Environmental stochasticity is known to be a destabilizing factor, increasing abundance fluctuations and extinction rates of populations. However, the stability of a community may benefit from the differential response of species to environmental variations due to the storage effect. This paper provides a systematic and comprehensive discussion of these two contradicting tendencies, using the metacommunity version of the recently proposed time-average neutral model of biodiversity which incorporates environmental stochasticity and demographic noise and allows for extinction and speciation. We show that the incorporation of demographic noise into the model is essential to its applicability, yielding realistic behavior of the system when fitness variations are relatively weak. The dependence of species richness on the strength of environmental stochasticity changes sign when the correlation time of the environmental variations increases. This transition marks the point at which the storage effect no longer succeeds in stabilizing the community.
Speciation is the "elephant in the room" of community ecology. As the ultimate source of biodiversity, its integration in ecology's theoretical corpus is necessary to understand community assembly. Yet, speciation is often completely ignored or stripped of its spatial dimension. Recent approaches based on network theory have allowed ecologists to effectively model complex landscapes. In this study, we use this framework to model allopatric and parapatric speciation in networks of communities and focus on the relationship between speciation, richness, and the spatial structure of communities. W…
Life-history tradeoffs among species are major drivers of community assembly. Most studies investigate how tradeoffs promote deterministic coexistence of species. It remains unclear how tradeoffs may instead promote historically contingent exclusion of species, where species dominance is affected by initial abundances, causing alternative community states. Focusing on the establishment-longevity tradeoff, we study the transient dynamics and equilibrium outcomes of competitive interactions in a simulation model of plant community assembly. We show that, in this model, the establishment-longevit…
The dynamics of two competing species in a finite size community is one of the most studied problems in population genetics and community ecology. Stochastic fluctuations lead, inevitably, to the extinction of one of the species, but the relevant timescale depends on the underlying dynamics. The persistence time of the community has been calculated for neutral models, where the only drive of the system is drift (demographic stochasticity) and for models with strong selection. Following recent analyses that stress the importance of environmental stochasticity in empirical systems, we present he…
Population analysis is persistently challenging but important, leading to the determination of diversity and function prediction of microbial community members. Here we detail our bioinformatics methods for analyzing population distribution and diversity in large microbial communities. This was achieved via (i) a homology based method for robust phylotype determination, equaling the classification accuracy of the Ribosomal Database Project (RDP) classifier, but providing improved associations of closely related sequences; (ii) a comparison of different clustering methods for achieving more acc…
It has been a century since the species-area relationship (SAR) was first proposed as a power law to explain how species richness scales with area. There have been many attempts to explain the origin of this predominant form. Apart from the power law, numerous empirical studies also report a semi-log form of the SAR, but very few have addressed its incidence. In this work, we test whether these relationships could emerge from the assembly of large random communities on island-like systems. We reformulate the generalized Lotka-Volterra model by introducing an area parameter that determines the …
Understanding the forces shaping ecological communities is crucially important to basic science and conservation. In recent years, considerable progress was made in explaining communities using simple and general models, with neutral theory as a prominent example. However, while successful in explaining static patterns such as species abundance distributions, the neutral theory was criticized for making unrealistic predictions of fundamental dynamic patterns. Here we incorporate environmental stochasticity into the neutral framework, and show that the resulting generalized neutral theory is ca…
Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sam…
We study the effects of demographic stochasticity on the long-term dynamics of biological coevolution models of community assembly. The noise is induced in order to check the validity of deterministic population dynamics. While mutualistic communities show little dependence on the stochastic population fluctuations, predator-prey models show strong dependence on the stochasticity, indicating the relevance of the finiteness of the populations. For a predator-prey model, the noise causes drastic decreases in diversity and total population size. The communities that emerge under influence of the …
Species accumulation curves (SAC), i.e. the relationship between species richness and the number of sampling units in a given community, can be used to describe diversity patterns while accounting for the well-known scale-dependence of species richness. Despite their value, the functional form and the parameters of SAC, as well as their determinants, have barely been investigated in plant communities, particularly in drylands. We characterized the SAC of perennial plant communities from 233 dryland ecosystems from six continents by comparing the fit of major functions (power-law, logarithmic a…
High-diversity assemblages are very common in nature, and yet the factors allowing for the maintenance of biodiversity remain obscure. The competitive exclusion principle and May's complexity-diversity puzzle both suggest that a community can support only a small number of species, turning the spotlight at the dynamics of local patches or islands, where stable and uninvadable (SU) subsets of species play a crucial role. Here we map the community SUs question to the geometric problem of finding maximal cliques of the corresponding graph. We solve for the number of SUs as a function of the speci…
Over the past century, nonlinear difference and differential equations have been used to understand conditions for species coexistence. However, these models fail to account for random fluctuations due to demographic and environmental stochasticity which are experienced by all populations. I review some recent mathematical results about persistence and coexistence for models accounting for each of these forms of stochasticity. Demographic stochasticity stems from populations and communities consisting of a finite number of interacting individuals, and often are represented by Markovian models …
Competition is the main driver of population dynamics, which shapes the genetic composition of populations and the assembly of ecological communities. Neutral models assume that all the individuals are equivalent and that the dynamics is governed by demographic (shot) noise, with a steady state species abundance distribution (SAD) that reflects a mutation-extinction equilibrium. Recently, many empirical and theoretical studies emphasized the importance of environmental variations that affect coherently the relative fitness of entire populations. Here we consider two generic time-averaged neutr…
Self-organized pattern synchronization modulated by stochasticity in coupled plankton ecosystems
School of Ecology, Sun Yat-sen University（中山大学生态系统学院）；School of Physics, Sun Yat-sen University（中山大学物理学院）；School of Mathematical Sciences, Shanghai Jiao Tong University（上海交通大学数学科学学院）
We used a metacommunity of 49 discrete communities of aquatic invertebrates to analyze the dynamical relationship between community and metacommunity species distributions as a test of the neutral theory of biodiversity and biogeography. At the community scale, observed variation in species richness and relative abundance was greater than predicted by neutral models, and revealed important differences among species in competitive ability and tolerance for predation. At the metacommunity scale, species with metacommunity proportions of less than 0.01% (38% of the observed metacommunity) were co…
Determining the relative importance of environmental factors, biotic interactions and stochasticity in assembling and maintaining species-rich communities remains a major challenge in ecology. In plant communities, interactions between individuals of different species are expected to leave a spatial signature in the form of positive or negative spatial correlations over distances relating to the spatial scale of interaction. Most studies using spatial point process tools have found relatively little evidence for interactions between pairs of species. More interactions tend to be detected in co…
Beta-diversity has been repeatedly shown to decline with increasing elevation, but the causes of this pattern remain unclear, partly because they are confounded by coincident variation in alpha- and gamma-diversity. We used 8,795 forest vegetation-plot records from the Czech National Phytosociological Database to compare the observed patterns of beta diversity to null-model expectations (beta-deviation) controlling for the effects of alpha- and gamma-diversity. We tested whether \b{eta}-diversity patterns along a 1,200 m elevation gradient exclusively depend on the effect of varying species po…
${\bf Background:}$ The early growth dynamics of the West African Ebola virus epidemic has been qualitatively different for Guinea, Sierra Leone and Liberia. However, it is important to understand these disparate dynamics as trends of a single epidemic spread over regions with similar geographic and cultural aspects, with likely common parameters for transmission rates and the reproduction number $R_0$. ${\bf Methods:}$ We combine a discrete, stochastic SEIR model with a two-scale community network model to demonstrate that the different regional trends may be explained by different community …
Environmental heterogeneity is a determining factor of the structure of biological communities. Thus, understanding the distribution of species along environmental gradients provides assistance to conservation. The goal of this study was to determine the distribution pattern of the herbaceous community in three areas of the Southern Amazon. Sampling was conducted in three modules totaling 39 permanent plots according to the protocol of collection of the Program for Research in Biodiversity. All herbaceous and ground hemiepiphyte subjects above 5 cm were recorded. Multivariate analyses were use…
