Community differentiation on landscapes: drift, migration and speciation

Theories of the differentiation of ecological communities on landscapes have typically not considered evolutionary dynamics. Here we analytically study the expected differentiation among local communities in a large metacommunity, undergoing speciation, ecological drift and intercommunity dispersal, in the context of neutral theory. We demonstrate that heterogeneity in species diversity and abundance arises among communities when local communities are small and intercommunity migration is infrequent. We propose a new measure to describe community differentiation, defined as the average correlation or the average probability (C_st) that two randomly sampled individuals of the same species within local communities are from the same ancestor. The effects of driving forces (migration, mutation, and ecological drift) are incorporated into the two-level hierarchical community structure in a finite island model of neutral communities. Community differentiation can increase the effective metacommunity size or the Hubbell's fundamental species diversity in the metacommunity by a factor (1−C_st)⁻¹. Significant community differentiation arises when C_st≠0. Intercommunity migration promotes species diversity in local communities but reduce species diversity in the metacommunity. In either the finite or infinite island case, one can estimate the number of intercommunity migrants by using multiple local community datasets when the speciation is negligible in the neutral local communities, or by using the metacommunity dataset when the speciation is included in the local neutral communities. These results highlight the significance of the evolutionary mechanisms in generating heterogeneous communities in the absence of complicated ecological processes on large landscapes.     

Hubbell's fundamental biodiversity parameter and the Simpson diversity index

Central to Hubbell's neutral theory of biodiversity is a universal, dimensionless fundamental biodiversity parameter that is the product of community size and speciation rate. One of the most important discoveries of Hubbell's theory is that the species‐abundance distribution and the species–area relationship of the neutral metacommunity is completely determined by this fundamental biodiversity parameter, although the diversity patterns of the local community are collectively determined by the biodiversity parameter and migration. Using the relative abundance of species and following the concept of heterozygosity of population genetics, here we developed an analytical relationship between this biodiversity parameter and the well‐known Simpson diversity index. This relationship helps bridge the evolutionary aspect of biodiversity to the ecological and statistical aspect of the diversity. The relationship between these two parameters suggests that diversity patterns of the metacommunity can also be equally described by the Simpson index. This relationship provides an alternative approach to interpret and estimate the fundamental biodiversity parameter for the metacommunity.     

群落生态学的中性理论

生物多样性的分布格局和维持机制一直是群落生态学研究的核心问题,其中的关键是物种的共存机制。长期以来,生态位分化的思想在这一研究领域占据着主导地位。然而这一理论在解释热带雨林很高的物种多样性时遇到了困难。而以Hubbell为代表提出的群落中性漂变理论则假定在同一营养级物种构成的群落中不同物种的不同个体在生态学上可看成是完全等同的;物种的多度随机游走,群落中的物种数取决于物种灭绝和物种迁入/新物种形成之间的动态平衡。在这一假定之下,该理论预言了两种统计分布。一种是集合群落在点突变形成新物种的模式下其各个物种相对多度服从对数级数分布,而受扩散限制的局域群落以及按照随机分裂为新物种模式形成的集合群落则服从零和多项式分布。与生态位理论相反,中性理论不以种间生态位差异作为研究群落结构的出发点,而是以物种间在个体水平上的对等性作为前提。该理论第一次从基本生态学过程(出生、死亡、迁移、物种分化)出发,给出了群落物种多度分布的机理性解释,同时其预测的物种多度分布格局在实际群落中也得到了广泛的印证。因此,中性理论自诞生以来便在生态学界引发了极大的反响,也包括一些反对的声音。该文重点综述了关于中性理论的假设、预测和物种形成模式等方面的最新研究进展,包括中性理论本身的发展、关于中性理论的假设和预测的合理性检验以及在集合群落尺度上物种分化模式的讨论;并指出未来发展方向可能是在生态位理论和中性理论之间架起一座桥梁,同时发展包含随机性的群落生态位模型,以及允许种间差异的近中性模型。     

Neutral theory in community ecology

One of the central goals of community ecology is to understand the forces that maintain species diversity within communities. The traditional niche-assembly theory asserts that species live together in a community only when they differ from one another in resource uses. But this theory has some difficulties in explaining the diversity often observed in specie-rich communities such as tropical forests. As an alternative to the niche theory, Hubbell and other ecologists introduced a neutral model. Hubbell argues that the number of species in a community is controlled by species extinction and immigration or speciation of new species. Assuming that all individuals of all species in a trophically similar com-munity are ecologically equivalent, Hubbell's neutral theory predicts two important statistical distributions. One is the asymptotic log-series distribution for the metacommunities under point mutation speciation, and the other is the zero-sum multinomial distribution for both local communities under dispersal limitation and metacommunities under random fission speciation. Unlike the niche-assembly theory, the neutral theory takes similarity in species and individuals as a starting point for investigating species diversity. Based on the fundamental processes of birth, death, dispersal and spe-ciation, the neutral theory provided the first mechanistic explanation of species abundance distribution commonly observed in natural communities. Since the publication of the neutral theory, there has been much discussion about it, pro and con. In this paper, we summarize recent progress in the assumption, prediction and speciation mode of the neutral theory, including progress in the theory itself, tests about the assumption of the theory, prediction and speciation mode at the metacommunity level. We also suggest that the most important task in the future is to bridge the niche-assembly theory and the neutral theory, and to add species differences to the neutral theory and more stochasticity to the niche theory.     

Neutral theory in community ecology

One of the central goals of community ecology is to understand the forces that maintain species diversity within communities. The traditional niche-assembly theory asserts that species live together in a community only when they differ from one another in resource uses. But this theory has some difficulties in explaining the diversity often observed in specie-rich communities such as tropical forests. As an alternative to the niche theory, Hubbell and other ecologists introduced a neutral model. Hubbell argues that the number of species in a community is controlled by species extinction and immigration or speciation of new species. Assuming that all individuals of all species in a trophically similar community are ecologically equivalent, Hubbell’s neutral theory predicts two important statistical distributions. One is the asymptotic log-series distribution for the metacommunities under point mutation speciation, and the other is the zero-sum multinomial distribution for both local communities under dispersal limitation and metacommunities under random fission speciation. Unlike the niche-assembly theory, the neutral theory takes similarity in species and individuals as a starting point for investigating species diversity. Based on the fundamental processes of birth, death, dispersal and speciation, the neutral theory provided the first mechanistic explanation of species abundance distribution commonly observed in natural communities. Since the publication of the neutral theory, there has been much discussion about it, pro and con. In this paper, we summarize recent progress in the assumption, prediction and speciation mode of the neutral theory, including progress in the theory itself, tests about the assumption of the theory, prediction and speciation mode at the metacommunity level. We also suggest that the most important task in the future is to bridge the niche-assembly theory and the neutral theory, and to add species differences to the neutral theory and more stochasticity to the niche theory. __________ Translated from Journal of Plant Ecology, 2006, 30(5): 868–877 [译自:植物生态学报]     

Beta diversity in spatially implicit neutral models: a new way to assess species migration

The spatially implicit neutral model (SINM) of S. P. Hubbell predicts species' abundance distributions at two levels: local communities where extinction balances immigration, characterized by the immigration number I, and the metacommunity, a source pool of migrants where speciation balances extinction. Previously, a plot's I was estimated from its species abundance distribution. Here, we relate neutral theory to the additive partitioning of species diversity and calculate the immigration rate into different plots from the variation in species composition among them. We revisit the G(ST) statistic of population genetics to introduce a new version, G(ST)(k), conditional on each community sample k. We derive an analytical expectation of G(ST)(k) as a function of the local immigration number, I(k), under a generalized version of the SINM, which allows the pool of migrants to deviate from the large-scale speciation-extinction balance. Simulations and field data suggest that G(ST)(k) provides reasonable estimates of immigration numbers, which were compared with the results from alternative likelihood-based estimations.     

Species abundance distribution and dynamics in two locally coupled communities

This study considered a model for species abundance dynamics in two local community (or islands) connected to a regional metacommunity. The model was analyzed using continuous probabilistic technique that employs Kolmogorov-Fokker-Planck forward equation to derive the probability density of the species abundance in the two local communities. Using this technique, we proposed a classification for the species abundance dynamics in the local communities. This classification was made based on such characteristics as immigration intensity, species representation in the metacommunity and the size of local communities. We further distinguished several different scenarios for species abundance dynamics using different ecological characteristics such as species persistence, extinction and monodominance in one or both local communities. The similarity of the species abundance distributions between the two local communities was studied using the correlation coefficient between species abundances in two local communities. The correlation is a function of migration rates between local communities and between local and metacommunity. Immigration between local communities drives the homogenization of the local communities, while immigration from the metacommunity will differentiate them. This community subdivision model provides useful insights for studying the effect of landscape fragmentation on species diversity.     

Linking dispersal, immigration and scale in the neutral theory of biodiversity

In the classic spatially implicit formulation of Hubbell's neutral theory of biodiversity a local community receives immigrants from a metacommunity operating on a relatively slow timescale, and dispersal into the local community is governed by an immigration parameter m . A current problem with neutral theory is that m lacks a clear biological interpretation. Here, we derive analytical expressions that relate the immigration parameter m to the geometry of the plot defining the local community and the parameters of a dispersal kernel. Our results facilitate more rigorous and extensive tests of the neutral theory: we conduct a test of neutral theory by comparing estimates of m derived from fits to empirical species abundance distributions to those derived from dispersal kernels and find acceptable correspondence; and we generate a new prediction of neutral theory by investigating how the shapes of species abundance distributions change theoretically as the spatial scale of observation changes. We also discuss how our main analytical results can be used to assess the error in the mean-field approximations associated with spatially implicit formulations of neutral theory.     

Metacommunity speciation models and their implications for diversification theory

The emergence of new frameworks combining evolutionary and ecological dynamics in communities opens new perspectives on the study of speciation. By acknowledging the relative contribution of local and regional dynamics in shaping the complexity of ecological communities, metacommunity theory sheds a new light on the mechanisms underlying the emergence of species. Three integrative frameworks have been proposed, involving neutral dynamics, niche theory, and life history trade‐offs respectively. Here, we review these frameworks of metacommunity theory to emphasise that: (1) studies on speciation and community ecology have converged towards similar general principles by acknowledging the central role of dispersal in metacommunities dynamics, (2) considering the conditions of emergence and maintenance of new species in communities has given rise to new models of speciation embedded in the metacommunity theory, (3) studies of diversification have shifted from relating phylogenetic patterns to landscapes spatial and ecological characteristics towards integrative approaches that explicitly consider speciation in a mechanistic ecological framework. We highlight several challenges, in particular the need for a better integration of the eco‐evolutionary consequences of dispersal and the need to increase our understanding on the relative rates of evolutionary and ecological changes in communities.     

Demographic trade-offs determine species abundance and diversity

Aims Much recent theory has focused on the role of neutral processes in assembling communities, but the basic assumption that all species are demographically identical has found little empirical support. Here, we show that the framework of the current neutral theory can easily be generalized to incorporate species differences so long as fitness equivalence among individuals is maintained through trade-offs between birth and death.Methods Our theory development is based on a careful reformulation of the Moran model of metacommunity dynamics in terms of a non-linear one-step stochastic process, which is described by a master equation.Important findings We demonstrate how fitness equalization through demographic trade-offs can generate significant macroecological diversity patterns, leading to a very different interpretation of the relation between Fisher's α and Hubbell's fundamental biodiversity number. Our model shows that equal fitness (not equal demographics) significantly promotes species diversity through strong selective sieving of community membership against high-mortality species, resulting in a positive association between species abundance and per capita death rate. An important implication of demographic trade-off is that it can partly explain the excessively high speciation rates predicted by the neutral theory of the stronger symmetry. Fitness equalization through demographic trade-offs generalizes neutral theory by considering heterospecific demographic difference, thus representing a significant step toward integrating the neutral and niche paradigms of biodiversity.     

Dispersal, edaphic fidelity and speciation in species-rich Western Australian shrublands: evaluating a neutral model of biodiversity

Over evolutionary time, the number of species in a community reflects the balance between the rate of speciation and the rate of extinction. Over shorter time‐scales local species richness is also affected by how often species move into and out of the local community. These processes are at the heart of Hubbell's ‘unified neutral theory of biodiversity’ ( Hubbell 2001 ). Hubbell's spatially implicit, dispersal‐limited neutral model is the most widely used of the many implementations of neutral theory and it provides an estimate of the rate of speciation in a metacommunity (if metacommunity size is known) and the rate at which species migrate into the local community from the wider metacommunity. Recently, this neutral model has been used to compare rates of speciation and migration in the species‐rich fynbos of South Africa and in neotropical forests. Here we use new analytical methods for estimating the neutral model's parameters to infer speciation and dispersal rates for three sites in species‐rich sclerophyll shrublands (equivalent to fynbos) in Western Australia (WA). Our estimates suggest that WA shrublands are intermediate between fynbos and tropical rainforest in terms of speciation and dispersal. Although a weak test, the model predicts species abundance distributions and species accumulation curves similar to those observed at the three sites. The neutral model's predictions also remain plausible when confronted with independent data describing: (1) known edaphic relationships between sites, (2) estimates of metacommunity species richness and (3) rates of speciation among resprouters and nonsprouters. Two of the site pairs, however, show species turnovers significantly different from those predicted by the spatially implicit form of the neutral model that we use. This suggests that non‐neutral processes, in this case probably edaphic specialisation, are important in the WA shrubland metacommunity. The neutral model predicts similar rates of speciation in resprouter and sprouter taxa, a finding supported by recent molecular phylogenies. Finally, when converted into temporally scaled speciation rates and species longevities, the estimates produced by the neutral model seem implausible. The apparent departure from neutrality in the turnover of species between some sites and the implausible temporal dynamics may be due to the particular model chosen and does not reduce the significance of our other results, which confirm that local dispersal limitation, coupled with broader scale edaphic fidelity, combine to structure this biodiverse metacommunity.     

Disentangling the effects of local and regional processes on biodiversity patterns through taxon‐contingent metacommunity network analysis

Metacommunity theory, which has gained a central position in ecology, accounts for the role of migration in patterns of diversity among communities at different scales. Community isolation has a main role in this theory, but is difficult to estimate empirically, partly due to the taxon‐dependent nature of dispersal. Landscapes could be perceived as either fragmented or connected for organisms with contrasting dispersal abilities. Indeed, the dispersal ability of a taxon, and the spatial scale at which eco‐evolutionary processes shape local diversity, determine a taxon‐dependent metacommunity network. In this paper, we introduce a methodology using graph theory to define this taxon‐dependent metacommunity network and then to estimate the isolation of local communities. We analyzed the relative importance of local conditions versus community isolation as determinants of community richness for 25 taxa inhabiting 18 temporary ponds. Although local factors have been the foci of most previous empirical and theoretical considerations, we demonstrate that the metacommunity network is an equally important contributor to local diversity. We also found that the relative effect of local conditions and the metacommunity network depend on body size and taxon abundance. Local diversity of larger species was more affected by patch isolation, while taxon abundances were associated with positive or negative effects of isolation. Our results provide empirical support for the proposed role of metacommunity networks as determinants of community diversity and show the taxon‐dependent nature of these networks.     

Reconciling neutral community models and environmental filtering: theory and an empirical test

It is widely believed that the neutral theory of biodiversity cannot be used for parameter inference if the assumption of neutrality is not met. The goal of this work is to extend this neutral framework to quantify the intensity of recruitment limitation (limited dispersal plus environmental filtering) in natural species assemblages. We model several local communities as part of a larger metacommunity, and we assume that neutrality holds in each local community, but not in the metacommunity. The immigration rate m does not only reflect dispersal limitation into a given local community, but also the intensity of environmental filtering. We develop a novel statistical method to infer the immigration parameter m in each local community. Using simulated datasets, we show that m indeed depends on both dispersal limitation and on the intensity of environmental filtering. We then apply this method to a network of tropical tree plots in central Panama. Inferred recruitment rates m were positively correlated with the fraction of trees dispersed by mammals, and with annual rainfall, possibly due to a weaker environmental filtering as rainfall increases. Finally, m, as estimated from trees greater than 1 cm trunk diameter, were significantly larger than an estimation based on trees greater than 10 cm trunk diameter. This suggests a cumulative effect of environmental filtering upon trees throughout their ontogeny.     

Asymmetry in species regional dispersal ability and the neutral theory

The neutral assumption that individuals of either the same or different species share exactly the same birth, death, migration, and speciation probabilities is fundamental yet controversial to the neutral theory. Several theoretical studies have demonstrated that a slight difference in species per capita birth or death rates can have a profound consequence on species coexistence and community structure. Whether asymmetry in migration, a vital demographic parameter in the neutral model, plays an important role in community assembly still remains unknown. In this paper, we relaxed the ecological equivalence assumption of the neutral model by introducing differences into species regional dispersal ability. We investigated the effect of asymmetric dispersal on the neutral local community structure. We found that per capita asymmetric dispersal among species could reduce species richness of the local community and result in deviations of species abundance distributions from those predicted by the neutral model. But the effect was moderate compared with that of asymmetries in birth or death rates, unless very large asymmetries in dispersal were assumed. A large difference in species dispersal ability, if there is, can overwhelm the role of random drift and make local community dynamics deterministic. In this case, species with higher regional dispersal abilities tended to dominate in the local community. However, the species abundance distribution of the local community under asymmetric dispersal could be well fitted by the neutral model, but the neutral model generally underestimated the fundamental biodiversity number but overestimated the migration rate in such communities.     

Demographic analysis of Hubbell's neutral theory of biodiversity

Hubbell's neutral model is increasingly applied in both theoretical and empirical studies but so far little attention has been paid to the ecological mechanisms that determine species diversity in neutral communities. In this contribution we use a stochastic individual-based Markovian model to provide an explicit derivation of Hubbell's local community model from the fundamental processes of reproduction, mortality, and immigration, and show that such derivation provides important insights on the mechanisms regulating species diversity that cannot be obtained from the original model and its previous extensions. One important insight is that the basic parameters of Hubbell's model, community size (J) and the probability that a dying individual will be replaced by an immigrant (m), cannot be considered independent and that their interdependency leads to a counterintuitive trade-off between community size and species diversity. We further demonstrate that Hubbell's treatment of community size as a free parameter hides fundamental mechanisms that influence species diversity through their effect on the size of the community. For example, while in Hubbell's model immigration can only increase species diversity by promoting colonization rates, the demographic derivation shows that immigration can also promote species diversity by reducing extinction rates. Our demographic derivation also unifies previous contrasting predictions about the effect of reproduction on species diversity by showing that both positive and negative effects are possible, and that the balance between the two effects depends on the size of the community. The demographic derivation also reconciles an apparent contradiction between Hubbell's theory and patch occupancy theory, and integrates three previously proposed mechanisms of species diversity, the More Individuals Hypothesis, the rescue effect, and the dilution effect, within a single, unified framework.     

Species diversity in neutral metacommunities: a network approach

Biologists seek an understanding of the processes underlying spatial biodiversity patterns. Neutral theory links those patterns to dispersal, speciation and community drift. Here, we advance the spatially explicit neutral model by representing the metacommunity as a network of smaller communities. Analytic theory is presented for a set of equilibrium diversity patterns in networks of communities, facilitating the exploration of parameter space not accessible by simulation. We use this theory to evaluate how the basic properties of a metacommunity – connectivity, size, and speciation rate – determine overall metacommunity γ -diversity, and how that is partitioned into α - and β -components. We find spatial structure can increase γ -diversity relative to a well-mixed model, even when θ is held constant. The magnitude of deviations from the well-mixed model and the partitioning into α - and β -diversity is related to the ratio of migration and speciation rates. γ -diversity scales linearly with metacommunity size even as α - and β -diversity scale nonlinearly with size.     

A novel genealogical approach to neutral biodiversity theory

Current neutral theory in community ecology views local biodiversity as a result of the interplay between speciation, extinction and immigration. Simulations and a mean‐field approximation have been used to study this neutral theory. As simulations have limitations of convergence and the mean‐field approximation ignores dependencies between species’ abundances when applied to species‐abundance data, there is still no final conclusion whether the neutral theory or the traditional lognormal model describes community structure best. We present a novel analytical framework, based on the genealogy of individuals in the local community, to overcome the problems of previous approaches, and show, using Bayesian statistics, that the lognormal model provides a slightly better fit to the species‐abundance distribution of a much‐discussed tropical tree community. A key feature of our approach is that it shows the tight link between genetic and species diversity, which creates important perspectives to future integration of evolutionary and community ecological theory.     

Neutral processes and species sorting in benthic microalgal community assembly: effects of tidal resuspension

Benthic microalgae (BMA) provide vital food resources for heterotrophs and stabilize sediments with their extracellular secretions. A central goal in ecology is to understand how processes such as species interactions and dispersal, contribute to observed patterns of species abundance and distribution. Our objectives were to assess the effects of sediment resuspension on microalgal community structure. We tested whether taxa‐abundance distributions could be predicted using neutral community models (NCMs) and also specific hypotheses about passive migration: (i) As migration decreases in sediment patches, BMA α‐diversity will decrease, and (ii) As migration decreases, BMA community dissimilarity (β‐diversity) will increase. Co‐occurrence indices (checkerboard score and variance ratio) were also computed to test for deterministic factors, such as competition and niche differentiation, in shaping communities. Two intertidal sites (mudflat and sand bar) differing in resuspension regime were sampled throughout the tidal cycle. Fluorometry and denaturing gradient gel electrophoresis were utilized to investigate diatom community structure. Observed taxa‐abundances fit those predicted from NCMs reasonably well (R² of 0.68–0.93), although comparisons of observed local communities to artificial randomly assembled communities rejected the null hypothesis that diatom communities were assembled solely by stochastic processes. No co‐occurrence tests indicated a significant role for competitive exclusion or niche partitioning in microalgal community assembly. In general, predictions about relationships between migration and species diversity were supported for local community dynamics. BMA at low tide (lowest migration) exhibited reduced α‐diversity as compared to periods of immersion at both mudflat and sand bar sites. β‐diversity was higher during low tide emersion on the mudflat, but did not differ temporally at the sand bar site. In between‐site metacommunity comparisons, low‐ and high‐resuspension sites exhibited distinct community compositions while the low‐energy mudflats contained higher microalgal biomass and greater α‐diversity. To our knowledge this is the first study to test the relevance of neutral processes in structuring marine microalgal communities. Our results demonstrate a prominent role for stochastic factors in structuring local BMA community assembly, although unidentified nonrandom processes also appear to play some role. High passive migration, in particular, appears to help maintain species diversity and structure communities in both sand and muddy habitats.     

Dispersal rates affect species composition in metacommunities of Sarracenia purpurea inquilines

Dispersal among local communities can have a variety of effects on species composition and diversity at local and regional scales. Local conditions (e.g., resource and predator densities) can have independent effects, as well as interact with dispersal, to alter these patterns. Based on metacommunity models, we predicted that local diversity would show a unimodal relationship with dispersal frequency. We manipulated dispersal frequencies, resource levels, and the presence of predators (mosquito larvae) among communities found in the water-filled leaves of the pitcher plant Sarracenia purpurea. Diversity and abundance of species of the middle trophic level, protozoa and rotifers, were measured. Increased dispersal frequencies significantly increased regional species richness and protozoan abundance while decreasing the variance among local communities. Dispersal frequency interacted with predation at the local community scale to produce patterns of diversity consistent with the model. When predators were absent, we found a unimodal relationship between dispersal frequency and diversity, and when predators were present, there was a flat relationship. Intermediate dispersal frequencies maintained some species in the inquiline communities by offsetting extinction rates. Local community composition and the degree of connectivity between communities are both important for understanding species diversity patterns at local and regional scales.