Null model analysis of species associations using abundance data

The influence of negative species interactions has dominated much of the literature on community assembly rules. Patterns of negative covariation among species are typically documented through null model analyses of binary presence/absence matrices in which rows designate species, columns designate sites, and the matrix entries indicate the presence (1) or absence (0) of a particular species in a particular site. However, the outcome of species interactions ultimately depends on population-level processes. Therefore, patterns of species segregation and aggregation might be more clearly expressed in abundance matrices, in which the matrix entries indicate the abundance or density of a species in a particular site. We conducted a series of benchmark tests to evaluate the performance of 14 candidate null model algorithms and six covariation metrics that can be used with abundance matrices. We first created a series of random test matrices by sampling a metacommunity from a lognormal species abundance distribution. We also created a series of structured matrices by altering the random matrices to incorporate patterns of pairwise species segregation and aggregation. We next screened each algorithm-index combination with the random and structured matrices to determine which tests had low Type I error rates and good power for detecting segregated and aggregated species distributions. In our benchmark tests, the best-performing null model does not constrain species richness, but assigns individuals to matrix cells proportional to the observed row and column marginal distributions until, for each row and column, total abundances are reached. Using this null model algorithm with a set of four covariance metrics, we tested for patterns of species segregation and aggregation in a collection of 149 empirical abundance matrices and 36 interaction matrices collated from published papers and posted data sets. More than 80% of the matrices were significantly segregated, which reinforces a previous meta-analysis of presence/absence matrices. However, using two of the metrics we detected a significant pattern of aggregation for plants and for the interaction matrices (which include plant-pollinator data sets). These results suggest that abundance matrices, analyzed with an appropriate null model, may be a powerful tool for quantifying patterns of species segregation and aggregation.     

Simulating wildfire patterns using a small-world network model

This paper presents the development and validation results of a weighted small-world network model designed to simulate fire patterns in real heterogeneous landscapes. Fire spread is simulated on a gridded landscape, a mosaic in which each cell represents an area of the land surface. In this model, the interaction between burning and non-burning cells (here, due to flame radiation) may extend well beyond nearest neighbors, and depends on local conditions of wind, topography, and vegetation. An approach based on the coupling of the solid flame model with the Monte Carlo method is used to predict the radiative heat flux from the flame generated by the burning of each combustible cell to its neighbors. The weighting procedure takes into account latency (a combustible cell will only ignite when it has accumulated enough energy along time) and flaming persistence of burning cells. The model is applied to very different fire scenarios: a historical Mediterranean fire that occurred in southeastern France in 2005 and experimental fires conducted in arid savanna fuels in South Africa in 1992. Model results are found to be in agreement with real fire patterns, in terms both of rate of spread, and of the area and shape of the burn. This work also shows that the fractal properties of fire patterns predicted by the model are similar to those observed from satellite images of three other Mediterranean fire scars.     

The effect of species response form on species distribution model prediction and inference

Ecological theory and current evidence support the validity of various species response curves according to a variety of environmental gradients. Various methods have been developed for building species distribution models but it is not well known how these methods perform under various assumptions about the form of the underlying species response. It is also not well known how spatial correlation in species occurrence affects model performance. These effects were investigated by applying an environmental envelope method (BIOCLIM) and three regression-based methods: logistic regression (LR), generalized additive modelling (GAM), and classification and regression tree (CART) to simulated species occurrence data. Each simulated species was constructed as a sum of responses with varying weights. Three basic species response curves were assumed: Gaussian (bell-shaped), Beta (skew) and linear. The two non-linear responses conform to standard ecological niche theory. All three responses were applied in turn to three simulated environmental variables, each with varying degrees of spatial autocorrelation. GAM produced the most consistent model performance over all forms of simulated species response. BIOCLIM and CART were inclined to underrate the performance of variables with a linear response. BIOCLIM was less sensitive to data density. LR was susceptible to model misspecification. The use of a linear function in LR underestimated the performance of variables with non-linear species response and contributed to increased spatial autocorrelation in model residuals. Omission of important environmental variables with non-linear species response also contributed to increased spatial autocorrelation in model residuals. Adding a spatial autocovariate term to the LR model (autologistic model) reduced the spatial autocorrelation and improved model performance, but did not correct the misidentification of the dominant environmental determinant. This is to be expected since the autologistic approach was designed primarily for prediction and not for inference. Given that various forms of species response to environmental determinants arise commonly in nature: (1) higher order functions should always be tested when applying LR in modelling species distribution; (2) spatial autocorrelation in species distribution model residuals can indicate that environmental determinants with non-linear response are missing from the model; and (3) deficiencies in LR model performance due to model misspecification can be addressed by adding a spatial autocovariate to the model, but care should be taken when interpreting the coefficients of the model parameters.     

Contrasting feeding patterns among species of fish larvae from the tropical Andaman Sea

Feeding habits of tropical fish larvae were analysed in a comparative study of four species (Scorpaenodes sp., Carangoides sp., Acanthocepola sp. and Cynoglossus sp.) from the Andaman Sea. We investigated morphological characteristics and their potential influence on larval feeding, and looked for common patterns in larval prey preference. Gut contents of a total of 300 larvae were examined and compared with local zooplankton composition. The feeding habits of the investigated larvae shared a number of characteristics. During ontogeny both the preferred prey size and the number of prey in the gut increased, and across all larval size classes the relative prey size spectrum stayed constant, of approximately the same magnitude for all four species. On the other hand, larval feeding also differed in a number of aspects, especially differences in the taxonomic composition of preferred prey were apparent. Scorpaenodes sp. preferred abundant and large prey taxa, Acanthocepola sp. and Carangoides sp. preferred large, but less common prey taxa, while Cynoglossus sp., which had the relatively smallest mouth size, preferred smaller sized prey groups. Hence, the findings indicate that from an offset of common characteristics, especially related to prey size preference, larvae have their individual feeding patterns related to specific morphology and patterns of distribution.Communicated by M. Kühl, Helsingør     

Stronger predation in the tropics shapes species richness patterns in marine communities

Species interactions are widely assumed to be stronger at lower latitudes, but surprisingly few experimental studies test this hypothesis, and none ties these processes to observed patterns of species richness across latitude. We report here the first experimental field test that predation is both stronger and has a disproportionate effect on species richness in the tropics relative to the temperate zone. We conducted predator-exclusion experiments on communities of sessile marine invertebrates in four regions, which span 32 degrees latitude, in the western Atlantic Ocean and Caribbean Sea. Over a three-month timescale, predation had no effect on species richness in the temperate zone. In the tropics, however, communities were from two to over ten times more species-rich in the absence of predators than when predators were present. While micro-and macro-predators likely compete for the limited prey resource in the tropics, micropredators alone were able to exert as much pressure on the invertebrate communities as the full predator community. This result highlights the extent to which exposure to even a subset of the predator guild can significantly impact species richness in the tropics. Patterns were consistent in analyses that included relative and total species abundances. Higher species richness in the absence of predators in the tropics was also observed when species occurrences were pooled across two larger spatial scales, site and region, demonstrating a consistent scaling relationship. These experimental results show that predation can both limit local species abundances and shape patterns of regional coexistence in the tropics. When preestablished diverse tropical communities were then exposed to predation for different durations, ranging from one to several days, species richness was always reduced. These findings confirmed that impacts of predation in the tropics are strong and consistent, even in more established communities. Our results offer empirical support for the long-held prediction that predation pressure is stronger at lower latitudes. Furthermore, we demonstrate the magnitude to which variation in predation pressure can contribute to the maintenance of tropical species diversity.     

Insights on plant interaction between dominating species from patterns of plant association: expected covariance of pin-point cover measurements of two species

It has been suggested that in order to infer ecological processes from observed patterns of species abundance we need to investigate the covariance in species abundance. Consequently, an expression for the expected covariance of pin-point cover measurements of two species is developed. By comparing the observed covariance with the expected covariance we get a new type of information on the spatial arrangement of two species. Here the discrepancy between the observed and expected covariance may be thought of as a measure of the spatial configuration of the two species that may indicate underling ecological processes. The method is applied in a case study of Calluna vulgaris and Deschampsia flexuosa on dry heathland sites. The observed covariance of Calluna and Deschampsia at the level of the sites was positively and significantly correlated with the expected covariance. Negative covariance was observed on sites where both Calluna and Deschampsia had a high cover, which is in agreement with the notion that both species form distinct patches. Oppositely, at sites where both species have a low cover, we found that both the expected and observed covariance were positive. The proposed measure for the expected covariance of two species does capture information on the combined spatial configuration of the two species if the species are common. We show how this may be relevant for understanding the underlying ecological processes leading to the observed covariance.     

A hierarchical analysis of terrestrial ecosystem model Biome-BGC: Equilibrium analysis and model calibration

The increasing complexity of ecosystem models represents a major difficulty in tuning model parameters and analyzing simulated results. To address this problem, this study develops a hierarchical scheme that simplifies the Biome-BGC model into three functionally cascaded tiers and analyzes them sequentially. The first-tier model focuses on leaf-level ecophysiological processes; it simulates evapotranspiration and photosynthesis with prescribed leaf area index (LAI). The restriction on LAI is then lifted in the following two model tiers, which analyze how carbon and nitrogen is cycled at the whole-plant level (the second tier) and in all litter/soil pools (the third tier) to dynamically support the prescribed canopy. In particular, this study analyzes the steady state of these two model tiers by a set of equilibrium equations that are derived from Biome-BGC algorithms and are based on the principle of mass balance. Instead of spinning-up the model for thousands of climate years, these equations are able to estimate carbon/nitrogen stocks and fluxes of the target (steady-state) ecosystem directly from the results obtained by the first-tier model. The model hierarchy is examined with model experiments at four AmeriFlux sites. The results indicate that the proposed scheme can effectively calibrate Biome-BGC to simulate observed fluxes of evapotranspiration and photosynthesis; and the carbon/nitrogen stocks estimated by the equilibrium analysis approach are highly consistent with the results of model simulations. Therefore, the scheme developed in this study may serve as a practical guide to calibrate/analyze Biome-BGC; it also provides an efficient way to solve the problem of model spin-up, especially for applications over large regions. The same methodology may help analyze other similar ecosystem models as well.     

Hidden genetic diversity in a key model species of coral

A total of 43 colonies of the scleractinian coral Pocillopora damicornis from lagoonal and reef slope sites in the western Indian Ocean (WIO) region were genetically characterised at one nuclear and two mitochondrial sequence markers and six microsatellite loci. Both mitochondrial and microsatellite data support the existence of two reciprocally monophyletic clusters (F- and NF-types) and provide evidence of the existence of two cryptic species of P. damicornis on reefs in WIO region and put current morphological delineation and geographical boundaries of P. damicornis and Pocillopora molokensis into question. The results add to ongoing studies on the phylogeny and phylogeography within the genus Pocillopora, which all point towards a range of unresolved morphological and molecular species boundaries. Nuclear phylogenies derived from the present and previously published sequences show evidence for incomplete lineage sorting and/or introgressive hybridisation between Pocillopora morphospecies. However, the two WIO types largely remain in separate clusters, further supporting the theory that these represent two different species.     

Aquatic plant community invasibility and scale-dependent patterns in native and invasive species richness

Invasive species richness often is negatively correlated with native species richness at the small spatial scale of sampling plots, but positively correlated in larger areas. The pattern at small scales has been interpreted as evidence that native plants can competitively exclude invasive species. Large-scale patterns have been understood to result from environmental heterogeneity, among other causes. We investigated species richness patterns among submerged and floating-leaved aquatic plants (87 native species and eight invasives) in 103 temperate lakes in Connecticut (northeastern USA) and found neither a consistently negative relationship at small (3-m2) scales, nor a positive relationship at large scales. Native species richness at sampling locations was uncorrelated with invasive species richness in 37 of the 60 lakes where invasive plants occurred; richness was negatively correlated in 16 lakes and positively correlated in seven. No correlation between native and invasive species richness was found at larger spatial scales (whole lakes and counties). Increases in richness with area were uncorrelated with abiotic heterogeneity. Logistic regression showed that the probability of occurrence of five invasive species increased in sampling locations (3 m2, n = 2980 samples) where native plants occurred, indicating that native plant species richness provided no resistance against invasion. However, the probability of three invasive species' occurrence declined as native plant density increased, indicating that density, if not species richness, provided some resistance with these species. Density had no effect on occurrence of three other invasive species. Based on these results, native species may resist invasion at small spatial scales only in communities where density is high (i.e., in communities where competition among individuals contributes to community structure). Most hydrophyte communities, however, appear to be maintained in a nonequilibrial condition by stress and/or disturbance. Therefore, most aquatic plant communities in temperate lakes are likely to be vulnerable to invasion.     

物种分布宽度对种子植物物种丰富度垂直分布格局及"中间膨胀效应"的影响

物种丰富度的垂直分布格局是生态学研究的重要课题之一.文章以云南楚雄地区为例探讨物种分布宽度对种子植物物种丰富度垂直分布格局及"中间膨胀效应"的影响.利用大尺度的物种分布数据建立物种分布数据库,同时结合地形信息,分析了研究区域内物种丰富度的海拔分布格局以及"中间膨胀效应"对该格局的影响.在此基础上,探讨了物种分布宽度对楚雄地区种子植物物种丰富度垂直分布格局及"中间膨胀效应"的影响.结果表明,随着海拔的升高,物种丰富度先增加,后下降,呈单峰分布格局.物种分布宽度的相互重叠,即"中间膨胀效应"对物种多样性的垂直分布格局具有显著影响.随着物种分布宽度的增加,"中间膨胀效应"以及各物种组对物种丰富度垂直分布格局的影响均呈显著增加趋势,这说明"中间膨胀效应"和物种丰富度的垂直分布格局更多地取决于分布宽度较大的物种.     

A strategy for species introduction into evolving model ecosystems

Using a recently developed technique, a realistic method of introducing species into an evolving ecosystem simulation model is presented. A single unit, preemption strength, provides an index which combines strictly preemptive and strictly head-of-the-line colonization strategies. An optimization of priority strategies is presented. The relevance of the realistically evolving model to the stability-complexity problem is emphasized.     

Zooplankton responses to hypoxia: behavioral patterns and survival of three species of calanoid copepods

Seasonally recurrent and persistent hypoxic events in semi-enclosed coastal waters are characterized by bottom-water dissolved oxygen (d.o.) concentrations of < 2.0 ml l⁻¹. Shifts in the distribution patterns of zooplankters in association with these events have been documented, but the mechanisms responsible for these shifts have not been investigated. This study assessed interspecific differences in responses to hypoxia by several species of calanoid copepods common off Turkey Point, Florida, USA: Labidocera aestiva (Wheeler) (a summer/fall species), Acartia tonsa (Dana) (a ubiquitous year-round species), and Centropages hamatus (Lilljeborg) (a winter/spring species). Under conditions of moderate to severe hypoxia 24-h survival experiments were conducted for adults and nauplii of these species from August 1994 to October 1995. Experiments on adults used a flow-through system to maintain constant d.o. concentrations. Adults of A. tonsa showed no decline in survival with d.o. as low as 1.0 ml l⁻¹, sharp declines in survival at d.o. = 0.9 to 0.6 ml l⁻¹, and 100% mortality with d.o. = 0.5 ml l⁻¹. Adults of L. aestiva and C. hamatus were more sensitive to oxygen depletion: both species experienced significant decreases in survival for d.o. = 1.0 ml l⁻¹. Nauplii of L. aestiva and A. tonsa showed no significant mortality with d.o. = 1.1 to 1.5 ml␣l⁻¹ and d.o. = 0.24 to 0.5 ml l⁻¹, respectively. In addition, experiments investigating behavioral avoidance of moderate to severe hypoxia were carried out for adults of all three species. None of the three species effectively avoided either severely hypoxic (d.o. < 0.5 ml l⁻¹) or moderately hypoxic (d.o. ≈ 1.0 ml l⁻¹) bottom layers in stratified columns. These results suggest that in␣nearshore areas where development of zones of d.o. < 1.0 ml l⁻¹ may be sudden, widespread, or unpredictable, patterns of reduced copepod abundance in bottom waters may be due primarily to mortality rather than avoidance. Received: 31 August 1996 / Accepted: 24 September 1996     

Including spatial contiguity information in the analysis of multispecific patterns

In this paper we analyse an ordination method in which spatial contiguity information is included. The original method, proposed by Ver Hoef and Glenn-Lewin (1989), is extended, using graphs to describe spatial contiguity for several sampling schemes where locations are given. Extensions for two dimensional grids and for the case of discrete measures of abundance are analysed. Applications to simulated transect frequency data and real data collected on a regular grid are reported.     

Dynamic analysis of commercial fishing model

We investigate a quadratic commercial fishing model in this paper. The results imply that fishing capital investment is nonexplosive, the fishery resources are nonextinctive, and the solution of the bionomic system is globally stable within an invariant region.     

Plasticity in circadian activity patterns of mesocarnivores in Southwestern Europe: implications for species coexistence

Limiting similarity theory predicts that competing species must segregate along one or more dimensions of their ecological niche in order to coexist. In predator communities, interspecific interactions are influenced by a diversity of factors; therefore, the behavioural patterns of composing species will differ due to locally adapted interactions. We deployed 32–41 camera-traps in five study areas across the Iberian Peninsula to investigate the temporal relations between mesocarnivores in SW Europe. The selection for a period of the diel cycle and plasticity in activity patterns was evaluated using the Jacobs Selection Index (JSI) and the coefficient of activity overlap (?₁). Furthermore, we investigated whether temporal shifts can facilitate coexistence by reducing activity overlap. Seven species of mesocarnivores were detected and were assigned into one of three behaviourally distinct groups: diurnal (JSI_day?≥?0.8), strictly nocturnal (JSI_night?≥?0.8) or facultative nocturnal species (0.4?≥?JSI_night?>?0.8). Most species exhibited substantial flexibility, which allowed them to locally adapt their foraging strategies (intraspecific ?₁?=?0.70–0.77). Mean Δ₁ from all interspecific pairwise comparisons was negatively correlated with the number of carnivore species with ≥10 detections (r ?0.76, p?=?0.02). Our results suggest that temporal segregation is likely to play an important role in facilitating mesocarnivore coexistence, especially with increasing community complexity, where most species’ activity peaks were asynchronous. These results contribute to understanding the dynamics and behavioural strategies of coexisting mesocarnivores, crucial for forecasting the possible outcomes of conservation or management actions.     

Interactions between environment, species traits, and human uses describe patterns of plant invasions

Although invasive alien species (IAS) are a major threat to biodiversity, human health, and economy, our understanding of the factors controlling their distribution and abundance is limited. Here, we determine how environmental factors, land use, life-history traits of the invaders, residence time, origin, and human usage interact to shape the spatial pattern of invasive alien plant species in South Africa. Relationships between the environmental factors and the extrinsic and intrinsic attributes of species were investigated using RLQ analysis, a multivariate method for relating a species-attribute table to an environmental table by way of a species presence/absence table. We then clustered species according to their position on the RLQ axes, and tested these groups for phylogenetic independence. The first three axes of the RLQ explained 99% of the variation and were strongly related to the species attributes. The clustering showed that, after accounting for environmental factors, the spatial pattern of IAS in South Africa was driven by human uses, life forms, and reproductive traits. The seven clusters of species strongly reflected geographical distribution, but also intrinsic species attributes and patterns of human use. Two of the clusters, centered on the genera Acacia and Opuntia, were phylogenetically non-independent. The remaining clusters comprised species of diverse taxonomic affinities, but sharing traits facilitating invasion in particular habitats. This information is useful for assessing the extent to which the potential spread of recent introductions can be predicted by considering the interaction of their biological attributes, region of origin, and human use.     

The spread of marine non-indigenous species via recreational boating: A conceptual model for risk assessment based on fault tree analysis

Recreational vessel movements are increasingly recognised as an important pathway for the spread of non-indigenous species (NIS) in marine environments. Research on risks posed by recreational vessels has focused on external hull fouling, yet a number of studies reveal the potential for NIS to also be transferred by a range of other vessel components. This paper uses fault tree analysis as a framework for incorporating input from a panel of international experts, to elucidate the consecutive steps that must occur for NIS to be introduced from different components of recreational boats. Our conceptual model reveals the complexity of the invasion process even when only the ‘release’ phase is considered (i.e. the release of NIS from an infected vessel into a new area). The model highlights that, in addition to external fouling of the ‘hull’ (hull, rudder and propeller), important vessel components may also include fouling, sediment or water released from the deck, internal spaces, anchors and fishing/diving gear. The extent to which these components are important is situation-specific, and depends on attributes of the vessel, location and NIS present. Hence, the comprehensive model described here could be modified or simplified to reflect the attributes that are relevant to particular circumstances. We demonstrate this principle using examples of three NIS: the colonial tunicate Didemnum vexillum and the Asian kelp Undaria pinnatifida that both have established in Port Nelson New Zealand after vessel-mediated spread, and the clubbed tunicate Styela clava that was detected on a vessel hull in the port but is not known to have established. Although the modelling and assessment of some of the events identified in the fault trees would be difficult or unrealistic, it is important to acknowledge them in order to provide a comprehensive risk assessment tool. Even where risks are largely unknown, difficult to quantify, or reflect stochastic events, this does not necessarily preclude management intervention.