Age-dependent extinction and the neutral theory of biodiversity.

Red Queen (RQ) theory states that adaptation does not protect species from extinction because their competitors are continually adapting alongside them. RQ was founded on the apparent independence of extinction risk and fossil taxon age, but analytical developments have since demonstrated that age-dependent extinction is widespread, usually most intense among young species. Here, we develop ecological neutral theory as a general framework for modeling fossil species survivorship under incomplete sampling. We show that it provides an excellent fit to a high-resolution dataset of species durations for Paleozoic zooplankton and more broadly can account for age-dependent extinction seen throughout the fossil record. Unlike widely used alternative models, the neutral model has parameters with biological meaning, thereby generating testable hypotheses on changes in ancient ecosystems. The success of this approach suggests reinterpretations of mass extinctions and of scaling in eco-evolutionary systems. Intense extinction among young species does not necessarily refute RQ or require a special explanation but can instead be parsimoniously explained by neutral dynamics operating across species regardless of age.

Neutrality in plant-herbivore interactions.

Understanding the distribution of herbivore damage among leaves and individual plants is a central goal of plant-herbivore biology. Commonly observed unequal patterns of herbivore damage have conventionally been attributed to the heterogeneity in plant quality or herbivore behaviour or distribution. Meanwhile, the potential role of stochastic processes in structuring plant-herbivore interactions has been overlooked. Here, we show that based on simple first principle expectations from metabolic theory, random sampling of different sizes of herbivores from a regional pool is sufficient to explain patterns of variation in herbivore damage. This is despite making the neutral assumption that herbivory is caused by randomly feeding herbivores on identical and passive plants. We then compared its predictions against 765 datasets of herbivory on 496 species across 116° of latitude from the Herbivory Variability Network. Using only one free parameter, the estimated attack rate, our neutral model approximates the observed frequency distribution of herbivore damage among plants and especially among leaves very well. Our results suggest that neutral stochastic processes play a large and underappreciated role in natural variation in herbivory and may explain the low predictability of herbivory patterns. We argue that such prominence warrants its consideration as a powerful force in plant-herbivore interactions.

Pólya-splitting distributions as stationary solutions of multivariate birth-death processes under extended neutral theory.

Multivariate count distributions are crucial for the inference of ecological processes underpinning biodiversity. In particular, neutral theory provides useful null distributions allowing the evaluation of adaptation or natural selection. In this paper, we build a broader family of multivariate distributions: the Polya-splitting distributions. We show that they emerge naturally as stationary distributions of a multivariate birth-death process. This family of distributions is a consistent extension of non-zero sum neutral models based on a master equation approach. It allows considering both total abundance of the community and relative abundances of species. We emphasize that this family is large enough to encompass various dependence structures among species. We also introduce the strong closure under addition property that can be useful to generate nested multi-level dependence structures. Although all Pólya splitting distributions do not share this property, we provide numerous example verifying it. They include the previously known example with independent species, and also new ones with alternative dependence structures. Overall, we advocate that Polya-splitting distribution should become a part of the classic toolbox for the analysis of multivariate count data in ecology, providing alternative approaches to joint species distribution framework. Comparatively, our approach allows to model dependencies between species at the observation level, while the classical JSDM's model dependencies at the latent process strata.

Epistasis Creates Invariant Sites and Modulates the Rate of Molecular Evolution.

Invariant sites are a common feature of amino acid sequence evolution. The presence of invariant sites is frequently attributed to the need to preserve function through site-specific conservation of amino acid residues. Amino acid substitution models without a provision for invariant sites often fit the data significantly worse than those that allow for an excess of invariant sites beyond those predicted by models that only incorporate rate variation among sites (e.g., a Gamma distribution). An alternative is epistasis between sites to preserve residue interactions that can create invariant sites. Through computer-simulated sequence evolution, we evaluated the relative effects of site-specific preferences and site-site couplings in the generation of invariant sites and the modulation of the rate of molecular evolution. In an analysis of ten major families of protein domains with diverse sequence and functional properties, we find that the negative selection imposed by epistasis creates many more invariant sites than site-specific residue preferences alone. Further, epistasis plays an increasingly larger role in creating invariant sites over longer evolutionary periods. Epistasis also dictates rates of domain evolution over time by exerting significant additional purifying selection to preserve site couplings. These patterns illuminate the mechanistic role of epistasis in the processes underlying observed site invariance and evolutionary rates.

Colonization-persistence trade-offs in natural bacterial communities.

Fitness equalizing mechanisms, such as trade-offs, are recognized as one of the main factors promoting species coexistence in community ecology. However, they have rarely been explored in microbial communities. Although microbial communities are highly diverse, the coexistence of their multiple taxa is largely attributed to niche differences and high dispersal rates, following the principle 'everything is everywhere, but the environment selects'. We use a dynamical stochastic model based on the theory of island biogeography to study highly diverse bacterial communities over time across three different systems (soils, alpine lakes and shallow saline lakes). Assuming fitness equalization mechanisms, here we newly analytically derive colonization-persistence trade-offs, and report a signal of such trade-offs in natural bacterial communities. Moreover, we show that different subsets of species in the community drive this trade-off. Rare taxa, which are occasional and more likely to follow independent colonization/extinction dynamics, drive this trade-off in the aquatic communities, while the core sub-community did it in the soils. We conclude that equalizing mechanisms may be more important than previously recognized in bacterial communities. Our work also emphasizes the fundamental value of dynamical models for understanding temporal patterns and processes in highly diverse communities.

Stochastic and Deterministic Assembly Processes in Seamount Microbial Communities.

Seamounts are ubiquitous in the ocean. However, little is known about how seamount habitat features influence the local microbial community. In this study, the microbial populations of sediment cores from sampling depths of 0.1 to 35 cm from 10 seamount summit sites with a water depth of 1,850 to 3,827 m across the South China Sea (SCS) Basin were analyzed. Compared with nonseamount ecosystems, isolated seamounts function as oases for microbiomes, with average moderate to high levels of microbial abundance, richness, and diversity, and they harbor distinct microbial communities. The distinct characteristics of different seamounts provide a high level of habitat heterogeneity, resulting in the wide range of microbial community diversity observed across all seamounts. Using dormant thermospores as tracers to study the effect of dispersal by ocean currents, the observed distance-decay biogeography across different seamounts shaped simultaneously by the seamounts' naturally occurring heterogeneous habitat and the limitation of ocean current dispersal was found. We also established a framework that links initial community assembly with successional dynamics in seamounts. Seamounts provide resource-rich and dynamic environments, which leads to a dominance of stochasticity during initial community establishment in surface sediments. However, a progressive increase in deterministic environmental selection, correlated with resource depletion in subsurface sediments, leads to the selective growth of rare species of surface sediment communities in shaping the subsurface community. Overall, the study indicates that seamounts are a previously ignored oasis in the deep sea. This study also provides a case study for understanding the microbial ecology in globally widespread seamounts. IMPORTANCE Although there are approximately 25 million seamounts in the ocean, surprisingly little is known about seamount microbial ecology. We provide evidence that seamounts are island-like habitats harboring microbial communities distinct from those of nonseamount habitats, and they exhibit a distance-decay pattern. Environmental selection and dispersal limitation simultaneously shape the observed biogeography. Coupling empirical data with a null mode revealed a shift in the type and strength, which controls microbial community assembly and succession from the seamount surface to the subsurface sediments as follows: (i) community assembly is initially primarily driven by stochastic processes such as dispersal limitation, and (ii) changes in the subsurface environment progressively increase the importance of environmental selection. This case study contributes to the mechanistic understanding essential for a predictive microbial ecology of seamounts.

Neutral theory: applicability and neutrality of clinical study endpoints where a disease-specific instrument is available.

BACKGROUND: There is a pressing need to improve the accuracy of rare disease clinical study endpoints. Neutral theory, first described here, can be used to assess the accuracy of endpoints and improve their selection in rare disease clinical studies, reducing the risk of patient misclassification. METHODS: Neutral theory was used to assess the accuracy of rare disease clinical study endpoints and the resulting probability of false positive and false negative classifications at different disease prevalence rates. Search strings were extracted from the Orphanet Register of Rare Diseases using a proprietary algorithm to conduct a systematic review of studies published until January 2021. Overall, 11 rare diseases with one disease-specific disease severity scale (133 studies) and 12 rare diseases with more than one disease-specific disease severity scale (483 studies) were included. All indicators from clinical studies were extracted, and Neutral theory was used to calculate their match to disease-specific disease severity scales, which were used as surrogates for the disease phenotype. For those with more than one disease-severity scale, endpoints were compared with the first disease-specific disease severity scale and a composite of all later scales. A Neutrality score of > 1.50 was considered acceptable. RESULTS: Around half the clinical studies for half the rare diseases with one disease-specific disease severity score (palmoplantar psoriasis, achalasia, systemic lupus erythematosus, systemic sclerosis and Fournier's gangrene) met the threshold for an acceptable match to the disease phenotype, one rare disease (Guillain-Barré syndrome) had one study with an acceptable match, and four diseases (Behcet's syndrome, Creutzfeldt-Jakob disease, atypical hemolytic uremic syndrome and Prader-Willi syndrome) had no studies. Clinical study endpoints in almost half the rare diseases with more than one disease-specific DSS (acromegaly, amyotrophic lateral sclerosis, cystic fibrosis, Fabry disease and juvenile rheumatoid arthritis) were a better match to the composite, while endpoints in the remaining rare diseases (Charcot Marie Tooth disease, Gaucher disease Type I, Huntington's disease, Sjogren's syndrome and Tourette syndrome) were a worse match. Misclassifications varied with increasing disease prevalence. CONCLUSIONS: Neutral theory confirmed that disease-severity measurement needs improvement in rare disease clinical studies, especially for some diseases, and suggested that the potential for accuracy increases as the body of knowledge on a disease increases. Using Neutral theory to benchmark disease-severity measurement in rare disease clinical studies may reduce the risk of misclassification, ensuring that recruitment and treatment effect assessment optimise medicine adoption and benefit patients.

Effective Population Size Predicts Local Rates but Not Local Mitigation of Read-through Errors.

In correctly predicting that selection efficiency is positively correlated with the effective population size (Ne), the nearly neutral theory provides a coherent understanding of between-species variation in numerous genomic parameters, including heritable error (germline mutation) rates. Does the same theory also explain variation in phenotypic error rates and in abundance of error mitigation mechanisms? Translational read-through provides a model to investigate both issues as it is common, mostly nonadaptive, and has good proxy for rate (TAA being the least leaky stop codon) and potential error mitigation via "fail-safe" 3' additional stop codons (ASCs). Prior theory of translational read-through has suggested that when population sizes are high, weak selection for local mitigation can be effective thus predicting a positive correlation between ASC enrichment and Ne. Contra to prediction, we find that ASC enrichment is not correlated with Ne. ASC enrichment, although highly phylogenetically patchy, is, however, more common both in unicellular species and in genes expressed in unicellular modes in multicellular species. By contrast, Ne does positively correlate with TAA enrichment. These results imply that local phenotypic error rates, not local mitigation rates, are consistent with a drift barrier/nearly neutral model.

What does the distribution of fitness effects of new mutations reflect? Insights from plants.

The distribution of fitness effects (DFE) of new mutations plays a central role in molecular evolution. It is therefore crucial to be able to estimate it accurately from genomic data and to understand the factors that shape it. After a rapid overview of available methods to characterize the fitness effects of mutations, we review what is known on the factors affecting them in plants. Available data indicate that life history traits (e.g. mating system and longevity) have a major effect on the DFE. By contrast, the impact of demography within species appears to be more limited. These results remain to be confirmed, and methods to estimate the joint evolution of demography, life history traits, and the DFE need to be developed.

When the "satisficing" is the new "fittest": how a proscriptive definition of adaptation can change our view of cognition and culture.

Since Darwin's theory of evolution, adaptationism is frequently invoked to explain cognition and cultural processes. Adaptationism can be described as a prescriptive view, as phenotypes that do not optimize fitness should not be selected by natural selection. From an epistemological perspective, the principle of a prescriptive definition of adaptation seems incompatible with recent advances in epigenetics, evolutionary developmental biology, ethology, and genomics. From these challenges, a proscriptive view of adaptation has emerged, postulating that phenotypes that are not deleterious will be evolutionary maintained. In this epistemological investigation, we examine how the shift from adaptationism to a proscriptive view changes our view of cognition and culture. We argue that, while adaptationism leads to cognitivism and a view of culture as strategies to optimize overall fitness, the proscriptive definition favors embodied theories of cognition and a view of culture as the cumulative diffusion of behaviors allowed by the constraints of reproduction.

Tropical forests can maintain hyperdiversity because of enemies.

Explaining the maintenance of tropical forest diversity under the countervailing forces of drift and competition poses a major challenge to ecological theory. Janzen-Connell effects, in which host-specific natural enemies restrict the recruitment of juveniles near conspecific adults, provide a potential mechanism. Janzen-Connell is strongly supported empirically, but existing theory does not address the stable coexistence of hundreds of species. Here we use high-performance computing and analytical models to demonstrate that tropical forest diversity can be maintained nearly indefinitely in a prolonged state of transient dynamics due to distance-responsive natural enemies. Further, we show that Janzen-Connell effects lead to community regulation of diversity by imposing a diversity-dependent cost to commonness and benefit to rarity. The resulting species-area and rank-abundance relationships are consistent with empirical results. Diversity maintenance over long time spans does not require dispersal from an external metacommunity, speciation, or resource niche partitioning, only a small zone around conspecific adults in which saplings fail to recruit. We conclude that the Janzen-Connell mechanism can explain the maintenance of tropical tree diversity while not precluding the operation of other niche-based mechanisms such as resource partitioning.

Effect of Productivity on Community Size Explains the Latitudinal Diversity Gradient of South American Small Mammals.

AbstractAlthough many studies have shown that species richness increases from high to low latitudes (the latitudinal diversity gradient), the mechanisms responsible for generating and maintaining higher species richness in the tropics remain intensely debated. Here we investigate how the effects of temperature on speciation rates (kinetic effects) and the effects of productivity on community size (chemical effects) explain the latitudinal diversity gradient of South American small mammals. We implemented Bayesian models that integrate processes from the neutral and metabolic theories, comparing model predictions with empirical richness patterns. The neutral-metabolic model predicted the latitudinal richness gradient in South American small mammals. We found evidence that the effects of productivity on community size are more important for explaining differences in species richness than the effects of temperature on speciation rates. These results suggest that differences in species richness along latitudinal gradients are regulated primarily by the chemical effects of productivity on speciation-extinction dynamics.

Pan-tissue analysis of allelic alternative polyadenylation suggests widespread functional regulation.

Alternative polyadenylation (APA) is a major layer of gene regulation. However, it has recently been argued that most APA represents molecular noise. To clarify their functional relevance and evolution, we quantified allele-specific APA patterns in multiple tissues from an F1 hybrid mouse. We found a clearly negative correlation between gene expression and APA diversity for the 2,866 genes (24.9%) with a dominant polyadenylation site (PAS) usage above or equal to 90%, suggesting that their other PASs represent molecular errors. Among the remaining genes with multiple PASs, 3,971 genes (34.5%) express two or more isoforms with potentially functional importance. Interestingly, the genes with potentially functional minor PASs specific to neuronal tissues often express two APA isoforms with distinct subcellular localizations. Furthermore, our analysis of cis-APA divergence shows its pattern across tissues is distinct from that of gene expression. Finally, we demonstrate that the relative usage of alternative PASs is not only affected by their cis-regulatory elements, but also by potential coupling between transcriptional and APA regulation as well as competition kinetics between alternative sites.

Dispersal limitations and long-term persistence drive differentiation from haplotypes to communities within a tropical sky-island: Evidence from community metabarcoding.

Neutral theory proposes that dispersal stochasticity is one of the main drivers of local diversity. Haplotypes-level genetic variation can now be efficiently sampled from across whole communities, thus making it possible to test neutral predictions from the genetic to species-level diversity, and higher. However, empirical data is still limited, with the few studies to date coming from temperate latitudes. Here, we focus on a tropical mountain within the Transmexican Volcanic Belt to evaluate spatially fine-scale patterns of arthropod community assembly to understand the role of dispersal limitation and landscape features as drivers of diversity. We sampled whole-communities of arthropods for eight orders at a spatial scale ranging from 50 m to 19 km, using whole community metabarcoding. We explored multiple hierarchical levels, from individual haplotypes to lineages at 0.5, 1.5, 3, 5, and 7.5% similarity thresholds, to evaluate patterns of richness, turnover, and distance decay of similarity with isolation-by-distance and isolation-by-resistance (costs to dispersal given by landscape features) approaches. Our results showed that distance and altitude influence distance decay of similarity at all hierarchical levels. This holds for arthropod groups of contrasting dispersal abilities, but with different strength depending on the spatial scale. Our results support a model where local-scale differentiation mediated by dispersal constraints, combined with long-term persistence of lineages, is an important driver of diversity within tropical sky islands.

A nearly-neutral biallelic Moran model with biased mutation and linear and quadratic selection.

In this article, a biallelic reversible mutation model with linear and quadratic selection is analysed. The approach reconnects to one proposed by Kimura (1979), who starts from a diffusion model and derives its equilibrium distribution up to a constant. We use a boundary-mutation Moran model, which approximates a general mutation model for small effective mutation rates, and derive its equilibrium distribution for polymorphic and monomorphic variants in small to moderately sized populations. Using this model, we show that biased mutation rates and linear selection alone can cause patterns of polymorphism within and substitution rates between populations that are usually ascribed to balancing or overdominant selection. We illustrate this using a data set of short introns and fourfold degenerate sites from Drosophila simulans and Drosophila melanogaster.

Neutral theory: applicability and neutrality of using generic health-related quality of life tools in diseases or conditions where specific tools are available.

BACKGROUND: Health-related quality of life (HRQoL) tools are limited by the indicators included in the construct and variation in interpretation by different researchers. Neutral Theory describes the ideal construct that includes all relevant indicators and, therefore, complete accuracy, or neutrality. Neutral Theory can thereby provide the framework to develop or test constructs. To assess the application of Neutral Theory, the neutrality of generic tools (SF-36 and EQ-5D) at measuring HRQoL was compared to disease/condition-specific tools, with the latter considered surrogates for the Neutral construct. METHODS: Full descriptions of all disease/condition-specific HRQoL tools published on PubMed (to 01-Jul-19) were sourced. For each tool, the number of items with and without a direct match within the SF-36 and EQ-5D was recorded and the sensitivity/specificity calculated. RESULTS: The SF-36 and EQ-5D did not achieve a sensitivity/specificity both > 50% against any of the 163 disease/condition-specific tools identified. At 20% prevalence of poor HRQoL, the false positive rate (FPR) was > 75% for all but two tools against the SF-36 and six tools against the EQ-5D. Increasing poor HRQoL to 80%, 47 tools for the SF-36 and 48 tools for the EQ-5D had a FPR < 50%. For rare disease tools (< 1/2000 population; n = 17), sensitivity/specificity ranged from 0 to 40%/5-31% for the SF-36 and 0-22%/29-100% for the EQ-5D. For non-rare (n = 75) and symptom-specific tools (n = 71) sensitivity/specificity was: 0-100%/0-100% (SF-36) and 0-50%/0-100% (EQ-5D); and 0-60%/0-19% (SF-36) and 0-25%/0-100% (EQ-5D), respectively. No concordance was recorded for 18% (2/11) of results from studies of rare disease tools versus the SF-36 (no data vs EQ-5D). For non-rare, disease-specific tools, results were discordant for 30% (25/84) and 35% (23/65) of studies against the SF-36 and EQ-5D, respectively. For symptom-specific tools, corresponding results were 36% (24/66) and 16% (5/31). CONCLUSIONS: Generic HRQoL tools appear poorly correlated with disease/condition-specific tools, which indicates that adoption of Neutral Theory in the development and assessment of HRQoL tools could improve their relevance, accuracy, and utility in economic evaluations of health interventions.

Drivers of taxonomic, functional and phylogenetic diversities in dominant ground-dwelling arthropods of coastal heathlands.

Although functional and phylogenetic diversities are increasingly used in ecology for a variety of purposes, their relationship remains unclear, and this relationship likely differs among taxa, yet most recent studies focused on plants. We hypothesize that communities may be diverse in functional traits due to presence of: many phylogenetic lineages, trait divergence within lineages, many species and random functional variation among species, weak filtering of traits in favorable environments, or strong trait divergence in unfavorable environments. We tested these predictions for taxa showing higher (ants), or lower (spiders, ground beetles) degrees of competition and niche construction, both of which might decouple functional traits from phylogenetic position or from the environment. Studying > 11,000 individuals and 216 species from coastal heathlands, we estimated functional as minimum spanning trees using traits related to the morphology, feeding habits and dispersal, respectively. Relationships between functional and phylogenetic diversities were overall positive and strong. In ants, this relationship disappeared after accounting for taxonomic diversities and environments, whereas in beetles and spiders taxonomic diversity is related to functional diversity only via increasing phylogenetic diversity. Environmental constraints reduced functional diversity in ants, but affected functional diversity only indirectly via phylogenetic diversity (ground beetles) and taxonomic and then phylogenetic diversity (spiders and ground beetles). Results are consistent with phylogenetic conservatism in traits in spiders and ground beetles. In ants, in contrast, traits appear more phylogenetically neutral with any new species potentially representing a new trait state, tentatively suggesting that competition or niche construction might decouple phylogenetics from trait diversity.

Functional traits shape small mammal-helminth network: patterns and processes in species interactions.

Understanding the role of species traits in mediating ecological interactions and shaping community structure is a key question in ecology. In this sense, parasite population parameters allow us to estimate the functional importance of traits in shaping the strength of interactions among hosts and parasites in a network. The aim of this study was to survey and analyse the small mammal-helminth network in a forest reserve of the Brazilian Atlantic Forest in order to understand (i) how functional traits (type of parasite life cycle, site of infection in their host, host and parasite body length, host diet, host locomotor habit and host activity period) and abundance influence host­parasite interactions, (ii) whether these traits explain species roles, and (iii) if this relationship is consistent across different parasite population parameters (presence and absence, mean abundance and prevalence). Networks were modular and their structural patterns did not vary among the population parameters. Functional traits and abundance shaped the interactions observed between parasites and hosts. Host species abundance, host diet and locomotor habit affected their centrality and/or vulnerability to parasites. For helminths, infection niche was the main trait determining their central roles in the networks.

Ecological Processes Shaping Bulk Soil and Rhizosphere Microbiome Assembly in a Long-Term Amazon Forest-to-Agriculture Conversion.

Forest-to-agriculture conversion has been identified as a major threat to soil biodiversity and soil processes resilience, although the consequences of long-term land use change to microbial community assembly and ecological processes have been often neglected. Here, we combined metagenomic approach with a large environmental dataset, to (i) identify the microbial assembly patterns and, (ii) to evaluate the ecological processes governing microbial assembly, in bulk soil and soybean rhizosphere, along a long-term forest-to-agriculture conversion chronosequence, in Eastern Amazon. We hypothesized that (i) microbial communities in bulk soil and rhizosphere have different assembly patterns and (ii) the weight of the four ecological processes governing assembly differs between bulk soil and rhizosphere and along the chronosequence in the same fraction. Community assembly in bulk soil fitted most the zero-sum multinomial (ZSM) neutral-based model, regardless of time. Low to intermediate dispersal was observed. Decreasing influence of abiotic factors was counterbalanced by increasing influence of biotic factors, as the chronosequence advanced. Undominated ecological processes of dispersal limitation and variable selection governing community assembly were observed in this soil fraction. For soybean rhizosphere, community assembly fitted most the lognormal niche-based model in all chronosequence areas. High dispersal and an increasing influence of abiotic factors coupled with a decreasing influence of biotic factors were found along the chronosequence. Thus, we found a dominant role of dispersal process governing microbial assembly with a secondary effect of homogeneous selection process, mainly driven by decreasing aluminum and increased cations saturation in soil solution, due to long-term no-till cropping. Together, our results indicate that long-term no-till lead community abundances in bulk soil to be in a transient and conditional state, while for soybean rhizosphere, community abundances reach a periodic and permanent distribution state. Dominant dispersal process in rhizosphere, coupled with homogeneous selection, brings evidences that soybean root system selects microbial taxa via trade-offs in order to keep functional resilience of soil processes.

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.