A dynamical model of communities and a new species-abundance distribution

It is known to many field biologists that biosurveys of natural communities tend to produce a J-shaped curve when the numbers of species are plotted against abundance. In other words, when the number of species of abundance k is plotted against k (running from 1 to some large number), the resulting distribution peaks at the lowest abundance, then forms a concave ramp as it approaches zero at the far end of the abundance axis. Does this distribution represent a single formula operating behind the scenes, or does it represent several formulas, appropriate for different types of community? Or does it represent no particular formula at all? The research reported here has three components: (1) The analysis of a new dynamical system that simulates multispecies communities (producing J-curves in the process) and the derivation of the "logistic-J" distribution, as the underlying community equilibrium curve; (2) the summary of a general theory of sampling as a bridge between natural communities and samples of them; (3) the evaluation of extant proposals for species-abundance distributions by application of a general theory of sampling or by cross-comparison via 100 biosurveys randomly selected from the literature.     

综防区和化防区稻田害虫-天敌群落特性的研究——种-多度关系及群落统计量的生态效应

对数级数模式是描述稻田害虫-天敌群落种-多度分布的理想模式。资料表明两个呈单一对数级数分布的群落经混合扩大后仍为对数级数分布.Shannon-weaver多样性指数比其他指数有较强的判别力。但在大样本中,对群落组成的变化亦不敏感,采用对数级数分布的参数(?)作为多样性统计量较为合适。     

Species abundance distributions and richness estimations in fungal metagenomics--lessons learned from community ecology

Results of diversity and community ecology studies strongly depend on sampling depth. Completely surveyed communities follow log-normal distribution, whereas power law functions best describe incompletely censused communities. It is arguable whether the statistics behind those theories can be applied to voluminous next generation sequencing data in microbiology by treating individual DNA sequences as counts of molecular taxonomic units (MOTUs). This study addresses the suitability of species abundance models in three groups of plant-associated fungal communities - phyllosphere, ectomycorrhizal and arbuscular mycorrhizal fungi. We tested the impact of differential treatment of molecular singletons on observed and estimated species richness and species abundance distribution models. The arbuscular mycorrhizal community of 48 MOTUs was exhaustively sampled and followed log-normal distribution. The ectomycorrhizal (153 MOTUs) and phyllosphere (327 MOTUs) communities significantly differed from log-normal distribution. The fungal phyllosphere community in particular was clearly undersampled. This undersampling bias resulted in strong sensitivity to the exclusion of molecular singletons and other rare MOTUs that may represent technical artefacts. The analysis of abundant (core) and rare (satellite) MOTUs clearly identified two species abundance distributions in the phyllosphere data - a log-normal model for the core group and a log-series model for the satellite group. The prominent log-series distribution of satellite phyllosphere fungi highlighted the ecological significance of an infrequent fungal component in the phyllosphere community.     

Neutral theory in community ecology

One of the central goals of community ecology is to understand the forces that maintain species diversity within communities. The traditional niche-assembly theory asserts that species live together in a community only when they differ from one another in resource uses. But this theory has some difficulties in explaining the diversity often observed in specie-rich communities such as tropical forests. As an alternative to the niche theory, Hubbell and other ecologists introduced a neutral model. Hubbell argues that the number of species in a community is controlled by species extinction and immigration or speciation of new species. Assuming that all individuals of all species in a trophically similar community are ecologically equivalent, Hubbell’s neutral theory predicts two important statistical distributions. One is the asymptotic log-series distribution for the metacommunities under point mutation speciation, and the other is the zero-sum multinomial distribution for both local communities under dispersal limitation and metacommunities under random fission speciation. Unlike the niche-assembly theory, the neutral theory takes similarity in species and individuals as a starting point for investigating species diversity. Based on the fundamental processes of birth, death, dispersal and speciation, the neutral theory provided the first mechanistic explanation of species abundance distribution commonly observed in natural communities. Since the publication of the neutral theory, there has been much discussion about it, pro and con. In this paper, we summarize recent progress in the assumption, prediction and speciation mode of the neutral theory, including progress in the theory itself, tests about the assumption of the theory, prediction and speciation mode at the metacommunity level. We also suggest that the most important task in the future is to bridge the niche-assembly theory and the neutral theory, and to add species differences to the neutral theory and more stochasticity to the niche theory. __________ Translated from Journal of Plant Ecology, 2006, 30(5): 868–877 [译自:植物生态学报]     

物种多度格局研究进展

物种多度格局研究始于20世纪30年代,是种群生态学和群落生态学研究的起点。物种多度格局研究主要在两个水平上进行：1）初期研究主要集中于群落水平,希望在不同群落之间发现一个共同的整体格局来描述群落的组织结构。常用模型包括几何级数、对数级数、对数正态和断棍模型,不同模型代表了不同的生态学过程。2）目前转向重视物种水平,并以物种多度的区域分布规律及其生态学机制研究为主。物种分布区多度关系有正相关、无相关和负相关3种形式。局部多度高的物种一般趋于广布,而局部多度低的物种趋于受限分布。物种多度区域分布的生态位模型预测为单峰型,还经常会出现“热点地区”;而异质种群模型预测为双峰型。物种多度的区域分布主要由环境资源特性、物种生态位和扩散过程等因素决定。3）物种多度格局的时间变化与空间变异类似,代表了这些生态学过程的时间异质性。4）物种多度格局的尺度变化经常表现出自相似性,但该规律并非一直存在,因为生物多样性由不同尺度上的不同生态学过程决定。5）多度（稀有度）是物种保护的基本依据,而群落多度模型能够指示生态学和干扰过程变化对群落结构的影响。物种多度格局的模型手段仍需改进,机制研究尚不系统,应用研究亟待扩展,对于物种多度格局的深入理解将为揭示生物多样性分布机制和有效保护提供帮助。     

Patterns of abundance and co-occurrence in aquatic plant communities

Aquatic plants are well suited as subjects for studies on the distribution and abundance of co-occurring species, especially due to the simple structure of their communities, well defined toposequences and relatively easily measurable environmental factors. Here we show that underwater plants occurring in semi-natural lakes form stable communities, where species interactions dominate over dispersal dynamics to form a modular community structure with a high degree of zonation (turnover) and low within-module species richness. In turn, human-induced disturbance largely destroyed the modular structure. Our results indicate that (1) species abundance distributions (SADs) of underwater plant communities are well described by the lognormal model; (2) environmental characters did not significantly influence the SADs of underwater plant communities; (3) log-series SADs do not indicate specific types of community organization; (4) in our lake communities only few satellites (tourists) occur; (5) the co-occurrence of species is highly dependent on the turnover across lakes and water depth zones; and (6) species zonation is a function of lake properties.     

Development of a stochastic dynamic model for ecological indicators’ prediction in changed Mediterranean agroecosystems of north-eastern Portugal

A holistic stochastic dynamic model was developed by focusing on the interactions between conceptually isolated key-components, such as local passerine guilds and changes in habitat conditions, in Mediterranean agroecosystems of the “Terra Quente Transmontana region” (north-eastern Portugal). The ecological integrity of the typical patchwork of this region, with respect to land use, can be partly assessed by the observation of the occurrence of passerine guilds. These important indicators and state variables are the underlying database of our model. This model aimed the prediction of the ecological changes which can be expected when olive orchards are being intensified. The model proposed was preceded by a conventional multivariate statistical procedure (stepwise multiple regression analysis) performed to discriminate the significant relationships between guild richness and environmental variables. Since this statistical analysis is static, the dataset recorded from the field included true gradients of habitat changes. The model parameters were estimated from the results of the stochastic treatment and from regional data regarding tendencies within the use of land. A period of 50 years was considered. The final model provided some basis to analyse the responses of passerine guilds to the environmental scenarios that will characterize the new agroecosystems of the region. The model simulations were incorporated into a Geographical Information System (GIS) approach. The results of the simulation revealed a structural drift within the different guild richness in response to the expected gradient of habitat changes. The possible local extinction of several species within the less well-represented guilds, such as the steppe passerine species, may be associated with a predictable reduction in ecological integrity of the typical agroecosystems. Therefore, a new structure of the passerine communities indicates that future agroecosystems will diverge from the initial or actual ecological state.     

塔里木荒漠河岸林不同生境群落物种多度分布格局

为解释塔里木荒漠河岸林群落构建和物种多度分布格局形成的机理, 本文以塔里木荒漠河岸林2个不同生境(沙地、河漫滩) 4 ha固定监测样地为研究对象, 基于两样地物种调查数据, 采用统计模型(对数级数模型、对数正态模型、泊松对数正态分布模型、Weibull分布模型)、生态位模型(生态位优先占领模型、断棍模型)和中性理论模型(复合群落零和多项式模型、Volkov模型)拟合荒漠河岸林群落物种多度分布, 并用K-S检验与赤池信息准则(AIC)筛选最优拟合模型。结果表明: (1)随生境恶化(土壤水分降低), 植物物种多度分布曲线变化减小, 群落物种多样性、多度和群落盖度降低, 常见种数减少。(2)选用的3类模型均可拟合荒漠河岸林不同生境群落物种多度分布格局, 统计模型和中性理论模型拟合效果均优于生态位模型。复合群落零和多项式模型对远离河岸的干旱沙地生境拟合效果最好; 对数正态模型和泊松对数正态模型对洪水漫溢的河漫滩生境拟合效果最优; 中性理论模型与统计模型无显著差异。初步推断中性过程在荒漠河岸林群落构建中发挥着主导作用, 但模型拟合结果只能作为推断群落构建过程的必要非充分条件, 不能排除生态位过程的潜在作用。     

Starting the invasion pathway: the interaction between source populations and human transport vectors

Human transport hubs, such as shipping ports, airports and mail centers are important foci for the spread of non-indigenous species. High relative abundance in a transport hub has been proposed as a correlate of invasion success, since abundant species are thought more likely to colonize vectors and to be transported more frequently. We here evaluate the relative importance of vector characteristics and local source assemblages in determining the pool of species that is transported by hull fouling on recreational boats. We compared the resident fouling communities of three recreational boat harbors in Australia with the assemblages on the hulls of boats that travel between them. We used data on the recent travel and maintenance history of the boats to evaluate correlates of transport probability and the potential for intra-coastal spread of fouling organisms. Invertebrate assemblages on heavily fouled vessels reflected the composition of biotic assemblages within the marina in which they were moored, but by itself, relative abundance in the source port was not a reliable predictor of transport probability. More important was the age of the antifouling paint on the vessels’ hulls, which acted selectively on some groups of organisms. Movements of vessels were characterized by “fidelity” (vessels remaining close to homeport) interspersed with “promiscuity” (vessels traveling to a diverse pool of destinations). In an infested harbor, measures taken to increase the resistance of vectors to colonization by the invader should be effective in slowing the rate of spread to other locations, by decreasing the overall frequency of transport.     

Species richness and rarity of crane flies (Diptera, Tipuloidea) in a boreal mire

Species richness and abundance are central in biodiversity inventories and in measuring the structure of communities. Neglecting the assessment of sampling efficiency may lead to spurious estimates of species richness and conservation value. Our aim was to examine species richness, sampling effectiveness, species-abundance distribution (SAD) and rarity of a boreal, mire-dwelling crane fly (Diptera, Tipuloidea) assemblage in western Finland. 12 Malaise traps dispersed in 4 subplots and standardized sweep net samples were used to collect adult flies from the mire. A total of 23 species and 1,569 specimens were identified. In general all species richness estimators were highly correlated and indicated rather good sampling effort. Sample completeness, expressed as percentage of observed richness divided by estimated richness, was higher for mire-dwellers (mean 75 %) than for all species (mean 63 %). Crane fly assemblages of subplots and combined data fitted best with log-series SAD. Species spatial distribution was positively correlated with average abundance. In other words, the most abundant species occurred in the most of Malaise traps. Seven mire-dwelling species greatly outnumbered (94 % of the collected specimens) all other members in the assemblage, and only one observed species was rare by several definitions (local abundance, extent of occurrence in Finland and area of occupancy). Although the studied assemblage was characterized by commonness, five of the species have threatened status in Europe south of Finland. Separate species richness estimation of all species (vagrants and occasional species included) and focal species (here mire-dwellers) is supported if ecological information is available on the taxonomic group being studied.     

Impact of logging on the richness and diversity of forest butterflies in a tropical dry forest in Thailand

Studies on the impact of logging on tropical forest butterflies have been almost exclusively conducted in moist forest habitats. This study considers the impacts of small-scale logging on butterfly communities at three sites of varying disturbance intensity in a tropical dry forest in western Thailand. Butterfly species richness was similar at all sites, but the abundance of butterflies and diversity of the butterfly community decreased with increased logging disturbance. The recorded decrease in diversity at the relatively large sampling scale used lends further support to the hypothesis that disturbance effects are scale dependent. Species abundance data for butterflies fitted a log-normal distribution at all sites, but also a log-series distribution at the two disturbed sites. These analyses suggest a more complex butterfly community at the undisturbed site, but also that log-series and log-normal distributions may not to be sufficiently sensitive to be useful indicators of community changes following logging. Community ordination separates both the butterfly species and transect samples into three distinct regions corresponding to the three study locations. Ordination axes are correlated with tree density, understorey cover and understorey plant richness. Species with the smallest geographic ranges tend to be the least abundant and occurred most frequently in the undisturbed site. The observed diverging responses to disturbance among butterfly families diminishes the value of butterfly communities as biodiversity indicators, and forest managers should perhaps focus on restricted range species or of groups of recognized sensitive species for this purpose.     

长白山阔叶红松林草本层物种多度分布格局及其季节动态

草本层是森林生态系统的重要组成部分, 对维持森林生物多样性具有重要意义。本文以长白山阔叶红松(Pinus koraiensis)林25 ha固定监测样地为研究平台, 运用不同的统计模型(对数正态模型和对数级数模型)及机理模型(包括生态位模型: 断棍模型和生态位优先占领模型; 中性模型: 复合群落零和多项式模型和Volkov模型), 对不同季节草本物种多度分布进行拟合。采用Kolmogorov-Smirnov和AIC检验确定最优模型, 以揭示草本层物种多度分布格局随季节的变化规律, 探讨草本层物种组成与结构背后的生态学过程。结果表明: (1)草本层物种多度分布季节差异明显。春季各多度级物种数差异不大, 夏季中间种较多, 秋季则是稀有种较多; (2)模型拟合结果显示, 不同季节草本层物种多度分布的最优拟合模型相近。统计模型中对数级数模型表现最优, 机理模型中中性模型的拟合效果优于生态位模型。复合群落零和多项式模型较好地拟合了春夏季草本物种多度分布, Volkov模型较好地拟合了秋季草本物种多度分布。综上所述, 尽管长白山阔叶红松林草本植物不同季节的物种多度分布格局不尽一致, 但其背后的构建机制相似, 中性随机过程在草本层物种多样性维持过程中显得更为重要。     

Neutral theory in community ecology

One of the central goals of community ecology is to understand the forces that maintain species diversity within communities. The traditional niche-assembly theory asserts that species live together in a community only when they differ from one another in resource uses. But this theory has some difficulties in explaining the diversity often observed in specie-rich communities such as tropical forests. As an alternative to the niche theory, Hubbell and other ecologists introduced a neutral model. Hubbell argues that the number of species in a community is controlled by species extinction and immigration or speciation of new species. Assuming that all individuals of all species in a trophically similar com-munity are ecologically equivalent, Hubbell's neutral theory predicts two important statistical distributions. One is the asymptotic log-series distribution for the metacommunities under point mutation speciation, and the other is the zero-sum multinomial distribution for both local communities under dispersal limitation and metacommunities under random fission speciation. Unlike the niche-assembly theory, the neutral theory takes similarity in species and individuals as a starting point for investigating species diversity. Based on the fundamental processes of birth, death, dispersal and spe-ciation, the neutral theory provided the first mechanistic explanation of species abundance distribution commonly observed in natural communities. Since the publication of the neutral theory, there has been much discussion about it, pro and con. In this paper, we summarize recent progress in the assumption, prediction and speciation mode of the neutral theory, including progress in the theory itself, tests about the assumption of the theory, prediction and speciation mode at the metacommunity level. We also suggest that the most important task in the future is to bridge the niche-assembly theory and the neutral theory, and to add species differences to the neutral theory and more stochasticity to the niche theory.     

Identification of Specialists and Abundance-Occupancy Relationships among Intestinal Bacteria of Aves,Mammalia, and Actinopterygii

The coalescence of next-generation DNA sequencing methods, ecological perspectives, and bioinformatics analysis tools is rapidly advancing our understanding of the evolution and function of vertebrate-associated bacterial communities. Delineation of host-microbe associations has applied benefits ranging from clinical treatments to protecting our natural waters. Microbial communities follow some broad-scale patterns observed for macroorganisms, but it remains unclear how the specialization of intestinal vertebrate-associated communities to a particular host environment influences broad-scale patterns in microbial abundance and distribution. We analyzed the V6 region of 16S rRNA genes amplified from 106 fecal samples spanning Aves, Mammalia, and Actinopterygii (ray-finned fish). We investigated the interspecific abundance-occupancy relationship, where widespread taxa tend to be more abundant than narrowly distributed taxa, among operational taxonomic units (OTUs) within and among host species. In a separate analysis, we identified specialist OTUs that were highly abundant in a single host and rare in all other hosts by using a multinomial model without excluding undersampled OTUs a priori. We show that intestinal microbes in humans and other vertebrates display abundance-occupancy relationships, but because intestinal host-associated communities have undergone intense specialization, this trend is violated by a disproportionately large number of specialist taxa. Although it is difficult to distinguish the effects of dispersal limitations, host selection, historical contingency, and stochastic processes on community assembly, results suggest that intestinal bacteria can be shared among diverse hosts in ways that resemble the distribution of “free-living” bacteria in the extraintestinal environment.     

Spatial and temporal preferences for trans-splicing in Ciona intestinalis revealed by EST-based gene expression analysis

Ciona intestinalis is a useful model organism to analyze chordate development and genetics. However, unlike vertebrates, it shares a unique mechanism called trans-splicing with lower eukaryotes. In the computational analysis of trans-splicing in C. intestinalis we report here, we discovered that although the amount of non-trans-spliced and trans-spliced genes is usually equivalent, the expression ratio between the two groups varies significantly with tissues and developmental stages. Among the seven tissues studied, the observed ratios ranged from 2.53 in “gonad” to 19.53 in “endostyle”, and during development they increased from 1.68 at the “egg” stage to 7.55 at the “juvenile” stage. We further hypothesize that this enrichment in trans-spliced mRNAs in early developmental stages might be related to the abundance of trans-spliced mRNAs in “gonad”. Our analysis indicates that in C. intestinalis, although there may not exist strong fundamental requirements for genes to be trans-spliced, the populations of non-trans-spliced and trans-spliced genes are likely to be spatially and temporally regulated differently.     

Using species abundance models as indicators of habitat disturbance in tropical forests

1. In temperate communities, species abundance distributions have been used to detect ecosystem disturbance: in undisturbed habitats, distributions are claimed to generally fit log-normal models, whereas in disturbed habitats, distributions fit log-series models.
2. There is a growing literature on the effects of habitat disturbance in tropical ecosystems and several studies suggest that species abundance models may be useful in detecting disturbance, although data are lacking.
3. Nummelin (1998) claims that these models are not universal indicators of forest disturbance, but we highlight a number of problems with the data presented in Nummelin's study and conclude that it is too soon to dismiss these models. We discuss several important points arising from Nummelin's study which need to be considered if species abundance models are to be used appropriately.     

Interpreting Ecological Diversity Indices Applied to Terminal Restriction Fragment Length Polymorphism Data: Insights from Simulated Microbial Communities

Ecological diversity indices are frequently applied to molecular profiling methods, such as terminal restriction fragment length polymorphism (T-RFLP), in order to compare diversity among microbial communities. We performed simulations to determine whether diversity indices calculated from T-RFLP profiles could reflect the true diversity of the underlying communities despite potential analytical artifacts. These include multiple taxa generating the same terminal restriction fragment (TRF) and rare TRFs being excluded by a relative abundance (fluorescence) threshold. True community diversity was simulated using the lognormal species abundance distribution. Simulated T-RFLP profiles were generated by assigning each species a TRF size based on an empirical or modeled TRF size distribution. With a typical threshold (1%), the only consistently useful relationship was between Smith and Wilson evenness applied to T-RFLP data (TRF-E_var) and true Shannon diversity (H′), with correlations between 0.71 and 0.81. TRF-H′ and true H′ were well correlated in the simulations using the lowest number of species, but this correlation declined substantially in simulations using greater numbers of species, to the point where TRF-H′ cannot be considered a useful statistic. The relationships between TRF diversity indices and true indices were sensitive to the relative abundance threshold, with greatly improved correlations observed using a 0.1% threshold, which was investigated for comparative purposes but is not possible to consistently achieve with current technology. In general, the use of diversity indices on T-RFLP data provides inaccurate estimates of true diversity in microbial communities (with the possible exception of TRF-E_var). We suggest that, where significant differences in T-RFLP diversity indices were found in previous work, these should be reinterpreted as a reflection of differences in community composition rather than a true difference in community diversity.     

Statistical mechanics of relative species abundance

Statistical mechanics of relative species abundance (RSA) patterns in biological networks is presented. The theory is based on multispecies replicator dynamics equivalent to the Lotka–Volterra equation, with diverse interspecies interactions. Various RSA patterns observed in nature are derived from a single parameter related to productivity or maturity of a community. The abundance distribution is formed like a widely observed left-skewed lognormal distribution. It is also found that the “canonical hypothesis” is supported in some parameter region where the typical RSA patterns are observed. As the model has a general form, the result can be applied to similar patterns in other complex biological networks, e.g. gene expression.     

DeepCME: A deep learning framework for computing solution statistics of the chemical master equation

Stochastic models of biomolecular reaction networks are commonly employed in systems and synthetic biology to study the effects of stochastic fluctuations emanating from reactions involving species with low copy-numbers. For such models, the Kolmogorov’s forward equation is called the chemical master equation (CME), and it is a fundamental system of linear ordinary differential equations (ODEs) that describes the evolution of the probability distribution of the random state-vector representing the copy-numbers of all the reacting species. The size of this system is given by the number of states that are accessible by the chemical system, and for most examples of interest this number is either very large or infinite. Moreover, approximations that reduce the size of the system by retaining only a finite number of important chemical states (e.g. those with non-negligible probability) result in high-dimensional ODE systems, even when the number of reacting species is small. Consequently, accurate numerical solution of the CME is very challenging, despite the linear nature of the underlying ODEs. One often resorts to estimating the solutions via computationally intensive stochastic simulations. The goal of the present paper is to develop a novel deep-learning approach for computing solution statistics of high-dimensional CMEs by reformulating the stochastic dynamics using Kolmogorov’s backward equation. The proposed method leverages superior approximation properties of Deep Neural Networks (DNNs) to reliably estimate expectations under the CME solution for several user-defined functions of the state-vector. This method is algorithmically based on reinforcement learning and it only requires a moderate number of stochastic simulations (in comparison to typical simulation-based approaches) to train the “policy function”. This allows not just the numerical approximation of various expectations for the CME solution but also of its sensitivities with respect to all the reaction network parameters (e.g. rate constants). We provide four examples to illustrate our methodology and provide several directions for future research.     

Factors influencing community structure in a South American tank bromeliad fauna

We examined factors influencing the structure of naturally replicated, taxonomically unrestricted communities inhabiting South American tank bromeliads. We measured aspects of plant physical structure and collected the entire macroscopic fauna of 209 bromeliads from the Yasuní Scientific Reserve in lowland eastern Ecuador. We collected a total of 11 219 individuals of 354 morphospecies. The morphospecies abundance distribution of our sample was approximated by a log-series distribution dominated by rare morphospecies (57% of the morphospecies were represented by a single individual). Six methods for estimating the total number of bromeliad associated morphospecies in our study area gave results which varied by a factor of three, illustrating that caution should be exercised in interpreting the results of any single estimator. Variation in plant volume, number of leaves, detritus content, and water volume explained 62% of the variation in morphospecies richness among plants. Finally, there was a quadratic relationship between body mass and both individual abundance and morphospecies richness in our sample. These results illustrate an important role of both biotic and abiotic factors influencing the structure of taxonomically unrestricted, ecologically defined natural communities.