Twelve fundamental life histories evolving through allocation‐dependent fecundity and survival

An organism's life history is closely interlinked with its allocation of energy between growth and reproduction at different life stages. Theoretical models have established that diminishing returns from reproductive investment promote strategies with simultaneous investment into growth and reproduction (indeterminate growth) over strategies with distinct phases of growth and reproduction (determinate growth). We extend this traditional, binary classification by showing that allocation‐dependent fecundity and mortality rates allow for a large diversity of optimal allocation schedules. By analyzing a model of organisms that allocate energy between growth and reproduction, we find twelve types of optimal allocation schedules, differing qualitatively in how reproductive allocation increases with body mass. These twelve optimal allocation schedules include types with different combinations of continuous and discontinuous increase in reproduction allocation, in which phases of continuous increase can be decelerating or accelerating. We furthermore investigate how this variation influences growth curves and the expected maximum life span and body size. Our study thus reveals new links between eco‐physiological constraints and life‐history evolution and underscores how allocation‐dependent fitness components may underlie biological diversity.     

Diversity in times of adversity: probabilistic strategies in microbial survival games

Population diversification strategies are ubiquitous among microbes, encompassing random phase-variation (RPV) of pathogenic bacteria, viral latency as observed in some bacteriophage and HIV, and the non-genetic diversity of bacterial stress responses. Precise conditions under which these diversification strategies confer an advantage have not been well defined. We develop a model of population growth conditioned on dynamical environmental and cellular states. Transitions among cellular states, in turn, may be biased by possibly noisy readings of the environment from cellular sensors. For various types of environmental dynamics and cellular sensor capability, we apply game-theoretic analysis to derive the evolutionarily stable strategy (ESS) for an organism and determine when that strategy is diversification. We find that: (1) RPV, effecting a sort of Parrondo paradox wherein random alternations between losing strategies produce a winning strategy, is selected when transitions between different selective environments cannot be sensed, (2) optimal RPV cell switching rates are a function of environmental lifecycle asymmetries and environmental autocorrelation, (3) probabilistic diversification upon entering a new environment is selected when sensors can detect environmental transitions but have poor precision in identifying new environments, and (4) in the presence of excess additive noise, low-pass filtering is required for evolutionary stability. We show that even when RPV is not the ESS, it may minimize growth rate variance and the risk of extinction due to 'unlucky' environmental dynamics.     

The ideal free distribution: a review and synthesis of the game-theoretic perspective

The Ideal Free Distribution (IFD), introduced by Fretwell and Lucas in [Fretwell, D.S., Lucas, H.L., 1970. On territorial behavior and other factors influencing habitat distribution in birds. Acta Biotheoretica 19, 16-32] to predict how a single species will distribute itself among several patches, is often cited as an example of an evolutionarily stable strategy (ESS). By defining the strategies and payoffs for habitat selection, this article puts the IFD concept in a more general game-theoretic setting of the “habitat selection game”. Within this game-theoretic framework, the article focuses on recent progress in the following directions: (1) studying evolutionarily stable dispersal rates and corresponding dispersal dynamics; (2) extending the concept when population numbers are not fixed but undergo population dynamics; (3) generalizing the IFD to multiple species.For a single species, the article briefly reviews existing results. It also develops a new perspective for Parker’s matching principle, showing that this can be viewed as the IFD of the habitat selection game that models consumer behavior in several resource patches and analyzing complications involved when the model includes resource dynamics as well. For two species, the article first demonstrates that the connection between IFD and ESS is now more delicate by pointing out pitfalls that arise when applying several existing game-theoretic approaches to these habitat selection games. However, by providing a new detailed analysis of dispersal dynamics for predator-prey or competitive interactions in two habitats, it also pinpoints one approach that shows much promise in this general setting, the so-called “two-species ESS”. The consequences of this concept are shown to be related to recent studies of population dynamics combined with individual dispersal and are explored for more species or more patches.     

Microfragmentation concept explains non-positive environmental heterogeneity–diversity relationships

Although recent studies have revealed that the relationship between diversity and environmental heterogeneity is not always positive, as classical niche theory predicts, scientists have had difficulty interpreting these results from an ecological perspective. We propose a new concept—microfragmentation—to explain how small-scale heterogeneity can have neutral or even negative effect on species diversity. We define microfragmentation as a community level process of splitting habitat into a more heterogeneous environment that can have non-positive effects on the diversity through habitat loss and subsequent isolation. We provide support for the microfragmentation concept with results from spatially explicit heterogeneity–diversity model simulations, in which varying sets of species (with different ratios of specialist and generalist species) were modeled at different levels of configurational heterogeneity (meaning that only the habitat structure was changed, not its composition). Our results indicate that environmental heterogeneity can affect community diversity in the same way as fragmentation at the landscape level. Although generalist species might not be seriously affected by microfragmentation, the persistence of specialist species can be seriously disturbed by small-scale patchiness. The microfragmentation concept provides new insight into community level diversity dynamics and can influence conservation and management strategies.     

Evolution of pathogen virulence: the role of variation in host phenotype

Selection on pathogens tends to favour the evolution of growth and reproductive rates and a concomitant level of virulence (damage done to the host) that maximizes pathogen fitness. Yet, because hosts often pose varying selective environments to pathogens, one level of virulence may not be appropriate for all host types. Indeed, if a level of virulence confers high fitness to the pathogen in one host phenotype but low fitness in another host phenotype, alternative virulence strategies may be maintained in the pathogen population. Such strategies can occur either as polymorphism, where different strains of pathogen evolve specialized virulence strategies in different host phenotypes or as polyphenism, where pathogens facultatively express alternative virulence strategies depending on host phenotype. Polymorphism potentially leads to specialist pathogens capable of infecting a limited range of host phenotypes, whereas polyphenism potentially leads to generalist pathogens capable of infecting a wider range of hosts. Evaluating how variation among hosts affects virulence evolution can provide insight into pathogen diversity and is critical in determining how host pathogen interactions affect the phenotypic evolution of both hosts and pathogens.     

Functional diversity: back to basics and looking forward

Functional diversity is a component of biodiversity that generally concerns the range of things that organisms do in communities and ecosystems. Here, we review how functional diversity can explain and predict the impact of organisms on ecosystems and thereby provide a mechanistic link between the two. Critical points in developing predictive measures of functional diversity are the choice of functional traits with which organisms are distinguished, how the diversity of that trait information is summarized into a measure of functional diversity, and that the measures of functional diversity are validated through quantitative analyses and experimental tests. There is a vast amount of trait information available for plant species and a substantial amount for animals. Choosing which traits to include in a particular measure of functional diversity will depend on the specific aims of a particular study. Quantitative methods for choosing traits and for assigning weighting to traits are being developed, but need much more work before we can be confident about trait choice. The number of ways of measuring functional diversity is growing rapidly. We divide them into four main groups. The first, the number of functional groups or types, has significant problems and researchers are more frequently using measures that do not require species to be grouped. Of these, some measure diversity by summarizing distances between species in trait space, some by estimating the size of the dendrogram required to describe the difference, and some include information about species' abundances. We show some new and important differences between these, as well as what they indicate about the responses of assemblages to loss of individuals. There is good experimental and analytical evidence that functional diversity can provide a link between organisms and ecosystems but greater validation of measures is required. We suggest that non-significant results have a range of alternate explanations that do not necessarily contradict positive effects of functional diversity. Finally, we suggest areas for development of techniques used to measure functional diversity, highlight some exciting questions that are being addressed using ideas about functional diversity, and suggest some directions for novel research.     

Habitat size and number in multi-habitat landscapes: a model approach based on species-area curves

This paper discusses species diversity in simple multi-habitat environments. Its main purpose is to present simple mathematical and graphical models on how landscape patterns affect species numbers. The idea is to build models of species diversity in multi-habitat landscapes by combining species-area curves for different habitats. Predictions are made about how variables such as species richness and species overlap between habitats influence the proportion of the total landscape each habitat should constitute, and how many habitats it should be divided into in order to be able to sustain the maximal number of species. Habitat size and numbers are the only factors discussed here, not habitat spatial patterns. Among the predictions are: 1) where there are differences in species diversity between habitats, optimal landscape patterns contain larger proportions of species rich habitats. 2) Species overlap between habitats shifts the optimum further towards larger proportions of species rich habitat types. 3) Species overlap also shifts the optimum towards fewer habitat types. 4) Species diversity in landscapes with large species overlap is more resistant to changes in landscape (or reserve) size. This type of model approach can produce theories useful to nature and landscape management in general, and the design of nature reserves and national parks in particular.     

Mating games: the evolution of human mating transactions

We propose a new, evolutionary, game-theoretic model of conditionalhuman mating strategies that integrates currently disconnectedbodies of data into a single mathematically-explicit theoryof human mating transactions. The model focuses on the problemof how much resource a male must provide to a female to secureand retain her as a mate. By using bidding-game models, we showhow the male's minimally required resource incentive variesas a function of his own mate value, the value of the female,and the distribution of the mate values of their available alternativemates. The resulting theory parsimoniously accounts for strategicpluralism within the sexes, mate choice differences betweenthe sexes, and assortative mating, while generating a rich setof testable new predictions about human mating behavior.     

Effects of habitat simplification on assemblages of cavity nesting bees and wasps in a semiarid neotropical conservation area

Habitat complexity is directly correlated to insect diversity in most natural environments. Structural complexity reflects an increase in vertical stratification and plant diversity and often leads to a greater availability of floral resources and nesting sites. Efficient conservation strategies require understanding of how changes in habitat structure affect insects that provide essential ecosystem services. We analyzed how the diversity and species composition of bees and wasps that nest in pre-existing cavities is affected by habitat complexity. Our study was developed in the semiarid region of northeastern Brazil, in the Ubajara National Park and surrounding area. Four types of habitats within two physiognomies were sampled for two consecutive years. We used 120 trap-nest (9000 cavities) distributed in 40 sample points. Overall, 657 cavities were occupied by 11 species of bees, nine of wasps, and six of cleptoparasitic/parasitoids. Bees and wasp diversity increases with habitat complexity. While species richness was higher in more complex physiognomies, abundance was higher in disturbed areas. Species composition also varied with habitat structure. Habitat simplification has adverse effects on the diversity and composition of assemblages. These effects are stronger in more complex habitats indicating that conservation of humid habitats within semiarid areas is essential to maintain bee and wasp regional diversity.     

Finding spatial regularity in mosaic landscapes: two methods integrated

Two methods were employed to find spatial regularity in a complicated mountain landscape of Beijing, China on the basis of functional and structural affinities. The first approach applied Affinity Analysis based on species composition to landscape. The mosaic diversity of the landscape was 3.5298>3, which means the study landscape is complex and controlled by multiple environmental gradients. These landscape types were divided into 3 parts according to the mean affinity values of 0.2143 and 0.7857 (0.5±1 SD). Modal sites are the central types of the landscape, which include a zonal broad-leaved forest of the region and a conifer plantation replacing the former. Outliers are found in the highest altitude and the lowest, both have few species in common with the above two modal types. The remaining landscape types are intermediate sites, which are transitional between modals and outliers, broadly distributed throughout mountain environments. Neighbor types have more species in common than those more widely separated, which probably distributed adjacently in space or in similar quality habitat. The other method employed is the new TWINSPAN analysis by substituting spatial neighboring data of landscape types for species composition data. It clearly divided the landscape types into three groups, i.e., subalpine, middle and low mountain groups, which were correlated with altitude, as well as influenced by human disturbance. The new TWINSPAN classification method is more reliable in finding spatial gradient of patchy landscapes than affinity analysis; however, affinity analysis is useful in finding species diversity pattern and the importance of landscape types in a region. Integrating advantages of the two methods could supply complete and reliable information on how landscape types are distributed in space, which environmental gradient dominates the spatial distribution of the landscape types, as well as where important and unusual types are located.     

Explaining diversity of livestock-farming management strategies of multiple-job holders: importance of level of production objectives and role of farming in the household

We characterised the livestock-farming management strategies of multiple-job holders and identified which variables contributed most to the differentiation of these strategies. We hypothesised that they would mainly be differentiated by the contribution of the farming income to the total household income and the availability of the household members for farming. The multiple-job holding livestock-farmer's motivations, decisions and actions about both multiple-job holding and livestock farming were obtained in semi-directed interviews of 35 sheep farmers who held multiple jobs, on farm and off farm. They were synthesised into six variables characterising the diversity of the livestock-farming objectives and management guidelines. Thanks to a multiple factorial analysis, we showed that the diversity of the sheep-farming management strategies of multiple-job holders was better explained by two factors 'level of motivation of the farmer to get high technical results' and 'more personal fulfilling v. the family business conception of farming', than the factors we hypothesised. Within our sample, the performances ranged from 0.7 to 1.4 weaned lambs per ewe per year. Six sheep-farming management strategies were identified. They illustrated the importance of the level of production objectives and of farming income expectation, which were found to be independent, in explaining diversity. No direct relationship between farm work organisation and sheep-farming management strategy was identified. Explaining the diversity of the livestock-farming management strategies of multiple-job holders appears to require that all the benefits expected from farming and their hierarchy be identified before analysing how they are translated into production objectives and management guidelines.     

村落文化林与非文化林多尺度物种多样性加性分配

文化林是指村民按照文化传统、风俗习惯或宗教信仰自觉保护和管理的森林,具有一定社会文化功能。目前国内外对文化林物种多样性研究主要为定性描述,缺乏对文化林和非文化林生物多样性的定量比较及差异来源分析。利用物种多样性加性分配方法,将总的Gamma 多样性分成样格内的Alpha多样性以及样格间、样方间和林型间Beta多样性,对中国亚热带地区3个村落文化林的乔木层、灌木层、草本层和藤本层进行物种多样性的多尺度分析。调查发现:(1)文化林共有维管束植物296种,以苦槠,樟和米槠为优势种,非文化林共有维管束植物189种,以杉木、马尾松和毛竹为优势种。文化林乔木层和灌木层物种数显著高于非文化林,草本层和藤本层物种数差异不显著。(2)Beta多样性随尺度增大而增加,林型间Beta多样性最高,占区域总Gamma多样性的41.9%-62.8%,其次是样方间Beta多样性(18.6%-31.9%),对区域多样性贡献最小为样格内Alpha和样格间Beta多样性。(3)林型间的多样性对区域物种多样性的贡献中,文化林占主导作用,乔木层占54.4%-81.0%,灌木层占51.2%-60.2%,草本层占42.9%-64.1%,藤本层占49.9%-62.2%。(4) 物种累积-面积曲线表明,在各个尺度上,文化林物种多样性始终高于非文化林,从而在相同面积下保护了更多的物种。加性分配模型在多个空间尺度上阐明了Alpha和Beta多样性的变化,突出了文化林对区域物种多样性的贡献,对保护对象和保护范围的决策以及生物多样性的保护与恢复具有重要意义。     

Strategies to protect biological diversity and the evolutionary processes that sustain it

Conservation planning has tended to focus more on pattern (representation) than process (persistence) and, for the former, has emphasized species and ecosystem or community diversity over genetic diversity. Here I consider how best to incorporate knowledge of evolutionary processes and the distribution of genetic diversity into conservation planning and priority setting for populations within species and for biogeographic areas within regions. Separation of genetic diversity into two dimensions, one concerned with adaptive variation and the other with neutral divergence caused by isolation, highlights different evolutionary processes and suggests alternative strategies for conservation. Planning for both species and areas should emphasize protection of historically isolated lineages (Evolutionarily Significant Units) because these cannot be recovered. By contrast, adaptive features may best be protected by maintaining the context for selection, heterogeneous landscapes, and viable populations, rather than protecting specific phenotypes. A useful strategy may be to (1) identify areas that are important to represent species and (vicariant) genetic diversity and (2) maximize within these areas the protection of contiguous environmental gradients across which selection and migration can interact to maintain population viability and (adaptive) genetic diversity. These concepts are illustrated with recent results from analysis of a rainforest fauna from northeast Australia.     

The grammaticalization cycle of the progressive

A well-attested phenomenon in morpho-semantic change is known as the progressive cycle, which depicts a directed and cyclic pathway of a grammatical progressive marker through its emergence and disappearance inside the imperfective domain. Deo (2015) offers a model within the framework of evolutionary game theory to study the evolutionary dynamics of four preselected types of progressive-imperfective grammars. Based on her basic game-theoretic model, we investigate which types of grammars would emerge from the first principles in a population of agents under reinforcement learning. In our computational model, the actual progressive-imperfective cycle can be reconstructed from such atomic interactions between learner agents after the addition of several simple assumptions to the basic game-theoretic model.     

A consistent terminology for quantifying species diversity? Yes, it does exist

The prevailing terminological confusion around the concept ‘diversity’ has hampered accurate communication and caused diversity issues to appear unnecessarily complicated. In fact, a consistent terminology for phenomena related to (species) diversity is already available. When this terminology is adhered to, diversity emerges as an easily understood concept. It is important to differentiate between diversity itself and a diversity index: an index of something is just a surrogate for the thing itself. The conceptual problem of defining diversity also has to be separated from the practical problem of deciding how to adequately quantify diversity for a community of interest. In practice, diversity can be quantified for any dataset where units of observation (such as individuals) have been classified into types (such as species). All that needs to be known is what proportion of the observed units belong to a type of mean abundance. Diversity equals the inverse of this mean, and it quantifies the effective number of the types of interest. In ecology, interest often (but not always) focuses on species diversity. If the dataset consists of (or gets divided into) subunits, then the total effective number of species (gamma diversity) can be partitioned into the effective number of compositionally distinct subunits (beta diversity) and the mean effective number of species per such subunit (alpha diversity). Species richness is related to species diversity, but they are not the same thing; richness does not take the proportional abundances into account and is therefore the actual—rather than the effective—number of types. Most of the phenomena that have been called ‘beta diversity’ in the past do not quantify an effective number of types, so they should be referred to by names other than ‘diversity’ (for example, species turnover or differentiation).     

Thermodynamic constraints on the assembly and diversity of microbial ecosystems are different near to and far from equilibrium

Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. However, most of this interest has focused on developing coarse ecosystem-level maximisation principles, providing little insight into underlying mechanisms that lead to such emergent constraints. Microbial communities are a natural system to decipher this mechanistic basis because their interactions in the form of substrate consumption, metabolite production, and cross-feeding can be described explicitly in thermodynamic terms. Previous work has considered how thermodynamic constraints impact competition between pairs of species, but restrained from analysing how this manifests in complex dynamical systems. To address this gap, we develop a thermodynamic microbial community model with fully reversible reaction kinetics, which allows direct consideration of free-energy dissipation. This also allows species to interact via products rather than just substrates, increasing the dynamical complexity, and allowing a more nuanced classification of interaction types to emerge. Using this model, we find that community diversity increases with substrate lability, because greater free-energy availability allows for faster generation of niches. Thus, more niches are generated in the time frame of community establishment, leading to higher final species diversity. We also find that allowing species to make use of near-to-equilibrium reactions increases diversity in a low free-energy regime. In such a regime, two new thermodynamic interaction types that we identify here reach comparable strengths to the conventional (competition and facilitation) types, emphasising the key role that thermodynamics plays in community dynamics. Our results suggest that accounting for realistic thermodynamic constraints is vital for understanding the dynamics of real-world microbial communities.     

Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design

Combinatorial sequence optimization for protein design requires libraries of discrete side-chain conformations. The discreteness of these libraries is problematic, particularly for long, polar side chains, since favorable interactions can be missed. Previously, an approach to loop remodeling where protein backbone movement is directed by side-chain rotamers predicted to form interactions previously observed in native complexes (termed "motifs") was described. Here, we show how such motif libraries can be incorporated into combinatorial sequence optimization protocols and improve native complex recapitulation. Guided by the motif rotamer searches, we made improvements to the underlying energy function, increasing recapitulation of native interactions. To further test the methods, we carried out a comprehensive experimental scan of amino acid preferences in the I-AniI protein-DNA interface and found that many positions tolerated multiple amino acids. This sequence plasticity is not observed in the computational results because of the fixed-backbone approximation of the model. We improved modeling of this diversity by introducing DNA flexibility and reducing the convergence of the simulated annealing algorithm that drives the design process. In addition to serving as a benchmark, this extensive experimental data set provides insight into the types of interactions essential to maintain the function of this potential gene therapy reagent.     

Predators alter the scaling of diversity in prey metacommunities

Although predator effects on the number of locally coexisting species are well understood, there are few formal predictions of how these local predator effects influence patterns of prey diversity at larger spatial scales. Building on the theory of island biogeography, we develop a simple model that describes how predators can alter the scaling of diversity in prey metacommunities and compares the effects of generalist and specialist predators on regional prey diversity. Generalist predators, which consume prey randomly with respect to species identity, are predicted to reduce α‐diversity and increase β‐diversity thereby maintaining regional diversity (γ‐diversity). Alternatively, specialist predators, which filter out prey species intolerant of predators, are predicted to reduce bothα‐diversity andβ‐diversity by causing the same prey species to be extirpated in each locality, resulting in regional prey species extinctions and lower γ‐diversity. These distinct effects of generalist and specialist predators on prey diversity at different spatial scales are uniquely shaped by the extent of predation within those metacommunities. Overall, our model results make general predictions for how different types of predators can differentially affect prey diversity across spatial scales, allowing a more complete understanding of the possible implications of predator eradications or introductions for biodiversity.     

Combinatorial chemistry,automation and molecular diversity: new trends in the pharmaceutical industry

Combinatorial chemistry has emerged as a set of novel strategies for the synthesis of large sets of compounds (combinatorial libraries) for biological evaluation. Within a few years combinatorial chemistry has undergone a series of changes in trends, which are closely related to two important factors in libraries: numbers and quality. While the number of compounds in a library may be easily expressed, it is a lot more difficult to indicate the degree of quality of a library. This degree of quality can be split into two aspects : purity and diversity. The changing trends in combinatorial chemistry with respect to the strategies, the technologies, the libraries themselves (numbers and purity aspects) and the molecular diversity are outlined in this paper.     

A General Scheme to Predict Partner Control Mechanisms in Pairwise Cooperative Interactions Between Unrelated Individuals

Recent years have seen an explosion in the diversity of partner control mechanisms hypothesised to stabilise cooperative behaviour among unrelated individuals. Game theory suggests numerous strategies, each with specific decision rules that allow cooperators to control a non‐contributing partner. This diversity of hypothetical strategies seems likely to reflect diversity in the types of intraspecific cooperation and interspecific mutualism that exist in nature. It is therefore important to provide a framework that explains similarities and differences between the various hypothetical strategies and that predicts how key parameters that describe the natural history of natural systems favour different control mechanisms. We develop a novel unifying framework for pairwise interactions between unrelated individuals, in which we link specific control mechanisms to specific game structures. The latter are defined by unique combinations of the states of five parameters that describe investment, aspects of the payoff matrix, the number of interactions and partner choice. We find that specific control mechanisms potentially have utility in a limited number of game structures; conversely, each game structure may typically offer a few competing control mechanisms. Our framework offers theoreticians specific problems that await mathematical exploration, while at the same time offering empiricists guidelines for evaluating the game structure and corresponding control mechanisms in their systems.