A mathematical synthesis of niche and neutral theories in community ecology

The debate between niche-based and neutral community theories centers around the question of which forces shape predominantly ecological communities. Niche theory attributes a central role to niche differences between species, which generate a difference between the strength of intra- and interspecific interactions. Neutral theory attributes a central role to migration processes and demographic stochasticity. One possibility to bridge these two theories is to combine them in a common mathematical framework. Here we propose a mathematical model that integrates the two perspectives. From a niche-based perspective, our model can be interpreted as a Lotka-Volterra model with symmetric interactions in which we introduce immigration and demographic stochasticity. From a neutral perspective, it can be interpreted as Hubbell's local community model in which we introduce a difference between intra- and interspecific interactions. We investigate the stationary species abundance distribution and other community properties as functions of the interaction coefficient, the immigration rate and the strength of demographic stochasticity.     

Heterogeneity in dynamic species abundance models: the selective effect of extinction processes

There is often large variation in traits across the species of a community. In particular, variation in life history traits affecting population dynamics is likely to affect the species abundance distribution. Applying a dynamic and heterogeneous species abundance model we study how differences in extinction time for species in a community act as a force changing the distribution of dynamic parameters across species. This process may generate communities that are more heterogeneous then the heterogeneity measured as the species enter the community. Analytical results for some versions of the lognormal and gamma species abundance model are given as exemplifications of this process, together with stochastic simulations demonstrating the temporal changes in number of species and community heterogeneity through time.     

Colonization rules and spatial distributions in ecology

Because they are intuitive and mathematically straight-forward, colonization rules are often used to model spatial patterns in ecology. Colonization rules assign individuals to categories according to the locations of previous colonists. In this note, a compact introduction to colonization rules in ecology is presented with implications for autocorrelation and spatial distributions. I use the colonization rule approach to unify a diverse set of spatial and species diversity analyses, exploring future extensions to incorporate greater realism.     

A neutral model of edge effects

In this paper a spatially implicit neutral model for explaining the edge effects between habitats is proposed. To analyze this model we use two different approaches: a discrete approach that is based on the Master equation for a one step jump process and a continuous approach based on the approximation of the discrete jump process with the Kolmogorov-Fokker-Planck forward and backward equations. The discrete and continuous approaches are applied to analyze the species abundance distributions and the time to species extinction. Moreover, with the aid of the continuous approach a realistic classification of the behavior of species in local communities is developed. The species abundance dynamics at the edge between two distinct habitats is compared with those located in the homogeneous interior habitats using species abundance distributions and the first time to species extinction. We show that the structure of the links between local community and the metacommunity plays an important role on species persistence. Specifically, species at the edge between two distinct metacommunities have higher extinction rate than those in the interior habitats connected only to one metacommunity. Moreover, the same species might be persistent in the homogeneous interior habitat, but its probability of extinction from the edge local community could be very high.     

The effect of habitat stability on benthic invertebrate communities: the utility of species abundance distributions

Spatial and temporal patterns in the species abundance distribution of benthic invertebrate communities of 11 freshwater habitats (10 streams and a wind-swept lake shore) were examined with respect to habitat stability. Abundance patterns varied markedly between seasons at most sites. However, mean abundance distributions at 4 of the 5 unstable sites and the 2 most stable sites were dominated by one or two taxa with a large number of rare species, whereas sites of intermediate stability had more equitable distributions. Both the log series and log normal distributions were statistically indistinguishable, at the 5% level, from all the observed mean abundance patterns. In contrast, graphical comparisons of the observed and fitted distributions suggested the log series may be the better fit at most of the unstable sites and the two most stable sites, whereas the more equitable distribution at sites of intermediate stability suggested the log normal distribution was the better fit. If conditions at a site favoured one or two species, either through severe physical conditions, or through competitive superiority in the absence of disturbance then the log series distribution may result. However, if no species in the community was strongly advantaged over others, a log normal distribution should result. Given the discriminating power of the appropriate statistical test it may not, however, be possible to pick up these differences without graphical comparisons as well.     

Heterogeneous communities with lognormal species abundance distribution: Species-area curves and sustainability

Heterogeneous species abundance models are models in which the dynamics differ between species, described by variation among parameters defining the dynamics. Using a dynamic and heterogeneous species abundance model generating the lognormal species abundance distribution it is first shown that different degrees of heterogeneity may result in equivalent species abundance distributions. An alternative to Preston's canonical lognormal model is defined by assuming that reduction in resources, for example reduction in available area, increases the density regulation of each species. This leads to species-individual curves and species-area curves that are approximately linear in a double logarithmic plot. Preston's canonical parameter gamma varies little along these curves and takes values in the neighborhood of one. Quite remarkably, the curves, which define the sensitivity of the community to area reductions, are independent of the heterogeneity among species for this model. As a consequence, the curves can be estimated from a single sample from the community using the Poisson lognormal distribution. It is shown how to perform sensitivity analysis with respect to over-dispersion in sampling relative to the Poisson distribution as well as sampling intensity, that is, the fraction of the community sampled. The method is exemplified by analyzing three simulated data sets.     

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.     

Influence of dietary specialization and resource availability on geographical variation in abundance of butterflyfish

Empirical evidence indicates that both niche breadth and resource availability are key drivers of a species' local abundance patterns. However, most studies have considered the influence of either niche breath or resource availability in isolation, while it is the interactive effects that are likely to influence local abundance. We examined geographic variation in the feeding ecology and distribution of coral-feeding butterflyfish to determine the influence of dietary specialization and dietary resource availability on their local abundance. Dietary composition and abundance of five butterflyfish and coral dietary resource availability were determined at 45 sites across five locations (Lizard Island and Heron Island, Great Barrier Reef; Kimbe Bay, Papua New Guinea; Noumea, New Caledonia; and Moorea, French Polynesia). Multiple regression models using variables representative of total dietary resource availability, availability of specific dietary resources, and interspecific competition were used to determine the best predictors of local abundance across all sites and locations for each species. Factors influencing local abundance varied between butterflyfish with specialized and generalized diets. Dietary resource availability had the strongest influence on the abundance of Chaetodon trifascialis-the most specialized species. Local abundance of C. trifascialis was best predicted by availability of the Acropora corals that it preferentially feeds on. In contrast, abundance of generalist butterflyfish was poorly described by variation in availability of specific resources. Rather, indices of total dietary resource availability best predicted their abundance. Overall, multiple regression models only explained a small proportion of the variation in local abundance for all five species. Despite their relatively specialized diets, dietary resource availability has limited influence on the local abundance of butterflyfish. Only the most specialized species appear to be consistently limited by prey availability. Local and total abundance of species are influenced by a wide range of different factors and there is definite need to conduct independent species assessments.     

Species number, species abundance and body length relationships of arboreal beetles in Bornean lowland rain forest trees

ABSTRACT.

• 1 The relationships between number of species, abundance per species, and body length are examined for 859 species of beetles in samples of arthropods collected from ten Bornean lowland forest trees by insecticide fogging. Similar relationships are examined for different feeding guilds of these beetles, and for those beetles from different species of trees.
• 2 The data are used to construct four interrelated graphs, namely species: abundance, species: body length, population abundance: body length and total number of individuals: body length distributions.
• 3 In contrast to a number of previous studies, no consistent linear relationship between population density and body length was found for the Bornean beetles and it is suggested that, as in birds, the added dispersal ability of flight reduces critical population densities necessary for persistence in small species. Previous relationships between body weight and population abundance may also be artefacts of the way in which data were gathered.
• 4 Despite large samples, we failed to locate the mode in plots of the number of species in each abundance category (species: abundance distribution).
• 5 Species: body length and total number of individuals: body length plots were similar to those found in previous studies, although using data for Coleoptera alone may have produced a steeper decline in the total number of individuals as body size increases than is apparent in samples of all arthropods.
• 6 We present the first three-dimensional graph relating numbers of species, body lengths and population abundances. The surface of this three-dimensional relationship is relatively simple.

     

The evolutionary consequences of niche construction: a theoretical investigation using two-locus theory

This paper addresses the joint evolution of environment-altering (niche constructing) traits, and traits whose fitness depends on alterable sources of natural selection in environments. We explore the evolutionary consequences of this niche construction using a two-locus population genetic model. The novel conclusions are that niche construction can (1) cause evolutionary inertia and momentum, (2) lead to the fixation of otherwise deleterious alleles, (3) support stable polymorphisms where none are expected, (4) eliminate what would otherwise be stable polymorphisms, and (5) influence disequilibrium. The results suggest that the changes that organisms bring about in their niche can themselves be an important source of natural selection pressures, and imply that evolution may proceed in cycles of selection and niche construction.     

The relationships between abundance, range size and niche breadth in Central European tree species

Aim  Range size and niche breadth have been found to be positively related to abundance in many plant and animal groups. We tested these two relationships for the tree species flora of Central Europe; that is, for all 25 species that have their distribution centre in this region.
Location  Eurasia, with a focus on Central Europe.
Methods  We devised an abundance and niche variable classification system to transform the existing literature data into a semi-quantitative assessment of abundance and niche breadth (in terms of soil chemical and physical variables, and temperature) for each of the 25 tree species. Regression analyses between abundance, range size and niche breadth were conducted for the entire species sample and for subsets of species defined by their ecology or phylogeny.
Results  The relationship between abundance in the distribution centre and range size was weak for the Central European tree species. However, significant abundance–range size relationships were found for phylogenetically or ecologically more homogenous species groups (for example for trees of the order Rosales and for mid-successional tree species). Realized niche breadth was positively related to range size in the case of temperature, but not for soil-related variables. No relationship existed between niche breadth and abundance in the distribution centre.
Main conclusions  We hypothesize that the weak relationship between abundance and range size is primarily a consequence of substantial ecological and phylogenetic heterogeneity within this rather species-poor assemblage. The positive relationship between realized temperature niche breadth and range size emphasizes the strong influence of climatic variables on plant distribution patterns over continental or global scales.     

Cattle grazing, raptor abundance and small mammal communities in Mediterranean grasslands

Abundance and diversity of small mammals are usually affected strongly by grazing either due to decreased food availability or quality, decreased suitability of soil for building burrow systems due to trampling and/or due to increased predation risk in the structurally simpler grazed areas. We estimated the effects of grazing-induced changes in vegetation and soil and of increased predation on small mammals in a Mediterranean grassland landscape. We measured vegetation structure, soil compaction and small mammal abundance and species composition in 22 plots of 8 Sherman live traps each, arranged according to an unbalanced two-way ANOVA design with two grazing levels (grazed areas and cattle exclosures) and two predator abundance levels (increased densities of Eurasian kestrels Falco tinnunculus by means of nest boxes and control). Plots were sampled during 2 consecutive years in early summer and early fall. Exclosure from cattle increased significantly vegetation height and volume and decreased soil compaction. Grazing-induced changes in vegetation height and volume and in soil compaction produced strong effects on small mammal abundance and species richness. Increased kestrel densities did not have significant additive or interactive effects, with the effects of grazing-induced vegetation and soil gradients on abundance or richness of small mammals. Our results suggest that the effects of grazing on small mammal communities in Mediterranean montane grasslands were mainly due to reduced food availability and by negative effects of trampling on the suitability of soils for building burrow systems. Decreased food quality and increased predation in grazed areas seemed to play a minor role, if any. Reductions in stock densities would then favor generalist predator populations in Mediterranean grasslands through the expected positive effects of such reductions on the availability of food and burrows for small mammals.     

International Biodiversity Observation Year in Western-Pacific and Asian regions (DIWPA-IBOY): a case report on species rarity and spatio-temporal variability of species composition in Lepidoptera and Coleoptera communities from a temperate forest of northern Japan

An international project, DIWPA-IBOY, took place for simultaneously observing biodiversity throughout the Western-Pacific and Asian regions in 2001–2003, as one of the core projects for International Biodiversity Observation Year, a crosscutting network activity of DIVERSITAS (an international programme of biodiversity science). DIWPA-IBOY provides extensive data on species diversity obtained by the standardized method. Under this project, 51,742 individuals of Lepidoptera and 11,633 of Coleoptera were collected by light traps from the Tomakomai Experimental Forest of Hokkaido University, one of the core DIWPA-IBOY sites, in the cool-temperate region of northern Japan. Based on these data, this study examined the relative abundance distribution (RAD) to evaluate the amount of rare species in the Lepidoptera and Coleoptera communities. The beta diversities between sampling seasons, forest strata, and trap sites were also assessed to evaluate the spatio-temporal variability of species composition in these communities. In the analysis of the RAD, the best-fit model was selected from the log-Normal, Zipf–Mandelbrot, and Zipf models differing in the tail length of the RAD, i.e., the proportion of rare species. To explore the beta diversity between samples, the abundance-based Jaccard index with an unseen species estimator was calculated, and then a hierarchical clustering analysis was conducted. As a result of RAD analysis, the Coleoptera community was regarded as containing a larger proportion of rare species than the Lepidoptera community. The seasonal compartmentalization of the community, deduced from the beta-diversity analysis, was finer in Lepidoptera (seven assemblages recognized) than in Coleoptera (three assemblages). The spatial (vertical and horizontal) compartmentalization was negligible in both communities. The coincidence of the larger proportion of rare species and the lower beta diversity between seasons in the Coleoptera community was explained by the longer life spans of beetles compared to moths, based on the assumption that the length of life span acts as a temporal agent for mass effect on the analogy of the migration rate as a spatial agent for mass effect.     

Plant traits,species pools and the prediction of relative abundance in plant communities: a maximum entropy approach

Questions: To what extent can Shipley et al.'s original maximum entropy model of trait‐based community assembly predict relative abundances of species over a large (3000 km²) landscape? How does variation in the species pool affect predictive ability of the model? How might the effects of missing traits be detected? How can non‐trait‐based processes be incorporated into the model? Location: Central England. Material and Methods: Using 10 traits measured on 506 plant species from 1308 1‐m² plots collected over 3000 km² in central England, we tested one aspect of Shipley et al.'s original maximum entropy model of “pure” trait‐based community assembly (S₁), and modified it to represent both a neutral (S₂) and a hybrid (S₃) scenario of community assembly at the local level. Predictive ability of the three corresponding models was determined with different species pool sizes (30, 60, 100 and 506 species). Statistical significance was tested using a distribution‐free permutation test. Results: Predictive ability was high and significantly different from random expectations in S₁. Predictive ability was low but significant in S₂. Highest predictive ability occurred when both neutral and trait‐based processes were included in the model (S₃). Increasing the pool size decreased predictive ability, but less so in S₃. Incorporating habitat affinity (to indicate missing traits) increased predictive ability. Conclusions: The measured functional traits were significantly related to species relative abundance. Our results both confirm the generality of the original model but also highlight the importance of (i) taking into account neutral processes during assembly of a plant community, and (ii) properly defining the species pool.     

北京东灵山辽东栎(Quercus liaotungensis)林沿海拔梯度的物种多度分布

多度格局对理解群落结构具有重要意义。选用5个描述种-多度关系的生态位模型(断棍模型BSM、生态位优先占领模型NPM、生态位重叠模型ONM、随机分配模型RAM、优势优先模型DPM),分乔、灌、草3层分别对北京东灵山辽东栎林进行了研究。结果表明:在乔木层,沿海拔梯度从低海拔到高海拔,能很好地反映物种多度格局变异的模型有由RAM、NPM向DPM过渡的趋势;NPM和BSM均能较好地模拟灌木层的绝大多数海拔段,但NPM的效果更好;草本层以BSM的模拟效果最好。生态位模型可以反映出辽东栎林乔木层物种多度分布沿海拔存在的明显变异,而灌木层和草本层物种多度分布沿海拔梯度无明显变化或很难由生态位模型反映出来,是否引入新的模型方法,如中性模型、近中性模型,还有待于进一步研究。     

Position on slope,disturbance, and tree species coexistence in a Seasonal Semideciduous Forest in SE Brazil

We investigated the influence of position on a slope (plot relative elevation) and vegetation disturbance (the tallest tree height per plot) on community composition and diversity in a SE Brazilian Seasonal Semideciduous Forest (46°55′ W, 22°50′ S). Trees with dbh ≥5 cm were sampled in one hundred 10 × 10 m plots randomly placed in a 6.5-ha stand. Through partial Mantel test, floristic dissimilarities among plots (Jaccard index computed with species abundance in each plot) were correlated with environmental distances among plots (Euclidian distance index computed with relative elevation and the tallest tree height values in each plot). Relative elevation and the tallest tree per plot height were individually correlated with floristic gradients expressed by PCA axes scores using Pearson’s correlation coefficient. Through resampling, we compared diversity (richness, Berger-Parker D and Shannon H′) among plots in the drier (up) and moister (low) ends of the slope. Floristic dissimilarities were significantly correlated with environmental distances even after geographic distances among plots have been partialled out (r _m = 0.1274, p < 0.001). The first two PCA axes accounted for 22% of the total variance. After Bonferroni and Dutilleul’s corrections, axis 1 showed a marginally significant correlation with plot relative elevation (r = − 0.4097, p = 0.0309), and axis 2 was significantly correlated with the tallest tree height per plot (r = 0.2953, p = 0.0106). Position on the slope and vegetation disturbance were reliable predictors of community composition, thus suggesting the operation of niche assembly organizing processes. Richness and diversity (H′) decreased and dominance (D) increased with elevation on the slope. Dominance increase from D ₍₃₀₀₎ = 0.11 (confidence interval = 0.091–0.131) to D ₍₃₀₀₎ = 0.19 (CI = 0.165–0.210) surpassed the expected dominance increase based on the reduction of richness alone: D ₍₃₀₀₎ = 0.13 (CI = 0.110–0.140), thus highlighting the niche partitioning assembly of the community, especially among abundant species. Given the great amount of floristic variability remaining unexplained, stochastic processes, such as those related to dispersal limitation, may also have influence on the community composition. Therefore, both niche assembly and chance events can operate even on a fine local scale.     

Gene bionetworks involved in the epigenetic transgenerational inheritance of altered mate preference: environmental epigenetics and evolutionary biology

Background

Mate preference behavior is an essential first step in sexual selection and is a critical determinant in evolutionary biology. Previously an environmental compound (the fungicide vinclozolin) was found to promote the epigenetic transgenerational inheritance of an altered sperm epigenome and modified mate preference characteristics for three generations after exposure of a gestating female.

Results

The current study investigated gene networks involved in various regions of the brain that correlated with the altered mate preference behavior in the male and female. Statistically significant correlations of gene clusters and modules were identified to associate with specific mate preference behaviors. This novel systems biology approach identified gene networks (bionetworks) involved in sex-specific mate preference behavior. Observations demonstrate the ability of environmental factors to promote the epigenetic transgenerational inheritance of this altered evolutionary biology determinant.

Conclusions

Combined observations elucidate the potential molecular control of mate preference behavior and suggests environmental epigenetics can have a role in evolutionary biology.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-377) contains supplementary material, which is available to authorized users.     

The geography and ecology of plant speciation: range overlap and niche divergence in sister species

A goal of evolutionary biology is to understand the roles of geography and ecology in speciation. The recent shared ancestry of sister species can leave a major imprint on their geographical and ecological attributes, possibly revealing processes involved in speciation. We examined how ecological similarity, range overlap and range asymmetry are related to time since divergence of 71 sister species pairs in the California Floristic Province (CFP). We found that plants exhibit strikingly different age-range correlation patterns from those found for animals; the latter broadly support allopatric speciation as the primary mode of speciation. By contrast, plant sisters in the CFP were sympatric in 80% of cases and range sizes of sisters differed by a mean of 10-fold. Range overlap and range asymmetry were greatest in younger sisters. These results suggest that speciation mechanisms broadly grouped under ‘budding’ speciation, in which a larger ranged progenitor gives rise to a smaller ranged derivative species, are probably common. The ecological and reproductive similarity of sisters was significantly greater than that of sister–non-sister congeners for every trait assessed. However, shifts in at least one trait were present in 93% of the sister pairs; habitat and soil shifts were especially common. Ecological divergence did not increase with range overlap contrary to expectations under character displacement in sympatry. Our results suggest that vicariant speciation is more ubiquitous in animals than plants, perhaps owing to the sensitivity of plants to fine-scale environmental heterogeneity. Despite high levels of range overlap, ecological shifts in the process of budding speciation may result in low rates of fine-scale spatial co-occurrence. These results have implications for ecological studies of trait evolution and community assembly; despite high levels of sympatry, sister taxa and potentially other close relatives, may be missing from local communities.     

The roles of ecological and behavioral observation in species recognition among primates

Closely related living mammal species present numerous difficulties of recognition and delineation, not least because populations as well as individual organisms fulfill both genetic and economic functions. However, since species are often distributed geographically across multiple ecosystems or environments, it is evident that species as wholes, except where coterminous with the local populations of which they are composed, cannot be said to play unitary ecological roles. Aspects of the economic activity of organisms thus may not be admitted as elements in species recognition. Those who study the behavior of mammals in their natural habitats must therefore focus upon behaviors which preserve the genetic integrity of species if they wish to contribute to the systematic question of species identification. «Isolation» concepts of species are not served by data of this kind, since they emphasize interspecies discontinuities; the «recognition» concept of species, however, specifically focuses upon behaviors of this kind as they contribute to the «Specific-Mate Recognition System». Among primates such behaviors are likely to involve signalling of various kinds; where this is visual it is reasonable to expect to find morphological or chromatic correlates; where such cues are auditory or, to a lesser extent, olfactory, it is less probable that such correlates will be found to exist.     

Environmental control of plant species abundance in a microtidal Mediterranean saltmarsh

Question: To what extent are environmental factors the main determinants of species abundance in Mediterranean coastal marshlands? Location: The Llobregat delta, Barcelona, Spain. Methods: Vegetation relevés were performed and a set of water table and soil variables were periodically monitored in 43 sampling points randomly distributed in four marsh areas (sites) along a coastal–inland gradient. A canonical correspondence analysis (CCA) was performed to identify the primary water and soil correlates of species cover, after considering the effect of site and point spatial location. The realized niches of dominant species were modeled through GLMs performed on the first two axes of CCA. Niche overlapping among these species was compared with their coexistence, assessed through pairwise correlations of relative species cover in each sampling point. Results: Water and soil variables explained more of the variation in species' abundance than site and spatial position. Mean water table level, maximum water conductivity and sodium adsorption ratio (SAR), summarized in the two first CCA axes, explained 23.8% of the variability in species' cover. Arthrocnemum fruticosum, Phragmites australis subsp. australis, Juncus acutus, Spartina versicolor and Juncus maritimus dominated the vegetation stands. Niches obtained from GLM response curves showed moderate overlapping among all these species except for A. fruticosum. However, pairwise correlations were mainly negative or non‐significant, indicating low coincidence, and even segregation, between species' cover. Conclusions: The abundance of dominant plants in Mediterranean marshes is only partly explained by the environmental gradients summarized in niche models. The role of other factors such as facilitation or competition between species and random recruitment should be explored.