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This paper demonstrates that the differing social meanings held by linguistic features can result in an implicational relationship between them. Rates of (h) and (ing) are investigated in the casual speech of sixty-three speakers from a community with Cockney heritage: Debden, Essex. The indexicalities of h-dropping in Debden (signalling Cockney) are superordinate to and incorporate the indexicalities of g-dropping (working-class, “improper”), resulting in an implicational relationship. H-dropping implies g-dropping, but g-dropping can occur independently of h-dropping. This occurs in terms of co-variation at the between-speaker level and clustering effects at the within-speaker level which is measured through a novel approach using the number of phonemes as the denomination of distance. The features’ differing social meaning are also related to rates of change. Young speakers are shifting away from linguistic features which index Cockney heritage (h-dropping; the [-Iŋk] variant of -thing words) in favor of more general, southeastern, working-class norms (g-dropping).

Soil moisture is an important variable for land-climate and hydrological interactions. To investigate emergent large-scale, long-term interactions between soil moisture and other key hydro-climatic variables (precipitation, actual evapotranspiration, runoff, temperature), we analyze monthly values and anomalies of these variables in 1378 hydrological catchments across Europe over the period 1980–2010. The study distinguishes results for the main European climate regions, and tests how sensitive or robust they are to the use of three alternative observational and re-analysis datasets. Robustly across the European climates and datasets, monthly soil moisture anomalies correlate well with runoff anomalies, and extreme soil moisture and runoff values also largely co-occur. For precipitation, evapotranspiration, and temperature, anomaly correlation and extreme value co-occurrence with soil moisture are overall lower than for runoff. The runoff results indicate a possible new approach to assessing variability and change of large-scale soil moisture conditions by use of long-term time series of monitored catchment-integrating stream discharges.

Social interaction complexity makes humans unique. But in times of social deprivation this strength risks to expose important vulnerabilities. Human social neuroscience studies have placed a premium on the default network (DN). In contrast, hippocampus (HC) subfields have been intensely studied in rodents and monkeys. To bridge these two literatures, we here quantified how DN subregions systematically co-vary with specific HC subfields in the context of subjective social isolation (i.e., loneliness). By co-decomposition using structural brain scans of ∼40,000 UK Biobank participants, loneliness was specially linked to midline subregions in the uncovered DN patterns. These association cortex signatures coincided with concomitant HC patterns implicating especially CA1 and molecular layer. These patterns also showed a strong affiliation with the fornix white-matter tract and the nucleus accumbens. In addition, separable signatures of structural HC-DN co-variation had distinct associations with the genetic predisposition for loneliness at the population level.

Adaptation of viruses to their environments occurs through the acquisition of both novel Single-Nucleotide Variants (SNV) and recombination events including insertions, deletions, and duplications. The co-occurrence of SNVs in individual viral genomes during their evolution has been well-described. However, unlike covariation of SNVs, studying the correlation between recombination events with each other or with SNVs has been hampered by their inherent genetic complexity and a lack of bioinformatic tools. Here, we expanded our previously reported CoVaMa pipeline (v0.1) to measure linkage disequilibrium between recombination events and SNVs within both short-read and long-read sequencing datasets. We demonstrate this approach using long-read nanopore sequencing data acquired from Flock House virus (FHV) serially passaged in vitro. We found SNVs that were either correlated or anti-correlated with large genomic deletions generated by nonhomologous recombination that give rise to Defective-RNAs. We also analyzed NGS data from longitudinal HIV samples derived from a patient undergoing antiretroviral therapy who proceeded to virological failure. We found correlations between insertions in the p6Gag and mutations in Gag cleavage sites. This report confirms previous findings and provides insights on novel associations between SNVs and specific recombination events within the viral genome and their role in viral evolution.

Basal metabolic rate (BMR) represents the lowest level of aerobic metabolism in a resting, postabsorptive endotherm as measured within the thermoneutral zone. By contrast, maximal metabolic rate ([Formula: see text]max) reflects the upper limit of aerobic metabolism achieved during intensive exercise. As BMR and [Formula: see text]max define the boundaries of the possible levels of aerobic metabolism expressed by a normothermic individual, a key question is whether BMR and [Formula: see text]max are correlated. In the present study, we took repeated paired measurements of thermoneutral resting metabolic rate (RMRt) and [Formula: see text]max on 165 white-footed mice (Peromyscus leucopus). Over a single summer (May-October), repeatability (R ± SE) was low but statistically significant ([Formula: see text]) for both RMRt and [Formula: see text]max ([Formula: see text] for RMRt; [Formula: see text] for [Formula: see text]max). Willingness to run during the forced-exercise trials was also significantly repeatable ([Formula: see text]). At the residual level (within individual), RMRt and [Formula: see text]max tended to be positively correlated ([Formula: see text], [Formula: see text]), suggesting the presence of correlated phenotypic plasticity. By contrast, RMRt and [Formula: see text]max were significantly negatively correlated at the among-individual level ([Formula: see text]). To the extent that variation in RMRt reflects variation in BMR, the negative among-individual correlation does not corroborate the idea that a costly metabolic machinery is needed to support a high [Formula: see text]max. Future research should investigate the (genetic) relationship between RMRt (and BMR) and other energetically expensive behaviors and activities to better understand how energy is allocated within individuals.

Woody plant encroachment affects dry grasslands globally. To predict changes in biodiversity and ecosystem processes, it is important to understand how this process affects the functional composition of grassland organism groups. In this context, seminatural wooded meadows represent a form of experimental manipulation—where open grassland and woody patches co-occur in homogeneous environmental conditions due to human management decisions—which provides an opportunity to address the effect of woody plant encroachment on vegetation and soil biota. We used environmental DNA metabarcoding to address variation in plant, soil fungal, and soil animal communities in parallel. We also addressed functional groups of fungi—animal and plant pathogens, saprotrophs, decomposers, arbuscular mycorrhizal, ectomycorrhizal, endophytic, and other symbiotrophic fungi—and of soil animals—fungivores, bacterivores, litter feeders, root feeders, macro plant feeders, algal/lichen feeders, predators, and parasites. Co-variation between communities was detected from aboveground vegetation plots and metabarcoding of soil DNA, in terms of estimated richness and compositional patterns. Differences between open and wooded patches were most pronounced among plants and symbiotic fungi, whereas soil animals exhibited less marked differences. For most organisms, mean richness, as well as total richness per habitat type, was higher in open than wooded patches, but ectomycorrhizal fungi exhibited the opposite pattern. The functional structure of the soil biotic community, as characterized by the proportion of DNA sequences attributed to different functional groups, differed significantly between open and wooded grassland patches, with symbiotic fungi (arbuscular mycorrhizal, ectomycorrhizal, and other symbiotrophic [mostly orchid mycorrhizal] fungi) contributing most to the difference. This study supports the notion that a soil DNA-based metabarcoding approach can provide insights into the diversity and composition of multiple taxonomic groups in natural ecosystems. It also provides a first demonstration of the complex changes to the functional structure of the belowground community that accompany woody plant encroachment in grasslands. This research was supported by the University of Tartu (PLTOM20903) and the European Regional Development Fund (Centre of Excellence EcolChange).

The supply of fresh minerals to Earth’s surface by erosion is thought to modulate global climate by removing atmospheric carbon dioxide (CO2) through silicate weathering. In turn, weathering of accessory carbonate and sulfide minerals is a geologically-relevant CO2 source, which may dampen or reverse the effect of silicate weathering on climate. Although these weathering pathways commonly operate side by side, we lack quantitative constraints on their co-evolution across erosion-rate gradients. Using stream-water chemistry across a 3 order-of-magnitude erosion-rate gradient in shales and sandstones of southern Taiwan, here, we demonstrate that silicate, sulfide, and carbonate weathering are linked: Increasing sulfide oxidation generates sulfuric acid and boosts carbonate solubility whereas silicate weathering kinetics remain constant or even decline, perhaps due to buffering of the pH by carbonates. On timescales shorter than marine sulfide compensation, CO2 emission rates from weathering in rapidly-eroding terrain are more than twice the CO2 sequestration rates in slow-eroding terrain. On longer timescales, CO2 emissions are compensated, but CO2 sequestration rates do not increase with erosion, in contrast to assumptions in carbon cycle models. We posit that these patterns are broadly applicable to many Cenozoic mountain ranges that expose dominantly siliciclastic metasediments.

Climate change has a great impact on boreal ecosystems including Siberian larch forests. As a consequence of warming, larch grow is possible in areas where climate used to be too cold, leading to a shift of the tree line into more arctic regions. Most plants co-exist in symbiosis with heterotrophic organisms surrounding their root system. In arctic ecosystems, mycorrhizal fungi are a prerequisite for plant establishment and survival because they support nutrient uptake from nutrient-poor soils and maintain the water supply. Until now, however, knowledge about the co-variation of vegetation and fungi is poor. Certainly, the understanding of dynamic changes in biotic interactions is important to understand adaptation mechanisms of ecosystems to climate change.We investigated sedimentary ancient DNA from Lake Levinson Lessing, Taymyr Peninsula (Arctic Siberia, tundra), Lake Lama, Lake Kyutyunda (both northern Siberia, tundra-taiga transition zone) and Lake Bolshoe Toko (southern Siberia, forest area) covering the last about 45.000 years using ITS primers for fungi along with the chloroplast P6 loop marker for vegetation metabarcoding. We found changes in the fungal communities that are in broad agreement with vegetation turnover. To our knowledge, this is the first broad ecological study on lake sediment cores to analyze fungal biodiversity in relation to vegetation change on millennial time scales.

The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipogon wild rice; male parent Oryza sativa cultivated rice; their F1 progeny; and the F2, F3 and F4 self-crossing generations. Our results showed that the bacterial and fungal α-diversities of the hybrid F1 and self-crossing generations (F2, F3, F4) were closer to one of the two parental lines, which may indicate a role of the parental line in the diversity of the rhizosphere microbial community assembly. Self-crossing from F1 to F4 led to weak co-variation of the bacterial and fungal communities and distinct rhizosphere microbiomes. In the parental and self-crossing progenies, the reduction of community dissimilarity was higher for the fungal community than for the bacterial community.

Despite the well-known tradeoff between speed and accuracy, skilled people often demonstrate the ability to maintain high accuracy during fast movements. We focused on two strategies to improve accuracy, thereby increasing the reproducibility of individual parameters (certain parameters are maintained in low variability) and coordinating covariation among parameters (different parameters compensate each other's variability). The objective of this study was to determine whether coordinated covariation among release parameters is used for high accuracy by skilled baseball pitchers. A model was employed to simulate pitch location after eliminating the coordinated covariation by randomly reshuffling the release parameters, and the variability of simulated and measured pitch locations were compared. The results showed that there was no significant coordinated covariation for any of the release parameters for either the vertical or horizontal pitch location supports strategy of increasing the reproducibility of individual parameter. In addition, for the vertical pitch location, because there was coordinated covariation between the release angle and speed in slow pitching, it was suggested that, the higher speed the task requires, the more important the reproducibility of individual parameter becomes.

This study aimed to investigate and validate a noninvasive affordable cardiac output (CO) trend monitor intended for telemedicine applications. The approach of this work will widely increase the availability of CO measurements, currently only available through expensive hospital equipment. The estimation method of the CO trend is based on the transient analysis of a PPG (photoplethys-mography) signal during venous occlusion. The PPG signal is acquired with an LED and a photodiode as in typical pulse oximeters, whereas a pneumatic cuff and pressure pump implement the occlusion and release cycles. The CO trend is given by the relative comparison of different CO measurements of the same individual. All the components used in this work have been already integrated into a portable device with wireless communications so it can be suitable for telemedicine applications. Different measures were taken on different individuals at different times of the day, several days per week during some weeks. The CO trend consistently reflected the expected daily CO variation patterns and events such as food intake and mild physical activities. The proposed methodology can be used to determine sudden CO changes or to analyze the underlying overall CO trend with measurements taken over multiple days.

Summary CONAN is a web application developed to detect specificity determinants and function-related sites by amino acids co-variation networks analysis, emphasizing local coevolutionary constraints. The software allows the characterization of structurally and functionally relevant groups of residues and their relationship with subsets of sequences by automatic cross-referencing with GO terms, UniprotKb annotations and INTERPRO. Availability and implementation CONAN is free and open-source, being distributed in the terms of the GPLV3 license. The software is available as a web application and python script versions and can be accessed at http://bioinfo.icb.ufmg.br/conan. We also provide running instructions, the source code and a user guide.

Temporary changes in precipitation may lead to sustained and severe drought or massive floods in different parts of the world. Knowing variation in precipitation can effectively help the water resources decision-makers in water resources management. Large-scale circulation drivers have a considerable impact on precipitation in different parts of the world. In this research, the impact of El Ni\~no-Southern Oscillation (ENSO), Pacific Decadal Oscillation (PDO), and North Atlantic Oscillation (NAO) on seasonal precipitation over Iran was investigated. For this purpose, 103 synoptic stations with at least 30 years of data were utilized. The Spearman correlation coefficient between the indices in the previous 12 months with seasonal precipitation was calculated, and the meaningful correlations were extracted. Then the month in which each of these indices has the highest correlation with seasonal precipitation was determined. Finally, the overall amount of increase or decrease in seasonal precipitation due to each of these indices was calculated. Results indicate the Southern Oscillation Index (SOI), NAO, and PDO have the most impact on seasonal precipitation, respectively. Also, these indices have the highest impact on the precipitation in winter, autumn, spring, and summer, respectively. SOI has a diverse impact on winter precipitation compared to the PDO and NAO, while in the other seasons, each index has its special impact on seasonal precipitation. Generally, all indices in different phases may decrease the seasonal precipitation up to 100%. However, the seasonal precipitation may increase more than 100% in different seasons due to the impact of these indices. The results of this study can be used effectively in water resources management and especially in dam operation., Comment: 25 pages, 10 figures

Objective There is limited knowledge about how fatigue develops and worsens and what influences fluctuations in daily fatigue. Stress was found to influence fatigue, and being in a relationship seems to either increase or decrease stress depending on the couple interaction. In this study, co-variation of fatigue, self-reported stress, and biological stress markers in couples’ everyday lives was investigated. Specifically, we examined a) whether momentary couple interactions moderated dyadic outcomes and b) whether and how stress and relationship measures influenced individual momentary fatigue. Methods Forty heterosexual couples (age: 28 ± 5 years) reported subjective fatigue and stress levels 4 times a day for 5 consecutive days (1600 measures). Furthermore, participants reported whether they had interacted with their partner since the last data entry and, if so, they rated the valence of this interaction. Salivary cortisol (a measure of HPA axis activity) and alpha amylase (a measure of ANS activity) were analyzed as biological stress markers from saliva samples obtained at the same time points. Moment-to-moment data were analyzed using dyadic multilevel models to account for the nested design. Results Stress (women and men: p ≤ 0.001) and fatigue (women: p = .003, men: p = .020) showed patterns of co-variation within couples, especially if partners had interacted with each other since the previous data entry. Cortisol was also found to co-vary between partners (women: unstandardized coefficient (UC) = 0.12, p ≤ .001, men: UC = 0.18, p ≤ .001), whereas the regulation of alpha-amylase levels depending on the partner’s levels was only present in women (UC = 0.11, p = .002). Valence of couple interaction was negatively associated with fatigue (women: UC = −0.13, p ≤ .001, men: UC = −0.06, p = .011). There was no momentary association of fatigue with an individual’s own or the partner’s subjective or biological stress markers. Conclusions Fatigue and stress levels during the day seem to co-vary within couples. These associations were particularly strong when the partners had interacted with each other since the last measurement. These data underline the importance of social factors in fatigue and stress in everyday life.

Drivers of forest structure in central African rain forests are largely unknown. Using forest inventory data (3024 0.4-ha plots) in a forest concession of 154 456 ha in north-eastern Gabon covering an altitudinal gradient (from 485 to 1009 m asl), relationships between above-ground plot biomass and environmental variables (soil type, altitude, slope, aspect) and floristic composition (score given by an ordination method) were tested. After controlling for confounding variables, biomass was significantly related to altitude (with a modal response peaking at 346 Mg ha–1 on western slopes at an altitude of 707 m asl) and to aspect (additional 18.3 Mg ha–1 on eastern slopes) but not to floristic composition. Biomass and basal area responded differentially to the environment. Mean wood density was significantly related to soil, altitude and floristic composition, with a predicted minimum of 0.60 g cm–3 at an altitude of 1009 m asl in stands characterized by Scorodophloeus zenkeri and a maximum of 0.69 g cm–3 at an altitude of 458 m asl in monodominant Gilbertiodendron dewevrei stands. Variation in forest structure in the concession was primarily driven by altitude while floristic composition played a role in differentiating the variation in biomass and basal area.

Longitudinal deep sequencing of viruses can provide detailed information about intra-host evolutionary dynamics including how viruses interact with and transmit between hosts. Many analyses require haplotype reconstruction, identifying which variants are co-located on the same genomic element. Most current methods to perform this reconstruction are based on a high density of variants and cannot perform this reconstruction for slowly evolving viruses. We present a new approach, HaROLD (HAplotype Reconstruction Of Longitudinal Deep sequencing data), which performs this reconstruction based on identifying co-varying variant frequencies using a probabilistic framework. We test this method with synthetic data sets of mixed cytomegalovirus and norovirus genomes, demonstrating high accuracy when longitudinal samples are available.

Males of socially monogamous species can increase their siring success via within-pair and extra-pair fertilizations. In this study, we focused on the different sources of (co)variation between these siring routes, and asked how each contributes to total siring success. We quantified the fertilization routes to siring success, as well as behaviors that have been hypothesized to affect siring success, over a five-year period for a wild population of great tits Parus major. We considered siring success and its fertilization routes as "interactive phenotypes" arising from phenotypic contributions of both members of the social pair. We show that siring success is strongly affected by the fecundity of the social (female) partner. We also demonstrate that a strong positive correlation between extra-pair fertilization success and paternity loss likely constrains the evolution of these two routes. Moreover, we show that more explorative and aggressive males had less extra-pair fertilizations, whereas more explorative females laid larger clutches. This study thus demonstrates that (co)variation in siring routes is caused by multiple factors not necessarily related to characteristics of males. We thereby highlight the importance of acknowledging the multilevel structure of male fertilization routes when studying the evolution of male mating strategies.

Understanding the conformational propensities of proteins is key to solving many problems in structural biology and biophysics. The co-variation of pairs of mutations contained in multiple sequence alignments of protein families can be used to build a Potts Hamiltonian model of the sequence patterns which accurately predicts structural contacts. This observation paves the way to develop deeper connections between evolutionary fitness landscapes of entire protein families and the corresponding free energy landscapes which determine the conformational propensities of individual proteins. Using statistical energies determined from the Potts model and an alignment of 2896 PDB structures, we predict the propensity for particular kinase family proteins to assume a "DFG-out" conformation implicated in the susceptibility of some kinases to type-II inhibitors, and validate the predictions by comparison with the observed structural propensities of the corresponding proteins and experimental binding affinity data. We decompose the statistical energies to investigate which interactions contribute the most to the conformational preference for particular sequences and the corresponding proteins. We find that interactions involving the activation loop and the C-helix and HRD motif are primarily responsible for stabilizing the DFG-in state. This work illustrates how structural free energy landscapes and fitness landscapes of proteins can be used in an integrated way, and in the context of kinase family proteins, can potentially impact therapeutic design strategies.

This article provides a report on the state-of-the-art in the prediction of intra-molecular residue-residue contacts in proteins based on the assessment of the predictions submitted to the CASP11 experiment. The assessment emphasis is placed on the accuracy in predicting long-range contacts. Twenty-nine groups participated in contact prediction in CASP11. At least eight of them used the recently developed evolutionary coupling techniques, with the top group (CONSIP2) reaching precision of 27% on target proteins that could not be modeled by homology. This result indicates a breakthrough in the development of methods based on the correlated mutation approach. Successful prediction of contacts was shown to be practically helpful in modeling three-dimensional structures; in particular target T0806 was modeled exceedingly well with accuracy not yet seen for ab initio targets of this size (>250 residues). Proteins 2016; 84(Suppl 1):131-144. © 2015 Wiley Periodicals, Inc.

Atmospheric ultrafine particles (UFP; diameter 5 ms−1 or ΔT < 0 °C from LWTs produced more uniform and stronger relationships (R2 = 0.90; R2 = 0.93). Low wind speeds and positive vertical temperature gradients were most common during LWTs A, NW, N and NE. These weather types were also associated with the highest daily means of NOx (∼30 ppb) and PNC (∼10 000 # cm−3). A conclusion from this study is that NOx (but not PM10) is a good proxy for PNC especially during calm and stable conditions and that LWTs A, NW, N and NE are high risk weather types for elevated NOx and PNC.

Physical soil properties have a marked influence on the quality of forest sites and on the preconditions for forest growth and management. In this study, water retention characteristics (WRC) and related physical soil properties in addition to vegetation coverage and tree stand data were studied at upland forest sites in Finland. Fixed and mixed models between soil and site characteristics were formed to estimate physical and hydrologic soil characteristics and the site quality with indirect co-varying variables. In the present data, the site quality index (H100) shows a high coefficient of determination in respect to the temperature sum. It is also related to soil fine fraction content, topsoil pH and water retention at field capacity. The thickness of the humus layer is predictable from the pH and cover of xeric and mesic plant species. The soil fine fraction content (clay + silt) is closely related to water retention at field capacity, the soil layer and site type, and without WRC to the temperature sum and site index and type, as well as the slope angle. The soil bulk density is related to organic matter, depth (layer) or alternatively to organic matter, slope and field estimated textural class (fine, medium, coarse). Water retention characteristics were found to be best determinable by the fine fraction content, depth and bulk density. Water content and air-filled porosity at field capacity are closely related to the fine fraction. This study provides novel models for further investigations that aim at improved prediction models for forest growth, hydrology and trafficability.

The co-variation of rainfall and flow was assessed in four selected catchments of the River Nile which has two main sources including the White Nile (in the Equatorial region) and the Blue Nile (from the Ethiopian highlands). The selected catchments included Kyoga and Kagera (from the Equatorial region), as well as Blue Nile and Atbara (in Sudan and Ethiopia). In each catchment, the flow-rainfall co-variation was investigated at both seasonal and annual time scales. To explain aggregated variation at larger temporal scale while investigating the possible change in catchment behavior, which may interfere with the flow-rainfall relationship, rainfall-runoff modeling was done at daily time scale using data (falling within the period 1949–2003) from Kagera and Blue Nile i.e. the major catchment of each region where the River Nile emanates. Correlation analysis was conducted to assess how well the variation of flow and that of catchment-wide rainfall resonate. The co-occurrence of the changes in observed and simulated overland flow was examined using the quantile perturbation method (QPM). Trends in the model residuals were detected using the Mann–Kendal (MK) and cumulative rank difference (CRD) tests. The null hypothesis H0 (no correlation between rainfall and flow) was rejected at the significance level α of 5% for all the selected catchments. The temporal changes in terms of the QPM anomalies for both the observed and simulated flow were in a close agreement. The evidence to reject the H0 (no trend in the model residuals) was generally statistically insufficient at α = 5% for all the models and selected catchments considering both the MK and CRD tests. These results indicate that change in catchment behavior due to anthropogenic influence in the Nile basin over the selected time period was minimal. Thus, the overall rainfall-runoff generation processes of the catchments did not change in a significant way over the selected data period. The temporal flow variation could be attributed mainly to the rainfall variation. ispartof: Stochastic Environmental Research and Risk Assessment vol:32 issue:3 pages:623-641 status: published

The developmental instability (DI)-sexual selection hypothesis proposes that large size and symmetry in secondary sexual traits are favored by sexual selection because they reveal genetic quality. A critical prediction of this hypothesis is that there should exist negative correlations between trait fluctuating asymmetry (FA) and size of condition dependent sexual traits, condition dependent traits should reveal an organism’s overall health and vigor, and be influenced by a multitude of genetic loci. Here, we tested for the predicted negative FA-size correlations in the male sex comb of Drosophila bipectinata. Among field-caught males from five widely separated geographic localities, FA-size correlations were consistently positive, despite evidence that sex comb size is condition dependent. After controlling for trait size, FA was significantly negatively correlated with body size within several populations, indicating that developmental instability in the comb may reveal individual genetic quality. We suggest the possibility that condition dependent traits in some cases tap into independent units of the genome (a restricted set of genes), rather than signaling overall genetic properties of the organism. There were pronounced among-population differences in both comb FA and size, and these traits were positively correlated across populations, recapitulating the within-population patterns. We conclude that the results are inconsistent with the DI-sexual selection hypothesis, and discuss potential reasons for positive FA-size co-variation in sexual traits.

In order to understand the stoichiometric balance between foliar nitrogen (N) and phosphorus (P) on P-poor soils, we investigated how foliar N and P attributes (i.e. N and P concentrations in green and senesced leaves, N and P resorption efficiencies) of 30 tropical tree species co-vary along a gradient of soil P availability across three forests on Mount Kinabalu, Borneo. We found strong and positive correlations between foliar N and P in the concentrations and resorption efficiencies within each forest and across the three forests. Slopes of standardized major axis between foliar N and P concentrations for both green and senesced leaves were not different among the three forests, although the values of the scaling exponent in the relationships of foliar N to P across the three forests were significantly lower than 1. We suggest that down-regulation of N concentrations in green leaves on P-poor soils is one of several possible mechanisms explaining why N concentrations decrease with decreasing P concentrations in both green and senesced leaves toward a lower P availability in soils. On the other hand, the physiological and ecological reasons why N and P resorption efficiencies are positively correlated with each other across tree species remain unclear.

SUMMARY Spatiotemporal neural patterns depend on the physical structure of neural circuits. Neural plasticity can thus be associated with changes in the circuit structure. For example, newborn neurons migrate toward existing, already matured, neural networks in order to participate in neural computation. In the present study, we have conducted two experiments to investigate how neural migration is associated with the development of neural activity in primary dissociated cultures of neuronal cells. In Experiment 1, using a mature culture, a high-density CMOS microelectrode array was used to continuously monitor neural migration and activity for more than two weeks. Consequently, we found that even in mature neuronal cultures neurons moved 2.0 ± 1.0 μm a day and that the moving distance was negatively correlated with their firing rate, suggesting that neurons featuring low firing rates tend to migrate actively. In Experiment 2 using a co-culture of mature and immature neurons, we found that immature neurons moved more actively than matured neurons to achieve functional connections to other neurons. These findings suggest that neurons with low firing rates as well as newborn neurons actively migrate in order to establish their connections and function in a neuronal network.

Following up on the encouraging results of residue‐residue contact prediction in the CASP11 experiment, we present the analysis of predictions submitted for CASP12. The submissions include predictions of 34 groups for 38 domains classified as free modeling targets which are not accessible to homology‐based modeling due to a lack of structural templates. CASP11 saw a rise of coevolution‐based methods outperforming other approaches. The improvement of these methods coupled to machine learning and sequence database growth are most likely the main driver for a significant improvement in average precision from 27% in CASP11 to 47% in CASP12. In more than half of the targets, especially those with many homologous sequences accessible, precisions above 90% were achieved with the best predictors reaching a precision of 100% in some cases. We furthermore tested the impact of using these contacts as restraints in ab initio modeling of 14 single‐domain free modeling targets using Rosetta. Adding contacts to the Rosetta calculations resulted in improvements of up to 26% in GDT_TS within the top five structures.

In a multiple sequence alignment, sequence co-variations result from structural, functional, and/or phylogenetic constraints. Numerous methods have been developed to calculate co-variation scores, but few studies have compared these methods to identify which methods are best suited for the analysis of protein family divergence. Here, we give an overview of widely used methods and identify simple rules for selection of appropriate methods. Specifically, we found that methods such as OMES and ELSC-which favor pairs with intermediate entropy and covariation networks with hub structure-are well suited to reveal evolutionary information on family divergence. When applied to G protein-coupled receptors, these methods support an epistasis model of protein evolution in which, after a key mutation, co-evolution of several residues was necessary to restore and/or shift protein function.

Animal communication among competitors often relies on honest signaling such that displays of aggression accurately reflect an individual’s performance abilities. Moreover, the maintenance of honest signaling should be enhanced by the existence of consistent individual differences in behavior and performance, and individual-level correlations between them. Despite this, researchers studying honest signaling rarely measure behavioral repeatability. Here, we demonstrate that field behaviors of free-ranging lizards and a measure of locomotor performance in the laboratory are consistent among individuals (i.e. they were repeatable), although the magnitude of repeatability varies among traits. In addition, endurance appears to be correlated with display frequency in the field at the individual level, suggesting that display frequency is an honest signal of endurance. Interestingly, this correlation was strong for males, and non-existent for females. Our results extend previous studies of behavior‐performance relationships by identifying a sex-specific correlation between traits and by partitioning phenotypic correlations into between- and within-individual components. This analytical approach is emerging as a powerful tool for studying individual variation in behavior and physiology.

Upon varying parameters in a sensitivity analysis of a Bayesian network, the standard approach is to co-vary the parameters from the same conditional distribution such that their proportions remain the same. Alternative co-variation schemes are, however, possible. In this paper we investigate the properties of the standard proportional co-variation and introduce two alternative schemes: uniform and order-preserving co-variation. We theoretically investigate the effects of using alternative co-variation schemes on the so-called sensitivity function, and conclude that its general form remains the same under any linear co-variation scheme. In addition, we generalise the CD-distance for bounding global belief change to explicitly include the co-variation scheme under consideration. We prove a tight lower bound on this distance for parameter changes in single conditional probability tables.

Repeatability is an important concept in evolutionary analyses because it provides information regarding the benefit of repeated measurements and, in most cases, a putative upper limit to heritability estimates. Repeatability (R) of different aspects of energy metabolism and behavior has been demonstrated in a variety of organisms over short and long time intervals. Recent research suggests that consistent individual differences in behavior and energy metabolism might covary. Here we present new data on the repeatability of body mass, standard metabolic rate (SMR), voluntary exploratory behavior, and feeding rate in a semiaquatic salamander and ask whether individual variation in behavioral traits is correlated with individual variation in metabolism on a whole-animal basis and after conditioning on body mass. All measured traits were repeatable, but the repeatability estimates ranged from very high for body mass (R = 0.98), to intermediate for SMR (R = 0.39) and food intake (R = 0.58), to low for exploratory behavior (R = 0.25). Moreover, repeatability estimates for all traits except body mass declined over time (i.e., from 3 to 9 wk), although this pattern could be a consequence of the relatively low sample size used in this study. Despite significant repeatability in all traits, we find little evidence that behaviors are correlated with SMR at the phenotypic and among-individual levels when conditioned on body mass. Specifically, the phenotypic correlations between SMR and exploratory behavior were negative in all trials but significantly so in one trial only. Salamanders in this study showed individual variation in how their exploratory behavior changed across trials (but not body mass, SMR, and feed intake), which might have contributed to observed changing correlations across trials.

Summary 1. Standard metabolic rate (SMR) and maximal metabolic rate (MMR) are fundamental measures in ecology and evolution because they set the scope within which animals can perform activities that directly affect fitness. In ectotherms, both SMR and MMR are repeatable over time when measured at a single ambient temperature (Ta). 2. Many ectotherms encounter variable Ta from day to day and over their lifetime, yet it is currently unknown whether individual differences hold across an ecologically relevant range of Ta (i.e. thermal repeatability; RT). Moreover, it is possible that thermal sensitivity of SMR and MMR are important individual attributes, and correlated with one another, but virtually nothing is known about this at present. 3. We measured SMR and MMR across an ecologically relevant Ta gradient (i.e. from 10 to 25 °C) in wild-caught salamanders (Plethodon albagula) and found that RT was significant in both traits. SMR and MMR were also positively correlated, resulting in a lower RT in absolute and factorial aerobic scopes (AAS and FAS). 4. We found significant individual differences in thermal sensitivity for both SMR and MMR, but not for AAS and FAS. The intercept (at Ta =0 °C) and the slope of the thermal reaction norms were negatively correlated; individuals with low MR at low Ta had a higher thermal sensitivity. Finally, individuals with a high thermal sensitivity for SMR also had high thermal sensitivity for MMR. 5. Our results suggest that natural selection occurring over variable Ta may efficiently target the overall level of – and thermal sensitivity in – SMR and MMR. However, this may not be the case for metabolic scopes, as the positive correlation between SMR and MMR, in addition to their combined changes in response to Ta, yielded little individual variation in AAS and FAS. 6. Our results support the idea that organisms with low metabolism at low Ta have a high metabolic thermal sensitivity as a compensatory mechanism to benefit in periods of warmer environmental conditions. Hence, our study reveals the importance of considering within-individual variation in metabolism, as it may represent additional sources of adaptive (co)variation.

The adaptive benefits of extended phenotypic plasticity are imprecisely defined due to a paucity of experiments examining traits that are manipulable and measurable across environments. Spider webs are often used as models to explore the adaptive benefits of variations in extended phenotypes across environments. Nonetheless, our understanding of the adaptive nature of the plastic responses of spider webs is impeded when web architectures and silk physicochemical properties appear to co-vary. An opportunity to examine this co-variation is presented by modifying prey items while measuring web architectures and silk physiochemical properties. Here we performed two experiments to assess the nature of the association between web architectures and gluey silk properties when the orb web spider Argiope keyserlingi was fed a diet that varied in either mass and energy or prey size and feeding frequency. We found web architectures and gluey silk physicochemical properties to co-vary across treatments in both experiments. Specifically, web capture area co-varied with gluey droplet morphometrics, thread stickiness and salt concentrations when prey mass and energy were manipulated, and spiral spacing co-varied with gluey silk salt concentrations when prey size and feeding frequency were manipulated. We explained our results as A. keyserlingi plastically shifting its foraging strategy as multiple prey parameters simultaneously varied. We confirmed and extended previous work by showing that spiders use a variety of prey cues to concurrently adjust web and silk traits across different feeding regimes.

Speech production requires control for coordination among different articulatory organs. During the natural speech, the articulatory co-variation is more common rather than compensation, but the studies supporting this view are few. In this study, the coordination of lip and tongue articulation was examined during speech using articulatory data. Native speakers of Chinese served as subjects. Speech materials consisted of short Chinese sentences, which include words having the cardinal vowels at different locations in sentences with and without emphasis. Articulatory movements were recorded using Microsoft Kinect for Windows and Terason T3000 ultrasound systems. After movement collection, 3D lip shapes were extracted from planar and depth images to examine the degree of lip deformation, and mid-sagittal tongue contours were tracked on ultrasound images to observe tongue surface deformation. The results indicate the tendency of covariation between the lips and tongue rather than compensation, showing more extreme articulation of both for vowels at strong syllables than at weak syllables.

Advances in high-throughput sequencing (HTS) technologies have facilitated the assessment of the genetic diversity of heterogeneous virus populations at an unprecedented level of detail. However, the existence of technical errors confounds the identification of truthful variants. Here, we present a comparative approach for the identification of patterns of co-variation in deep-sequenced virus populations. In addition to sequencing errors, we account for other unknown sources of error by modeling the occurrences of patterns of mutations using the Dirichlet distribution as prior for the multinomial distribution.

Relationships between species diversity and genetic diversity, the two most important elements of biodiversity, have recently attracted considerable interest in the field of community genetics. The present study contributes to this issue by addressing three questions that seem to have been ignored so far, namely whether the use of (a) different diversity measures, of (b) different components of diversity, and of (c) different genetic traits may lead to different assessements of speciesgenetic diversity relationships. For this purpose, data on species composition and genetic traits were collected from the natural regeneration of nine forest communities, which consist of three pure and six mixed tree stands located in the Thuringian forest area. The genetic traits comprised one DNA (AFLP) and five isozyme traits all of which were determined in all species. In contrast to other studies, the species diversity was determined for two components, SD (species diversity) and NeS (effective number of genetically distinct species), and the genetic diversity was determined for three components, TSGD (the transspecific genetic diversity taken over all species of a community), ISGD and NGS (each describing a special average of intraspecific genetic diversity). Each component was quantified by measures of diversity representing four orders of the Renyi/Hillfamily. The orders correspond to the degree to which prevalence of types is considered in the diversity measure (at the lowest order, known as richness, prevalence is disregarded, with increasing order, the diversity measure reports prevalent types only). In our data, the diversity measured for each genetic trait separately showed a great range of variation across traits and components of diversity even in the same stand. The choice of the diversity component thus turned out to have a substantial effect on the assessment of the level of genetic diversity within stands. This prompted more detailed studies of the relationships between species and genetic diversity. Relationships were quantified with the help of the coefficient of co-variation, and the statistical significance of the co-variations was verified through permutation tests. The co-variations between SD and TSGD were found to be generally positive and in most cases significant, but the co-variation declined with increasing orders of diversity for most of the genetic traits. In contrast, the co-variation between SD and ISGD was not consistent for the four orders of diversity. In particular, the co-variations for the highest order were found to be negative for all traits. The results of our explorative study thus demonstrate that the assessment of levels of genetic diversity within stands as well as species-genetic interrelations critically depend on the choice of the diversity component, of the order of diversity, and of the genetic trait. These observations lend support to different and even opposing hypotheses on the processes potentially generating species-genetic relationships. Therefore, strategies in the conservation of biodiversity, for example, are suggested to be related more specifically to the components and orders of diversity to be safegarded and to consider the functions of genetic traits in relation to adaptationally relevant environmental factors.

Morpho-functional patterns are important drivers of phenotypic diversity given their importance in a fitness-related context. Although modularity of the mandible and skull has been studied extensively in mammals, few studies have explored shape co-variation between these two structures. Despite being developmentally independent, the skull and mandible form a functionally integrated unit. In the present paper we use 3D surface geometric morphometric methods allowing us to explore the form of both skull and mandible in its 3D complexity using the greater white-toothed shrew as a model. This approach allows an accurate 3D description of zones devoid of anatomical landmarks that are functionally important. Two-block partial least-squares approaches were used to describe the co-variation of form between skull and mandible. Moreover, a 3D biomechanical model was used to explore the functional consequences of the observed patterns of co-variation. Our results show the efficiency of the method in investigations of complex morpho-functional patterns. Indeed, the description of shape co-variation between the skull and the mandible highlighted the location and the intensity of their functional relationships through the jaw adductor muscles linking these two structures. Our results also demonstrated that shape co-variation in form between the skull and mandible has direct functional consequences on the recruitment of muscles during biting.

a b s t r a c t The present study examines possible relationships between changes in electroencephalogram (EEG) power and in working memory (WM) due to brain maturation. Scores on the phonological loop, visuospatial sketchpad and executive components of WM, measured by the Working Memory Test Battery for Children (WMTB-C), were correlated with the power spectral density (PSD) values on the spontaneous EEG from 1 to 46 Hz. In order to control for non-specific processes of visuomotor abilities, the reaction time (RT) variable was measured with an Oddball task. One hundred and sixty seven subjects (82 males and 85 females) between 6 and 26 years old participated in the study. Three minutes of spontaneous EEG were recorded. The WMTB-C and the Oddball task were also administered. The scores on each WM component increased and the RT in the Oddball decreased with age, while PSD values in the different frequencies decreased with age. Significant negative correlations between each of the components and the PSD were obtained. The maximal negative correlations were obtained in the theta (4–7 Hz) range. A bivariate linear model including theta PSD and RT explained most of the WM variance due to age. The results suggest that spontaneous EEG maturation is closely related to WM maturation, particularly in the theta range.

Plants usually express multiple chemical and mechanical defenses simultaneously. The interplay of these defenses is still poorly understood, as predictions range from negative associations such as allocation tradeoffs to positive correlations forming synergistic defense syndromes. Surprisingly, little empirical evidence exists on the co-variation of multiple plant defenses. In the present study, we analyzed different genotypes of lima bean (Phaseolus lunatus L.) for the expression of two direct chemical defenses [cyanogenic potential (constitutive), polyphenol oxidase activity (inducible)], two indirect chemical defenses [volatiles (VOCs) and extrafloral nectar (EFN; both inducible)] and a constitutive mechanical defense (hook-shaped trichomes). While the occurrence of trichomes was positively correlated with cyanogenesis, these traits showed a tradeoff with polyphenol oxidase activity, release of VOCs, and secretion of EFN. Hook-shaped trichomes were abundantly present in four of 14 genotypes investigated, and were found only in one monophyletic group of an AFLP-based tree, thus indicating a single evolutionary origin within the species. Our findings show that different lima bean genotypes express either one of two defense systems: 1) high constitutive defense via cyanogenesis and trichomes or 2) high inducible defense via VOCs, EFN, and PPO activity.

An earlier study of ours that used data collected in 1972 found that a single common factor accounted for the positive correlations among a number of adolescent problem behaviors, including problem drinking, marijuana use, delinquent-type behavior, and precocious sexual intercourse. The present maximum-likelihood factor analyses replicated this finding on new samples of male and female 11th- and 12th-grade students tested 13 years later, in 1985. The findings lend further support to the concept of a syndrome of problem behavior in adolescence.

Two major types of glycerol dialkyl glycerol tetraethers (GDGTs) are commonly used in paleoecological and paleoclimatological reconstructions: isoprenoidal and branched GDGTs. In aquatic environments, it was originally assumed that isoprenoidal GDGTs, especially crenarchaeol, derive mainly from aquatic Thaumarchaeota, while branched GDGTs are an allochthonous input derived from soil Bacteria. Recently, direct co-variation of crenarchaeol and branched GDGTs has been described in two marine sedimentary records, and this observation suggests that in situ production of branched GDGTs is possible at least in some aquatic environments. After investigating 30 published and unpublished data sets from downcore and surface sediments as well as sediment traps from 19 distinct regions around the world, we found a widespread significant correlation between concentrations of branched GDCTs and crenarchaeol (p

We are daily exposed to many different environmental contaminants. Mixtures of these contaminants could act together to induce more pronounced effects than the sum of the individual contaminants. To evaluate the effects of such mixtures, it is of importance to assess the co-variance amongst the contaminants. Thirty-seven environmental contaminants representing different classes were measured in blood samples from 1016 individuals aged 70 years. Hierarchical cluster analysis and principal component analysis were used to assess the co-variation among the contaminants. Within each identified cluster, possible marker contaminants were sought for. We validated our findings using data from the National Health and Nutrition Examination Survey (NHANES) 2003-2004 study. Two large clusters could be identified, one representing low/medium chlorinated polychlorinated biphenyls (PCBs) (≤6 chlorine atoms), as well as two pesticides and one representing medium/high chlorinated PCBs (≥6 chlorine atoms). PCBs 118 and 153 could be used as markers for the low/medium chlorinated cluster and PCBs 170 and 209 could be used as markers for the medium/high chlorinated cluster. This pattern was similar to data from the NHANES study. Apart from the PCBs, little co-variation was seen among the contaminants. Thus, a large number of chemicals have to be measured to adequately identify mixtures of environmental contaminants.

Visual strain and discomfort may contribute to the generation of work-related musculoskeletal disorders among e.g. computer workers. A positive correlation on a group level between eye-lens accommodation and trapezius muscle activity has been reported. In this study we investigated the possibility of a direct, fast, connection between lens accommodation and trapezius muscles activity. The subjects focused alternately on Near and Far targets, with a mean switch time of 5 s, through four different lenses. The cross-correlation, R(tau) was computed, between the time signals of accommodation and electromyography (EMG) from 23 subjects. In the overall mean R(tau) of 736 curves, a small but significant correlation peak (0.019) with a delay (of the EMG signal) of about 0.3 s, revealed a small common component in the two signals. Among the lenses, the positive lens (3.5 D), showed the highest correlation peak (0.040). The correlation may be caused by a direct "hard-wired" connection between the ciliary and trapezius muscles. But it could also be caused indirectly by the subject's need for a more stable head in a more demanding visual task. The latter is supported by the result that the correlation was the highest in the positive lens condition. The present correlation is however weak and it has probably a low practical importance.

Rumination is a maladaptive form of emotion regulation and seems to be the cognitive mechanism linking stress to depressive symptoms. However, it remains to be investigated whether individuals' variation in rumination in relation to the occurrence of stressful events (e.g., phasic co-variation between stressful events and rumination) prospectively predict the experience of depressive symptoms in lengthy follow-up moments. In this eighteen months prospective design, a large unselected sample of undergraduates was tested before, during, and after a period with prominent naturally occurring stressful events. The multilevel results show that the co-variation of stressful events and ruminative thinking predicts the experience of depressive symptoms at 3 and 15 months follow up moments, also when statistically controlling for baseline depressive symptoms. Moreover, the data demonstrate that the phasic elevations of rumination in relation to the occurrence of stressful events are more predictive of depressive symptoms compared with the stable aspects of rumination measured at one occasion. At the clinical level, the current findings seem to suggest a process-oriented intervention to target the phasic ruminative cognitions where individuals need to learn to control rumination exactly at moments of stress. (C) 2016 Elsevier Ltd. All rights reserved.