Comparative power law analysis for the spatial heterogeneity scaling of the hot‐spring microbiomes

Spatial heterogeneity is a fundamental property of any natural ecosystems, including hot spring and human microbiomes. Two important scales that spatial heterogeneity exhibits are population and community scales, and Taylor's power law (PL) and its extensions (PLEs) offer ideal quantitative models to assess population‐ and community‐level heterogeneities. Here we analyse 165 hot spring microbiome samples at the global scale that cover a wide range of temperatures (7.5–99°C) and pH levels (3.3–9). We explore a question of fundamental importance for measuring the spatial heterogeneity of the hot‐spring microbiome and further discuss their ecological implications: How do critical environmental factors such as temperature and pH influence the scaling of community spatial heterogeneity? We are particularly interested in the existence of a universal scaling model that is independent of environmental gradients. By applying PL and PLEs, we were able to obtain such scaling parameters of the hot spring at both community and population levels, which are temperature‐ and pH‐invariant. These findings suggest that while the hot‐spring microbiomes located at different regions may have different environmental conditions, they share a fundamental heterogeneity scaling parameter, analogically similar to the gravitational acceleration on Earth, which may vary slightly depending on altitude and latitude, but is invariant overall. In contrast, similar to the physics of the Moon and Earth, which have different gravitational accelerations, the hot spring and human microbiomes can have different scaling parameters as demonstrated in this study.     

Taylor's law and related allometric power laws in New Zealand mountain beech forests: the roles of space,time and environment

Taylor's law says that the variance of population density of a species is proportional to a power of mean population density. Density–mass allometry says that mean population density is proportional to a power of mean biomass per individual. These power laws predict a third, variance–mass allometry: the variance of population density of a species is proportional to a power of mean biomass per individual. We tested these laws using 10 censuses of New Zealand mountain beech trees in 250 plots over 30 years at spatial scales from 5 m to kilometers. We found that: 1) a single‐species forest not disrupted by humans obeyed all three laws; 2) random sampling explained the parameters of Taylor's law at a large spatial scale in 8 of 10 censuses, but not at a fine spatial scale; 3) larger spatial scale increased the exponent of Taylor's law and decreased the exponent of variance–mass allometry (this is the first empirical demonstration that the latter exponent depends on spatial scale), but affected the exponent of density–mass allometry slightly; 4) despite varying natural disturbance, the three laws varied relatively little over the 30 years; 5) self‐thinning and recruiting plots had significantly different intercepts and slopes of density–mass allometry and variance–mass allometry, but the parameters of Taylor's law were not usually significantly affected; and 6) higher soil calcium was associated with higher variance of population density in all censuses but not with a difference in the exponent of Taylor's law, while elevation above sea level and soil carbon‐to‐nitrogen ratios had little effect on the parameters of Taylor's law. In general, the three laws were remarkably robust. When their parameters were influenced by spatial scale and environmental factors, the parameters could not be species‐specific indicators. We suggest biological mechanisms that may explain some of these findings.     

A model of temporal distribution of Aphis gossypii (Glover) (Hem., Aphididae) on cotton

The spatio‐temporal distribution of Aphis gossypii (Glover) was studied for a 4‐year period in a plot of Gossypium hirsutum located in Bangui, Central African Republic. A study of the temporal evolution of the number of aphids by means of non‐linear regression indicated a rapid population increase during the first 8 weeks of cotton cultivation. The overdispersion of the aphids was found to be significant during most of the season. We tested three population dispersion models; Iwao's model and Taylor's power law describe the relationship between the mean m and variance σ² for the number of aphids, and the Nachman's model describes the functional dependence between m and the proportion p of non‐infested cotton plants. The results of these statistical tests indicate that only the Taylor's model was not rejected. The aphids’ aggregation increases with population density. The regression parameter confidence intervals for each of the 4 years of observation prove the stability of the Taylor's model. The model σ² = 45m^1.3 is recommended when the environmental and cultural conditions are similar to those of our study.     

Seasonal abundance, spatial distribution and sampling indices of thrip populations on cotton; a 4-year survey from central Greece

Abstract: Field studies were carried out in order to assess the populations of thrips on cotton leaves, by developing a sampling program to estimate the density with an acceptable level of precision. Thus, in a cotton field (1.1 ha) in central Greece, 45 leaves were collected (one leaf per cotton plant) at 10‐day intervals from May to September, for four consecutive growing seasons (1995–98). Five species of thrips were found: Frankliniella intonsa was the most abundant species followed by Thrips angusticeps, Thrips tabaci, Frankliniella occidentalis and Aeolothrips intermedius. Although considerable differences were observed in the population fluctuations among species, the highest population densities, for all species found, were recorded in July and August. As indicated by Taylor's power law estimates, all species presented aggregated distribution among sampling units. As this type of spatial pattern indicates, the accuracy obtained in estimating mean population density increased with the increase of the mean. Furthermore, the increase of the mean caused an exponential decrease in sample size. However, the precision level is acceptable only in high mean values, while at the same time the benefit from an increase in sample size is of no practical value.     

Ecological scaling laws link individual body size variation to population abundance fluctuation

Scaling research has seen remarkable progress in the past several decades. Many scaling relationships were discovered within and across individual and population levels, such as species–abundance relationship, Taylor's law, and density mass allometry. However none of these established patterns incorporate individual variation in the formulation. Individual body size variation is a key evolutionary phenomenon and closely related to ecological diversity and species adaptation. Using a macroecological approach, I test 57 Long‐Term Ecological Research data sets and show that a power‐law and a generalized power‐law function describe well the mean‐variance scaling of individual body mass. This relationship connects Taylor's law and density mass allometry, and leads to a new scaling pattern between the individual body size variation and population abundance fluctuation, which is confirmed using freshwater fish and forest tree data. Underlying mechanisms and implications of the proposed scaling relationships are discussed. This synthesis shows that integration and extension of existing ecological laws can lead to the discovery of new scaling patterns and complete our understanding of the relation between individual trait and population abundance. Synthesis Scaling relationships are useful for community ecology as they reveal ubiquitous patterns across different levels of biological organizations. This work extends and integrates two existing scaling laws: Taylor's law and density‐mass allometry, and derives a new variance allometry between individual body mass and population abundance. The result shows that diverse individual body size is associated with stable population fluctuation, reflecting the effect of individual traits on population characteristics. Confirmed by several empirical data sets, these scaling relationships suggest new ways to study the underlying mechanisms of Taylor's law and have profound implications for fisheries and other applied sciences.     

Human reproductive system microbiomes exhibited significantly different heterogeneity scaling with gut microbiome,but the intra-system scaling is invariant

Maintaining sexual reproduction in a highly competitive world is still one of the major mysteries of biology given the apparently high efficiency of asexual reproduction. Co-evolutionary theories such as the Red Queen hypothesis would suggest that the microbiomes in human reproductive systems, specifically the microbiomes contained in semen and vaginal fluids, should reach some level of homogeneity thanks to arguably the most conspicuous microbiome transmission between two sexes. The long-term sexual coevolution should favor the dynamic homogeneity or stability, which should also be beneficial for sexual reproduction such as sperm survival or fertilization on physiological/ecological time scale. We present a piece of quantitative evidence in the form of microbial community spatial heterogeneity to support the stability notion by analyzing three big datasets of the human vaginal, semen and gut microbiome. Methodologically, we applied a recent community-level extension to the classic Taylor's power law, which reached the rare status of ecological law and has found applications beyond biology. Both ecological and evolutionary theories, such as hologenome/holobiont and Red Queen, as well as consideration of first principles, would predict that microbiome transmissions between two sexes should have homogenizing effects on the composition and stability of the microbiomes in human reproductive systems, and therefore have similar variance structures. This is supported by the finding that the power law analysis revealed human vaginal and semen microbiomes exhibited the same scaling parameter size in their community spatial (inter-individual) heterogeneities, while the both exhibited significantly different heterogeneity scaling parameter size with the human gut microbiome.     

Use of Taylor's Power Law in examining the spatial distribution of free-livingBoophilus microplus (Acari: Ixodidae) larvae in pastures in Puerto Rico

Taylor's power law (y=am ^b) was used to analyze the spatial pattern ofBoophilus microplus (Canestrini) larvae in tropical pastures. The index of aggregationb was 2.75 and showed that larvae were highly aggregated. Theb-values differed significantly among certain pastures (LSD,P<0.05), and pasture type and use could have contributed to differences inb. The use of Taylor's power law to adjust for sampling inconsistencies that occur in tropical pastures where regimented sampling cannot always be followed is discussed.     

A new active piggyBac‐like element in Aphis gossypii

Abstract Nine piggyBac‐like elements (PLEs) were identified from the cotton aphid Aphis gossypii Glover. All the PLEs shared high sequence similarity with each other. However, eight of the nine PLEs were unlikely to encode functional transposase due to the existence of disruptive mutations within the coding regions. The other one PLE contained major characteristics of members in the piggyBac family, including TTAA target site duplications, inverted terminal repeats (ITRs), and an open reading frame (ORF) coding for a transposase with a putative DDD domain. This one with an intact transposase ORF was named AgoPLE1.1. The predicted transposase shared 47% similarity with that of Trichoplusia ni piggyBac IFP2. Phylogenetic analyses showed that AgoPLE1.1 was most related to the Heliothis virescens PLE1.1 (HvPLE1.1) element, with 45% and 60% similarity at the nucleotide and amino acid levels, respectively. A functional assay demonstrated that AgoPLE1.1 encoded a functional transposase and was able to cause precise excision in cell cultures. On the other hand, few genomic insertion polymorphisms of AgoPLE1 were observed in the genome of the cotton aphid. These observations suggested that AgoPLE1.1 was a PLE that invaded the cotton aphid genome in recent periods and retained its activity.     

Community fluctuations and local extinction in a planktonic food web

Determining statistical patterns irrespective of interacting agents (i.e. macroecology) is useful to explore the mechanisms driving population fluctuations and extinctions in natural food webs. Here, we tested four predictions of a neutral model on the distribution of community fluctuations (CF) and the distributions of persistence times (APT). Novel predictions for the food web were generated by combining (1) body size–density scaling, (2) Taylor's law and (3) low efficiency of trophic transference. Predictions were evaluated on an exceptional data set of plankton with 15 years of weekly samples encompassing c. 250 planktonic species from three trophic levels, sampled in the western English Channel. Highly symmetric non‐Gaussian distributions of CF support zero‐sum dynamics. Variability in CF decreased while a change from an exponential to a power law distribution of APT from basal to upper trophic positions was detected. Results suggest a predictable but profound effect of trophic position on fluctuations and extinction in natural communities.     

Power-law species–area relationships and self-similar species distributions within finite areas

The species–area relationship (SAR) is often expressed as a power law, which indicates scale invariance. It has been claimed that the scale invariance – or self‐similarity at the community level – is not compatible with the self‐similarity at the level of spatial distribution of individual species, because the power law would only emerge if distributions for all species had identical fractal dimensions (FD). Here we show that even if species differ in their FD, the resulting SAR is approximately linear on a log–log scale because observed spatial distributions are inevitably spatially restricted – a phenomenon we term the ‘finite‐area effect’. Using distribution atlases, we demonstrate that the apparent power law of SARs for central European birds is attributable to this finite‐area effect affecting species that indeed reveal self‐similar distributions. We discuss implications of this mechanism producing the SAR.     

Cloning and characterization of piggyBac- like elements in lepidopteran insects

PiggyBac-like elements (PLE) are widespread in variety of organisms, however, few of them are active or have an intact transposon structure. To further define the distribution PLEs in Lepidoptera, where the original active piggyBac IFP2 was discovered, and potentially isolate new functional elements, a survey for PLEs by PCR amplification and Southern dot blots was performed. Two new PLEs, AyPLE and AaPLE, were successfully isolated from the noctuid species, Agrotis ypsilon and Argyrogramma agnate, respectively. These elements were found to be closely related to each other by sequence similarity, and by sharing the same 16 bp inverted terminal repeat sequences. The AyPLE1.1 and AaPLE1.1 elements are structurally intact having characteristic TTAA target site duplications, inverted terminal repeats and intact open reading frames encoding putative transposases with the presumed piggyBac DDD domains, which are features consistent with autonomous functional transposons. Phylogenetic analysis revealed that AyPLE1.1 and AaPLE1.1 cluster with another noctuid species element, HaPLE1.1, suggesting a common ancestor for the three types of PLEs. This contributes to our understanding of the distribution and evolution of piggyBac in Lepidoptera.     

Whether larval amphibians school does not affect the parasite aggregation rule: testing the effects of host spatial heterogeneity in field and experimental studies

Almost all macroparasites show over‐dispersed infections within natural host populations such that most parasites are distributed among a few heavily‐infected individuals. Despite the importance of parasite aggregation for understanding system stability, the potential for population regulation, and super‐spreading events, many questions persist about its underlying drivers. Theoretically, aggregation results from heterogeneity in host exposure, resistance, and tolerance. However, few studies have examined how host spatial arrangement – which likely affects both parasite encounter and density‐dependent interactions – influences infection and dispersion, representing a critical gap in our current knowledge regarding the possible drivers of parasite aggregation. Using field data from over 165 ponds and 8000 hosts, we evaluated how the spatial clustering of amphibian larvae within ponds 1) varied among different amphibian species, and 2), affected the distribution of parasites within the host population using Taylor's power law. A complementary mesocosm experiment used field‐guided manipulations of the spatial arrangement of larval amphibians to create a gradient in host clustering while controlling host density, thereby testing for spatial effects on both infection success and aggregation by three different trematode species. Our field data indicated that larval amphibians exhibited significant spatial clustering that was well captured by Taylor's power law (R² 0.92 to 0.97 for different host species), but the residual variation only weakly correlated with observed patterns of trematode parasite over‐dispersion. Correspondingly, experimental manipulation of host clustering had no effects on parasite infection success or the degree of parasite aggregation among cages or mesocosms. Given the importance of parasite over‐dispersion for host populations and disease dynamics, we advocate for further investigations of host and parasite spatial aggregation, particularly studies that incorporate and/or control for heterogeneity in exposure and susceptibility.     

Linking the spatio‐temporal distribution of an edaphic crane fly to its heterogeneous soil environment

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Psychotic-Like Experiences and Nonsuidical Self-Injury in England: Results from a National Survey

BackgroundLittle is known about the association between psychotic-like experiences (PLEs) and nonsuicidal self-injury (NSSI) in the general adult population. Thus, the aim of this study was to examine the association using nationally-representative data from England.MethodsData from the 2007 Adult Psychiatric Morbidity Survey was analyzed. The sample consisted of 7403 adults aged ≥16 years. Five forms of PLEs (mania/hypomania, thought control, paranoia, strange experience, auditory hallucination) were assessed with the Psychosis Screening Questionnaire. The association between PLEs and NSSI was assessed by multivariable logistic regression. Hierarchical models were constructed to evaluate the influence of alcohol and drug dependence, common mental disorders, and borderline personality disorder symptoms on this association.ResultsThe prevalence of NSSI was 4.7% (female 5.2% and male 4.2%), while the figures among those with and without any PLEs were 19.2% and 3.9% respectively. In a regression model adjusted for sociodemographic factors and stressful life events, most types of PLE were significantly associated with NSSI: paranoia (OR 3.57; 95%CI 1.96–6.52), thought control (OR 2.45; 95%CI 1.05–5.74), strange experience (OR 3.13; 95%CI 1.99–4.93), auditory hallucination (OR 4.03; 95%CI 1.56–10.42), and any PLE (OR 2.78; 95%CI 1.88–4.11). The inclusion of borderline personality disorder symptoms in the models had a strong influence on the association between PLEs and NSSI as evidenced by a large attenuation in the ORs for PLEs, with only paranoia continuing to be significantly associated with NSSI. Substance dependence and common mental disorders had little influence on the association between PLEs and NSSI.ConclusionsBorderline personality disorder symptoms may be an important factor in the link between PLEs and NSSI. Future studies on PLEs and NSSI should take these symptoms into account.     

Testing for shared biogeographic history in the lower Central American freshwater fish assemblage using comparative phylogeography: concerted,independent, or multiple evolutionary responses?

A central goal of comparative phylogeography is determining whether codistributed species experienced (1) concerted evolutionary responses to past geological and climatic events, indicated by congruent spatial and temporal patterns (“concerted‐response hypothesis”); (2) independent responses, indicated by spatial incongruence (“independent‐response hypothesis”); or (3) multiple responses (“multiple‐response hypothesis”), indicated by spatial congruence but temporal incongruence (“pseudocongruence”) or spatial and temporal incongruence (“pseudoincongruence”). We tested these competing hypotheses using DNA sequence data from three livebearing fish species codistributed in the Nicaraguan depression of Central America (Alfaro cultratus, Poecilia gillii, and Xenophallus umbratilis) that we predicted might display congruent responses due to co‐occurrence in identical freshwater drainages. Spatial analyses recovered different subdivisions of genetic structure for each species, despite shared finer‐scale breaks in northwestern Costa Rica (also supported by phylogenetic results). Isolation‐with‐migration models estimated incongruent timelines of among‐region divergences, with A. cultratus and Xenophallus populations diverging over Miocene–mid‐Pleistocene while P. gillii populations diverged over mid‐late Pleistocene. Approximate Bayesian computation also lent substantial support to multiple discrete divergences over a model of simultaneous divergence across shared spatial breaks (e.g., Bayes factor [B₁₀] = 4.303 for Ψ [no. of divergences] > 1 vs. Ψ = 1). Thus, the data support phylogeographic pseudoincongruence consistent with the multiple‐response hypothesis. Model comparisons also indicated incongruence in historical demography, for example, support for intraspecific late Pleistocene population growth was unique to P. gillii, despite evidence for finer‐scale population expansions in the other taxa. Empirical tests for phylogeographic congruence indicate that multiple evolutionary responses to historical events have shaped the population structure of freshwater species codistributed within the complex landscapes in/around the Nicaraguan depression. Recent community assembly through different routes (i.e., different past distributions or colonization routes), and intrinsic ecological differences among species, has likely contributed to the unique phylogeographical patterns displayed by these Neotropical fishes.     

Local–regional boundary shifts in oribatid mite (Acari: Oribatida) communities: species–area relationships in arboreal habitat islands of a coastal temperate rain forest, Vancouver Island, Canada

Aim This study investigates the species–area relationship (SAR) for oribatid mite communities of isolated suspended soil habitats, and compares the shape and slope of the SAR with a nested data set collected over three spatial scales (core, patch and tree level). We investigate whether scale dependence is exhibited in the nested sampling design, use multivariate regression models to elucidate factors affecting richness and abundance patterns, and ask whether the community composition of oribatid mites changes in suspended soil patches of different sizes. Location Walbran Valley, Vancouver Island, Canada. Methods A total of 216 core samples were collected from 72 small, medium and large isolated suspended soil habitats in six western redcedar trees in June 2005. The relationship between oribatid species richness and habitat volume was modelled for suspended soil habitat isolates (type 3) and a nested sampling design (type 1) over multiple spatial scales. Nonlinear estimation parameterized linear, power and Weibull function regression models for both SAR designs, and these were assessed for best fit using R² and Akaike's information criteria (ΔAIC) values. Factors affecting oribatid mite species richness and standardized abundance (number per g dry weight) were analysed by anova and linear regression models. Results Sixty‐seven species of oribatid mites were identified from 9064 adult specimens. Surface area and moisture content of suspended soils contributed to the variation in species richness, while overall oribatid mite abundance was explained by moisture and depth. A power‐law function best described the isolate SAR (S = 3.97 × A^0.12, R² = 0.247, F_1,70 = 22.450, P < 0.001), although linear and Weibull functions were also valid models. Oribatid mite species richness in nested samples closely fitted a power‐law model (S = 1.96 × A^0.39, R² = 0.854, F_1,18 = 2693.6, P < 0.001). The nested SAR constructed over spatial scales of core, patch and tree levels proved to be scale‐independent. Main conclusions Unique microhabitats provided by well developed suspended soil accumulations are a habitat template responsible for the diversity of canopy oribatid mites. Species–area relationships of isolate vs. nested species richness data differed in the rate of accumulation of species with increased area. We suggest that colonization history, stability of suspended soil environments, and structural habitat complexity at local and regional scales are major determinants of arboreal oribatid mite species richness.     

Temporal and spatial dynamics of grapevine anthracnose and its relationship to pathogen survival

Anthracnose, caused by Elsinoë ampelina, is an economically important grapevine disease in south and southeast Brazil. Control is achieved by lime sulphur application during grapevine dormancy and foliar fungicide sprays until the berries are half-grown. This study assessed the temporal and spatial progress of grapevine anthracnose under field conditions in order to describe the disease dynamics and its relationship to pathogen survival. The experiment was carried out in a vineyard of table grape Vitis labrusca in Brazil, during the 2014 and 2015 growing seasons. The incidence of vines with diseased leaves, stems and berries and the disease severity on leaves were recorded from bud break to veraison. Monomolecular, logistic and Gompertz models were fitted by non-linear regression to the incidence and severity data over time to characterize the temporal progress. Ordinary runs, dispersion index, modified Taylor's power law and spatial hierarchy analyses were used to characterize the spatial pattern of diseased plants. The monomolecular model showed the best fit for the incidence progress, with disease progress rates ranging from 0.051 to 0.136 per day. In both seasons, the incidence of diseased plants reached 100% 1 month after bud break. However, the incidence of diseased leaves per plant was around 60% and leaf disease severity was lower than 5% for both years. Ordinary runs and dispersion index analyses revealed that diseased grapevines were distributed randomly on the majority of the assessment dates. Meanwhile, a slight aggregation of diseased vines was observed in the modified Taylor's power law analysis. Our results suggested that the progress of anthracnose incidence and severity over time was governed mainly by the income of the primary inoculum, which survived in the vineyard. Therefore, anthracnose control measures in Brazilian vineyards should be focused on the reduction in inoculum within the vineyard.     

Parasitic castration: host species preferences,size-selectivity and spatial heterogeneity

Summary This study investigates host-parasite population dynamics in a marine intertidal community of three barnacle host species (Balanus glandula, Chthamalus fissus andC. dalli). Our paper addresses the following questions: (1) Does prevalence (percentage parasitism) differ among the three host species? (2) What are the spatial and temporal population dynamics within the community? and (3) Does the parasite exhibit size-selective behaviour in any of the three host species? Significant differences in prevalence were found among the three host species; the parasitic castrator (Hemioniscus balani) most heavily infected the least abundant host. Parasitism occurred throughout the year and also showed significant spatial variation.H. balani showed size-selective parasitism inC. fissus, but not inC. dalli. Consequently, the population effects of parasitic castration inC. fissus depend both upon the host population size structure and the intensity of the parasite's size-selectivity.     

Metacommunity‐scale biodiversity regulation and the self‐organised emergence of macroecological patterns

There exist a number of key macroecological patterns whose ubiquity suggests that the spatio‐temporal structure of ecological communities is governed by some universal mechanisms. The nature of these mechanisms, however, remains poorly understood. Here, we probe spatio‐temporal patterns in species richness and community composition using a simple metacommunity assembly model. Despite making no a priori assumptions regarding biotic spatial structure or the distribution of biomass across species, model metacommunities self‐organise to reproduce well‐documented patterns including characteristic species abundance distributions, range size distributions and species area relations. Also in agreement with observations, species richness in our model attains an equilibrium despite continuous species turnover. Crucially, it is in the neighbourhood of the equilibrium that we observe the emergence of these key macroecological patterns. Biodiversity equilibria in models occur due to the onset of ecological structural instability, a population‐dynamical mechanism. This strongly suggests a causal link between local community processes and macroecological phenomena.