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

This paper describes a pattern of explanation prevalent in the biological sciences that I call a ‘lineage explanation’. The aim of these explanations is to make plausible certain trajectories of change through phenotypic space. They do this by laying out a series of stages, where each stage shows how some mechanism worked, and the differences between each adjacent stage demonstrates how one mechanism, through minor modifications, could be changed into another. These explanations are important, for though it is widely (...) accepted that there is an ‘incremental constraint’ on evolutionary change, in an important class of cases it is difficult to see how to satisfy this constraint. I show that lineage explanations answer important questions about evolutionary change, but do so by demonstrating differences between individuals rather than invoking population processes, such as natural selection.1. Introduction2. Turning a ‘Scale’ into a ‘Plume’3. Lineage Explanations in Biology3.1. The evolution of eyes3.2. The evolution of feathers4. The Two Dimensions of a Lineage Explanation4.1. The production dimension4.2. The continuity dimension4.3. The dual role of the parts5. Constraining the Explanations6. Operational and Generative Lineages7. Explaining Change Without Populations8. Conclusion. (shrink)

Frequent evolutionary birth and death events have created a large quantity of biologically important, lineage‐specific DNA within mammalian genomes. The birth and death of DNA sequences is so frequent that the total number of these insertions and deletions in the human population remains unknown, although there are differences between these groups, e.g. transposable elements contribute predominantly to sequence insertion. Functional turnover – where the activity of a locus is specific to one lineage, but the underlying DNA remains (...) conserved – can also drive birth and death. However, this does not appear to be a major driver of divergent transcriptional regulation. Both sequence and functional turnover have contributed to the birth and death of thousands of functional promoters in the human and mouse genomes. These findings reveal the pervasive nature of evolutionary birth and death and suggest that lineage‐specific regions may play an important but previously underappreciated role in human biology and disease. (shrink)

Mapping the paths that stem and progenitor cells take en route to differentiate and elucidating the underlying molecular controls are key goals in developmental and stem cell biology. However, with population level analyses it is difficult − if not impossible − to define the transition states and lineage trajectory branch points within complex developmental lineages. Single‐cell RNA‐sequencing analysis can discriminate heterogeneity in a population of cells and even identify rare or transient intermediates. In this review, we propose (...) that using these data, one can infer the lineage trajectories of individual stem cells and identify putative branch points. Clonal lineage tracing of stem cells allows one to define the outcome of differentiation. Integrating these single cell‐based approaches provides a robust strategy for establishing and testing models of how an individual stem cell changes through time to differentiate and self‐renew. (shrink)

This paper proposes a new and testable view about the nature of species and other evolving lineages, according to which they are feedback systems. On this view, it is a mistake to think gene flow, niche sharing, and trait frequency similarities between populations are among variables that interact to cause some further downstream variable that distinguishes evolving lineages from each other, some sort of “species cohesion” for example. Instead, gene flow, niche sharing, similarities between populations, and other causal variables feed (...) into each other—instances of these at earlier times help cause instances of these same variables at later times. And any lineage-identifying cohesion just is the recurrence or cycling of these feedback relations within metapopulations over generations. Such cohesion can then be represented as variable M within multi-dimensional variable spaces, where values of M vary dynamically with the frequency and magnitude of feedback relations. Related conditions for being a species or other evolving lineage are then clarified. To argue for the development and testing of this view, the paper shows how it improves upon others. (shrink)

Two or more independent species lineages can fuse through an evolutionary transition to form a single lineage, such as in the case of eukaryotic cells, lichens, and coral. The fusion of two or more independent lineages requires intermediary steps of increasing selective interdependence between these lineages. We argue a precursory selective regime of such a transition can be Multilevel Selection 1 (MLS1). We propose that intraspecies MLS1 can be extended to ecological multispecies arrangements. We develop a trait group selection (...) (MLS1) model applicable to multispecies mutualistic interactions. We then explore conditions under which such a model could apply to mutualistic relationships between pollinators and plants. We propose that MLS1 could drive transitions towards higher interdependency between mutualists and stabilise obligate mutualisms in the face of invasion by cheater variants. This represents a radical extension of multilevel selection theory, applying it to the evolution of multispecies populations, and indicating new avenues for researching ecological community evolution. (shrink)

For a population to undergo evolution by natural selection, it is assumed that the constituents of the population form parent-offspring lineages, that is, that they must reproduce. I challenge this assumption by dividing the notion of reproduction into two subprocesses, that is, multiplication and inheritance, that produce parent-offspring lineages between the parts of a population, and I show that their population-level roles, generation and memory, respectively, can be effected by processes that do not rely on such (...) local-level lineages. I further argue that these two population-level processes, not local parent-offspring lineages, are necessary conditions for a population to undergo Darwinian evolution. (shrink)

The project of this paper is to understand what a phylogenetic tree represents and to discuss some of the implications that this has for the practice of systematics. At least the first part of this task, if not both parts, might appear trivial—or perhaps better suited for a single page in a textbook rather than a scholarly research paper. But this would be a mistake. While the task of interpreting phylogenetic trees is often treated in a trivial way, their interpretation (...) is tied to foundational conceptual questions at the heart of systematics—questions whose answers are hotly disputed. I have previously argued that widely shared ideas about the meaning and interpretation of phylogenetic trees are inconsistent with species concepts other than some genealogical version of a phylogenetic species concept (Velasco 2008). Here I rely on a similar approach and concentrate on the implications of the necessary conditions underlying the inferences that we make using phylogenetic trees. I argue that common practices for the interpretation and use of trees are in conflict and that unacceptable principles about species as units of phylogeny must be given up. According to the view that I will develop, all phylogenetic trees depict the history of populations. The branches on trees represent collections of population lineages through time and the splits represent population lineage splits. This is true regardless of whether the tips of the trees are themselves populations, or are species or higher taxa. Although this conclusion might be paired naturally with a view that species must be monophyletic groups, this population-centric view of trees is independent of that view of species. If we still want to have species that are paraphyletic groups of populations, this is permissible as long as we also do not treat species as the units of phylogeny. This population-centric view opposes a species-centric view of phylogeny and might be called a “rank-free” approach since it entails that we do not need to determine which groups are species (which is partly a ranking question) in order to build a tree. This conclusion and the argument for it are meant to be consistent with, but not require, acceptance of the conclusions of Velasco (2008) regarding species. (shrink)

Biologists and philosophers have offered differing concepts of biological race. That is, they have offered different candidates for what a biological correlate of race might be; for example, races might be subspecies, clades, lineages, ecotypes, or genetic clusters. One thing that is striking about each of these proposals is that they all depend on a concept of population. Indeed, some authors have explicitly characterized races in terms of populations. However, including the concept of population into concepts of race (...) raises three puzzles, all having to do with time. In this paper, I extend the causal interactionist population concept (CIPC) by introducing some simple assumptions about how to understand populations through time. These assumptions help to shed light on the three puzzles, and in the process show that if we want to understand races in terms of populations, we will need to revise our concept(s) of race. (shrink)

Sex determination in mammals is mediated via the supporting cell lineage in the fetal gonad. In the very early stages of gonadal development, the fate of the supporting cell population is critically dependent on the expression of the male‐determining gene on the Y chromosome. If this gene is absent or fails to be expressed, or is expressed too late or in too small a number of supporting cells, all supporting cells (XX or XY) differentiate as pre‐follicle cells and (...) development proceeds along the female pathway. Supporting cells in which the male‐determining gene is expressed in a timely manner differentiate as pre‐Sertoli cells; given sufficient such cells, testis cords form and development proceeds in a male direction. If XX supporting cells are also present, a few may be recruited into the pre‐Sertoli population and participate in testis cord formation. The subsequent fate of pre‐follicle cells depends critically on interaction with the germ cell population in the developing gonad: absence of germ cells may lead to partial masculinization of the gonad, and/or to disappearance of the supporting cell component. (shrink)

Evolutionary conceptions of species place special weight on each species having dynamic independence as a unit of evolution. However, the idea that species have their own historical fates, tendencies, or roles has resisted systematic analysis. Growing evidence from population genomics shows that many paradigm species regularly engage in hybridization. How can species be defined in terms of independent evolutionary identities if their genomes are dynamically coupled through lateral exchange? I introduce the concept of a “composite lineage” to distinguish (...) species and subspecies on the basis of the proportion of a group’s heritable traits that are uncoupled from reproductive exchange. (shrink)

As part of a survey of the biological history of Alpine populations, the lineages of all the families of the Vallouise valley (a French of the Hautes Alpes) have been reconstructed over several centuries. The genealogies have been included in a computerized population record, known as 20th centuries)Canadian programme Analypop. Most of the professions of the family heads were included in the files. In this study, various profession groups were identified and their descents determined over successive generations. In this (...) mountain area, where over 92% of marriages took place among relatives during the 19th century, the profession groups modulated their descents according to chosen strategies, sometimes with considerable differences among groups but with a remarkable consistency of behaviour. Moreover, there was weak interpenetration in the descents of each profession at both the 2nd and 3rd generations. (shrink)

No later than ~500kya the population of Homo sapiens split into three lin¬eages of independently evolving human populations: Sapiens, Neanderthals and Den¬isovans. After several hundred thousands years, they met several times and interbred with low frequency. Evidence of coupling between them is found in fossil records of Neanderthal – Sapiens offspring and Neanderthal – Denisovans offspring. Moreover, the analysis of ancient and present-day population DNA shows that there were several significant gene flows between populations. Many introgressed sequences from (...) Denisovans and Neanderthals were identified in genomes of currently living populations. All these data, according to biological species definition, may in¬dicate that populations of H. sapiens sapiens and two extinct populations H. sapiens neanderthalensis and H. sapiens denisovensis are one species. Ontological transitions from pre-human beings to humans might have happened before the initial splitting of the Homo sapiens population or after the splitting during evolution of H. sapiens sapiens lineage in Africa. If the ensoulment of the first homo occurred in the evolving populations of H. sapiens sapiens, then occasionally mixed couples created relations that functioned as a family, in which children could have matured. (shrink)

What are species? One popular answer is that species are individuals. Here I develop another approach to thinking about species, an approach based on the notion of a lineage. A lineage is a sequence of reproducing entities, individuated in terms of its components. I argue that one can conceive of species as groups of lineages, either organism lineages or population lineages. Conceiving of species as groups of lineages resolves the problems that the individual conception of species is (...) supposed to resolve. It has added the virtue of focusing attention on the characteristic of species that is most relevant to understanding their role in evolutionary processes, namely, the lineage structure of species. (shrink)

This book is a comprehensive and unique text and reference in medical ethics. By far the most inclusive set of primary documents and articles in the field ever published, it contains over 100 selections. Virtually all pieces appear in their entirety, and a significant number would be difficult to obtain elsewhere. The volume draws upon the literature of history, medicine, philosophical and religious ethics, economics, and sociology. A wide range of topics and issues are covered, such as law and medicine, (...) truth-telling by the physician, research, population policy, genetics, abortion, dying, and individual rights in medical care. The selections span the centuries, beginning with material from the works of Hippocrates, continuing through Thomas Percival, John Stuart Mill, and Claude Bernard, down to modern commentators like Henry K. Beecher, Walsh McDermott, David L. Bazelon, Paul Freund, H. L. A. Hart, John Rawls, Paul Ramsey, Richard McCormick, Rashi Fein, and Bernard Barber. The text has eight major divisions, beginning with sections on the ethical dimensions of the physician-patient relationship in history; the moral bases of medical ethics; and regulation, compulsion, and protection of the consumer in clinical medicine and public health. Each of these sections includes key essays that appear for the first time. All of the book's major divisions contain primary documents: codes such as the Hippocratic Oath, Medieval Law for the Regulation of Medicine, and the first as well as the most recent code of the American Medical Association; court decisions, including those on Karen Quinlan and on abortion in the United States and West Germany; government documents such as the statement of the National Commission on the Protection of Human Subjects, the Tuskegee Syphilis Report, the British Parliamentary debate on euthanasia, and the Council of Europe on rights of the sick and dying; and various published guidelines such as the Harvard Medical School brain death criteria, the American Hospital Association on patient's rights, and Pope Pius XII on the prolongation of life. Cases that illustrate moral dilemmas are provided for discussion purposes. Each section is preceded by a succinct editor's introduction. The documents and essays are of practical value for practitioners and students in medicine, law, ethics, and counselling, and for individual patients and groups concerned with medical care. Through encompassing divergent viewpoints, the essays and primary documents were selected to encourage humane practices and deepen understanding of the multiple traditions that shaped and do shape the development of medicine. (shrink)

In this paper, we redefine the target of evolutionary explanations by proposing the “evosystem” as an alternative to populations, lineages and species. Evosystems account for changes in the distribution of heritable variation within individual Darwinian populations (evolution by natural selection, drift, or constructive neutral evolution), but also for changes in the networks of interactions within or between Darwinian populations and changes in the abiotic environment (whether these changes are caused by the organic entities or not). The evosystem can thereby become (...) a centerpiece for a redefined evolutionary science, that is, evolutionary studies, that apprehends through a single framework the variety of evolutionary processes that lie at various scales. To illustrate the importance of this broadened perspective on evolution, we use a case of antimicrobial resistance evolution: the spread of the blaNDM gene family and the related resistance to carbapenem antibiotics observed globally, and show how evolutionary studies can contribute to answering contemporary socially relevant challenges. (shrink)

Philosophers are approaching a consensus that biological individuality, including evolutionary individuality, comes in degrees. Graded evolutionary individuality presents a puzzle when juxtaposed with another widely embraced view: that evolutionary individuality follows from being a selectable member of a Darwinian population. Population membership is, on the orthodox view, a bivalent condition, so how can members of Darwinian populations vary in their degree of individuality? This article offers a solution to the puzzle, by locating difference in degree of evolutionary individuality (...) at the level of population lineages, some of which are more Darwinian than others. In doing so, it sheds light on graded individuality in overlapping and nested population lineages, such as those that arise in multilevel selection and symbiotic collectives. (shrink)

Philosophers are approaching a consensus that biological individuality, including evolutionary individuality, comes in degrees. Graded evolutionary individuality presents a puzzle when juxtaposed with another widely embraced view: that evolutionary individuality follows from being a selectable member of a Darwinian population. Population membership is, on the orthodox view, a bivalent condition, so how can members of Darwinian populations vary in their degree of individuality? This article offers a solution to the puzzle, by locating difference in degree of evolutionary individuality (...) at the level of population lineages, some of which are more Darwinian than others. In doing so, it sheds light on graded individuality in overlapping and nested population lineages, such as those that arise in multilevel selection and symbiotic collectives. (shrink)

In biological systematics, as well as in the philosophy of biology, species and higher taxa are individuated through their unique evolutionary origin. This is taken by some authors to mean that monophyly is a (relational) property not only of higher taxa, but also of species. A species is said to originate through speciation, and to go extinct when it splits into two daughter species (or through terminal extinction). Its unique evolutionary origin is said to bestow identity on a species through (...) time and change, and to render species names rigid designators. Species names are thus believed to function just like names of supraspecific taxa. However, large parts of the Web of Life are composed of species that do not have a unique evolutionary origin from a single population, lineage or stem-species. Further, monophyly is an ambiguous concept if it is defined simply in terms of ‘unique evolutionary origin’. Disambiguating the concept by defining a monophyletic taxon as ‘a taxon that includes the ancestor and all, and only, its descendant’ renders monophyly inapplicable to species. At the heart of the problem lies a fundamental distinction between species and monophyletic taxa, where species form mutually exclusive reticulated systems, while higher taxa form inclusive hierarchical systems. Examples are given both at the species level and below to illustrate the problems that result from the application of the monophyly criterion to species. The conclusion is that the concepts of exclusivity and monophyly should be treated as non-overlapping: exclusivity marks out a species synchronistically, i.e. in the present time. Monophyly marks out clades (groups of species) diachronistically, i.e. within an historical dimension. (shrink)

Biological lineages move through time, space, and each other. As they do, they diversify, diverge, and grade away from and into one another. One result of this is genealogical discordance; i.e., the lineages of a biological entity may have different histories. We see this on numerous levels, from microbial networks, to holobionts, to population-level lineages. This paper considers how genealogical discordance impacts our study of species. More specifically, I consider this in the context of three framing questions: (1) How, (...) if at all, does genealogical discordance challenge, modify, or revise how we conceive of species? (2) How has growing appreciation of genealogical discordance impacted scientific practice? Of systematics in particular? (3) How do lineages at different levels diverge and diversify? All told, genealogical discordance enriches and complicates our taxonomic ontology, as well as the practice of reconstructing phylogenies. This presents both challenges and opportunities for the study of divergence and diversification. (shrink)

One of the major developments in cancer research in recent years has been the construction of models that treat cancer as a cellular population subject to natural selection. We expand on this idea, drawing upon multilevel selection theory. Cancer is best understood in our view from a multilevel perspective, as both a by-product of selection at other levels of organization, and as subject to selection at several levels of organization. Cancer is a by-product in two senses. First, cancer cells (...) co-opt signaling pathways that are otherwise adaptive at the organismic level. Second, cancer is also a by-product of features distinctive to the metazoan lineage: cellular plasticity and modularity. Applying the multilevel perspective in this way permits one to explain transitions in complexity and individuality in cancer progression. Our argument is a reply to Germain’s scepticism towards the explanatory relevance of natural selection for cancer. The extent to which cancer fulfills the conditions for being a paradigmatic Darwinian population depends on the scale of analysis, and the details of the purported selective scenario. Taking a multilevel perspective clarifies some of the complexities surrounding how to best understand the relevance of evolutionary thinking in cancer progression. (shrink)

Transposable elements (TEs) are powerful facilitators of genome evolution, and hence of phenotypic diversity as they can cause genetic changes of great magnitude and variety. TEs are ubiquitous and extremely ancient, and although harmful to some individuals, they can be very beneficial to lineages. TEs can build, sculpt, and reformat genomes by both active and passive means. Lineages with active TEs or with abundant homogeneous inactive populations of TEs that can act passively by causing ectopic recombination are potentially fecund, adaptable, (...) and taxonate readily. Conversely, taxa deficient in TEs or possessing heterogeneous populations of inactive TEs may be well adapted in their niche, but tend to prolonged stasis and may risk extinction by lacking the capacity to adapt to change, or diversify. Because of recurring intermittent waves of TE infestation, available data indicate a compatibility with punctuated equilibrium, in keeping with widely accepted interpretations of evidence from the fossil record. We propose a general and holistic synthesis on how the presence of TEs within genomes makes them flexible and dynamic, so that genomes themselves are powerful facilitators of their own evolution. (shrink)

Cancer stem cells (CSC) represent malignant cell subsets in hierarchically organized tumors, which are selectively capable of tumor initiation and self‐renewal and give rise to bulk populations of non‐tumorigenic cancer cell progeny through differentiation. Robust evidence for the existence of prospectively identifiable CSC among cancer bulk populations has been generated using marker‐specific genetic lineage tracking of molecularly defined cancer subpopulations in competitive tumor development models. Moreover, novel mechanisms and relationships have been discovered that link CSC to cancer therapeutic resistance (...) and clinical tumor progression. Importantly, proof‐of‐principle for the potential therapeutic utility of the CSC concept has recently been provided by demonstrating that selective killing of CSC through a prospective molecular marker can inhibit tumor growth. Herein, we review these novel and translationally relevant research developments and discuss potential strategies for CSC‐targeted therapy in the context of resistance mechanisms and molecular pathways preferentially operative in CSC. (shrink)

Turkey, in direct lineage of the Ottoman Empire, experimented a particularly violent nation-building out of the imperial ashes. Non-Muslims corresponding to one fifth of its population have been annihilated for the creation of a homogeneous nation State. These crimes have never been accounted for, giving way to a culture of impunity, self-righteousness, contempt for the rule of law and justice which, over years, pushed the polity towards an illiberal if not totalitarian essence and praxis, domestically against its own (...) constituency and externally against neighbours through an extensive neo-imperial drive. Paradoxically, such an outcome seems to constitute a belated retribution for the unaccounted crimes. (shrink)

We hypothesize that as one of the most consequential events in evolution, primary endosymbiosis accelerates lineage divergence, a process we refer to as the endosymbiotic ratchet. Our proposal is supported by recent work on the photosynthetic amoeba, Paulinella, that underwent primary plastid endosymbiosis about 124 Mya. This amoeba model allows us to explore the early impacts of photosynthetic organelle (plastid) origin on the host lineage. The current data point to a central role for effective population size (Ne) (...) in accelerating divergence post‐endosymbiosis due to limits to dispersal and reproductive isolation that reduce Ne, leading to local adaptation. We posit that isolated populations exploit different strategies and behaviors and assort themselves in non‐overlapping niches to minimize competition during the early, rapid evolutionary phase of organelle integration. The endosymbiotic ratchet provides a general framework for interpreting post‐endosymbiosis lineage evolution that is driven by disruptive selection and demographic and population shifts. Also see the video abstract here: https://youtu.be/gYXrFM6Zz6Q. (shrink)

Here, we propose that the heterogeneity of mutational types in populations underpins alternative pathways of evolutionary adaptation. Point mutations, deletions, insertions, transpositions and duplications cause different biological effects and provide distinct adaptive possibilities. Experimental evidence for this notion comes from the mutational origins of adaptive radiations in large, clonal bacterial populations. Independent sympatric lineages with different phenotypes arise from distinct genetic events including gene duplication, different insertion sequence movements and several independent point mutations. The breadth of the mutational spectrum in (...) the ancestral population should be viewed as a form of bet‐hedging, reducing the risk of evolutionary dead ends and complementing the phenotypic and epigenetic heterogeneities that improve the survival capabilities of a population. Different mutational events arise from distinct cellular processes and are subject to separate environmental impacts, so the availability of any particular type of mutation may constrain or promote adaptive pathways in populations. (shrink)

Integrative mobile genetic elements (MGEs), such as transposons and insertion sequences, propagate within bacterial genomes, but persistence times in individual lineages are short. For long‐term survival, MGEs must continuously invade new hosts by horizontal transfer. Theoretically, MGEs that persist for millions of years in single lineages, and are thus subject to vertical inheritance, should not exist. Here we draw attention to an exception – a class of MGE termed REPIN. REPINs are non‐autonomous MGEs whose duplication depends on non‐jumping RAYT transposases. (...) Comparisons of REPINs and typical MGEs show that replication rates of REPINs are orders of magnitude lower, REPIN population size fluctuations correlate with changes in available genome space, REPIN conservation depends on RAYT function, and REPIN diversity accumulates within host lineages. These data lead to the hypothesis that REPINs form enduring, beneficial associations with eubacterial chromosomes. Given replicative nesting, our hypothesis predicts conflicts arising from the diverging effects of selection acting simultaneously on REPINs and host genomes. Evidence in support comes from patterns of REPIN abundance and diversity in two distantly related bacterial species. Together this bolsters the conclusion that REPINs are the genetic counterpart of mutualistic endosymbiotic bacteria. (shrink)

Different cell lineages growing in microgravity undergo a spontaneous transition leading to the emergence of two distinct phenotypes. By returning these populations in a normal gravitational field, the two phenotypes collapse, recovering their original configuration. In this review, we hypothesize that, once the gravitational constraint is removed, the system freely explores its phenotypic space, while, when in a gravitational field, cells are “constrained” to adopt only one favored configuration. We suggest that the genome allows for a wide range of “possibilities” (...) but it is unable per se to choose among them: the emergence of a specific phenotype is enabled by physical constraints that drive the system toward a preferred solution. These findings may help in understanding how cells and tissues behave in both development and cancer. In microgravity, cells undergo spontaneous and reversible transitions between different phenotypes. In the absence of physical constraints, living systems could yield bi-stable decisions. On the contrary, physical ‘boundaries’ constrain cells to acquire only a specific configuration by selecting and shaping different gene expression patterns provided by the intrinsic genetic stochasticity. (shrink)

Few issues cause academics to disagree more than gender and race, especially when topics are addressed in terms of biological differences. To conduct research in these areas or comment favorably on research can subject one to scorn. When these topics are addressed, they generally take the form of philosophical debates. Anthony Walsh focuses upon such debates and supporting research. He divides parties into biologists and social constructionists, arguing that biologists remain focused on laboratory work, while constructionists are acutely aware of (...) the impact of biologists in contested territories. "Science Wars" introduces the ideas motivating the parties and examines social constructionism and its issues with science. He explores arguments over conceptual tools scientists love and constructionists abhor, and he provides a solid discussion of the co-evolution of genes and culture. Walsh then focuses his attention on gender, how constructionists view it, and the neuroscience explanation of gender differences. Moving to race, Walsh looks at how some have tried to bury the concept of race, while others emphasize it. He considers definitions of race--essentialist, taxonomic, population, and lineage--as they have evolved from the time of the Enlightenment to the present. And finally, he attempts to bring the opposing sides together by pointing out what each can bring to a meaningful discussion. (shrink)

I argue that population-level selection does not necessarily have to be invoked to explain the polymorphism at the MHC locus. I argue that the authors' attempt to model operant conditioning in Darwinian terms faces a serious problem. Depending on how many operant responses we take to comprise a sequence, different conclusions about whether or not evolution is occurring in an operant lineage will be reached.

In recent years, the concept of evolvability has been gaining in prominence both within evolutionary developmental biology (evo-devo) and the broader field of evolutionary biology. Despite this, there remains considerable disagreement about what evolvability is. This article offers a solution to this problem. I argue that, in focusing too closely on the role played by evolvability as an explanandum in evo-devo, existing philosophical attempts to clarify the evolvability concept have been overly narrow. Within evolutionary biology more broadly, evolvability offers a (...) robust explanation for the evolutionary trajectories of populations. Evolvability is an abstract, robust, dispositional property of populations, which captures the joint causal influence of their internal features on the outcomes of evolution (as opposed to the causal influence of selection, which is often characterized as external). When considering the nature of the physical basis of this disposition, it becomes clear that the many existing definitions of evolvability at play within evo-devo should be understood as capturing only aspects of a much broader phenomenon. 1 Introduction2 The Problem of Evolvability3 The Theoretical Role of Evolvability in Evolutionary Biology3.1 The explanatory targets of evolutionary biology3.2 Selection-based explanations3.3 Lineage explanations3.4 Evolvability-based explanations3.5 What properties must evolvability have?4 What Evolvability Really Is4.1 Making sense of ft4.2 Making sense of x and b5 What of the Limbs? The Power of E6 Conclusion. (shrink)

The use of socially learned information (culture) is central to human adaptations. We investigate the hypothesis that the process of cultural evolution has played an active, leading role in the evolution of genes. Culture normally evolves more rapidly than genes, creating novel environments that expose genes to new selective pressures. Many human genes that have been shown to be under recent or current selection are changing as a result of new environments created by cultural innovations. Some changed in response to (...) the development of agricultural subsistence systems in the Early and Middle Holocene. Alleles coding for adaptations to diets rich in plant starch (e.g., amylase copy number) and to epidemic diseases evolved as human populations expanded (e.g., sickle cell and G6PD defi- ciency alleles that provide protection against malaria). Large-scale scans using patterns of linkage disequilibrium to detect recent selection suggest that many more genes evolved in response to agriculture. Genetic change in response to the novel social environment of contemporary modern societies is also likely to be occurring. The functional effects of most of the alleles under selection during the last 10,000 years are currently unknown. Also unknown is the role of paleoenvironmental change in regulating the tempo of hominin evolution. Although the full extent of culture-driven gene-culture coevolution is thus far unknown for the deeper history of the human lineage, theory and some evidence suggest that such effects were profound. Genomic methods promise to have a major impact on our understanding of gene-culture coevolution over the span of hominin evolutionary history. (shrink)

We address the controversy in the literature concerning the definition of holobionts and the apparent constraints on their evolution using concepts from community population genetics. The genetics of holobionts, consisting of a host and diverse microbial symbionts, has been neglected in many discussions of the topic, and, where it has been discussed, a gene-centric, species-centric view, based in genomic conflict, has been predominant. Because coevolution takes place between traits or genes in two or more species and not, strictly speaking, (...) between species, it may affect some traits but not others in either host or symbiont. Moreover, when interacting species pairs are embedded in a larger community, indirect ecological effects can alter the expected pairwise dynamics. Mode of symbiont transmission and the degree of host inbreeding both affect the extent of microbial mixing across host lineages and thereby the degree to which selection on one trait of either partner affects other aspects of a holobiont phenotype. We discuss several potential defining criteria for holobionts using community genetics and population genetics models, suggesting their application and limitations. Using community genetics models, we show how conflict between genomes can be self-limiting, while cooperation and mutualism tend to be self-accelerating. It is likely that this bias in the evolutionary dynamics of interaction between hosts and symbionts is an important feature of holobionts. This bias in the evolutionary dynamic could contribute to explaining the absence of cheaters from natural mutualisms, although cheaters are predicted by gene-centered conflict theory to cause the evolutionary instability of mutualisms. Additionally, it may help explain the more frequent origin of mutualisms from parasitic than from free-living systems, an evolutionary trajectory opposite to that predicted by genome conflict theory. (shrink)

This article challenges the orthodox view that there is and can be no scientifically valid concept of race applicable to human beings by presenting a candidate scientific concept of biological race. The populationist concept of race specifies that a “race” is a subdivision of Homo sapiens—a group of populations that exhibits a distinctive pattern of genetically transmitted phenotypic characters and that belongs to an endogamous biological lineage initiated by a geographically separated and reproductively isolated founding population. The viability (...) of the PRC is shown by demonstrating its capacity to withstand a wide range of objections. A common theme is that the objections turn on misconceptions of the idea of a scientific concept of race. The final section argues that the PRC will not foster racism. (shrink)

In recent years, the concept of evolvability has been gaining in prominence both within evolutionary developmental biology (evo-devo) and the broader field of evolutionary biology. Despite this, there remains considerable disagreement about what evolvability is. This article offers a solution to this problem. I argue that, in focusing too closely on the role played by evolvability as an explanandum in evo-devo, existing philosophical attempts to clarify the evolvability concept have been overly narrow. Within evolutionary biology more broadly, evolvability offers a (...) robust explanation for the evolutionary trajectories of populations. Evolvability is an abstract, robust, dispositional property of populations, which captures the joint causal influence of their internal features on the outcomes of evolution (as opposed to the causal influence of selection, which is often characterized as external). When considering the nature of the physical basis of this disposition, it becomes clear that the many existing definitions of evolvability at play within evo-devo should be understood as capturing only aspects of a much broader phenomenon. 1 Introduction2 The Problem of Evolvability3 The Theoretical Role of Evolvability in Evolutionary Biology 3.1 The explanatory targets of evolutionary biology 3.2 Selection-based explanations 3.3 Lineage explanations 3.4 Evolvability-based explanations 3.5 What properties must evolvability have?4 What Evolvability Really Is 4.1 Making sense of ft 4.2 Making sense of x and b5 What of the Limbs? The Power of E6 Conclusion. (shrink)

This paper reviews the debate about behavioral modernity in our species, listing counterexamples to the thesis that there was a dramatic change to the minds of Cro-Magnon sapiens in Europe in the Upper Paleolithic. It is argued that we were probably behaviorally modern from about 150,000 years ago, and that aspects of this mentality were apparent in developments in tool technologies and hunting practices across the prior Homo lineage. Key behaviors expressive of behavioral modernity include practical reasoning about the (...) past and future and role-differentiated rights-based cooperation, which are more obvious in their effects than is the vague but much-used notion of symbolic thinking. Behavioral modernity leads to technological innovation but is not sufficient to maintain such innovations in face of population loss and environmental instability, which along with the vagaries of preservation explains why the archaeological record of behavioral modernity in our species is patchy until the Upper Paleolithic. (shrink)

This paper analyzes recent attempts to reject reproduction with lineage formation as a necessary condition for evolution by means of natural selection :560–570, 2008; Stud Hist Philos Sci Part C Stud Hist Philos Biol Biomed Sci 42:106–114, 2011; Bourrat in Biol Philos 29:517–538, 2014; Br J Philos Sci 66:883–903, 2015; Charbonneau in Philos Sci 81:727–740, 2014; Doolittle and Inkpen in Proc Natl Acad Sci 115:4006–4014, 2018). Building on the strengths of these attempts and avoiding their pitfalls, it is argued (...) that a robust formulation of evolution by natural selection without reproduction can be established. The main contribution of this paper is a reformulation of Lewontin’s three principles stating that minimal evolution by natural selection occurs when two conditions are met in a population: fitness-related variation and memory. Paradigmatic evolution by natural selection, which can generate adaptations, takes place when an additional condition is present, namely regeneration. (shrink)

Evolution and life phenomena can be understood as results of history, i.e., as outcomes of cohabitation and collective memory of populations of autonomous entities across many generations and vast extent of time. Hence, evolution of distinct lineages of life can be considered as isomorphic with that of cultures. I argue here that cultures and culture-like systems – human culture, natural languages, and life forms – always draw from history, memory, experience, internal dynamics, etc., transforming themselves creatively into new patterns, never (...) foreseen before. This is possible thanks to the fact that all forms of life are descendants of life. Ontogeny and speciation in various lineages draw from continuous re-interpretation of conservative genetic/generic “texts”, as well as from changes of the interpretative process itself. The result is continuous appearances of new lineages-cultures and/or communities-cultures, in a semiotic process of re-interpretation and inventing new ways of living. The topic is developed here on the backgrounds of ideas presented by R. A. Rappaport in “Ritual and religion in the making of humanity” and J. Flegr in “Frozen evolution”. (shrink)

The foundations of systematics lie in ontology, not in subjective epistemology. Systems and their elements should be distinguished from classes; only the latter are constructed from similarities. The term classification should be restricted to ordering into classes; ordering according to systematic relations may be called systematization.The theory of organization levels portrays the real world as a hierarchy of open systems, from energy quanta to ecosystems; followingHartmann these systems as extended in time are considered the primary units of reality. Organization levels (...) should be distinguished from levels of differentiation within each organization level.Certain biological systems, such as species, continue to be misinterpreted as classes, particularly by logicians unfamiliar with modern biological theory. Replacement of Aristotelian definitions of species by “polytypic” definitions achieves nothing, because species are individual systems which can be defined from an ontological viewpoint only as wholes. The dispute whether classes are real per se or only in individuals is of no scientific importance; irrespective of which view is taken, any ordering of physical objects into classes constitutes an hypothesis about the structure of the real world.The distinction between essential and contingent characters is relevant only to classification. There are no universal rules for evaluating characters for purposes of systematization. Character statements do not form separate linear sequences. The search for “unit characters” in an absolute sense is futile. All real characters are reducible to relations and are in principle measurable, although there are limitations on the extent to which this can be presently achieved.The concept of the sexual species is fundamental to theories of biosystematics. Sexual species may be defined as lineages consisting at any given time of series of populations between which genetic exchange can occur and delimited in time by two successive processes of speciation. Linnaean nomenclature needs modification; in its traditional form it is appropriate only to non-truncated hierarchies, whereas real phylogenies form truncated hierarchies. In consequence of the distinction between systematization and classification it is concluded that, while taxa may be classified into age classes or evolutionary grades, their limits as taxa can be no different in either case. Classification into evolutionary grades remains an imprecise endeavour, since no general measure of evolutionary differentiation has been devised.The spatial and temporal extent of ecosystems, the postulated basic units of ecosystematics, remains unclarified. Nevertheless there are grounds for expecting progress in this field as the energetic relations between organisms become better understood. Biotic communities are not “abstract” classes, but systematic units. Physiognomic classification should not be confused with systematization of plant communities; both approaches contribute to an understanding of vegetational structure. (shrink)

The cumulative open-endedness of human cultures represents a major break with the social traditions of nonhuman species. As traditions are altered and the modifications retained along the cultural lineage, human populations are capable of producing complex traits that no individual could have figured out on its own. For cultures to produce increasingly complex traditions, improvements and modifications must be kept for the next generations to build upon. High-fidelity transmission would thus act as a ratchet, retaining modifications and allowing the (...) historical buildup of complex traditions. Mechanisms acting against slippage are important, of course, but cultures also need to move forward for the ratchet to retain anything important. In this article, I argue that studies of modification-generating processes and the many ways they shape cumulative culture have been overlooked. Key to a better understanding of cultural modification processes is taking seriously that cultural traditions consist of complex, hierarchically structured recipes. Taking such structures seriously and assessing the different ways they can vary in cultural design space, a novel picture for the onset of cumulative cultural evolution emerges. I argue that a possible impediment for cumulative culture in nonhuman animals may in fact reside not so much in the fidelity of their social transmission but rather in the constraints, internal and external, on their capacity to modify complex, hierarchically structured cultural recipes. (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)

Maximum Parsimony (MP) and Maximum Likelihood (ML) are two methods for evaluating which phlogenetic tree is best supported by data on the characteristics of leaf objects (which may be species, populations, or individual organisms). MP has been criticized for assuming that evolution proceeds parsimoniously -- that if a lineage begins in state i and ends in state j, the way it got from i to j is by the smallest number of changes. MP has been criticized for needing to (...) assume some model or other of the evolutionary process even though biologists often do not know what that process really is. This paper critically evaluates both criticisms. (shrink)

Because human cognition is creative and socially situated, knowledge accumulates, diffuses, and gets applied in new contexts, generating cultural analogs of phenomena observed in population genetics such as adaptation and drift. It is therefore commonly thought that elements of culture evolve through natural selection. However, natural selection was proposed to explain how change accumulates despite lack of inheritance of acquired traits, as occurs with template-mediated replication. It cannot accommodate a process with significant retention of acquired or horizontally (e.g. socially) (...) transmitted traits. Moreover, elements of culture cannot be treated as discrete lineages because they constantly interact and influence one another. It is proposed that what evolves through culture is the mind; ideas and artifacts are merely reflections of its current evolved state. Interacting minds transform (in part) through through a non-Darwinian autopoietic process similar to that by which early life evolved, involving not survival of the fittest but actualization of their potential. (shrink)

Markov models of evolution describe changes in the probability distribution of the trait values a population might exhibit. In consequence, they also describe how entropy and conditional entropy values evolve, and how the mutual information that characterizes the relation between an earlier and a later moment in a lineage’s history depends on how much time separates them. These models therefore provide an interesting perspective on questions that usually are considered in the foundations of physics—when and why does entropy (...) increase and at what rates do changes in entropy take place? They also throw light on an important epistemological question: are there limits on what your observations of the present can tell you about the evolutionary past? (shrink)

In their 1987 Nature publication, “Mitochondrial DNA and Human Evolution,” Rebecca Cann, Mark Stoneking, and Allan C. Wilson gave a new reconstruction of human evolution on the basis of differences in mitochondrial DNA among contemporary human populations. This phylogeny included an African common ancestor for all human mitochondrial DNA (mtDNA) lineages, and Cann et al.’s reconstruction became known as the “Out of Africa” hypothesis. Since mtDNA is inherited exclusively through the maternal line, the common ancestor who was first branded African (...) Eve later became known as Mitochondrial Eve (mtEve, for short). -/- In this paper, I show that mtEve was not a single, successful, or purely scientific discovery. Instead, she was produced many times and in many ways, each of which informed the next. Importantly, though Wilson and colleagues heralded mitochondrial DNA as a source of certainty, objectivity, and consensus for evolutionary inference, their productions of Mitochondrial Eve depended as much on popular assumptions about the certainty of maternal inheritance as they did on new molecular and computational tools. This recognition lets us reevaluate the complex consequences of these productions, which, like mtEve herself, could not be confined to a purely social, material, or scientific dimension. (shrink)

In the maximal form of indirect development found in many taxa of marine invertebrates, embryonic cell lineages of fixed fate and limited division capacity give rise to the larval structures. The adult arises from set‐aside cells in the larva that are held out from the early embryonic specification processes, and that retain extensive proliferative capacity. We review the locations and fates of set‐aside cells in two protostomes, a lophophorate and a deuterostome. The distinct adult body plans of many phyla develop (...) from homologous set‐aside cells within homologous larvae. We argue that the stocks from which these phyla arose utilized these respective larvae, and the diversity of their adult body plans reflects diverse pattern formation processes executed in their set‐aside cell populations. Chordates and arthropods develop directly, but share adult characters with indirectly developing phyla. Thus the deuterostome and protostome stocks that were ancestral to chordates and arthropods, respectively, also utilized maximal indirect development. (shrink)

Paul Griffiths and John Matthewson argue that selected effects play the key role in determining whether a state is pathological. In response, it is argued that a selected effects account faces a number of difficulties in light of modern genomic research. Firstly, a modern history approach to selection is problematic as a basis for assigning function to human traits in light of the small population sizes in the hominin lineage, which imply that selection has played a limited role (...) in shaping these genomes in the evolutionarily recent past. Secondly, determining both the genetic basis of disease and selective histories of the various alleles involved may be experimentally intractable. Thirdly, the existence of “selected disorders” is well supported, and yet on the other hand many other common diseases may not reduce evolutionary fitness. In summary, the biological ends promoted by natural selection, as best modeled in recent research, do not adequately ground a concept of dysfunction that aligns well with the interests of human health. (shrink)