Universal scaling of species‐abundance distributions across multiple scales

The scale‐dependent species abundance distribution (SAD) is fundamental in ecology, but few spatially explicit models of this pattern have thus far been studied. Here we show spatially explicit neutral model predictions for SADs over a wide range of spatial scales, which appear to match empirical patterns qualitatively. We find that the assumption of a log‐series SAD in the metacommunity made by spatially implicit neutral models can be justified with a spatially explicit model in the large area limit. Furthermore, our model predicts that SADs on multiple scales are characterized by a single, compound parameter that represents the ratio of the survey area to the species’ average biogeographic range (which is in turn set by the speciation rate and the dispersal distance). This intriguing prediction is in line with recent empirical evidence for a universal scaling of the species‐area curve. Hence we hypothesize that empirical SAD patterns will show a similar universal scaling for many different taxa and across multiple spatial scales.     

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.     

Dispersal stochasticity mediates species richness in source–sink metacommunities

Although it is well‐known that dispersal of organisms within a metacommunity will influence patterns of coexistence and richness, theoretical and experimental studies generally assume that dispersal rates are constant through time. However, dispersal is often a highly variable process that can vary seasonally and/or when stochastic events (e.g. wind storms, droughts, floods) occur. Using a well‐known source–sink metacommunity model, we present novel predictions for local and regional species richness when stochasticity in dispersal is expressly considered. We demonstrate that dispersal stochasticity alters some of the predictions obtained with constant dispersal; the peak of the predicted hump‐shaped relationship between dispersal and local species richness is diminished and shifted towards higher values of dispersal. Dispersal stochasticity increases extinction probabilities of inferior competitor species particularly in metacommunities subjected to severe isolation events (i.e. decreases of dispersal) or homogenization events (i.e. sudden increases of dispersal). Our results emphasize how incorporating dispersal stochasticity into theoretical predictions will broaden our understanding of metacommunities dynamics and their responses to natural and human‐related disturbances.     

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 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]     

Understanding how biodiversity unfolds through time under neutral theory

Theoretical predictions for biodiversity patterns are typically derived under the assumption that ecological systems have reached a dynamic equilibrium. Yet, there is increasing evidence that various aspects of ecological systems, including (but not limited to) species richness, are not at equilibrium. Here, we use simulations to analyse how biodiversity patterns unfold through time. In particular, we focus on the relative time required for various biodiversity patterns (macroecological or phylogenetic) to reach equilibrium. We simulate spatially explicit metacommunities according to the Neutral Theory of Biodiversity (NTB) under three modes of speciation, which differ in how evenly a parent species is split between its two daughter species. We find that species richness stabilizes first, followed by species area relationships (SAR) and finally species abundance distributions (SAD). The difference in timing of equilibrium between these different macroecological patterns is the largest when the split of individuals between sibling species at speciation is the most uneven. Phylogenetic patterns of biodiversity take even longer to stabilize (tens to hundreds of times longer than species richness) so that equilibrium predictions from neutral theory for these patterns are unlikely to be relevant. Our results suggest that it may be unwise to assume that biodiversity patterns are at equilibrium and provide a first step in studying how these patterns unfold through time.     

Dispersal and the transition to sympatry in vertebrates

Under allopatric speciation models, a key step in the build-up of species richness is population dispersal leading to the co-occurrence of previously geographically isolated forms. Despite its central importance for community assembly, the extent to which the transition from spatial segregation (allopatry or parapatry) to coexistence (sympatry) is a predictable process, or alternatively one governed by chance and the vagaries of biogeographic history, remains poorly understood. Here, we use estimated divergence times and current patterns of geographical range overlap among sister species to explore the evolution of sympatry in vertebrates. We show that rates of transition to sympatry vary predictably according to ecology, being faster in marine or strongly dispersive terrestrial clades. This association with organism vagility is robust to the relative frequency of geographical speciation modes and consistent across taxonomic scales and metrics of dispersal ability. These findings reject neutral models of dispersal assembly based simply on evolutionary age and are not predicted by the main alternative view that range overlap is primarily constrained by biotic interactions. We conclude that species differences in dispersal limitation are fundamental in organizing the assembly of ecological communities and shaping broad-scale patterns of biodiversity over space and time.     

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.     

The effects of species pool,dispersal and competition on the diversity–productivity relationship

Aim The diversity–productivity relationship is a controversial issue in ecology. Diversity is sometimes seen to increase with productivity but a unimodal relationship has often been reported. Competitive exclusion was cited initially to account for the decrease of diversity at high productivity. Subsequently, the roles of evolutionary history (species pool size) and dispersal rate have been acknowledged. We explore how the effects of species pool, dispersal and competition combine to produce different diversity–productivity relationships. Methods We use a series of simulations with a spatially explicit, individual‐based model. Following empirical expectations, we used four scenarios to characterize species pool size along the productivity gradient (uniformly low and high, linear increase and unimodal). Similarly, the dispersal rate varied along the productivity gradient (uniformly low and high, and unimodal). We considered both neutral communities and communities with competitive exclusion. Results and main conclusions Our model predicts that competitive interactions will result in unimodal diversity–productivity relationships. The model often predicts unimodal patterns in neutral communities as well, although the decline in richness at high productivity is less than in competing communities. A positive diversity–productivity relationship is simulated for neutral communities when the species pool size increases with productivity and the dispersal rate is high. This scenario is probably more widespread in nature than the others since positive diversity–productivity relationships have been observed more frequently than previously expected, especially in the tropics and for woody species. Our simulated effects of species pool, dispersal and competition on diversity patterns can be linked to empirical observations to uncover mechanisms behind the diversity–productivity relationship.     

Spatial processes that maintain biodiversity in plant communities

The composition of communities of sessile organisms, and the change in species diversity with time, is a spatially explicit phenomenon. Three spatial factors clearly affect diversity: (1) the structure and heterogeneity of the landscape that limits species immigration and ultimate community size; (2) neighborhood interactions that determine colonization and extinction rates and influence residence times of local populations; and (3) disturbances that open spatially contiguous areas for recolonization by less abundant species. The importance of these three factors was first reviewed and then examined with a spatially explicit, multi-species model of plant dispersal, competition and establishment, with an assumption of neutrality (all species had equivalent life histories) that reduced the initial dimensionality of the problem. The simulations assumed that the probability of immigration was a linear function of mainland abundance and distance to islands, similar to the equilibrium theory of island biogeography and the unified neutral theory of biodiversity. The rate of increase in species richness was not constant across island sizes, declining as island area became very large. This pattern was explained by the spatial dynamics of colonization and establishment, a non-random process that cannot be explained by passive sampling alone. Simulations showed that population establishment depended critically on rare long-distance dispersal events while population persistence was achieved by the formation of aggregated species distributions that developed through restricted dispersal and local competitive interactions. Nevertheless, species richness always declined to a single species in the absence of disturbances, while up to 40 species could persist to 10,000 years when spatially dependent mortality was added. Further explorations with spatially explicit models will be required to fully appreciate the consequence of land use change and altered disturbance regimes on patterns of species distribution and the maintenance of diversity.     

Theory predicts a rapid transition from niche-structured to neutral biodiversity patterns across a speciation-rate gradient

A central challenge in community ecology is to predict patterns of biodiversity with mechanistic models. The neutral model of biodiversity is a simple model that appears to provide parsimonious and accurate predictions of biodiversity patterns in some ecosystems, even though it ignores processes such as species interactions and niche structure. In a recent paper, we used analytical techniques to reveal why the mean predictions of the neutral model are robust to niche structure in high diversity but not low-diversity ecosystems. In the present paper, we explore this phenomenon further by generating stochastic simulated data from a spatially implicit hybrid niche-neutral model across different speciation rates. We compare the resulting patterns of species richness and abundance with the patterns expected from a pure neutral and a pure niche model. As the speciation rate in the hybrid model increases, we observe a surprisingly rapid transition from an ecosystem in which diversity is almost entirely governed by niche structure to one in which diversity is statistically indistinguishable from that of the neutral model. Because the transition is rapid, one prediction of our abstract model is that high-diversity ecosystems such as tropical forests can be approximated by one simple model—the neutral model—whereas low-diversity ecosystems such as temperate forests can be approximated by another simple model—the niche model. Ecosystems that require the hybrid model are predicted to be rare, occurring only over a narrow range of speciation rates.     

Patterns of species ranges, speciation, and extinction

The exact nature of the relationship among species range sizes, speciation, and extinction events is not well understood. The factors that promote larger ranges, such as broad niche widths and high dispersal abilities, could increase the likelihood of encountering new habitats but also prevent local adaptation due to high gene flow. Similarly, low dispersal abilities or narrower niche widths could cause populations to be isolated, but such populations may lack advantageous mutations due to low population sizes. Here we present a large-scale, spatially explicit, individual-based model addressing the relationships between species ranges, speciation, and extinction. We followed the evolutionary dynamics of hundreds of thousands of diploid individuals for 200,000 generations. Individuals adapted to multiple resources and formed ecological species in a multidimensional trait space. These species varied in niche widths, and we observed the coexistence of generalists and specialists on a few resources. Our model shows that species ranges correlate with dispersal abilities but do not change with the strength of fitness trade-offs; however, high dispersal abilities and low resource utilization costs, which favored broad niche widths, have a strong negative effect on speciation rates. An unexpected result of our model is the strong effect of underlying resource distributions on speciation: in highly fragmented landscapes, speciation rates are reduced.     

How Neutral is Ecology?

Neutral ecological theory comes in two flavors—a two-stage model with space implicit and a spatially explicit version. Reconciliation of the two flavors has proven problematic. Panmixis, an implicit assumption of the two-stage model, is neither realistic for nor supported by tropical forest trees. However, in spatially explicit versions, stochastic species input in local communities is still necessary to retain high species richness. A unified theory of biodiversity must include both stochasticity and relevant ecological mechanisms.     

The causes of species richness patterns across space, time, and clades and the role of "ecological limits"

A major goal of research in ecology and evolution is to explain why species richness varies across habitats, regions, and clades. Recent reviews have argued that species richness patterns among regions and clades may be explained by "ecological limits" on diversity over time, which are said to offer an alternative explanation to those invoking speciation and extinction (diversification) and time. Further, it has been proposed that this hypothesis is best supported by failure to find a positive relationship between time (e.g., clade age) and species richness. Here, I critically review the evidence for these claims, and propose how we might better study the ecological and evolutionary origins of species richness patterns. In fact, ecological limits can only influence species richness in clades by influencing speciation and extinction, and so this new "alternative paradigm" is simply one facet of the traditional idea that ecology influences diversification. The only direct evidence for strict ecological limits on richness (i.e., constant diversity over time) is from the fossil record, but many studies cited as supporting this pattern do not, and there is evidence for increasing richness over time. Negative evidence for a relationship between clade age and richness among extant clades is not positive evidence for constant diversity over time, and many recent analyses finding no age-diversity relationship were biased to reach this conclusion. More comprehensive analyses strongly support a positive age-richness relationship. There is abundant evidence that both time and ecological influences on diversification rates are important drivers of both large-scale and small-scale species richness patterns. The major challenge for future studies is to understand the ecological and evolutionary mechanisms underpinning the relationships between time, dispersal, diversification, and species richness patterns.     

How likely is speciation in neutral ecology?

Patterns of biodiversity predicted by the neutral theory rely on a simple phenomenological model of speciation. To further investigate the effect of speciation on neutral biodiversity, we analyze a spatially explicit neutral model based on population genetics. We define the metacommunity as a system of populations exchanging migrants, and we use this framework to introduce speciation with little or no gene flow (allopatric and parapatric speciation). We find that with realistic mutation rates, our metacommunity model driven by neutral processes cannot support more than a few species. Adding natural selection in the population genetics of speciation increases the number of species in the metacommunity, but the level of diversity found in the Barro Colorado Island is difficult to reach.     

An integrative framework of coexistence mechanisms in competitive metacommunities

Species distribution in a metacommunity varies according to their traits, the distribution of environmental conditions and connectivity among localities. These ingredients contribute to coexistence across spatial scales via species sorting, patch dynamics, mass effects and neutral dynamics. These mechanisms however seldom act in isolation and the impact of landscape configuration on their relative importance remains poorly understood. We present a new model of metacommunity dynamics that simultaneously considers these four possible mechanisms over spatially explicit landscapes and propose a statistical approach to partition their contribution to species distribution. We find that landscape configuration can induce dispersal limitations that have negative consequences for local species richness. This result was more pronounced with neutral dynamics and mass effect than with species sorting or patch dynamics. We also find that the relative importance of the four mechanisms varies not only among landscape configurations, but also among species, with some species being mostly constrained by dispersal and/or drift and others by sorting. Changes in landscape properties might lead to a shift in coexistence mechanisms and, by extension, to a change in community composition. This confirms the importance of considering landscape properties for conservation and management. Our results illustrate the idea that ecological communities are the results of multiple mechanisms acting at the same time and complete our understanding of spatial processes in competitive metacommunities.     

Can the tropical conservatism hypothesis explain temperate species richness patterns? An inverse latitudinal biodiversity gradient in the New World snake tribe Lampropeltini

Aim  A latitudinal gradient in species richness, defined as a decrease in biodiversity away from the equator, is one of the oldest known patterns in ecology and evolutionary biology. However, there are also many known cases of increasing poleward diversity, forming inverse latitudinal biodiversity gradients. As only three processes (speciation, extinction and dispersal) can directly affect species richness in areas, similar factors may be responsible for both classical (high tropical diversity) and inverse (high temperate diversity) gradients. Thus, a modified explanation for differential species richness which accounts for both patterns would be preferable to one which only explains high tropical biodiversity.
Location  The New World.
Methods  We test several proposed ecological, temporal, evolutionary and spatial explanations for latitudinal diversity gradients in the New World snake tribe Lampropeltini, which exhibits its highest biodiversity in temperate regions.
Results  We find that an extratropical peak in species richness is not explained by latitudinal variation in diversification rate, the mid-domain effect, or Rapoport's rule. Rather, earlier colonization and longer duration in the temperate zones allowing more time for speciation to increase biodiversity, phylogenetic niche conservatism limiting tropical dispersal and the expansion of the temperate zones in the Tertiary better explain inverse diversity gradients in this group.
Main conclusions  Our conclusions are the inverse of the predictions made by the tropical conservatism hypothesis to explain higher biodiversity near the equator. Therefore, we suggest that the processes invoked are not intrinsic to the tropics but are dependent on historical biogeography to determine the distribution of species richness, which we refer to as the 'biogeographical conservatism hypothesis'.     

Searching for mechanisms of synchrony in spatially structured gamebird populations

1.  Time series data on five species of gamebird from the Dolomitic Alps were used to examine the relative importance of dispersal and common stochastic events in causing synchrony between spatially structured populations.
2.  Cross-correlation analysis of detrended time series was used to describe the spatial pattern of fluctuations in abundance, while standardized time series were used to describe both fluctuations and the trend in abundance. There were large variations in synchrony both within and between species and only weak negative relationships with distance.
3.  Species in neighbouring habitats were more likely to be in synchrony than species separated by several habitats. Species with similar density-dependent structure were more likely to be in synchrony.
4.  In order to estimate the relative importance of dispersal and environmental stochasticity, we modelled the spatial dynamics of each species using two different approaches. First, we used estimating functions and bootstrapping of time series data to calculate the relative importance of dispersal and stochastic effects for each species. Second, we estimated the intensity of environmental stochasticity from climatic records during the breeding season and then modelled the dispersal rate and dispersal distance for each species. The two models exhibited similar results for rock ptarmigan, black grouse, hazel grouse and rock partridge, while contrasting patterns were observed for capercaillie.
5.  The results suggest that environmental stochasticity plays the dominant role in synchronizing the fluctuations of these galliform species, although there will also be some dispersal between populations.     

Neutral community dynamics, the mid-domain effect and spatial patterns in species richness

The mid‐domain effect (MDE) aims to explain spatial patterns in species richness invoking only stochasticity and geometrical constraints. In this paper, we used simulations to show that its main qualitative prediction, a hump‐shaped pattern in species richness, converges to the expectation of a spatially bounded neutral model when communities are linked by short‐distance migration. As these two models can be linked under specific situations, neutral theory may provide a mechanistic population level basis for MDE. This link also allows establishing in which situations MDE patterns are more likely to be found. Also, in this situation, MDE models could be used as a first approximation to understand the role of both stochastic (ecological drift and migration) and deterministic (adaptation to environmental conditions) processes driving the spatial structure of species richness.     

Species richness and evolutionary niche dynamics: a spatial pattern-oriented simulation experiment

Evolutionary processes underlying spatial patterns in species richness remain largely unexplored, and correlative studies lack the theoretical basis to explain these patterns in evolutionary terms. In this study, we develop a spatially explicit simulation model to evaluate, under a pattern-oriented modeling approach, whether evolutionary niche dynamics (the balance between niche conservatism and niche evolution processes) can provide a parsimonious explanation for patterns in species richness. We model the size, shape, and location of species' geographical ranges in a multivariate heterogeneous environmental landscape by simulating an evolutionary process in which environmental fluctuations create geographic range fragmentation, which, in turn, regulates speciation and extinction. We applied the model to the South American domain, adjusting parameters to maximize the correspondence between observed and predicted patterns in richness of about 3,000 bird species. Predicted spatial patterns, which closely resemble observed ones (r2=0.795), proved sensitive to niche dynamics processes. Our simulations allow evaluation of the roles of both evolutionary and ecological processes in explaining spatial patterns in species richness, revealing the enormous potential of the link between ecology and historical biogeography under integrated theoretical and methodological frameworks.