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Species abundances are undoubtedly the most widely available macroecological data, but can we use them to distinguish among several models of community structure? Here we present a Bayesian analysis of species‐abundance data that yields a full joint probability distribution of each model's parameters plus a relatively parameter‐independent criterion, the posterior Bayes factor, to compare these models. We illustrate our approach by comparing three classical distributions: the zero‐sum multinomial (ZSM) distribution, based on Hubbell's neutral model, the multivariate Poisson lognormal distribution (MPLN), based on niche arguments, and the discrete broken stick (DBS) distribution, based on MacArthur's broken stick model. We give explicit formulas for the probability of observing a particular species‐abundance data set in each model, and argue that conditioning on both sample size and species count is needed to allow comparisons between the two distributions. We apply our approach to two neotropical communities (trees, fish). We find that DBS is largely inferior to ZSM and MPLN for both communities. The tree data do not allow discrimination between ZSM and MPLN, but for the fish data ZSM (neutral model) overwhelmingly outperforms MPLN (niche model), suggesting that dispersal plays a previously underestimated role in structuring tropical freshwater fish communities. We advocate this approach for identifying the relative importance of dispersal and niche‐partitioning in determining diversity of different ecological groups of species under different environmental conditions. 相似文献
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Major shifts in many ecosystem-level properties of tropical forests have been observed, but the processes driving these changes are poorly understood. The forest on Barro Colorado Island (BCI) exhibited a 20% decrease in the number of trees and a 10% increase in average diameter. Using a metabolism-based zero-sum framework, we show that increases in per capita resource use at BCI, caused by increased tree size and increased temperature, compensated for the observed declines in abundance. This trade-off between abundance and average resource use resulted in no net change in the rate resources are fluxed by the forest. Observed changes in the forest are not consistent with other hypotheses, including changes in overall resource availability and existing self-thinning models. The framework successfully predicts interrelated changes in size, abundance and temperature, indicating its utility for understanding changes in the structure and dynamics of ecosystems. 相似文献
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Vascular epiphytes form a diverse group of almost 30 000 species, yet theory concerning their community structure is still largely lacking. We therefore employed the simplest models of biodiversity, (near-)neutral models, to generate hypotheses concerning their community structure. With recently developed tools for (near-)neutral models we analyzed species abundance data from many samples in Central and South America which we divided into four metacommunities (Mesoamerica, Central America, Amazonia and Paraná), where for each metacommunity we considered two subsets differing in dispersal syndrome: an animal-dispersed guild and a wind-dispersed guild. We considered three models differing in the underlying speciation mode. Across all metacommunities, we found observed patterns to be indistinguishable from patterns generated by neutral or near-neutral processes. Furthermore, we found that subdivision in different dispersal guilds was often supported, with recruitment limitation being stronger for animal-dispersed species than for wind-dispersed species. This is the first time that (near-)neutral theory has been applied to epiphyte communities. Future efforts with additional data sets and more refined models are expected to further improve our understanding of community structure in epiphytes and will have to test the generality of our findings. 相似文献
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Aims Neutral theory consists of a suite of models that assume ecological equivalence among individual organisms. They have been most commonly applied to tropical forest tree communities either as null models or as approximations. Neutral models typically only include reproductive adults; therefore, fitting to empirical tree community data requires defining a reproductive-size threshold, which for trees is usually set arbitrarily to a diameter at breast height (DBH) of 100 mm. The inevitable exclusion of some reproductive adults and inclusion of some saplings cause a non-random sampling bias in neutral model fits. Here, we investigate this problem and resolve it by introducing simple age structure into a neutral model.Methods We compared the performance and sensitivity of DBH threshold of three variants of a spatially explicit neutral model: the traditional model, a model incorporating random sampling and a model with two distinct age classes—reproductive adults and saplings. In the age-structured model, saplings are offspring from adults that disperse according to a Gaussian dispersal kernel around the adults. The only extra parameter is the ratio of adults to saplings, which is not a free parameter but directly measurable. We used species–area relationships (SARs) to explore the predicted effect of saplings on the species richness at different scales in our model. We then evaluated the three model variations to find the parameters required to maintain the observed level of species richness in the 50-ha plot on Barro Colorado Island (BCI). We repeated our analysis filtering the data at different minimum tree-size thresholds in order to find the effect this threshold has on our results. Lastly, we used empirical species–individual relationships (SIRs) to test the pre-existing hypothesis that environmental filtering is the primary cause of differences between the assemblage of saplings and that of adults on BCI.Important findings Our age-structured neutral model was characterized by SARs that were insensitive to the presence of saplings at large scales and highly sensitive to them at small scales. Both models without age structure were highly sensitive to the DBH threshold chosen in a way that could not be explained based on random samplings alone. The age-structured neutral model, which allowed for non-random sampling based on life stage, was consistent with species richness observations. Our analysis of empirical SIRs did not support environmental filtering as a dominant force, but it did show evidence for other differences between age classes. Age can now be easily incorporated into future studies of neutral models whenever there is a concern that a sample is not entirely composed of reproductive adult individuals. More generally, we suggest that modeling studies using tree data subject to a minimum size threshold should consider the sensitivity of their results to that threshold. 相似文献
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2008～2009年连续2年系统调查了番茄、茄子、棉花、大豆、玉米等寄主植物上烟粉虱种群发生的时间与空间动态。结果表明：不同寄主植物上的烟粉虱成虫及其伪蛹数量有显著性差异,其密度大小依次为：茄子>棉花>番茄>大豆>玉米。其中,在玉米上除了发现极少量的成虫逗留外,没有发现烟粉虱的卵及若虫。在发生的时间序列上,烟粉虱成虫及伪蛹的数量呈现为先逐渐上升后又下降的变化过程,发生高峰期集中在8月5日到8月31日,9月初以后烟粉虱数量慢慢减少。在空间分布上,表现为烟粉虱成虫喜食寄主的上部叶片。统计分析显示,寄主对烟粉虱成虫和伪蛹的数量的影响极显著,而年份对其数量的影响没有显著差异。由此得出的烟粉虱发生和达到高峰的时间,可为烟粉虱预测预报和区域性综合治理提供重要理论依据。 相似文献
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Assuming equality of genotypic effects over different loci, this paper provides an ML procedure for estimating genetic parameters for quantitative traits from autotetraploid self-fertilized populations. The results are illustrated by computer generated data involving P1, P2, F2, B1 and B2 populations. 相似文献
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An implicit assumption of standard line transect methodology is that detection probabilities depend solely on the perpendicular distance of detected objects to the transect line. Heterogeneity in detection probabilities is commonly minimized using stratification, but this may be precluded by small sample sizes. We develop a general methodology which allows the effects of multiple covariates to be directly incorporated into the estimation procedure using a conditional likelihood approach. Small sample size properties of estimators are examined via simulations. As an example the method is applied to eastern tropical Pacific dolphin sightings data. 相似文献
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Ryan A. Chisholm Richard Condit K. Abd. Rahman Patrick J. Baker Sarayudh Bunyavejchewin Yu‐Yun Chen George Chuyong H. S. Dattaraja Stuart Davies Corneille E. N. Ewango C. V. S. Gunatilleke I. A. U. Nimal Gunatilleke Stephen Hubbell David Kenfack Somboon Kiratiprayoon Yiching Lin Jean‐Remy Makana Nantachai Pongpattananurak Sandeep Pulla Ruwan Punchi‐Manage Raman Sukumar Sheng‐Hsin Su I‐Fang Sun H. S. Suresh Sylvester Tan Duncan Thomas Sandra Yap 《Ecology letters》2014,17(7):855-865
Long‐term surveys of entire communities of species are needed to measure fluctuations in natural populations and elucidate the mechanisms driving population dynamics and community assembly. We analysed changes in abundance of over 4000 tree species in 12 forests across the world over periods of 6–28 years. Abundance fluctuations in all forests are large and consistent with population dynamics models in which temporal environmental variance plays a central role. At some sites we identify clear environmental drivers, such as fire and drought, that could underlie these patterns, but at other sites there is a need for further research to identify drivers. In addition, cross‐site comparisons showed that abundance fluctuations were smaller at species‐rich sites, consistent with the idea that stable environmental conditions promote higher diversity. Much community ecology theory emphasises demographic variance and niche stabilisation; we encourage the development of theory in which temporal environmental variance plays a central role. 相似文献
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Recently, three different models have been proposed to explain the distribution of abundances in natural communities: the self‐similarity model; the zero‐sum ecological drift model; and the occasional–frequent species model of Magurran and Henderson. Here we study patterns of relative abundance in a large community of forest Hymenoptera and show that it is indeed possible to divide the community into a group of frequent species and a group of occasional species. In accordance with the third model, frequent species followed a lognormal distribution. Relative abundances of the occasional species could be described by the self‐similarity model, but did not follow a log‐series as proposed by the occasional–frequent model. The zero‐sum ecological drift model makes no explicit predictions about frequent and occasional species but the abundance distributions of the hymenopteran species did not show the excess of rare species predicted by this model. Separate fits of this model to the frequent and to the occasional species were worse than the respective fits of the lognormal and the self‐similarity model. 相似文献
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There have been several attempts to build a unified framework for macroecological patterns. However, these have mostly been based either on questionable assumptions or have had to be parameterized to obtain realistic predictions. Here, we propose a new model explicitly considering patterns of aggregated species distributions on multiple spatial scales, the property which lies behind all spatial macroecological patterns, using the idea we term 'generalized fractals'. Species' spatial distributions were modelled by a random hierarchical process in which the original 'habitat' patches were randomly replaced by sets of smaller patches nested within them, and the statistical properties of modelled species assemblages were compared with macroecological patterns in observed bird data. Without parameterization based on observed patterns, this simple model predicts realistic patterns of species abundance, distribution and diversity, including fractal-like spatial distributions, the frequency distribution of species occupancies/abundances and the species–area relationship. Although observed macroecological patterns may differ in some quantitative properties, our concept of random hierarchical aggregation can be considered as an appropriate null model of fundamental macroecological patterns which can potentially be modified to accommodate ecologically important variables. 相似文献
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Does Mother Nature really prefer rare species or are log‐left‐skewed SADs a sampling artefact? 总被引：1，自引：1，他引：1
Brian J. McGill 《Ecology letters》2003,6(8):766-773
Intensively sampled species abundance distributions (SADs) show left‐skew on a log scale. That is, there are too many rare species to fit a lognormal distribution. I propose that this log‐left‐skew might be a sampling artefact. Monte Carlo simulations show that taking progressively larger samples from a log‐unskewed distribution (such as the lognormal) causes log‐skew to decrease asymptotically (move towards ?∞) until it reaches the level of the underlying distribution (zero in this case). In contrast, accumulating certain types of repeated small samples results in a log‐skew that becomes progressively more log‐left‐skewed to a level well beyond the underlying distribution. These repeated samples correspond to samples from the same site over many years or from many sites in 1 year. Data from empirical datasets show that log‐skew generally goes from positive (right‐skewed) to negative (left‐skewed) as the number of temporally or spatially replicated samples increases. This suggests caution when interpreting log‐left‐skew as a pattern that needs biological interpretation. 相似文献
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Jofre Carnicer Lluís Brotons Daniel Sol Pedro Jordano 《Global Ecology and Biogeography》2007,16(6):709-719
Aim To consider the role of local colonization and extinction rates in explaining the generation and maintenance of species richness gradients at the regional scale.
Location A Mediterranean biome (oak forests, deciduous forests, shrublands, pinewoods, firwoods, alpine heathlands, crops) in Catalonia, Spain.
Methods We analysed the relative importance of direct and indirect effects of community size in explaining species richness gradients. Direct sampling effects of community size on species richness are predicted by Hubbell's neutral theory of biodiversity and biogeography. The greater the number of individuals in a locality, the greater the number of species expected by random direct sampling effects. Indirect effects are predicted by the abundance–extinction hypothesis, which states that in more productive sites increased population densities and reduced extinction rates may lead to high species richness. The study system was an altitudinal gradient of forest bird species richness.
Results We found significant support for the existence of both direct and indirect effects of community size in species richness. Thus, both the neutral and the abundance–extinction hypotheses were supported for the altitudinal species richness gradient of forest birds in Catalonia. However, these mechanisms seem to drive variation in species richness only in low-productivity areas; in high-productivity areas, species richness was uncorrelated with community size and productivity measures.
Main conclusions Our results support the existence of a geographical mosaic of community-based processes behind species richness gradients, with contrasting abundance–extinction dynamics and sampling effects in areas of low and high productivity. 相似文献
Location A Mediterranean biome (oak forests, deciduous forests, shrublands, pinewoods, firwoods, alpine heathlands, crops) in Catalonia, Spain.
Methods We analysed the relative importance of direct and indirect effects of community size in explaining species richness gradients. Direct sampling effects of community size on species richness are predicted by Hubbell's neutral theory of biodiversity and biogeography. The greater the number of individuals in a locality, the greater the number of species expected by random direct sampling effects. Indirect effects are predicted by the abundance–extinction hypothesis, which states that in more productive sites increased population densities and reduced extinction rates may lead to high species richness. The study system was an altitudinal gradient of forest bird species richness.
Results We found significant support for the existence of both direct and indirect effects of community size in species richness. Thus, both the neutral and the abundance–extinction hypotheses were supported for the altitudinal species richness gradient of forest birds in Catalonia. However, these mechanisms seem to drive variation in species richness only in low-productivity areas; in high-productivity areas, species richness was uncorrelated with community size and productivity measures.
Main conclusions Our results support the existence of a geographical mosaic of community-based processes behind species richness gradients, with contrasting abundance–extinction dynamics and sampling effects in areas of low and high productivity. 相似文献
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The traditional sampling method for estimating frequency (the number of sub-quadrats containing a basal part of the organisms) is compared, using both computer simulations and direct comparison in the field, to two new methods that use a compound series of variable-sized concentric sub-quadrats. Both the new frequency-score and the new importance-score methods are closer approximations of density than is the standard frequency method, and the estimates produced by both of the new methods are less affected by the choice of sub-quadrat size and the spatial distribution (dispersion) of the organisms (i.e. clumping and regularity). Thus, the two nested-quadrat methods appear to ameliorate the usual frequency limitations associated with sub-quadrat size and organism dispersion, by the use of a range of different sub-quadrat sizes. This is important in community studies, where the component species may show a wide range of densities and dispersions. Both of the new methods are easily employed in the field. The importance-score method involves no more sampling effort than does standard qualitative (presence-absence) sampling, and it can therefore be used to sample a larger quadrat area than would normally be used for frequency sampling. This makes the method much more cost-effective as a means of estimating abundance, and it allows a greater number of the rarer species to be included in the sampling. The frequency-score method is more time-consuming, but it is capable of detecting more subtle community patterns. This means that it is particularly useful for the study of species-poor communities or where small variations in composition need to be detected. 相似文献
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Anchi Wu Xiangwen Deng Honglin He Xiaoli Ren Yiran Jing Wenhua Xiang Shuai Ouyang Wende Yan Xi Fang 《Ecology and evolution》2019,9(9):5338-5347
To quantify and assess the processes underlying community assembly and driving tree species abundance distributions(SADs) with spatial scale variation in two typical subtropical secondary forests in Dashanchong state‐owned forest farm, two 1‐ha permanent study plots (100‐m × 100‐m) were established. We selected four diversity indices including species richness, Shannon–Wiener, Simpson and Pielou, and relative importance values to quantify community assembly and biodiversity. Empirical cumulative distribution and species accumulation curves were utilized to describe the SADs of two forests communities trees. Three types of models, including statistic model (lognormal and logseries model), niche model (broken‐stick, niche preemption, and Zipf‐Mandelbrodt model), and neutral theory model, were estimated by the fitted SADs. Simulation effects were tested by Akaike's information criterion (AIC) and Kolmogorov–Smirnov test. Results found that the Fagaceae and Anacardiaceae families were their respective dominance family in the evergreen broad‐leaved and deciduous mixed communities. According to original data and random sampling predictions, the SADs were hump‐shaped for intermediate abundance classes, peaking between 8 and 32 in the evergreen broad‐leaved community, but this maximum increased with size of total sampled area size in the deciduous mixed community. All niche models could only explain SADs patterns at smaller spatial scales. However, both the neutral theory and purely statistical models were suitable for explaining the SADs for secondary forest communities when the sampling plot exceeded 40 m. The results showed the SADs indicated a clear directional trend toward convergence and similar predominating ecological processes in two typical subtropical secondary forests. The neutral process gradually replaced the niche process in importance and become the main mechanism for determining SADs of forest trees as the sampling scale expanded. Thus, we can preliminarily conclude that neutral processes had a major effect on biodiversity patterns in these two subtropical secondary forests but exclude possible contributions of other processes. 相似文献
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Summary Many well‐known methods are available for estimating the number of species in a forest community. However, most existing methods result in considerable negative bias in applications, where field surveys typically represent only a small fraction of sampled communities. This article develops a new method based on sampling with replacement to estimate species richness via the generalized jackknife procedure. The proposed estimator yields small bias and reasonably accurate interval estimation even with small samples. The performance of the proposed estimator is compared with several typical estimators via simulation study using two complete census datasets from Panama and Malaysia. 相似文献
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Summary A number of species richness estimators have been developed under the model that individuals (or sampling units) are sampled with replacement. However, if sampling is done without replacement so that no sampled unit can be repeatedly observed, then the traditional estimators for sampling with replacement tend to overestimate richness for relatively high-sampling fractions (ratio of sample size to the total number of sampling units) and do not converge to the true species richness when the sampling fraction approaches one. Based on abundance data or replicated incidence data, we propose a nonparametric lower bound for species richness in a single community and also a lower bound for the number of species shared by multiple communities. Our proposed lower bounds are derived under very general sampling models. They are universally valid for all types of species abundance distributions and species detection probabilities. For abundance data, individuals' detectabilities are allowed to be heterogeneous among species. For replicated incidence data, the selected sampling units (e.g., quadrats) need not be fully censused and species can be spatially aggregated. All bounds converge correctly to the true parameters when the sampling fraction approaches one. Real data sets are used for illustration. We also test the proposed bounds by using subsamples generated from large real surveys or censuses, and their performance is compared with that of some previous estimators. 相似文献