Neutral Theory Research Articles

Non-Equilibrium ϕ4 theory for networks: towards memory formations with quantum brain dynamics

We investigate the time evolution of quantum fields in neutral scalar ϕ4 theory for open systems with the central region and the multiple reservoirs (networks) as a toy model of quantum field theory of the brain. First we investigate the Klein–Gordon (KG) equations and the Kadanoff–Baym (KB) equations in open systems in d + 1 dimensions. Next, we introduce the kinetic entropy current and provide the proof of the H-theorem for networks. Finally, we solve the KG and the KB equations numerically in spatially homogeneous systems in 1 + 1 dimensions. We find that decoherence, entropy saturation and chemical equilibration all occur during the time evolution in the networks. We also show how coherent field transfer takes place in the networks.

Modeling community assembly on growing habitat “islands”: a case study on trees and their vascular epiphyte communities

The number of available sites for establishment is a key determinant of species richness on habitat islands. While most theoretical studies assume habitat size or capacity to be constant, many natural habitats are characterized by dynamic growth in capacity over ecological timescales. A case in point is provided by trees that serve as habitat for vascular and non-vascular epiphytes. Here, we develop a modeling framework, based on neutral theory, to address the effects of habitat growth on community development, i.e., species richness and abundance. The model is parameterized to the situation of vascular epiphyte communities in tropical lowland forests and includes stochastic reproduction, death, and immigration events from a larger metacommunity. Using numerical simulations, we explore the proportion of growing sites occupied by individuals, the number of empty unoccupied sites, as well as changes in species abundances, species richness, colonization and extinction rates, and the dependence on the abundance in the metacommunity throughout the growth of the habitat. Our analysis suggests two characteristic phases of community development in a growing habitat: (i) an initial phase, characterized by a rapid buildup of empty sites, a slow increase in species abundance, and a fast increase in species richness, and (ii) a second phase, in which the number of empty sites reaches an equilibrium, species richness is accumulating very slowly, while the number of individuals increases unabatedly with habitat capacity.

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.

Bulklike band-offset mystery solved through energy minimization: Lessons from perovskite oxide heterojunctions

The formation of band offset (BO) at isovalent semiconductor heterojunctions has been branded ``bulklike'' because of an insensitivity of the BO to the interface orientation and atomic structure and a transitivity in BOs. Even though tunability and nontransitivity of BO are frequently found for heterovalent interfaces, empirical theories with built-in bulklike characteristics have thus far dominated the explanation of experimental BOs. Presently, the distribution of charge density and the formation of BO at a large number of interfaces between lattice-matched perovskite oxides are studied in detail using density functional theory. Ionic screening is found to dominate the formation of the BO, as a sharp dependence of the (apparently tunable) BO on atomic structure for unrelaxed interfaces is essentially washed out upon lattice relaxation. Numerical experimentation with deliberate embedding of dipolar layers in perovskite oxides and their interfaces corroborates the effectiveness of ionic screening. The relaxed, converged (bulklike) BOs are found to be in good agreement with the prediction of the neutral polyhedra theory (NPT). The success of the NPT, presently for ionic interfaces and previously for covalent zinc-blende interfaces, unmasks a possible connection between the partition into neutral symmetric cells and the energy-minimization requirement on the interface charge distribution. The independence of the BO on interface specifics, i.e., bulklike behavior, is shown to stem directly from such a property of charge distribution with minimized electrostatic energy. As energy minimization governs the formation of charge distribution in general, NPT is expected to describe the band offset of a wide variety of material interfaces.

A simple spatially explicit neutral model explains the range size distribution of reef fishes

AbstractAimThe great variation in range sizes among species has fascinated ecologists for decades. Reef‐associated fish species live in highly spatially structured habitats and adopt a wide range of dispersal strategies. We consequently expect species with greater dispersal ability to occupy larger ranges. However, empirical evidence for such a positive relationship between dispersal and range size remains scarce. Here, we unveil the role of dispersal on the range size distribution of reef‐associated fishes using empirical data and a novel spatially explicit model.LocationTropical Eastern Pacific.Major taxa studiedReef‐associated fishes.Time periodUnderlying records are from the 20th and 21st centuries.MethodsWe estimated range size distributions for all reef‐associated fishes separated into six guilds, each with different dispersal abilities. We used a one‐dimensional spatially explicit neutral model, which simulates the distribution of species along a linear and contiguous coastline, to explore the effect of dispersal, speciation and sampling on the distribution of range sizes. Our model incorporates biologically important long‐distance dispersal events with a fat‐tailed dispersal kernel and also adopts a more realistic gradual “protracted” speciation process than originally used in neutral theory. We fitted the model to the empirical data using an approximate Bayesian computation approach, with a sequential Monte Carlo algorithm.ResultsStochastic birth, death, speciation and dispersal events alone can accurately explain empirical range size distributions for six different guilds of tropical, reef‐associated fishes. Variation in range size distributions among guilds are explained purely by differences in dispersal ability with the best dispersers being distributed over larger ranges.Main conclusionsNeutral processes and guild‐specific dispersal ability provide a general explanation for both within‐ and across‐guild range size variation. Our results support the theoretically expected, but empirically much debated, hypothesis that high dispersal capacity promotes the establishment of large range size.

Modelling incomplete neutralisation with weighted phonetic constraints

Incomplete neutralisation presents a problem for classical modular feed-forward grammars: it results in surface phonetic distinctions between phonologically neutralised segments. This paper argues for a model of incomplete neutralisation using two independently motivated theoretical devices: paradigm uniformity and weighted phonetic constraints. A case study is presented, showing that Japanese monomoraic lengthening results in incomplete neutralisation: when monomoraic nouns with short vowels are lengthened to fill a bimoraic minimality requirement, they reach a duration intermediate between that of unlengthened short vowels and underlyingly long vowels. The Japanese case has properties distinct from other classically cited examples of incomplete neutralisation such as final devoicing, which are not predicted by previous theories of neutralisation. The Weighted Paradigm Uniformity theory of incomplete neutralisation is shown to make four unique predictions, and is argued to better capture the typology of incomplete neutralisation.

Spatial scale modulates the inference of metacommunity assembly processes.

The abundance and distribution of species across the landscape depend on the interaction between local, spatial, and stochastic processes. However, empirical syntheses relating these processes to spatiotemporal patterns of structure in metacommunities remain elusive. One important reason for this lack of synthesis is that the relative importance of the core assembly processes (dispersal, selection, and drift) critically depends on the spatial grain and extent over which communities are studied. To illustrate this, we simulated different aspects of community assembly on heterogeneous landscapes, including the strength of response to environmental heterogeneity (inherent to niche theory) vs. dispersal and stochastic drift (inherent to neutral theory). We show that increasing spatial extent leads to increasing importance of niche selection, whereas increasing spatial grain leads to decreasing importance of niche selection. The strength of these scaling effects depended on environment configuration, dispersal capacity, and niche breadth. By mapping the variation observed from the scaling effects in simulations, we could recreate the entire range of variation observed within and among empirical studies. This means that variation in the relative importance of assembly processes among empirical studies is largely scale dependent and cannot be directly compared. The scaling coefficient of the relative contribution of assembly processes, however, can be interpreted as a scale-integrative estimate to compare assembly processes across different regions and ecosystems. This emphasizes the necessity to consider spatial scaling as an explicit component of studies intended to infer the importance of community assembly processes.

A neutral evolution test derived from a theoretical amino acid substitution model

A neutral evolution model that explicitly considers codons, amino acids, and the degeneracy of the genetic code is developed. The model is built from nucleotides up to amino acids, and it represents a refinement of the neutral theory of molecular evolution. The model is based on a stochastic process that leads to a stationary probability distribution of amino acids. The latter is used as a neutral test of evolution. We provide some examples for assessing the neutrality test for a small set of protein sequences. The Jukes-Cantor model is generalized to deal with amino acids and it is compared with our neutral model, along with the empirical BLOSUM62 substitution model. The neutral test provides a baseline to which the evolution of any protein can be analyzed, and it clearly helps in discerning putative amino acids with unexpected frequencies that might be under positive or negative selection. Our model and neutral test are as universal as the standard genetic code.

Functional traits of acquisitive invasive woody species differ from conservative invasive and native species

One of the most important sources of invasiveness is species’ functional traits and their variability. However there are still few studies on invasive tree species traits conducted along resource gradients that allow for a comparison of acquisitive and conservative strategies. We aimed to assess the differences in trait variation among native alien conservative and alien acquisitive tree species along resource availability gradients (soil fertility and light availability) and to assess the traits variability of the species studied along resources availability gradients. Our study compared invasive tree species in Europe (Prunusserotina Ehrh. Quercusrubra L. and Robiniapseudoacacia L.) with their native competitors (Acerpseudoplatanus L. A.platanoides L. Quercuspetraea (Matt.) Liebl. and Fagussylvatica L.). The study was conducted on 1329 seedlings and saplings collected in a system of 372 study plots in W Poland. For each individual we assessed leaf stem and root mass ratios total biomass leaf area ratio specific leaf area and projected leaf area. Two invasive species (P.serotina and R.pseudoacacia) represented a more acquisitive strategy than native species – along litter pH and light availability gradients these species had higher leaf mass fraction specific leaf area and leaf area ratio. In contrast Q.rubra had the highest total biomass and root mass fraction. Alien species usually had higher coefficients of variation of studied traits. This suggests that relatively high projected leaf area as a way of filling space and outcompeting native species may be reached in two ways – biomass allocation to leaves and control of leaf morphology or by overall growth rate. High variability of invasive species traits also suggests randomness in seedling survival which similarly to the neutral theory of invasion highlights the necessity of including randomness in modelling biological invasions.

The gut microbiota heterogeneity and assembly changes associated with the IBD

Inflammatory bowel disease (IBD) is an immunologically mediated disease and may be caused by abnormal immunological response to gut microbes. Although several studies on the ecological changes associated with IBD, such as community diversities, were reported, no previous studies have investigated the changes in the spatial heterogeneity and the mechanism of community assembly of the gut microbiota associated with IBD. In the present study, we first applied the Taylor’s power law extensions to compare the community spatial heterogeneity between the gut microbial communities of the IBD patients and those of the healthy individuals. We found that the community spatial heterogeneity of gut microbiota in IBD patients is slightly lower than in the healthy individuals. This finding suggests that IBD may lower the spatial heterogeneity of gut microbiota, possibly via lowering the abundance of dominant species. We further applied the neutral theory of biodiversity to comparatively investigate the community assembly and diversity maintenance of the gut microbiota with and without IBD, and our application suggested that deterministic factors such as host immunity should be dominant forces shaping gut microbiota assembly, and diseases such as IBD may not be strong enough to change the trend set by the deterministic host factors.

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes

BackgroundThe nearly neutral theory of molecular evolution predicts that the efficacy of natural selection increases with the effective population size. This prediction has been verified by independent observations in diverse taxa, which show that life-history traits are strongly correlated with measures of the efficacy of selection, such as the dN/dS ratio. Surprisingly, avian taxa are an exception to this theory because correlations between life-history traits and dN/dS are apparently absent. Here we explore the role of GC-biased gene conversion on estimates of substitution rates as a potential driver of these unexpected observations.ResultsWe analyze the relationship between dN/dS estimated from alignments of 47 avian genomes and several proxies for effective population size. To distinguish the impact of GC-biased gene conversion from selection, we use an approach that accounts for non-stationary base composition and estimate dN/dS separately for changes affected or unaffected by GC-biased gene conversion. This analysis shows that the impact of GC-biased gene conversion on substitution rates can explain the lack of correlations between life-history traits and dN/dS. Strong correlations between life-history traits and dN/dS are recovered after accounting for GC-biased gene conversion. The correlations are robust to variation in base composition and genomic location.ConclusionsOur study shows that gene sequence evolution across a wide range of avian lineages meets the prediction of the nearly neutral theory, the efficacy of selection increases with effective population size. Moreover, our study illustrates that accounting for GC-biased gene conversion is important to correctly estimate the strength of selection.

Entitled to Embezzlement? The Case of Successful Executives Working for Rich Heirs

ABSTRACTIn family firms, there is a distinction between family members and nonfamily members. Research reviewed in this article indicates that family firms tend to be operated to enhance the well-being of owning families and their members. Nonfamily executives are often treated as second-class individuals in the organization. There is an asymmetrical distribution of power among family and nonfamily. From the theory of convenience, we apply equity theory in the motivational dimension, principal–agent theory in the opportunity dimension, and neutralization theory in the willingness dimension to shed light on deviant behaviors by nonfamily executives in family firms. We present two case studies from Norway – a former CEO and a former CFO in family firms – who both were sentenced to prison for embezzlement.

Multivariate morphometrics, quantitative genetics, and neutral theory: Developing a "modern synthesis" for primate evolutionary morphology.

Anthropologists are increasingly turning to explicit model-bound evolutionary approaches for understanding the morphological diversification of humans and other primate lineages. Such evolutionary morphological analyses rely on three interconnected conceptual frameworks; multivariate morphometrics for quantifying similarity and differences among taxa, quantitative genetics for modeling the inheritance and evolution of morphology, and neutral theory for assessing the likelihood that taxon diversification is due to stochastic processes such as genetic drift. Importantly, neutral theory provides a framework for testing more parsimonious explanations for observed morphological differences before considering more complex adaptive scenarios. However, the consistency with which these concepts are applied varies considerably, which mirrors some of the theoretical obstacles faced during the "modern synthesis" of classical population genetics in the early 20th century. Here, each framework is reviewed and some potential stumbling blocks to the full conceptual integration of multivariate morphometrics, quantitative genetics, and neutral theory are considered.

Quantifying the Scientific Cost of Ambiguous Terminology in Community Ecology

Fundamental terms in the field of ecology are ambiguous, with multiple meanings associated with them. While this could lead to confusion, discord, or even tests that violate core assumptions of a given theory or model, this ambiguity could also be a feature that allows for new knowledge creation through the interconnected nature of concepts. We approached this debate from a quantitative perspective, and investigated the cost of ambiguity related to definitions of ecological units in ecology related to the general term “community.” We did a meta-analysis of tests associated with two bodies of literature, Hubbell’s unified neutral theory of biodiversity and biogeography and Diamond’s assembly rules, that rely on a specific ecological unit that assumes that species are existing within a local area and that they have overlapping resource needs. We predicted that if ambiguous terminology is widespread, then researchers will have tested them with many different ecological units, that in addition some of these ecological units will violate the core assumptions of the theory, and finally that the overall level of support for a theory will be stronger if appropriate ecological units were used. We found that indeed multiple different ecological units were used in the literature to test both theories, with 65 percent appropriate ecological units for neutral theory tests, and only 6 percent for assembly rule tests. Finally, there was some evidence that the support for a theory depended on whether appropriate ecological units were used for neutral tests, but there was not enough data for the assembly rule tests. These results thus show that ambiguous terminology in ecology is having measurable effects on research and is not of solely philosophical concern. We advocate that authors be explicit in their writing and outline core assumptions of theories, that researchers apply these consistently in their tests, and that readers be attentive to what is written and cognizant of their potential biases.

The Aims and Structures of Ecological Research Programs

Neutral Theory is controversial in ecology. Ecologists and philosophers have diagnosed the source of the controversy as: its false assumption that individuals in different species within the same trophic level are ecologically equivalent, its conflict with Competition Theory and the adaptation of species, its role as a null hypothesis, and as a Lakatosian research programme. In this paper, I show why we should instead understand the conflict at the level of research programs which involve more than theory. The Neutralist and Competitionist research programs borrow and construct theories, models, and experiments for various aims and given their home ecological systems. I present a holistic and pragmatic view of the controversy that foregrounds the interrelation between many kinds of practices and decisions in ecological research.

Fractal analysis of flavonoids in complex chemical compositions in extracts of Chamaedaphne calyculata (L.) Moench (ericaceae) in oligotrophic swamps of Western Siberia

Evaluated the possibility of organizing the biosynthesis of plant adaptogens-flavonoids from the standpoint of the theory of neutrality. We assumed that the biosynthesis of flavonoids and low-molecular compounds with similar physicochemical properties is neutral with respect to microfluctuations of environmental conditions. Leaf extracts Chamaedaphne calyculata (L.) Moench from natural populations oligotrophic swamps the Middle Ob region (Western Siberia) was studied by method HPLC-high performance liquid chromatography. The samples to carry out the HPLC analyses were taken in ecologically equivalent swamp areas. Chromatograms differed in the number of peaks, the time of their release, and the area of particular peaks. The hierarchy constructing procedure from single up to combined chromatograms, where peaks from 1, 2, 3, 5, and 9 chromatograms were placed on the common time scale of the peaks release, was carried out for fractal analysis. The number of peaks varied from 21-30 in particular chromatograms up to 76 peaks in a generalized united chromatogram. The complex of calculation procedures has shown that all chromatograms obtained from Chamaedaphne calyculata plants are stochastic fractals, where the independent variables are the number, the size (area) and release time of each particular peak. In the presence of the fractal properties of the flavonoid system, it is necessary to analyze the possibility of implementing both neutral and deterministic variants of the synthesis of this or that flavonoid.

Implications of Two Opposing Variations of Neutral Theory

This letter discusses the difference between neutral theory as an observation of present evolutionary dynamics compared to neutral theory as a more-or-less comprehensive theory of evolution. The letter suggests that prior information, not neutral evolution itself, creates the patterns in the genome in ways that make the dynamics described by neutral theory possible in modern organisms.

Neutral technical progress and the measure of value: along the Kaldor–Kennedy line

Abstract In this paper, I investigate the question of ‘the effect of progress upon distribution’ based on the analyses of Hicks, Robinson, Harrod, Salter, Kaldor, Samuelson and Kennedy. The paper aims to address a neglected and controversial theoretical argument on neutral technical progress related to the measure of value that preceded and then continued to the period of the Cambridge Capital Theory Controversy. I focus on Kennedy’s writings and his solutions to the complications between the measure of value and technical progress. Important intuitions behind the measure of value are crucial to the formulation of neutral technical progress in both the post-Keynesian and the neoclassical-Keynesian endogenous growth models. The paper concludes with mathematical illustrations of neutral technical progress theories.

Does God roll dice? Neutrality and determinism in evolutionary ecology

A tension between perspectives that emphasize deterministic versus stochastic processes has sparked controversy in ecology since pre-Darwinian times. The most recent manifestation of the contrasting perspectives arose with Hubbell’s proposed “neutral theory”, which hypothesizes a paramount role for stochasticity in ecological community composition. Here we shall refer to the deterministic and the stochastic perspectives as the niche-based and neutral-based research programs, respectively. Our goal is to represent these perspectives in the context of Lakatos’ notion of a scientific research program. We argue that the niche-based program exhibits all the characteristics of a robust, progressive research program, including the ability to deal with disconfirming data by generating new testable predictions within the program. In contrast, the neutral-based program succeeds as a mathematical tool to capture, as epiphenomena, broad-scale patterns of ecological communities but appears to handle disconfirming data by incorporating hypotheses and assumptions from outside the program, specifically, from the niche-based program. We conclude that the neutral research program fits the Lakatosian characterization of a degenerate research program.

Degeneracy and genetic assimilation in RNA evolution

BackgroundThe neutral theory of Motoo Kimura stipulates that evolution is mostly driven by neutral mutations. However adaptive pressure eventually leads to changes in phenotype that involve non-neutral mutations. The relation between neutrality and adaptation has been studied in the context of RNA before and here we further study transitional mutations in the context of degenerate (plastic) RNA sequences and genetic assimilation. We propose quasineutral mutations, i.e. mutations which preserve an element of the phenotype set, as minimal mutations and study their properties. We also propose a general probabilistic interpretation of genetic assimilation and specialize it to the Boltzmann ensemble of RNA sequences.ResultsWe show that degenerate sequences i.e. sequences with more than one structure at the MFE level have the highest evolvability among all sequences and are central to evolutionary innovation. Degenerate sequences also tend to cluster together in the sequence space. The selective pressure in an evolutionary simulation causes the population to move towards regions with more degenerate sequences, i.e. regions at the intersection of different neutral networks, and this causes the number of such sequences to increase well beyond the average percentage of degenerate sequences in the sequence space. We also observe that evolution by quasineutral mutations tends to conserve the number of base pairs in structures and thereby maintains structural integrity even in the presence of pressure to the contrary.ConclusionsWe conclude that degenerate RNA sequences play a major role in evolutionary adaptation.