Predictions Of Neutral Model Research Articles

Response of salivary microbiome to temporal, environmental, and surface characteristics under in vitro exposure

The microbiome of saliva stains deposited at crime scenes and in everyday settings is valuable for forensic investigations and environmental ecology. However, the dynamics and applications of microbial communities in these saliva stains have not been fully explored. In this study, we analyzed saliva samples that were exposed to indoor conditions for up to 1 year and to different carriers (cotton, sterile absorbent cotton swab, woolen, dacron) in both indoor and outdoor environments for 1 month using high-throughput sequencing. The analysis of microbial composition and Mfuzz clustering showed that the salivary flora, specifically Streptococcus (cluster7), which was associated with microbial contamination, remained stable over short periods of time. However, prolonged exposure led to significant differences due to the invasion of environmental bacteria such as Pseudomonas and Achromobacter. The growth and colonization of environmental flora were promoted by humidity. The neutral model predictions indicated that the assembly of salivary microbial communities in outdoor environments was significantly influenced by stochastic processes, with environmental characteristics having a greater impact on community change compared to surface characteristics. By incorporating data from previous studies on fecal and vaginal secretion microbiology, we developed RF and XGBoost classification models that achieved high accuracy (>98 %) and AUC (>0.8). Additionally, a RF regression model was created to determine the time since deposition (TsD) of the stains. Time inference models yielded a mean absolute error (MAE) of 7.1 days for stains exposed for 1 year and 14.2 h for stains exposed for 14 days. These findings enhance our understanding of the changes in the microbiome of saliva stains over time, in different environments, and on different surfaces. They also have potential applications in assessing potential microbial contamination, identifying body fluids, and inferring the time of deposition.

Viral diversity is linked to bacterial community composition in alpine stream biofilms

Biofilms play pivotal roles in fluvial ecosystems, yet virtually nothing is known about viruses in these communities. Leveraging an optimized sample-to-sequence pipeline, we studied the spatiotemporal turnover of dsDNA viruses associated with stream biofilms and found an astounding diversity to be structured by seasons and along the longitudinal gradient in the stream. While some vOTUs were region- or season-specific, we also identified a large group of permanent biofilm phages, taxonomically dominated by Myoviridae. Comparison of the observed viral distribution with predictions based on neutral community assembly indicated that chance and dispersal may be important for structuring stream biofilm viral communities. Deviation from neutral model predictions suggests that certain phages distribute efficiently across distant locations within the stream network. This dispersal capacity appears to be linked to EPS depolymerases that enable phages to efficiently overcome the biofilm barrier. Other phages, particularly vOTUs classified as Siphoviridae, appear locally overrepresented and to rely on a lysogenic life cycle, potentially to exploit the spatial distribution of bacterial populations in stream biofilms. Overall, biofilm viral and bacterial community turnover were significantly coupled. Yet, viral communities were linked to the presence of the most abundant bacterial community members. With this work, we provide a foundational ecological perspective on factors that structure viral diversity in stream biofilms and identify potentially important viral traits related to the biofilm mode of life.

Drifting to the top? Disentangling mechanisms influencing the turnover rate of popular music

ABSTRACT What causes turnover on the Billboard charts? The neutral model of cultural evolution, which assumes that taste is transmitted via an unbiased copying process, provides precise predictions regarding expected popularity distributions and turnover within a popularity-ranked list. Recent advances in this line make it possible to characterize the likelihood of music taste transmission mechanisms by investigating departures of observed turnover rates from neutral model predictions. Here, I bias the neutral model to investigate four alternative conceptions of individual music taste transmission (song quality, individual status, social network, and anticonformist) and use agent-based simulations to examine the impact on turnover. I then compare modeled with empirical turnover data from the Billboard Hot 100 over the period from 1958 to 2021 and find that observed turnover patterns are reproduced only in an anticonformist model simulating the systematic rejection of the most popular songs. This finding was unexpected and challenges the notion of a generalized “preference for the popular.” Overall, this study contributes to ongoing debates regarding the mechanisms involved in the transmission of taste and the mechanics of fashion change.

Experimental field test of the influence of generalist stingless bees (Meliponini) on the topology of a bee–flower mutualistic network in the tropics

1. Generalists are assumed to play a key role in structuring and stabilising animal–plant mutualistic networks. Until now, analyses on the effects of generalists have been based on empirical field data or simulations. The present natural field experiment manipulated the abundance of a generalist and abundant stingless bee [Melipona (Eomelipona) marginata] to determine the effects on the mutualistic network.2. Networks were generated, and associated metrics were used for comparing replicate plots with and without the insertion of stingless bee nests.3. Unweighted metrics and the basic qualitative structural pattern of networks (high nestedness, very low modularity and specialisation) was not affected by experimental variation in stingless bee abundance because they exert strong basal effects on the plant–pollinator community under natural conditions of abundance. Still, increased abundance caused significant variation in weighted nestedness and modularity and community‐level specialisation.4. Supporting predictions of neutral models, increased abundance of the stingless bee led to an increase in most of its specific metrics, expressing the expansion of its realised trophic niche.5. During this process, specialist and other generalist bees were affected in different ways. More plant species became even more dependent on this stingless bee (increased asymmetry).6. Long‐term effects could not be inferred directly from instantaneous values of network metrics. Nonetheless, the increased abundance of the generalist stingless bee may both reduce the local level of ecological specialisation in the short term and affect the spatial distribution of less abundant and/or specialist bee species and plants in the long term.

Testing the neutral theory of biodiversity with the microbiome dataset from cystic fibrosis patients

Cystic fibrosis (CF) is a hereditary disease that is characterized by defective mucociliary clearance, airway obstruction, chronic infection, and persistent inflammation. Cystic fibrosis pulmonary exacerbation (CFPE) majorly causes the morbidity of CF patients. Although CF has been demonstrated to change the composition of lung microbial community, previous studies have not made efforts to study the differences in the mechanism of assembly and diversity maintenance of lung microbial community in CF patients. In this study, we applied the neutral theory of biodiversity to comparatively investigate the assembly and diversity maintenance of the lung microbial community before and after the antibiotic treatment by reanalyzing the dataset from Fodor et al's study. We found that no one sample in the lung microbial communities of the sputum samples of Exacerbation group, nor those of End-of-treatment group satisfied the predictions of neutral model, suggesting that the neutral-process does not dominate in CF patients before and after antibiotic treatments. By comparing the biodiversity parameter between Exacerbation and End-of-treatment group, we found that the former had the significantly higher biodiversity, but the change in diversity parameter is slight and the P value is close to.05 (P value = .41). Therefore, our second finding is that although CFPE may increase the biodiversity of lung microbial community, the change is not essential.

Ecological filtering or random extinction? Beta‐diversity patterns and the importance of niche‐based and neutral processes following habitat loss

Although both niche‐based and neutral processes are involved in community assembly, most models on the effects of habitat loss are stochastic, assuming neutral communities mainly affected by ecological drift and random extinction. Given that habitat loss is considered the most important driver of the current biodiversity crisis, unraveling the processes underlying the effects of habitat loss is critical from both a theoretical and an applied perspective. Here we unveil the importance of niche‐based and neutral processes to species extinction and community assembly across a gradient of habitat loss, challenging the predictions of neutral models. We draw on a large dataset containing the distribution of 3653 individuals of 42 species, representing 35% of the small mammal species of the Atlantic Forest hotspot, obtained in 68 sites across three continuously‐forested landscapes and three adjacent 10 000‐ha fragmented landscapes differing in the amount of remaining forest (50%, 30% and 10%). By applying a null‐model approach, we investigated β‐diversity patterns by detecting deviations of observed community similarity from the similarity between randomly assembled communities. Species extinction following habitat loss was decidedly non‐random, in contrast to the notion that fragmented communities are mainly driven by ecological drift. Instead, habitat loss led to a strong biotic homogenization. Moreover, species composition changed abruptly at the same level of landscape‐scale habitat loss that has already been associated with a drastic decline in species richness. Habitat loss, as other anthropogenic disturbances, can thus be seen as a strong ecological filter that increases (rather than decreases) the importance of deterministic processes in community assembly. As such, critical advances for the development of conservation science lie on the incorporation of the relevant niche traits associated with extinction proneness into models of habitat loss. The results also underscore the fundamental importance of pro‐active measures to prevent human‐modified landscapes surpassing critical ecological thresholds.

Biases in cultural transmission shape the turnover of popular traits

The neutral model of cultural evolution, which assumes that copying is unbiased, provides precise predictions regarding frequency distributions of traits and the turnover within a popularity-ranked list. Here we study turnover in ranked lists and identify where the turnover departs from neutral model predictions to detect transmission biases in three different domains: color terms usage in English language 20th century books, popularity of early (1880–1930) and recent (1960–2010) USA baby names, and musical preferences of users of the Web site Last.fm. To help characterize the type of transmission bias, we modify the neutral model to include a content-based bias and two context-based biases (conformity and anti-conformity). How these modified models match real data helps us to infer, from population scale observations, when cultural transmission is biased, and, to some extent, what kind of biases are operating at individual level.

The Co-Occurrence of Species and the Co-Diversity of Sites in Neutral Models of Biodiversity

Patterns of co-occurrence of species are widely used to assess the fit of ecological neutral models to empirical patterns. The mathematically equivalent patterns of co-diversity of sites, in contrast, have been considered only indirectly and analyses normally are focused on the spatial distribution of species richness, rather than on the patterns of species sharing. Here we use two analytical tools (range-diversity plots and rank plots) to assess the predictions of simple neutral models in relation to patterns of co-occurrence and co-diversity. Whereas a fully stochastic null model predicts zero average among species and among sites, neutral models generate systems with low levels of covariance among species and high levels of positive covariance among sites. These patterns vary with different combinations of dispersal and speciation rates, but are always linked to the shape, symmetry, and spread of the range-size and species-richness frequency distributions. Non-homogeneous patterns of diversity and distribution arise in neutral models because of the spatial arrangement of sites and their concomitant similarity, which is reflected also in the spread of the range-size frequency distribution. The nearly null covariance among species, in contrast, implies low variance in species richness of sites and very slim frequency distributions. In real world assemblages of Mexican volant and non-volant mammals, patterns of range-size and species-richness frequency distribution are similar to those generated by neutral models. However, when the comparison includes the covariance both for species (co-occurrence) and for sites (co-diversity), empirical patterns differ significantly from the predictions of neutral models. Because of the mathematical links between the covariance in the distribution of species and the variance of species-richness values and between the covariance in species sharing among sites and the variance of range-size values, a full understanding of patterns of diversity calls for the simultaneous analysis of co-occurrence and co-diversity.

Universal scaling of species‐abundance distributions across multiple scales

The scale‐dependent species abundance distribution (SAD) is fundamental in ecology, but few spatially explicit models of this pattern have thus far been studied. Here we show spatially explicit neutral model predictions for SADs over a wide range of spatial scales, which appear to match empirical patterns qualitatively. We find that the assumption of a log‐series SAD in the metacommunity made by spatially implicit neutral models can be justified with a spatially explicit model in the large area limit. Furthermore, our model predicts that SADs on multiple scales are characterized by a single, compound parameter that represents the ratio of the survey area to the species’ average biogeographic range (which is in turn set by the speciation rate and the dispersal distance). This intriguing prediction is in line with recent empirical evidence for a universal scaling of the species‐area curve. Hence we hypothesize that empirical SAD patterns will show a similar universal scaling for many different taxa and across multiple spatial scales.

Species Differences Drive Nonneutral Structure in Pleistocene Coral Communities

Although ecological assemblages frequently depart from neutral model predictions, these discrepancies have not been unambiguously attributed to neutral theory's core assumption: that community structure is primarily the result of chance variation in birth, death, speciation, and dispersal, rather than the manifestation of demographic differences among species. Using coral communities in Barbados from four time periods during the Pleistocene, we demonstrate that the neutral theory cannot explain coral community similarity distributions, species' regional abundance distributions, or their local occupancy. Furthermore, discrepancies between the neutral theory and the observed communities can be attributed to violation of the core assumption of species equivalence. In particular, species' variable growth rates are driving departures from neutral predictions. Our results reinforce an understanding of reef coral community assembly that invokes trade-offs in species' demographic strategies. The results further suggest that conservation management actions will fail if they are based on the neutral assumption that different coral species are equally able to create live coral cover in the shallow-water reef environment. These findings highlight the importance of developing biodiversity theory that can parsimoniously incorporate species differences in coral reef communities, rather than further elaborating neutral theory.

Herbivores on a dominant understory shrub increase local plant diversity in rain forest communities

Indirect effects of trophic interactions on biodiversity can be large and common, even in complex communities. Previous experiments with dominant understory Piper shrubs in a Costa Rican rain forest revealed that increases in herbivore densities on these shrubs caused widespread seedling mortality as a result of herbivores moving from Piper to seedlings of many different plant genera. We tested components of the Janzen-Connell hypothesis by conducting focused studies on the effects of specialist and generalist Piper herbivores on local seedling diversity. Whereas specialist herbivores are predicted to increase mortality to neighboring seedlings that are closely related to the source plant, true generalists moving from source plants may cause density-dependent mortality of many species, and possibly increase richness if new species replace abundant species that have been thinned by herbivores. Therefore, we hypothesized that seedling richness would be greater in understory control plots created in patches of Piper that had normal densities of generalist herbivores compared to plots from which we removed generalist herbivores manually from all Piper shrubs. After 15 months, generalist-herbivore-removal plots had > 40% fewer seedlings, > 40% fewer species, and 40% greater seedling evenness, on average, than control plots with generalist herbivores intact. Using a complementary approach in unmanipulated plots in four forests, we used path analysis to test for a positive association between seedling diversity and herbivore damage on Piper species. In unmanipulated plots, for both generalist and specialist herbivores, our data were significant fits to the causal model that Piper herbivores decrease evenness and increase plant species richness, corroborating the experimental results. Because herbivores changed how individuals were apportioned among the species and families present (lower evenness), one interpretation of these associations between herbivores on Piper shrubs and local seedling richness is that high seedling mortality in dominant families allowed the colonization or survival of less common species. If interspecific or apparent competition allowed for a relative increase in species richness, then the Janzen-Connell hypothesis may extend its predictions to generalist seedling predators. We speculate that apparent competition may explain some of the deviations from neutral model predictions, especially at small scales.

Herbivores on a dominant understory shrub increase local plant diversity in rain forest communities

Indirect effects of trophic interactions on biodiversity can be large and common, even in complex communities. Previous experiments with dominant understory Piper shrubs in a Costa Rican rain forest revealed that increases in herbivore densities on these shrubs caused widespread seedling mortality as a result of herbivores moving from Piper to seedlings of many different plant genera. We tested components of the Janzen-Connell hypothesis by conducting focused studies on the effects of specialist and generalist Piper herbivores on local seedling diversity. Whereas specialist herbivores are predicted to increase mortality to neighboring seedlings that are closely related to the source plant, true generalists moving from source plants may cause density-dependent mortality of many species, and possibly increase richness if new species replace abundant species that have been thinned by herbivores. Therefore, we hypothesized that seedling richness would be greater in understory control plots created in patches of Piper that had normal densities of generalist herbivores compared to plots from which we removed generalist herbivores manually from all Piper shrubs. After 15 months, generalist-herbivore-removal plots had >40% fewer seedlings, >40% fewer species, and 40% greater seedling evenness, on average, than control plots with generalist herbivores intact. Using a complementary approach in unmanipulated plots in four forests, we used path analysis to test for a positive association between seedling diversity and herbivore damage on Piper species. In unmanipulated plots, for both generalist and specialist herbivores, our data were significant fits to the causal model that Piper herbivores decrease evenness and increase plant species richness, corroborating the experimental results. Because herbivores changed how individuals were apportioned among the species and families present (lower evenness), one interpretation of these associations between herbivores on Piper shrubs and local seedling richness is that high seedling mortality in dominant families allowed the colonization or survival of less common species. If interspecific or apparent competition allowed for a relative increase in species richness, then the Janzen-Connell hypothesis may extend its predictions to generalist seedling predators. We speculate that apparent competition may explain some of the deviations from neutral model predictions, especially at small scales.

Dispersal, edaphic fidelity and speciation in species‐rich Western Australian shrublands: evaluating a neutral model of biodiversity

Over evolutionary time, the number of species in a community reflects the balance between the rate of speciation and the rate of extinction. Over shorter time‐scales local species richness is also affected by how often species move into and out of the local community. These processes are at the heart of Hubbell's ‘unified neutral theory of biodiversity’ (Hubbell 2001). Hubbell's spatially implicit, dispersal‐limited neutral model is the most widely used of the many implementations of neutral theory and it provides an estimate of the rate of speciation in a metacommunity (if metacommunity size is known) and the rate at which species migrate into the local community from the wider metacommunity. Recently, this neutral model has been used to compare rates of speciation and migration in the species‐rich fynbos of South Africa and in neotropical forests. Here we use new analytical methods for estimating the neutral model's parameters to infer speciation and dispersal rates for three sites in species‐rich sclerophyll shrublands (equivalent to fynbos) in Western Australia (WA). Our estimates suggest that WA shrublands are intermediate between fynbos and tropical rainforest in terms of speciation and dispersal. Although a weak test, the model predicts species abundance distributions and species accumulation curves similar to those observed at the three sites. The neutral model's predictions also remain plausible when confronted with independent data describing: (1) known edaphic relationships between sites, (2) estimates of metacommunity species richness and (3) rates of speciation among resprouters and nonsprouters. Two of the site pairs, however, show species turnovers significantly different from those predicted by the spatially implicit form of the neutral model that we use. This suggests that non‐neutral processes, in this case probably edaphic specialisation, are important in the WA shrubland metacommunity. The neutral model predicts similar rates of speciation in resprouter and sprouter taxa, a finding supported by recent molecular phylogenies. Finally, when converted into temporally scaled speciation rates and species longevities, the estimates produced by the neutral model seem implausible. The apparent departure from neutrality in the turnover of species between some sites and the implausible temporal dynamics may be due to the particular model chosen and does not reduce the significance of our other results, which confirm that local dispersal limitation, coupled with broader scale edaphic fidelity, combine to structure this biodiverse metacommunity.

Gypsy moth response to landscape structure differs from neutral model predictions: implications for invasion monitoring

Simulations of dispersal across computer-generated neutral landscapes have generated testable predictions about the relationship between dispersal success and landscape structure. Models predict a threshold response in dispersal success with increasing habitat fragmentation. A threshold is defined as an abrupt, disproportionate decline in dispersal success at a certain proportion of habitat in the landscape. To identify potential empirical threshold responses in invasion success to landscape structure, we quantified the relationship between progression of the gypsy moth (Lymantria dispar) invasion wavefront across Michigan (1985–1996) and the structure of the Michigan landscape using two indices of invasion success and six landscape metrics. We also examined the effect of scale of analysis and choice of land cover characterization on our results by repeating our analysis at three scales using two different land cover maps. Contrary to simulation model predictions, thresholds in invasion success did not correspond closely with thresholds in landscape structure metrics. Increased variation in invasion success indices at smaller scales of analysis also suggested that invasion success should be studied at larger spatial extents (≥75 km2) than would be appropriate for characterizing individual dispersal events. The predictions of individual dispersal models across neutral landscapes may have limited applications for the monitoring and management of vagile species with excellent dispersal capabilities such as the gypsy moth.

Coral reef diversity refutes the neutral theory of biodiversity

The global decline of coral reefs highlights the need to understand the mechanisms that regulate community structure and sustain biodiversity in these systems. The neutral theory, which assumes that individuals are demographically identical regardless of species, seeks to explain ubiquitous features of community structure and biodiversity patterns. Here we present a test of neutral-theory predictions with the use of an extensive species-level data set of Indo-Pacific coral communities. We show that coral assemblages differ markedly from neutral-model predictions for patterns of community similarity and the relative abundance of species. Within local communities, neutral models do not fit relative abundance distributions as well as the classical log-normal distribution. Relative abundances of species across local communities also differ markedly from neutral-theory predictions: coral communities exhibit community similarity values that are far more variable, and lower on average, than the neutral theory can produce. Empirical community similarities deviate from the neutral model in a direction opposite to that predicted in previous critiques of the neutral theory. Instead, our results support spatio-temporal environmental stochasticity as a major driver of diversity patterns on coral reefs.

Interactions between Habitat Abundance and Configuration: Experimental Validation of Some Predictions from Percolation Theory

Recent neutral landscape models derived from percolation theory predict that a landscape with sparse but contagious habitat coverage is functionally equivalent to one with more abundant but randomly situated habitat patches. We tested this prediction in a field experiment that determined how habitat-patch abundance and configuration affect landscape use by animals. Using a 2 × 2 factorial design in a 25-m 2 landscape, we created four treatments by varying the ratio of habitat (grass) to non-habitat (sand) patches (10%:90% vs 20%:80%) and the clustering of grass habitat patches (random vs contagious). We then followed the movements of tenebrionid beetles (Coleoptera: Tenebrionidae) through these experimental landscapes and measured their pathway characteristics. Our results were largely consistent with neutralmodel predictions, in that the amount of habitat present had a greater influence than did habitat configuration and habitat abundance exerted its strongest influence on movement behaviours when habitat was sparse, regardless of spatial pattern. However, we also detected interactions between the amount and spatial arrangement of habitat patches that reflected how beetles responded to certain landscape-level properties of different abundances and configurations of habitat: average habitat-patch size and the distance between patches were better predictors of beetle responses than were the average number of patches or the amount of patch edge (perimeter) within a treatment. Because of such latent influences of landscape-level habitat properties, our results have important implications for conservation efforts that endeavour to preserve landscape function by maintaining some minimum amount of habitat coverage. Interactions between habitat abundance and configuration complicate the detection and definition of landscape function, illustrating the need for a spatially realistic approach in habitat management.

Community structure of estuarine meiobenthos

Meiofaunal samples were collected from intertidal mudflats in the lower, middle and upper reaches of the Tamar estuary, South West England in April and October, 1982. Species abundance and biomass patterns of nematodes and copepods did not follow the expected trends in relation to salinity: the lowest species diversity (below neutral model predictions), the steepest ranked species abundance curves and the greatest departure from the theoretical lognormal distribution of numbers and biomass of individuals among species were found at the middle rather than the upper site. Huston's (1979) dynamic equilibrium hypothesis is invoked to explain these phenomena, but the hypothesis remains to be tested. Intense macrofaunal predation and disturbance, together with more pronounced environmental fluctuations, may eliminate competitive exclusion at the upper site resulting in a relatively high species diversity. The absence of such population reduction mechanisms at the middle site results in competitive exclusion and lowered diversity. The major nematode species at the upper site have certain opportunistic characteristics, and at the middle site conservative characteristics, which support the contention that these are respectively successional and climax communities. The lower site may represent an intermediate successional stage with the highest diversity. The apparent correlation between the abundances of 3 copepod and 1 nematode species with changes in salinity at the middle and upper sites between April and October is thought to result from passive suspension and transport of these species upstream during the summer: there is a distinct fine-scale vertical stratification of species in the sediment at the middle site, with the species in question having an extreme surficial distribution.

Reanalysis of Caswell's Neutral Models

In an important and much quoted paper Caswell (1976) derived models of community structure (the numbers of individuals and species) that did not involve biological interactions. From these neutral models he contended that biological interactions depress values of the Shannon-Wiener diversity index below model predictions in tropical bird, insect, and tree communities and that values equal to predictions obtain for temperate birds and forest trees. Caswell's conclusion was that biological interactions lead to less diverse communities than neutral-model predictions, and diversity is depressed more where abiotic factors have only slight influence on biological interactions. Such conclusions are in marked contrast to the traditional views that high diversity in particular is generated by biological interactions. Using Caswell's neutral model other workers have also found that diversity is less than neutral-model predictions in, e.g., marine benthic communities (Rainer 1981). (An example purporting to support the traditional view [Gray 1978] was shown by Rainer to be due to the use of an incorrect logarithm base, and this data set also supported Caswell's contention.) It seemed to us improbable that all examples should consistently be equal to or below neutral-model predictions, and this led us to reexamine Caswell's model. In most communities species are patchily distributed, and the total abundance of a species is the sum of the abundances in all patches. Because of the multiplicity of factors that influence any given species, the distribution of species within any patch will be rather unpredictable. A species having been eliminated from a patch may recolonize by migrating from other patches. Thus, extinction over ecological time is generally a local phenomenon. The two species-abundance distributions that have been shown to fit a large number of different assemblages are the logseries distribution and the lognormal distribution. Frequently it is impossible to determine which of these two distributions is more apt, since they both give excellent fits to the data. In a survey of stochastic models of population growth, Kendall (1948) pointed out that the success of fitting the logseries to entomological data implies that the density of the abundances must be in the form

Temporal patterns in the structure of macrobenthic communities of an Australian estuary

The benthic fauna of a small estuary was examined to test hypotheses about community structure and environmental stress (foreign, or natural but excessive, perturbations in the environment). Quantitative samples were collected at approximately 2-month intervals over 18 months from Cabbage Tree Basin, Port Hacking, New South Wales. The sites sampled ranged from the intertidal to a central basin subject to deoxygenation of the bottom water. The species composition of the intertidal and shallow-water sites was more stable than that of the deeper sites, due to the presence of short-lived opportunistic species at the deeper sites after periods of deoxygenation. There were no obvious changes in species composition associated with temperature minima or maxima. No changes directly associated with reduced salinity after rainfall were found, although heavy rainfall prior to the sampling period may have reduced the number of species at some sites. The stable community structure and species composition at the intertidal and shallow-water sites indicated that greater environmental harshness does not necessarily imply less faunal stability. Differences in diversity among these sites were interpreted as evidence that biological accommodation was responsible for a reduction in diversity from values predicted by the neutral model. At a deeper site, diversity was close to neutral model predictions. It is suggested that the ecotone point in a stressed community may be characterized by diversity values that are in agreement with neutral model predictions. The statistical properties of the measures of diversity and evenness were not important for their interpretation. Biomass-based measures indicated patterns that were often different from frequency-based measures.