Neutral Theory Model Research Articles

Distinct strategies of the habitat generalists and specialists in the Arctic sediments: Assembly processes, co-occurrence patterns, and environmental implications

Microorganisms could be classified as habitat generalists and specialists according to their niche breadth, uncovering their survival strategy is a crucial topic in ecology. Here, differences in environmental adaptation, community assemblies, co-occurrence patterns, and ecological functions between generalists and specialists were explored in the Arctic marine sediments. Compared to specialists, generalists showed lower alpha diversity but stronger environmental adaption, and dispersal limitation contributed more to the community assembly of specialists (74 %) than generalists (46 %). Furthermore, the neutral theory model demonstrated that generalists (m = 0.20) had a higher immigration rate than specialists (m = 0.02), but specialists exhibited more complex co-occurrence patterns than generalists. Our results also found that generalists may play more important roles in C, N, S metabolism but are weaker in carbon fixation and xenobiotic biodegradation and metabolism. This study would broaden our understanding of bacterial generalists' and specialists' survival strategies, and further reveal their ecological functions in marine sediments.

Species Sorting and Neutral Theory Analyses Reveal Archaeal and Bacterial Communities Are Assembled Differently in Hot Springs.

Although the recognition of archaea as one of the three kingdoms in the tree of life has been nearly a half-century long, the comparative investigations on their ecological adaptations with bacteria have been limited. The mechanisms of their community assembly and diversity maintenance in hot springs have not been addressed. The mechanistic study is critical not only for understanding the hot-spring microbiome structure and dynamics, but also for shedding light on their evolutionary adaptations. We applied the neutral theory model and species sorting paradigm of metacommunity theory to investigate how hot-spring microbial communities were assembled, how their diversities were maintained, and how the temperature and pH influence these mechanisms. Through rigorous statistical tests based on the neutral theory and species sorting paradigm, we found (i) According to the neutral theory, archaeal and bacterial communities are assembled differently, with stochastic neutral force playing a more significant role in archaeal communities than in bacterial communities (neutrality-rate = 52.9 vs. 15.8%, p-value < 0.05). (ii) Temperature and pH account for rather limited (<10%) variations in hot-spring microbiomes based on the species sorting paradigm. The pH has more significant influences than temperature on archaeal communities, and both pH and temperature have similarly low influences on bacterial community structure. (iii) We postulate that the differences between archaea and bacteria are likely due to the longer evolutionary history and better adaptation of archaea to host spring environments.

Responses of species abundance distribution patterns to spatial scaling in subtropical secondary forests.

To quantify and assess the processes underlying community assembly and driving tree species abundance distributions(SADs) with spatial scale variation in two typical subtropical secondary forests in Dashanchong state‐owned forest farm, two 1‐ha permanent study plots (100‐m × 100‐m) were established. We selected four diversity indices including species richness, Shannon–Wiener, Simpson and Pielou, and relative importance values to quantify community assembly and biodiversity. Empirical cumulative distribution and species accumulation curves were utilized to describe the SADs of two forests communities trees. Three types of models, including statistic model (lognormal and logseries model), niche model (broken‐stick, niche preemption, and Zipf‐Mandelbrodt model), and neutral theory model, were estimated by the fitted SADs. Simulation effects were tested by Akaike's information criterion (AIC) and Kolmogorov–Smirnov test. Results found that the Fagaceae and Anacardiaceae families were their respective dominance family in the evergreen broad‐leaved and deciduous mixed communities. According to original data and random sampling predictions, the SADs were hump‐shaped for intermediate abundance classes, peaking between 8 and 32 in the evergreen broad‐leaved community, but this maximum increased with size of total sampled area size in the deciduous mixed community. All niche models could only explain SADs patterns at smaller spatial scales. However, both the neutral theory and purely statistical models were suitable for explaining the SADs for secondary forest communities when the sampling plot exceeded 40 m. The results showed the SADs indicated a clear directional trend toward convergence and similar predominating ecological processes in two typical subtropical secondary forests. The neutral process gradually replaced the niche process in importance and become the main mechanism for determining SADs of forest trees as the sampling scale expanded. Thus, we can preliminarily conclude that neutral processes had a major effect on biodiversity patterns in these two subtropical secondary forests but exclude possible contributions of other processes.

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.

Does colorectal cancer significantly influence the assembly of gut microbial communities?

Colorectal cancer (CRC) is the third commonest malignant tumor. Previous studies have revealed that the composition change of the human gut microbiome, measured by community diversity, is associated with the progression of CRC. However, a further question, whether or not the mechanism of community assembly and diversity maintenance of the gut microbiome is influenced by CRC has not been addressed. To address this question, we applied Hubbell’s neutral theory for biodiversity to reanalyze the dataset from Wang et al.’s (2012) study of the gut microbiome sampled from 46 CRC patients and 56 healthy individuals. Our reanalysis presents two important findings. Firstly, our analysis demonstrated that only around 4% (4/102) samples (in total of both the CRC and control groups) have their species abundance distribution (SAD) satisfied the prediction of the neutral theory null model. No significant difference in the number of the samples satisfying the neutral null model was detected between the healthy individuals and CRC patients, suggesting that the nature or mechanism of community assembly and diversity maintenance of the gut microbiome is not significantly influenced by CRC. That is, the stochasticity of survival, reproduction and migration of gut microbes, as implied by the neutral theory model, does not play a significant role in shaping the community assembly and diversity maintenance. We further infer that the alternative hypothesis to the neutral null model, i.e., the deterministic niche differentiations should be the driving forces that shape the assembly and diversity maintenance of the gut microbiome in both the healthy individuals and CRC patients. Secondly, although CRC does not seem to influence the nature of community assembly, we postulate that it may indirectly influence the outcome (i.e., the community composition as measured by community diversity) of the community assembly, possibly by influencing niche differentiations. This postulation is supported by our second finding: the diversity of the gut microbiome in CRC patients is significantly lower than that in the healthy individuals as demonstrated by the fundamental diversity parameter (θ) of the neutral theory model. This second finding offers an independent confirmation of the relationship between the CRC disease and diversity of the gut microbiome, about which existing studies have presented conflicting evidences. Finally, we suggest that hybrid modeling which integrates both the neutral and niche theories should be explored in future studies to further understanding of the CRC influence on the human gut microbiome.

Environmental factors and underlying mechanisms of tree community assemblages of pine-oak mixed forests in the Qinling Mountains, China

Understanding the mechanisms of assembly of tree communities is very important for restoring and managing pine-oak mixed forests in the Qinling Mountains, China, but the essential mechanisms remain largely unexplored. The objective of this research was to uncover the underlying mechanisms of species coexistence and to identify the key environmental factors influencing the tree community assemblages in these forests. We investigated tree species and 15 environmental factors of topography, soil properties, and stand development of pine-oak mixed forests at an elevation of 1000-2000 m a.s.l. in the Qinling Mountains. Six classical models for the distribution of species abundance were used to fit the observed distributions; a clustering analysis was conducted to divide the ecological species groups, and a redundancy analysis examined the relationship between species assemblages and various environmental factors. Zipf-Mandelbrot, neutral-theory, log-normal, and Zipf models performed well in fitting the patterns of species-abundance distribution in the pine-oak mixed forests, which was related to the complexity of the community structure of the forests. A special combination of the Zipf-Mandelbrot and neutral-theory models, however, best explained the mechanism of species coexistence for the forests and indicated that these forests were progressive successional communities able to maintain stable development during succession. In addition, multiple factors controlled the tree community assemblage of pine-oak mixed forests in the mountainous regions, although available potassium, slope aspect, average tree DBH, and slope position were significant environmental variables.

Distribution of species abundance of evergreen and deciduous woody plants in the evergreen broad-leaved forests at Tiantong, Zhejiang

Species abundance distribution (SAD) delineates abundance of all species sampled within a community. As one major stepping stone in understanding the community, the generation mechanisms of SAD have attracted much attention. Evergreen and deciduous plants are two types of species with distinct phenological traits and growth strategies. They widely coexist in evergreen broad-leaved forests (EBLFs). Compared to deciduous plants, evergreen species have slightly lower species richness but substantially higher abundance and basal area in the 20 ha EBLF plot at Tiantong. This study independently analyzing their SAD characteristics provided a new perspective on the understanding of species diversity maintenance in EBLFs. Therefore, in order to compare SADs and determine reasons for differences, an empirical cumulative distri·研究报告· 630 生 物 多 样 性 Biodiversity Science 第 24 卷 bution function (ECDF) was utilized to describe the SADs of evergreen and deciduous trees in Tiantong plot. A Kolmogorov-Smirnov test (K-S test) was employed to detect the significance of these differences. Additionally, three types of models, including statistic model (log-normal model and log-series model), niche model (broken-stick model and niche preemption model) and neutral theory model (metacommunity zero-sum multinomial distribution model and Volkov model), were used to fit the SAD of each lifeform. The K-S test and AIC values were applied to test the goodness of fit for each model. We found that the differences in SAD between the two life forms were not significant based on the results of the K-S test. Among the three types of models, the neutral theory model was the best fitting model, and the niche model was the poorest fit. Thus we conclude that evergreen and deciduous trees had similar SAD patterns, although they differed in species richness and abundance. However, the model fitting results were found to be a necessary but insufficient condition in understanding the maintenance mechanism of biodiversity. Hence we may only preliminarily conclude that neutral processes had a major effect on the generation of biodiversity patterns of both evergreen and deciduous trees, whereas the possible contributions made by other processes, such as niche differentiations, could not be excluded and measured by this method.

Cytoplasmic polymorphism and evolutionary history of plum cultivars: Insights from chloroplast DNA sequence variation of trnL-trnF spacer and aggregated trnL intron & trnL-trnF spacer.

We screened for polymorphisms of the non-coding region of plastid DNA in plum trees. Sequencing data from the trnL-trnF chloroplast region were used to reveal a pattern of diversity, establish phylogenetic relationships, and test the selection pressure or evolutionary demography scenario for plastome DNA. The size of the non-coding regions varied from 398 to 563 and 865 to 1084 bases pairs for the trnL-trnF spacer and combined sequences, respectively. The average GC contents were 33.8 and 34.4% in the spacer and pooled sequences, respectively. Genetic distances calculated within the plums were 0.077 and 0.254, on average, for the trnL spacer and combined sequences, respectively. The neighbor-joining trees showed clustering relationships among cultivars that were independent of their geographic origins and designations. The neutrality tests and site-frequency spectra indicated that spacer and pooled sequences fit the neutral theory model at equilibrium between mutation and genetic drift and reject the hypothesis of a recent demographic expansion. The mismatch distribution shows variation patterns, thus providing evidence of an important genetic diversity explained by an excess of intermediate variants that occurred in the sequences analyzed. Further implications of the findings with regard to plum germplasm management and its utilization in breeding programs are also discussed.

Species abundance distribution patterns of &lt;I&gt;Pinus tabulaeformis&lt;/I&gt; forest in Huoshan Mountain of Shanxi Province, China

Aims Determination of species abundance distribution is important in research on species diversity. Our major objective was to determine species abundance distribution models to advance understanding of distribution mechanisms and to assist preservation of biological diversity. Methods Based on data collected from field surveys, we examined the species abundance patterns of tree, shrub and herb layers in Pinus tabulaeformis forest in Huoshan Mountain, Shanxi Province. We used niche preemption (NPM), broken stick (BSM) and overlapping niche (ONM) models and two species abundance statistical models (log-series distribution model (LSD) and log-normal distribution model (LN)) and neutral theory model (NT). The simulation effects were verified by Chi-square tests, Likelihood-ratios (L-R) tests, Kolmogorov-Smirnov (K-S) tests and Akaike Information Criterion (AIC). Important findings The best niche model for the tree layer is NPM, because it had the smallest AIC value and no significant difference (p > 0.05) between the theory predictions and observed species abundance distributions. The next best is ONM; BSM does not fit the tree layer. All three niche models are suitable for the shrub layer. ONM is the best for the herb layer, followed by BSM and NPM. LSD is good for understanding distribution mechanisms in Pinus tabulaeformis forest. LN can fit both the herb and shrub layers, but not the tree layer. NT cannot explain any layer. These findings indicate that the community has relatively few dense species and more sparse species, the species richness and diversity indices of the tree and shrub layers are much smaller than those of the herb layer, and the community evenness is relatively smaller. We conclude that one model cannot fit differ- ent data but that more than one model can fit the same data even for the same layer. Therefore, we should choose different models to study the species abundances of forest communities. We suggest that these methods might be useful for the protection of the biodiversity of forest dominated by Pinus tabulaeformis.

TOWARD A SELECTION THEORY OF MOLECULAR EVOLUTION

The Neutral Theory Models describing the dynamics of genetic variants with no effect on fitness—so-called neutral models—have been around almost as long as the field of population genetics (Fisher 1922; Wright 1931). Decades after the first models were introduced Motoo Kimura gave a complete description of the dynamics of neutral mutations in finite populations, using mathematical tools borrowed from particle physics (Kimura 1955). Although the elegance of this and other results from Kimura and colleagues were uncontested, their applicability to data seemed remote until experiments revealed enormous amounts of molecular genetic variation, both within and between species (Zuckerkandl and Pauling 1965; Harris 1966; Lewontin and Hubby 1966). The observed levels of variation appeared inconsistent with models that proposed selective effects for all or most mutations, and what has become known as the Neutral Theory of Molecular Evolution was born (Kimura 1968; King and Jukes 1969; Kimura and Ohta 1971). Despite contentious argument over the validity of the Neutral Theory (Kimura 1983; Gillespie 1991), it has become the predominant framework for research in population genetics and molecular evolution for almost 40 years. Increasingly complex models describing the expected patterns of variation within and between species allow researchers to ask about the evolutionary processes acting in nature, both at single loci and in increasingly large datasets encompassing all or most genes in a genome. The Neutral Theory provides a theoretical basis for understanding DNA variation with clear, testable hypotheses and an array of statistical tools that distinguish natural selection from random genetic drift (Kreitman 2000; Nielsen 2001; Hahn 2007). However, the recent paper by Begun and colleagues (Begun et al. 2007) should finally begin to change people’s view of this scientific paradigm. Although results inconsistent with the Neutral Theory have been mounting for some time (see below), the field has continued to use it as a foundation for understanding the molecular world. As the first true “population genomic” dataset, the results of Begun et al. force us to see that the central predictions of the Neutral Theory do not hold in natural populations. Far from just the half-caught glimpses of nonneutral evolution afforded by studies of limited numbers of loci, by sequencing the whole genomes of multiple lines of Drosophila simulans this work should cause a major shift in how we interpret DNA variation within populations and among species. As the conclusions of this article are appropriately cautious with respect to the implications of the work, I will use this essay to provide a wider view of the importance of these results and a synthesis with previous results. To do this I will address the two major tenets of the Neutral Theory, and how increasing amounts of data are showing that these claims and their attendant predictions do not hold for the vast majority of genes and species. I also argue that the implications of our continued use of neutral models are dire—at

Neutral theory models ofS-wave π-π scattering fulfilling rigorous conditions

Neutral theory models ofS-wave π-π scattering fulfilling rigorous conditions