Phenoptosis,another specialized neologism,or the mark of a widespread revolution?

The classical approach of evolutionism is based on the concept of the survival of the fittest individuals. More and more data indicate that natural selection often acts with supra-individual mechanisms favoring genes and actions harmful for the individual. The most striking type of cases is when an individual kills himself or his offspring by actions genetically determined or favored. The neologism “phenoptosis” describes these events and implicates that they are not evolutionary anomalies but physiological phenomena determined by natural selection. The most important and familiar kind of phenoptosis, the “slow phenoptosis” or aging, which is currently considered an inevitable and scarcely changeable event, is transformed by this different interpretation into a function, in principle modifiable and manageable. Perhaps, the neologism “phenoptosis” will represent, together with the term supra-individual selection, the mark of a vital enrichment of evolutionism, conceived in broader terms of which the individual selection is just a particular case, and will be referred to as the brand and the standard for the start of a new era.     

Macro- and microevolution of bacteria in symbiotic systems

Using the examples of diverse interactions among prokaryotes and eukaryotes, the relationships between molecular and population mechanisms of evolution of symbiotic bacteria are addressed. Their circulation in host-environment systems activates microevolutionary factors that direct combinative or reductive genome evolution in facultative, ecologically obligatory, and genetically obligatory symbioses. Due to intense systemic intra-genome rearrangements and horizontal gene transfer, two types of gene systems evolve in these bacteria: (1) controlling the pathogenesis-like processes of host recognition and penetration and (2) responsible for mutualistic interactions that are related to nitrogen fixation and its transfer to the host. The evolution of gene systems of type 1 is directed by individual (Darwinian, frequency-dependent) selection, which is responsible for gene-for-gene interactions between the partners. In the evolution of the type 2 systems, group (interdeme, kin) selection plays the key role, being responsible for the development of bacterial traits beneficial for the host. Using the legume--rhizobia symbiosis as an example, it is shown that evolution of mutualism can be described in terms of biological altruism, whose regularities are common for intraspecific and interspecific relationships. Macroevolutionary rearrangements of bacterial genomes result from the structural changes in their populations, wherein various selection modes are combined with stochastic processes (genetic drift, population waves) induced in the symbiotic systems.     

Macro- and microevolution of bacteria in symbiotic systems

Using the examples of diverse interactions among prokaryotes and eukaryotes, the relationships between molecular and population mechanisms of evolution of symbiotic bacteria are addressed. Their circulation in host-environment systems activates microevolutionary factors that direct combinative or reductive genome evolution in facultative, ecologically obligatory, and genetically obligatory symbioses. It is shown on the example of symbiosis of rhizobia with legumes, that due to intensive systemic intra-genome rearrangements and horizontal gene transfer, two types of gene systems evolve in these bacteria: (1) controlling the pathogenesis-like processes of host recognition and penetration and (2) responsible for mutualistic interactions that are related to nitrogen fixation and its transfer to the host. The evolution of gene systems of type 1 is directed by individual (Darwinian, frequency-dependent) selection, which is responsible for gene-for-gene interactions between the partners. In the evolution of the type 2 systems, group (interdeme, kin) selection plays the key role, being responsible for the development of bacterial traits beneficial for the host. It is shown that evolution of mutualism can be described in terms of biological altruism, whose regularities are common for intraspecific and interspecific relationships. Macroevolutionary rearrangements of bacterial genomes result from the structural changes in their populations, wherein various selection modes are combined with stochastic processes (genetic drift, population waves) induced in the symbiotic systems.     

The hologenome concept: we need to incorporate function

Are we in the midst of a paradigm change in biology and have animals and plants lost their individuality, i.e., are even so-called ‘typical’ organisms no longer organisms in their own right? Is the study of the holobiont—host plus its symbiotic microorganisms—no longer optional, but rather an obligatory path that must be taken for a comprehensive understanding of the ecology and evolution of the individual components that make up a holobiont? Or are associated microbes merely a component of their host’s environment, and the holobiont concept is just a beautiful idea that does not add much or anything to our understanding of evolution? This article explores different aspects of the concept of the holobiont. We focus on the aspect of functional integration, a central holobiont property, which is only rarely considered thoroughly. We conclude that the holobiont comes in degrees, i.e., we regard the property of being a holobiont as a continuous trait that we term holobiontness, and that holobiontness is differentiated in several dimensions. Although the holobiont represents yet another level of selection (different from classical individual or group selection because it acts on a system that is composed of multiple species), it depends on the grade of functional integration whether or not the holobiont concept helps to cast light on the various degrees of interactions between symbiotic partners.     

Sex and aging: A comparison between two phenoptotic phenomena

Phenoptosis is a phenomenon that is genetically programmed and favored by natural selection, and that determines death or increased risk of death (fitness reduction) for the individual that manifests it. Aging, here defined as agerelated progressive mortality increase in the wild, if programmed and favored by natural selection, falls within the definition of phenoptosis. Sexual reproduction (sex), as for the involved individuals determines fitness reduction and, in some species, even certain death, also falls within the definition of phenoptosis. In this review, sex and aging are analyzed as phenoptotic phenomena, and the similarities between them are investigated. In particular, from a theoretical standpoint, the genes that cause and regulate these phenomena: (i) require analyses that consider both individual and supra-individual selection because they are harmful in terms of individual selection, but advantageous (that is, favored by natural selection) in particular conditions of supra-individual selection; (ii) determine a higher velocity of and greater opportunities for evolution and, therefore, greater evolutionary potential (evolvability); (iii) are advantageous under ecological conditions of K-selection and with finite populations; (iv) are disadvantageous (that is, not favored by natural selection) under ecological conditions of r-selection and with unlimited populations; (v) are not advantageous in all ecological conditions and, so, species that reproduce asexually or species that do not age are predicted and exist.     

Comparative analysis of experimental testing procedures for the elicitation of rescue actions in ants

Rescue behavior is observed when 1 individual provides help to another individual in danger. Most reports of rescue behavior concern ants (Formicidae), in which workers rescue each other from various types of entrapment. Many of these entrapment situations can be simulated in the laboratory using an entrapment bioassay, in which ants confront a single endangered nest mate entrapped on a sandy arena by means of an artificial snare. Here, we compared numerous characteristics of rescue actions (contact between individuals, digging around the entrapped individual, pulling at its body parts, transport of the sand covering it, and biting the snare entrapping it) in Formica cinerea ants. We performed entrapment tests in the field and in the laboratory, with the latter under varying conditions in terms of the number of ants potentially engaged in rescue actions and the arena substrate (marked or unmarked by ants’ pheromones). Rescue actions were more probable and pronounced in the field than in the laboratory, regardless of the type of test. Moreover, different test types in the laboratory yielded inconsistent results and showed noteworthy variability depending on the tested characteristic of rescue. Our results illustrate the specifics of ant rescue actions elicited in the natural setting, which is especially important considering the scarcity of field data. Furthermore, our results underline the challenges related to the comparison of results from different types of entrapment tests reported in the available literature. Additionally, our study shows how animal behavior differs in differing experimental setups used to answer the same questions.     

The life form concept and the use in the analysis of life cycle evolutionary strategies

The life form is a generalized morphoecological characteristic of an animal giving an idea of the organism as a whole, its position and function and functional role in the ecosystem. This characteristic is inherent to a species or to a group of congeneric species (for applied goal it is better to use a genus, not species) considered in the framework of higher taxon (from family to type). The principal contradiction of life form concept is determined by the existence of ontogenetic stages and changes of life forms during the whole life of individual. It is usually assumed that the concept of life form should be applied only to the adult stage, thus ignoring the integral character of the life cycle as indivisible unit of selection, evolution and functioning in ecosystem. We propose that a morphologically specific ontogenetic of a given species should be used as an elementary lowest unit in the classification of life forms. Thus it can be considered as integrated internally structured morphoecological unit in time and multidimensional space of abiotic and biotic environmental factors. As an example we describe the types of reproductive strategies and classification of elementary (ontogenetic) life forms in cephalopods. We present characteristics of the life cycle of some typical cephalopod species inhabiting different biotopes and having different models of locomotion, feeding, reproduction and development.     

面向实践的生态用地内涵、多维度分类体系

生态用地是保障我国国土生态安全格局、建设生态文明基础,是土地资源研究领域的热点问题。其内涵与分类界定是深化生态用地研究与实践的前提,也是该研究领域的难点。根据国内外现有研究,挖掘生态用地的内涵与分类特征。基于此,重新阐释了生态用地的内涵,提出功能主导性、尺度依赖性、区域特殊性、等级性和可操作性等五大分类原则,构建了面向管理实践的多维度生态用地分类体系,即基础性生态用地、保全性生态用地、生产性生态用地和生活性生态用地4大类、10个一级类和15个二级类。同时在分类体系中明确了各生态用地地类的适用尺度与范围。多维度生态用地分类体系的构建,将有利于国家和地方制定生态用地管理政策,便于深入生态用地及其生态系统服务研究。     

Obligatory Effort [Hishtadlut] as an Explanatory Model: A Critique of Reproductive Choice and Control

Studies on reproductive technologies often examine women’s reproductive lives in terms of choice and control. Drawing on 48 accounts of procreative experiences of religiously devout Jewish women in Israel and the US, we examine their attitudes, understandings and experiences of pregnancy, reproductive technologies and prenatal testing. We suggest that the concept of hishtadlut—”obligatory effort”—works as an explanatory model that organizes Haredi women’s reproductive careers and their negotiations of reproductive technologies. As an elastic category with negotiable and dynamic boundaries, hishtadlut gives ultra-orthodox Jewish women room for effort without the assumption of control; it allows them to exercise discretion in relation to medical issues without framing their efforts in terms of individual choice. Haredi women hold themselves responsible for making their obligatory effort and not for pregnancy outcomes. We suggest that an alternative paradigm to autonomous choice and control emerges from cosmological orders where reproductive duties constitute “obligatory choices.”     

Signal behavior in cranes (the Siberian Crane Sarcogeranus leucogeranus, the White-naped Crane Grus vipio, and the Red-crowned Crane Grus japonensis) in the context of the ritualization hypothesis

Signal behavior of three crane species was chosen to test the logic of the ritualization hypothesis. Its claims to explain the origin and functioning of the “highly ritualized” communication signals in birds are discussed. It is shown that such signals are observed in a wide range of situations, including those in the absence of a social partner for communication (perceiver). In its presence a signal may be performed in a way that it cannot be perceived by the partner. The same actions (“ritualized preening”) vary in length and intensity, and such variability is present in nearly all situations. In each situation, it is difficult to discriminate between the ritualized preening and actual comfort behavior. It may take place even when a social partner is present. Short preening that may be readily considered as ritualized signals are more common in the all situations, including those with an absent partner. The endogenous cyclicity in unison calling by mates indicates that communication cannot be regarded as a simple exchange of signals in accordance to the ‘stimulus-reaction’ principle. Similar actions by the more ancestral Siberian Crane may appear to be more ritualized than in the evolutionary advanced Red-crowned Crane. All these findings contradict the concept of emancipation and ritualization of behavioral actions during evolution and selection for increasing communication efficiency. According to that hypothesis, during this process such actions, due to selection for more efficient communication, evolve into discrete meaningful communication signals (displays). They stand out against the background of the monotonous, unexpressive (non-signal) everyday behavior and thus appear as the main carriers of information serving principal communication functions. A more realistic approach seems to be the understanding of communication as a process of a continuous mutual fine-tuning of the social partners’ behavioral attitudes towards each other. In either participant, its behavior is an integral structure, inseparable into categories of more or less important signals (flow of behavior). Even minor changes in performance by one individual reflect alteration in its motivational state which, in its turn, changes that of the other participant and the subsequent lines of its behavior.     

A critical approach to the definition of Darwinian units of selection

What are the biological units of selection? In fact, the notion of "unit of selection" (UOS) is blurred by ambiguity and controversy. To further evaluate the biological entities that are the objects of natural selection, three novel conceptual criteria (holism, minimalism, functionalism) are critically applied; they reveal, in addition to the self-evident case of the "individual," at least six distinct types of UOSs. These UOSs do not always have a defined structural organization; they can be parts of a living organism, a cohesive group of conspecifics, a multiunit entity, a totipotent cell, a DNA fragment, or a whole organism. UOS types diversify by amalgamation or parcelation processes of apparent entities. Therefore, previous attempts to characterize the UOSs solely on some morphological levels (gene, individual, group) without applying stringent criteria have failed to cope with the structural variations of natural phenomena and have led to the ambiguity of terms used.     

Death to the bad guys: Targeting cancer via Apo2L/TRAIL

All higher organisms consist of an ordered society of individual cells that must communicate to maintain and regulate their functions. This is achieved through a complex but highly regulated network of hormones, chemical mediators, chemokines and other cytokines, acting as ligands for intra or extra-cellular receptors. Ligands and receptors of the tumor necrosis factor (TNF) superfamilies are examples of signal transducers, whose integrated actions influence the development, homeostasis and adaptive responses of many cells and tissue types. Apo2L/TRAIL is one of several members of the tumour necrosis factor superfamily that induce apoptosis through the engagement of death receptors. Apo2L/TRAIL interacts with an unusually complex receptor system, which in humans comprises two death receptors and three decoy receptors. This molecule has received considerable attention recently because of the finding that many cancer cell types are sensitive to Apo2L/TRAIL-induced apoptosis, while most normal cells appear to be resistant to this action of Apo2L/TRAIL. In this review, we specifically emphasise on the actions of Apo2L/TRAIL with respect to its apoptotic signaling pathways and summarise what is known about its physiological role. The potential therapeutic usefulness of Apo2L/TRAIL, especially in combination with chemotherapeutic agents, is also discussed in some detail.     

Evolutionary origin of RNA editing

The term "RNA editing" encompasses a wide variety of mechanistically and phylogenetically unrelated processes that change the nucleotide sequence of an RNA species relative to that of the encoding DNA. Two general classes of editing, substitution and insertion/deletion, have been described, with all major types of cellular RNA (messenger, ribosomal, and transfer) undergoing editing in different organisms. In cases where RNA editing is required for function (e.g., to generate a translatable open reading frame in a mRNA), editing is an obligatory step in the pathway of genetic information expression. How, when, and why individual RNA editing systems originated are intriguing biochemical and evolutionary questions. Here I review briefly what is known about the biochemistry, genetics, and phylogenetics of several very different RNA editing systems, emphasizing what we can deduce about their origin and evolution from the molecular machinery involved. An evolutionary model, centered on the concept of "constructive neutral evolution", is able to account in a general way for the origin of RNA editing systems. The model posits that the biochemical elements of an RNA editing system must be in place before there is an actual need for editing, and that RNA editing systems are inherently mutagenic because they allow potentially deleterious or lethal mutations to persist at the genome level, whereas they would otherwise be purged by purifying selection.     

Lamarckism and epigenetic inheritance: a clarification

Since the 1990s, the terms “Lamarckism” and “Lamarckian” have seen a significant resurgence in biological publications. The discovery of new molecular mechanisms (DNA methylation, histone modifications, RNA interference, etc.) have been interpreted as evidence supporting the reality and efficiency of the inheritance of acquired characters, and thus the revival of Lamarckism. The present paper aims at giving a critical evaluation of such interpretations. I argue that two types of arguments allow to draw a clear distinction between the genuine Lamarckian concept of inheritance of acquired characters and transgenerational epigenetic inheritance. The first concerns the explanandum of the processes under consideration: molecular mechanisms of transgenerational epigenetic inheritance are understood as evolved products of natural selection. This means that the kind of inheritance of acquired characters they might be responsible for is an obligatory emergent feature of evolution, whereas traditional Lamarckisms conceived the inheritance of acquired characters as a property inherent in living matter itself. The second argument concerns the explanans of the inheritance of acquired characters: in light of current knowledge, epigenetic mechanisms are not able to drive adaptive evolution by themselves. Emergent Lamarckian phenomena would be possible if and only if individual epigenetic variation allowed the inheritance of acquired characters to be a factor of unlimited change. This implies specific requirements for epigenetic variation, which I explicitly define and expand upon. I then show that given current knowledge, these requirements are not empirically grounded.     

Evolutionary stability: States and strategies

Different aspects and modifications of the definition of an evolutionarily stable (ES) strategy that have been considered in the literature can be incorporated in a unifying concept which regards the population context. This concept of evolutionary stability will generally characterize population states in both pure- and mixed-strategist models. In particular, it includes ES strategies, represented as a phenotype unique in an ES population. For an important class of mixed-strategist models, no strict ESS can exist. This will be the case whenever the success of an individual strategy is considered to follow as an average from the successes of its behavioural components. Instead, ESS results may be obtained from what will be called a “degenerate” form of the model, which is simply an ESS model on the level of elementary actions. Then, however, the correct interpretation of an ESS is not an individual phenotype but rather a population mixture of elementary actions. If an ES state exists in a mixed-strategist model it may be determined by an equilibrium condition; if there is an ES strategy, a different approach—mainly maximum considerations—is needed for finding it. An equilibrium condition does not hold for the components of an ES strategy straightforwardly; but it can be derived in terms of an auxiliary ESS model that considers first-order effects of the components. Several examples illustrate the significance of these results. Particularly, two models on “Games between Relatives” are reconsidered in order to display both their formal interrelation and the different meaning of their results in the context of mixed-strategist models.     

A unified view of the initiation of protein synthesis

The mechanism of the initiation of protein synthesis is discussed in terms of two different hypotheses in which each emphasized a different possible element of the process: the Shine-Dalgarno (SD) hypothesis ascribed an essential role to recognition of the SD segment by the ribosomal RNA; it is supported by a variety of experiments but conflicting evidence negates its obligatory nature. In contrast, our hypothesis highlighted the role of the structure of the mRNA and proposes that the initiation codon is selected by virtue of its unique accessibility. The rationale for the importance of accessibility in the selection of the initiation site is discussed. An analysis and a recapitulation of the initiation process and ribosomal specificity are presented. The apparent conflicts with the SD hypothesis are resolved in a unified mechanism where accessibility is the dominant factor.     

The genome‐centric concept: resynthesis of evolutionary theory

Modern biology has been heavily influenced by the gene‐centric concept. Paradoxically, this very concept – on which bioresearch is based – is challenged by the success of gene‐based research in terms of explaining evolutionary theory. To overcome this major roadblock, it is essential to establish new theories, to not only solve the key puzzles presented by the gene‐centric concept, but also to provide a conceptual framework that allows the field to grow. This paper discusses a number of paradoxes and illustrates how they can be addressed by the genome‐centric concept in order to further resynthesize evolutionary theory. In particular, methodological breakthroughs that analyze genome evolution are discussed. The multiple interactions among different levels of a complex system provide the key to understanding the relationship between self‐organization and natural selection. Darwinian natural selection applies to the biological level due to its unique genetic and heterogeneous features, but does not simply or directly apply to either the lower non‐living level or higher intellectual society level. At the complex bio‐system level, the genome context (the entire package of genes and their genomic physical relationship or genomic topology), not the individual genes, defines the system and serves as the principle selection platform for evolution.     

The expected efficiencies of some methods of selection of components for inter-genotypic mixtures

Summary The gains in yields of mixtures expected to follow various methods of selection of components from populations of randomly constituted mixtures are formulated in terms of a statistical model and a model of first-order inter-plant competition. The types of selection investigated include that among whole mixtures and among groups or individual components on a within-mixture or unrestricted basis, or on the basis of the yields of sets of mixtures to which the group or individual is common. In all cases the sizes of mixture used for selection and for measurement of gain may differ. While evaluation of components in groups or whole mixtures allows selection for component interactions, gains are lower overall because of the reduction in variance caused by grouping. Gains due to interaction are lost if the components are pooled after selection, as in a population improvement programme. Individual selection carries some risk of negative gains, but these are reduced if assessment is made on an unrestricted rather than within-mixture basis. When second and higher order competitive interactions are absent, monoculture assessment is expected to be an efficient means of selection of components for binary and tertiary mixtures.     

ON MULTILEVEL SELECTION AND KIN SELECTION: CONTEXTUAL ANALYSIS MEETS DIRECT FITNESS

When Hamilton defined the concept of inclusive fitness, he specifically was looking to define the fitness of an individual in terms of that individual's behavior, and the effects of its’ behavior on other related individuals. Although an intuitively attractive concept, issues of accounting for fitness, and correctly assigning it to the appropriate individual make this approach difficult to implement. The direct fitness approach has been suggested as a means of modeling kin selection while avoiding these issues. Whereas Hamilton's inclusive fitness approach assigns to the focal individual the fitness effects of its behavior on other related individuals, the direct fitness approach assigns the fitness effects of other actors to the focal individual. Contextual analysis was independently developed as a quantitative genetic approach for measuring multilevel selection in natural populations. Although the direct fitness approach and contextual analysis come from very different traditions, both methods rely on the same underlying equation, with the primary difference between the two approaches being that the direct fitness approach uses fitness optimization modeling, whereas with contextual analysis, the same equation is used to solve for the change in fitness associated with a change in phenotype when the population is away from the optimal phenotype.     

Scale dependency and functional response in moose habitat selection

Habitat selection can be influenced by the distribution of the habitat types in the landscape as well as net gain in visiting patches of resources, causing individual variation in habitat selection. Moreover, the hypothesis of functional response in habitat selection predicts that the degree of selection of a resource depends on its relative availability. We used radio-telemetry data from individual moose on an island off the coast of northern Norway to evaluate whether the selection of habitat types at the landscape scale differed from the choice of habitat types within the home range, and investigated the functional response in habitat selection by relating individual habitat selection to home range characteristics. At the landscape scale, moose selected for habitat types that provided both good forage and cover, with small differences between sex and age groups. At the home range scale, all individuals selected habitat types that were associated with cover and low human impact. Habitat selection was not modified by local moose density, but was related to home range size at both spatial scales. Larger home ranges contained larger proportions of non-preferred habitat types compared to smaller home ranges. At the home range scale, the selection for a habitat type decreased with its relative availability, indicating a functional response in habitat selection. This suggests that habitat selection is modified by home range size, which influences the availability of habitat types and shapes individual habitat selection patterns. Our results support previous suggestions that analyses of habitat or resource selection should follow a multi-scale approach. Both the relative availability of habitat types as well as individual variation in home range size should be accounted for in order to disentangle the complex mechanisms that contribute to shape patterns of resource selection in animals.