Hybrid niche-neutral models outperform an otherwise equivalent neutral model for fitting coral reef data

Tang, Junfeng; Zhou, Shurong

doi:10.1016/j.jtbi.2012.10.019

Cited by 15 publications

(67 citation statements)

References 35 publications

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“…Despite contrasting opinions on the value of neutral theory [1,2], it is now generally accepted that neutral and niche processes interact in natural communities and both contribute towards the structure of species assemblages [3]. The relative roles of neutral and niche processes have been shown to differ across spatio-temporal scales [4,5] and modelling these processes in combination (composite models) better represents biological patterns than neutral or niche models alone [6,7]. Two composite-model approaches have been used to jointly examine niche and neutral processes in communities.…”

Section: Introductionmentioning

confidence: 99%

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Beyond the continuum: a multi-dimensional phase space for neutral–niche community assembly

2015

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Neutral and niche processes are generally considered to interact in natural communities along a continuum, exhibiting community patterns bounded by pure neutral and pure niche processes. The continuum concept uses niche separation, an attribute of the community, to test the hypothesis that communities are bounded by pure niche or pure neutral conditions. It does not accommodate interactions via feedback between processes and the environment. By contrast, we introduce the Community Assembly Phase Space (CAPS), a multidimensional space that uses community processes (such as dispersal and niche selection) to define the limiting neutral and niche conditions and to test the continuum hypothesis. We compare the outputs of modelled communities in a heterogeneous landscape, assembled by pure neutral, pure niche and composite processes. Differences in patterns under different combinations of processes in CAPS reveal hidden complexity in neutral-niche community dynamics. The neutral-niche continuum only holds for strong dispersal limitation and niche separation. For weaker dispersal limitation and niche separation, neutral and niche processes amplify each other via feedback with the environment. This generates patterns that lie well beyond those predicted by a continuum. Inferences drawn from patterns about community assembly processes can therefore be misguided when based on the continuum perspective. CAPS also demonstrates the complementary information value of different patterns for inferring community processes and captures the complexity of community assembly. It provides a general tool for studying the processes structuring communities and can be applied to address a range of questions in community and metacommunity ecology.

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Section: Introductionmentioning

confidence: 99%

“…A phenomenological approach involves directly modelling the abundance of species using differential equations and probability distributions, taking interactions between species into account (e.g. [6,[8][9][10]). By contrast, a mechanistic approach is based on a 'filter & 2015 The Author(s) Published by the Royal Society.…”

Section: Introductionmentioning

confidence: 99%

Beyond the continuum: a multi-dimensional phase space for neutral–niche community assembly

2015

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“…To explore the mechanisms of microbial community construction and diversity maintenance, niche theory and neutral theory can be applied to illustrate the role of stochastic and deterministic forces. Hubbell (2001) initially applied the unified neutral theory of biodiversity and biogeography (UNTB) to explain community construction mechanisms, with many researchers subsequently extending and challenging traditional neutral and niche theories (Etienne, 2005(Etienne, , 2007Hubbell 2006;Volkov, 2003Volkov, , 2007Sloan et al, 2006Sloan et al, , 2007McGill, 2003;Harris et al, 2017;Tang & Zhou, 2013, Li & Ma 2016Burns 2016). For example, Sloan et al (2006Sloan et al ( , 2007) extended Hubbell's discrete neutral theory to a continuous version to test large microbiomes.…”

Section: Introductionmentioning

confidence: 99%

“…We take advantage of this feature to detect the potential correlation between tumor development and bacterial species competitiveness. We also used another pair of models, i.e., multi-site neutral (MSN) (Harris et al, 2017) and niche-neutral hybrid models (NNH) (Tang & Zhou, 2013), to evaluate the relative significance of stochastic neutral drifts vs. deterministic niche selection in driving community assembly and shaping the diversity patterns of the breast tissue microbiome. The MSN by Harris et al (2017) is a major computational advance to Hubbell's classic UNTB because it allows for simultaneously estimation of the migrations rates among large number of sites (local communities), which was a significant computational challenge until recently.…”

Section: Introductionmentioning

confidence: 99%

“…The summary results of fittingTang & Zhou (2013) NNH (niche-neutral hybrid) model to the breast microbiomes, excerpted from Tables S3 and S4 in the OSI where the full fitting results from 1000 or 100 times of re-sampling were exhibited * J: average number of individuals per niche (local community) in each metacommunity, S: average species number per niche (local community) in each metacommunity, θ: average fundamental biodiversity parameter per niche (local community) in each metacommunity, m: average of migration coefficients, x: average of birth to death ratio, γ: average of migration rate, R 2 : goodness-of-fit index, χ 2 : c 2 -value of chi-squared test for observed value against predicted value, p-value for χ 2 -test; when p > 0.05, metacommunity satisfies NNH model. Last two columns are number and percentage of local communities (niches) that passed local neutrality test.…”

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A theoretic approach to the breast tissue microbiomes under tumor influences with near-neutral, neutral and niche-neutral hybrid models

Sam

2020

Preprint

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Background: The structure and dynamics of breast tissue microbiomes can have far-reaching influences on women’s health, particularly on breast tumor development. However, there is currently little understanding on the ecological processes that shape the structure and dynamics of breast tissue microbiomes.Methods: Here we fill the gap by applying three metacommunity models for investigating the community assembly and diversity maintenance, including Sloan near neutral model, Harris et al. multisite neutral and Tang & Zhou niche-neutral hybrid models to reanalyze the 16s-rRNA sequencing datasets of 23 healthy, 12 benign tumor, and 33 malignant tumor tissue samples. To remedy the practical difficulty in collecting tissue microbiome samples, we adopted a sophisticated random re-sampling (up to 1000 times) scheme in applying the three metacommunity models for analyzing the patterns in the breast tissue microbiomes. Results: First, we found that, at the community/metacommunity levels, the mechanisms of microbiome assembly and diversity maintenance of breast tissue microbiomes were predominantly driven by stochastic drifts of bacteria demography (division, death and dispersal of bacterial cells), whereas the deterministic selection forces such as tumor progression were insignificant. However, at species level, on average, approximately 10% and 5% species were above (positively-selected) and below (negatively-selected) neutral, respectively. Furthermore, malignant tumor may raise the positively selected species up to 17%. Second, malignant tumor appears to inhibit microbial dispersal as evidenced by lowered migration rates, compared with the migration in normal and benign tumor tissues.Conclusions: The mechanisms of microbiome assembly and diversity maintenance of breast tissue microbiomes were predominantly driven by stochastic drifts, and malignant tumor may inhibit microbial dispersal. These theoretic findings can be inspirational for further investigating the relationships between tissue microbiomes and breast tumor progression/development.

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Emergent niche structuring leads to increased differences from neutrality in species abundance distributions

Rael

D’Andrea

Barabás

et al. 2018

Ecology

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Species abundance distributions must reflect the dynamic processes involved in community assembly, but whether and when specific processes lead to distinguishable signals is not well understood. Biodiversity and species abundances may be shaped by a variety of influences, but particular attention has been paid to competition, which can involve neutral dynamics, where competitor abundances are governed only by demographic stochasticity and immigration, and dynamics driven by trait differences that enable stable coexistence through the formation of niches. Key recent studies of the species abundance patterns of communities with niches employ simple models with pre-imposed niche structure. These studies suggest that species abundance distributions are insensitive to the relative contributions of niche and neutral processes, especially when diversity is much higher than the number of niches. Here we analyze results from a stochastic population model with competition driven by trait differences. With this model, niche structure emerges as clumps of species that persist along the trait axis, and leads to more substantial differences from neutral species abundance distributions than have been previously shown. We show that heterogeneity in "between-niche" interaction strength (i.e., in the strength of competition between species in different niches) plays the dominant role in shaping the species abundances along the trait axis, acting as a biotic filter favoring species at the centers of niches. Furthermore, we show that heterogeneity in "within-niche" interactions (i.e., in the competition between species in the same niche) counteracts the influence of heterogeneity in "between-niche" interactions on the SAD to some degree. Our results suggest that competitive interactions that produce niches can also influence the shapes of SADs.

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Hybrid niche-neutral models outperform an otherwise equivalent neutral model for fitting coral reef data

Cited by 15 publications

References 35 publications

Beyond the continuum: a multi-dimensional phase space for neutral–niche community assembly

Beyond the continuum: a multi-dimensional phase space for neutral–niche community assembly

A theoretic approach to the breast tissue microbiomes under tumor influences with near-neutral, neutral and niche-neutral hybrid models

Emergent niche structuring leads to increased differences from neutrality in species abundance distributions

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