The mystery of the mystery of common genetic diseases

Common monogenic genetic diseases, ones that have unexpectedly high frequencies in certain populations, have attracted a great number of conflicting evolutionary explanations. This paper will attempt to explain the mystery of why two particularly extensively studied common genetic diseases, Tay Sachs disease and cystic fibrosis, remain evolutionary mysteries despite decades of research. I review the most commonly cited evolutionary processes used to explain common genetic diseases: reproductive compensation, random genetic drift (in the context of founder effect), and especially heterozygote advantage. The latter process has drawn a particularly large amount of attention, having so successfully explained the elevated frequency of sickle cell anemia in malaria-endemic areas. However, the empirical evidence for heterozygote advantage in other common genetic diseases is quite weak. I introduce and illustrate the significance of a hierarchy of genetic disease phenomena found within the genetic disease explanations, which include the phenomena: single mutation variants of a common genetic disease, single genetic diseases, and classes of diseases with related phenotypic effects. I demonstrate that some of the confusion over the explanations of common genetic diseases can be traced back to confusions over which phenomena are being explained. I proceed to briefly evaluate the existing evidence for two common human genetic diseases: Tay Sachs disease and cystic fibrosis. The above considerations will ultimately shed light on why these diseases’ evolutionary explanations remain so deeply unresolved after so such a great volume of research.     

Methodological Problems in Evolutionary Biology. XII. Against Evolutionary Ethics

Evolutionary ethics has recently become popular again. Some of its representatives elaborate new attempts to derive ethics from evolutionary biology. The attempts, like previous ones, fail because they commit the naturalistic fallacy. Premises from evolutionary biology together with normative premises also do not justify ethical principles. Other representatives argue that evolutionary considerations imply that ethics cannot be justified at all. Their arguments presuppose an unacceptable form of foundationalism. In principle, evolutionary biology might explain some aspects of morality, but in practice explanations are hard to come by. All this does not imply that evolutionary theory is irrelevant in normative settings. To the contrary, it may help us devise guidelines in environmental policy and health care policy. It is to be hoped that evolutionary ethicists will divert their research efforts to the elaboration of such guidelines.     

Predicting trait values and measuring selection in complex life histories: reproductive allocation decisions in Soay sheep

Accurate prediction of life history phenomena and characterisation of selection in free-living animal populations are fundamental goals in evolutionary ecology. In density regulated, structured populations, where individual state influences fate, simple and widely used approaches based on individual lifetime measures of fitness are difficult to justify. We combine recently developed structured population modelling tools with ideas from modern evolutionary game theory (adaptive dynamics) to understand selection on allocation of female reproductive effort to singletons or twins in a size-structured population of feral sheep. In marked contrast to the classical selection analyses, our model-based approach predicts that the female allocation strategy is under negligible directional selection. These differences arise because classical selection analysis ignores components of offspring fitness and fails to consider selection over the complete life cycle.     

Four misunderstandings about cultural attraction

Cultural attraction theory (CAT) is a research agenda the purpose of which is to develop causal explanations of cultural phenomena. CAT is also an evolutionary approach to culture, in the sense that it treats culture as a population of items of different types, with the frequency of tokens of those types changing over time. Now more than 20 years old, CAT has made many positive contributions, theoretical and empirical, to the naturalization of the social sciences. In consequence of this growing impact, CAT has, in recent years, been the subject of critical discussion. Here, we review and respond to these critiques. In so doing, we also provide a clear and concise introduction to CAT. We give clear characterizations of CAT's key theoretical notions, and we outline how these notions are derived from consideration of the natural character of cultural phenomena (Box 1 ). This naturalistic quality distinguishes CAT from other evolutionary approaches to culture.     

Simple minds: a qualified defence of associative learning

Using cooperation in chimpanzees as a case study, this article argues that research on animal minds needs to steer a course between 'association-blindness'-the failure to consider associative learning as a candidate explanation for complex behaviour-and 'simple-mindedness'-the assumption that associative explanations trump more cognitive hypotheses. Association-blindness is challenged by the evidence that associative learning occurs in a wide range of taxa and functional contexts, and is a major force guiding the development of complex human behaviour. Furthermore, contrary to a common view, association-blindness is not entailed by the rejection of behaviourism. Simple-mindedness is founded on Morgan's canon, a methodological principle recommending 'lower' over 'higher' explanations for animal behaviour. Studies in the history and philosophy of science show that Morgan failed to offer an adequate justification for his canon, and subsequent attempts to justify the canon using evolutionary arguments and appeals to simplicity have not been successful. The weaknesses of association-blindness and simple-mindedness imply that there are no short-cuts to finding out about animal minds. To decide between associative and yet more cognitive explanations for animal behaviour, we have to spell them out in sufficient detail to allow differential predictions, and to test these predictions through observation and experiment.     

Fluctuation Induces Evolutionary Branching in a Mathematical Model of Ecosystems

Ecological systems are always subjected to various environmental fluctuations. They evolve under these fluctuations and the resulting systems are robust against them. The diversity in ecological systems is also acquired through the evolution. How do the fluctuations affect the evolutionary processes? Do the fluctuations have direct impact on the species diversity in ecological systems? In the present paper, we investigate the relation between the environmental fluctuation and the evolution of species diversity with a mathematical model of evolutionary ecology. In the model, individual organisms compete for a single restricted resource and the temporal fluctuation in the resource supply is introduced as the environmental fluctuation. The evolutionary process is represented by the mutational change of genotypes which determines their resource utilization strategies. We found that when the environmental state is switched form static to fluctuating conditions, the initial closely related population distributed around the genotype adapted for the static environment is destabilized and divided into two groups in the genotype space; i.e., the evolutionary branching is induced by the environmental fluctuation. The consequent multiple species structures is evolutionary stable at the presence of the fluctuation. We perform the evolutionary invasion analysis for the phenomena and illustrate the mechanisms of the branchings. The results indicate a novel process of increasing the species diversity via evolutionary branching, and the analysis reveals the mechanisims of the branching preocess as the response to the environmental fluctuation. The robustness of the evolutionary process is also discussed.     

Are Probabilities Necessary For Evolutionary Explanations?

Several philosophers of science have advanced an instrumentalist thesis about the use of probabilities in evolutionary biology. I investigate the consequences of instrumentalism on evolutionary explanations. I take issue with Barbara Horan's (1994) argument that probabilities are unnecessary to explain evolutionary change given the underlying deterministic character of evolutionary processes. First, I question Horan's deterministic assumption. Then, I attempt to undermine her Laplacian argument by demonstrating that whether probabilities are necessary depends upon the sort of questions one is asking.     

Convergent exaptation and adaptation in solitary island lizards

Independent evolutionary lineages often display similar characteristics in comparable environments. Three kinds of historical hypotheses could explain this convergence. The first is adaptive and evolutionary: nonrandom patterns may result from analogous evolutionary responses to shared conditions. The second explanation is exaptive and ecological: species may be filtered by their suitability for a particular type of environment. The third potential explanation is a null hypothesis of random colonization from a historically nonrandom source pool. Here we demonstrate that both exaptation and adaptation have produced convergent similarity in different size-related characters of solitary island lizards. Large sexual size dimorphism results from adaptive response to solitary existence; uniform, intermediate size results from ecological filtering of potential colonizers. These results demonstrate the existence of deterministic exaptive convergence and suggest that convergent phenomena may require historical explanations that are ecological as well as evolutionary.     

Developmental plasticity and evolutionary explanations

Developmental plasticity looks like a promising bridge between ecological and developmental perspectives on evolution. Yet, there is no consensus on whether plasticity is part of the explanation for adaptive evolution or an optional “add‐on” to genes and natural selection. Here, we suggest that these differences in opinion are caused by differences in the simplifying assumptions, and particular idealizations, that enable evolutionary explanation. We outline why idealizations designed to explain evolution through natural selection prevent an understanding of the role of development, and vice versa. We show that representing plasticity as a reaction norm conforms with the idealizations of selective explanations, which can give the false impression that plasticity has no explanatory power for adaptive evolution. Finally, we use examples to illustrate why evolutionary explanations that include developmental plasticity may in fact be more satisfactory than explanations that solely refer to genes and natural selection.     

Robustness and evolution: concepts, insights and challenges from a developmental model system

Robustness, the persistence of an organismal trait under perturbations, is a ubiquitous property of complex living systems. We here discuss key concepts related to robustness with examples from vulva development in the nematode Caenorhabditis elegans. We emphasize the need to be clear about the perturbations a trait is (or is not) robust to. We discuss two prominent mechanistic causes of robustness, namely redundancy and distributed robustness. We also discuss possible evolutionary causes of robustness, one of which does not involve natural selection. To better understand robustness is of paramount importance for understanding organismal evolution. Part of the reason is that highly robust systems can accumulate cryptic variation that can serve as a source of new adaptations and evolutionary innovations. We point to some key challenges in improving our understanding of robustness.     

Warfare in an evolutionary perspective

The importance of warfare for human evolution is hotly debated in anthropology. Some authors hypothesize that warfare emerged at least 200,000–100,000 years BP, was frequent, and significantly shaped human social evolution. Other authors claim that warfare is a recent phenomenon, linked to the emergence of agriculture, and mostly explained by cultural rather than evolutionary forces. Here I highlight and critically evaluate six controversial points on the evolutionary bases of warfare. I argue that cultural and evolutionary explanations on the emergence of warfare are not alternative but analyze biological diversity at two distinct levels. An evolved propensity to act aggressively toward outgroup individuals may emerge irrespective of whether warfare appeared early/late during human evolution. Finally, I argue that lethal violence and aggression toward outgroup individuals are two linked but distinct phenomena, and that war and peace are complementary and should not always be treated as two mutually exclusive behavioral responses.     

The evolutionary ecology of metacommunities

Research on the interactions between evolutionary and ecological dynamics has largely focused on local spatial scales and on relatively simple ecological communities. However, recent work demonstrates that dispersal can drastically alter the interplay between ecological and evolutionary dynamics, often in unexpected ways. We argue that a dispersal-centered synthesis of metacommunity ecology and evolution is necessary to make further progress in this important area of research. We demonstrate that such an approach generates several novel outcomes and substantially enhances understanding of both ecological and evolutionary phenomena in three core research areas at the interface of ecology and evolution.     

Why are defensive toxins so variable? An evolutionary perspective

Defensive toxins are widely used by animals, plants and micro-organisms to deter natural enemies. An important characteristic of such defences is diversity both in the quantity of toxins and the profile of specific defensive chemicals present. Here we evaluate evolutionary and ecological explanations for the persistence of toxin diversity within prey populations, drawing together a range of explanations from the literature, and adding new hypotheses. We consider toxin diversity in three ways: (1) the absence of toxicity in a proportion of individuals in an otherwise toxic prey population (automimicry); (2) broad variation in quantities of toxin within individuals in the same population; (3) variation in the chemical constituents of chemical defence. For each of these phenomena we identify alternative evolutionary explanations for the persistence of variation. One important general explanation is diversifying (frequency- or density-dependent) selection in which either costs of toxicity increase or their benefits decrease with increases in the absolute or relative abundance of toxicity in a prey population. A second major class of explanation is that variation in toxicity profiles is itself nonadaptive. One application of this explanation requires that predator behaviour is not affected by variation in levels or profiles of chemical defence within a prey population, and that there are no cost differences between different quantities or forms of toxins found within a population. Finally, the ecology and life history of the animal may enable some general predictions about toxin variation. For example, in animals which only gain their toxins in their immature forms (e.g. caterpillars on host plants) we may expect a decline in toxicity during adult life (or at least no change). By contrast, when toxins are also acquired during the adult form, we may for example expect the converse, in which young adults have less time to acquire toxicity than older adults. One major conclusion that we draw is that there are good reasons to consider within-species variation in defensive toxins as more than mere ecological noise. Rather there are a number of compelling evolutionary hypotheses which can explain and predict variation in prey toxicity.     

Effects of epistasis on phenotypic robustness in metabolic pathways

It is an open question whether phenomena such as phenotypic robustness to mutation evolve as adaptations or are simply an inherent property of genetic systems. As a case study, we examine this question with regard to dominance in metabolic physiology. Traditionally the conclusion that has been derived from Metabolic Control Analysis has been that dominance is an inevitable property of multi-enzyme systems and hence does not require an evolutionary explanation. This view is based on a mathematical result commonly referred to as the flux summation theorem. However it is shown here that for mutations involving finite changes (of any magnitude) in enzyme concentration, the flux summation theorem can only hold in a very restricted set of conditions. Using both analytical and simulation results we show that for finite changes, the summation theorem is only valid in cases where the relationship between genotype and phenotype is linear and devoid of non-linearities in the form of epistasis. Such an absence of epistasis is unlikely in metabolic systems. As an example, we show that epistasis can arise in scenarios where we assume generic non-linearities such as those caused by enzyme saturation. In such cases dominance levels can be modified by mutations that affect saturation levels. The implication is that dominance is not a necessary property of metabolic systems and that it can be subject to evolutionary modification.     

A biologically plausible model of early visual motion processing II: Psychophysical application

We test the model of early visual processing introduced in the companion paper by simulating a range of psychophysical phenomena. We present new data concerning our ability to discriminate the speed of drifting gratings when spatiotemporally apertured in a variety of ways. We shall investigate the role played by the aperture in modifying the grating's behaviour from its idealisation as a pure Fourier component and show that this is not negligible. Other phenomena which we simulate and explain relate to the way perceived velocity is influenced by contrast and spatial frequency. Many of our explanations are couched in terms of the relative number of cells occurring within each locale of the Fourier domain. This use of the cell density map is a unifying concept and avoids the necessity for a range of separate mechanisms. We argue that a neurophysiologically detailed model is necessary in order to explain psychophysical data (Weber fractions) which vary over less than an order of magnitude, and small deviations from veridical encoding of velocity.     

The QTN program and the alleles that matter for evolution: all that's gold does not glitter

The search for the alleles that matter, the quantitative trait nucleotides (QTNs) that underlie heritable variation within populations and divergence among them, is a popular pursuit. But what is the question to which QTNs are the answer? Although their pursuit is often invoked as a means of addressing the molecular basis of phenotypic evolution or of estimating the roles of evolutionary forces, the QTNs that are accessible to experimentalists, QTNs of relatively large effect, may be uninformative about these issues if large‐effect variants are unrepresentative of the alleles that matter. Although 20th century evolutionary biology generally viewed large‐effect variants as atypical, the field has recently undergone a quiet realignment toward a view of readily discoverable large‐effect alleles as the primary molecular substrates for evolution. I argue that neither theory nor data justify this realignment. Models and experimental findings covering broad swaths of evolutionary phenomena suggest that evolution often acts via large numbers of small‐effect polygenes, individually undetectable. Moreover, these small‐effect variants are different in kind, at the molecular level, from the large‐effect alleles accessible to experimentalists. Although discoverable QTNs address some fundamental evolutionary questions, they are essentially misleading about many others.     

Students’ Mental Models of Evolutionary Causation: Natural Selection and Genetic Drift

In an effort to understand how to improve student learning about evolution, a focus of science education research has been to document and address students?? naive ideas. Less research has investigated how students reason about alternative scientific models that attempt to explain the same phenomenon (e.g., which causal model best accounts for evolutionary change?). Within evolutionary biology, research has yet to explore how non-adaptive factors are situated within students?? conceptual ecologies of evolutionary causation. Do students construct evolutionary explanations that include non-adaptive and adaptive factors? If so, how are non-adaptive factors structured within students?? evolutionary explanations? We used clinical interviews and two paper and pencil instruments (one open-response and one multiple-choice) to investigate the use of non-adaptive and adaptive factors in undergraduate students?? patterns of evolutionary reasoning. After instruction that included non-adaptive causal factors (e.g., genetic drift), we found them to be remarkably uncommon in students?? explanatory models of evolutionary change in both written assessments and clinical interviews. However, consistent with many evolutionary biologists?? explanations, when students used non-adaptive factors they were conceptualized as causal alternatives to selection. Interestingly, use of non-adaptive factors was not associated with greater understanding of natural selection in interviews or written assessments, or with fewer naive ideas of natural selection. Thus, reasoning using non-adaptive factors appears to be a distinct facet of evolutionary thinking. We propose a theoretical framework for an expert?Cnovice continuum of evolutionary reasoning that incorporates both adaptive and non-adaptive factors, and can be used to inform instructional efficacy in evolutionary biology.     

Some implications of paleoecology for contemporary ecology

The paleoecological record allows contemporary ecologists to put current phenomena into the context of a longer time-frame, thereby providing the opportunity to evaluate the importance of slowly operating processes, past cyclic or unusual events, disturbance regimes, and historically constrained phenomena. We briefly outline the environmental history of the Quaternary, discuss the spatial and temporal resolution of the paleoecological evidence for biotic change, and summarize data relevant to such current issues as the nature of the biotic community, the role of disturbance, stability versus rapid change, evolutionary theory, explanations of species diversity, and refugia theory. Finally, we offer examples of the utility of paleoecological techniques for ecologists and environmental scientists.