On the role of cross-immunity and vaccines on the survival of less fit flu-strains

A pathogen's route to survival involves various mechanisms including its ability to invade (host's susceptibility) and its reproductive success within an invaded host ("infectiousness"). The immunological history of an individual often plays an important role in reducing host susceptibility or it helps the host mount a faster immunological response de facto reducing infectiousness. The cross-immunity generated by prior infections to influenza A strains from the same subtype provide a significant example. The results of this paper are based on the analytical study of a two-strain epidemic model that incorporates host isolation (during primary infection) and cross-immunity to study the role of invasion mediated cross-immunity in a population where a precursor related strain (within the same subtype, i.e. H3N2, H1N1) has already become established. An uncertainty and sensitivity analysis is carried out on the ability of the invading strain to survive for given cross-immunity levels. Our findings indicate that it is possible to support coexistence even in the case when invading strains are "unfit", that is, when the basic reproduction number of the invading strain is less than one. However, such scenarios are possible only in the presence of isolation. That is, appropriate increments in isolation rates and weak cross-immunity can facilitate the survival of less fit strains. The development of "flu" vaccines that minimally enhance herd cross-immunity levels may, by increasing genotype diversity, help facilitate the generation and survival of novel strains.     

Hutchinson revisited: Patterns of density regulation and the coexistence of strong competitors

Ecologists have long been searching for mechanisms of species coexistence, particularly since G.E. Hutchinson raised the ‘paradox of the plankton’. A promising approach to solve this paradox and to explain the coexistence of many species with strong niche overlap is to consider over-compensatory density regulation with its ability to generate endogenous population fluctuations.Previous work has analysed the role of over-compensation in coexistence based on analytical approaches. Using a spatially explicit time-discrete simulation model, we systematically explore the dynamics and conditions for coexistence of two species. We go beyond the analytically accessible range of models by studying the whole range of density regulation from under- to very strong over-compensation and consider the impact of spatial structure and temporal disturbances. In particular, we investigate how coexistence can emerge in different types of population growth models.We show that two strong competitors are able to coexist if at least one species exhibits over-compensation. Analysing the time series of population dynamics reveals how the differential responses to density fluctuations of the two competitors lead to coexistence: The over-compensator generates density fluctuations but is the inferior competitor at strong amplitudes of those fluctuations; the competitor, therefore, becomes frequent and dampens the over-compensator's amplitudes, but it becomes inferior under dampened fluctuations.These species interactions cause a dynamic alternation of community states with long-term persistence of both species. We show that a variety of population growth models is able to reproduce this coexistence although the particular parameter ranges differ among the models. Spatial structure influences the probability of coexistence but coexistence is maintained for a broad range of dispersal parameters.The flexibility and robustness of coexistence through over-compensation emphasize the importance of nonlinear density dependence for species interactions, and they also highlight the potential of applying more flexible models than the classical Lotka-Volterra equations in community ecology.     

Coexistence in a competitive parasitoid-host system

The main objective of this work is to determine the conditions for coexistence and competitive exclusion in a discrete model for a community of three species: a stage-structured host and two competing parasitoids sharing the same host developmental stage. Coexistence of the community of the species is found to depend on the host life history parameters in the first place, and on competitive ability and parasitoid efficiency in the second place. In particular, parasitoids equilibrium densities are defined by the size of the refuge. Extinction is expected with low growth rate and with low adult survival. Host life histories are also associated with oscillations in population density, and depending on the combination of host adult survival from one generation to the next and host growth rate, the minimum of fluctuations approaches zero, implying a higher potential risk of extinction because of stochastic factors. Our results suggest that equally reduced survival of parasitoids in hosts parasitized by both species determines extinction of the parasitoid with lower population density, in contrast to the case when both parasitoids benefit with 50% of all doubly parasitized hosts, leading to the hypothesis that a community where competitors in multiparasitized hosts die, easily becomes extinct. Competitive exclusion is expected for highly asymmetric competitive interactions, independent of population densities, allowing us to hypothesize that coexistence of competitors in systems with limited resources and refuges is associated with a clearly defined competitive hierarchy.     

北美CHIHUAHUAN荒漠旗尾更格卢鼠(DIPODOMYS SPECTABILIS)的种群生态学

本文提供了1978—1985年美国亚利桑那州Chihuahuan荒漠旗尾更格卢鼠(Dipodomys spectabilis)种群的密度、体重、繁殖、扩散和寿命的标志重捕资料。较长的寿命、较重的体重、低繁殖力和喜巢行为标志着它的灵活的生活史,这种生活史使该鼠的种群密度适应荒漠环境的变化而变化。本文还比较了与旗尾更格卢鼠共同生活于同一地区的同属物种麦利阿姆更格卢鼠(Merriam's kangaroo rat, Dipodomys merriami)的生活史性状的差异,这些差异使这两个同属物种能利用不同资源或以不同方式利用相同资源,从而保证了它们的共同生存。     

An expanded modern coexistence theory for empirical applications

Understanding long‐term coexistence of numerous competing species is a longstanding challenge in ecology. Progress requires determining which processes and species differences are most important for coexistence when multiple processes operate and species differ in many ways. Modern coexistence theory (MCT), formalised by Chesson, holds out the promise of doing that, but empirical applications remain scarce. We argue that MCT's mathematical complexity and subtlety have obscured the simplicity and power of its underlying ideas and hindered applications. We present a general computational approach that extends our previous solution for the storage effect to all of standard MCT's spatial and temporal coexistence mechanisms, and also process‐defined mechanisms amenable to direct study such as resource partitioning, indirect competition, and life history trade‐offs. The main components are a method to partition population growth rates into contributions from different mechanisms and their interactions, and numerical calculations in which some mechanisms are removed and others retained. We illustrate how our approach handles features that have not been analysed in the standard framework through several case studies: competing diatom species under fluctuating temperature, plant–soil feedbacks in grasslands, facilitation in a beach grass community, and niche differences with independent effects on recruitment, survival and growth in sagebrush steppe.     

Recent advances in ecological stoichiometry: insights for population and community ecology

Conventional theories of population and community dynamics are based on a single currency such as number of individuals, biomass, carbon or energy. However, organisms are constructed of multiple elements and often require them (in particular carbon, phosphorus and nitrogen) in different ratios than provided by their resources; this mismatch may constrain the net transfer of energy and elements through trophic levels. Ecological stoichiometry, the study of the balance of elements in ecological processes, offers a framework for exploring ecological effects of such constraints. We review recent theoretical and empirical studies that have considered how stoichiometry may affect population and community dynamics. These studies show that stoichiometric constraints can affect several properties of populations (e.g. stability, oscillations, consumer extinction) and communities (e.g. coexistence of competitors, competitive interactions between different guilds). We highlight gaps in general knowledge and focus on areas of population and community ecology where incorporation of stoichiometric constraints may be particularly fruitful, such as studies of demographic bottlenecks, spatial processes, and multi-species interactions. Finally, we suggest promising directions for new research by recommending potential study systems (terrestrial insects, detritivory-based webs, soil communities) to improve our understanding of populations and communities. Our conclusion is that a better integration of stoichiometric principles and other theoretical approaches in ecology may allow for a richer understanding of both population and community structure and dynamics.     

Frequency-dependent community dynamics driven by sexual interactions

Research in community ecology has tended to focus on trophic interactions (e.g., predation, resource competition) as driving forces of community dynamics, and sexual interactions have often been overlooked. Here we discuss how sexual interactions can affect community dynamics, especially focusing on frequency-dependent dynamics of horizontal communities (i.e., communities of competing species in a single ecological guild). By combining mechanistic and phenomenological models of competition, we place sexual reproduction into the framework of modern coexistence theory. First, we review how population dynamics of two species competing for two resources can be represented by the Lotka–Volterra competition model as well as frequency dynamics, and how niche differentiation and overlap produce negative and positive frequency-dependence (i.e., stable coexistence and priority effect), respectively. Then, we explore two situations where sexual interactions change the frequency-dependence in community dynamics: (1) reproductive interference, that is, negative interspecific interactions due to incomplete species recognition in mating trials, can promote positive frequency-dependence and (2) density-dependent intraspecific adaptation load, that is, reduced population growth rates due to adaptation to intraspecific sexual (or social) interactions, produces negative frequency-dependence. We show how reproductive interference and density-dependent intraspecific adaptation load can decrease and increase niche differences in the framework of modern coexistence theory, respectively. Finally, we discuss future empirical and theoretical approaches for studying how sexual interactions and related phenomena (e.g., reproductive interference, intraspecific adaptation load, and sexual dimorphism) driven by sexual selection and conflict can affect community dynamics.     

Compensatory responses of vital rates attenuate impacts of competition on population growth and promote coexistence

Competition is among the most important factors regulating plant population and community dynamics, but we know little about how different vital rates respond to competition and jointly determine population growth and species coexistence. We conducted a field experiment and parameterised integral projection models to model the population growth of 14 herbaceous plant species in the absence and presence of neighbours across an elevation gradient (284 interspecific pairs). We found that suppressed individual growth and seedling establishment contributed the most to competition-induced declines in population growth, although vital rate contributions varied greatly between species and with elevation. In contrast, size-specific survival and flowering probability and seed production were frequently enhanced under competition. These compensatory vital rate responses were nearly ubiquitous (occurred in 92% of species pairs) and significantly reduced niche overlap and stabilised coexistence. Our study highlights the importance of demographic processes for regulating population and community dynamics, which has often been neglected by classic coexistence theories.     

Competitive exclusion and limiting similarity: a unified theory

Robustness of coexistence against changes of parameters is investigated in a model-independent manner by analyzing the feedback loop of population regulation. We define coexistence as a fixed point of the community dynamics with no population having zero size. It is demonstrated that the parameter range allowing coexistence shrinks and disappears when the Jacobian of the dynamics decreases to zero. A general notion of regulating factors/variables is introduced. For each population, its impact and sensitivity niches are defined as the differential impact on, and the differential sensitivity towards, the regulating variables, respectively. Either the similarity of the impact niches or the similarity of the sensitivity niches results in a small Jacobian and in a reduced likelihood of coexistence. For the case of a resource continuum, this result reduces to the usual "limited niche overlap" picture for both kinds of niche. As an extension of these ideas to the coexistence of infinitely many species, we demonstrate that Roughgarden's example for coexistence of a continuum of populations is structurally unstable.     

Comparative demographics of a Hawaiian forest bird community

Estimates of demographic parameters such as survival and reproductive success are critical for guiding management efforts focused on species of conservation concern. Unfortunately, reliable demographic parameters are difficult to obtain for any species, but especially for rare or endangered species. Here we derived estimates of adult survival and recruitment in a community of Hawaiian forest birds, including eight native species (of which three are endangered) and two introduced species at Hakalau Forest National Wildlife Refuge, Hawai?i. Integrated population models (IPM) were used to link mark–recapture data (1994–1999) with long‐term population surveys (1987–2008). To our knowledge, this is the first time that IPM have been used to characterize demographic parameters of a whole avian community, and provides important insights into the life history strategies of the community. The demographic data were used to test two hypotheses: 1) arthropod specialists, such as the ‘Akiapōlā‘au Hemignathus munroi, are ‘slower’ species characterized by a greater relative contribution of adult survival to population growth, i.e. lower fecundity and increased adult survival; and 2) a species’ susceptibility to environmental change, as reflected by its conservation status, can be predicted by its life history traits. We found that all species were characterized by a similar population growth rate around one, independently of conservation status, origin (native vs non‐native), feeding guild, or life history strategy (as measured by ‘slowness’), which suggested that the community had reached an equilibrium. However, such stable dynamics were achieved differently across feeding guilds, as demonstrated by a significant increase of adult survival and a significant decrease of recruitment along a gradient of increased insectivory, in support of hypothesis 1. Supporting our second hypothesis, we found that slower species were more vulnerable species at the global scale than faster ones. The possible causes and conservation implications of these patterns are discussed.     

A criterion for permanent coexistence of species,with an application to a two-prey one-predator system

The question of whether all species in a multispecies community governed by differential equations can persist for all time is one of the most important in theoretical ecology. However, criteria for this property vary widely, asymptotic stability and global asymptotic stability being two of the conditions most widely used. In fact neither of these criteria appears to reflect intuitive concepts of persistence in a satisfactory manner: the first because it is only a local condition, the second because it rules out cyclic behavior. We argue here that a more realistic criterion is that of “permanent coexistence,” which essentially requires that there should be a region separated from the boundary (corresponding to a zero value of the population of at least one species) which all orbits enter and remain within. A mathematical technique for establishing permanent coexistence is illustrated by an application to the long-standing problem of predator-mediated coexistence in a two-prey one-predator community.     

Dynamic process,spatial pattern and species coexistence in plants

The significance of dynamic processes of individual genets/ramets for the spatial pattern of plant species and community structure is discussed. It is suggested that under a different mode of competition (symmetric vs. asymmetric), spatial distribution of individuals, initial size distribution at the establishment stage and boundary conditions as recruitment influence differently the species coexistence pattern. It is therefore important to consider the mode of competition for the study of community structure. To know the mode and degree of intra- and interspecific competition, the dynamic processes of individual genets/ramets must be studied by following the growth, mortality and recruitment of each genet/ramet of each component species in a plant community. The models and methods of plant population ecology are therefore useful also for plant community ecology.     

Mutualism in a community context: the positive feedback between an ant–aphid mutualism and a gall-making midge

Although mutualisms are widespread and often described in natural history accounts, their ecological influences on other community members remain largely unexplored. Many of these influences are likely a result of indirect effects. In this field study, we investigated the indirect effects of an ant–aphid mutualism on the abundance, survival rates and parasitism rates of a co-occurring herbivore. Rabdophaga salicisbrassicoides (Diptera: Cecidomyiidae) induces rosette galls on the developing shoots of Salix exigua trees, and populations can reach outbreak densities (up to 1,000 galls/stem) in central Washington State (USA). Ant-tended aphids feed on these same stems and often feed on gall tissue. In this study we used a combination of manipulative experiments and observational surveys to test the hypothesis that the abundances of aphids, ants, and galls have positive and reciprocal effects on one another, in a manner that would create a positive feedback loop in population growth. In addition, we examined whether the combined presence of ants and aphids reduces parasitism rates for the gallers. In support of the positive feedback loop hypothesis, aphids enjoyed higher population growth rates in the presence of ants and galls, the presence of ants and aphids resulted in increased abundance of galls, and the abundances of ants, aphids and galls were all positively correlated with one another. However, the mechanism underlying the positive effect of ants and aphids on galler density remains unknown, as the mutualism did not affect parasitism rates. More broadly, this study demonstrates that mutualisms can have significant and complex indirect effects on community and population ecology.     

Relative Importance of Vital Rates to Population Dynamics of Wood Ducks

The wood duck (Aix sponsa) is a common and important cavity-nesting duck in North America; however, we know very little about how changes in vital rates influence population growth rate (λ). We used estimates of fertility and survival of female wood ducks from our nest-box studies in South Carolina, Alabama, and Georgia, USA, to create a stage-based matrix population model. We conducted perturbation analyses and ranked elasticity values to examine the relative importance of 17 component vital rates to λ. Female survival is influenced by nest success, so we recognized this female heterogeneity in our analyses. Four vital rates showed the greatest importance to λ. Analytic elasticities were greatest for breeding season and nonbreeding season survival of females that nested successfully, followed by nest success and female recruitment to the breeding population. Differences in female quality were important to λ. Next, we used process variation of vital rates and conducted life-stage simulation analyses (LSA) followed by variance decomposition to determine the amount of variation in λ explained by each vital rate. Female recruitment to the breeding population explained 57.7% of the variation in λ followed by nest success (11.4%), and breeding and nonbreeding season survival of females that nested successfully (9.3% and 9.4%, respectively). Together these 4 vital rates explained 88% of the variation in λ. Mean asymptotic population growth rate (λ = 0.80 ± 0.08 [SD]) from LSA revealed a declining population. Recruitment of females hatched from nest boxes was insufficient to sustain the nest-box population. However, including yearling (SY) females that were produced outside of nest boxes (i.e., immigrants) increased recruitment rates 1.5 to 2 times more than when only SY females recruited from nest boxes were included. Future research that examines how emigration and immigration interact with survival and reproduction to influence local population dynamics of wood ducks will be important for identifying the value of nest-box programs to wood duck conservation and management. © 2019 The Wildlife Society.     

The role of pollen limitation on the coexistence of two dioecious, wind-pollinated, closely related shrubs in a fluctuating environment

Elucidating the mechanisms of species coexistence is a crucial goal in ecology. Theory suggests that, when resource abundance fluctuates, coexistence can be achieved if each species in a competing pair is better at exploiting resources at opposite extremes of a fluctuating resource spectrum. Nonetheless, the proximal mechanisms allowing coexistence remain largely unexplored. In a previous paper, we showed that the coexistence of two Atriplex species was facilitated by their varying demographic response (in survival, growth and recruitment) to fluctuation in water availability. Here we explore the effect of spatial distribution, and pollen and resource limitation on the reproductive success (production of viable seeds) of the same two species. An analysis of their spatial distribution showed that Atriplex acanthocarpa had a clumped distribution, which is thought to increase the effectiveness of pollination in wind-pollinated plants, while Atriplex canescens had a random distribution, a pattern expected to restrict wind-pollination success. A pollen and resource (water and nutrients) addition experiment implemented through a repeated-measures design demonstrated that seed viability of A. canescens was both pollen and resource limited, but that these effects were negligible in A. acanthocarpa. Under natural conditions, pollen limitation restricted seed number in A. canescens to only one-third of that recorded when manual pollination was performed. By decreasing its fecundity (and consequent potential seedling recruitment), pollen limitation reverses the competitive advantage of A. canescens over A. acanthocarpa when the limiting resource (water) is abundant and seedling recruitment takes place. To our knowledge, our study of this congeneric pair in the Chihuahuan Desert is the first to document a link between pollen limitation and species coexistence.     

Diversity of biological rhythm and food web stability

How ecosystem biodiversity is maintained remains a persistent question in the field of ecology. Here, I present a new coexistence theory, i.e. diversity of biological rhythm. Circadian, circalunar and circannual rhythms, which control short- and long-term activities, are identified as universal phenomena in organisms. Analysis of a theoretical food web with diel, monthly and annual cycles in foraging activity for each organism shows that diverse biological cycles play key roles in maintaining complex communities. Each biological rhythm does not have a strong stabilizing effect independently but enhances community persistence when combined with other rhythms. Biological rhythms also mitigate inherent destabilization tendencies caused by food web complexity. Temporal weak interactions due to hybridity of multiple activity cycles play a key role toward coexistence. Polyrhythmic changes in biological activities in response to the Earth''s rotation may be a key factor in maintaining biological communities.     

鼎湖山南亚热带常绿阔叶林不同树种存活对邻体组成的响应差异

理解群落结构和动态的主导机制是生态学研究的基本目标之一。群落内树种的存活受到其邻近树木的显著影响。为探究不同树种的存活对邻体组成的响应差异, 本研究基于鼎湖山南亚热带阔叶林20 ha森林动态监测样地中常见的90个树种的存活监测数据和功能性状数据, 建立了一系列关于邻体效应的树种存活模型。结果表明: 约58%的树种存活对邻体组成有敏感的响应, 共存树种间的功能性状差异影响着50%的树种存活动态。不同树种对邻体组成的响应差异与其耐阴性相关, 耐阴能力较弱的树种更倾向于表现出对邻体的敏感性。低比叶面积、高叶干物质含量、木材密度和最大胸径意味着较强的耐阴能力, 与光资源利用策略有关的生态位分化可能是邻域尺度上物种共存的原因。本研究为量化邻体间的相互作用和解释局域群落的物种共存提供了新的视角。     

Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

To completely understand the ecology of a bacterial community, we need to identify its ecologically distinct populations (ecotypes). The greatest promise for enumerating a community's constituent ecotypes is held by molecular approaches that identify bacterial ecotypes as DNA sequence clusters. These approaches succeed when ecotypes correspond with sequence clusters, but some models of bacterial speciation predict a one-to-many and others a many-to-one relationship between ecotypes and sequence clusters. A further challenge is that sequence-based phylogenies often contain a hierarchy of clusters and subclusters within clusters, and there is no widely accepted theory to guide systematists and ecologists to the size of cluster most likely to correspond to ecotypes. While present systematics attempts to use universal thresholds of sequence divergence to help demarcate species, the recently developed 'community phylogeny' approach assumes no universal thresholds, but demarcates ecotypes based on the analysis of a lineage's evolutionary dynamics. Theory-based approaches like this one can give a conceptual framework as well as operational criteria for hypothesizing the identity and membership of ecotypes from sequence data; ecology-based approaches can then confirm that the putative ecotypes are actually ecologically distinct. Bacterial ecotypes that are demonstrated to have a history of coexistence as ecologically distinct lineages (based on sequence analysis) and as a prognosis of future coexistence (based on ecological differences), are the fundamental units of bacterial ecology and evolution, and should be recognized by bacterial systematics.     

Sexual reproduction and diversity: Connection between sexual selection and biological communities via population dynamics

Sexual reproduction is a mysterious phenomenon. Most animals and plants invest in sexual reproduction, even though it is more costly than asexual reproduction. Theoretical studies suggest that occasional or conditional use of sexual reproduction, involving facultative switching between sexual and asexual reproduction, is the optimal reproductive strategy. However, obligate sexual reproduction is common in nature. Recent studies suggest that the evolution of facultative sexual reproduction is prevented by males that coerce females into sexual fertilization; thus, sexual reproduction has the potential to enforce costs on a given species. Here, the effect of sex on biodiversity is explored by evaluating the reproductive costs arising from sex. Sex provides atypical selection pressure that favors traits that increase fertilization success, even at the expense of population growth rates, that is, sexual selection. The strength of sexual selection depends on the density of a given species. Sexual selection often causes strong negative effects on the population growth rates of species that occur at high density. Conversely, a species that reduces its density is released from this negative effect, and so increases its growth rate. Thus, this negative density-dependent effect on population growth that arises from sexual selection could be used to rescue endangered species from extinction, prevent the overgrowth of common species and promote the coexistence of competitive species. Recent publications on sexual reproduction provide several predictions related to the evolution of reproductive strategies, which is an important step toward integrating evolutionary dynamics, demographic dynamics and community dynamics.