Neutral Theory Research Articles

Reproduction, development, asymmetry and late eye regression in the Brazilian cave catfish Ituglanis passensis (Siluriformes, Trichomycteridae): evidence contributing to the neutral mutation theory

The troglobitic (exclusively subterranean source population) catfish Ituglanis passensis (Siluriformes, Trichomycteridae) is endemic to the Passa Três Cave, São Domingos karst area, Rio Tocantins basin, Central Brazil. This unique population presents variably reduced eyes and melanic pigmentation. We describe reproduction and early development in this species based on a spontaneous (non-induced) reproductive-event that occurred in the laboratory in January–February, 2009, while simultaneously comparing with data from the cave-habitat and a previous reproductive event. Egg laying was parceled. Egg-size and number were within variations observed in epigean congeners. Larvae behavior and growth is described. A single surviving specimen was monitored over two years. Eye-regression started late, one year after birth, and followed a pattern of stasis phases intercalated with slow growth and fluctuating asymmetric rates. Late eye regression, associated with asymmetry in eye development and intra-population variability of troglomorphic traits, as shown by several Brazilian subterranean fishes, provide support for the Neutral Mutation Theory.

The Shape of Species Abundance Distributions Across Spatial Scales

Species abundance distributions (SADs) describe community structure and are a key component of biodiversity theory and research. Although different distributions have been proposed to represent SADs at different scales, a systematic empirical assessment of how SAD shape varies across wide scale gradients is lacking. Here, we examined 11 empirical large-scale datasets for a wide range of taxa and used maximum likelihood methods to compare the fit of the logseries, lognormal, and multimodal (i.e., with multiple modes of abundance) models to SADs across a scale gradient spanning several orders of magnitude. Overall, there was a higher prevalence of multimodality for larger spatial extents, whereas the logseries was exclusively selected as best fit for smaller areas. For many communities the shape of the SAD at the largest spatial extent (either lognormal or multimodal) was conserved across the scale gradient, despite steep declines in area and taxonomic diversity sampled. Additionally, SAD shape was affected by species richness, but we did not detect a systematic effect of the total number of individuals. Our results reveal clear departures from the predictions of two major macroecological theories of biodiversity for SAD shape. Specifically, neither the Neutral Theory of Biodiversity (NTB) nor the Maximum Entropy Theory of Ecology (METE) are able to accommodate the variability in SAD shape we encountered. This is highlighted by the inadequacy of the logseries distribution at larger scales, contrary to predictions of the NTB, and by departures from METE expectation across scales. Importantly, neither theory accounts for multiple modes in SADs. We suggest our results are underpinned by both inter- and intraspecific spatial aggregation patterns, highlighting the importance of spatial distributions as determinants of biodiversity patterns. Critical developments for macroecological biodiversity theories remain in incorporating the effect of spatial scale, ecological heterogeneity and spatial aggregation patterns in determining SAD shape.

On the Unfounded Enthusiasm for Soft Selective Sweeps III: The Supervised Machine Learning Algorithm That Isn't.

In the last 15 years or so, soft selective sweep mechanisms have been catapulted from a curiosity of little evolutionary importance to a ubiquitous mechanism claimed to explain most adaptive evolution and, in some cases, most evolution. This transformation was aided by a series of articles by Daniel Schrider and Andrew Kern. Within this series, a paper entitled “Soft sweeps are the dominant mode of adaptation in the human genome” (Schrider and Kern, Mol. Biol. Evolut. 2017, 34(8), 1863–1877) attracted a great deal of attention, in particular in conjunction with another paper (Kern and Hahn, Mol. Biol. Evolut. 2018, 35(6), 1366–1371), for purporting to discredit the Neutral Theory of Molecular Evolution (Kimura 1968). Here, we address an alleged novelty in Schrider and Kern’s paper, i.e., the claim that their study involved an artificial intelligence technique called supervised machine learning (SML). SML is predicated upon the existence of a training dataset in which the correspondence between the input and output is known empirically to be true. Curiously, Schrider and Kern did not possess a training dataset of genomic segments known a priori to have evolved either neutrally or through soft or hard selective sweeps. Thus, their claim of using SML is thoroughly and utterly misleading. In the absence of legitimate training datasets, Schrider and Kern used: (1) simulations that employ many manipulatable variables and (2) a system of data cherry-picking rivaling the worst excesses in the literature. These two factors, in addition to the lack of negative controls and the irreproducibility of their results due to incomplete methodological detail, lead us to conclude that all evolutionary inferences derived from so-called SML algorithms (e.g., S/HIC) should be taken with a huge shovel of salt.

Asking the Wrong Question in Explaining Tropical Diversity

Enhancement of plant diversity via the Janzen-Connell mechanism is often measured relative to neutral models that ignore species' competitive differences. Recent modelling indicates this mechanism is ineffective when included in models incorporating species' demographic variations. This suggests we have been asking the wrong questions when measuring the effectiveness of diversity-enhancing mechanisms.

Circumglobal distribution of fish environmental DNA in coral reefs

Coral reefs host the highest fish diversity on Earth despite covering less than 0.1% of the ocean’s seafloor. At the same time they are also extremely threatened. Data syntheses over decades of surveys estimate the total number of coral reef fishes to vary from 2,400 to 8,000 species distributed among roughly 100 families. But this diversity remains largely unknown. Here, we investigated how environmental DNA (eDNA) could describe the distribution of fish diversity in coral reefs. We generated 504,457,267 raw 12S ribosomal DNA (rDNA) sequence reads from 251 samples (2,693 PCR replicates) collected at 25 sites in 145 stations covering five regions across the Indian, Pacific and Atlantic Oceans. Bioinformatic analysis clustered these sequences into 2,160 molecular operational taxonomic units (MOTUs) corresponding to distinct species (Marques 2020) We compared our results, with visual census surveys from Reef Life Survey, on 2,813 transects in tropical regions. Our outcomes demonstrate the capacity of eDNA metabarcoding from water samples to reconstruct well-known biogeographic patterns of fish diversity on coral reefs, such as species richness gradients towards the coral triangle, and family proportion stability across sites (Bellwood and Hughes 2001). Additionally, eDNA survey data documented a higher fish species (16%) and family (50%) diversity than estimates obtained with underwater visual surveys carried out on 20 times more sites. MOTU richness per family retrieved with eDNA closely matched fish species richness within families recorded in visual census data. However, eDNA revealed higher richness of reef-associated species and species from adjacent habitats, of cryptobenthic or nocturnal species, but also of pelagic and wide-ranging species. eDNA survey data showed that fish diversity is characterized by spatially heterogeneous species assemblages among regions, with more dissimilarity among adjacent coral reefs than detected with visual survey data. Unlike visual surveys, eDNA metabarcoding revealed the same prevalence of rarity as expected under the neutral theory of biodiversity, suggesting the predominance of random processes and ecological equivalence within trophic groups at large scale to explain fish biodiversity patterns on coral reefs. Our study demonstrates how sequencing eDNA from water provides a rapid and effective approach to characterize and assess coral reef diversity across large spatial scales, thereby also uncovering hidden biodiversity patterns.

Very large-scale gap distances of atmospheric pressure dielectric barrier glow discharge using semiconductor materials

Very large-scale gap distances of atmospheric pressure dielectric barrier discharge (DBD) in glow mode are obtained through semiconductor materials. The maximum value of the gap distance is up to 70 mm. Based on the feature of the cathode sheath, Auger neutralization theory, the trapped electron and the accumulated charge in the DBD system, the secondary electron emission is one of the primary reasons for very large-scale gap distances of the DBD to produce glow discharge. Furthermore, the contribution of the effective capacitance, the gas voltage and the discharge power are also discussed. Significant for the research are the development and the practical applications of atmospheric pressure glow discharge in the DBD with very large-scale gap distances.

Self-deception as a technique of neutralisation: an analysis of the subjective account of a white-collar criminal

Neutralisation theory suggests that wrongdoers will rationalise their wrongdoing in such a way that allows them to maintain their views of themselves as moral law-abiding people. Though regularly applied since it first emerged as an aspect of differential association theory, it has rarely been extended beyond its original conceptualisation. Moreover, scholars rarely consider the subjective belief systems of criminals or their own accounts of their wrongdoing, when applying this theory. This is particularly true of white-collar criminals where there is a dearth of scholarship analysing how they respond to their own criminality. This article addresses these criticisms by analysing how self-deception may operate as a technique of neutralisation for white-collar criminals, anchoring and applying this extension in a specific case study on white-collar crime, from the subjective perspective of the criminal. It analyses the case of Kareem Serageldin, often considered the only banker jailed in the US for having some role in causing the financial crisis. The Serageldin case is used as a lens to extend and apply neutralisation theory in the field of white-collar crime, exploring how Serageldin distorted the facts of his wrongdoing, deceiving both himself and the court, to minimise his responsibility for his crime.

Rare prokaryotic sub-communities dominate the complexity of ecological networks and soil multinutrient cycling during long-term secondary succession in China's Loess Plateau

Unraveling the succession of microbial communities is a core ecological research topic. Yet few studies have focused on how long-term secondary succession affects the functional profiles and ecological processes of abundant and rare microbial subcommunities. Here, we used amplicon sequencing and GeoChip analysis to explore the ecological functions of abundant and rare biospheres and their correlation with soil multinutrient cycling. Samples for this study were collected from a well-established secondary succession chronosequence that spans >30 years of dryland ecosystem development on the Loess Plateau of China. Although both abundant and rare subcommunities shifted with succession, the changing of beta-diversity of the microbial communities was primarily driven by species replacement of the rare biosphere. Phylogenetic changes of abundant and rare taxa were associated with their functional traits, which dominated the diversity-related selection along all succession ages. Neutral theory analysis indicated that the assemblage of abundant taxa over all successional ages was regulated by dispersal homogenizing and ecological drift. The null model revealed that homogeneous and variable selection were the dominant assembly processes for rare subcommunities compared with abundant species. pH and nitrogen content were the paramount drivers determining the assembly of microbial communities and functional genes, consistent with the importance of environmental filtering. Furthermore, the rare biosphere had a paramount role in the entire ecological network and was the major driver for most soil processes such as C, N, and S cycling. Nonetheless, a significant portion of soil P cycling was regulated by abundant taxa. Collectively, our study provides insight into the mechanisms underlying microbial community assembly and soil microbe-driven functional changes in biogeochemical processes during secondary succession.

From NiSi2 experiments to density functional theory calculations: How the Schottky barrier mystery was solved

A cloud of mystery hung over the formation mechanism of the Schottky barrier height (SBH) for many decades. The experimental discovery of an insensitivity of the SBH of polycrystalline metal-semiconductor (MS) interfaces to the metal work function (WF), known as “Fermi-level pinning (FLP),” prompted the proposal of many empirical interface state models, which dominated the theoretical scenes of SBH research for decades. The reliance on empiricism in this field is curious because being a direct consequence of charge distribution at MS interfaces, the magnitude of the SBH should be predictable from principles that govern charge distribution in general, i.e., chemistry. With experimental work on epitaxial NiSi2/Si interfaces more than three decades ago that showed a sharp dependence of the SBH on atomic structure, the shroud covering the FLP mystery began to lift. Subsequently, SBHs of polycrystalline MS interfaces were widely recognized to be inhomogeneous, meaning that the FL was never “pinned” after all. The insensitivity of the SBH to metal WF was also shown to be in agreement with bond polarization that can be expected at the MS interface. Even though theoretical calculation was able to numerically reproduce SBHs for specific interfaces, it has not been possible to quantitatively predict/explain the SBH from chemical principles. That has remained the state of the affairs for SBH for the last two decades, until very recently, when density functional theory calculations demonstrated that SBH could be quantitatively predicted from basic chemical principles, provided the traditional analysis method, based on the Schottky–Mott model, was abandoned and a newly proposed neutral polyhedra theory was adopted. Through the same study, the cause for the FLP effect and the apparent experimental “pinning level” were also identified. It appears that the SBH mystery is finally over. This article chronicles important advances in the last four decades on different fronts of research that finally brought in a scientifically based understanding of the formation of the SBH.

Scaling of causal neural avalanches in a neutral model

Neural avalanches are collective firings of neurons that exhibit emergent scale-free behavior. Understanding the nature and distribution of these avalanches is an important element in understanding how the brain functions. We study a model of neural avalanches for which the dynamics are governed by neutral theory. The neural avalanches are defined using causal connections between the firing neurons. We analyze the scaling of causal neural avalanches as the critical point is approached from the absorbing phase. By using cluster analysis tools from percolation theory, we characterize the critical properties of the neural avalanches. We identify the tuning parameters consistent with experiments. The scaling hypothesis provides a unified explanation of the power laws which characterize the critical point. The critical exponents characterizing the avalanche distributions and divergence of the response functions are consistent with the predictions of the scaling hypothesis. We use a universal scaling function for the avalanche profile to find that the firing rates for avalanches of different durations show data collapse after appropriate rescaling. We also find data collapse for the avalanche distribution functions, which is stronger evidence of criticality than just the existence of power laws. Critical slowing-down and power law relaxation of avalanches is observed as the system is tuned to its critical point. We discuss how our results motivate future empirical studies of criticality in the brain.

Redrawing the Boundaries: R. Dvorkin’s Interpretativism in the Light of Traditional Typologies of Legal Theorizing

Introduction: the paper is devoted to the interpretative concept of the outstanding American jurist Ronald Dworkin, formulated in his “Law’s Empire” (1986) and a number of other works. The subject of the paper is the characteristic of R. Dvorkin’s methodological approach. As its basis the author uses the interpretation of a “methodological model” of the thinker, proposed by the Mexican researcher Imer Flores, which is valuable for the effort to relate a (polemical and only partly explicit) approach of the American jurist with the classical criteria system of the typology of legal doctrines. Accordingly, the paper aims to identify (using the general scientific and specific scientific methods) R. Dworkin’s interpretativism in the context of the basic divisions of legal theories in modern Western (Anglo-American) jurisprudence, as well as to establish the impact of interpretativism on existing legaltheoretical typologies. As a result, the paper, first, outlines the key ideas of R. Dworkin’s doctrine, and secondly, examines I. Flores’s interpretation of the content and meaning of the interpretive methodology, thirdly, assesses the validity of such an interpretation with the justification of the status of interpretativism in the system of classical types of legal theorizing and its methodological implications. As a general conclusion, the paper argues for the status of R. Dworkin’s doctrine as a private and normative jurisprudence of the “internal point of view”. I. Flores’s thesis about the unification of traditional types of legal theories in interpretativism and transcending the dichotomy between positivism and natural law is disputed. Interpretativism challenges the established system of criteria for differentiating legal theories, rejecting a number of relevant methodological perspectives, primarily a general descriptive and morally neutral theory of law. By defending a necessary connection between law and morality, interpretativism, in fact, legitimizes the claims of natural-law concepts as to a proper explanation of “law as it is”, transferring their long-standing dispute with positivism to a new – methodological – level.

Neutral theory for competing attention in social networks

We used an ecological approach based on a neutral model to study the competition for attention in an online social network. This novel approach allow us to analyze some ecological patterns that has also an insightful meaning in the context of information ecosystem. Specifically, we focus on the study of patterns related with the persistence of a meme within the network and the capacity of the system to sustain coexisting memes. Not only are we able of doing such analysis in an approximated continuum limit, but also we get exact results of the finite-size discrete system.

Island songbirds as windows into evolution in small populations

Due to their limited ranges and inherent isolation, island species have long been recognized as crucial systems for tackling a range of evolutionary questions, including in the early study of speciation.1,2 Such species have been less studied in the understanding of the evolutionary forces driving DNA sequence evolution. Island species usually have lower census population sizes (N) than continental species and, supposedly, lower effective population sizes (Ne). Given that both the rates of change caused by genetic drift and by selection are dependent upon Ne, island species are theoretically expected to exhibit (1) lower genetic diversity, (2) less effective natural selection against slightly deleterious mutations,3,4 and (3) a lower rate of adaptive evolution.5-8 Here, we have used a large set of newly sequenced and published whole-genome sequences of Passerida species (14 insular and 11 continental) to test these predictions. We confirm that island species exhibit lower census size and Ne, supporting the hypothesis that the smaller area available on islands constrains the upper bound of Ne. In the insular species, we find lower nucleotide diversity in coding regions, higher ratios of non-synonymous to synonymous polymorphisms, and lower adaptive substitution rates. Our results provide robust evidence that the lower Ne experienced by island species has affected both the ability of natural selection to efficiently remove weakly deleterious mutations and also the adaptive potential of island species, therefore providing considerable empirical support for the nearly neutral theory. We discuss the implications for both evolutionary and conservation biology.

Quantitative explanation of the Schottky barrier height

Eight decades ago, Schottky proposed that the energy barrier at the metal-semiconductor interface, which now bears his name, should be compared with the difference of two surface quantities, the work function (WF) of the metal and the ionization potential of the semiconductor. This tradition of plotting and modeling the Schottky barrier height (SBH) against the metal WF has been followed ever since. However, success in general quantitative understanding of the SBH from physical principles has been limited, and empirical models are still relied upon. Here, we show that the stumbling block that has prevented a broadly applicable physical explanation of the SBH is the presence of surface dipole terms, inherently included in the traditional, Schottky-Mott styled analyses. By removing these surface contributions with the help of the recently developed neutral polyhedra theory, we show that the SBHs calculated for a very large number of epitaxial interfaces between metals and zinc-blende semiconductors are quantitatively explained from general chemical principles. Amazingly, SBHs calculated for 17 different semiconductors fit onto the same universal plot. Previously, SBHs needed to be grouped according to the semiconductor before analyses could be conducted separately for, and with empirical parameters specific to, each semiconductor. This work shows that the mechanism for SBH formation at metal-semiconductor interface is none other than the same chemistry responsible for charge distribution in molecules. There is no need for empirical modeling once the traditional beginning-point of SBH analysis is abandoned and the proposed new one is used.

Myxomycetes of the Caramoan Islands and an update on the species found in the Bicol Peninsula, Philippines

The main objective of this study was to characterize the assemblages of myxomycetes on isolated Philippine islands through a correlational study using geographical and ecological distance in the Caramoan Islands, including an updated checklist of the myxomycetes of the Bicol Peninsula. Four islands of varying sizes and distances from each other, but all within relatively close proximity to the mainland of the Bicol Peninsula, were surveyed. A combination of traditional and more contemporary ecological tools was used to analyze diversity indices among and between the islands. Among the four islands, Matukad Island recorded the highest species richness (46.8) and taxonomic diversity index (2.6), while ranking next to Lahos island in terms of species diversity (7.9). Pairwise comparisons using community similarity indices and clustering analysis consistently showed that Lahos and Matukad are the most similar to each other, while also being closer to one another but situated farthest from the mainland. On the other hand, the two smallest islands, which were also closest to each other and to the mainland, grouped together using clustering analysis but recorded the lowest pairwise percentage similarity value. The ecological patterns in this study appear to follow the unified neutral theory of biodiversity and biogeography more than the insular biogeography theory. In addition, this study added 16 new morphospecies to the list of myxomycetes known from the Bicol Peninsula, which brings the total to 73, including one new record for the country [Lamproderma arcyrioides (Sommerf.) Rostaf.] KEYWORDS: slime molds, insular, biodiversity, paleotropics, unified netural theory

New paradigm of the Russian labor market in the context of the formation of an inclusive economy and a new gender order

The author considers the profound changes that have occurred in the Russian labor market during the transition from a transitive economy to an inclusive one and the expanding influence of the emerging gender order, the theoretical concept of which is the theory of gender neutrality. A new paradigm for the development of the Russian labor market is proposed, which meets the radically changed economic and social conditions for the development of socio-gender labor resources in the conditions of digitalization. According to the author, a new multi-vector structure has formed in the Russian economic space, consisting of four closely interrelated markets: labor, employment, professions, and educational services. The labor market and the employment market have become the epicenter of the development of social inclusion and an inclusive economy, which have presented qualitatively different requirements for socio-gender labor resources. The complex interrelations between the four segments of the new structuration are analyzed as deep structural changes and tectonic shifts in the formation of socio-gender labor resources, the implementation of their social functions, and the reformatting of social mechanisms for managing ongoing processes. The inertial view of the labor market as a single social space does not correspond to the realities of its modern development. The article reveals the essence of the new social structuration in the context of the theory of Giddens, its architectonics, logistics of development, dialectics, and social multidimensionality. The trends in the development of a new social structuration are evaluated through the standpoint of the formation of a new gender order and the theory of gender neutrality.

Stability among cyclic change in an Antipodean pond and bolster heath system 1983–2017

A long-term study of a bolster heath–pond system at Newdegate Pass, Mount Field, Tasmania, was designed to test a theory of cyclical dynamics and to determine why there was constancy in the proportions of species in stable mosaic bolster heath, while their individual distributions changed. Groups of permanent plots were monitored approximately once every 5 years between 1983 and 2017, in apparently stable, apparently colonising, apparently recovering and apparently degrading bolster heath. The putatively stable sites exhibited an average of 37% spatial turnover in the three early 5-year periods, with reciprocal replacements between many pairs of species; however, there was little evidence of long-term directional change except for expansion of a gymnosperm shrub across the top of the bolster mosaic at one site. This pattern suggests a cyclical succession of species in the stable mosaic; however, the mechanism driving cyclicity remains unclear, with facilitation, competition and stochastic processes being implicated at different times and locations. These cyclic changes were likely to have been largely endogenous, given the variability and autocorrelations in relative growth rates of the stable mosaic over short horizontal distances, conforming with neutral theory. The process of dam vegetation loss after draining was rapid, as was vegetation colonisation of the floor of one dam and recovery from fire. On a putatively colonising site on rocky ground, changes were subdued but directionally consistent with the previously proposed model, which was consistent with all long-term observations.

Natural Selection as the Sum over all Histories

As evolution can be connected to the principle of least action, and if it is depicted in evolution-space versus time then it corresponds to the direction of ultimate causation. As an organism evolves and follows a path of proximate causation, if the vector is closely parallel to that of the Ultimate Causation then the changes will confer desirable attributes which will lead to further development. If, however, the variations do not occur in a direction close to that of the ultimate causation vector the evolved organism will quickly die out. Therefore Natural Selection may be viewed as similar to Feynman’s “sum over all histories”. This approach is compatible with both Neutral Theory and Selection, as it includes both positive and negative mutations and selection. Therefore, the principle of least action gives a direction, but not a purpose, to evolution.

Problems of Acid / Alkali Neutralization Theory in Cleaning

Problems of Acid / Alkali Neutralization Theory in Cleaning

Real communities of virtual plants explain biodiversity on just three assumptions

Abstract To illuminate mechanisms supporting diversity in plant communities, we construct 2D cellular automata and ‘grow’ virtual plants in real experiments. The plants are 19 different, fully validated functional types drawn from universal adaptive strategy theory. The scale of approach is far beyond that of even the most ambitious investigations in the physical world. By simulating 496 billion plant–environment interactions, we succeed in creating conditions that sustain high diversity realistically and indefinitely. Our simulations manipulate the levels of, and degree of heterogeneity in the supply of, resources, external disturbances and invading propagules. We fail to reproduce this outcome when we adopt the assumptions of unified neutral theory. The 19 functional types in our experiments respond in complete accordance with universal adaptive strategy theory. We find that spatial heterogeneity is a strong contributor to long-term diversity, but temporal heterogeneity is less so. The strongest support of all comes when an incursion of propagules is simulated. We enter caveats and suggest further directions for working with cellular automata in plant science. We conclude that although (i) the differentiation of plant life into distinct functional types, (ii) the presence of environmental heterogeneity and (iii) the opportunity for invasion by propagules can all individually promote plant biodiversity, all three appear to be necessary simultaneously for its long-term maintenance. Though further, and possibly more complex, sets of processes could additionally be involved, we consider it unlikely that any set of conditions more minimal than those described here would be sufficient to deliver the same outcome.