Reconciling niche and neutrality through the Emergent Group approach

Both niche and neutral theories have been suggested as potential frameworks for modelling biodiversity. Niche models assume that biological traits represent evolutionary adaptations and define individuals in terms of functional trade-offs. Neutral models assume that all individuals at a single trophic level are functionally equivalent on a per capita basis with respect to their birth, death, dispersal and speciation. The opinion of many researchers is that neutral and niche processes operate simultaneously to generate diversity without knowing how the unification of both models can be achieved. Recently, several theoretical papers have reported evidence on the evolutionary emergence of niche structures shaping the emergence of groups of similar species. In this way, an Emergent Group is defined as a set of species that have a similar functional niche owing to a convergent ecological strategy. Central to the Emergent Group concept are the assumptions of functional equivalence within and of functional divergence between Emergent Groups. Within an Emergent Group, species richness is subject to a zero-sum rule set by the balance between the rate of individual loss and of immigration. Between Emergent Groups, tradeoffs such as seed size/seedling competitivity, investment in reproductive system/investment in vegetative systems or competitive ability/predator invulnerability are cornerstones of the evolutionary divergence. Delineating Emergent Groups amounts to reaching a compromise between maximizing niche differentiation (i.e. maximizing differences in functional tradeoffs) between Emergent Groups and maximizing neutrality within Emergent Groups. Up to now, the Emergent Group concept has been mostly proposed by theoretical scientists but it should be tested by empirical ecologists. The way in which niche and neutral models could be combined provides a profitable opportunity for theoretical and empirical scientists to collaborate fruitfully.     

The impact of neutrality, niche differentiation and species input on diversity and abundance distributions

We present a spatially-explicit generalization of Hubbell's model of community dynamics in which the assumption of neutrality is relaxed by incorporating dispersal limitation and habitat preference. In simulations, diversity and species abundances were governed by the rate at which new species were introduced (usually called 'speciation') and nearly unaffected by dispersal limitation and habitat preference. Of course, in the absence of species input, diversity is maintained solely by niche differences. We conclude that the success of the neutral model in predicting the abundance distribution has nothing to do with neutrality, but rather with the species-introduction process: when new species enter a community regularly as singletons, the typical J-shaped abundance distribution, with a long tail of rare species, is always observed, whether species differ in habitat preferences or not. We suggest that many communities are indeed driven by the introduction process, accounting for high diversity and rarity, and that species differences may be largely irrelevant for either.     

Estimation and Tests for Departures from Rao-Structured Covariance Matrices

For linear models, a measure of departure of a variance-covariance matrix from Rao-structure (Rao, 1967) is proposed. Relevant estimation and testing problems are discussed. Illustrative examples are also presented.     

Differences in above-ground resource acquisition and niche overlap between a model invader (Phragmites australis) and resident plant species: measuring the role of fitness and niche differences in the field

Biological Invasions - Identifying the mechanisms that result in a “high impact” invasive species can be difficult. Coexistence theory suggests that detrimental invasive species can be...     

Neural differentiation of embryonic stem cells is induced by signalling from non-neural niche cells.

BACKGROUND/AIMS: Embryonic stem cell (ESC) transplantation offers new therapeutic strategies for neurodegenerative diseases and injury. However, the mechanisms underlying integration and differentiation of engrafted ESCs are poorly understood. This study elucidates the influence of exogenous signals on ESC differentiation using in vitro modelling of non-stem/stem cell interactions. METHODS: Murine ESCs were co-cultured with endothelial cells and astrocytes or conditioned medium obtained from endothelial or astrocyte cultures. After 7 days of co-culture isolated RNA was analysed using RT-PCR for the expression of pluripotency marker oct-4, neural progenitor marker nestin, and neurofilament (NFL), an early marker of neuronal lineage commitment. The presence of the glial cell surface marker A2B5 was determined in ESCs by flow cytometry. RESULTS: Neuronal differentiation was inhibited in ESCs when grown in close vicinity to cerebral endothelial or glial cells. Under these conditions, ESC differentiation was predominantly directed towards a glial fate. However, treatment of ESCs with endothelial cell- or astrocyte-conditioned medium promoted neuronal as well as glial differentiation. CONCLUSION: Our results indicate that ESC fate is determined by endothelial and glial cells that comprise the environmental niche of these stem cells in vivo. The direction of differentiation processes appears to be dependent on humoral factors secreted by adjacent cell lines.     

Physical fitness differences between prepubescent boys and girls

The purpose of this study was to analyze in which physical capabilities boys and girls are closer or distant. An additional objective was to find which of the body fat, physical activity, and somatotype factors have a greater effect on prepubescent children's physical fitness. This was a cross-sectional study involving 312 children (10.8 ± 0.4 years). The physical fitness assessment employed sets of aerobic fitness, strength, flexibility, speed, agility, and balance. The boys presented higher values in all selected tests, except tests of balance and flexibility, in which girls scored better. Gender differences in the physical fitness were greatest in the explosive strength of upper (p ≤ 0.01, η(p)(2) = 0.09) and lower limbs (p ≤ 0.01, η(p)(2) = 0.08), although with a medium-size effect of gender, and smaller in the abdominal (p > 0.05, η(p)(2) = 0.007) and upper limbs (p > 0.05, η(p)(2) = 0.003) muscular endurance, and trunk extensor strength and flexibility (p > 0.05, η(p)(2) = 0.001). The endomorphic (p ≤ 0.01, η(p)(2) = 0.26) in the girls, and the ectomorphic (p ≤ 0.01, η(p)(2) = 0.31) and mesomorphic (p ≤ 0.01, η(p)(2) = 0.26) in the boys, had the high-sized effect on the physical fitness. The physical activity in the girls, and the endomorphic and body fat in the boys, did not have a significant effect. These findings can help in the planning of activities that take into account the success and motivation of both boys and girls and thus increase levels of physical activity and physical fitness at school. However, in prepubescent children, one cannot neglect the influence of genetic determinism, observed from the morphoconstitutional point of view.     

Statistical differences between relative quantitative molecular fingerprints from microbial communities

Molecular fingerprints of microbial communities are a common method for the analysis and comparison of environmental samples. The significance of differences between microbial community fingerprints was analyzed considering the presence of different phylotypes and their relative abundance. A method is proposed by simulating coverage of the analyzed communities as a function of sampling size applying a Cramér-von Mises statistic. Comparisons were performed by a Monte Carlo testing procedure. As an example, this procedure was used to compare several sediment samples from freshwater ponds using a relative quantitative PCR-DGGE profiling technique. The method was able to discriminate among different samples based on their molecular fingerprints, and confirmed the lack of differences between aliquots from a single sample.     

On the determination of relative fitness from frequencies of genotypes in subsequent generations

Summary An algebraic treatment of reproduction and selection processes in populations of diploids with discrete generation cycles is presented. The main objective was a determination of the conditions under which the selection coefficients for the various genotypes can be determined solely on the basis of known frequencies of genotypes in two subsequent generations. In part two, to be published later, the statistical properties of a special fitness estimator, proposed by Hayman, are considered. Confidence intervals and tests of significance concerning hypotheses about fitness are established and checked by computer simulation studies.

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Zusammenfassung Für Reproduktions- und Selektionsvorgänge in Populationen diploider Organismen mit diskreter Generationenfolge wird eine algebraische Darstellung gegeben. Das Interesse konzentriert sich dabei auf die Frage, unter welchen Bedingungen die Selektionskoeffizienten der verschiedenen Genotypen aus den Genotypenfrequenzen zweier aufeinander folgender Generationen allein bestimmt werden können. Im zweiten Teil der Arbeit, der später veröffentlicht wird, werden die statistischen Eigenschaften einer speziellen, von Hayman aufgestellten Schätzfunktion untersucht. Hierbei werden Konfidenzintervalle und Signifikanzteste für Fitnesswerte betrachtet und mit Hilfe von Simulationsstudien geprüft.

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Gekürzte Fassung einer der Mathem.-naturwiss. Fakultät der Universität Tübingen eingereichten Dissertationsschrift (Teil I).     

On the determination of relative fitness from frequencies of genotypes in subsequent generations

Summary In part I of this paper (Theoret. Appl. Genetics 40, p. 11–17) an algebraic treatment of reproduction and selection processes in populations of diploids was given. Here the statistical properties of a special fitness estimator, which is due to Hayman, are considered. Confidence intervals and tests of significance concerning hypotheses about fitnesses are established and checked by computer simulation studies in part III.

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Zusammenfassung Im ersten Teil dieser Arbeit^* wurde eine alge-Darstellung von Reproduktions- und Selektionsvorgängen in Populationen diploider Organismen gegeben. Im zweiten Teil werden die statistischen Eigenschaften einer speziellen, von Hayman stammenden Schätzfunktion für die Fitness betrachtet. Es werden verschiedene Möglichkeiten zur Be-rechnung von Konfidenzintervallen und zur Durch-führung von Signifikanztesten angegeben und mit Hilfe von Simulationsstudien geprüft.

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Gekürzte Fassung einer der Mathem.-naturwiss. Fakultät der Universität Tübingen eingereichten Dissertationsschrift (Teil II und III).     

同地共栖三种鼠耳蝠食性差异及其生态位分化

2005年9—11月在贵州省安龙县笃山乡暗河村,分析了共栖同一山洞3种鼠耳蝠的形态特征和食性。在体型上,华南水鼠耳蝠体重为(4.46±0.53)g,前臂长为(34.63±1.45)mm;毛腿鼠耳蝠体重为(5.15±1.76)g,前臂长为(35.20±1.07)mm;西南鼠耳蝠体重为(10.94±0.87)g,前臂长为(45.21±1.15)mm。3种鼠耳蝠的体重两两之间差异显著,西南鼠耳蝠与另外2种鼠耳蝠的前臂长相比两两之间差异显著。在食物组成上,华南水鼠耳蝠主要捕食近水面活动的双翅目及其幼虫,体积百分比和频次百分比分别为79.7%和100%;毛腿鼠耳蝠主要捕食双翅目和小型鞘翅目,体积百分比分别占59.6%和28.8%,频次百分比分别为91.3%和80.1%;西南鼠耳蝠的食物组成主要为近地面或在地表活动的鞘翅目步甲科和埋葬虫科昆虫,体积百分比和频次百分比分别为80.8%和100%;3种鼠耳蝠食物组成存在显著差异。结果表明,同地共栖3种鼠耳蝠除了形态结构上出现差异,食物组成也存在明显的差异。据此,推测3种鼠耳蝠可能采取不同的捕食生境和捕食策略,从而导致捕食生态位分离,避免出现激烈竞争,使得3种近缘鼠耳蝠能够同地共栖。     

Bubbles Are Departures from Equilibrium Housing Markets: Evidence from Singapore and Taiwan

The housing prices in many Asian cities have grown rapidly since mid-2000s, leading to many reports of bubbles. However, such reports remain controversial as there is no widely accepted definition for a housing bubble. Previous studies have focused on indices, or assumed that home prices are lognomally distributed. Recently, Ohnishi et al. showed that the tail-end of the distribution of (Japan/Tokyo) becomes fatter during years where bubbles are suspected, but stop short of using this feature as a rigorous definition of a housing bubble. In this study, we look at housing transactions for Singapore (1995 to 2014) and Taiwan (2012 to 2014), and found strong evidence that the equilibrium home price distribution is a decaying exponential crossing over to a power law, after accounting for different housing types. We found positive deviations from the equilibrium distributions in Singapore condominiums and Zhu Zhai Da Lou in the Greater Taipei Area. These positive deviations are dragon kings, which thus provide us with an unambiguous and quantitative definition of housing bubbles. Also, the spatial-temporal dynamics show that bubble in Singapore is driven by price pulses in two investment districts. This finding provides a valuable insight for policymakers on implementation and evaluation of cooling measures.     

Expected relative fitness and the adaptive topography of fluctuating selection

Wright's adaptive topography describes gene frequency evolution as a maximization of mean fitness in a constant environment. I extended this to a fluctuating environment by unifying theories of stochastic demography and fluctuating selection, assuming small or moderate fluctuations in demographic rates with a stationary distribution, and weak selection among the types. The demography of a large population, composed of haploid genotypes at a single locus or normally distributed phenotypes, can then be approximated as a diffusion process and transformed to produce the dynamics of population size, N, and gene frequency, p, or mean phenotype, . The expected evolution of p or is a product of genetic variability and the gradient of the long-run growth rate of the population, , with respect to p or . This shows that the expected evolution maximizes , the mean Malthusian fitness in the average environment minus half the environmental variance in population growth rate. Thus, as a function of p or represents an adaptive topography that, despite environmental fluctuations, does not change with time. The haploid model is dominated by environmental stochasticity, so the expected maximization is not realized. Different constraints on quantitative genetic variability, and stabilizing selection in the average environment, allow evolution of the mean phenotype to undergo a stochastic maximization of . Although the expected evolution maximizes the long-run growth rate of the population, for a genotype or phenotype the long-run growth rate is not a valid measure of fitness in a fluctuating environment. The haploid and quantitative character models both reveal that the expected relative fitness of a type is its Malthusian fitness in the average environment minus the environmental covariance between its growth rate and that of the population.     

Sex-biased immunity is driven by relative differences in reproductive investment

Sex differences in immunity are often observed, with males generally having a weaker immune system than females. However, recent data in a sex-role-reversed species in which females compete to mate with males suggest that sexually competitive females have a weaker immune response. These findings support the hypothesis that sexual dimorphism in immunity has evolved in response to sex-specific fitness returns of investment in traits such as parental investment and longevity, but the scarcity of data in sex-reversed species prevents us from drawing general conclusions. Using an insect species in which males make a large but variable parental investment in their offspring, we use two indicators of immunocompetence to test the hypothesis that sex-biased immunity is determined by differences in parental investment. We found that when the value of paternal investment was experimentally increased, male immune investment became relatively greater than that of females. Thus, in this system, in which the direction of sexual competition is plastic, the direction of sex-biased immunity is also plastic and appears to track relative parental investment.     

Malaria in Africa: vector species' niche models and relative risk maps

A central theoretical goal of epidemiology is the construction of spatial models of disease prevalence and risk, including maps for the potential spread of infectious disease. We provide three continent-wide maps representing the relative risk of malaria in Africa based on ecological niche models of vector species and risk analysis at a spatial resolution of 1 arc-minute (9 185 275 cells of approximately 4 sq km). Using a maximum entropy method we construct niche models for 10 malaria vector species based on species occurrence records since 1980, 19 climatic variables, altitude, and land cover data (in 14 classes). For seven vectors (Anopheles coustani, A. funestus, A. melas, A. merus, A. moucheti, A. nili, and A. paludis) these are the first published niche models. We predict that Central Africa has poor habitat for both A. arabiensis and A. gambiae, and that A. quadriannulatus and A. arabiensis have restricted habitats in Southern Africa as claimed by field experts in criticism of previous models. The results of the niche models are incorporated into three relative risk models which assume different ecological interactions between vector species. The "additive" model assumes no interaction; the "minimax" model assumes maximum relative risk due to any vector in a cell; and the "competitive exclusion" model assumes the relative risk that arises from the most suitable vector for a cell. All models include variable anthrophilicity of vectors and spatial variation in human population density. Relative risk maps are produced from these models. All models predict that human population density is the critical factor determining malaria risk. Our method of constructing relative risk maps is equally general. We discuss the limits of the relative risk maps reported here, and the additional data that are required for their improvement. The protocol developed here can be used for any other vector-borne disease.     

Temporal niche dynamics, relative abundance and phylogenetic signal of coexisting species

The coexistence of similar species accounts for some 30% of diversity within communities, yet the coexistence and relative abundance of similar species is a continuing ecological conundrum. Using close phylogenetic relatedness as a measure of similarity, we previously demonstrated that neither classic niche theory nor neutral theory can explain the relative abundances of co-occurring pairs of similar tree species in a diverse tropical forest. Here, we show that the stable, focused competition of a temporal niche dynamic fits the distribution of observed fractional abundances (pairwise relative abundances). Previously published, independent evidence of temporal dynamics in this community supports our results; our model identifies additional criteria for field tests of differential sensitivity (DS) temporal dynamics. The success of temporal dynamics at explaining the observed distribution—and the failure of alternative hypotheses to do so—indicates that current diagnostics of community structure and assembly needs general re-examination. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Quantifying the relative importance of niches and neutrality for coexistence in a model microbial system

1.  Ecologists have identified two types of processes promoting species coexistence: stabilizing mechanisms (niche differentiation and related processes) that increase negative intraspecific interactions relative to negative interspecific interactions, and equalizing mechanisms (neutrality) that minimize the differences in species' demographic parameters. It has been theoretically and empirically shown that the two types of mechanisms can operate simultaneously; however, their relative importance remains unstudied although this is a key question in the synthesis of niche and neutral theories.
2.  We experimentally quantified the relative importance of niche and neutral mechanisms in promoting phenotypic diversity in a model microbial system involving different phenotypes of the bacterium Pseudomonas fluorescens . Initially isogenic populations of the bacterium can diversify into a series of major and minor classes of phenotypes that can be treated as analogues of species. We estimated the relative population growth rate when rare of 32 phenotypes from six replicate microcosms. Each phenotype was assessed in a re-assembled microcosm in which the relative densities of all phenotypes remained the same except for the focal one which was reduced in frequency. A growth rate advantage when rare was considered evidence of non-neutral processes.
3.  Approximately one-third of the phenotypes had a growth rate advantage when rare while the remaining two-thirds showed neutral or near-neutral dynamics. Furthermore, there was overall little evidence that productivity increased with phenotypic diversity.
4.  Our results suggest that niche and neutral processes may simultaneously contribute to the maintenance of biodiversity, with the latter playing a more important role in our system, and that the operation of niche mechanisms does not necessarily lead to a positive biodiversity effect on ecosystem properties.     

Invasion of drug and pesticide resistance is determined by a trade-off between treatment efficacy and relative fitness

Drug and pesticide resistance are among the most pressing problems facing public, animal and plant health today. In order to design effective resistance management strategies it is imperative to identify criteria for the invasion of resistant forms. Two key determinants of the ability of a resistant pest or pathogen to invade are any inherent fitness costs to the resistant subpopulation, and the effect of treatment on the sensitive and resistant subpopulations. For two generic classes of model which encompass many of the standard models in this field, we summarize relative fitness and treatment efficacy via two simple parameters, and demonstrate that invasion of resistance depends critically on a trade-off between them. Thresholds for invasion are derived when the effect of treatment is a constant reduction in the life-history parameters of the pathogen, and when treatment efficacy varies periodically with the repeated application and subsequent decay of the chemical.     

Biodiversity, phenology and temporal niche differences between native- and novel exotic-dominated grasslands

Many exotic species have been introduced or have escaped into grasslands where they form ‘novel ecosystems’ of species with no evolutionary history of interaction. Novel ecosystems are good model systems for understanding how diversity maintenance mechanisms might differ between species with a history of interaction (natives) and species without a history (exotics) in cases where exotics originated from several continents. We tested for lower species diversity and richness in exotic grasslands and found a negative correlation between species diversity measures and proportion of exotic species across 15 grasslands in an observational study in Texas. We then planted 9-species mixtures of all native or all exotics under ambient or elevated summer precipitation to compare dynamics of diversity and to test if exotic species respond more strongly to altered resource availability. Species diversity was lower in communities of exotic than native species by the second year. Reduced diversity in exotic communities resulted from lower complementarity and higher temporal niche overlap among species and occurred in both ambient and irrigated plots. In general, summer irrigation had additive positive effects and did not interact with native–exotic status. Exotic species and communities had much earlier green-up during spring than natives, and altered inter-correlations among phenology variables. There were no differences in flowering dates. Taken together, our results suggest that rapid and synchronous growth may increase niche overlap among exotic species and reduce local diversity in exotic-dominated grassland communities. Earlier green-up by exotics may complicate attempts to ascertain relationships between phenology and climate. An increase in exotic species may cause earlier green-up regardless of any climate change effects and our results suggest that phenology networks should take a species-based rather than an ecosystem approach to evaluate green-up if the abundance of exotics increases within the time-frame in question. These differences between native and exotic species and communities should be considered in future management and restoration projects.     

On the relationship between the load and the variance of relative fitness

Background  

Operation of natural selection can be characterized by a variety of quantities. Among them, variance of relative fitness V and load L are the most fundamental.     

Artificial niche substrates for embryonic and induced pluripotent stem cell cultures

Stem cells possess the ability to self-renew and differentiate into other cell types. In vivo, stem cells reside in their own anatomic niches in a defined physiological environment, from which they are released to differentiate into a required cell type when deemed appropriate. While a resident within the niche, the stem cell receives signals that in turn maintain the cell in a pluripotent state. In addition, the niche also provides nourishment to the cell. Physically, the niche also serves to anchor the cell via various ECM components and cell-adhesion molecules. Therefore, in vitro models that replicate the in vivo niche will lead to a better understanding of stem cell fate and turnover. In turn, this will help inform attempts to culture stem cells in vitro on artificial niche-like substrates. In this review, we have highlighted recent studies describing artificial niche-like substrates used to culture embryonic and induced pluripotent stem cells in vitro.