Stochastic process drives the dissimilarity in biodiversity patterns between Pinus kwangtungensis coniferous forest and evergreen deciduous broad-leaved mixed forest in karst area.

Pinus kwangtungensis is an endangered evergreen conifer tree species, and its in situ conservation has been considered one of the most critical issues. However, relative protection is limited by the lack of understanding of its community structure and underlying assembly processes. To study how the species diversity and assembly processes of Pinus kwangtungensis coniferous forest (CF) differed with regional climax community, this study established a series forest dynamic plots both in CF and evergreen deciduous broadleaved mixed forest (EDBM). By performing comparison analysis and PER-SIMPER approaches, we quantified the differences in species diversity and community assembly rules. The results showed that the species α-diversity of CF differed greatly from the EDBM both in species richness and evenness. In addition, the stochastic process acted a more important role in determining species composition, indicating the uncertainty in presence of species. The soil phosphorus and changeable calcium content were the main factors driving the differences in biodiversity, which the importance of soil nutrient factors in driving species composition. Our study highlighted that we should consider the community structure and ecological process when conducting conservation of Pinus kwangtungensis.

Variations in species diversity patterns and community assembly rules among vegetation types in the karst landscape.

The various vegetation types in the karst landscape have been considered the results of heterogeneous habitats. However, the lack of a comprehensive understanding of regional biodiversity patterns and the underlying ecological processes limits further research on ecological management. This study established forest dynamic plots (FDPs) of the dominant vegetation types (shrubland, SL; mixed tree and shrub forest, MTSF; coniferous forest, CF; coniferous broadleaf mixed forest, CBMF; and broadleaf forest, BF) in the karst landscape and quantified the species diversity patterns and potential ecological processes. The results showed that in terms of diversity patterns, the evenness and species richness of the CF community were significantly lower than other vegetation types, while the BF community had the highest species richness. The other three vegetation types showed no significant variation in species richness and evenness. However, when controlling the number of individuals of FDPs, the rarefied species richness showed significant differences and ranked as BF > SL > MTSF > CBMF > CF, highlighting the importance of considering the impacts of abundance. Additionally, the community assembly of climax communities (CF or BF) was dominated by stochastic processes such as species dispersal or species formation, whereas deterministic processes (habitat filtering) dominated the secondary forests (SL, MTSF, and CBMF). These findings proved that community assembly differs mainly between the climax community and other communities. Hence, it is crucial to consider the biodiversity and of the potential underlying ecological processes together when studying regional ecology and management, particularly in heterogeneous ecosystems.

How do species richness and its component dependence vary along the natural restoration in extremely heterogeneous forest ecosystems?

Giant habitat heterogeneity is an important factor contributing to the high species richness (SR) in karst forests. Yet, the driving factor behind the alterations in SR patterns during natural restoration remains unclear. In this study, we established the forest dynamics plots along the natural restoration sequence (including shrub-tree mixed forest stage (SC), secondary forest stage (SG) and old-growth forest sage (OG)) in degraded karst forests to compare the SR and the dependence on its components (including total community abundance, species abundance distribution (SAD), and conspecific spatial aggregation (CSA)) among stages of natural restoration. By evaluating the degree of contribution of the components to local SR and rarefied SR, we found that the SG exhibited the highest local SR, while the rarefied SR remained increasing along the restoration sequence after controlling the sample size. At SC-SG stage, SAD and CSA contributed negatively to the differences in SR, while abundance made a positive contribution to SR differences. At SG-OG, abundance contributed positively to the difference in SR at all scales, while SAD contributed negatively at small scales. No significant contribution of CSA was found at observed scales. In addition, local SR varied more significantly with PIE than with abundance. Our research emphasizes the importance of eliminating the influence of abundance on species richness in forest ecology and management, as well as the significance of separately evaluating the components that shape the diversity patterns.

Assessing the sensitivity and resistance of communities in a changing environment.

We propose that the ecological resilience of communities to permanent changes of the environment can be based on how variation in the overall abundance of individuals affects the number of species. Community sensitivity is defined as the ratio between the rate of change in the log expected number of species and the rate of change in the log expected number of individuals in the community. High community sensitivity means that small changes in the total abundance strongly impact the number of species. Community resistance is the proportional reduction in expected number of individuals that the community can sustain before expecting to lose one species. A small value of community resistance means that the community can only endure a small reduction in abundance before it is expected to lose one species. Based on long-term studies of four bird communities in European deciduous forests at different latitudes large differences were found in the resilience to environmental perturbations. Estimating the variance components of the species abundance distribution revealed how different processes contributed to the community sensitivity and resistance. Species heterogeneity in the population dynamics was the largest component, but its proportion varied among communities. Species-specific response to environmental fluctuations was the second major component of the variation in abundance. Estimates of community sensitivity and resistance based on data only from a single year were in general larger than those based on estimates from longer time series. Thus, our approach can provide rapid and conservative assessment of the resilience of communities to environmental changes also including only short-term data. This study shows that a general ecological mechanism, caused by increased strength of density dependence due to reduction in resource availability, can provide an intuitive measure of community resilience to environmental variation. Our analyses also illustrate the importance of including specific assumptions about how different processes affect community dynamics. For example, if stochastic fluctuations in the environment affect all species in a similar way, the sensitivity and resistance of the community to environmental changes will be different from communities in which all species show independent responses.

Understory vegetation diversity patterns of Platycladus orientalis and Pinus elliottii communities in Central and Southern China.

As a vital component of arbor forests, understory vegetation serves as an essential buffer zone for storing carbon due to its strong capacity for community regeneration. This study aimed to identify the diversity pattern and construction mechanism of Platycladus orientalis and Pinus elliottii understory vegetation based on large-scale sample surveys. The Bayesian Information Criterion value of species abundance distribution (SAD) indicated that the Zipf and Zipf-Mandelbrot models were the best-fitting models. The SAD and gambin fitting results suggested that the Pi. elliottii community had a more balanced structure, with most species being relatively abundant. The multiple regression tree model detected four and six indicator species in P. orientalis and Pi. elliottii communities, respectively. The α-diversity index increased with a rise in altitude and showed a wavy curve with latitude. Linear regression between the ß diversity and environmental and geographic distance indicated that the P. orientalis and Pi. elliottii understory communities tended to be dominated by different ecological processes. The partition of ß diversity indicated that both communities were dominated by turnover processes, which were caused by environmental classification or spatial constraints. This study helped to understand the diversity maintenance in the P. orientalis and Pi. elliottii understory vegetation communities, and will benefit for diversity restoration and conservation of pure conifer forests.

Temporal change in functional rarity in marine fish assemblages.

Recent research has uncovered rapid compositional and structural reorganization of ecological assemblages, with these changes particularly evident in marine ecosystems. However, the extent to which these ongoing changes in taxonomic diversity are a proxy for change in functional diversity is not well understood. Here we focus on trends in rarity to ask how taxonomic rarity and functional rarity covary over time. Our analysis, drawing on 30 years of scientific trawl data, reveals that the direction of temporal shifts in taxonomic rarity in two Scottish marine ecosystems is consistent with a null model of change in assemblage size (i.e. change in numbers of species and/or individuals). In both cases, however, functional rarity increases, as assemblages become larger, rather than showing the expected decrease. These results underline the importance of measuring both taxonomic and functional dimensions of diversity when assessing and interpreting biodiversity change.

On the shape and origins of the freshwater species-area relationship.

The species-area relationship (SAR) has over a 150-year-long history in ecology, but how its shape and origins vary across scales and organisms remains incompletely understood. This is the first subcontinental freshwater study to examine both these properties of the SAR in a spatially explicit way across major organismal groups (diatoms, insects, and fish) that differ in body size and dispersal capacity. First, to describe the SAR shape, we evaluated the fit of three commonly used models, logarithmic, power, and Michaelis-Menten. Second, we proposed a hierarchical framework to explain the variability in the SAR shape, captured by the parameters of the SAR model. According to this framework, scale and species group were the top predictors of the SAR shape, climatic factors (heterogeneity and median conditions) represented the second predictor level, and metacommunity properties (intraspecific spatial aggregation, γ-diversity, and species abundance distribution) the third predictor level. We calculated the SAR as a sample-based rarefaction curve using 60 streams within landscape windows (scales) in the United States, ranging from 160,000 to 6,760,000 km2 . First, we found that all models provided good fits (R2 ≥ 0.93), but the frequency of the best-fitting model was strongly dependent on organism, scale, and metacommunity properties. The Michaelis-Menten model was most common in fish, at the largest scales, and at the highest levels of intraspecific spatial aggregation. The power model was most frequent in diatoms and insects, at smaller scales, and in metacommunities with the lowest evenness. The logarithmic model fit best exclusively at the smallest scales and in species-poor metacommunities, primarily fish. Second, we tested our framework with the parameters of the most broadly used SAR model, the log-log form of the power model, using a structural equation model. This model supported our framework and revealed that the SAR slope was best predicted by scale- and organism-dependent metacommunity properties, particularly spatial aggregation, whereas the intercept responded most strongly to species group and γ-diversity. Future research should investigate from the perspective of our framework how shifts in metacommunity properties due to climate change may alter the SAR.

A multi-level exploration of the relationship between temperature and species diversity: Two cases of marine phytoplankton.

The relationship between temperature (T) and diversity is one of the most important issues in ecology. It provides a key direction not only for exploring the determinants of diversity's patterns, but also for understanding diversity's responses to climate change. Previous studies suggested that T-diversity relationships could be positive, negative, or unimodal. Although these studies accumulated many informative achievements, they might be unsatisfied due to (1) investigating inadequate range of T, (2) selecting incomplete diversity metrics, and (3) making insufficiently detailed analysis of correlation. In this study, species diversity is estimated by four most commonly used diversity metrics and three parameters of species abundance distribution (SAD), and two global datasets of marine phytoplankton (covering a wider range of T) are used to evaluate the T-diversity relationships according to a piecewise model. Results show that all aspects of diversity (except evenness) have the similar relationship with T in the range of lower T, noting that diversity significantly increases as T increases. However, in the range of higher T, diversity may significantly decrease or nearly constant, which indicates that their relationships may be the unimodal or asymptotic. The asymptotic relationship found by this study is assumed that increasing diversity with T will gradually approach the Zipf's law (1:1/2:1/3…). If such assumption can be verified by future investigations, the intrinsic mechanism of the asymptotic relationship is likely to be crucial in understanding the T-diversity relationships.

Analyzing dynamic species abundance distributions using generalized linear mixed models.

Understanding the mechanisms of ecological community dynamics and how they could be affected by environmental changes is important. Population dynamic models have well known ecological parameters that describe key characteristics of species such as the effect of environmental noise and demographic variance on the dynamics, the long-term growth rate, and strength of density regulation. These parameters are also central for detecting and understanding changes in communities of species; however, incorporating such vital parameters into models of community dynamics is challenging. In this paper, we demonstrate how generalized linear mixed models specified as intercept-only models with different random effects can be used to fit dynamic species abundance distributions. Each random effect has an ecologically meaningful interpretation either describing general and species-specific responses to environmental stochasticity in time or space, or variation in growth rate and carrying capacity among species. We use simulations to show that the accuracy of the estimation depends on the strength of density regulation in discrete population dynamics. The estimation of different covariance and population dynamic parameters, with corresponding statistical uncertainties, is demonstrated for case studies of fish and bat communities. We find that species heterogeneity is the main factor of spatial and temporal community similarity for both case studies.

An Evolutionary and Ecological Community Model for Distribution of Phenotypes and Abundances among Competing Species.

AbstractHere, we propose a theory for the structure of communities of competing species. We include ecologically realistic assumptions, such as density dependence and stochastic fluctuations in the environment, and analyze how evolution caused by r- and K-selection will affect the packing of species in the phenotypic space as well as the species abundance distribution. Species-specific traits have the same matrix G of additive genetic variances and covariances, and evolution of mean traits is affected by fluctuations in population size of all species. In general, the model produces a shape of the distributions of log abundances that is skewed to the left, which is typical of most natural communities. Mean phenotypes of the species in the community are distributed approximately uniformly on the surface of a multidimensional sphere. However, environmental stochasticity generates selection that deviates species slightly from this surface; nonetheless, phenotypic distribution will be different from a random packing of species. This model of community evolution provides a theoretical framework that predicts a relationship between the structure of the phenotypic space and the form of species abundance distributions that can be compared against time series of variation in community structure.

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The statistical model (log-normal model), niche models (Zipf model, broken stick mo-del, niche preemption model), and neutral model were used to fit the species-abundance distribution patterns based on the measurements of environmental factors and inventory data of trees with DBH≥1 cm in a 1.5 hm2 plot in the primary forest (PF) and a 1.5 hm2 plot in the secondary forest (SF). The results showed that species-abundance distribution was affected by habitat heterogeneity in Q. aliena var. acutiserrata forest. Topography had a predominant impact on the species-abundance distribution in PF. Species distribution was affected by both neutral and niche processes, with neutral process having a less prominent effect in large convexity habitats. While the neutral model was rejected by the K-S and Chi-square test in low convexity habitats, the species-abundance distribution satisfied the assumption of niche theory. Niche process and neutral process were equally important in the community in areas with steep slopes, while niche differentiation was the dominant in flat areas. In SF, the main factors affecting species distribution were soil nutrients. The niche process was the mainly ecological process affected species-abundance distribution in habitats with high soil available phosphorus, while the niche and neutral processes existed simultaneously in habitats with low soil phosphorus availability. There was a significant scale effect on the species-abundance distribution pattern of Q. aliena var. acutiserrata forests in Taibai Mountain. The niche and neutral processes could protect the species-abundance distribution at the 20 m×20 m scale in PF, while the niche process could explain the species-abundance distribution at the 40 m×40 m and 70 m×70 m scales. The niche and neutral processes combined acted on the species abundance distribution at the 20 m×20 m, 40 m×40 m and 70 m×70 m scales in SF, with niche process being more important than neutral process. Moreover, besides the scale and habitat heterogeneity, the species-abundance distribution patterns of Q. aliena var. acutiserrata forests differed significantly between primary forest and secondary forest under anthropogenic disturbance.

Disentangling Environmental Effects on the Tree Species Abundance Distribution and Richness in a Subtropical Forest.

As a transitional vegetation type between evergreen broadleaved forest and deciduous broadleaved forest, evergreen-deciduous broadleaved mixed forest is composed of diverse plant species. This distinctive forest is generally distributed in mountainous areas with complex landforms and heterogeneous microenvironments. However, little is known about the roles of environmental conditions in driving the species diversity patterns of this forest. Here, based on a 15-ha plot in central China, we aimed to understand how and to what extent topographical characteristics and soil nutrients regulate the number and relative abundance of tree species in this forest. We measured environmental factors (terrain convexity, slope, soil total nitrogen, and phosphorus concentrations) and species diversity (species abundance distribution and species richness) in 20 m × 20 m subplots. Species abundance distribution was characterized by skewness, Berger-Parker index, and the proportion of singletons. The generalized additive model was used to examine the variations in diversity patterns caused by environmental factors. The structural equation model was used to assess whether and how topographical characteristics regulate species diversity via soil nutrients. We found that soil nutrients had significant negative effects on species richness and positive effects on all metrics of species abundance distribution. Convexity had significant positive effects on species richness and negative effects on all metrics of species abundance distribution, but these effects were mostly mediated by soil nutrients. Slope had significant negative effects on skewness and the Berger-Parker index, and these effects were almost independent of soil nutrients. Soil nutrients and topographical characteristics together accounted for 9.5-17.1% of variations in diversity patterns and, respectively, accounted for 8.9-13.9% and 3.3-10.7% of the variations. We concluded that soil nutrients were more important than topographical factors in regulating species diversity. Increased soil nutrient concentration led to decreased taxonomic diversity and increased species dominance and rarity. Convexity could be a better proxy for soil nutrients than slope. Moreover, these abiotic factors played limited roles in regulating diversity patterns, and it is possible that the observed patterns are also driven by some biotic and abiotic factors not considered here.

A multiscale framework for disentangling the roles of evenness, density, and aggregation on diversity gradients.

Disentangling the drivers of diversity gradients can be challenging. The Measurement of Biodiversity (MoB) framework decomposes scale-dependent changes in species diversity into three components of community structure: species abundance distribution (SAD), total community abundance, and within-species spatial aggregation. Here we extend MoB from categorical treatment comparisons to quantify variation along continuous geographic or environmental gradients. Our approach requires sites along a gradient, each consisting of georeferenced plots of abundance-based species composition data. We demonstrate our method using a case study of ants sampled along an elevational gradient of 28 sites in a mixed deciduous forest of the Great Smoky Mountains National Park, USA. MoB analysis revealed that decreases in ant species richness along the elevational gradient were associated with decreasing evenness and total number of species, which counteracted the modest increase in richness associated with decreasing spatial aggregation along the gradient. Total community abundance had a negligible effect on richness at all but the finest spatial grains, SAD effects increased in importance with sampling effort, and the aggregation effect had the strongest effect at coarser spatial grains. These results do not support the more-individuals hypothesis, but they are consistent with a hypothesis of stronger environmental filtering at coarser spatial grains. Our extension of MoB has the potential to elucidate how components of community structure contribute to changes in diversity along environmental gradients and should be useful for a variety of assemblage-level data collected along gradients.

Scale-dependent impact of land management on above- and belowground biodiversity.

Land management is known to have consequences for biodiversity; however, our synthetic understanding of its effects is limited due to highly variable results across studies, which vary in the focal taxa and spatial grain considered, as well as the response variables reported. Such synthetic knowledge is necessary for management of agroecosystems for high diversity and function.To fill this knowledge gap, we investigated the importance of scale-dependent effects of land management (LM) (pastures vs. meadows), on plant and soil microbe diversity (fungi and bacteria) across 5 study sites in Central Germany. Analyses included diversity partitioning of species richness and related biodiversity components (i.e., density of individuals, species-abundance distribution, and spatial aggregation) at two spatial grains (α- and γ-scale, 1 m2 and 16 km2, respectively).Our results show scale-dependent patterns in response to LM to be the norm rather than the exception and highlight the importance of measuring species richness and its underlying components at multiple spatial grains.Our outcomes provide new insight to the complexity of scale-dependent responses within and across taxonomic groups. They suggest that, despite close associations between taxa, LM responses are not easily extrapolated across multiple spatial grains and taxa. Responses of biodiversity to LM are often driven by changes to evenness and spatial aggregation, rather than by changes in individual density. High-site specificity of LM effects might be due to a variety of context-specific factors, such as historic land management, identity of grazers, and grazing regime. Synthesis and applications: Our results suggest that links between taxa are not necessarily strong enough to allow for generalization of biodiversity patterns. These findings highlight the importance of considering multiple taxa and spatial grains when investigating LM responses, while promoting management practices that do the same and are tailored to local and regional conditions.

Niche and Neutrality Work Differently in Microbial Communities in Fluidic and Non-fluidic Ecosystems.

This data-intensive study investigated the delicate balance of niche and neutrality underlying microbial communities in freshwater ecosystems through comprehensive application of high-throughput sequencing, species abundance distribution (SAD), and the neutral community model (NCM), combined with species diversity and phylogenetic measures, which unite the traditional and microbial ecology. On the genus level, 45.10% and 41.18% of the water samples could be explained by the log-normal and Volkov model respectively, among which 31.37% could fit both models. Meanwhile, 55.56% of the sediment samples could be depicted by the log-normal model, and Volkov-fitted samples comprised only 13.33%. Besides, operational taxonomic units (OTUs) from water samples fit Sloan's neutral model significantly better than those in sediment. Therefore, it was concluded that deterministic processes played a great role in both water and sediment ecosystems, whereas neutrality was much more involved in water assemblages than in non-fluidic sediment ecosystems. Secondly, log-normal fitted samples had lower phylogenetic species variability (PSV) than Volkov-fitted ones, indicating that niche-based communities were more phylogenetically clustered than neutrally assembled counterparts. Additionally, further testing showed that the relative richness of rare species was vital to SAD modeling, either niche-based or neutral, and communities containing fewer rare species were more easily captured by theoretical SAD models.

FragSAD: A database of diversity and species abundance distributions from habitat fragments.

Habitat destruction is the single greatest anthropogenic threat to biodiversity. Decades of research on this issue have led to the accumulation of hundreds of data sets comparing species assemblages in larger, intact, habitats to smaller, more fragmented, habitats. Despite this, little synthesis or consensus has been achieved, primarily because of non-standardized sampling methodology and analyses of notoriously scale-dependent response variables (i.e., species richness). To be able to compare and contrast the results of habitat fragmentation on species' assemblages, it is necessary to have the underlying data on species abundances and sampling intensity, so that standardization can be achieved. To accomplish this, we systematically searched the literature for studies where abundances of species in assemblages (of any taxa) were sampled from many habitat patches that varied in size. From these, we extracted data from several studies, and contacted authors of studies where appropriate data were collected but not published, giving us 117 studies that compared species assemblages among habitat fragments that varied in area. Less than one-half (41) of studies came from tropical forests of Central and South America, but there were many studies from temperate forests and grasslands from all continents except Antarctica. Fifty-four of the studies were on invertebrates (mostly insects), but there were several studies on plants (15), birds (16), mammals (19), and reptiles and amphibians (13). We also collected qualitative information on the length of time since fragmentation. With data on total and relative abundances (and identities) of species, sampling effort, and affiliated meta-data about the study sites, these data can be used to more definitively test hypotheses about the role of habitat fragmentation in altering patterns of biodiversity. There are no copyright restrictions. Please cite this data paper and the associated Dryad data set if the data are used in publications.

Plant species dominance increases pollination complementarity and plant reproductive function.

Worldwide, anthropogenic change is causing biodiversity loss, disrupting many critical ecosystem functions. Most studies investigating the relationship between biodiversity and ecosystem functioning focus on species richness, predominantly within the context of productivity-related functions. Consequently, there is limited understanding of how other biodiversity measures, such as species evenness (the distribution of abundance among species), affect complex multitrophic functions such as pollination. We explore the effect of species evenness on the ecosystem function of pollination using a controlled experiment with selected plants and insects in flight cages. We manipulated the relative abundances of plant and pollinator species, while holding species richness, composition, dominance order, and total abundance constant. Then, we tested how numerical species evenness affected network structure and consequently, seed production, in our artificial communities. Contrary to our expectation, numerical dominance in plant communities increased complementarity in pollinator use (reduced pollinator sharing) among plant species. As predicted by theory, this increased complementarity resulted in higher seed production for the most dominant and rare plant species in our cages. Our results show that in a controlled experimental setting, numerical species evenness can alter important aspects of plant-pollinator networks and plant reproduction, irrespective of species richness, composition, and total abundance. Extending this understanding of how species evenness affects ecosystem functioning to natural systems is crucial as anthropogenic disturbances continue to alter species' abundances, likely disrupting ecosystem functions long before extinctions occur.

Derivations of the Core Functions of the Maximum Entropy Theory of Ecology.

The Maximum Entropy Theory of Ecology (METE), is a theoretical framework of macroecology that makes a variety of realistic ecological predictions about how species richness, abundance of species, metabolic rate distributions, and spatial aggregation of species interrelate in a given region. In the METE framework, "ecological state variables" (representing total area, total species richness, total abundance, and total metabolic energy) describe macroecological properties of an ecosystem. METE incorporates these state variables into constraints on underlying probability distributions. The method of Lagrange multipliers and maximization of information entropy (MaxEnt) lead to predicted functional forms of distributions of interest. We demonstrate how information entropy is maximized for the general case of a distribution, which has empirical information that provides constraints on the overall predictions. We then show how METE's two core functions are derived. These functions, called the "Spatial Structure Function" and the "Ecosystem Structure Function" are the core pieces of the theory, from which all the predictions of METE follow (including the Species Area Relationship, the Species Abundance Distribution, and various metabolic distributions). Primarily, we consider the discrete distributions predicted by METE. We also explore the parameter space defined by the METE's state variables and Lagrange multipliers. We aim to provide a comprehensive resource for ecologists who want to understand the derivations and assumptions of the basic mathematical structure of METE.

Environmental filtering explains a U-shape latitudinal pattern in regional ß-deviation for eastern North American trees.

The underlying drivers of ß-diversity along latitudinal gradients have been unclear. Previous studies have focused on ß-diversities calculated at a local scale and shed limited light on regional ß-diversity. We tested the much-debated effects of range size vs. environmental filtering on the ß-gradient using data from the US Forest Inventory Analysis Program. We showed that the drivers of the ß-gradient were scale dependent. At the local scale species spatial patterns contributed little to the ß-gradient, whereas at the regional scale spatial patterns dominated the gradient and a U-shape latitudinal relationship for the standardised ß-diversity deviation was revealed. The relationship can be explained by spatial variation in climate and soil texture, thus supporting the environmental filtering hypothesis. But it is inconsistent with Rapoport's rule about the effect of range size on ß-gradient. These results resolve the debate on whether species spatial distributions contribute to ß-gradient and attest the importance of environmental filtering in determining regional ß-diversity.

A Cross-Scale Neutral Theory Approach to the Influence of Obesity on Community Assembly of Human Gut Microbiome.

Background: The implications of gut microbiome to obesity have been extensively investigated in recent years although the exact mechanism is still unclear. The question whether or not obesity influences gut microbiome assembly has not been addressed. The question is significant because it is fundamental for investigating the diversity maintenance and stability of gut microbiome, and the latter should hold a key for understanding the etiological implications of gut microbiome to obesity. Methods: In this study, we adopt a dual neutral theory modeling strategy to address this question from both species and community perspectives, with both discrete and continuous neutral theory models. The first neutral theory model we apply is Hubbell's neutral theory of biodiversity that has been extensively tested in macro-ecology of plants and animals, and the second we apply is Sloan's neutral theory model that was developed particularly for microbial communities based on metagenomic sequencing data. Both the neutral models are complementary to each other and integrated together offering a comprehensive approach to more accurately revealing the possible influence of obesity on gut microbiome assembly. This is not only because the focus of both neutral theory models is different (community vs. species), but also because they adopted two different modeling strategies (discrete vs. continuous). Results: We test both the neutral theory models with datasets from Turnbaugh et al. (2009). Our tests showed that the species abundance distributions of more than ½ species (59-69%) in gut microbiome satisfied the prediction of Sloan's neutral theory, although at the community level, the number of communities satisfied the Hubbell's neutral theory was negligible (2 out of 278). Conclusion: The apparently contradictory findings above suggest that both stochastic neutral effects and deterministic environmental (host) factors play important roles in shaping the assembly and diversity of gut microbiome. Furthermore, obesity may just be one of the host factors, but its influence may not be strong enough to tip the balance between stochastic and deterministic forces that shape the community assembly. Finally, the apparent contradiction from both the neutral theories should not be surprising given that there are still near 30-40% species that do not obey the neutral law.