Neutral Theory Research Articles

Emergent neutrality in consumer-resource dynamics.

Neutral theory assumes all species and individuals in a community are ecologically equivalent. This controversial hypothesis has been tested across many taxonomic groups and environmental contexts, and successfully predicts species abundance distributions across multiple high-diversity communities. However, it has been critiqued for its failure to predict a broader range of community properties, particularly regarding community dynamics from generational to geological timescales. Moreover, it is unclear whether neutrality can ever be a true description of a community given the ubiquity of interspecific differences, which presumably lead to ecological inequivalences. Here we derive analytical predictions for when and why non-neutral communities of consumers and resources may present neutral-like outcomes, which we verify using numerical simulations. Our results, which span both static and dynamical community properties, demonstrate the limitations of summarizing distributions to detect non-neutrality, and provide a potential explanation for the successes of neutral theory as a description of macroecological pattern.

Consuming Worker Exploitation? Accounts and Justifications for Consumer (In)action to Modern Slavery

While research has examined the plight of vulnerable workers, the role of consumers who drive demand for slave-based services and products has been largely neglected. This is an important gap given both historical evidence of the effectiveness of 18th and 19th century anti-slavery consumer activism and recent attempts to regulate slavery through harnessing consumer power, such as the UK’s Modern Slavery Act 2015. This article draws on data from in-depth interviews with 40 consumers, to identify their understanding of modern slavery, before revealing the neutralising and legitimising techniques they use to justify their (in)action. Our findings contribute to, and extend, neutralisation theory by exploring its applicability in this unique context. We also position techniques of legitimisation as central to understanding how modern slavery is tolerated through a variety of discursive and institutional factors.

A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques.

Human gut microbiome could translocate to other tissues, and the relocation triggered by HIV/SIV infection has received increasing attention. However, the underlying mode of this translocation, whether it is deterministic or random (passive) process, is not clear, not to mention quantitative estimation of the relocation probability and rates. Using multi-tissue microbiome datasets collected from SIV-infected macaques, originally reported by Klase etal. (2015), we apply Hubbell's unified neutral theory of biodiversity (UNTB) implemented by Harris etal. (2017) in the form of multi-site neutral (MSN) model to explore the translocation mode and rates of the gut microbiome. We found that (i) The translocation from gastrointestinal tract to tissues was driven by stochastic (neutral) forces as revealed by 100% neutrality-passing rates with MSN testing; (ii) The translocation probability from gastrointestinal tract to tissues is significantly larger than the baseline dispersal rates occurring within gastrointestinal tract (0.234vs. 0.006 at the phylum level, P< 0.001). (iii) Approximately, 23% of phyla and 55% of genera were migrated from gastrointestinal tract to the tissues (liver and mesenteric lymph nodes). Our findings offer the first interpretation of the microbial translocation mode from gastrointestinal tract to tissues, and the first estimates of the translocation probability and level.

Counterbalancing the time-dependent effect on the human mitochondrial DNA molecular clock

BackgroundThe molecular clock is an important genetic tool for estimating evolutionary timescales. However, the detection of a time-dependent effect on substitution rate estimates complicates its application. It has been suggested that demographic processes could be the main cause of this confounding effect. In the present study, I propose a new algorithm for estimating the coalescent age of phylogenetically related sequences, taking into account the observed time-dependent effect on the molecular rate detected by others.ResultsBy applying this method to real human mitochondrial DNA trees with shallow and deep topologies, I obtained significantly older molecular ages for the main events of human evolution than were previously estimated. These ages are in close agreement with the most recent archaeological and paleontological records favoring the emergence of early anatomically modern humans in Africa 315 ± 34 thousand years ago (kya) and the presence of recent modern humans outside of Africa as early as 174 ± 48 thousand years ago. Furthermore, during the implementation process, I demonstrated that in a population with fluctuating sizes, the probability of fixation of a new neutral mutant depends on the effective population size, which is in better accordance with the fact that under the neutral theory of molecular evolution, the fate of a molecular mutation is mainly determined by random drift.ConclusionsI suggest that the demographic history of populations has a more decisive effect than purifying selection and/or mutational saturation on the time-dependent effect observed for the substitution rate, and I propose a new method that corrects for this effect.

Towards an improved understanding of molecular evolution: the relative roles of selection, drift, and everything in between.

A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus comprehension of historical and contemporary processes driving phenotypic change and adaptation. A fundamental difficulty lies in distinguishing sites targeted by selection from both sites linked to these targets and sites fully independent of selection. These three categories of sites necessitate attention in light of the debate over the relative importance of selection versus neutrality and the neutral theory. Modern genomic insights have proved that complex processes such as linkage, demography, and biased gene conversion complicate our understanding of the role of neutral versus selective processes in evolution. In this perspective, we first highlight the importance of the genomic and (a)biotic context of new mutations to identify the targets of natural selection. We then present mechanisms that may constrain the evolution of genomes and bias the inference of selection. We discuss these mechanisms within the two critical levels that they occur: the population level and the molecular level. We highlight that they should be taken into account to correctly distinguish sites across the genome subject to selective or non-selective forces and stress that a major current field-wide goal is to quantify the absolute importance of these mechanisms.

Neutral excitation density-functional theory: an efficient and variational first-principles method for simulating neutral excitations in molecules

We introduce neutral excitation density-functional theory (XDFT), a computationally light, generally applicable, first-principles technique for calculating neutral electronic excitations. The concept is to generalise constrained density functional theory to free it from any assumptions about the spatial confinement of electrons and holes, but to maintain all the advantages of a variational method. The task of calculating the lowest excited state of a given symmetry is thereby simplified to one of performing a simple, low-cost sequence of coupled DFT calculations. We demonstrate the efficacy of the method by calculating the lowest single-particle singlet and triplet excitation energies in the well-known Thiel molecular test set, with results which are in good agreement with linear-response time-dependent density functional theory (LR-TDDFT). Furthermore, we show that XDFT can successfully capture two-electron excitations, in principle, offering a flexible approach to target specific effects beyond state-of-the-art adiabatic-kernel LR-TDDFT. Overall the method makes optical gaps and electron-hole binding energies readily accessible at a computational cost and scaling comparable to that of standard density functional theory. Owing to its multiple qualities beneficial to high-throughput studies where the optical gap is of particular interest; namely broad applicability, low computational demand, and ease of implementation and automation, XDFT presents as a viable candidate for research within materials discovery and informatics frameworks.

Changes in the roles of spatial and environmental processes in the structuring of rodent metacommunities

We studied the role of spatial (regional) and environmental (local) processes in the structuring of rodent metacommunities in three contiguous ecoregions that share the same species pool. The two northern ecoregions are mainly affected by anthropogenic processes (agriculture and urbanization) while the southern one is mainly affected by natural processes (flood and drought pulses). Local communities were described based on the analysis of 77 samples of barn owl pellets. To identify which processes (patch dynamics, species sorting, mass effect or neutral theory) structure each metacommunity we evaluated the percentage of variance explained by space (spatial arrangement of communities) and environment (topography, climate and land cover) in three Variation Partitioning Redundancy Analyses. The percentage of variance in rodent metacommunities composition explained by space and environment was between 38 and 61%, and was significant in all three analyses. The pure space fraction was significant for two of the three ecoregions, while the pure environmental fraction was significant for all three ecoregions. The processes that structure rodent metacommunities change across the region. In all three ecoregions the species sorting played a key role, while, mass effect was a structuring factor for northern metacommunities. These results can be explained by species-specific dispersal characteristics and environmental filtering.

Proof of dispersion relations for the amplitude in theories with a compactified space dimension

The analyticity properties of the scattering amplitude in the nonforward direction are investigated for a field theory in the manifold R3,1 ⨂ S1. The theory is obtained from a massive, neutral scalar field theory of mass m0 defined in flat five dimensional spacetime upon compactification on a circle, S1. The resulting theory is endowed with a massive scalar field which has the lowest mass, m0, as of the original five dimensional theory and a tower of massive Kaluza-Klein states. We derive nonforward dispersion relations for scattering of the excited Kaluza-Klein states in the Lehmann-Symanzik-Zimmermann formulation of the theory. In order to accomplish this object, first we generalize the Jost-Lehmann-Dyson theorem for a relativistic field theory with a compact spatial dimension. Next, we show the existence of the Lehmann-Martin ellipse inside which the partial wave expansion converges. The scattering amplitude satisfies fixed-t dispersion relations when |t| lies within the Lehmann-Martin ellipse.

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.

Inhibition of competitive exclusion due to phytoplankton dispersion: a contribution for solving Hutchinson's paradox

G. E. Hutchinson raised the paradox of how a number of phytoplankton species competing for the same resources are able to coexist in a relatively isotropic environment. As a key for solving the paradox, we focused on the limiting similarity which prohibits the coexistence of similar species. We expected that the limiting similarity will be mitigated by some factors which are not represented in traditional theoretical studies but can be represented if we use a three-dimensional (3D) model. The use of a 3D model enables us to explore the limiting similarity without using the controversial assumption connecting niche overlap with the competitive exclusion in previous theoretical studies. Furthermore, while constant or no dispersion is given in theoretical studies, it is explicitly represented in a 3D model. The coexistence of similar species in 3D environments was explored by dividing a target persistent species in a quasi-equilibrium community into 80 subspecies, which were slightly different from one another at the optimum temperature for population growth. In the experiments, we found cases in which several dozens of species having nearly-overlapping niches coexist stably at a point for over 80 years. The comparison of experiments with and without dispersion by oceanic currents revealed that dispersion negates the progress of competitive exclusion or significantly delays the exclusion. The result that species having nearly-overlapping niches are able to coexist also highlights the crucial role of the specific rate in determining the number of coexisting species. If the number of coexisting species is not determined by the limiting similarity, it will be determined by the frequency of speciation events, as in the neutral theory.

The role of selection in the evolution of blindness in cave fish

AbstractThe forces driving regression of biologically functionless traits remain disputed. There is ongoing debate regarding whether selection, as opposed to disuse and neutral mutations, is involved in this process. Cave species are of particular relevance for study in this regard because in continuous darkness all traits that depend on information from light, such as eyes, dark pigmentation and certain behaviours, abruptly lose their function. Recently, strong selection driving reduction has again been proposed, which relied on modelling analyses based on assumptions such as immigration of surface alleles into the cave forms or no fitness difference existing between Astyanax surface and cave fish. The validity of these assumptions, often applied to reject neutral processes in functionless traits, is questioned in this review. Morphological variation in a trait resulting from genetic variability is typical of biologically functionless traits and is particularly notable in phylogenetically young cave species. It is the most evident indicator of loss of selection, which normally enforces uniformity to guarantee optimal functionality. Phenotypic and genotypic variability in Astyanax cave fish eyes does not derive from genetic introgression by the surface form, but from regressive mutations not being eliminated by selection. This matches well with the principles of Kimura’s neutral theory of molecular evolution.

Critical Network Structures and Medical Ecology Mechanisms Underlying Human Microbiome-Associated Diseases.

SummaryA fundamental problem in studies on human microbiome-associated diseases (MADs) is to understand the relationships between microbiome structures and health status of hosts. For example, species diversity metrics have been routinely evaluated in virtually all studies on MADs, yet a recent meta-analysis revealed that, in only approximately one-third of the cases, diversity and diseases were related. In this study, we ask whether Hubbell's neutral theory (supplemented with the normalized stochasticity ratio [NSR]) or critical microbiome network structures may offer better alternatives. Whereas neutral theory and NSR focus on stochastic processes, we use core/periphery and high-salience skeleton networks to evaluate deterministic, asymmetrical niche effects, assuming that all species or their interactions were not “born” equal and focusing on non-neutral, critical network structures. We found that properties of critical network structures are more indicative of disease effects. Finally, seven findings (mechanisms, interpretations, and postulations) regarding medical ecology mechanisms underlying MADs were summarized.

Systematic Literature Review of Information Security Compliance Behaviour Theories

The paper aims to identify behavioural theories that influence information security policies compliance behaviour. A systematic review of empirical studies from eleven online databases (ACM digital library, Emerald Insight, IEEE Xplore digital library, Springer link, Science direct, Scopus, Web of Science, Oxford academic journals, SAGE journals, Taylor & Francis and Wiley online library) are conducted. This review identified 29 studies met its criterion for inclusion. The investigated theories were extracted and analysed. Total of 19 theories have been identified and studied concerning to security policy compliance behaviour. The result indicated that the most established theories in information security compliance behaviour studies are the Theory of Planned Behavior and Protection Motivation theory. Meanwhile, General Deterrence Theory, Neutralization theory, Social Bond Theory / Social Control Theory are used moderately in this research area. Less explored theories are namely Self Determination Theory, Knowledge, Attitude, and Behavior, Social Cognitive Theory, Involvement Theory, Health belief model, Theory of Interpersonal Behavior, Extended Parallel Processing Model, Organisational Control Theory, Psychological Reactance Theory, Norm Activation Theory, Organizational Behaviour Theory, Cognitive Evaluation Theory and Extended Job Demands-Resources. The results from this review may guide the development and evaluation of theories promoting information security compliance behaviours. This will further contribute in the development of an integrated theory of information security compliance behaviour.

Patterns of association of native and exotic boring polychaetes on the southeastern Pacific coast of Chile: the combined importance of negative, positive and random interactions.

BackgroundStudies of biological invasions focus on negative interactions between exotic and native biotas, emphasizing niche overlap between species and competitive exclusion. However, the effects of positive interactions and coexistence are poorly known. In this study we evaluate the importance of positive, negative, or random species associations in explaining the coexistence of native and exotic boring polychaetes inhabiting invertebrate hosts, on the southeastern Pacific coast of Chile. We assess three hypotheses to explain the observed patterns: positive species interactions, weak competitive interactions, and competitive intransitivity.MethodologyTo assess the potential effect of competition between native and exotic polychaetes we analyzed patterns of co-occurrence of species pairs in northern and southern regions, using the metric of the probabilistic model. Since biotic interactions can affect not only native species, we also evaluated correlations between native and exotic polychaete abundance, using reduced major axis regression linear models. To assess the transitivity of competitive hierarchies we used metrics and analytical methods based on abundance matrices to estimate species competition and patch transition matrices.ResultsOn average 50% of the species pairs presented significant weak negative associations, all associated with the exotic species Polydora rickettsi; the remaining 50% had random associations, and none showed positive associations. However, the relationship of abundance between native and exotic boring polychates supports a tendency towards coexistence. At local and regional scales, we observed the presence of a transitive network competition structure, where the exotic boring polychaete, P. rickettsi was generally the dominant species.ConclusionsOur results support that native and exotic boring polychaete species coexist through weak competitive interactions. Nevertheless, the large number of random interactions observed indicates that species coexistence can be accounted for by stochastic processes, as proposed by neutral theory. Coexistence may be a frequent result of interactions between native and exotic species, although less apparent than competitive exclusion. Thus, the probabilistic point-of-view used here provides a statistical tool for evaluating coexistence as a result of exotic and native species’ interactions, an idea which has been proposed in invasion ecology, but largely lacks empirical support and methodologies for detecting underlying mechanisms. Finally, we found evidence that P. rickettsi is a successful invader by being competitively dominant, but not excluding other species.

I want it my way: Using consumerism and neutralization theory to understand students’ cyberslacking behavior

In the age of instant connectivity, it is often difficult to detach students from the Internet and technology. This study examines the role of consumerism and neutralization on the cyberslacking behavior of students in a classroom environment. This study offers a unique and integrative understanding of the impact of consumerism on neutralization behavior to understand the intention of students to use the Internet and technology in class for non-class activities. An online survey of 303 university students from United States was conducted. The study finds a positive and a significant relationship of consumerism with all the five neutralization techniques used by students to engage in cyberslacking. Except for condemnation of the condemners, the rest of the neutralization techniques were found to have a positive and a significant impact on student’s intention to engage in cyberslacking behavior. This study would extend the existing literature by expanding the concepts and theory of consumerism and neutralization to cyberslacking behavior in the classroom. The findings demonstrated several theoretical and practical implications that are discussed in the article.

Bioinformatic Detection of Positive Selection Pressure in Plant Pathogens: The Neutral Theory of Molecular Sequence Evolution in Action.

The genomes of plant pathogenic fungi and oomycetes are often exposed to strong positive selection pressure. During speciation, shifts in host range and preference can lead to major adaptive changes. Furthermore, evolution of total host resistance to most isolates can force rapid evolutionary changes in host-specific pathogens. Crop pathogens are subjected to particularly intense selective pressures from monocultures and fungicides. Detection of the footprints of positive selection in plant pathogen genomes is a worthwhile endeavor as it aids understanding of the fundamental biology of these important organisms. There are two main classes of test for detection of positively selected alleles. Tests based on the ratio of non-synonymous to synonymous substitutions per site detect the footprints of multiple fixation events between divergent lineages. Thus, they are well-suited to the study of ancient adaptation events spanning speciations. On the other hand, tests that scan genomes for local fluctuations in allelic diversity within populations are suitable for detection of recent positive selection in populations. In this review, I briefly describe some of the more widely used tests of positive selection and the theory underlying them. I then discuss various examples of their application to plant pathogen genomes, emphasizing the types of genes that are associated with signatures of positive selection. I conclude with a discussion of the practicality of such tests for identification of pathogen genes of interest and the important features of pathogen ecology that must be taken into account for accurate interpretation.

Methylation-driven model for analysis of dinucleotide evolution in genomes

BackgroundCpGs, the major methylation sites in vertebrate genomes, exhibit a high mutation rate from the methylated form of CpG to TpG/CpA and, therefore, influence the evolution of genome composition. However, the quantitative effects of CpG to TpG/CpA mutations on the evolution of genome composition in terms of the dinucleotide frequencies/proportions remain poorly understood.ResultsBased on the neutral theory of molecular evolution, we propose a methylation-driven model (MDM) that allows predicting the changes in frequencies/proportions of the 16 dinucleotides and in the GC content of a genome given the known number of CpG to TpG/CpA mutations. The application of MDM to the 10 published vertebrate genomes shows that, for most of the 16 dinucleotides and the GC content, a good consistency is achieved between the predicted and observed trends of changes in the frequencies and content relative to the assumed initial values, and that the model performs better on the mammalian genomes than it does on the lower-vertebrate genomes. The model’s performance depends on the genome composition characteristics, the assumed initial state of the genome, and the estimated parameters, one or more of which are responsible for the different application effects on the mammalian and lower-vertebrate genomes and for the large deviations of the predicted frequencies of a few dinucleotides from their observed frequencies.ConclusionsDespite certain limitations of the current model, the successful application to the higher-vertebrate (mammalian) genomes witnesses its potential for facilitating studies aimed at understanding the role of methylation in driving the evolution of genome dinucleotide composition.

From Drift to Draft: How Much Do Beneficial Mutations Actually Contribute to Predictions of Ohta's Slightly Deleterious Model of Molecular Evolution?

Since its inception in 1973, the slightly deleterious model of molecular evolution, also known as the nearly neutral theory of molecular evolution, remains a central model to explain the main patterns of DNA polymorphism in natural populations. This is not to say that the quantitative fit to data are perfect. A recent study used polymorphism data from Drosophila melanogaster to test whether, as predicted by the nearly neutral theory, the proportion of effectively neutral mutations depends on the effective population size (Ne). It showed that a nearly neutral model simply scaling with Ne variation across the genome could not alone explain the data, but that consideration of linked positive selection improves the fit between observations and predictions. In the present article, we extended the work in two main directions. First, we confirmed the observed pattern on a set of 59 species, including high-quality genomic data from 11 animal and plant species with different mating systems and effective population sizes, hence a priori different levels of linked selection. Second, for the 11 species with high-quality genomic data we also estimated the full distribution of fitness effects (DFE) of mutations, and not solely the DFE of deleterious mutations. Both Ne and beneficial mutations contributed to the relationship between the proportion of effectively neutral mutations and local Ne across the genome. In conclusion, the predictions of the slightly deleterious model of molecular evolution hold well for species with small Ne, but for species with large Ne, the fit is improved by incorporating linked positive selection to the model.

Analyzing snapshot diversity patterns with the Neutral Theory can show functional groups' effects on community assembly.

A central question of community ecology is to understand how the interplay between processes of the Neutral Theory (e.g., immigration and ecological drift) and niche-based processes (e.g., environmental filtering, intra- and interspecific density dependence) shape species diversity in competitive communities. The articulation between these two categories of mechanisms can be studied through the lens of the intermediate organizational level of "functional groups" (FGs), defined as clusters of species with similar traits. Indeed, FGs stress ecological differences among species and are thus likely to unravel non-neutral interactions within communities. Here we presented a novel approach to explore how FGs affect species coexistence by comparing species and functional diversity patterns. Our framework considers the Neutral Theory as a mechanistic null hypothesis. It assesses how much the functional diversity deviates from species diversity in communities, and compares this deviation, called the "average functional deviation," to a neutral baseline. We showed that the average functional deviation can indicate reduced negative density dependence or environmental filtering among FGs. We validated our framework using simulations illustrating the two situations. We further analyzed tropical tree communities in Western Ghats, India. Our analysis of the average functional deviation revealed environmental filtering between deciduous and evergreen FGs along a broad rainfall gradient. By contrast, we did not find clear evidence for reduced density dependence among FGs. We predict that applying our approach to new case studies where environmental gradients are milder and FGs are more clearly associated to resource partitioning should reveal the missing pattern of reduced density dependence among FGs.

Coupled wire model of Z2×Z2 orbifold quantum Hall states

We construct a coupled wire model for a sequence of non-Abelian quantum Hall states occurring at filling factors $\nu=2/(2M+q)$ with integers $M$ and even(odd) integers $q$ for fermionic(bosonic) states. They are termed $Z_2 \times Z_2$ orbifold states, which have a topological order with a neutral sector described by the $c=1$ orbifold conformal field theory (CFT) at radius $R_{\rm orbifold}=\sqrt{p/2}$ with even integers $p$. When $p=2$, the state can be viewed as two decoupled layers of Moore-Read (MR) state, whose neutral sector is described by the Ising $\times$ Ising CFT and contains a $Z_2 \times Z_2$ fusion subalgebra. We demonstrate that orbifold states with $p>2$, also containing a $Z_2 \times Z_2$ fusion algebra, can be obtained by coupling together an array of MR $\times$ MR wires through local interactions. The corresponding charge spectrum of quasiparticles is also examined. The orbifold states constructed here are complementary to the $Z_4$ orbifold states, whose neutral edge theory is described by orbifold CFT with odd integer $p$ and contains a $Z_4$ fusion algebra.