Direct and indirect transgenerational effects alter plant-herbivore interactions

Theory suggests that environmental effects with transgenerational consequences, including rapid evolution and maternal effects, may affect the outcome of ecological interactions. However, indirect effects occur when interactions between two species are altered by the presence of a third species, and can make the consequences of transgenerational effects difficult to predict. We manipulated the presence of insect herbivores and the competitor Medicago polymorpha in replicated Lotus wrangelianus populations. After one generation, we used seeds from the surviving Lotus to initiate a reciprocal transplant experiment to measure how transgenerational effects altered ecological interactions between Lotus, Medicago, and insect herbivores. Herbivore leaf damage and Lotus fecundity were dependent on both parental and offspring environmental conditions. The presence of insect herbivores and Medicago in the parental environment resulted in transgenerational changes in herbivore resistance, but these effects were non-additive, likely as a result of indirect effects in the parental environment. Indirect transgenerational effects interacted with more immediate ecological indirect effects to affect Lotus fecundity. These results suggest that explanations of ecological patterns require an understanding of transgenerational effects and that these effects may be difficult to predict in species-rich, natural communities where indirect effects are prevalent.     

Analysis of genetic effects on nutrient quality traits in indica rice

Nine cytoplasmic male-sterile lines and five restorer lines were used in an incomplete diallel cross to analyze seed effects, cytoplasmic effects, and maternal gene effects on nutrient quality traits of indica rice (Oryza sauva L.). The results indicated that nutrient quality traits were controlled by cytoplasmic and maternal effects as well as by seed direct effects. Maternal effects for lysine content (LC), lysine index (LI), and the ratio of lysine content to protein content (RLP) were more important than seed direct effects, while protein content (PC) and protein index (PI) were mainly affected by seed direct effects. Cytoplasmic effects accounted for 2.41–20.80% of the total genetic variation and were significant for all nutrient quality traits. Additive genetic effects were much more important than dominance effects for all of the traits studied, so that selection could be applied for these traits in early generations.     

Match and mismatch: Integrating consumptive effects of predators,prey traits,and habitat selection in colonizing aquatic insects

Predators are a particularly critical component of habitat quality, as they affect survival, morphology, behavior, population size, and community structure through both consumptive and non‐consumptive effects. Non‐consumptive effects can often exceed consumptive effects, but their relative importance is undetermined in many systems. Our objective was to determine the consumptive and non‐consumptive effects of a predaceous aquatic insect, Notonecta irrorata, on colonizing aquatic beetles. We tested how N. irrorata affected survival and habitat selection of colonizing aquatic beetles, how beetle traits contributed to their vulnerability to predation by N. irrorata, and how combined consumptive and non‐consumptive effects affected populations and community structure. Predation vulnerabilities ranged from 0% to 95% mortality, with size, swimming, and exoskeleton traits generating species‐specific vulnerabilities. Habitat selection ranged from predator avoidance to preferentially colonizing predator patches. Attraction of Dytiscidae to N. irrorata may be a natural ecological trap given similar cues produced by these taxa. Hence, species‐specific habitat selection by prey can be either predator‐avoidance responses that reduce consumptive effects, or responses that magnify predator effects. Notonecta irrorata had both strong consumptive and non‐consumptive effects on populations and communities, while combined effects predicted even more distinct communities and populations across patches with or without predators. Our results illustrate that an aquatic invertebrate predator can have functionally unique consumptive effects on prey, attracting and repelling prey, while prey have functionally unique responses to predators. Determining species‐specific consumptive and non‐consumptive effects is important to understand patterns of species diversity across landscapes.     

Effects of tracking devices on individual birds – a review of the evidence

We review long‐term patterns of tracking device use and the reporting of the effects of such devices on individual birds. We assessed > 3400 primary references including > 1500 containing information as to whether effects were looked for and reported. Numbers of papers published increased at 4.4% yr^–1. Research on foraging and energetics focussed on seabirds while work on habitat use and dispersal was focussed mainly on landbirds. Migration was the most common study topic overall and increased markedly from the turn of the century in all three bird groups. The proportion of studies reporting effects of devices on individuals declined at > 1% yr^–1, while the proportion of studies providing no information on effects increased by ca 0.7% yr^–1. The presence of a control group increased the likelihood of a study reporting effects, (45 vs 33%). We modelled the probability of reporting effects separately for three bird groups and two attachment durations. Occurrence of effects was significantly related to attachment method (4 models), year (4 models) and relative device mass (1 model). Invasive attachment methods were associated with a high incidence of effects while tail and leg attachments showed relatively few effects. Probabilities of reporting effects declined over time and increased with relative device mass, however there was no device mass threshold below which effects were not observed. Approaches designed to minimize potential effects of devices on individual birds and to improve scientific rigour have advanced substantially. Nevertheless ca 55% of studies contained no information on potential effects and in many more documentation was inadequate. We call for more systematic documentation of potential effects in peer‐reviewed publications to support more rigorous science and to further improve bird welfare.     

Mesopredator suppression by an apex predator alleviates the risk of predation perceived by small prey

Predators can impact their prey via consumptive effects that occur through direct killing, and via non-consumptive effects that arise when the behaviour and phenotypes of prey shift in response to the risk of predation. Although predators'' consumptive effects can have cascading population-level effects on species at lower trophic levels there is less evidence that predators'' non-consumptive effects propagate through ecosystems. Here we provide evidence that suppression of abundance and activity of a mesopredator (the feral cat) by an apex predator (the dingo) has positive effects on both abundance and foraging efficiency of a desert rodent. Then by manipulating predators'' access to food patches we further the idea that apex predators provide small prey with refuge from predation by showing that rodents increased their habitat breadth and use of ‘risky′ food patches where an apex predator was common but mesopredators rare. Our study suggests that apex predators'' suppressive effects on mesopredators extend to alleviate both mesopredators'' consumptive and non-consumptive effects on prey.     

Genetic and heterosis analysis for important agronomic traits of Chinese vegetable mustard (<Emphasis Type="Italic">Brassica juncea</Emphasis>) in different environments

Genetic effects and genotype by environment (GE) interaction effects for some important agronomic traits of Chinese vegetable mustard were analyzed by using a genetic model including additive, dominance, additive × additive effects and their interaction effects with the environment. Four variations of Chinese vegetable mustard as parental lines and their F_1s, F_2s were evaluated in two locations. It was revealed that the agronomic traits of Chinese vegetable mustard were mainly controlled by genetic effects except plant weight (PW) and leaf weight (LW) were observed to be more affected by GE interaction effects. Among the genetic effects, additive effects took the main proportion for tiller number (TN), leaf number (LN), leaf breadth (LB) and LW; dominance effects were the main components of PW, leaf length (LL), root weight (RW) and plant height (PH); additive × additive effects were the main components of plant breadth (PB). Among the GE interaction effects, additive × environment interaction effects mainly affected LB, LW and RW, while PW, LL, PH and PB were mainly controlled by dominance × environment interaction effects. Besides, additive × additive × environment interaction was the main factor, which controlled TN and LN of Chinese vegetable mustard. For heterosis analyses, TN, LN, LB and LW of Chinese vegetable mustard showed positive H_PM and negative H_PB. The other traits showed positive H_PM and H_PB. Heterosis arising from GE interaction was found to varying degree for different environments. It was shown that genetic heterosis and GE interaction effects were important factors for agronomic traits in Chinese vegetable mustard.     

A comparison of maternal effects and current environment on vital rates of Aphis nerii, the milkweed–oleander aphid

Abstract.  1. Non-Mendelian maternal effects, the effects of maternal phenotype or environment on offspring phenotype, have been documented in numerous taxa. By affecting offspring vital rates (birth, death, and movement), maternal effects have the potential to influence population dynamics. However, relatively few studies have directly linked maternal phenotype or environment to offspring vital rates. Additionally, even fewer studies have compared the magnitude of across-generation effects (i.e. maternal effects) to within-generation effects.
2. Because of their telescoping generations, aphids can be strongly influenced by maternal effects. The effects of maternal density and maternal host-plant species on offspring survival, fecundity, and alate formation were investigated experimentally in Aphis nerii , the milkweed–oleander aphid.
3. Additionally, the relative strength of maternal effects were compared with those operating within a generation. Therefore, in another set of experiments, the effects of current density and host-plant species (within-generation effects) on aphid vital rates were examined.
4. While maternal effects were present, within-generation effects were much stronger and more strongly influenced aphid vital rates. Within a generation, aphids exhibited density-dependent survival, fecundity, and alate formation and these effects varied among host-plant species.
5. These results indicate that while maternal effects have the potential to affect population dynamics, this potential is not always met. Additionally, the current environment, not the environment of previous generations, more strongly impacts population dynamics.     

Epigenetic modifications in radiation-induced non-targeted effects and their clinical significance

BackgroundIonizing radiation (IR) plays an important role in the diagnosis and treatment of cancer. Besides the targeted effects, the non-targeted effects, which cause damage to non-irradiated cells and genomic instability in normal tissues, also play a role in the side effects of radiotherapy and have been shown to involve both alterations in DNA sequence and regulation of epigenetic modifications.Scope of reviewWe summarize the recent findings regarding epigenetic modifications that are involved in radiation-induced non-targeted effects as well as their clinical significance in radiotherapy and radioprotection.Major conclusionsEpigenetic modifications play an important role in both the realization and modulation of radiobiological effects. However, the molecular mechanisms underlying non-targeted effects still need to be clarified.General significanceA better understanding of the epigenetic mechanisms related to radiation-induced non-targeted effects will guide both individualized clinical radiotherapy and individualized precise radioprotection.     

Direct and transgenerational effects of an experimental heatwave on early life stages in a freshwater snail

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Predator‐driven elemental cycling: the impact of predation and risk effects on ecosystem stoichiometry

Empirical evidence is beginning to show that predators can be important drivers of elemental cycling within ecosystems by propagating indirect effects that determine the distribution of elements among trophic levels as well as determine the chemical content of organic matter that becomes decomposed by microbes. These indirect effects can be propagated by predator consumptive effects on prey, nonconsumptive (risk) effects, or a combination of both. Currently, there is insufficient theory to predict how such predator effects should propagate throughout ecosystems. We present here a theoretical framework for exploring predator effects on ecosystem elemental cycling to encourage further empirical quantification. We use a classic ecosystem trophic compartment model as a basis for our analyses but infuse principles from ecological stoichiometry into the analyses of elemental cycling. Using a combined analytical‐numerical approach, we compare how predators affect cycling through consumptive effects in which they control the flux of nutrients up trophic chains; through risk effects in which they change the homeostatic elemental balance of herbivore prey which accordingly changes the element ratio herbivores select from plants; and through a combination of both effects. Our analysis reveals that predators can have quantitatively important effects on elemental cycling, relative to a model formalism that excludes predator effects. Furthermore, the feedbacks due to predator nonconsumptive effects often have the quantitatively strongest impact on whole ecosystem elemental stocks, production and efficiency rates, and recycling fluxes by changing the stoichiometric balance of all trophic levels. Our modeling framework predictably shows how bottom‐up control by microbes and top‐down control by predators on ecosystems become interdependent when top predator effects permeate ecosystems.     

Analysis on additive effects and additive-by-additive epistatic effects of QTLs for yield traits in a recombinant inbred line population of rice

A linkage map consisting of 158 DNA markers were constructed by using a recombinant inbred line (RIL) population derived from the indica-indica rice cross Zhenshan 97B 2 Milyang 46. Quantitative trait loci (QTLs) conditioning grain yield and five yield component traits were determined at the one-locus and two-locus levels, and genotype-by-environment (GE) interactions were analyzed. Thirty-one QTLs were detected to have significant additive effects for yield traits, of which 12 also exhibited significant epistatic effects. Sixteen significant additive-by-additive (AA) interactions were detected, of which nine occurred between QTLs with own additive effects (M_epQTLs), four occurred between QTLs showing epistatic effects only (epQTLs), and three occurred between M_epQTLs and epQTLs. Significant GE interactions were found for six QTLs with additive effects and one AA interaction. Generally, the contributions to the phenotypic variation were higher due to QTL main effects than to epistatic effects. The detection of additive effects and AA effects of a QTL interfered with each other, indicating that the detection of QTLs with main effects, as well as the magnitude and directions of the additive effects, might vary depending on their interactions with other loci.     

The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study

Genome-wide association studies (GWAS) have identified more than 100 genetic variants contributing to BMI, a measure of body size, or waist-to-hip ratio (adjusted for BMI, WHR_adjBMI), a measure of body shape. Body size and shape change as people grow older and these changes differ substantially between men and women. To systematically screen for age- and/or sex-specific effects of genetic variants on BMI and WHR_adjBMI, we performed meta-analyses of 114 studies (up to 320,485 individuals of European descent) with genome-wide chip and/or Metabochip data by the Genetic Investigation of Anthropometric Traits (GIANT) Consortium. Each study tested the association of up to ~2.8M SNPs with BMI and WHR_adjBMI in four strata (men ≤50y, men >50y, women ≤50y, women >50y) and summary statistics were combined in stratum-specific meta-analyses. We then screened for variants that showed age-specific effects (G x AGE), sex-specific effects (G x SEX) or age-specific effects that differed between men and women (G x AGE x SEX). For BMI, we identified 15 loci (11 previously established for main effects, four novel) that showed significant (FDR<5%) age-specific effects, of which 11 had larger effects in younger (<50y) than in older adults (≥50y). No sex-dependent effects were identified for BMI. For WHR_adjBMI, we identified 44 loci (27 previously established for main effects, 17 novel) with sex-specific effects, of which 28 showed larger effects in women than in men, five showed larger effects in men than in women, and 11 showed opposite effects between sexes. No age-dependent effects were identified for WHR_adjBMI. This is the first genome-wide interaction meta-analysis to report convincing evidence of age-dependent genetic effects on BMI. In addition, we confirm the sex-specificity of genetic effects on WHR_adjBMI. These results may provide further insights into the biology that underlies weight change with age or the sexually dimorphism of body shape.     

Genetic and heterosis analysis for cooking quality traits of indica rice in different environments

Genetic effects and genotype×environment (GE) interaction effects on the cooking quality traits of indica rice (Oryza sativa L.) were analyzed based on a genetic model for quantitative traits of triploid endosperm in cereal crops. Nine cytoplasmic male-sterile lines as females and 5 restoring lines as males were used in an incomplete diallel cross over 2 years. The cooking quality traits studied were observed to be mainly controlled by genetic effects, but GE interaction effects, especially for amylose content (AC) and alkali spreading score (ASS), were also indicated. Among the genetic effects, seed direct effects and maternal effects were the main components of AC and ASS, respectively; cytoplasmic effects were the main components of gel consistency (GC). Among the GE interaction effects, AC and ASS were mainly affected by maternal interaction effects and GC by direct interaction effects. Additive effects and/or additive interaction effects were the main factors controlling the performance of rice cooking quality traits except for GC which was affected by dominant interaction effects. For AC and GC, there were seed heterosis and/or maternal heterosis. The predicated genetic effects indicated that four parents were better than the others in improving the rice cooking quality traits of the progenies. It was shown that genetic heterosis and GE interaction heterosis were important, especially for amylose content trait in early season indica rice.     

Sulfur dioxide,a double-faced molecule in mammals

Sulfur dioxide (SO₂) is a common air pollutant and is detrimental to many organs. Its toxic effects including oxidative damage, deoxyribonucleic acid (DNA) damage and inflammation have been extensively studied. However, recent studies showed that SO₂ can be generated endogenously in mammals. In contrast to the toxic effects of SO₂, protective effects have also been found in mammals. Endogenous SO₂ has antioxidant, anti-inflammatory, anti-hypertension, and anti-atherogenic effects and regulates vascular tone and cardiac function in mammals. SO₂ may have a dual role in regulating physiological and pathophysiological effects in mammals. The biological effects of SO₂ in mammals are reviewed in this study.     

Are species differences in maternal effects arising from maternal care adaptive?

Parental care benefits offspring through maternal effects influencing their development, growth and survival. However, although parental care in general is likely the result of adaptive evolution, it does not follow that specific differences in the maternal effects that arise from care are also adaptive. Here, we used an interspecific cross‐fostering design in the burying beetle species Nicrophorus orbicollis and N. vespilloides, both of which have elaborate parental care involving direct feeding of regurgitated food to offspring, to test whether maternal effects are optimized within a species and therefore adaptive. Using a full‐factorial design, we first demonstrated that N. orbicollis care for offspring longer regardless of recipient species. We then examined offspring development and mass in offspring reared by hetero‐ or conspecific parents. As expected, there were species‐specific direct effects independent of the maternal effects, as N. orbicollis larvae were larger and took longer to develop than N. vespilloides regardless of caregiver. We also found significant differences in maternal effects: N. vespilloides maternal care caused more rapid development of offspring of either species. Contrary to expectations if maternal effects were species‐specific, there were no significant interactions between caretaker and recipient species for either development time or mass, suggesting that these maternal effects are general rather than optimized within species. We suggest that rather than coadaptation between parents and offspring performance, the species differences in maternal effects may be correlated with direct effects, and that their evolution is driven by selection on those direct effects.     

Maternal effects and the outcome of interspecific competition

1. Maternal environmental effects create lagged population responses to past environments. Although they are ubiquitous and vary in expression across taxa, it remains unclear if and how their presence alters competitive interactions in ecological communities.
2. Here, we use a discrete‐time competition model to simulate how maternal effects alter competitive dynamics in fluctuating and constant environments. Further, we explore how omitting maternal effects alter estimates of known model parameters from observational time series data.
3. Our simulations demonstrate that (i) maternal effects change competitive outcomes, regardless of whether competitors otherwise interact neutrally or exhibit non‐neutral competitive differences, (ii) the consequences of maternal effects for competitive outcomes are mediated by the temporal structure of environmental variation, (iii) even in constant conditions, competitive outcomes are influenced by species'' maternal effects strategies, and (iv) in observational time series data, omitting maternal effects reduces variation explained by models and biases parameter estimates, including competition coefficients.
4. Our findings demonstrate that the ecological consequences of maternal effects hinge on the competitive environment. Evolutionary biologists have long recognized that maternal effects can be an important but often overlooked strategy buffering populations from environmental change. We suggest that maternal effects are similarly critical to ecology and call for research into maternal effects as drivers of dynamics in populations and communities.

     

Contrasting effects of hemiparasites on ecosystem processes: can positive litter effects offset the negative effects of parasitism?

Hemiparasites are known to influence community structure and ecosystem functioning, but the underlying mechanisms are not well studied. Variation in the impacts of hemiparasites on diversity and production could be due to the difference in the relative strength of two interacting pathways: direct negative effects of parasitism and positive effects on N availability via litter. Strong effects of parasitism should result in substantial changes in diversity and declines in productivity. Conversely, strong litter effects should result in minor changes in diversity and increased productivity. We conducted field-based surveys to determine the association of Castilleja occidentalis with diversity and productivity in the alpine tundra. To examine litter effects, we compared the decomposition of Castilleja litter with litter of four other abundant plant species, and examined the decomposition of those four species when mixed with Castilleja. Castilleja was associated with minor changes in diversity but almost a twofold increase in productivity and greater foliar N in co-occurring species. Our decomposition trials suggest litter effects are due to both the rapid N loss of Castilleja litter and the effects of mixing Castilleja litter with co-occurring species. Castilleja produces litter that accelerates decomposition in the alpine tundra, which could accelerate the slow N cycle and boost productivity. We speculate that these positive effects of litter outweigh the effects of parasitism in nutrient-poor systems with long-lived hemiparasites. Determining the relative importance of parasitism and litter effects of this functional group is crucial to understand the strong but variable roles hemiparasites play in affecting community structure and ecosystem processes.     

A framework for evolutionary systems biology

Background  

Many difficult problems in evolutionary genomics are related to mutations that have weak effects on fitness, as the consequences of mutations with large effects are often simple to predict. Current systems biology has accumulated much data on mutations with large effects and can predict the properties of knockout mutants in some systems. However experimental methods are too insensitive to observe small effects.     

Assembly-history dynamics of a pitcher-plant protozoan community in experimental microcosms

Background

History drives community assembly through differences both in density (density effects) and in the sequence in which species arrive (sequence effects). Density effects arise from predictable population dynamics, which are free of history, but sequence effects are due to a density-free mechanism, arising solely from the order and timing of immigration events. Few studies have determined how components of immigration history (timing, number of individuals, frequency) alter local dynamics to determine community assembly, beyond addressing when immigration history produces historically contingent assembly.

Methods/Findings

We varied density and sequence effects independently in a two-way factorial design to follow community assembly in a three-species aquatic protozoan community. A superior competitor, Colpoda steinii, mediated alternative community states; early arrival or high introduction density allowed this species to outcompete or suppress the other competitors (Poterioochromonas malhamensis and Eimeriidae gen. sp.). Multivariate analysis showed that density effects caused greater variation in community states, whereas sequence effects altered the mean community composition.

Conclusions

A significant interaction between density and sequence effects suggests that we should refine our understanding of priority effects. These results highlight a practical need to understand not only the “ingredients” (species) in ecological communities but their “recipes” as well.     

<Emphasis Type="Italic">Acroptilon repens</Emphasis>, an Asian invader,has stronger competitive effects on species from America than species from its native range

The ability to competitively suppress native species is key to successful invasion. Since invasions involve an increase in abundance or dominance of a species in its non-native range, competitive effects might be expected to be stronger in the non-native range of an invader; however, there have been few comparisons of the competitive effects of invasive plants on species from invaded ranges versus species from native ranges. We compared the competitive and allelopathic effects of Acroptilon repens on native North American species to effects on related species from the native range of Acroptilon in Uzbekistan. We also compared the competitive interactions among these North American and Eurasian species, in the absence of Acroptilon, examining the hypothesis that particular regional species pools may show differences in competitive ability. The results showed that Acroptilon had stronger competitive effects against native North American species than against species native to Uzbekistan. There was no difference in the competitive effects among Eurasians and North Americans. The effects of leachates collected from Acroptilon roots were weak but more negative on species from North America than on species from Uzbekistan. Our results suggest that inherently stronger competitive and allelopathic effects of Acroptilon on North American plants than on plants from its native range may contribute to its invasive success.