Physical models of biological information and adaptation

The bio-informational equivalence asserts that biological processes reduce to processes of information transfer. In this paper, that equivalence is treated as a metaphor with deeply anthropomorphic content of a sort that resists constitutive-analytical definition, including formulation within mathematical theories of information. It is argued that continuance of the metaphor, as a quasi-theoretical perspective in biology, must entail a methodological dislocation between biological and physical science. It is proposed that a general class of functions, drawn from classical physics, can serve to eliminate the anthropomorphism. Further considerations indicate that the concept of biological adaptation is central to the general applicability of the informational idea in biology; a non-anthropomorphic treatment of adaptive phenomena is suggested in terms of variational principles.     

Adaptation or exaptation? The case of the human hand

A controversy of relevance to the study of biological form involves the concept of adaptation. This controversy is illustrated by the structure and function of the human hand. A review of the principal definitions of adaptation points to two main problems: (1) they are qualitative and make reference to the whole structure (or substructural feature) and (2) they are based on the idea of natural selection as a moulding factor. The first problem would be solved by a definition that encompasses quantitative measures of the effects of selection, drawing on new advances in the comparative method. The second problem is deeper and presents greater conceptual difficulties. I will argue that the idea of natural selection as a moulding factor depends on the notion of a genetic program for development. But regarding the hand, experimental evidence on limb development challenges the idea of a genetic program for skeletal pattern formation, undermining a simple application of standard adaptationist concepts. These considerations lead to a revised definition of adaptation and interpretation of the evolutionary determinants of the hand’s form.     

Adaptive physiological processes in the host during gastrointestinal parasitism

Parasite infection of the gastrointestinal tract with helminths or protozoa induces detrimental effects on host tissues and host physiology, which have been extensively studied and reviewed. However, parasitism of the digestive system is also associated with adaptive, compensatory phenomena based on changes in host physiology or structures and which tend to counterbalance the negative consequences. The objective of this review is to describe these adaptive processes and their possible underlying mechanisms. Different processes which tend to attenuate the effect of either the loss of appetite, the intestinal malabsorption or the increased tissue losses have been assessed. These processes have been reported both for helminth and protozoan infections, where they present similar characteristics. The mechanisms involved in the adaptation to parasitism remain largely unidentified. The role of feedback mechanisms based on host regulation, possibly through gastrointestinal hormones, has been raised. On the other hand, some data support the proposal that parasites themselves may initiate some of the adaptive processes and consequently favour their own survival. These adaptive phenomena appear to be an essential component in the dynamic balance between host and parasites. Also, parasite infections represent unique models to study the adaptation of the gastrointestinal tract to aggressors.     

Comparison and adaptation.

It has sometimes been suggested that the term adaptation should be reserved for differences with a known genetic basis. We argue that adaptation should be defined by its effects rather than by its causes as any difference between two phenotypic traits (or trait complexes) which increases the inclusive fitness of its carrier. This definition implies that some adaptations may arise by means other than natural selection. It is particularly important to bear this in mind when behavioural traits are considered. Critics of the 'adaptationist programme' have suggested that an important objection to many adaptive explanations is that they rely on ad-hoc arguments concerning the function of previously observed differences. We suggest that this is a less important problem (because evolutionary explanations generally claim some sort of generality and are therefore testable) than the difficulties arising from confounding variables. These are more widespread and more subtle than is generally appreciated. Not all differences between organisms are directly adapted to ecological variation. The form of particular traits usually constrains the form of value that other traits can take, presenting several obstacles to attempts to relate variation in morphological or behavioural characteristics directly to environmental differences. We describe some of the repercussions of differences in body size among vertebrates and ways in which these can be allowed for. In addition, a variety of evolutionary processes can produce non-adaptive differences between organisms. One way of distinguishing between these and adaptations is to investigate adaptive trends in phylogenetically different groups of species.     

Synergy between adaptive management and participatory modelling: The two processes as interconnected spirals

The management of social-ecological systems often presents a complex and wicked problem due to interactions between natural processes and varied, sometimes opposing, stakeholder goals. The adaptive management and participatory modelling processes are often used either to manage or in support of the management of social-ecological systems but are not always used in concert. We suggest that these processes are naturally complementary with overlapping components and between-process feedback. As such, we advocate that adaptive management should make use of participatory modelling for the management of social-ecological systems to increase stakeholder communication, confidence, and participation, streamline management strategy development, and improve management strategy application and durability. We present a translation of the typical adaptive management cycle concept to a spiral format, as well as a representation of adaptive management and participatory modelling proceeding together as interconnected spirals.     

A practical guide to measuring local adaptation

Patterns of local adaptation are expected to emerge when selection is spatially heterogeneous and sufficiently strong relative to the action of other evolutionary forces. The observation of local adaptation thus provides important insight into evolutionary processes and the adaptive divergence of populations. The detection of local adaptation, however, suffers from several conceptual, statistical and methodological issues. Here, we provide practical recommendations regarding (1) the definition of local adaptation, (2) the analysis of transplant experiments and (3) the optimisation of the experimental design of local adaptation studies. Together, these recommendations provide a unified approach for measuring local adaptation and understanding the adaptive divergence of populations in a wide range of biological systems.     

Adaptation and the origin of species

As reflected in the title of his masterwork On the Origin of Species, Darwin proposed that adaptation is the primary mechanism of speciation. On this, Darwin was criticized for his neglect of reproductive isolation, his lack of appreciation for the role of geographic barriers, his failure to distinguish varieties from species, and his typological species concept. Two developments since Darwin, the biological species concept of Ernst Mayr and the methods of Coyne and Orr for estimating the contribution of different barriers to the total reproductive isolation, provide a framework for reconciling Darwin's view on the primacy of adaptation in speciation with later proposals that emphasize reproductive isolation. A review of the few studies that have estimated the contributions of multiple isolating barriers suggests that habitat isolation and other barriers that operate before hybrid formation are much stronger than intrinsic postzygotic isolation. In light of these data, I suggest that Darwin's focus on adaptation in the origin of species was essentially correct, a conclusion that calls for future studies that explore the links between adaptation and speciation, in particular, ecogeographic isolating barriers that result from adaptive divergence in habitat use. The recent revival in thinking about ecological factors and adaptive divergence in the origin of species echoes Darwin's much-criticized "principle of divergence" and suggests that the emerging views from today's naturalists are not so different from those espoused by Darwin some 150 years ago.     

Interactions between species and environments from incomplete information

There are two contradictory aspects of the adaptive process in evolution. The first is that species must optimally increase their own fitness in a given environment. The second is that species must maintain their variation to be ready to respond to changing environments. In a strict sense, these two aspects might consider to be mutually exclusive. If species are optimally adapted, then the variation in the species that is suboptimal decreases and vice versa. To resolve this dilemma, species must find a balance between optimal adaptation and robust adaptation. Finding the balance between these processes requires both the local and global complete, static information. However, the balance between the processes must be dynamic. In this study, we propose a model that illustrates dynamic negotiation between the global and local information using lattice theory. The dynamic negotiation between these two levels results in an overestimate of fitness for each species. The overestimation of fitness in our model represents the multiplicity of fitness which is sometimes discussed as the exaptation. We show that species in our model demonstrate the power law of the lifespan distribution and 1/f fluctuation for the adaptive process. Our model allows for a balance between optimal adaptation and robust adaptation without any arbitrary parameters.     

Distinct Motor Strategies Underlying Split-Belt Adaptation in Human Walking and Running

The aim of the present study was to elucidate the adaptive and de-adaptive nature of human running on a split-belt treadmill. The degree of adaptation and de-adaptation was compared with those in walking by calculating the antero-posterior component of the ground reaction force (GRF). Adaptation to walking and running on a split-belt resulted in a prominent asymmetry in the movement pattern upon return to the normal belt condition, while the two components of the GRF showed different behaviors depending on the gaits. The anterior braking component showed prominent adaptive and de-adaptive behaviors in both gaits. The posterior propulsive component, on the other hand, exhibited such behavior only in running, while that in walking showed only short-term aftereffect (lasting less than 10 seconds) accompanied by largely reactive responses. These results demonstrate a possible difference in motor strategies (that is, the use of reactive feedback and adaptive feedforward control) by the central nervous system (CNS) for split-belt locomotor adaptation between walking and running. The present results provide basic knowledge on neural control of human walking and running as well as possible strategies for gait training in athletic and rehabilitation scenes.     

The generation of variation and the developmental basis for evolutionary novelty

Organisms exhibit an incredible diversity of form, a fact that makes the evolution of novelty seemingly self-evident. However, despite the "obvious" case for novelty, defining this concept in evolutionary terms is highly problematic, so much so that some have suggested discarding it altogether. Approaches to this problem tend to take either an adaptation- or development-based perspective, but we argue here that an exclusive focus on either of these misses the original intent of the novelty concept and undermines its practical utility. We propose instead that for a feature to be novel, it must have evolved both by a transition between adaptive peaks on the fitness landscape and that this transition must have overcome a previous developmental constraint. This definition focuses novelty on the explanation of apparently difficult or low-probability evolutionary transitions and highlights how the integration of developmental and functional considerations are necessary to evolutionary explanation. It further reinforces that novelty is a central concern not just of evolutionary developmental biology (i.e., "evo-devo") but of evolutionary biology more generally. We explore this definition of novelty in light of four examples that range from the obvious to subtle. J. Exp. Zool. (Mol. Dev. Evol.) 318B:501-517, 2012. ? 2012 Wiley Periodicals, Inc.     

Ethanol resistance in Drosophila melanogaster has increased in parallel cold‐adapted populations and shows a variable genetic architecture within and between populations

Understanding the genetic properties of adaptive trait evolution is a fundamental crux of biological inquiry that links molecular processes to biological diversity. Important uncertainties persist regarding the genetic predictability of adaptive trait change, the role of standing variation, and whether adaptation tends to result in the fixation of favored variants. Here, we use the recurrent evolution of enhanced ethanol resistance in Drosophila melanogaster during this species’ worldwide expansion as a promising system to add to our understanding of the genetics of adaptation. We find that elevated ethanol resistance has evolved at least three times in different cooler regions of the species’ modern range—not only at high latitude but also in two African high‐altitude regions. Applying a bulk segregant mapping framework, we find that the genetic architecture of ethanol resistance evolution differs substantially not only between our three resistant populations, but also between two crosses involving the same European population. We then apply population genetic scans for local adaptation within our quantitative trait locus regions, and we find potential contributions of genes with annotated roles in spindle localization, membrane composition, sterol and alcohol metabolism, and other processes. We also apply simulation‐based analyses that confirm the variable genetic basis of ethanol resistance and hint at a moderately polygenic architecture. However, these simulations indicate that larger‐scale studies will be needed to more clearly quantify the genetic architecture of adaptive evolution and to firmly connect trait evolution to specific causative loci.     

Natural transformation increases the rate of adaptation in the human pathogen Helicobacter pylori

Gene exchange between individuals can lead to profound evolutionary effects at both the genomic and population levels. These effects have sparked widespread interest in examining the specific adaptive benefits of recombination. Although this work has primarily focused on the benefits of sex in eukaryotes, it is assumed that similar benefits of genetic exchange apply across eukaryotes and prokaryotes. Here we report a direct test of this assumption using the naturally transformable human gastric pathogen Helicobacter pylori as a model organism. We show that genetic exchange accelerates adaptation to a novel laboratory environment within bacterial populations and that a general adaptive advantage exists for naturally transformable strains when transfer occurs among conspecific backgrounds. This finding demonstrates that there are generalized benefits to adaptation in both eukaryotes and prokaryotes even though the underlying processes are mechanistically different.     

Limits to local adaptation in six populations of the annual plant Diodia teres

* Local adaptation is common, but tests for adaptive differentiation frequently compare populations from strongly divergent environments, making it unlikely that any influence of stochastic processes such as drift or mutation on local adaptation will be detected. Here, the hypothesis that local adaptation is more likely to develop when the native environments of populations are more distinct than when they are similar was tested. * A reciprocal transplant experiment including two populations from each of three habitats was conducted to determine the pattern of local adaptation. In addition to testing for local adaptation at the population level, the hypothesis was tested that local adaptation is more common between populations from different habitats than between populations from the same habitat. * Local adaptation was not common, but more evidence was found of local adaptation between populations from different habitats than between populations from the same habitat. Two instances of foreign genotype fitness advantage confirm that stochastic processes such as drift can limit local adaptation. * These results are consistent with the hypothesis that stochastic processes can inhibit local adaptation but are more likely to be overwhelmed by natural selection when populations occur in divergent environments.     

STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION

Comparative studies tend to differ from optimality and functionality studies in how they treat adaptation. While the comparative approach focuses on the origin and change of traits, optimality studies assume that adaptations are maintained at an optimum by stabilizing selection. This paper presents a model of adaptive evolution on a macroevolutionary time scale that includes the maintenance of traits at adaptive optima by stabilizing selection as the dominant evolutionary force. Interspecific variation is treated as variation in the position of adaptive optima. The model illustrates how phylogenetic constraints not only lead to correlations between phylogenetically related species, but also to imperfect adaptations. From this model, a statistical comparative method is derived that can be used to estimate the effect of a selective factor on adaptive optima in a way that would be consistent with an optimality study of adaptation to this factor. The method is illustrated with an analysis of dental evolution in fossil horses. The use of comparative methods to study evolutionary trends is also discussed.     

Landscape genetics of plants

Landscape genetics is the amalgamation of landscape ecology and population genetics to help with understanding microevolutionary processes such as gene flow and adaptation. In this review, we examine why landscape genetics of plants lags behind that of animals, both in number of studies and consideration of landscape elements. The classical landscape distance/resistance approach to study gene flow is challenging in plants, whereas boundary detection and the assessment of contemporary gene flow are more feasible. By contrast, the new field of landscape genetics of adaptive genetic variation, establishing the relationship between adaptive genomic regions and environmental factors in natural populations, is prominent in plant studies. Landscape genetics is ideally suited to study processes such as migration and adaptation under global change.     

Internodons as equivalence classes in genealogical networks: building-blocks for a rigorous species concept

Among the options suggested in phylogenetic systematics to solve the species problem is the Hennigian or internodal species concept. This concept interprets species as parts of the genealogical network of individual organisms between two successive permanent splits or between a permanent split and an extinction event. Though this option is at present not favoured by phylogeneticists, we believe that, to solve the species problem, there is no alternative to finding a satisfactory partition of the genealogical network. In previous work a formal definition has been developed of Hennigian or internodal species (called internodons here), based on a logical relation between individual organisms. In this paper, we prove that this definition indeed partitions genealogical networks exhaustively into mutually exclusive entities, by showing that the defining relation is an equivalence relation. Although internodons should not themselves be seen as species, they are essential building-blocks for any satisfying species concept.     

The cost to plants of different strategies of adaptation to stress and the alleviation of stress by increasing assimilation

Summary The fitter of two species that use different strategies to overcome the same stress may be the one that expends the least resources to cope with this stress. However, this concept has proven difficult to quantify. It is proposed here that the increase in maintenance respiration in response to stress factors such as high temperature, salinity or a high-oxygen atmosphere (one indirect effect of which is nitrogen deficiency) may provide a measure of the cost of adaptation, in terms of expenditure of assimilated carbon. A corrolary to this is that, where it can be shown that an adaptive strategy results in the expenditure of assimilates, adaptation may be enhanced by increasing carbon assimilation. Results are presented supporting the hypothesis and its corrolary.     

Genomic Signatures for Species-Specific Adaptation in Lake Victoria Cichlids Derived from Large-Scale Standing Genetic Variation

The cichlids of Lake Victoria are a textbook example of adaptive radiation, as >500 endemic species arose in just 14,600 years. The degree of genetic differentiation among species is very low due to the short period of time after the radiation, which allows us to ascertain highly differentiated genes that are strong candidates for driving speciation and adaptation. Previous studies have revealed the critical contribution of vision to speciation by showing the existence of highly differentiated alleles in the visual opsin gene among species with different habitat depths. In contrast, the processes of species-specific adaptation to different ecological backgrounds remain to be investigated. Here, we used genome-wide comparative analyses of three species of Lake Victoria cichlids that inhabit different environments—Haplochromis chilotes, H. sauvagei, and Lithochromis rufus—to elucidate the processes of adaptation by estimating population history and by searching for candidate genes that contribute to adaptation. The patterns of changes in population size were quite distinct among the species according to their habitats. We identified many novel adaptive candidate genes, some of which had surprisingly long divergent haplotypes between species, thus showing the footprint of selective sweep events. Molecular phylogenetic analyses revealed that a large fraction of the allelic diversity among Lake Victoria cichlids was derived from standing genetic variation that originated before the adaptive radiation. Our analyses uncovered the processes of species-specific adaptation of Lake Victoria cichlids and the complexity of the genomic substrate that facilitated this adaptation.     

Quick adaptation of the myocardium and autonomic nervous regulation of the cardiac rhythm in 10- to 11-year-old children operating a computer

A study of quick adaptation of the myocardium of subjects operating a computer, depending on the adaptive capacities of the body, was conducted in 100 children with ages varying between 10 and 11 years using the electrocardiography method for the analysis of heart rate variability. Significant differences in the bioelectrical processes in the myocardium and autonomic nervous regulation of the cardiac rhythm (CR) were found in children with different adaptive capacities of the body. Quick adaptation to the operator activity in children with a good adaptive capacity is characterized by intensification of atrial activity and metabolic processes in the myocardium, as well as by a shortened duration of the cardiac cycle due to a shorter diastolic time, determined by increased sympathetic influences on the CR. In children with a decreased adaptive capacity, a decrease in the atrial excitability and myocardial metabolism, an increase in the systolic time, a decrease in the diastolic time, and an increase in parasympathetic influences on the CR are observed.     

The phenomenology of niche evolution via quantitative traits in a 'black-hole' sink

Previous studies of adaptive evolution in sink habitats (in which isolated populations of a species cannot persist deterministically) have highlighted the importance of demographic constraints in slowing such evolution, and of immigration in facilitating adaptation. These studies have relied upon either single-locus models or deterministic quantitative genetic formulations. We use individual-based simulations to examine adaptive evolution in a 'black-hole' sink environment where fitness is governed by a polygenic character. The simulations track both the number of individuals and their multi-locus genotypes, and incorporate, in a natural manner, both demographic and genetic stochastic processes. In agreement with previous studies, our findings reveal the central parts played by demographic constraints and immigration in adaptation within a sink (adaptation is more difficult in environments with low absolute fitness, and higher immigration can accelerate adaptation). A novel finding is that there is a 'punctuational' pattern in adaptive evolution in sink environments. Populations typically stay maladapted for a long time, and then rapidly shift into a relatively adapted state, in which persistence no longer depends upon recurrent immigration.