Empirical patterns of environmental variation favor adaptive transgenerational plasticity

Effects of parental environment on offspring traits have been well known for decades. Interest in this transgenerational form of phenotypic plasticity has recently surged due to advances in our understanding of its mechanistic basis. Theoretical research has simultaneously advanced by predicting the environmental conditions that should favor the adaptive evolution of transgenerational plasticity. Yet whether such conditions actually exist in nature remains largely unexplored. Here, using long‐term climate data, we modeled optimal levels of transgenerational plasticity for an organism with a one‐year life cycle at a spatial resolution of 4 km² across the continental United States. Both annual temperature and precipitation levels were often autocorrelated, but the strength and direction of these autocorrelations varied considerably even among nearby sites. When present, such environmental autocorrelations render offspring environments statistically predictable based on the parental environment, a key condition for the adaptive evolution of transgenerational plasticity. Results of our optimality models were consistent with this prediction: High levels of transgenerational plasticity were favored at sites with strong environmental autocorrelations, and little‐to‐no transgenerational plasticity was favored at sites with weak or nonexistent autocorrelations. These results are among the first to show that natural patterns of environmental variation favor the evolution of adaptive transgenerational plasticity. Furthermore, these findings suggest that transgenerational plasticity is likely variable in nature, depending on site‐specific patterns of environmental variation.     

Trophic plasticity of Antarctic echinoids under contrasted environmental conditions

Echinoids are common members of Antarctic zoobenthos, and different groups can show important trophic diversity. As part of the ANT-XXIX/3 cruise of RV Polarstern, trophic plasticity of sea urchins was studied in three neighbouring regions (Drake Passage, Bransfield Strait and Weddell Sea) featuring several depth-related habitats offering different trophic environments to benthic consumers. Three families with contrasting feeding habits (Cidaridae, Echinidae and Schizasteridae) were studied. Gut content examination and stable isotopes ratios of C and N suggest that each of the studied families showed a different response to variation in environmental and food conditions. Schizasteridae trophic plasticity was low, and these sea urchins were bulk sediment feeders relying on sediment-associated organic matter in all regions and/or depth-related habitats. Cidaridae consumed the most animal-derived material. Their diet varied according to the considered area, as sea urchins from Bransfield Strait relied mostly on living and/or dead animal material, while specimens from Weddell Sea fed on a mixture of dead animal material and other detritus. Echinidae also showed important trophic plasticity. They fed on various detrital items in Bransfield Strait, and selectivity of ingested material varied across depth-related habitats. In Weddell Sea, stable isotopes revealed that they mostly relied on highly ¹³C-enriched food items, presumably microbially reworked benthic detritus. The differences in adaptive strategies could lead to family-specific responses of Antarctic echinoids to environmental and food-related changes.     

RNA-mediated transgenerational inheritance in ciliates and plants

In the age of next-generation sequencing (NGS) and with the availability of whole sequenced genomes and epigenomes, some attention has shifted from purely sequence-based studies to those of heritable epigenetic modifications. Transgenerational inheritance can be defined as heritable changes to the state of DNA that may be passed on to subsequent generations without alterations to the underlying DNA sequence. Although this phenomenon has been extensively studied in many systems, studies of transgenerational inheritance in mammals and other higher-level eukaryotes may be complicated by the fact that many epigenetic marks are reprogrammed during sexual reproduction. This, by definition, may obscure our interpretation of what is in fact truly transgenerational. Therefore, in this mini review, we discuss what is currently known in the field about transgenerational epigenetic inheritance in ciliates and plants, with a particular emphasis on RNA-mediated processes and changes in chromatin states.     

Management and sperm production of boars under differing environmental conditions

The management of boars to ensure good sperm production under differing environmental conditions is a major concern for pig keepers in both tropical countries and countries where there are extreme environmental changes. Such changes create stress in animals and influence the production of spermatozoa. High temperatures during hot summer months may result in lower feed consumption and create stresses that result in the inhibition of spermatogenesis. Although tropical countries do not have a problem with major variations in day length, this can cause problems such as decreased litter size and infertility in other regions of the world. Evaporative cooling systems built into boar accommodation are often used to reduce fluctuations in both temperature and humidity during the hot and humid months seen in tropical countries. The system has become popular in AI boar studs, where it is reported to reduce stress and improve feed consumption. Other management factors, such as housing comfort, social contact, mating conditions and the frequency of mating, are also very important boar management aids that assist good quality semen production; these will be covered briefly in this review. This review will consider primarily those management factors, for example, the management of temperature and humidity using evaporative cooling systems and other techniques that enable AI boar studs to maximize sperm fertility through adjustments to the environment.     

Role of epigenetics in developmental biology and transgenerational inheritance

The molecular mechanisms involved in developmental biology and cellular differentiation have traditionally been considered to be primarily genetic. Environmental factors that influence early life critical windows of development generally do not have the capacity to modify genome sequence, nor promote permanent genetic modifications. Epigenetics provides a molecular mechanism for environment to influence development, program cellular differentiation, and alter the genetic regulation of development. The current review discusses how epigenetics can cooperate with genetics to regulate development and allow for greater plasticity in response to environmental influences. This impacts area such as cellular differentiation, tissue development, environmental induced disease etiology, epigenetic transgenerational inheritance, and the general systems biology of organisms and evolution.     

Evolution of environmental cues for phenotypic plasticity

Phenotypically plastic characters may respond to multiple variables in their environment, but the evolutionary consequences of this phenomenon have rarely been addressed theoretically. We model the evolution of linear reaction norms in response to several correlated environmental variables, in a population undergoing stationary environmental fluctuations. At evolutionary equilibrium, the linear combination of environmental variables that acts as a developmental cue for the plastic trait is the multivariate best linear predictor of changes in the optimum. However, the reaction norm with respect to any single environmental variable may exhibit nonintuitive patterns. Apparently maladaptive, or hyperadaptive plasticity can evolve with respect to single environmental variables, and costs of plasticity may increase, rather than reduce, plasticity in response to some variables. We also find conditions for the evolution of an indirect environmental indicator that affects expression of a plastic phenotype, despite not influencing natural selection on it.     

Selected aspects of transgenerational epigenetic inheritance and resetting in plants

Transgenerational epigenetic inheritance (TEI), which is the inheritance of expression states and thus traits that are not determined by the DNA sequence, is often postulated but the molecular mechanisms involved are only rarely verified. This especially applies to the heritability of environmentally induced traits, which have gained interest over the last years. Here we will discuss selected examples of epigenetic inheritance in plants and artificially divide them according to the occurrence of inter-generational resetting. The decision which epigenetic marks are reset and which ones are not is crucial for the understanding of TEI. We will consider examples of epialleles found in natural populations and epialleles induced by genetic and/or environmental factors used in experimental setups.     

Gene bionetworks involved in the epigenetic transgenerational inheritance of altered mate preference: environmental epigenetics and evolutionary biology

Background

Mate preference behavior is an essential first step in sexual selection and is a critical determinant in evolutionary biology. Previously an environmental compound (the fungicide vinclozolin) was found to promote the epigenetic transgenerational inheritance of an altered sperm epigenome and modified mate preference characteristics for three generations after exposure of a gestating female.

Results

The current study investigated gene networks involved in various regions of the brain that correlated with the altered mate preference behavior in the male and female. Statistically significant correlations of gene clusters and modules were identified to associate with specific mate preference behaviors. This novel systems biology approach identified gene networks (bionetworks) involved in sex-specific mate preference behavior. Observations demonstrate the ability of environmental factors to promote the epigenetic transgenerational inheritance of this altered evolutionary biology determinant.

Conclusions

Combined observations elucidate the potential molecular control of mate preference behavior and suggests environmental epigenetics can have a role in evolutionary biology.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-377) contains supplementary material, which is available to authorized users.     

Large-scale mapping of sequence-function relations in small regulatory RNAs reveals plasticity and modularity

Two decades into the genomics era the question of mapping sequence to function has evolved from identifying functional elements to characterizing their quantitative properties including, in particular, their specificity and efficiency. Here, we use a large-scale approach to establish a quantitative map between the sequence of a bacterial regulatory RNA and its efficiency in modulating the expression of its targets. Our approach generalizes the sort-seq method, introduced recently to analyze promoter sequences, in order to accurately quantify the efficiency of a large library of sequence variants. We focus on two small RNAs (sRNAs) in E. coli, DsrA and RyhB, and their regulation of both repressed and activated targets. In addition to precisely identifying functional elements in the sRNAs, our data establish quantitative relationships between structural and energetic features of the sRNAs and their regulatory activity, and characterize a large set of direct and indirect interactions between nucleotides. A core of these interactions supports a model where specificity can be enhanced by a rigid molecular structure. Both sRNAs exhibit a modular design with limited cross-interactions, dividing the requirements for structural stability and target binding among modules.     

Maternal adaptations and inheritance in the transgenerational programming of adult disease

Adverse exposures in utero have long been linked with an increased susceptibility to adult cardio-renal and metabolic diseases. Clear gender differences exist, whereby growth-restricted females, although exhibiting some phenotypic modifications, are often protected from overt disease outcomes. One of the greatest physiological challenges facing the female gender, however, is that of pregnancy; yet little research has focused on the outcomes associated with this, as a potential 'second-hit' for those who were small at birth. We review the limited evidence suggesting that pregnancy may unmask cardio-renal and metabolic disease states and the consequences for long-term maternal health in females who were born small. Additionally, a growing area of research in this programming field is in the transgenerational transmission of low birth weight and disease susceptibility. Pathways for transmission might include an abnormal adaptation to pregnancy by the growth-restricted mother and/or inheritance via the parental germline. Strategies to optimise the pregnancy environment and/or prevent the consequences of inheritance of programmed deficits and dysfunction are of critical importance for future generations.     

Changes in morphological plasticity of Ulva prolifera under different environmental conditions: A laboratory experiment

The large-scale green tides, consisting mainly of Ulva prolifera, have invaded the coastal zones of western Yellow Sea each year since 2008, resulting in tremendous impacts on the local environment and economy. A large number of studies have been conducted to investigate the physiological traits of U. prolifera to explain its dominance in the green tides. However, little has been reported regarding the response of U. prolifera to changing environmental factors via morphological variation. In our experiments, we found remarkable morphological acclimation of U. prolifera to various temperature (20 and 25 °C) and salinity (10, 20, and 30) conditions. U. prolifera had more, but shorter branches when they were cultured at lower temperature and salinity conditions. To investigate the significance of these morphological variations in its acclimation to changes of environmental factors, physiological and biochemical traits of U. prolifera grown under different conditions were measured. Higher temperature increased the relative growth rate while salinity did not affect it. On the other hand, higher temperature did not enhance the net photosynthetic rate whilst lower salinity did. The increased net photosynthetic rate at lower salinity conditions could be attributed to more photosynthetic pigments—chlorophyll a, chlorophyll b, and carotenoids—in thalli due to there being more branches at lower salinity conditions. Increased numbers of branches and thus an increased intensity of thalli may be helpful to protect thalli from increased osmotic pressure caused by lower salinity, but it led to more shading. In order to capture enough light when being shaded, thalli of U. prolifera synthesized more photosynthetic pigments at lower salinity levels. In addition, higher temperature increased nitrate reductase activity and soluble protein content but variations in salinity did not impose any effect on them. Our results demonstrate conclusively that U. prolifera can acclimatize in the laboratory to the changes of environmental factors (salinity and temperature) by morphology-driven physiological and biochemical variation. We suggest that the morphological plasticity of U. prolifera may be an important factor for it to outcompete other algal species in a changing ocean.     

细菌sRNA对环境胁迫的响应机制

细菌小RNA (Small RNAs,sRNAs)是一类长度大约在40?400个核酸之间,不编码蛋白质的RNA,在细菌适应环境方面起重要的调节作用。当环境中温度、营养、外膜蛋白、pH、铁等条件改变时,sRNA常常通过连接双组分信号转导系统和调节蛋白,来传递压力信号并调节应激响应,其作用方式一般是通过碱基互补配对的方式与靶mRNA结合,从而调控靶mRNA的翻译和稳定性;或直接与靶标蛋白质结合,调节靶标蛋白质的生物活性。本文总结了细菌在多种环境压力下,sRNA的调控响应机制。     

Triacontanol as a dynamic growth regulator for plants under diverse environmental conditions

Triacontanol (TRIA) being an endogenous plant growth regulator facilitates numerous plant metabolic activities leading to better growth and development. Moreover, TRIA plays essential roles in alleviating the stress-accrued alterations in crop plants via modulating the activation of the stress tolerance mechanisms. The present article critically focuses on the role of exogenously applied TRIA in morpho-physiology and biochemistry of plants for example, in terms of growth, photosynthesis, enzymatic activity, biofuel synthesis, yield and quality under normal and stressful conditions. This article also enlightens the mode of action of TRIA and its interaction with other phytohormones in regulating the physio-biochemical processes in counteracting the stress-induced damages in plants.

     

The mechanisms of transgenerational inheritance and their potential contribution to human phenotypes

As of today, classical genetics has already completed the majority of groundwork to describe the laws of inheritance, identify the causes of many human diseases, and dissect the mechanisms of transfer of genetic information from parents to offspring. However, recent studies indicate that inheritance of phenotypic traits may also occur through nongenetic factors, in particular, through epigenetic factors, that manifest their effects in a transgenerational fashion. This review discusses findings in the area of transgenerational inheritance that open a new era in modern genetics. We discuss the mechanisms of transgenerational inheritance, including DNA methylation, histone modifications, and noncoding RNA transfer, and give an overview of the approaches to detect transgenerational effects in humans.     

Role of phenotypic plasticity and population differentiation in adaptation to novel environmental conditions

Species can adapt to new environmental conditions either through individual phenotypic plasticity, intraspecific genetic differentiation in adaptive traits, or both. Wild emmer wheat, Triticum dicoccoides, an annual grass with major distribution in Eastern Mediterranean region, is predicted to experience in the near future, as a result of global climate change, conditions more arid than in any part of the current species distribution. To understand the role of the above two means of adaptation, and the effect of population range position, we analyzed reaction norms, extent of plasticity, and phenotypic selection across two experimental environments of high and low water availability in two core and two peripheral populations of this species. We studied 12 quantitative traits, but focused primarily on the onset of reproduction and maternal investment, which are traits that are closely related to fitness and presumably involved in local adaptation in the studied species. We hypothesized that the population showing superior performance under novel environmental conditions will either be genetically differentiated in quantitative traits or exhibit higher phenotypic plasticity than the less successful populations. We found the core population K to be the most plastic in all three trait categories (phenology, reproductive traits, and fitness) and most successful among populations studied, in both experimental environments; at the same time, the core K population was clearly genetically differentiated from the two edge populations. Our results suggest that (1) two means of successful adaptation to new environmental conditions, phenotypic plasticity and adaptive genetic differentiation, are not mutually exclusive ways of achieving high adaptive ability; and (2) colonists from some core populations can be more successful in establishing beyond the current species range than colonists from the range extreme periphery with conditions seemingly closest to those in the new environment.     

Transgenerational inheritance of sexual attractiveness via small RNAs enhances evolvability in C. elegans

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