Untangling the mechanisms of cryptic species coexistence in a nematode community through individual-based modelling

Cryptic species are morphologically identical but genetically distinct, and are prominent across numerous phyla. The coexistence of such closely related species on local scales would seem to run counter to traditional coexistence and competition theory; it has been hypothesized as a consequence of differences in their resource use or tolerances to environmental conditions. We developed an individual-based model of a community of three cryptic Litoditis marina (nematode) species, to understand how individual-level interspecific and intraspecific interactions might explain the coexistence of these closely related species. The model incorporates individuals' reproduction, competition, dispersal and resource use. Data characterizing the cryptic species (growth rates, dispersal ability, competitive interactions and responses to changing environmental conditions) were obtained from laboratory experiments involving both mono- and multispecific nematode cultures, and are used to parameterize the model. Simulation studies are used to investigate which individual-level mechanisms of dispersal and interaction lead to the characteristic population-level patterns observed experimentally. Our results highlight the key role of intraspecific competition in mediating dispersal and therefore co-occurrence of the cryptic species. The differences in dispersal also influence the response of the cryptic species to competition, a combination of factors that provides an explanation for their co-occurrence. These results provide insights into how changes in individual-level processes can be amplified to affect population-level co-occurrence.     

Scaling up from local competition to regional coexistence across two scales of spatial heterogeneity: insect larvae in the fruits of Apeiba membranacea

Species that live in patchy and ephemeral habitats can compete strongly for resources within patches at a small scale. The ramifications of these interactions for population dynamics and coexistence at regional scales will depend on the intraspecific and interspecific distributions of individuals among patches. Spatial heterogeneity due to independent aggregation of competitors among patchy habitats is an important mechanism maintaining species diversity. I describe regional patterns of aggregation for four species of insect larvae in the fruits of Apeiba membranacea, a Neotropical rainforest tree. This aggregation results from variation in densities at a small scale (among the fruits under a single tree), compounded by significant variation among trees in both mean densities and degrees of aggregation. Both the degrees of aggregation and mean densities are statistically independent within and across species at both spatial scales. I evaluate the regional consequences of these spatial patterns by using maximum likelihood methods to parameterize a model that includes both explicit measures of the strength of competition and spatial variation at both within- and among-tree spatial scales. Despite strong competitive interactions among these species, during 2 years the observed spatial variation at both scales combined was sufficient to explain the coexistence of these species, although other coexistence mechanisms may also operate simultaneously. The observed spatial variation at small spatial scales may not be sufficient for coexistence, indicating the importance of considering multiple sources of spatial heterogeneity when scaling up from experiments that investigate local interactions to regional patterns of coexistence.     

Spatial heterogeneity of mortality and temporal fluctuation in fertility promote coexistence but not vice versa: a random-community approach

Both spatial heterogeneity and temporal fluctuation of the environment are important mechanisms promoting species coexistence, but they work in different manners. We consider many pairs of species with randomly generated survivorship and fertility in the lottery model, and examine how the variability in demographic processes affects the outcome of competition. The results are: [1] Coexistence is easier if habitat difference in mortality is greater, or if year-to-year variation in reproductive rate is larger. But neither habitat-difference in fertility nor temporal variation in mortality promotes coexistence. [2] Mean fertility does not affect the outcome if CV remains constant. In contrast, enhanced mean mortality decreases the fraction of coexisting pairs if the environment fluctuates temporally. [3] We also investigate the effect of limited dispersal of propagules between habitats. Compared with the complete mixing case, the fraction of coexisting pairs is clearly enhanced if the spatial heterogeneity is the major source of environmental variation, but shows slight increase if the temporal fluctuation is dominant. We conclude that spatial heterogeneity is likely to work more effectively in promoting species coexistence than temporal fluctuation, especially when the species suffer relatively high mortality, and disperse their propagules in a limited spatial scale.     

Scaling up from local competition to regional coexistence across two scales of spatial heterogeneity: insect larvae in the fruits of <Emphasis Type="Italic">Apeiba membranacea</Emphasis>

Species that live in patchy and ephemeral habitats can compete strongly for resources within patches at a small scale. The ramifications of these interactions for population dynamics and coexistence at regional scales will depend on the intraspecific and interspecific distributions of individuals among patches. Spatial heterogeneity due to independent aggregation of competitors among patchy habitats is an important mechanism maintaining species diversity. I describe regional patterns of aggregation for four species of insect larvae in the fruits of Apeiba membranacea, a Neotropical rainforest tree. This aggregation results from variation in densities at a small scale (among the fruits under a single tree), compounded by significant variation among trees in both mean densities and degrees of aggregation. Both the degrees of aggregation and mean densities are statistically independent within and across species at both spatial scales. I evaluate the regional consequences of these spatial patterns by using maximum likelihood methods to parameterize a model that includes both explicit measures of the strength of competition and spatial variation at both within- and among-tree spatial scales. Despite strong competitive interactions among these species, during 2 years the observed spatial variation at both scales combined was sufficient to explain the coexistence of these species, although other coexistence mechanisms may also operate simultaneously. The observed spatial variation at small spatial scales may not be sufficient for coexistence, indicating the importance of considering multiple sources of spatial heterogeneity when scaling up from experiments that investigate local interactions to regional patterns of coexistence.     

Distance-limited dispersal promotes coexistence at habitat boundaries: reconsidering the competitive exclusion principle

Understanding the conditions for the stable coexistence of different alleles or species is a central topic in theoretical evolution and ecology. Different causes for stable polymorphism or species coexistence have already been identified but they can be grouped into a limited number of general processes. This article is devoted to the presentation and illustration of a new process, which we call 'habitat boundary polymorphism', and which relies on two key ingredients: habitat heterogeneity and distance-limited dispersal. Under direct competition and with fixed population densities, we show that this process allows for the equilibrium coexistence of more than n types in a n-habitat environment. Distance-limited dispersal indeed creates local maladaptation at habitat edges, which leaves room for the invasion of more generalist alleles or species. This mechanism provides a generic yet neglected process for the maintenance of polymorphism or species coexistence.     

Consequences of varying regional heterogeneity in source–sink metacommunities

Although the influence of dispersal on coexistence mechanisms in metacommunities has received great emphasis, few studies have addressed how such influence is affected varying regional heterogeneity. We present a mechanistic model of resource competition in a metacommunity based on classical models of plant competition for limiting resources. We defined regional heterogeneity as the differences in resource supply rates (or resource availabilities) across local communities. As suggested by previous work, the highest diversify occurred at intermediate levels of dispersal among local communities. However our model shows how the effects of dispersal depend on the amount of heterogeneity among local communities and vice versa. Both regional and local species richness were the highest when heterogeneity was intermediate. We suggest that empirical studies that found no evidence for source–sink or mass effects at the community level may have examined communities with limited ranges of dispersal and regional heterogeneity. This model of species coexistence contributes to a broader understanding of patterns in real communities.     

At what scales does aggregated dispersal lead to coexistence?

Aggregation during dispersal can allow persistence of weak competitors, by creating conditions where stronger competitors are more likely to interact with conspecifics than with heterospecifics. However, aggregation mechanisms operate over a wide range of spatial scales, and species experience space in very different ways. The net effect of dispersal aggregation on coexistence will depend on how these scales interact. We show that it is possible to approximate the effects of aggregated dispersal on coexistence by considering three empirically measurable parameters: the spatial scale of interaction (how strongly competition drops off with distance), the spatial scale of aggregation (how large propagule packets are), and the temporal scale of aggregation (how frequently packets arrive). We use a novel metacommunity moment closure based on this approximation and stochastic simulations to show that aggregated dispersal allows for coexistence only when the stronger competitor is both aggregated and interacts at the same or a smaller spatial scale than the weaker competitor. When species interact and are aggregated at the same scales, coexistence outcomes are only weakly sensitive to the absolute scales of interaction and aggregation, as long as the scale of interaction is smaller than the scale of aggregation. However, coexistence is sensitive to the time‐scale of aggregation: increasing the frequency of packet arrival substantially reduces the region of fitness inequalities where both species persist. Finally, coexistence is less likely and global extinction of both competitors is more frequent when aggregation is fixed (with a constant number of propagules per packet), compared to density‐dependent (number of propagules increases with adult density).     

Coexistence of plant species in a biodiversity hotspot is stabilized by competition but not by seed predation

Understanding the mechanisms of species coexistence is a key task for ecology. Recent theory predicts that both competition and predation (which causes apparent competition among prey) can either promote or limit species coexistence. Both mechanisms cause negative interactions between individuals, and each mechanism promotes stable coexistence if it causes negative interactions to be stronger between conspecifics than between heterospecifics. However, the relative importance of competition and predation for coexistence in natural communities is poorly known. Here, we study how competition and apparent competition via pre‐dispersal seed predators affect the long‐term fecundity of Protea shrubs in the fire‐prone Fynbos biome (South Africa). These shrubs store all viable seeds produced since the last fire in fire‐proof cones. Competitive effects on cone number and pre‐dispersal seed predation reduce their fecundity and can thus limit recruitment after the next fire. In 27 communities comprising 49 990 shrubs of 22 Protea species, we measured cone number and per‐cone seed predation rate of 2154 and 1755 focal individuals, respectively. Neighbourhood analyses related these measures to individual‐based community maps. We found that conspecific neighbours had stronger competitive effects on cone number than heterospecific neighbours. In contrast, apparent competition via seed predators was comparable between conspecifics and heterospecifics. This indicates that competition stabilizes coexistence of Protea species, whereas pre‐dispersal seed predation does not. Larger neighbours had stronger competitive effects and neighbours with large seed crops exerted stronger apparent competition. For 97% of the focal plants, competition reduced fecundity more than apparent competition. Our results show that even in communities of closely related and ecologically similar species, intraspecific competition can be stronger than interspecific competition. On the other hand, apparent competition through seed predators need not have such a stabilizing effect. These findings illustrate the potential of ‘community demography’, the demographic study of multiple interacting species, for understanding plant coexistence.     

Disappearing refuges in time and space: how environmental change threatens species coexistence

Understanding the impacts of environmental changes on species survival is a major challenge in ecological research, especially when shifting from single- to multispecies foci. Here, we apply a spatially explicit two-species simulation model to analyze the effects of geographic range shifting and habitat isolation on different coexistence mechanisms. The model explicitly considers dispersal, local competition, and growth on a single resource. Results highlight that both range shifting and habitat isolation severely impact coexistence. However, the strength of these impacts depends on the underlying coexistence mechanisms. Neutrally coexisting species are particularly sensitive to habitat isolation, while stabilized coexistence through overcompensatory density regulation is much more sensitive to range shifting. We conclude that, at the community level, the response to environmental change sensitively depends on the underlying coexistence mechanisms. This suggests that predictions and management recommendations should consider differences between neutral versus stabilized community structures whenever possible.     

Contrasting effects of space and environment on functional and phylogenetic dissimilarity in a tropical forest

Aims The evolutionary history and functional traits of species can illuminate ecological processes supporting coexistence in diverse forest communities. However, little has been done in decoupling the relative importance of these mechanisms on the turnover of phylogenetic and functional characteristics across life stages and spatial scales. Therefore, this study aims to estimate the contribution of environment and dispersal on the turnover of phylogenetic and functional diversity across life stages and spatial scales, in order to build a coherent picture of the processes responsible for species coexistence.     

Trait‐based tests of coexistence mechanisms

Recent functional trait studies have shown that trait differences may favour certain species (environmental filtering) while simultaneously preventing competitive exclusion (niche partitioning). However, phenomenological trait‐dispersion analyses do not identify the mechanisms that generate niche partitioning, preventing trait‐based prediction of future changes in biodiversity. We argue that such predictions require linking functional traits with recognised coexistence mechanisms involving spatial or temporal environmental heterogeneity, resource partitioning and natural enemies. We first demonstrate the limitations of phenomenological approaches using simulations, and then (1) propose trait‐based tests of coexistence, (2) generate hypotheses about which plant functional traits are likely to interact with particular mechanisms and (3) review the literature for evidence for these hypotheses. Theory and data suggest that all four classes of coexistence mechanisms could act on functional trait variation, but some mechanisms will be stronger and more widespread than others. The highest priority for future research is studies of interactions between environmental heterogeneity and trait variation that measure environmental variables at within‐community scales and quantify species' responses to the environment in the absence of competition. Evidence that similar trait‐based coexistence mechanisms operate in many ecosystems would simplify biodiversity forecasting and represent a rare victory for generality over contingency in community ecology.     

Evolution of resource specialisation in competitive metacommunities

Spatial environmental heterogeneity coupled with dispersal can promote ecological persistence of diverse metacommunities. Does this premise hold when metacommunities evolve? Using a two‐resource competition model, we studied the evolution of resource‐uptake specialisation as a function of resource type (substitutable to essential) and shape of the trade‐off between resource uptake affinities (generalist‐ to specialist‐favouring). In spatially homogeneous environments, evolutionarily stable coexistence of consumers is only possible for sufficiently substitutable resources and specialist‐favouring trade‐offs. Remarkably, these same conditions yield comparatively low diversity in heterogeneous environments, because they promote sympatric evolution of two opposite resource specialists that, together, monopolise the two resources everywhere. Consumer diversity is instead maximised for intermediate trade‐offs and clearly substitutable or clearly essential resources, where evolved metacommunities are characterised by contrasting selection regimes. Taken together, our results present new insights into resource‐competition‐mediated evolutionarily stable diversity in homogeneous and heterogeneous environments, which should be applicable to a wide range of systems.     

Spatial heterogeneity, source-sink dynamics, and the local coexistence of competing species

Patch occupancy theory predicts that a trade-off between competition and dispersal should lead to regional coexistence of competing species. Empirical investigations, however, find local coexistence of superior and inferior competitors, an outcome that cannot be explained within the patch occupancy framework because of the decoupling of local and spatial dynamics. We develop two-patch metapopulation models that explicitly consider the interaction between competition and dispersal. We show that a dispersal-competition trade-off can lead to local coexistence provided the inferior competitor is superior at colonizing empty patches as well as immigrating among occupied patches. Immigration from patches that the superior competitor cannot colonize rescues the inferior competitor from extinction in patches that both species colonize. Too much immigration, however, can be detrimental to coexistence. When competitive asymmetry between species is high, local coexistence is possible only if the dispersal rate of the inferior competitor occurs below a critical threshold. If competing species have comparable colonization abilities and the environment is otherwise spatially homogeneous, a superior ability to immigrate among occupied patches cannot prevent exclusion of the inferior competitor. If, however, biotic or abiotic factors create spatial heterogeneity in competitive rankings across the landscape, local coexistence can occur even in the absence of a dispersal-competition trade-off. In fact, coexistence requires that the dispersal rate of the overall inferior competitor not exceed a critical threshold. Explicit consideration of how dispersal modifies local competitive interactions shifts the focus from the patch occupancy approach with its emphasis on extinction-colonization dynamics to the realm of source-sink dynamics. The key to coexistence in this framework is spatial variance in fitness. Unlike in the patch occupancy framework, high rates of dispersal can undermine coexistence, and hence diversity, by reducing spatial variance in fitness.     

Plant species coexistence at local scale in temperate swamp forest: test of habitat heterogeneity hypothesis

It has been suggested that a heterogeneous environment enhances species richness and allows for the coexistence of species. However, there is increasing evidence that environmental heterogeneity can have no effect or even a negative effect on plant species richness and plant coexistence at a local scale. We examined whether plant species richness increases with local heterogeneity in the water table depth, microtopography, pH and light availability in a swamp forest community at three local spatial scales (grain: 0.6, 1.2 and 11.4 m). We also used the variance partitioning approach to assess the relative contributions of niche-based and other spatial processes to species occurrence. We found that heterogeneity in microtopography and light availability positively correlated with species richness, in accordance with the habitat heterogeneity hypothesis. However, we recorded different heterogeneity-diversity relationships for particular functional species groups. An increase in the richness of bryophytes and woody plant species was generally related to habitat heterogeneity at all measured spatial scales, whereas a low impact on herbaceous species richness was recorded only at the 11.4 m scale. The distribution of herbaceous plants was primarily explained by other spatial processes, such as dispersal, in contrast to the occurrence of bryophytes, which was better explained by environmental factors. Our results suggest that both niche-based and other spatial processes are important determinants of the plant composition and species turnover at local spatial scales in swamp forests.     

Productivity, dispersal and the coexistence of intraguild predators and prey

A great deal is known about the influence of dispersal on species that interact via competition or predation, but very little is known about the influence of dispersal on species that interact via both competition and predation. Here, I investigate the influence of dispersal on the coexistence and abundance-productivity relationships of species that engage in intraguild predation (IGP: competing species that prey on each other). I report two key findings. First, dispersal enhances coexistence when a trade-off between resource competition and IGP is strong and/or when the Intraguild Prey has an overall advantage, and impedes coexistence when the trade-off is weak and/or when the Intraguild Predator has an overall advantage. Second, the Intraguild Prey's abundance-productivity relationship depends crucially on the dispersal rate of the Intraguild Predator, but the Intraguild Predator's abundance-productivity relationship is unaffected by its own dispersal rate or that of the Intraguild Prey. This difference arises because the two species engage in both a competitive interaction as well as an antagonistic (predator-prey) interaction. The Intraguild Prey, being the intermediate consumer, has to balance the conflicting demands of resource acquisition and predator avoidance, while the Intraguild Predator has to contend only with resource acquisition. Thus, the Intraguild Predator's abundance increases monotonically with resource productivity regardless of either species' dispersal rate, while the Intraguild Prey's abundance-productivity relationship can increase, decrease, or become hump-shaped with increasing productivity depending on the Intraguild Predator's dispersal rate. The important implication is that a species' trophic position determines the effectiveness of dispersal in sampling spatial environmental heterogeneity. The dispersal behavior of a top predator is likely to have a stronger effect on coexistence and spatial patterns of abundance than the dispersal behavior of an intermediate consumer.     

Spatiotemporal population distributions and their implications for species coexistence in a variable environment

A population experiences environmental variation both directly, through effects on life history parameters such as fecundity, and indirectly, through effects on the population distributions of competitors and thus on the distribution of competition. Which spatial and temporal scales of environmental variation most influence the coexistence of two species thus depends in part on the degree to which the resident population responds to different scales of variation. In this paper, I calculate an approximation for a spatiotemporal population distribution as the result of a filter function convolved with the environmental variation. I find that there is no straightforward connection between spatial or temporal scales inherent to an organism's life history, such as mean lifetime or dispersal distance, and the population's sensitivity to variation at different scales. Rather, life history traits interact sensitively with the way environmental variation affects the organism. I comment on the implications for variation-mediated coexistence.     

Plant species richness and environmental heterogeneity in a mountain landscape: effects of variability and spatial configuration

The loss of biodiversity has become a matter of urgent concern and a better understanding of local drivers is crucial for conservation. Although environmental heterogeneity is recognized as an important determinant of biodiversity, this has rarely been tested using field data at management scale. We propose and provide evidence for the simple hypothesis that local species diversity is related to spatial environmental heterogeneity. Species partition the environment into habitats. Biodiversity is therefore expected to be influenced by two aspects of spatial heterogeneity: 1) the variability of environmental conditions, which will affect the number of types of habitat, and 2) the spatial configuration of habitats, which will affect the rates of ecological processes, such as dispersal or competition. Earlier, simulation experiments predicted that both aspects of heterogeneity will influence plant species richness at a particular site. For the first time, these predictions were tested for plant communities using field data, which we collected in a wooded pasture in the Swiss Jura mountains using a four-level hierarchical sampling design. Richness generally increased with increasing environmental variability and "roughness" (i.e. decreasing spatial aggregation). Effects occurred at all scales, but the nature of the effect changed with scale, suggesting a change in the underlying mechanisms, which will need to be taken into account if scaling up to larger landscapes. Although we found significant effects of environmental heterogeneity, other factors such as history could also be important determinants. If a relationship between environmental heterogeneity and species richness can be shown to be general, recently available high-resolution environmental data can be used to complement the assessment of patterns of local richness and improve the prediction of the effects of land use change based on mean site conditions or land use history.     

Active dispersal is differentially affected by inter‐ and intraspecific competition in closely related nematode species

Competition is one of the main drivers of dispersal, which can be an important mechanism to achieve permanent or temporal coexistence of multiple species. This coexistence can be achieved by a dispersal‐competition tradeoff, spatial store effects or neutral dynamics. Here we test the effect of inter‐ and intraspecific competition on dispersal of four species of the marine nematode species complex Litoditis marina. A previous study in closed microcosms without a possibility for dispersal had demonstrated pronounced interspecific competition, leading to the exclusion of one species. We now investigated whether 1) the dispersal is affected by interspecific interactions, by intraspecific competition (density) or by food availability, 2) the dispersal dynamics influence assemblage composition and can lead to co‐occurrence of the species, and 3) the abiotic environment (here salinity) can affect these dynamics. We show that density is the main driver for dispersal in two of the four species. Dispersal of a third species always started at the same time irrespective of density, whereas in the fourth species interspecific interactions accelerated dispersal. Remarkably, this fourth species was not a strong competitor, suggesting that a dispersal–competition tradeoff does not explain the observed coexistence. Salinity did not alter the timing of dispersal when interspecific interactions were present but did affect assemblage composition. Consequently, spatial store effects may influence coexistence. All four species co‐occurred in fairly stable abundances throughout the present experiment indicating the importance of species specific dispersal strategies for coexistence. Co‐occurrence can be facilitated because competition is postponed or avoided by dispersal. Neutral dynamics also played a role as intra‐ and interspecific competition were of similar importance in three of the four species. We conclude that dispersal is a driver of the coexistence of closely related nematode species, and that population density and interspecific interactions shape these dynamics.     

Spatial patterns and coexistence mechanisms in systems with unidirectional flow

River ecosystems are the prime example of environments where unidirectional flow influences the dispersal of individuals. Spatial patterns of community composition and species replacement emerge from complex interplays of hydrological, geochemical, biological, and ecological factors. Local processes affecting algal dynamics are well understood, but a mechanistic basis for large scale emerging patterns is lacking. To understand how these patterns could emerge in rivers, we analyze a reaction-advection-diffusion model for two competitors in heterogeneous environments. The model supports waves that invade upstream up to a well-defined "upstream invasion limit". We discuss how these waves are produced and present their key properties. We suggest that patterns of species replacement and coexistence along spatial axes reflect stalled waves, produced from diffusion, advection, and species interactions. Emergent spatial scales are plausible given parameter estimates for periphyton. Our results apply to other systems with unidirectional flow such as prevailing winds or climate-change scenarios.     

Fluctuating Environments and Phytoplankton Community Structure: A Stochastic Model

Spatial heterogeneity in organism and resource distributions can generate temporal heterogeneity in resource access for simple organisms like phytoplankton. The role of temporal heterogeneity as a structuring force for simple communities is investigated via models of phytoplankton with contrasting life histories competing for a single fluctuating resource. A stochastic model in which environmental and demographic stochasticity are treated separately is compared with a model with deterministic resource variation to assess the importance of stochasticity. When compared with the deterministic model, the stochastic model allows for coexistence over a wider range of parameter values (or life-history types). The model suggests that demographic stochasticity alone is far more important in increasing the possibility of coexistence than environmental stochasticity alone. However, the combined effects of both types of stochasticity produce the largest likelihood of coexistence. Finally, the influence of relative nutrient levels and nutrient pulse frequency on these results is addressed. We relate our findings to variable environment theory with evidence for both relative nonlinearity and the storage effect acting in this model. We show for the first time that temporal dynamics generated by demographic stochasticity may operate like the storage effect at particular spatial scales.