Evolutionarily singular strategies and the adaptive growth and branching of the evolutionary tree

We present a general framework for modelling adaptive trait dynamics in which we integrate various concepts and techniques from modern ESS-theory. The concept of evolutionarily singular strategies is introduced as a generalization of the ESS-concept. We give a full classification of the singular strategies in terms of ESS-stability, convergence stability, the ability of the singular strategy to invade other populations if initially rare itself, and the possibility of protected dimorphisms occurring within the singular strategy's neighbourhood. Of particular interest is a type of singular strategy that is an evolutionary attractor from a great distance, but once in its neighbourhood a population becomes dimorphic and undergoes disruptive selection leading to evolutionary branching. Modelling the adaptive growth and branching of the evolutionary tree can thus be considered as a major application of the framework. A haploid version of Levene's soft selection model is developed as a specific example to demonstrate evolutionary dynamics and branching in monomorphic and polymorphic populations.     

Eco-evolutionary feedbacks,adaptive dynamics and evolutionary rescue theory

Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps.     

The mast cell: an evolutionary perspective

This review article is an attempt to trace the evolution of mast cells (MCs). These immune cells have been identified in all vertebrate classes as single‐lobed cells containing variable amounts of membrane‐bound secretory granules which store a large series of mediators, namely histamine, proteases, cytokines and growth factors. Other MC features, at least in mammals, are the c‐kit receptor for the stem cell factor and the high‐affinity receptor, FcεRI, for immunoglobulin E (IgE). The c‐kit receptor also has been identified in fish MCs. The FcεRI receptor seems to be a more recent acquisition in MC phylogenesis given that IgE originated in mammalian species. Tryptase and histamine have also been recognized in MCs of teleost fish. Thus, a cell population with the overall characteristics of higher vertebrate MCs is identifiable in the most evolutionarily advanced fish species. Two potential MC progenitors have been identified in ascidians (urochordates which appeared approximately 500 million years ago): the basophil/MC‐like granular haemocyte and the test cell. Both contain histamine and heparin, and provide defensive functions. Some granular haemocytes in Arthropoda also closely approximate the ultrastructure of modern MCs. The origin of MCs is probably to be found in a leukocyte ancestor operating in the context of a primitive local innate immunity and involved in phagocytic and killing activity against pathogens. From this type of defensive cell, the MC phylogenetic progenitor evolved into a tissue regulatory and remodelling cell, which was incorporated into the networks of recombinase activating genes (RAG)‐mediated adaptive immunity in the Cambrian era, some 550 million years ago. Early MCs probably appeared in the last common ancestor we shared with hagfish, lamprey and sharks about 450‐500 million years ago.     

Innate immunity in early chordates and the appearance of adaptive immunity

In the urochordate Ciona intestinalis some membrane Immunoglobulin superfamily members with ancestral features of antigen receptors are homologs of vertebrate adhesion molecules acting as virus receptors. They include the following: the junction adhesion molecule (reovirus receptor) (JAM), the Cortical thymocyte marker of Xenopus (CTX family) (Coxsackie's virus receptor) and the poliovirus receptor (PVR). In humans these genes belong to the same linkage group, of which 4 paralogous groups exist. This situation is consistent with the notion that the Ciona set of genes would correspond to a preduplication state. In addition, the human region 3q13 and its paralogs, harbour genes remotely related to the nectin family that can be detected in Protostomes (human CRTAM and CD80-86 related to Drosophila Beat). In addition, this linkage group contains several CDs important for the immune system CD166, CD47 and many members of the tetraspanin family. The VC1-like core of the nectin is homologous to the VCI core of the MHC-linked tapasin and to the VC1 segments of, for example, specific antigen receptors of vertebrates, and could be related to a primitive antigen receptor gene. It is suggested that the virus binding property of the members of this family was exploited, and that they were recruited in the vertebrate immune system following the introduction of the somatic rearrangement machinery. In this way the adaptive immune system could have developed from a set of receptors involved in a primitive local innate immunity involving NF-kappaB-mediated apoptosis.     

A conceptual framework of evolutionary novelty and innovation

Since 1990 the recognition of deep homologies among metazoan developmental processes and the spread of more mechanistic approaches to developmental biology have led to a resurgence of interest in evolutionary novelty and innovation. Other evolutionary biologists have proposed central roles for behaviour and phenotypic plasticity in generating the conditions for the construction of novel morphologies, or invoked the accessibility of new regions of vast sequence spaces. These approaches contrast with more traditional emphasis on the exploitation of ecological opportunities as the primary source of novelty. This definitional cornucopia reflects differing stress placed on three attributes of novelties: their radical nature, the generation of new taxa, and ecological and evolutionary impact. Such different emphasis has led to conflating four distinct issues: the origin of novel attributes (genes, developmental processes, phenotypic characters), new functions, higher clades and the ecological impact of new structures and functions. Here I distinguish novelty (the origin of new characters, deep character transformations, or new combinations) from innovation, the ecological and evolutionary success of clades. Evidence from the fossil record of macroevolutionary lags between the origin of a novelty and its ecological success demonstrates that novelty may be decoupled from innovation, and only definitions of novelty based on radicality (rather than generativity or consequentiality) can be assessed without reference to the subsequent history of the clade to which a novelty belongs. These considerations suggest a conceptual framework for novelty and innovation, involving: (i) generation of the potential for novelty; (ii) the formation of novel attributes; (iii) refinement of novelties through adaptation; (iv) exploitation of novelties by a clade, which may coincide with a new round of ecological or environmental potentiation; followed by (v) the establishment of innovations through ecological processes. This framework recognizes that there is little empirical support for either the dominance of ecological opportunity, nor abrupt discontinuities (often caricatured as ‘hopeful monsters’). This general framework may be extended to aspects of cultural and social innovation.     

Infection with Haemonchus contortus in sheep and the role of adaptive immunity in selection of the parasite

1988. Infection with Haemonchus contortus in sheep and the role of adaptive immunity in selection of the parasite. International Journal for Parasitology 18: 1071–1075. A series of infections with Haemonchus contortus in immune and non-immune sheep gave no indication that successive generations of the parasite were selected for the enhanced ability to cope with host-protective immunity. Separate subpopulations of the parasite were passaged through individual immune sheep and were compared at each generation with infections by the pooled populations in an additional panel of immune sheep. The experiment ceased when infections became too low to allow the production of sufficient infective larvae for reinfection. Results showed that H. contortus is unable to make adjustments to the immune status of a given sheep. Attention is thus diverted from the process through which host identifies self and non-self and from the histocompatibility system as the targets for possible antigen-mimicry by H. contortus.     

An evolutionary perspective on physical attractiveness

Everyday experience suggests that physical attractiveness is important in personal—and especially sexual—relationships. This impression is confirmed by a large body of social psychological research.^1,2 Cross-cultural surveys and ethnographic accounts show that concern with the attractiveness of potential mates is also common in non-Western societies and in tribal and peasant cultures.³ However, social psychologists and anthropologists have often had a hard time explaining why attractiveness should count for so much, or why some features rather than others should seem particularly attractive. The theoretical difficulties in accounting for physical attraction are brought out in a Brazilian saying, “Beleza nâo pôe na mesa” (“Good looks don't put anything on the table”), which points to the absence of any evident practical advantage to choosing an attractive mate. Faced with these difficulties, a growing number of researchers in biology, psychology, and anthropology have turned to the modern theory of sexual selection, which has been highly successful in explaining nonhuman animals attractions to traits of no direct ecological utility. In this article, I survey recent efforts to apply the theory of sexual selection to human physical attraction.     

Improvement of adaptive immunity by antigen-carrying biodegradable nanoparticles

One of the most important aspects in vaccine development is to induce potent antigen-specific immune responses. In this study, we examined the immunological activities of antigen-carrying biodegradable poly(γ-glutamic acid) (γ-PGA) nanoparticles (NPs) in mice. The immunization with ovalbumin (OVA)-carrying γ-PGA NPs (OVA-NPs) could induce significant expansion of antigen-specific CD8⁺ T cells. Unlike complete Freund’s adjuvant, subcutaneous (s.c.) inoculation of OVA-NPs to footpad did not generate injection site swelling. Although OVA-NPs could induce both antigen-specific cellular and humoral immune responses, the dominant induction of either cellular or humoral immunity was found to depend on their administration routes. Strong antibody production was observed by s.c. immunization, yet no antibody was identified by intranasal immunization. Thus, γ-PGA NPs are a safe and efficient antigen carrier with unique immunological properties.     

The effect of maternal care on child survival: a demographic, genetic, and evolutionary perspective

Models of population dynamics generally assume that child survival is independent of maternal survival. However, in humans, the death of a mother compromises her immature children's survival because children require postnatal care. A child's survival therefore depends on her mother's survival in years following her birth. Here, we provide a model incorporating this relationship and providing the number of children surviving until maturity achieved by females at each age. Using estimates of the effect that a mother's death has on her child's survival until maturity, we explore the effect of the model on population dynamics. Compared to a model that includes a uniform child survival probability, our model slightly raises the finite rate of increase lambda and modifies generation time and the stable age structure. We also provide estimates of selection on alleles that change the survival of females. Selection is higher at all adult ages in our model and remains significant after menopause (at ages for which the usual models predict neutrality of such alleles). Finally, the effect of secondary caregivers who compensate maternal care after the death of a mother is also emphasized. We show that allocare (as an alternative to maternal care) can have a major effect on population dynamics and is likely to have played an important role during human evolution.     

细胞自噬与机体免疫机制及抗微生物感染的关系

细胞自噬作为细胞的一种生理机制,一方面为细胞提供再生资源,一方面也可以作为防御机制抵抗微生物的感染和寄生。本文对它与先天性免疫、适应性免疫的关系做了综述,并探讨了自噬与微生物感染的关系。本文为我们理解细胞自噬在机体抗感染机制中的作用提供了帮助,也为我们研究感染性疾病治疗药物开启新的视野。     

The adaptive legacy of human evolution: A search for the environment of evolutionary adaptedness

The growth of evolutionary psychology has led to renewed interest in what might be the significant evolutionary heritage of people living today, and in the extent to which humans are suited to a particular adaptive environment—the EEA. The EEA, though, is a new tool in the battery of evolutionary concepts, and it is important both that it is scrutinized for its utility, and that the actual reconstructions of the environments in which humans and hominids evolved are based on sound palaeobiological inference and an appropriate use of the phylogenetic context of primate evolution.     

An evolutionary perspective on the kinome of malaria parasites

Malaria parasites belong to an ancient lineage that diverged very early from the main branch of eukaryotes. The approximately 90-member plasmodial kinome includes a majority of eukaryotic protein kinases that clearly cluster within the AGC, CMGC, TKL, CaMK and CK1 groups found in yeast, plants and mammals, testifying to the ancient ancestry of these families. However, several hundred millions years of independent evolution, and the specific pressures brought about by first a photosynthetic and then a parasitic lifestyle, led to the emergence of unique features in the plasmodial kinome. These include taxon-restricted kinase families, and unique peculiarities of individual enzymes even when they have homologues in other eukaryotes. Here, we merge essential aspects of all three malaria-related communications that were presented at the Evolution of Protein Phosphorylation meeting, and propose an integrated discussion of the specific features of the parasite's kinome and phosphoproteome.     

An evolutionary perspective on the regulation of carpel development

The carpel, or female reproductive organ enclosing the ovules, is one of the major evolutionary innovations of the flowering plants. The control of carpel development has been intensively studied in the model eudicot species Arabidopsis thaliana. This review traces the evolutionary history of genes involved in carpel development by surveying orthologous genes in taxa whose lineages separated from that of A. thaliana at different levels of the phylogenetic tree of the seed plants. Some aspects of the control of female reproductive development are conserved between the flowering plants and their sister group, the gymnosperms, indicating the presence of these in the common ancestor of the extant seeds plants, some 300 million years ago. Gene duplications that took place in the pre-angiosperm lineage, before the evolution of the first flowering plants, provided novel gene clades of potential importance for the origin of the carpel. Subsequent to the appearance of the first flowering plants, further gene duplications have led to sub-functionalization events, in which pre-existing reproductive functions were shared between paralogous gene clades. In some cases, fluidity in gene function is evident, leading to similar functions in carpel development being controlled by non-orthologous genes in different taxa. In other cases, gene duplication events have created sequences that evolved novel functions by the process of neo-functionalization, thereby generating biodiversity in carpel and fruit structures.     

An evolutionary perspective on the 'death hormone'hypothesis in plants

Many plants die after first reproduction, as if committing suicide, a phenomenon known as 'monocarpic senescence'. The process is different from the ageing seen in most animals. A 'death hormone'has been proposed to explain the phenomenon, both for plants and also separately for animals. This paper considers for plants whether and how such a death hormone could have evolved.
Monocarpic senescence has sometimes been attributed to starvation of the vegetative parts for photosynthate or mineral nutrients, by nutrient diversion to developing fruit. In this case, no evolutionary problem arises. In other cases, the phenomenon seems to be one of programmed senescence, since details of the process conflict with an explanation in terms of nutrient diversion, since there is apparently a hormonal senescence signal, and since, e.g., the same type of senescence occurs even in male plants that do not bear fruit.
A range of evolutionary mechanisms are considered, by which a death hormone could have evolved: species selection, kin selection, direct Darwinian selection, pleiotropy, functional correlation, orthogenesis, genetic drift and founder effects. The two most likely are identified as: (1) kin selection, in which the mother plant dies, and thus facilitates establishment of her offspring, and (2) selection for efficiency of assimilate mobilisation. Neither of these explanations seems completely satisfactory.     

An evolutionary perspective of biological invasions

The workshop on the Evolutionary Perspective of Biological Invasions in Terrestrial Ecosystems was held in Halle, Germany from 30 September to 3 October 2002.     

Inflammatory bowel disease requires the interplay between innate and adaptive immune signals

Inflammatory bowl disease （IBD） is a type 1 T helper cell （Th1）-mediated autoimmune disease. Various studies have revealed that environmental pathogens also play a significant role in the initiation and progression of this disease. Interestingly, the pathogenesis of IBD has been shown to be related to nitric oxide （NO） released from innate immune cells. Although NO is known to be highly toxic to the gut epithelia, there is very little information about the regulation of NO production, One major question in the etiology of IBD is how Thl cells and pathogens interact in the induction of IBD. In present study, we focused on the regulation of NO. We show that macrophages require both interferon-γ, （IFN-γ）-mediated and TLR4-mediated signals for the production of NO, which causes inflammation in the intestine and subsequently IBD. Thus, IBD is the result of concerted actions of innate immune signals, such as the binding of LPS to TLR-4, and adaptive immune signals, such as IFN-γ produced by Thl cells.     

Innate and adaptive immune proteins in the preen gland secretions of male house sparrows

Recent studies have demonstrated that preen oil acts to reduce or eliminate feather-associated bacteria. The mechanisms underlying this antibacterial activity, however, are incompletely understood. In addition to the activity of alcohols (i.e. 3,7-dimethyloctan-1-ol), recent research has suggested that antimicrobial peptides may underlie the antibacterial activity of preen oil. Here, we document the presence of innate and adaptive immune proteins, lysozyme and immunoglobulin Y (IgY), in the preen oil of house sparrows Passer domesticus. We suggest lysozyme functions as an antimicrobial agent, with potentially important impacts against Gram-positive feather degrading bacteria. Furthermore, both lysozyme and IgY likely act in local immune defence of the preen gland, and may also play a role in regulating the local microbiome, with potentially important consequences for chemical communication and signalling. Our findings suggest that the preen gland and its secretions should be considered an integral part of the body's first line of defence against invading infections.     

跨区域森林生态补偿的演化博弈分析——基于主体功能区的视角

新常态下,我国的森林生态环境承载力已经达到或接近上限,森林资源存在乱砍乱伐现象和林区政府监管乏力问题,究其根源是缺乏森林保护和补偿的驱动机制。在中央政府投入大量物力和财力的同时,其他利益相关主体却存在不同利益诉求和行为导向冲突,跨区域森林生态补偿难以实现,因此利用演化博弈模型厘清森林生态环境保护与补偿行动中保护主体、受益主体和中央政府的关系,有助于突破跨区域森林生态保护补偿困境,形成良好的行动机制。分析主体功能区利益群体逻辑关系的基础上,构建保护地区政府和受益地区政府的演化博弈模型,分别研究未引入"约束-激励"机制和引入"约束-激励"机制下的主体行为特征及其影响因素,剖析不同情形地方政府间的博弈决策行为。研究结果表明,在未引入中央政府"约束-激励"机制的情况下,跨区域生态补偿无法实现,保护地区政府会通过权衡保护森林资源收益和机会成本进行策略选择,当保护森林资源的净收益为正时,即使没有受益地区生态补偿,保护地区政府仍然有足够的激励保护森林资源,当保护森林资源的净收益为负时,两类政府群体容易陷入森林生态治理的"囚徒困境",而"约束-激励"机制的引入可以实现森林生态保护补偿的帕累托改进,通过中央政府惩罚、奖励金额的限制能够实现最优稳定均衡策略。