Limiting similarity revisited

We reinvestigate the validity of the limiting similarity principle via numerical simulations of the Lotka–Volterra model. A Gaussian competition kernel is employed to describe decreasing competition with increasing difference in a one-dimensional phenotype variable. The simulations are initiated by a large number of species, evenly distributed along the phenotype axis. Exceptionally, the Gaussian carrying capacity supports coexistence of all species, initially present. In case of any other, distinctly different, carrying capacity functions, competition resulted in extinction of all, but a few species. A comprehensive study of classes of fractal-like carrying capacity functions with different fractal exponents was carried out. The average phenotype differences between surviving species were found to be roughly equal to the competition width. We conclude that, despite the existence of exceptional cases, the classical picture of limiting similarity and niche segregation is a good rule of thumb for practical purposes.     

Using Range-Wide Abundance Modeling to Identify Key Conservation Areas for the Micro-Endemic Bolson Tortoise (Gopherus flavomarginatus)

A widespread biogeographic pattern in nature is that population abundance is not uniform across the geographic range of species: most occurrence sites have relatively low numbers, whereas a few places contain orders of magnitude more individuals. The Bolson tortoise Gopherus flavomarginatus is endemic to a small region of the Chihuahuan Desert in Mexico, where habitat deterioration threatens this species with extinction. In this study we combined field burrows counts and the approach for modeling species abundance based on calculating the distance to the niche centroid to obtain range-wide abundance estimates. For the Bolson tortoise, we found a robust, negative relationship between observed burrows abundance and distance to the niche centroid, with a predictive capacity of 71%. Based on these results we identified four priority areas for the conservation of this microendemic and threatened tortoise. We conclude that this approach may be a useful approximation for identifying key areas for sampling and conservation efforts in elusive and rare species.     

环境和扩散对草地群落构建的影响

植物群落构建机制是生态学研究的热点之一.长久以来这个难题并没有得到很好的解释,且争议较多.生态位理论或中性理论,或是二者的共同作用,这样的结论在不同的研究中都有印证.以黄土高原子午岭地区的草地群落为例,对3种不同的草地群落(5a的弃耕地、阴坡和阳坡的草地)进行了野外群落学调查,采用Mantel test和主轴邻距法(PCNM)分析方法,研究了空间地理距离和环境资源差异对于草本植物群落分布的影响,结果表明:地理距离和环境差异共同解释了群落组成相似性的79.3％,剔除环境因子的影响,地理距离解释了群落组成相似性的33.8％;而剔除地理距离的影响,环境因子解释了群落组成相似性的14.2％.无论是生态位理论还是中性理论,其在黄土高原草本群落构建过程中都有作用,但中性理论扮演了更为重要的角色.     

Perturbation Biology: Inferring Signaling Networks in Cellular Systems

We present a powerful experimental-computational technology for inferring network models that predict the response of cells to perturbations, and that may be useful in the design of combinatorial therapy against cancer. The experiments are systematic series of perturbations of cancer cell lines by targeted drugs, singly or in combination. The response to perturbation is quantified in terms of relative changes in the measured levels of proteins, phospho-proteins and cellular phenotypes such as viability. Computational network models are derived de novo, i.e., without prior knowledge of signaling pathways, and are based on simple non-linear differential equations. The prohibitively large solution space of all possible network models is explored efficiently using a probabilistic algorithm, Belief Propagation (BP), which is three orders of magnitude faster than standard Monte Carlo methods. Explicit executable models are derived for a set of perturbation experiments in SKMEL-133 melanoma cell lines, which are resistant to the therapeutically important inhibitor of RAF kinase. The resulting network models reproduce and extend known pathway biology. They empower potential discoveries of new molecular interactions and predict efficacious novel drug perturbations, such as the inhibition of PLK1, which is verified experimentally. This technology is suitable for application to larger systems in diverse areas of molecular biology.     

Effect of habitat degradation on competition,carrying capacity,and species assemblage stability

Changes in species’ trophic niches due to habitat degradation can affect intra‐ and interspecific competition, with implications for biodiversity persistence. Difficulties of measuring species’ interactions in the field limit our comprehension of competition outcomes along disturbance gradients. Thus, information on how habitat degradation can destabilize food webs is scarce, hindering predictions regarding responses of multispecies systems to environmental changes. Seagrass ecosystems are undergoing degradation. We address effects of Posidonia oceanica coverage reduction on the trophic organization of a macroinvertebrate community in the Tyrrhenian Sea (Italy), hypothesizing increased trophic generalism, niche overlap among species and thus competition and decreased community stability due to degraded conditions. Census data, isotopic analysis, and Bayesian mixing models were used to quantify the trophic niches of three abundant invertebrate species, and intra‐ and interspecific isotopic and resource‐use similarity across locations differing in seagrass coverage. This allowed the computation of (1) competition strength, with respect to each other and remaining less abundant species and (2) habitat carrying capacity. To explore effects of the spatial scale on the interactions, we considered both individual locations and the entire study area (“‘meadow scale”). We observed that community stability and habitat carrying capacity decreased as P. oceanica coverage declined, whereas niche width, similarity of resource use and interspecific competition strength between species increased. Competition was stronger, and stability lower, at the meadow scale than at the location scale. Indirect effects of competition and the spatial compartmentalization of species interactions increased stability. Results emphasized the importance of trophic niche modifications for understanding effects of habitat loss on biodiversity persistence. Calculation of competition coefficients based on isotopic distances is a promising tool for describing competitive interactions in real communities, potentially extendible to any subset of ecological niche axes for which specimens’ positions and pairwise distances can be obtained.     

Hydrological connectivity structures concordant plant and animal assemblages according to niche rather than dispersal processes

1. Understanding the processes that structure community assembly across landscapes is fundamental to ecology and for predicting and managing the consequences of anthropogenically induced changes to ecosystems. 2. We assessed the community similarity of fish, macroinvertebrate and vegetation communities against geographic distances ranging from 4 to 480 km (i.e. distance–decay relationships) to determine the balance between local environmental factors and regional dispersal processes, and thus whether species‐sorting (niche processes) or dispersal limitation (neutral processes) was more important in structuring these assemblages in Australia’s wet‐dry tropics. We investigated whether the balance between niche and dispersal processes depended on the degree of hydrological connectivity, predicting that dispersal processes would be more important at connected sites, and also whether there was spatial concordance among these three assemblage types. 3. There was significant but weak spatial concordance among the study communities, suggesting limited potential for surrogacy among them. Distance–decay in community similarity was not observed for any study assemblage at perennial sites, suggesting dispersal was not limiting and assemblages were structured more strongly by local niche processes at these connected sites. At intermittent sites, weak distance–decay relationships for each assemblage type were confounded by significant relationships with environmental dissimilarity, suggesting that dispersal limitation contributed, albeit weakly, to niche processes in structuring our three study assemblages at disconnected sites. 4. Two environmental factors, flow regime and channel width, explained significant proportions of variation in all three assemblages, potentially contributing to the observed spatial concordance between them and representing local environmental gradients along which these communities re‐assemble after the wet season, according to niche rather than dispersal processes.     

Predicting Phenotypic Diversity and the Underlying Quantitative Molecular Transitions

During development, signaling networks control the formation of multicellular patterns. To what extent quantitative fluctuations in these complex networks may affect multicellular phenotype remains unclear. Here, we describe a computational approach to predict and analyze the phenotypic diversity that is accessible to a developmental signaling network. Applying this framework to vulval development in C. elegans, we demonstrate that quantitative changes in the regulatory network can render ~500 multicellular phenotypes. This phenotypic capacity is an order-of-magnitude below the theoretical upper limit for this system but yet is large enough to demonstrate that the system is not restricted to a select few outcomes. Using metrics to gauge the robustness of these phenotypes to parameter perturbations, we identify a select subset of novel phenotypes that are the most promising for experimental validation. In addition, our model calculations provide a layout of these phenotypes in network parameter space. Analyzing this landscape of multicellular phenotypes yielded two significant insights. First, we show that experimentally well-established mutant phenotypes may be rendered using non-canonical network perturbations. Second, we show that the predicted multicellular patterns include not only those observed in C. elegans, but also those occurring exclusively in other species of the Caenorhabditis genus. This result demonstrates that quantitative diversification of a common regulatory network is indeed demonstrably sufficient to generate the phenotypic differences observed across three major species within the Caenorhabditis genus. Using our computational framework, we systematically identify the quantitative changes that may have occurred in the regulatory network during the evolution of these species. Our model predictions show that significant phenotypic diversity may be sampled through quantitative variations in the regulatory network without overhauling the core network architecture. Furthermore, by comparing the predicted landscape of phenotypes to multicellular patterns that have been experimentally observed across multiple species, we systematically trace the quantitative regulatory changes that may have occurred during the evolution of the Caenorhabditis genus.     

Coevolution in resource-limited competition communities

A coevolutionary model of species packing is developed which allows evolutionary adjustment in both niche position and within-phenotype niche width of from one of three competing species. The environment is specified as a single resource dimension x and availability of resources along x is given by a Gaussian curve with parameters ($\text{x}\text{?}{}_{\mathrm{R}}\text{and}\text{σ}{}_{\mathrm{R}}$). The model predicts that for S species the ratio of optimal niche width (?) to σ_R is roughly independent of σ_R and can be approximated by $\text{1}\text{S}$ when the competitors are completely resource limited. Niche separation ($\text{d}\text{?}\text{w}\text{?}$) increases only moderately with increases in resource diversity σ_R and is greater for two than for three competing species. To the extent that the competitors do not utilize all resources, both optimal niche separation and niche width decrease. Many of the general trends in niche width and niche separation predicted by this coevolutionary model parallel those from optimal foraging theory and limiting similarity models of community structure. The coevolutionary model stands out, however, in the singularly high values predicted for niche separation, making coevolved communities highly invadeable. Hence, the theory suggests, as some empirical evidence indicates, that coevolved competition communities can only exist as such on remote islands or in other habitats which might be free from invasion by outside species. For such communities, resource diversity (σ_R) should have much less effect on species packing than either species number itself or the extent that these competitors are resource limited.     

Walking variability during continuous pseudo-random oscillations of the support surface and visual field

Walking on uneven surfaces or while undergoing perturbations has been associated with increased gait variability in both modeling and human studies. Previous gait research involving continuous perturbations has focused on sinusoidal oscillations, which can result in individuals predicting the perturbation and/or entraining to it. Therefore, we examined the effects of continuous, pseudo-random support surface and visual field oscillations on 12 healthy, young participants. Participants walked in a virtual reality environment under no perturbation (NOP), anterior–posterior (AP) walking surface and visual oscillation and mediolateral (ML) walking surface and visual oscillation conditions. Participants exhibited shorter (p≤0.005), wider (p<0.001) and faster (p<0.001) steps relative to NOP during ML perturbations and shorter (p≤0.005) and wider (p<0.001) steps during AP perturbations. Step length variability and step width variability both increased relative to NOP during all perturbation conditions (p<0.001) but exhibited greater increases for the ML perturbations (p<0.001). Participants exhibited greater trunk position variability and trunk velocity variability in the ML direction than in the AP direction during ML perturbations relative to NOP (p<0.001). Significantly greater variability in the ML direction indicates that to maintain stability, participants needed to exert greater control in the ML direction. This observation is consistent with prior modeling predictions. The large and consistent responses observed during ML visual and walking surface perturbations suggest potential for application during gait training and patient assessment.     

Limiting similarity and Darwin’s naturalization hypothesis: understanding the drivers of biotic resistance against invasive plant species

Several hypotheses have been proposed to explain biotic resistance of a recipient plant community based on reduced niche opportunities for invasive alien plant species. The limiting similarity hypothesis predicts that invasive species are less likely to establish in communities of species holding similar functional traits. Likewise, Darwin’s naturalization hypothesis states that invasive species closely related to the native community would be less successful. We tested both using the invasive alien Ambrosia artemisiifolia L. and Solidago gigantea Aiton, and grassland species used for ecological restoration in central Europe. We classified all plant species into groups based on functional traits obtained from trait databases and calculated the phylogenetic distance among them. In a greenhouse experiment, we submitted the two invasive species at two propagule pressures to competition with communities of ten native species from the same functional group. In another experiment, they were submitted to pairwise competition with native species selected from each functional group. At the community level, highest suppression for both invasive species was observed at low propagule pressure and not explained by similarity in functional traits. Moreover, suppression decreased asymptotically with increasing phylogenetic distance to species of the native community. When submitted to pairwise competition, suppression for both invasive species was also better explained by phylogenetic distance. Overall, our results support Darwin’s naturalization hypothesis but not the limiting similarity hypothesis based on the selected traits. Biotic resistance of native communities against invasive species at an early stage of establishment is enhanced by competitive traits and phylogenetic relatedness.     

Phytoplankton responses to repeated pulse perturbations imposed on a trend of increasing eutrophication

While eutrophication remains one of the main pressures acting on freshwater ecosystems, the prevalence of anthropogenic and nature‐induced stochastic pulse perturbations is predicted to increase due to climate change. Despite all our knowledge on the effects of eutrophication and stochastic events operating in isolation, we know little about how eutrophication may affect the response and recovery of aquatic ecosystems to pulse perturbations. There are multiple ways in which eutrophication and pulse perturbations may interact to induce potentially synergic changes in the system, for instance, by increasing the amount of nutrients released after a pulse perturbation. Here, we performed a controlled press and pulse perturbation experiment using mesocosms filled with natural lake water to address how eutrophication modulates the phytoplankton response to sequential mortality pulse perturbations; and what is the combined effect of press and pulse perturbations on the resistance and resilience of the phytoplankton community. Our experiment showed that eutrophication increased the absolute scale of the chlorophyll‐a response to pulse perturbations but did not change the proportion of the response relative to its pre‐event condition (resistance). Moreover, the capacity of the community to recover from pulse perturbations was significantly affected by the cumulative effect of sequential pulse perturbations but not by eutrophication itself. By the end of the experiment, some mesocosms could not recover from pulse perturbations, irrespective of the trophic state induced by the press perturbation. While not resisting or recovering any less from pulse perturbations, phytoplankton communities from eutrophying systems showed chlorophyll‐a levels much higher than non‐eutrophying ones. This implies that the higher absolute response to stochastic pulse perturbations in a eutrophying system may increase the already significant risks for water quality (e.g., algal blooms in drinking water supplies), even if the relative scale of the response to pulse perturbations between eutrophying and non‐eutrophying systems remains the same.     

Detection of perturbation phases and developmental stages in organisms from DNA microarray time series data

Available DNA microarray time series that record gene expression along the developmental stages of multicellular eukaryotes, or in unicellular organisms subject to external perturbations such as stress and diauxie, are analyzed. By pairwise comparison of the gene expression profiles on the basis of a translation-invariant and scale-invariant distance measure corresponding to least-rectangle regression, it is shown that peaks in the average distance values are noticeable and are localized around specific time points. These points systematically coincide with the transition points between developmental phases or just follow the external perturbations. This approach can thus be used to identify automatically, from microarray time series alone, the presence of external perturbations or the succession of developmental stages in arbitrary cell systems. Moreover, our results show that there is a striking similarity between the gene expression responses to these a priori very different phenomena. In contrast, the cell cycle does not involve a perturbation-like phase, but rather continuous gene expression remodeling. Similar analyses were conducted using three other standard distance measures, showing that the one we introduced was superior. Based on these findings, we set up an adapted clustering method that uses this distance measure and classifies the genes on the basis of their expression profiles within each developmental stage or between perturbation phases.     

Distance decay of similarity in freshwater communities: do macro‐ and microorganisms follow the same rules?

Aim An intensively debated issue in macroecology is whether unicellular organisms show biogeographic patterns different from those of macroorganisms. One aspect of this debate addresses beta diversity, that is, do microbial organisms exhibit distance‐decay patterns similar to those of macroorganisms? And if so, is the decay of community similarity caused by spatially limited dispersal or by niche‐related factors? We studied the community similarity of stream diatoms, macroinvertebrates and bryophytes across the same set of sites in relation to environmental and geographic distance. Location A geographical gradient of c. 1100 km in Finland. Methods We first identified the subset of environmental variables that produced the highest correlation with community similarities for each taxonomic group. Based on these variables, we used partial Mantel tests to separate the independent influences of environmental and geographical distance for distance decay of community similarity, separately for diatoms, bryophytes and macroinvertebrates. Finally, macroinvertebrates were divided into three groups based on their different dispersal categories and a partial Mantel test was used to assess whether each of these groups were differently affected by environmental versus geographic distance, i.e. is dispersal a key factor in tests of niche versus neutral models. Results The level of environmental control was by far the strongest for diatoms; however, all groups were controlled more by environmental factors than by limited dispersal. Macroinvertebrate species with low dispersal ability were significantly related to geographic distance, while more effective dispersers showed no relationship to geography but were instead strongly related to environmental distance. Main conclusions Our results suggest that patterns between macro‐ and microorganisms are not fundamentally different, but the level of environmental control varies according to dispersal ability. The relative importance of niche versus dispersal processes is not simply a function of organism size but other traits (e.g. life‐history type, dispersal capacity) may obscure this relationship.     

Ecological niche variation in the Wilson's warbler Cardellina pusilla complex

Wilson's warbler comprises three subspecies separated into two geographic groups: C. p. pusilla that breeds in eastern North America; and C. p. pileolata and C. p. chryseola that breed in western North America. Given the differences between the groups in genetics, morphology, habitat use, and population decline, we tested for ecological niche similarity in both their breeding and wintering distribution using niche modeling based on temperature and precipitation data. We first conducted an inter‐prediction approach considering the percent of summer and winter localities of one group that are predicted by the potential distribution of the alternate group. We also applied a null model approach that compares self‐predictions and pseudoreplicates of each group to indicate similarity, divergence, or indeterminate niche overlap. Finally, we compared ecological distances between and within groups using the Gower similarity equation. We found that the western group had an ecological niche of broader climatic conditions, while the eastern group had a narrower ecological niche. The inter‐prediction approach showed that, for both summering and wintering ranges, ecological niche models of the western group predicted ～50% of the observed distribution of the eastern group, whereas eastern group models predicted < 18% of the western group distribution. The null model approach found that similarity in ecological niches was indeterminate, possibly due to the large area occupied by the two groups; but it suggests a more restricted set of climatic conditions of the eastern group distribution. However, the Gower coefficients demonstrated that the ecological distance between the two geographic groups was larger than the ecological distance within groups, indicating distinct ecological niches. Overall, our results support the hypothesis that the eastern and western groups of Wilson's warbler are two cryptic species; this should be taken into consideration for future analyses, particularly with respect to vulnerability categorization and conservation efforts.     

Morphological Similarity and Ecological Overlap in Two Rotifer Species

Co-occurrence of cryptic species raises theoretically relevant questions regarding their coexistence and ecological similarity. Given their great morphological similitude and close phylogenetic relationship (i.e., niche retention), these species will have similar ecological requirements and are expected to have strong competitive interactions. This raises the problem of finding the mechanisms that may explain the coexistence of cryptic species and challenges the conventional view of coexistence based on niche differentiation. The cryptic species complex of the rotifer Brachionus plicatilis is an excellent model to study these questions and to test hypotheses regarding ecological differentiation. Rotifer species within this complex are filtering zooplankters commonly found inhabiting the same ponds across the Iberian Peninsula and exhibit an extremely similar morphology—some of them being even virtually identical. Here, we explore whether subtle differences in body size and morphology translate into ecological differentiation by comparing two extremely morphologically similar species belonging to this complex: B. plicatilis and B. manjavacas. We focus on three key ecological features related to body size: (1) functional response, expressed by clearance rates; (2) tolerance to starvation, measured by growth and reproduction; and (3) vulnerability to copepod predation, measured by the number of preyed upon neonates. No major differences between B. plicatilis and B. manjavacas were found in the response to these features. Our results demonstrate the existence of a substantial niche overlap, suggesting that the subtle size differences between these two cryptic species are not sufficient to explain their coexistence. This lack of evidence for ecological differentiation in the studied biotic niche features is in agreement with the phylogenetic limiting similarity hypothesis but requires a mechanistic explanation of the coexistence of these species not based on differentiation related to biotic niche axes.     

Trip recovery strategies following perturbations of variable duration

Appropriately responding to mechanical perturbations during gait is critical to maintain balance and avoid falls. Tripping perturbation onset during swing phase is strongly related to the use of different recovery strategies; however, it is insufficient to fully explain how strategies are chosen. The dynamic interactions between the foot and the obstacle may further explain observed recovery strategies but the relationship between such contextual elements and strategy selection has not been explored. In this study, we investigated whether perturbation onset, duration and side could explain strategy selection for all of swing phase. We hypothesized that perturbations of longer duration would elicit lowering and delayed-lowering strategies earlier in swing phase than shorter perturbations. We developed a custom device to trip subjects multiple times while they walked on a treadmill. Seven young, healthy subjects were tripped on the left or right side at 10% to 80% of swing phase for 150 ms, 250 ms or 350 ms. Strategies were characterized by foot motion post-perturbation and identified by an automated algorithm. A multinomial logistic model was used to investigate the effect of perturbation onset, side, and the interaction between duration and onset on recovery strategy selection. Side perturbed did not affect strategy selection. Perturbation duration interacted with onset, limiting the use of elevating strategies to earlier in swing phase with longer perturbations. The choice between delayed-lowering and lowering strategies was not affected by perturbation duration. Although these variables did not fully explain strategy selection, they improved the prediction of strategy used in response to tripping perturbations throughout swing phase.     

Primate communities are structured more by dispersal limitation than by niches

1.?A major goal in community ecology is to identify mechanisms that govern the assembly and maintenance of ecological communities. Current models of metacommunity dynamics differ chiefly in the relative emphasis placed on dispersal limitation and niche differentiation as causal mechanisms structuring ecological communities. Herein we investigate the relative roles of these two mechanisms in structuring primate communities in Africa, South America, Madagascar and Borneo. 2.?We hypothesized that if dispersal limitation is important in structuring communities, then community similarity should depend on geographical proximity even after controlling for ecological similarity. Conversely, if communities are assembled primarily through niche processes, then community similarity should be determined by ecological similarity regardless of geographical proximity. 3.?We performed Mantel and partial Mantel tests to investigate correlations among primate community similarity, ecological distance and geographical distance. Results showed significant and strongly negative relationships between diurnal primate community similarity and both ecological similarity and geographical distance in Madagascar, but significant and stronger negative relationships between community similarity and geographical distance in African, South American and Bornean metacommunities. 4.?We conclude that dispersal limitation is an important determinant of primate community structure and may play a stronger role in shaping the structure of some terrestrial vertebrate communities than niche differentiation. These patterns are consistent with neutral theory. We recommend tests of functional equivalence to determine the extent to which neutral theory may explain primate community composition.     

Niches in the Anthropocene: passerine assemblages show niche expansion from natural to urban habitats

Human‐mediated habitat transformation is increasingly evident around the world. Yet, how this transformation influences species’ niche width and overlap remains unclear. On the one hand, human‐mediated habitat transformation promotes increased species similarity through trait‐based filtering, and an increased prevalence of generalist species with broad niches, resulting in functional homogenization. On the other hand, species that colonize transformed habitats could use empty niches, resulting in decreased species similarity and an expansion of assemblage‐level niche space. Here we explore these two alternatives in eight highly diverse passerine assembles in natural, rural and urban habitats in south and southwest China, a rapidly developing region of the world. Based on stable isotopes, we found that species’ niche width increased from natural to human‐made habitats, but there were no differences in niche overlap among habitats. Therefore, we found evidence for niche expansion, with generalists appearing to use empty niches created by human habitat modification, and with assemblages being comprised of complementary species. Further research is needed to determine whether increased between‐ or within‐individual niche variation is the main driver of niche expansion in transformed habitats.     

Effects of amplitude and predictability of perturbations to the arm on anticipatory and reactionary muscle responses to maintain balance

Disturbances to balance arising from forces applied to the upper limb have received relatively little attention compared to disturbances arising from support surface perturbations. In this study we applied fast ramp perturbations to the hand in anterior, posterior, medial and lateral directions. The effects of perturbation predictability and amplitude on the postural response of upper limb, trunk and lower limb muscles were investigated. Perturbations were applied either in blocks of constant amplitude and direction (predictable) or with direction and amplitude varying randomly (random) from trial to trial. The spatial-temporal patterns of anticipatory muscle activation under the predictable condition and the reactionary responses following the perturbation under both conditions were similarly organized. The size of the response increased systematically with the perturbation magnitude for both anticipatory and reactionary changes in muscle activation. However, the slope of the relation between perturbation amplitude and the magnitude of the change in muscle activation was greater when perturbations were predictable than when they were randomly selected. The timing of both the anticipatory and reactionary increases in muscle activation was invariant across perturbation amplitudes. The characteristics of the reactionary responses have a similar organization to the long latency muscle responses to support surface perturbations.