A method of phylogenetic reconstruction as proposed by a number of scientists of the Senckenberg Research Institute is discussed. The method is based on functional-morphological studies, the evolutionary adaptation principle of Bock and Von Wahlert (1965) and so-called model reconstruction. It is argued in this paper that direction of the adaptation process cannot be determined because of lack of knowledge about particular selective forces and that theories of model reconstruction are not open to contradiction in the (...) sense of Popperian falsification. Although it has been claimed that the method provides the only valid directional argument for morphoclines in cladistic studies, it remains unclear how to proceed when morphoclines show contradictory polarities. Moreover, it is doubtful whether polarities of morphoclines can be determined independently of phylogenetic hypotheses, and also whether the use of multistate morphoclines is methodologically valid. By relying on a particular evolutionary theory, i.e. the neo-Darwinian theory, and consequently assigning natural selection as the major agent of directional progress, the Senckenburg method of phylogenetic reconstruction restricts itself to microevolutionary change and, therefore, cannot be used when other hypotheses on the evolutionary process appear to explain the speciation process more plausibly, i.e. hypotheses on macroevolution. Furthermore, it is an unproved statement that evolution always proceeds according to the principle of economy. (shrink)

I attempt to raise questions regarding elements of systematics—primarily in the realm of phylogenetic reconstruction—in order to provoke discussion on the current state of affairs in this discipline, and also evolutionary biology in general: e.g., conceptions of homology and homoplasy, hypothesis testing, the nature of and objections to Hennigian “phylogenetic systematics”, and the schism between Darwinian descendants of the “modern evolutionary synthesis” and their supposed antagonists, cladists and punctuationalists.

The conditions are outlined under which the body construction of annelids could have been transformed into that of arthropods. As an adaptation to a vagile life and an uptake of food by filtering particles from the sediment, the body was more and more flattened. Thus lateral protrusions, the subsequent pleurotergites, developed, and the parapodia were shifted to a more ventral position and could differentiate into the branched limbs typical for arthropods. This is the condition under which parts of the body (...) wall were kept immobile, so that they could become sclerotized in the form of rigid plates. (shrink)

Reconstructing the Past seeks to clarify and help resolve the vexing methodological issues that arise when biologists try to answer such questions as whether human beings are more closely related to chimps than they are to gorillas. It explores the case for considering the philosophical idea of simplicity/parsimony as a useful principle for evaluating taxonomic theories of evolutionary relationships. For the past two decades, evolutionists have been vigorously debating the appropriate methods that should be used in systematics, the field that (...) aims at reconstructing phylogenetic relationships among species. This debate over phylogenetic inference, Elliott Sober observes, raises broader questions of hypothesis testing and theory evaluation that run head on into long standing issues concerning simplicity/parsimony in the philosophy of science. Sober treats the problem of phylogenetic inference as a detailed case study in which the philosophical idea of simplicity/parsimony can be tested as a principle of theory evaluation. Bringing together philosophy and biology, as well as statistics, Sober builds a general framework for understanding the circumstances in which parsimony makes sense as a tool of phylogenetic inference. Along the way he provides a detailed critique of parsimony in the biological literature, exploring the strengths and limitations of both statistical and nonstatistical cladistic arguments. (shrink)

This chapter contains sections titled: Introduction From Art to Science: An Introduction to Schools of Thought How to Infer Phylogeny, Or, Why Some Cladists Aren't “Cladists” Summary and Synthesis Acknowledgment References.

Cultural phylogenetics has made remarkable progress by relying on methods originally developed in biology. But biological and cultural evolution do not always proceed according to the same principles. So what, if anything, could justify the use of phylogenetic methods to reconstruct the evolutionary history of culture? In this paper, we describe models used to assess the reliability of inference methods and show how these models play an underappreciated role in addressing that question. The notion of reliability is of course (...) central to these models. As we explain, a common way of understanding reliability is in terms of low error rates. A careful look at case studies in cultural phylogenetics suggests that reliability models partly corroborate this understanding of reliability but also raises points of tension. We conclude by hinting at a few ways forward. (shrink)

Phylogenetics is the study and reconstruction of evolutionary history and is filled with numerous foundational issues of interest to philosophers. This paper briefly introduces some central concepts in the field, describes some of the main methods for inferring phylogenies, and provides some arguments for the superiority of model-based methods such as Likelihood and Bayesian methods over nonparametric methods such as parsimony. It also raises some underdeveloped issues in the field of interest to philosophers.

Taking its clues from Popperian philosophy of science, cladistics adopted a number of assumptions of the empiricist tradition. These include the identification of a dichotomy between observation reports and theoretical statements and its subsequent abandonment on the basis of the insight that all observation reports are theory-laden. The neglect of the ‘context of discovery’, which is the step of theory (hypothesis) generation. The emphasis on coherentism in the ‘context of justification’, which is the step of evaluation of the relative merits (...) of alternative theories. The appeal to a total evidence approach in phylogenetic inference. And finally, a silence about causation, which results in an instrumentalist approach to phylogeny reconstruction. This paper explores how these empiricist assumptions are embedded in phylogenetic systematics, and why these assumptions are problematic for cladists (or any taxonomists). (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)

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)

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)

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)

American archaeology has long been focused on reconstructing past cultures through the description and chronological ordering of items found in the archaeological record. This goal was most evident starting in the early 20th century through what became known as culture history, which in retrospect produced results based on common sense and ethnographic analogues rather than on formal theory. By the mid-1930s, some culture historians realized the lack of testability in their conclusions and began exploring Darwinian evolutionary theory as an alternative. (...) However, their efforts were often ignored or ridiculed, and it wasn’t until the early 1980s that evolutionary theory and associated methods began to play significant roles in archaeology. This acceptance grew from the development of a genetics-based theory of cultural transmission and the introduction of phylogenetic methods into anthropology and archaeology. These methods offered the necessary means for distinguishing between simple historical continuity—one thing following another chronologically—and heritable continuity—how one thing is related to another in terms of descent. Two concepts that play key roles in the reconstruction of cultural phylogenies are tradition and lineage, the former representing patterns of phylogenetic relationship and the latter patterns of genealogical descent. (shrink)

Bayesianism and likelihoodism are two of the most important frameworks philosophers of science use to analyse scientific methodology. However, both frameworks face a serious objection: much scientific inquiry takes place in highly idealized frameworks where all the hypotheses are known to be false. Yet, both Bayesianism and likelihoodism seem to be based on the assumption that the goal of scientific inquiry is always truth rather than closeness to the truth. Here, I argue in favour of a verisimilitude framework for inductive (...) inference. In the verisimilitude framework, scientific inquiry is conceived of, in part, as a process where inference methods ought to be calibrated to appropriate measures of closeness to the truth. To illustrate the verisimilitude framework, I offer a reconstruction of parsimony evaluations of scientific theories, and I give a reconstruction and extended analysis of the use of parsimony inference in phylogenetics. By recasting phylogenetic inference in the verisimilitude framework, it becomes possible to both raise and address objections to phylogenetic methods that rely on parsimony. 1Introduction2Problems with the Law of Likelihood3Introducing Verisimilitude-Based Inference4Examples of Verisimilitude-Based Inference Procedures4.1Parsimony inference over theories4.2Parsimony inference in phylogenetics5Conclusion. (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)

Chimpanzees, but very few other animals, figure prominently in attempts to reconstruct the evolution of uniquely human traits. In particular, the chimpanzee is used to identify traits unique to humans, and thus in need of reconstruction; to initialize the reconstruction, by taking its state to reflect the state of the last common ancestor of humans and chimpanzees; as a baseline against which to test evolutionary hypotheses. Here I point out the flaws in this three-step procedure, and show how (...) they can be overcome by taking advantage of much broader phylogenetic comparisons. More specifically, I explain how such comparisons yield more reliable estimations of ancestral states and how they help to resolve problems of underdetermination inherent to chimpocentric accounts. To illustrate my points, I use a recent chimpocentric argument by Kitcher. (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)

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)

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)

A distinction is drawn between property causation and token causation. According to the former, a positive causal factor in a population raises the probability of its effects within "background contexts". The latter, which concerns "actual physical connections" between token events, is not explicated here although its distinctness from the first concept and its importance are discussed. The applicability of both is illustrated by two currently controversial issues in evolutionary theory -- the units of selection controversy and the use of parsimony (...) as an inference rule in phylogenetic reconstruction. (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)

Sexual size dimorphism is generally associated with sexual selection via agonistic male competition in nonhuman primates. These primate models play an important role in understanding the origins and evolution of human behavior. Human size dimorphism is often hypothesized to be associated with high rates of male violence and polygyny. This raises the question of whether human dimorphism and patterns of male violence are inherited from a common ancestor with chimpanzees or are uniquely derived. Here I review patterns of, and causal (...) models for, dimorphism in humans and other primates. While dimorphism in primates is associated with agonistic male mate competition, a variety of factors can affect male and female size, and thereby dimorphism. The causes of human sexual size dimorphism are uncertain, and could involve several non-mutually-exclusive mechanisms, such as mate competition, resource competition, intergroup violence, and female choice. A phylogenetic reconstruction of the evolution of dimorphism, including fossil hominins, indicates that the modern human condition is derived. This suggests that at least some behavioral similarities with Pan associated with dimorphism may have arisen independently, and not directly from a common ancestor. (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)

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)

Biology and the social sciences share an interest in phylogeny. Biologists know that living species are descended from past species, and use the pattern of similarities among living species to reconstruct the history of phylogenetic branching. Social scientists know that the beliefs, values, practices, and artifacts that characterize contemporary societies are descended from past societies, and some social science disciplines, linguistics and cross cultural anthropology for example, have made use of observed similarities to reconstruct cultural histories. Darwin appreciated that (...) his theory of descent with modification had many similarities of pattern and process to the already well developed field of historical linguistics. In many other areas of social science, however, phylogenetic reconstruction has not played a central role. (shrink)

Visual self-recognition is often controversially cited as an indicator of self-awareness and assessed with the mirror-mark test. Great apes and humans, unlike small apes and monkeys, have repeatedly passed mirror tests, suggesting that the underlying brain processes are homologous and evolved 14-18 million years ago. However, neuroscientific, developmental, and clinical dissociations show that the medium used for self-recognition (mirror vs photograph vs video) significantly alters behavioral and brain responses, likely due to perceptual differences among the different media and prior experience. (...) On the basis of this evidence and evolutionary considerations, we argue that the visual self-recognition skills evident in humans and great apes are a byproduct of a general capacity to collate representations, and need not index other aspects of self-awareness. (shrink)

The present work analyzes the controversy within biological systematics regarding the status of cladistics. The use of the parsimony method for phylogenetic reconstruction has been defended by appealing to a methodological principle of simplicity, as well as to empirical principles that external to systematics. I propose new kind of approach, which consists in considering it an empirical theory, thus justifying its application by its empirical success. To defend this point, a formal structuralist reconstruction of cladistics will be (...) provided, which will help clarify what its central empirical statements are. At the same time, I show how these principles have been used to test that theory using experimental phylogenies. (shrink)

The origin and progress of multicellularity, which is one of the crucial steps in the evolution of life, remains unclear and stringent phylogenetic reconstruction of the process is difficult. However, further theoretical considerations of the problem could be useful for the creation of a verifiable hypothesis. Sex as a ubiquitous biological phenomenon is usually considered as something entirely linked with reproduction. This is mostly true for modem multicellular organisms, but at the earliest stage of evolution of eukaryotes it (...) was not so. At that time the sexual process had nothing to do with reproduction, and only later, sex and reproduction merged together.One of the aims of this paper is to consider the sexual process as a likely basis for the establishment of multicellularity and to discuss the early stages of evolution of the multicellularity from this perspective. It is suggested that mitotic reproduction of cells at different stages of the sexual cycle of unicellular ancestors might be the starting points for independent transition to multicellularity in different taxa. Numerous consequences of these transitions, including evolution of bisexuality and development of novel meiotic functions in animals, are discussed. (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)

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)

Significant amounts of wealth have been exchanged as part of marriage settlements throughout history. Although various models have been proposed for interpreting these practices, their development over time has not been investigated systematically. In this paper we use a Bayesian MCMC phylogenetic comparative approach to reconstruct the evolution of two forms of wealth transfers at marriage, dowry and bridewealth, for 51 Indo-European cultural groups. Results indicate that dowry is more likely to have been the ancestral practice, and that a (...) minimum of four changes to bridewealth is necessary to explain the observed distribution of the two states across the cultural groups. (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)

Recent theoretical work has identified a tightly-constrained sense in which genes carry representational content. Representational properties of the genome are founded in the transmission of DNA over phylogenetic time and its role in natural selection. However, genetic representation is not just relevant to questions of selection and evolution. This paper goes beyond existing treatments and argues for the heterodox view that information generated by a process of selection over phylogenetic time can be read in ontogenetic time, in the (...) course of individual development. Recent results in evolutionary biology, drawn both from modelling work, and from experimental and observational data, support a role for genetic representation in explaining individual ontogeny: both genetic representations and environmental information are read by the mechanisms of development, in an individual, so as to lead to adaptive phenotypes. Furthermore, in some cases there appears to have been selection between individuals that rely to different degrees on the two sources of information. Thus, the theory of representation in inheritance systems like the genome is much more than just a coherent reconstruction of information talk in biology. Genetic representation is a property with considerable explanatory utility. (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)

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)

The theory and practice of contemporary comparative biology and phylogeny reconstruction (systematics) emphasizes algorithmic aspects but neglects a concern for the evidence. The character data used in systematics to formulate hypotheses of relationships in many ways constitute a black box, subject to uncritical assessment and social influence. Concerned that such a state of affairs leaves systematics and the phylogenetic theories it generates severely underdetermined, we investigate the nature of the criteria of homology and their application to character conceptualization (...) in the context of transformationist and generative paradigms. Noting the potential for indeterminacy in character conceptualization, we conclude that character congruence (the coherence of character statements) relative to a hierarchy is a necessary, but not a sufficient, condition for phylogeny reconstruction. Specifically, it is insufficient due to the lack of causal grounding of character hypotheses. Conceptualizing characters as homeostatic property cluster natural kinds is in accordance with the empirical practice of systematists. It also accounts for the lack of sharpness in character conceptualization, yet requires character identification and re-identification to be tied to causal processes. (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)

Phylogenies are increasingly being used to investigate human history, diversification and cultural evolution. While using phylogenies in this way is not new, new modes of analysis are being applied to inferring history, reconstructing past states, and examining processes of change. Phylogenies have the advantage of providing a way of creating a continuous history of all current populations, and they make a large number of analyses and hypothesis tests possible even when other forms of historical information are patchy or nonexistent. In (...) common with approaches taken in other historical sciences, phylogenetics is a way of reconstructing past and processes using the traces left in the present day. Trees, based on DNA, language, cultural traits, or other evidence, are now sprouting all over the academic landscape. The increasing use of phylogenetic analysis to understand human cultural evolution has been embraced by some, and scorned by others. The purpose of this article is not to review methods and applications of phylogenetic analyses, nor to consider the growing field of cultural phylogenetics, but, more broadly, to explore how we interpret phylogenies as narratives about human diversification. The first half of the article deals with meaning: phylogenies are often interpreted as histories, but a bifurcating tree is at best an abstract representation of history, and its connections to past events and processes is dependent on the data used, the assumptions made in the analysis, and the degree to which nodes in the tree (where one lineage splits into two) can be connected to change and movement in real populations. The second half of the article explores the purpose of phylogenies: a tree does not have to be a literal history of human lineages in order to be useful for investigating processes of human diversification. Phylogenies should not be read as accurate records of history, but as a way of exploring plausible explanations for current patterns of diversity. Phylogenies provide important information that can be used to test ideas about human diversity, and can help to guard against errors of inference arising from statistical artifacts. (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)

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)

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)

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)

The concept that renders morphology a tool for phylogeny reconstruction is homology. The concept of homology is rooted in pre-evolutionary idealistic morphology. The claim that the goal of idealistic morphology was the seriability of form may sound paradoxical given that this discipline proceeded within a framework of strictly delimited types. But the types only demarcate where seriability starts and where it comes to an end. Carl Gegenbaur’s was recognized as a milestone in idealistic morphology. A comparison with the second (...) edition of 1870 illustrates Gegenbaur’s turn to evolutionary morphology. The methodology remained the same–seriability of form–but the series was no longer merely descriptive or conceptual but now a historical, evolutionary one. Gegenbaur emphasized that seriability of form was possible not only between species of the same type, but also between parts of organisms of the same type. Pursuing this project, he found that different parts of organisms evolve at different rates, resulting in an incongruence between the series of parts relative to the series of species under comparison. This incongrence was called chevauchement des spécialisations by Louis Dollo, Spezialisationskreuzungen by Othenio Abel, and heterobathmy of characters by Armen Takhtajan. Willi Hennig, the founder of modern methods in phylogenetic systematics, discovered that the heterobathmy of characters was a precondition for the establishment of the phylogenetic relationships based on shared derived characters. The result was a replacement of the search for ancestors by a search for relative degrees of phylogenetic relationships. (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)

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)

Exceptionally preserved fossils are the product of complex interplays of biological and geological processes including burial, autolysis and microbial decay, authigenic mineralization, diagenesis, metamorphism, and finally weathering and exhumation. Determining which tissues are preserved and how biases affect their preservation pathways is important for interpreting fossils in phylogenetic, ecological, and evolutionary frameworks. Although laboratory decay experiments reveal important aspects of fossilization, applying the results directly to the interpretation of exceptionally preserved fossils may overlook the impact of other key processes (...) that remove or preserve morphological information. Investigations of fossils preserving non-biomineralized tissues suggest that certain structures that are decay resistant are rarely preserved, and decay-prone structures can fossilize, albeit rarely. As we review here, decay resistance is an imperfect indicator of fossilization potential, and a suite of biological and geological processes account for the features preserved in exceptional fossils. Organisms decayed experimentally in seawater have been used as direct analogs for soft-bodied fossil taxa, with fossils representing a snapshot of a particular stage of decay. We argue that numerous geological and biological processes account for fossilization and that all of these should be considered when reconstructing extinct organisms. (shrink)

Fossil organisms offer our only direct insight into how the distinctive body plans of extant organisms were assembled. However, realizing the potential evolutionary significance of fossils can be hampered by controversy over their interpretation. Here, as a guide to evaluating palaeontological debates, we outline the process and pitfalls of fossil interpretation. The physical remains of controversial fossils should be reconstructed before interpreting homologies, and choice of interpretative model should be explicit and justified. Extinct taxa lack characters diagnostic of extant clades (...) because the characters had not yet evolved, because of secondary loss, or because they have rotted away. The latter, if not taken into account, will lead to the spurious assignment of fossils to basally branching clades. Conflicting interpretations of fossils can often be resolved by considering all the steps in the process of anatomical analysis and phylogenetic placement, although we must accept that some fossil organisms are simply too incompletely preserved for their evolutionary significance to be realized. (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)

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)

Evidence of cultural influences on cognition is accumulating, but untangling these cultural influences from one another or from non-cultural influences has remained a challenging task. As between-group differences are neither a sufficient nor a necessary indicator of cultural impact, cross-cultural comparisons in isolation are unable to furnish any cogent conclusions. This shortfall can be compensated by taking a diachronic perspective that focuses on the role of culture for the emergence and evolution of our cognitive abilities. Three strategies for reconstructing early (...) human cognition are presented: the chaîne opératoire approach and its extension to brain-imaging studies, large-scale extrapolations, and phylogenetic comparative methods. While these strategies are reliant on our understanding of present-day cognition, they conversely also have the potential to advance this understanding in fundamental ways. (shrink)