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.     

Characterizing species co-occurrence patterns of imperfectly detected stream fishes to inform species reintroduction efforts

Species reintroduction efforts can improve the recovery of imperiled species, but successful implementation of this conservation strategy requires a thorough understanding of the abiotic and biotic factors influencing species viability. Species interactions are especially understudied, in particular by omitting the effect of imperfect detection on negative, neutral, or positive associations within a community. Using repeat surveys from 5 southern Ontario, Canada, Great Lakes tributaries, we quantified species co-occurrence patterns with the eastern sand darter (ESD) (Ammocrypta pellucida), listed as federally threatened, and characterized how imperfect detection during sampling can influence inference regarding these relationships. We used a probabilistic framework that included 3 approaches of increasing complexity: probabilistic co-occurrence analysis ignoring imperfect detection; single-species occupancy models with subsequent co-occurrence analysis; and 2-species occupancy models. We then used our occupancy models to predict suitable sites for potential future reintroduction efforts while considering the influence of negative species interactions. Based on the observed data, ESD showed several positive associations with co-occurring species; however, species associations differed when imperfect detection was considered. Specifically, a negative association between ESD and rosyface shiner (Notropis rubellus) was observed only after accounting for imperfect detection in the Grand River. Alternatively, positive associations in the Grand River between ESD and northern hogsucker (Hypentelium nigricans) and silver shiner (Notropis photogenis) were observed regardless of whether imperfect detection was accounted for. Our models predicted several potential reintroduction sites for ESD in formerly occupied watersheds with high levels of certainty. Overall, our results demonstrate the importance of investigating imperfect detection and species co-occurrence when planning reintroduction efforts.     

The role of time and species identities in spatial patterns of species richness and conservation

Many conservation actions are justified on the basis of managing biodiversity. Biodiversity, in terms of species richness, is largely the product of rare species. This is problematic because the intensity of sampling needed to characterize communities and patterns of rarity or to justify the use of surrogates has biased sampling in favor of space over time. However, environmental fluctuations interacting with community dynamics lead to temporal variations in where and when species occur, potentially affecting conservation planning by generating uncertainty about results of species distribution modeling (including range determinations), selection of surrogates for biodiversity, and the proportion of biodiversity composed of rare species. To have confidence in the evidence base for conservation actions, one must consider whether temporal replication is necessary to produce broad inferences. Using approximately 20 years of macrofaunal data from tidal flats in 2 harbors, we explored variation in the identity of rare, common, restricted range, and widespread species over time and space. Over time, rare taxa were more likely to increase in abundance or occurrence than to remain rare or disappear and to exhibit temporal patterns in their occurrence. Space–time congruency in ranges (i.e., spatially widespread taxa were also temporally widespread) was observed only where samples were collected across an environmental gradient. Fifteen percent of the taxa in both harbors changed over time from having spatially restricted ranges to having widespread ranges. Our findings suggest that rare species can provide stability against environmental change, because the majority of species were not random transients, but that selection of biodiversity surrogates requires temporal validation. Rarity needs to be considered both spatially and temporally, as species that occur randomly over time are likely to play a different role in ecosystem functioning than those exhibiting temporal structure (e.g., seasonality). Moreover, temporal structure offers the opportunity to place management and conservation activities within windows of maximum opportunity.     

Effects of crowding due to habitat loss on species assemblage patterns

Terrestrial animals are negatively affected by habitat loss, which is assessed on a landscape scale, whereas secondary effects of habitat loss, such as crowding, are usually disregarded. Such impacts are inherently hard to address and poorly understood, and there is a growing concern that they could have dire consequences. We sampled birds throughout a deforestation process to assess crowding stress in an adjacent habitat remnant in the southern Brazilian Atlantic Forest. Crowding is expected of highly mobile taxa, especially given the microhabitat heterogeneity of Neotropical forests, and we hypothesized that the arrival of new individuals or species in refuges shifts assemblage patterns. We used point counts to obtain bird abundances in a before-after-control-impact design sampling of a deforestation event. Temporal changes in taxonomic and functional diversity were examined with metrics used to assess alpha and beta diversity, turnover of taxonomic and functional similarity, and taxonomic and functional composition. Over time increased abundance of some species altered the Simpson index and affected the abundance-distribution of traits in the habitat remnant. Taxonomic composition and functional composition changed in the remnant, and thus bird assemblages changed over time. Taxonomic and functional metrics indicated that fugitives affected resident assemblages in refuges, and effects endured >2 years after the deforestation processes had ceased. Dissimilarity of taxonomic composition between pre- and postdeforestation assemblages increased, whereas functional composition reverted to preimpact conditions. We found that ecological disruptions resulted from crowding and escalated into disruptions of species’ assemblages and potentially compromising ecosystem functioning. It is important to consider crowding effects of highly mobile taxa during impact assessments, especially in large-scale infrastructure projects that may affect larger areas than is assumed.     

Diverging response patterns of terrestrial and aquatic species to hydromorphological restoration

Although experiences with ecological restoration continue to accumulate, the effectiveness of restoration for biota remains debated. We complemented a traditional taxonomic analysis approach with information on 56 species traits to uncover the responses of 3 aquatic (fish, macroinvertebrates, macrophytes) and 2 terrestrial (carabid beetles, floodplain vegetation) biotic groups to 43 hydromorphological river restoration projects in Germany. All taxonomic groups responded positively to restoration, as shown by increased taxonomic richness (10–164%) and trait diversity (habitat, dispersal and mobility, size, form, life history, and feeding groups) (15–120%). Responses, however, were stronger for terrestrial than aquatic biota, and, contrary to our expectation, taxonomic responses were stronger than those of traits. Nevertheless, trait analysis provided mechanistic insights into the drivers of community change following restoration. Trait analysis for terrestrial biota indicated restoration success was likely enhanced by lateral connectivity and reestablishment of dynamic processes in the floodplain. The weaker response of aquatic biota suggests recovery was hindered by the persistence of stressors in the aquatic environment, such as degraded water quality, dispersal constraints, and insufficient hydromorphological change. Therefore, river restoration requires combined local- and regional-scale approaches to maximize the response of both aquatic and terrestrial organisms. Due to the contrasting responses of aquatic and terrestrial biota, the planning and assessment of river restoration outcomes should consider effects on both components of riverine landscapes.     

A phenomenological model without dispersal kernel to model species migration

Phenomenological approaches to model species migration are usually based on kernel-based methods. These methods require a good knowledge of the dispersal agent behaviour for a given species. They also calculate the location of individuals independently to each other (except the mother plant) and then suppress some of them according to additional interactions such as competition, facilitation and recruitment. In this paper, we propose to use a new phenomenological method, the Gibbs method, to model tree species migration at large scale. The Gibbs method handles the location of adult individuals in terms of pairwise interactions described by a potential function. This function summarizes the set of known and unknown factors determining the spatial distribution of the individuals (or cohorts). The principle of the Gibbs method is to minimize the sum of all pairwise interactions, also called the cost function, in order to optimize the spatial point pattern according to the chosen potential function.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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