What ecological factors shape species-area curves in neutral models?
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ABSTRACT:
SUBMITTER: Cencini M
PROVIDER: S-EPMC3366919 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:A fundamental challenge in ecology is to understand the mechanisms that govern patterns of relative species abundance. Previous numerical simulations have suggested that complex niche-structured models produce species abundance distributions (SADs) that are qualitatively similar to those of very simple neutral models that ignore differences between species. However, in the absence of an analytical treatment of niche models, one cannot tell whether the two classes of model produce the same patterns via similar or different mechanisms. We present an analytical proof that, in the limit as diversity becomes large, a strong niche model give rises to exactly the same asymptotic form of SAD as the neutral model, and we verify the analytical predictions for a Panamanian tropical forest data set. Our results strongly suggest that neutral processes drive patterns of relative species abundance in high-diversity ecological communities, even when strong niche structure exists. However, neutral theory cannot explain what generates high diversity in the first place, and it may not be valid in low-diversity communities. Our results also confirm that neutral theory cannot be used to infer an absence of niche structure or to explain ecosystem function.
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Project description:The "binormal" model is the most frequently used tool for parametric receiver operating characteristic (ROC) analysis. The binormal ROC curves can have "improper" (non-concave) shapes that are unrealistic in many practical applications, and several tools (eg, PROPROC) have been developed to address this problem. However, due to the general robustness of binormal ROCs, the improperness of the fitted curves might carry little consequence for inferences about global summary indices, such as the area under the ROC curve (AUC). In this work, we investigate the effect of severe improperness of fitted binormal ROC curves on the reliability of AUC estimates when the data arise from an actually proper curve.We designed theoretically proper ROC scenarios that induce severely improper shape of fitted binormal curves in the presence of well-distributed empirical ROC points. The binormal curves were fitted using maximum likelihood approach. Using simulations, we estimated the frequency of severely improper fitted curves, bias of the estimated AUC, and coverage of 95% confidence intervals (CIs). In Appendix?S1, we provide additional information on percentiles of the distribution of AUC estimates and bias when estimating partial AUCs. We also compared the results to a reference standard provided by empirical estimates obtained from continuous data.We observed up to 96% of severely improper curves depending on the scenario in question. The bias in the binormal AUC estimates was very small and the coverage of the CIs was close to nominal, whereas the estimates of partial AUC were biased upward in the high specificity range and downward in the low specificity range. Compared to a non-parametric approach, the binormal model led to slightly more variable AUC estimates, but at the same time to CIs with more appropriate coverage.The improper shape of the fitted binormal curve, by itself, ie, in the presence of a sufficient number of well-distributed points, does not imply unreliable AUC-based inferences.
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Project description:Many metagenomic sequencing studies have observed the presence of closely related bacterial species or genotypes in the same microbiome. Previous attempts to explain these patterns of microdiversity have focused on the abiotic environment, but few have considered how biotic interactions could drive patterns of microbiome diversity. We dissected the patterns, processes, and mechanisms shaping the ecological distributions of three closely related Staphylococcus species in cheese rind biofilms. Paradoxically, the most abundant species (S. equorum) is the slowest colonizer and weakest competitor based on growth and competition assays in the laboratory. Through in vitro community reconstructions, we determined that biotic interactions with neighboring fungi help resolve this paradox. Species-specific stimulation of the poor competitor by fungi of the genus Scopulariopsis allows S. equorum to dominate communities in vitro as it does in situ Results of comparative genomic and transcriptomic experiments indicate that iron utilization pathways, including a homolog of the S. aureus staphyloferrin B siderophore operon pathway, are potential molecular mechanisms underlying Staphylococcus-Scopulariopsis interactions. Our integrated approach demonstrates that fungi can structure the ecological distributions of closely related bacterial species, and the data highlight the importance of bacterium-fungus interactions in attempts to design and manipulate microbiomes.ImportanceDecades of culture-based studies and more recent metagenomic studies have demonstrated that bacterial species in agriculture, medicine, industry, and nature are unevenly distributed across time and space. The ecological processes and molecular mechanisms that shape these distributions are not well understood because it is challenging to connect in situ patterns of diversity with mechanistic in vitro studies in the laboratory. Using tractable cheese rind biofilms and a focus on coagulase-negative staphylococcus (CNS) species, we demonstrate that fungi can mediate the ecological distributions of closely related bacterial species. One of the Staphylococcus species studied, S. saprophyticus, is a common cause of urinary tract infections. By identifying processes that control the abundance of undesirable CNS species, cheese producers will have more precise control on the safety and quality of their products. More generally, Staphylococcus species frequently co-occur with fungi in mammalian microbiomes, and similar bacterium-fungus interactions may structure bacterial diversity in these systems.
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Project description:Aim:Area thresholds, at which the form of the species-area relationship (SAR) changes abruptly, have played an important role in the theoretical framework of conservation biogeography and biodiversity research. The application of piecewise regressions has been advocated as a rigorous statistical technique to identify such thresholds within SARs, but a large variety of piecewise models remains untested. We explore the prevalence and number of thresholds in SARs and examine whether the currently widely used method for detecting the small island effect (SIE) is robust. Location:Global. Taxon:We consider all multicellular taxa based on the criteria of datasets selection. Methods:We apply 15 regression models, including linear regression and piecewise regressions with two and three segments to 68 global island datasets that are sourced from the literature. Results:The number of area thresholds in SARs varied among groups and correlated positively with area range of a studied system. Under the AIC or AICc criterion, three-segment piecewise models were more prevalent, whereas under the BIC criterion, two-segment piecewise models were more prevalent. From the results of Aegean Sea isopods, West Indies herpetofauna, and Australian Islands mammals, we found evidence that the traditional criteria for detection of SIEs are not robust. Main conclusions:Our study demonstrates that (a) to detect an SIE, the comparison should use as many models as possible, including not only variants with and without a left-horizontal part, but also those with two and more segments; (b) naive use of the traditional two-segment piecewise regressions may cause poor estimations of both slope and breakpoint values; (c) the number of thresholds increases with the area range of a studied system; (d) conservation biologists and applied ecologists should determine the number of area thresholds when estimating the precise species-area patterns and making management strategies in fragmented landscapes.
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Project description:Among the greatest challenges facing the conservation of plants and animal species in protected areas are threats from a rapidly changing climate. An altered climate creates both challenges and opportunities for improving the management of protected areas in networks. Increasingly, quantitative tools like species distribution modeling are used to assess the performance of protected areas and predict potential responses to changing climates for groups of species, within a predictive framework. At larger geographic domains and scales, protected area network units have spatial geoclimatic properties that can be described in the gap analysis typically used to measure or aggregate the geographic distributions of species (stacked species distribution models, or S-SDM). We extend the use of species distribution modeling techniques in order to model the climate envelope (or "footprint") of individual protected areas within a network of protected areas distributed across the 48 conterminous United States and managed by the US National Park System. In our approach we treat each protected area as the geographic range of a hypothetical endemic species, then use MaxEnt and 5 uncorrelated BioClim variables to model the geographic distribution of the climatic envelope associated with each protected area unit (modeling the geographic area of park units as the range of a species). We describe the individual and aggregated climate envelopes predicted by a large network of 163 protected areas and briefly illustrate how macroecological measures of geodiversity can be derived from our analysis of the landscape ecological context of protected areas. To estimate trajectories of change in the temporal distribution of climatic features within a protected area network, we projected the climate envelopes of protected areas in current conditions onto a dataset of predicted future climatic conditions. Our results suggest that the climate envelopes of some parks may be locally unique or have narrow geographic distributions, and are thus prone to future shifts away from the climatic conditions in these parks in current climates. In other cases, some parks are broadly similar to large geographic regions surrounding the park or have climatic envelopes that may persist into near-term climate change. Larger parks predict larger climatic envelopes, in current conditions, but on average the predicted area of climate envelopes are smaller in our single future conditions scenario. Individual units in a protected area network may vary in the potential for climate adaptation, and adaptive management strategies for the network should account for the landscape contexts of the geodiversity or climate diversity within individual units. Conservation strategies, including maintaining connectivity, assessing the feasibility of assisted migration and other landscape restoration or enhancements can be optimized using analysis methods to assess the spatial properties of protected area networks in biogeographic and macroecological contexts.
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Project description:The study aimed to examine the effects of different numbers of presences and frequencies (proportions) of occurrences of species in a plot data set of forest vegetation on the species response curves and their niche attributes, based on Huisman-Olff-Fresco models (HOF). We modeled responses of 72 to 105 herbaceous forest species along a pH gradient under 14 different random sampling scenarios by varying the number of presences and absences used for model fitting. Mean niche attributes were calculated from 100 repetitive runs for each scenario and species. Re-prediction success of HOF models among the repetitive runs was highest when the total number of plots was high and the frequency of occurrences was low. With low plot numbers and high frequencies, less complicated model types (no response or monotonically increasing/decreasing responses) predominate. Measures of species niche boundaries (limits & borders) and niche width were strongly influenced by changes in sampling characteristics. With an increasing number of presences and an increasing frequency, limits and borders shifted to more extreme values, leading to wider niches. In contrast, species optima showed almost no change between the scenarios. Thus, the detected ecological response of a species often depends on the size of the data set and the relation between presences and absences of a species. In general, high data quantities are required for reliable response curve modeling with HOF models, which prevents the assessment of the responses of many rare species. To avoid undesired bias by differing sampling characteristics when comparing niches between different species or between data sets, the data basis used for model fitting should be adjusted according to the niche attribute in question, for example by keeping the frequency of the species constant.
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