innovations provide evidence of common ancestry—more clearly than did systematists, and if there had been more cross-fertilization among these fields the cladistic revolution in systematics might well have taken place in the nineteenth century. ¶ Although historical linguists and stemmaticists have in some respects had sounder theory than have systematists, at least until recently, they have also had the practical problem of very large amounts of data, a problem not often faced by systematists until the advent of molecular sequencing. The opportunity now exists for systematists to contribute to the theory and practice of linguistics and stemmatics, their sister disciplines in historical reconstruction, through application of our commonly used computer programs for tree estimation. Preliminary results from the application of numerical cladistic analysis to a large stemmatic data set have been very encouraging, and have already generated much discussion in the stemmatics community. (shrink)

By combining state‐of‐the‐art approaches in ancient genomics, Meyer and co‐workers have reconstructed the mitochondrial sequence of an archaic hominin that lived at Sierra de Atapuerca, Spain about 400,000 years ago. This achievement follows recent advances in molecular anthropology that delivered the genome sequence of younger archaic hominins, such as Neanderthals and Denisovans. Molecular phylogenetic reconstructions placed the Atapuercan as a sister group to Denisovans, although its morphology suggested closer affinities with Neanderthals. In addition to possibly challenging our (...) interpretation of the fossil record, this study confirms that genomic information can be recovered from extremely damaged DNA molecules, even in the presence of significant levels of human contamination. Together with the recent characterization of a 700,000‐year‐old horse genome, this study opens the Middle Pleistocene to genomics, thereby extending the scope of ancient DNA to the last million years. (shrink)

In a recent paper,(1) palaeontologist Mike Benton claimed that our ability to reconstruct accurately the tree of Life may not have improved significantly over the last 100 years. This implies that the cladistic and molecular revolutions may have promulgated as much bad “black box” science as rigorous investigation. Benton's assessment was based on the extent to which cladograms (typically constructed with reference only to distributions of character states) convey the same narrative as the geochronological ages of fossil taxa (...) (an independent data set). Fossil record quality varies greatly between major clades, and the palaeontological dating “yardstick” may be more appropriate for some groups than others. BioEssays 24:203–207, 2002. © 2002 Wiley Periodicals, Inc.; DOI 10.1002/bies.10065. (shrink)

MacDonald and Kreitman (1991) propose a test of the neutral mutationrandom drift (NM-RD) hypothesis, the central claim of the neutral theory of molecular evolution. The test involves generating predictions from the NM-RD hypothesis about patterns of molecular substitutions. Alternative selection hypotheses predict that the data will deviate from the predictions of the NM-RD hypothesis in specifiable ways. To conduct the test Mac- Donald and Kreitman examine the evolutionary dynamics of the alcohol dehydrogenase (Adh) gene in three species of (...) Drosophila. The test compares the number of DNA sequence changes between species and within species. The number of DNA differences is an indicator of the evolutionary rate of the Adh gene. Based on the test they conclude that there is strong evidence for adaptive protein evolution at particular sites in the gene. Understanding the test requires some basic knowledge about molecular terms and the predictions of neutral theory. The two important terms are fixed differences and polymorphisms. These are determined by comparing DNA sequences made up of thousands of individual nucleotide sites. A site that is unchanged within a species but different from a related species counts as a fixed difference. These are mutations that occur in some common ancestor of the lineage such that all descendants inherit the change. A site that differs within a species counts as a polymorphism. Determining the number of fixed differences and polymorphisms requires placing 1 each individual gene sequence onto a phylogenetic tree. A coalescent tree charts the ancestral relationships for a set of individual gene sequences. Sequences sampled from within a species form a within-species tree. The common ancestors of each within-species tree form a between-species tree. A detected difference counts as a polymorphism or a fixed difference depending on where it occurs in the phylogenetic tree (cf. Table 1). The test uses the numbers of polymorphisms and fixed differences as indicators of evolutionary rates.. (shrink)

Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today’s literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of (...) prokaryote phylogeny and its apparent failure to achieve integration within broader tree-of-life accounts of evolutionary history. Despite the fact that integrated databases exist of molecules pertinent to the phylogenetic reconstruction of all lineages of life, and even though the same methods can be used to construct phylogenies wherever the organisms fall on the tree of life, prokaryote phylogeny remains at best only partly integrated within tree-of-life efforts. I will examine why integration does not occur, compare it with integrative practices in animal and other eukaryote phylogeny, and reflect on whether there might be different expectations of what integration should achieve. Finally, I will draw some general conclusions about integration and its function as a ‘meta-heuristic’ in the normative commitments guiding scientific practice. (shrink)

Adaptive immunity is unique to the vertebrates, and the molecules involved (including immunoglobulins, T cell receptors and the major histocompatibility complex molecules) seem to have diversified very rapidly early in vertebrate history. Reconstruction of gene phylogenies has yielded insights into the evolutionary origin of a number of molecular systems, including the complement system and the major histocompatibility complex (MHC). These analyses have indicated that the C5 component of complement arose by gene duplication prior to the divergence of C3 (...) and C4, which suggests that the alternative complement pathway was the first to evolve. In the case of the MHC, phylogenetic analysis supports the hypothesis that MHC class II molecules evolved before class I molecules. The fact that the MHC‐linked proteasome components that specifically produce peptides for presentation by class I MHC appear to have originated before the separation of jawed and jawless vertebrates suggests that the MHC itself may have been present at this time. Immmune system gene families have evolved by gene duplication, interlocus recombination and (in some cases) positive Darwinian selection favoring diversity at the amino acid level. (shrink)

In this paper, I analyze George Gaylord Simpson's response to the molecularization of evolutionary biology from his unique perspective as a paleontologist. I do so by exploring his views on early attempts to reconstruct phylogenetic relationships among primates using molecular data. Particular attention is paid to Simpson's role in the evolutionary synthesis of the 1930s and 1940s, as well as his concerns about the rise of molecular biology as a powerful discipline and world-view in the 1960s. I (...) argue that Simpson's belief in the supremacy of natural selection as the primary driving force of evolution, as well as his view that biology was a historical science that seeks ultimate causes and highlights contingency, prevented him from acknowledging that the study of molecular evolution was an inherently valuable part of the life sciences. (shrink)

We examine three critical aspects of Popper’s formulation of the ‘ Logic of Scientific Discovery ’—evidence, content and degree of corroboration—and place these concepts in the context of the Tree of Life (ToL) problem with particular reference to molecular systematics. Content, in the sense discussed by Popper, refers to the breadth and scope of existence that a hypothesis purports to explain. Content, in conjunction with the amount of available and relevant evidence, determines the testability, or potential degree of (...) corroboration, of a statement; content distinguishes scientific hypotheses from metaphysical assertions. Degree of corroboration refers to the relative and tentative confidence assigned to one hypothesis over another, based upon the performance of each under critical tests. Here we suggest that systematists attempt to maximize content and evidence to increase the potential degree of corroboration in all phylogenetic endeavors. Discussion of this “total evidence” approach leads to several interesting conclusions about generating ToL hypotheses. (shrink)

Recent studies of the evolution of religion have revealed the cognitive underpinnings of belief in supernatural agents, the role of ritual in promoting cooperation, and the contribution of morally punishing high gods to the growth and stabilization of human society. The universality of religion across human society points to a deep evolutionary past. However, specific traits of nascent religiosity, and the sequence in which they emerged, have remained unknown. Here we reconstruct the evolution of religious beliefs and behaviors in early (...) modern humans using a global sample of hunter-gatherers and seven traits describing hunter-gatherer religiosity: animism, belief in an afterlife, shamanism, ancestor worship, high gods, and worship of ancestors or high gods who are active in human affairs. We reconstruct ancestral character states using a time-calibrated supertree based on published phylogenetic trees and linguistic classification and then test for correlated evolution between the characters and for the direction of cultural change. Results indicate that the oldest trait of religion, present in the most recent common ancestor of present-day hunter-gatherers, was animism, in agreement with long-standing beliefs about the fundamental role of this trait. Belief in an afterlife emerged, followed by shamanism and ancestor worship. Ancestor spirits or high gods who are active in human affairs were absent in early humans, suggesting a deep history for the egalitarian nature of hunter-gatherer societies. There is a significant positive relationship between most characters investigated, but the trait “high gods” stands apart, suggesting that belief in a single creator deity can emerge in a society regardless of other aspects of its religion. (shrink)

Historical sciences like evolutionary biology reconstruct past events by using the traces that the past has bequeathed to the present. Markov chain theory entails that the passage of time reduces the amount of information that the present provides about the past. Here we use a Moran process framework to show that some evolutionary processes destroy information faster than others. Our results connect with Darwin’s principle that adaptive similarities provide scant evidence of common ancestry whereas neutral and deleterious similarities do better. (...) We also describe how the branching in phylogenetic trees affects the information that the present supplies about the past. (shrink)

Sponges branch basally in the metazoan phylogenetic tree and are believed to be composed of four distinct lineages with still uncertain relationships. Indeed, some molecular studies propose that Homoscleromorpha may be a fourth Sponge lineage, distinct from Demospongiae in which they were traditionally classified. They harbour many features that distinguish them from other sponges and are more evocative of those of the eumetazoans. They are notably the only sponges to possess a basement membrane with collagen IV and (...) specialized cell‐junctions, thus possessing true epithelia. Among Homoscleromorphs, we have chosen Oscarella lobularis as a model species. This common and easily accessible sponge is characterized by relatively simple histology and cell composition, absence of skeleton, and strongly pronounced epithelial structure. In this review, we explore the specific features that make O. lobularis a promising homoscleromorph sponge model for evolutionary and developmental researches. (shrink)

Biological species are spatio-temporally localized entities. This fact led to the concept of species as individuals [11], [14], and, at the same time, to the refutation of essentialism in evolutionary biology and taxonomy. On the other hand, molecular biology is compatible with essentialisms of chemistry and physics. The new concept of "historical essences", which is presented in this paper, tries to reconcile antiessentialism of evolutionary biology with essentialism of molecular biology. Historical essences are those parts of genetic information (...) which determine characters relevant for the identification of a taxon. Since membership in a particular taxon is defined by the sharing of the most recent common ancestor, historical essences correspond to the genetic information responsible for the creation of such common ancestor. Historical essences, which are spatiotemporally localized, generate a particular arrangement of spatiotemporally unrestricted processes which lead to the creation, maintenance and reproduction of organisms. These arrangements are results of fortuitous confluence of biological and extrabiological circumstances . In historical essences such a sequence of historical contingencies is "conserved", which allows molecular taxonomy to reconstruct the phylogenetic relationships. The concept of historical essences can be seen as a post-Darwinian modification of the original Aristotleś term of essence - "to-ti-en-einai". (shrink)

Since Darwin, a genetic continuity of morphological and behavioral traits between all living beings has been taken for granted. This paper describes eight irreducible classes of descriptive traits on the basis of the presence or absence of (a) repetitivity, (b) correlation with natural environment properties and (c) inner integration. It is argued that some of these classes should neither be used in taxonomy nor in phylogenetic reconstructions. The remaining classes imply an inner dynamic indivisibility on the one hand, and (...) an evident relation to the concept of the reaction norm on the other. These implications, in turn, may lead to the recognition of much broader „natural species” units which embrace forms usually grouped within a genus or family. Morphological and behavioral gaps between such „natural species” have to be considered in relation to the rather mysterious developmental, integrative and adaptive potential of a particular natural species. Paleontological data seem to confirm the existence of such gaps. This introduces a serious objection to the theory of common descent and to the cognitive utility of the macro- and megaevolutionary „phylogenetic trees.”. (shrink)

Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn’s account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn’s relevance (...) to this controversy, we add a social analysis of the scientists involved to the historical and philosophical debates. We conclude that while Kuhn’s account may capture aspects of the pattern of an episode of scientific change, he has little to say about how the process of generating new understandings is occurring in evolutionary microbiology. Once Kuhn’s application is limited to that of an initial investigative probe into how scientific problem-solving occurs, his disciplinary scope becomes broader. (shrink)

Evidence and Evolution has four chapters: (1) Evidence, (2) Intelligent Design, (3) Natural Selection, and (4) Common Ancestry. The first chapter develops tools that are used in the rest of the book, though more ideas about evidence are added. In Chapter 1, I endorse a pluralistic outlook—Bayesianism is fine in some inference problems, likelihoodism in others, and AIC in still others. In Chapter Two, on intelligent design, I try to develop the strongest possible formulation of the design argument for the (...) existence of God, after which I criticize the argument so conceived. This second chapter also attempts to resuscitate the concept of testability. Chapter 3, on natural selection, discusses how to evaluate competing hypotheses on evolution mechanisms and evaluate the use of the principle of common cause, molecular data, and cladistic parsimony. Chapter 4 is on common ancestry: what it means to say that all life on earth has a common ancestor, and s. Why should the similarity of two species be evidence that they have a common ancestor? The chapter concludes with a discussion of how biologists use cladistic parsimony to infer phylogenetic trees and compare it with explicit statistical approaches. (shrink)

Although Bayesian methods are widely used in phylogenetic systematics today, the foundations of this methodology are still debated among both biologists and philosophers. The Bayesian approach to phylogenetic inference requires the assignment of prior probabilities to phylogenetic trees. As in other applications of Bayesian epistemology, the question of whether there is an objective way to assign these prior probabilities is a contested issue. This paper discusses the strategy of constraining the prior probabilities of phylogenetic trees by (...) means of the Principal Principle. In particular, I discuss a proposal due to Velasco (Biol Philos 23:455–473, 2008) of assigning prior probabilities to tree topologies based on the Yule process. By invoking the Principal Principle I argue that prior probabilities of tree topologies should rather be assigned a weighted mixture of probability distributions based on Pinelis’ (P Roy Soc Lond B Bio 270:1425–1431, 2003) multi-rate branching process including both the Yule distribution and the uniform distribution. However, I argue that this solves the problem of the priors of phylogenetic trees only in a weak form. (shrink)

In this paper, I show how idealizations contribute to social activities in science, such as the recruitment of experts to a research project. These contributions have not been explicitly discussed by recent philosophical accounts of scientific idealization. These accounts have focused on how idealizations influence activities like scientific theorization, explanation, and modeling. Other accounts focus on how idealizations influence policy-making and science communication. I expand these accounts by exploring the uses of idealized phylogenetic trees in science. Trees are not (...) only useful for improving our understanding and public communication of evolutionary history, but they also help with the organization of laboratories and collaboration among scientists. Attending to the relation between idealizations and these social practices in science matters. It can help us understand why idealized models become entrenched and why certain social practices change over time. (shrink)

Bayesian methods have become among the most popular methods in phylogenetics, but theoretical opposition to this methodology remains. After providing an introduction to Bayesian theory in this context, I attempt to tackle the problem mentioned most often in the literature: the “problem of the priors”—how to assign prior probabilities to tree hypotheses. I first argue that a recent objection—that an appropriate assignment of priors is impossible—is based on a misunderstanding of what ignorance and bias are. I then consider different (...) methods of assigning prior probabilities to trees. I argue that priors need to be derived from an understanding of how distinct taxa have evolved and that the appropriate evolutionary model is captured by the Yule birth–death process. This process leads to a well-known statistical distribution over trees. Though further modifications may be necessary to model more complex aspects of the branching process, they must be modifications to parameters in an underlying Yule model. Ignoring these Yule priors commits a fallacy leading to mistaken inferences both about the trees themselves and about macroevolutionary processes more generally. (shrink)

The article reconstructs the main lines of three hypotheses in the current literature concerning the evolutionary pace which characterized the natural history of human language: the “continuist” and gradualist perspective, the “discontinuist” and evolution-free perspective, and the “punctuationist” view. This current debate appears to have a long history, which starts at least from Darwin’s time. The article highlights the similarities between the old and the modern debates in terms of history of ideas, and it shows the current limits of each (...) of these perspectives. In the final part, we present an alternative approach which considers human language not as a single trait, but as the result of a mosaic of different elements, some of which recently evolved, and some others gradually evolved and phylogenetically ancient. When matched with a tree thinking and comparative perspective, this view suggests that expressions of symbolic and linguistic behaviors in other human species could have preceded the more complex and systematic behaviors showed by Homo sapiens. (shrink)

In the last thirty years systematics has transformed itself from a discipline concerned with classification into a discipline concerned with reconstructing the evolutionary history of life. This transformation has been driven by cladistic analysis, a set of techniques for reconstructing evolutionary trees. Long interested in the large-scale structure of evolutionary history, cladistically oriented systematists have recently begun to apply "tree thinking" to problems near the species level. ¶ In any local ("non-dimensional") situation species are usually well-defined, but across space (...) and time the grouping of populations into species is often problematic. Three views of species are in common use today, the biological species concept, the evolutionary species concept, and the phylogenetic species concept. Each of these has strengths and weaknesses, but no matter which is applied, exact counts of the number of species in any extended area will always be ambiguous no matter how much factual information is available. This ambiguity arises because evolution is an historical process, and the grouping of organisms into species always depends to some extent upon expectations of the future behavior of those organisms and their descendants, expectations that cannot be evaluated in the present. The existence and special character of the species problem is itself one of the central pieces of evidence for evolution. (shrink)

The reconstruction of ensemble d–f of the Akhmîm Papyrus, better known as the Strasbourg Papyrus, which attests approximately eighteen of the over seventy new lines of Empedocles’ physical poem, has drawn the attention of scholars over recent years. Thanks to the good condition of the papyrus and the coincidence with two Empedoclean lines, already known from the indirect tradition, ensemble d–f 1–10a presents a well-restored text and an intelligible sense. In contrast, because of the damaged state of the papyrus, (...) the restoration of d–f 10b–18 is more complicated. These lines seem to describe a life-generative process, but what process was Empedocles talking about? Some resemblances between these papyrus lines and the lines of another Empedoclean fragment, DK 31 B 62, have suggested to scholars, notably to A. Martin and O. Primavesi in 1999 and M. Rashed in 2011, that the lines of the papyrus depict, just like DK 31 B 62, the generation of whole-natured beings. Other scholars, however, such as R. Janko in 2004 and A. Laks and G.W. Most in 2016, show more caution and leave the possibility open that Empedocles is here talking about the generation of something else. (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)

The fundamental Hennigian principle, grouping solely on synapomorphy, is seldom used in modern phylogenetics. In the submitted paper, we apply this principle in reanalyzing five datasets comprising 197 complete plastid genomes (plastomes). We focused on the latter because plastome-based DNA sequence data gained dramatic popularity in molecular systematics during the last decade. We show that pattern-cladistic analyses based on complete plastid genome sequences can successfully resolve affinities between plant taxa, simultaneously simplifying both the genomic and analytical frameworks of (...) class='Hi'>phylogenetic studies. We developed “Matrix to Newick” (M2N), a program to represent the standard molecular alignment of plastid genomes in the form of trees or relationships directly. Thus, massive plastome-based DNA sequence data can be successfully represented in a relational form rather than as a standard molecular alignment. Application of methods of median supertree construction (the Average Consensus method has been used as an example in this study) or Maximum Parsimony analysis to relational representations of plastome sequence data may help systematist to avoid the complicated assumption-based frameworks of Maximum Likelihood or Bayesian phylogenetics that are most used today in massive plastid sequence data analyses. We also found that significant amounts of pure genomic information that typically accommodate the majority of current plastid phylogenomic studies can be effectively dropped by systematists if they focus on the pattern-cladistics or relational analyses of plastome-based molecular data. The proposed pattern-cladistic approach is a powerful and straightforward heuristic alternative to modern plastome-based phylogenetics. (shrink)

We show that, contrary to long-standing assumptions, syntactic traits, modeled here within the generative biolinguistic framework, provide insights into deep-time language history. To support this claim, we have encoded the diversity of nominal structures using 94 universally definable binary parameters, set in 69 languages spanning across up to 13 traditionally irreducible Eurasian families. We found a phylogenetic signal that distinguishes all such families and matches the family-internal tree topologies that are safely established through classical etymological methods and datasets. (...) We have retrieved “near-perfect” phylogenies, which are essentially immune to homoplastic disruption and only moderately influenced by horizontal convergence, two factors that instead severely affect more externalized linguistic features, like sound inventories. This result allows us to draw some preliminary inferences about plausible/implausible cross-family classifications; it also provides a new source of evidence for testing the representation of diversity in syntactic theories. (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)

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)

Given the pervasiveness of gene sharing in evolution and the extent of homology across the tree of life, why is everything not homologous with everything else? The continuity and overlapping genetic contributions to diverse traits across lineages seem to imply that no discrete determination of homology is possible. Although some argue that the widespread overlap in parts and processes should be acknowledged as “partial” homology, this threatens a broad base of presumed comparative morphological knowledge accepted by most biologists. Following (...) a long scientific tradition, we advocate a strategy of “theoretical articulation” that introduces further distinctions to existing concepts to produce increased contrastive resolution among the labels used to represent biological phenomena. We pursue this strategy by drawing on successful patterns of reasoning from serial homology at the level of gene sequences to generate an enriched characterization of serial homology as a hierarchical, phylogenetic concept. Specifically, we propose that the concept of serial homology should be applied primarily to repeated but developmentally individualized body parts, such as cell types, differentiated body segments, or epidermal appendages. For these characters, a phylogenetic history can be reconstructed, similar to families of paralogous genes, endowing the notion of serial homology with a hierarchical, phylogenetic interpretation. On this basis, we propose a five-fold theoretical classification that permits a more fine-grained mapping of diverse trait-types. This facilitates answering the question of why everything is not homologous with everything else, as well as how novelty is possible given that any new character possesses evolutionary precursors. We illustrate the fecundity of our account by reference to debates over insect wing serial homologs and vertebrate paired appendages. (shrink)