Non-additive Interactions Research Articles

Honey Bee Colonies Headed by Hyperpolyandrous Queens Have Improved Brood Rearing Efficiency and Lower Infestation Rates of Parasitic Varroa Mites.

A honey bee queen mates on wing with an average of 12 males and stores their sperm to produce progeny of mixed paternity. The degree of a queen’s polyandry is positively associated with measures of her colony’s fitness, and observed distributions of mating number are evolutionary optima balancing risks of mating flights against benefits to the colony. Effective mating numbers as high as 40 have been documented, begging the question of the upper bounds of this behavior that can be expected to confer colony benefit. In this study we used instrumental insemination to create three classes of queens with exaggerated range of polyandry– 15, 30, or 60 drones. Colonies headed by queens inseminated with 30 or 60 drones produced more brood per bee and had a lower proportion of samples positive for Varroa destructor mites than colonies whose queens were inseminated with 15 drones, suggesting benefits of polyandry at rates higher than those normally obtaining in nature. Our results are consistent with two hypotheses that posit conditions that reward such high expressions of polyandry: (1) a queen may mate with many males in order to promote beneficial non-additive genetic interactions among subfamilies, and (2) a queen may mate with many males in order to capture a large number of rare alleles that regulate resistance to pathogens and parasites in a breeding population. Our results are unique for identifying the highest levels of polyandry yet detected that confer colony-level benefit and for showing a benefit of polyandry in particular toward the parasitic mite V. destructor.

The regulatory element READ1 epistatically influences reading and language, with both deleterious and protective alleles

BackgroundReading disability (RD) and language impairment (LI) are heritable learning disabilities that obstruct acquisition and use of written and spoken language, respectively. We previously reported that two risk haplotypes, each...

Is There a Nonadditive Interaction Between Spontaneous and Evoked Activity? Phase-Dependence and Its Relation to the Temporal Structure of Scale-Free Brain Activity.

The aim of our study was to use functional magnetic resonance imaging to investigate how spontaneous activity interacts with evoked activity, as well as how the temporal structure of spontaneous activity, that is, long-range temporal correlations, relate to this interaction. Using an extremely sparse event-related design (intertrial intervals: 52-60 s), a novel blood oxygen level-dependent signal correction approach (accounting for spontaneous fluctuations using pseudotrials) and phase analysis, we provided direct evidence for a nonadditive interaction between spontaneous and evoked activity. We demonstrated the discrepancy between the present and previous observations on why a linear superposition between spontaneous and evoked activity can be seen by using co-occurring signals from homologous brain regions. Importantly, we further demonstrated that the nonadditive interaction can be characterized by phase-dependent effects of spontaneous activity, which is closely related to the degree of long-range temporal correlations in spontaneous activity as indexed by both power-law exponent and phase-amplitude coupling. Our findings not only contribute to the understanding of spontaneous brain activity and its scale-free properties, but also bear important implications for our understanding of neural activity in general.

Restoring fish ecological quality in estuaries: Implication of interactive and cumulative effects among anthropogenic stressors

Estuaries are subjected to multiple anthropogenic stressors, which have additive, antagonistic or synergistic effects. Current challenges include the use of large databases of biological monitoring surveys (e.g. the European Water Framework Directive) to help environmental managers prioritizing restoration measures. This study investigated the impact of nine stressor categories on the fish ecological status derived from 90 estuaries of the North East Atlantic countries. We used a random forest model to: 1) detect the dominant stressors and their non-linear effects; 2) evaluate the ecological benefits expected from reducing pressure from stressors; and 3) investigate the interactions among stressors. Results showed that largest restoration benefits were expected when mitigating water pollution and oxygen depletion. Non-additive effects represented half of pairwise interactions among stressors, and antagonisms were the most common. Dredged sediments, flow changes and oxygen depletion were predominantly implicated in non-additive interactions, whereas the remainder stressors often showed additive impacts. The prevalence of interactive impacts reflects a complex scenario for estuaries management; hence, we proposed a step-by-step restoration scheme focusing on the mitigation of stressors providing the maximum of restoration benefits under a multi-stress context.

Interactions of genetic variants reveal inverse modulation patterns of dopamine system on brain gray matter volume and resting-state functional connectivity in healthy young adults.

Different genotypic combinations of COMT and DRD2 can generate multiple subgroups with different levels of dopamine signaling. Its modulations on brain properties can be investigated by analyzing the combined gene effects of COMT and DRD2. However, the inherent association between modulation patterns of the dopamine system on structural and functional properties of the brain remains unknown. In 294 healthy young adults, we investigated both additive and non-additive interactions of COMT and DRD2 on gray matter volume (GMV) and resting-state functional connectivity (rsFC) using a voxel-based analysis. We found a significant non-additive COMT × DRD2 interaction in the right dorsal anterior cingulate cortex (dACC), exhibiting an inverted U-shape modulation by dopamine signaling. We also found a significant non-additive COMT × DRD2 interaction in the rsFC between the right dACC and precuneus, displaying a U-shape modulation by dopamine signaling. Moreover, this rsFC was negatively correlated with the GMV of the right dACC. Although the additive interaction did not pass corrections for multiple comparisons, we also found a trend towards an inverse modulation pattern and a negative correlation between the GMV and rsFC of the right inferior frontal gyrus. No genotypic differences were detected in any assessments of the cognition, mood and personality. These findings suggest that healthy young adults without optimal dopamine signaling may maintain their normal behavioral performance via a functional compensatory mechanism in response to structural deficit due to genetic variation.Electronic supplementary materialThe online version of this article (doi:10.1007/s00429-015-1134-4) contains supplementary material, which is available to authorized users.

Association of SLC2A9 genotype with phenotypic variability of serum urate in pre-menopausal women.

The SLC2A9 gene, that encodes a renal uric acid reuptake transporter, has genetic variants that explain ∼3% of variance in urate levels. There are previous reports of non-additive interaction between SLC2A9 genotype and environmental factors which influence urate control. Therefore, our aim was to further investigate the general phenomenon that such non-additive interactions contribute to genotype-specific association with variance at SLC2A9. Data from 14135 European individuals were used in this analysis. The measure of variance was derived from a ranked inverse normal transformation of residuals obtained by regressing known urate-influencing factors (sex, age, and body mass index) against urate. Variant rs6449173 showed the most significant effect on serum urate variance at SLC2A9 (P = 7.9 × 10-14), which was maintained after accounting for the effect on average serum urate levels (P = 0.022). Noting the stronger effect in a sub-cohort that consisted of pre-menopausal women and younger men, the participants were stratified into males and pre-menopausal and post-menopausal women. This revealed a strong effect on variance in pre-menopausal women (P = 3.7 × 10-5) with a weak effect in post-menopausal women (P = 0.032) and no effect in men (P = 0.22). The T-allele of rs6449173, which associates with increased urate levels, was associated with the greater variance in urate. There was a non-additive interaction between rs6449173 genotype and female gender in control of serum urate levels that was driven by a greater increase in urate levels associated with the T-allele in women. Female hormones, and/or other factors they influence or are associated with (such as iron levels, temperature, testosterone) interact with SLC2A9 genotype in women to determine urate levels. The association of SLC2A9 with greater variance in pre-menopausal women may reflect the cyclical changes resulting from menstruation.

Density-functional approach to the three-body dispersion interaction based on the exchange dipole moment.

We implement and compute the density functional nonadditive three-body dispersion interaction using a combination of Tang-Karplus formalism and the exchange-dipole moment model of Becke and Johnson. The computation of the C9 dispersion coefficients is done in a non-empirical fashion. The obtained C9 values of a series of noble atom triplets agree well with highly accurate values in the literature. We also calculate the C9 values for a series of benzene trimers and find a good agreement with high-level ab initio values reported recently in the literature. For the question of damping of the three-body dispersion at short distances, we propose two damping schemes and optimize them based on the benzene trimers data, and the fitted analytic potentials of He3 and Ar3 trimers fitted to the results of high-level wavefunction theories available from the literature. Both damping schemes respond well to the optimization of two parameters.

Identifying interactions among reforestation success drivers: A case study from the Philippines

Reforestation is an expensive undertaking. It is a long-term, complex, and trans-disciplinary process and it involves uncertainties and changing conditions. There is also a complex array of drivers (including biophysical, technical, socio-economic, institutional, and management drivers) that affect reforestation success. Previous research has documented the independent effects of biophysical and technical, environmental and socio-economic drivers on reforestation success. However, research over the last decade has revealed that the outcome of multiple factor interactions is commonly non-additive (i.e. synergies and antagonisms). Therefore, in order to provide better decision support for reforestation planning and policy setting it is necessary to understand the interactive effects that drivers have on reforestation success. To understand these interactive effects, we developed a Bayesian network model based on data collected from 43 reforestation projects on Leyte Island, the Philippines. Non-additive interactions among reforestation success drivers (i.e. synergies and antagonisms) were found to account for up to 90% of interactions tested. This result suggests an urgent need to account for these non-additive interactions in reforestation policy and planning in order to avoid unanticipated outcomes, wasted effort and missed opportunities.

Statistically significant deviations from additivity: What do they mean in assessing toxicity of mixtures?

There is increasing attention from scientists and policy makers to the joint effects of multiple metals on organisms when present in a mixture. Using root elongation of lettuce (Lactuca sativa L.) as a toxicity endpoint, the combined effects of binary mixtures of Cu, Cd, and Ni were studied. The statistical MixTox model was used to search deviations from the reference models i.e. concentration addition (CA) and independent action (IA). The deviations were subsequently interpreted as ‘interactions’. A comprehensive experiment was designed to test the reproducibility of the ‘interactions’. The results showed that the toxicity of binary metal mixtures was equally well predicted by both reference models. We found statistically significant ‘interactions’ in four of the five total datasets. However, the patterns of ‘interactions’ were found to be inconsistent or even contradictory across the different independent experiments. It is recommended that a statistically significant ‘interaction’, must be treated with care and is not necessarily biologically relevant. Searching a statistically significant interaction can be the starting point for further measurements and modeling to advance the understanding of underlying mechanisms and non-additive interactions occurring inside the organisms.

A traits-based test of the home-field advantage in mixed-species tree litter decomposition

Litter often decomposes faster in its environment of origin (at 'home') than in a foreign environment ('away'), which has become known as the home-field advantage (HFA). However, many studies have highlighted the conditional nature of the HFA, suggesting that current understanding of this phenomenon is not yet sufficient to generalize across systems. The HFA hypothesis was tested for mono-specific and mixed-species litter using a tree-based experiment that manipulated the functional identity and diversity of the host tree community. Litter types of varying quality were transplanted between several host tree communities and decomposition rates were measured using litterbags. Since the decomposer community should respond to traits of the litter input and not their taxonomic identity, a traits-based index of litter-tree similarity was developed. Mono-specific litter exhibited HFA, but when the same litter was decomposed in mixture, this trend was not observed. Mixed-species litter decomposed on average no faster or slower than monoculture litter and exhibited both positive and negative species interactions. These non-additive interactions of decomposition rates in mixture were influenced by the degree of similarity between litter and tree traits. Both synergistic and antagonistic interactions decreased in magnitude with increasing litter-tree similarity such that mixture rates were predictable from monocultures. The HFA occurred more strongly for mono-specific litter than for the litter types mixed together because interactions between species may have masked this effect. However, when expressed as a function of trait similarity between litters and tree communities, the HFA was not detected.

Intersecting transcription networks constrain gene regulatory evolution.

Epistasis—the non-additive interactions between different genetic loci—constrains evolutionary pathways, blocking some and permitting others1–8. For biological networks such as transcription circuits, the nature of these constraints and their consequences are largely unknown. Here we describe the evolutionary pathways of a transcription network that controls the response to mating pheromone in yeasts9. A component of this network, the transcription regulator Ste12, has evolved two different modes of binding to a set of its target genes. In one group of species, Ste12 binds to specific DNA binding sites, while in another lineage it occupies DNA indirectly, relying on a second transcription regulator to recognize DNA. We show, through the construction of various possible evolutionary intermediates, that evolution of the direct mode of DNA binding was not directly accessible to the ancestor. Instead, it was contingent on a lineage-specific change to an overlapping transcription network with a different function, the specification of cell type. These results show that analyzing and predicting the evolution of cis-regulatory regions requires an understanding of their positions in overlapping networks, as this placement constrains the available evolutionary pathways.

Social evolution and genetic interactions in the short and long term

The evolution of social traits remains one of the most fascinating and feisty topics in evolutionary biology even after half a century of theoretical research. W.D. Hamilton shaped much of the field initially with his 1964 papers that laid out the foundation for understanding the effect of genetic relatedness on the evolution of social behavior. Early theoretical investigations revealed two critical assumptions required for Hamilton’s rule to hold in dynamical models: weak selection and additive genetic interactions. However, only recently have analytical approaches from population genetics and evolutionary game theory developed sufficiently so that social evolution can be studied under the joint action of selection, mutation, and genetic drift. We review how these approaches suggest two timescales for evolution under weak mutation: (i) a short-term timescale where evolution occurs between a finite set of alleles, and (ii) a long-term timescale where a continuum of alleles are possible and populations evolve continuously from one monomorphic trait to another. We show how Hamilton’s rule emerges from the short-term analysis under additivity and how non-additive genetic interactions can be accounted for more generally. This short-term approach reproduces, synthesizes, and generalizes many previous results including the one-third law from evolutionary game theory and risk dominance from economic game theory. Using the long-term approach, we illustrate how trait evolution can be described with a diffusion equation that is a stochastic analogue of the canonical equation of adaptive dynamics. Peaks in the stationary distribution of the diffusion capture classic notions of convergence stability from evolutionary game theory and generally depend on the additive genetic interactions inherent in Hamilton’s rule. Surprisingly, the peaks of the long-term stationary distribution can predict the effects of simple kinds of non-additive interactions. Additionally, the peaks capture both weak and strong effects of social payoffs in a manner difficult to replicate with the short-term approach. Together, the results from the short and long-term approaches suggest both how Hamilton’s insight may be robust in unexpected ways and how current analytical approaches can expand our understanding of social evolution far beyond Hamilton’s original work.

Non-additive effects of intra- and interspecific competition between two larval salamanders.

Assessment of the relative strengths of intra- and interspecific competition has increased in recent years and is critical to understanding the importance of competition. Yet, whether intra- and interspecific competition can have non-additive effects has rarely been tested. The resulting fitness consequences of such non-additive interactions are important to provide the context necessary to advance our understanding of competition theory. We compared the strength of additive and non-additive intra- and interspecific competition by manipulating densities of a pair of larval salamanders (Ambystoma talpoideum and A. maculatum) in experimental mesocosms within a response surface design. Intraspecific density had the strongest effect on the strength of competition for both species, and few observed comparisons indicated interspecific competition was an important factor in predicting body size, growth or larval period length of either species. Non-additive effects of intra- and interspecific competition influenced some response variables, including size and mass at metamorphosis in A. maculatum, but at a reduced strength compared to intraspecific effects alone. Intraspecific competition was thus the dominant biotic interaction, but non-additive effects also impact the outcome of competition in these species, validating the importance of testing for and incorporating non-additive density effects into competition models.

Acute toxicity of binary and ternary mixtures of Cd, Cu, and Zn to Daphnia magna.

Standard static-exposure acute lethality tests were conducted with Daphnia magna neonates exposed to binary or ternary mixtures of Cd, Cu, and Zn in moderately hard reconstituted water that contained 3 mg dissolved organic carbon/L added as Suwannee River fulvic acid. These experiments were conducted to test for additive toxicity (i.e., the response to the mixture can be predicted by combining the responses obtained in single-metal toxicity tests) or nonadditive toxicity (i.e., the response is less than or greater than additive). Based on total metal concentrations (>90% dissolved) the toxicity of the tested metal mixtures could be categorized into all 3 possible additivity categories: less-than-additive toxicity (e.g., Cd-Zn and Cd-Cu-Zn mixtures and Cd-Cu mixtures when Cu was titrated into Cd-containing waters), additive toxicity (e.g., some Cu-Zn mixtures), or more-than-additive toxicity (some Cu-Zn mixtures and Cd-Cu mixtures when Cd was titrated into Cu-containing waters). Exposing the organisms to a range of sublethal to supralethal concentrations of the titrated metal was especially helpful in identifying nonadditive interactions. Geochemical processes (e.g., metal-metal competition for binding to dissolved organic matter and/or the biotic ligand, and possibly supersaturation of exposure waters with the metals in some high-concentration exposures) can explain much of the observed metal-metal interactions. Therefore, bioavailability models that incorporate those geochemical (and possibly some physiological) processes might be able to predict metal mixture toxicity accurately.

The adsorption of a mixture of particles with non-additive interactions: a Monte Carlo study

The adsorption of binary mixtures with non-additive lateral interactions has been studied through grand canonical Monte Carlo simulations in the framework of the lattice-gas model. The traditional assumption of additive lateral interactions is replaced with a more general one including non-pairwise interactions. It is assumed that the energy linking a certain atom with any of its nearest neighbors strongly depends on the state of occupancy in the first coordination sphere of such an adatom. The process has been monitored through the adsorption isotherms and the differential heats of adsorption. Different combinations of both inter- and intra-species interactions have been considered in the analysis. Interesting behaviors were observed and discussed in terms of the low temperature phases formed in the system.

Strong electronic polarization of the C60 fullerene by imidazolium-based ionic liquids: accurate insights from Born-Oppenheimer molecular dynamic simulations.

Fullerenes are known to be polarizable due to their strained carbon-carbon bonds and high surface curvature. The electronic polarization of fullerenes is steadily of practical importance because it leads to non-additive interactions and, therefore, to unexpected phenomena. For the first time, hybrid density functional theory (HDFT) powered Born-Oppenheimer molecular dynamics (BOMD) simulations have been conducted to observe electronic polarization and charge transfer phenomena in the C60 fullerene at finite temperature (350 K). The non-additive phenomena are fostered by the three selected imidazolium-based room-temperature ionic liquids (RTILs). We conclude that although charge transfer appears nearly negligible in these systems, electronic polarization is indeed significant, leading to a systematically positive effective electrostatic charge on the C60 fullerene: +0.14e in [MMIM][Cl], +0.21e in [MMIM][NO3], and +0.17e in [MMIM][PF6]. These results are, to a certain extent, unexpected and provide a motivation for considering novel C60-RTILs systems. HDFT BOMD is a powerful tool for investigating electronic effects in RTIL and fullerene containing nuclear-electronic systems.

Epistatic adaptive evolution of human color vision.

Establishing genotype-phenotype relationship is the key to understand the molecular mechanism of phenotypic adaptation. This initial step may be untangled by analyzing appropriate ancestral molecules, but it is a daunting task to recapitulate the evolution of non-additive (epistatic) interactions of amino acids and function of a protein separately. To adapt to the ultraviolet (UV)-free retinal environment, the short wavelength-sensitive (SWS1) visual pigment in human (human S1) switched from detecting UV to absorbing blue light during the last 90 million years. Mutagenesis experiments of the UV-sensitive pigment in the Boreoeutherian ancestor show that the blue-sensitivity was achieved by seven mutations. The experimental and quantum chemical analyses show that 4,008 of all 5,040 possible evolutionary trajectories are terminated prematurely by containing a dehydrated nonfunctional pigment. Phylogenetic analysis further suggests that human ancestors achieved the blue-sensitivity gradually and almost exclusively by epistasis. When the final stage of spectral tuning of human S1 was underway 45–30 million years ago, the middle and long wavelength-sensitive (MWS/LWS) pigments appeared and so-called trichromatic color vision was established by interprotein epistasis. The adaptive evolution of human S1 differs dramatically from orthologous pigments with a major mutational effect used in achieving blue-sensitivity in a fish and several mammalian species and in regaining UV vision in birds. These observations imply that the mechanisms of epistatic interactions must be understood by studying various orthologues in different species that have adapted to various ecological and physiological environments.

Polarization versus temperature in pyridinium ionic liquids.

Electronic polarization and charge transfer effects play a crucial role in thermodynamic, structural, and transport properties of room-temperature ionic liquids (RTILs). These nonadditive interactions constitute a useful tool for tuning physical chemical behavior of RTILs. Polarization and charge transfer generally decay as temperature increases, although their presence should be expected over an entire condensed state temperature range. For the first time, we use three popular pyridinium-based RTILs to investigate temperature dependence of electronic polarization in RTILs, based on a nonperiodic electronic density description for a cation-anion pair. Atom-centered density matrix propagation molecular dynamics, supplemented by a weak coupling to an external bath, is used to simulate the temperature impact on system properties. We show that, quite surprisingly, nonadditivity in the cation-anion interactions changes negligibly between 300 and 900 K, while the average dipole moment increases due to thermal fluctuations of geometries. Our results contribute to the fundamental understanding of electronic effects in the condensed phase of ionic systems and foster progress in physical chemistry and engineering.

On the Nature and Evolutionary Impact of Phenotypic Robustness Mechanisms.

Biologists have long observed that physiological and developmental processes are insensitive, or robust, to many genetic and environmental perturbations. A complete understanding of the evolutionary causes and consequences of this robustness is lacking. Recent progress has been made in uncovering the regulatory mechanisms that underlie environmental robustness in particular. Less is known about robustness to the effects of mutations, and indeed the evolution of mutational robustness remains a controversial topic. The controversy has spread to related topics, in particular the evolutionary relevance of cryptic genetic variation. This review aims to synthesize current understanding of robustness mechanisms and to cut through the controversy by shedding light on what is and is not known about mutational robustness. Some studies have confused mutational robustness with non-additive interactions between mutations (epistasis). We conclude that a profitable way forward is to focus investigations (and rhetoric) less on mutational robustness and more on epistasis.

Effects of near‐future ocean acidification, fishing, and marine protection on a temperate coastal ecosystem

Understanding ecosystem responses to global and local anthropogenic impacts is paramount to predicting future ecosystem states. We used an ecosystem modeling approach to investigate the independent and cumulative effects of fishing, marine protection, and ocean acidification on a coastal ecosystem. To quantify the effects of ocean acidification at the ecosystem level, we used information from the peer-reviewed literature on the effects of ocean acidification. Using an Ecopath with Ecosim ecosystem model for the Wellington south coast, including the Taputeranga Marine Reserve (MR), New Zealand, we predicted ecosystem responses under 4 scenarios: ocean acidification + fishing; ocean acidification + MR (no fishing); no ocean acidification + fishing; no ocean acidification + MR for the year 2050. Fishing had a larger effect on trophic group biomasses and trophic structure than ocean acidification, whereas the effects of ocean acidification were only large in the absence of fishing. Mortality by fishing had large, negative effects on trophic group biomasses. These effects were similar regardless of the presence of ocean acidification. Ocean acidification was predicted to indirectly benefit certain species in the MR scenario. This was because lobster (Jasus edwardsii) only recovered to 58% of the MR biomass in the ocean acidification + MR scenario, a situation that benefited the trophic groups lobsters prey on. Most trophic groups responded antagonistically to the interactive effects of ocean acidification and marine protection (46%; reduced response); however, many groups responded synergistically (33%; amplified response). Conservation and fisheries management strategies need to account for the reduced recovery potential of some exploited species under ocean acidification, nonadditive interactions of multiple factors, and indirect responses of species to ocean acidification caused by declines in calcareous predators.