Collective behavior and nongenetic inheritance allow bacterial populations to adapt to changing environments.

Collective behaviors require coordination among a group of individuals. As a result, individuals that are too phenotypically different from the rest of the group can be left out, reducing heterogeneity, but increasing coordination. If individuals also reproduce, the offspring can have different phenotypes from their parent(s). This raises the question of how these two opposing processes-loss of diversity by collective behaviors and generation of it through growth and inheritance-dynamically shape the phenotypic composition of an isogenic population. We examine this question theoretically using collective migration of chemotactic bacteria as a model system, where cells of different swimming phenotypes are better suited to navigate in different environments. We find that the differential loss of phenotypes caused by collective migration is environment-dependent. With cell growth, this differential loss enables migrating populations to dynamically adapt their phenotype compositions to the environment, enhancing migration through multiple environments. Which phenotypes are produced upon cell division depends on the level of nongenetic inheritance, and higher inheritance leads to larger composition adaptation and faster migration at steady state. However, this comes at the cost of slower responses to new environments. Due to this trade-off, there is an optimal level of inheritance that maximizes migration speed through changing environments, which enables a diverse population to outperform a nondiverse one. Growing populations might generally leverage the selection-like effects provided by collective behaviors to dynamically shape their own phenotype compositions, without mutations.

(Epi)mutation Rates and the Evolution of Composite Trait Architectures.

AbstractMutation rates vary widely along genomes and across inheritance systems. This suggests that complex traits-resulting from the contributions of multiple determinants-might be composite in terms of the underlying mutation rates. Here we investigate through mathematical modeling whether such a heterogeneity may drive changes in a trait's architecture, especially in fluctuating environments, where phenotypic instability can be beneficial. We first identify a convexity principle related to the shape of the trait's fitness function, setting conditions under which composite architectures should be adaptive or, conversely and more commonly, should be selected against. Simulations reveal, however, that applying this principle to realistic evolving populations requires taking into account pervasive epistatic interactions that take place in the system. Indeed, the fate of a mutation affecting the architecture depends on the (epi)genetic background, which itself depends on the current architecture in the population. We tackle this problem by borrowing the adaptive dynamics framework from evolutionary ecology-where it is routinely used to deal with such resident/mutant dependencies-and find that the principle excluding composite architectures generally prevails. Yet the predicted evolutionary trajectories will typically depend on the initial architecture, possibly resulting in historical contingencies. Finally, by relaxing the large population size assumption, we unexpectedly find that not only the strength of selection on a trait's architecture but also its direction depend on population size, revealing a new occurrence of the recently identified phenomenon coined "sign inversion."

Nongenetic individuality, changeability, and inheritance in bacterial behavior.

Isogenic populations often display remarkable levels of phenotypic diversity even in constant, homogeneous environments. Such diversity results from differences between individuals ("nongenetic individuality") as well as changes during individuals' lifetimes ("changeability"). Yet, studies that capture and quantify both sources of diversity are scarce. Here we measure the swimming behavior of hundreds of Escherichia coli bacteria continuously over two generations and use a model-independent method for quantifying behavior to show that the behavioral space of E. coli is low-dimensional, with variations occurring mainly along two independent and interpretable behavioral traits. By statistically decomposing the diversity in these two traits, we find that individuality is the main source of diversity, while changeability makes a smaller but significant contribution. Finally, we show that even though traits of closely related individuals can be remarkably different, they exhibit positive correlations across generations that imply nongenetic inheritance. The model-independent experimental and theoretical framework developed here paves the way for more general studies of microbial behavioral diversity.

Signatures of polygenic adaptation align with genome-wide methylation patterns in wild strawberry plants.

Epigenetic inheritance can drive adaptive evolution independently of DNA sequence variation. However, to what extent epigenetic variation represents an autonomous evolutionary force remains largely elusive. Through gene ontology and comparative analyses of genomic and epigenomic variation of wild strawberry plants raised in distinct drought settings, we characterised genome-wide covariation between single nucleotide polymorphisms (SNPs) and differentially methylated cytosines (DMCs). Covariation between SNPs and DMCs was independent of genomic proximity, but instead associated with fitness-related processes such as stress responses, genome regulation and reproduction. We expected this functional SNP-DMC covariation to be driven by adaptive evolution canalising SNP and DMC variation, but instead observed significantly lower covariation with DMCs for adaptive rather than for neutral SNPs. Drought-induced DMCs frequently co-varied with tens of SNPs, suggesting high genomic redundancy as a broad potential basis for polygenic adaptation of gene expression. Our findings suggest that stress-responsive DMCs initially co-vary with many SNPs under increased environmental stress, and that natural selection acting upon several of these SNPs subsequently reduces standing covariation with stress-responsive DMCs. Our study supports DNA methylation profiles that represent complex quantitative traits rather than autonomous evolutionary forces. We provide a conceptual framework for polygenic regulation and adaptation shaping genome-wide methylation patterns in plants.

The thermal environment of sperm affects offspring success: a test of the anticipatory paternal effects hypothesis in the blue mussel.

There has been an explosion of recent evidence that environments experienced by fathers or their ejaculates can influence offspring phenotypes (paternal effects). However, little is known about whether such effects are adaptive, which would have far-reaching implications for the many species facing rapidly changing environments. For example, some arguments suggest paternal effects might be a source of cross-generational plasticity, preparing offspring to face similar conditions to their father (anticipatory hypothesis). Alternatively, ejaculate-mediated effects on offspring may be non-adaptive by-products of stress. Here, we conduct an experiment to distinguish between these predictions, exposing ejaculates of the externally fertilizing mussel Mytilus galloprovincialis to ambient (19°C) and high (24°C) temperatures, then rearing offspring groups in temperatures that match and mismatch those of sperm. We find that, overall, high temperature-treated sperm induced higher rates of normal offspring development and higher success in transitioning to second-stage larvae, which may represent adaptive epigenetic changes or selection on sperm haplotypes. However, the progeny of high temperature-treated sperm did not perform better than those of ambient temperature-treated sperm when rearing temperatures were high. Overall, these findings offer little support for the anticipatory hypothesis and suggest instead that beneficial paternal effects may be eroded when offspring develop under stressful conditions.

Indirect parental effects on offspring viability by egg-derived fluids in an external fertilizer.

The capacity for parents to influence offspring phenotypes via nongenetic inheritance is currently a major area of focus in evolutionary biology. Intriguing recent evidence suggests that sexual interactions among males and females, both before and during mating, are important mediators of such effects. Sexual interactions typically extend beyond gamete release, involving both sperm and eggs, and their associated fluids. However, the potential for gamete-level interactions to induce nongenetic parental effects remains under-investigated. Here, we test for such effects using an emerging model system for studying gamete interactions, the external fertilizer Mytilus galloprovincialis. We employed a split-ejaculate design to test whether exposing sperm to egg-derived chemicals (ECs) from a female would affect fertilization rate and offspring viability when those sperm were used to fertilize a different female's eggs. We found separate, significant effects of ECs from non-fertilizing females on both fertilization rate and offspring viability. The offspring viability effect indicates that EC-driven interactions can have nongenetic implications for offspring fitness independent of the genotypes inherited by those offspring. These findings provide a rare test of indirect parental effects driven exclusively by gamete-level interactions, and to our knowledge the first evidence that such effects occur via the gametic fluids of females.

An Integrative Framework for Understanding the Mechanisms and Multigenerational Consequences of Transgenerational Plasticity.

Transgenerational plasticity (TGP) occurs when the environment experienced by a parent influences the development of their offspring. In this article, we develop a framework for understanding the mechanisms and multi-generational consequences of TGP. First, we conceptualize the mechanisms of TGP in the context of communication between parents (senders) and offspring (receivers) by dissecting the steps between an environmental cue received by a parent and its resulting effects on the phenotype of one or more future generations. Breaking down the problem in this way highlights the diversity of mechanisms likely to be involved in the process. Second, we review the literature on multigenerational effects and find that the documented patterns across generations are diverse. We categorize different multigenerational patterns and explore the proximate and ultimate mechanisms that can generate them. Throughout, we highlight opportunities for future work in this dynamic and integrative area of study.

Ecological divergence of wild strawberry DNA methylation patterns at distinct spatial scales.

Epigenetic change is considered relatively unstable and short-lived, raising questions of its contribution to long-term adaptive potential. However, epigenetic modifications can accumulate in the presence of environmental stress, resulting in beneficial epigenetic memories where environments are challenging. Diverging epigenetic memories have been observed across large spatial scales, and can persist through multiple generations. It is unknown, however, to what extent epigenetic variation contributes to fine-scale population structure and evolution. We compared DNA methylation patterns between a steep, altitudinal gradient (<2 km) and a wide spatial gradient (>500 km) using whole genome bisulphite sequencing data from 30 Fragaria vesca plants germinated and grown in controlled conditions. To assess the stability of spatial epigenetic variation in the presence of an environmental stressor, we applied acute drought stress to part of the plants and quantified drought-induced changes in DNA methylation signatures. We find that epigenetic memories and genomic islands of epigenetic divergence arise even at fine spatial scale, and that distinct spatial scales are featured by distinct epigenetic patterns. For example, demethylation of transposable elements consistently occurred at the large but not the fine spatial scale, while methylation differentiation for most biological processes were shared between spatial scales. Acute drought stress did not result in significant epigenetic differentiation. Our results indicate that population history, rather than short-term environmental stress, plays a dominant role in shaping epigenetic signatures. Specifically, repeated historical stress levels associated with heterogeneous environmental conditions may be required for acquiring a stable epigenetic memory and for coping with future environmental change.

Offspring phenotype is shaped by the nonsperm fraction of semen.

In a large majority of animal species, the only contribution of males to the next generation has been assumed to be their genes (sperm). However, along with sperm, seminal plasma contains a wide array of extracellular factors that have many important functions in reproduction. Yet, the potential intergenerational effects of these factors are virtually unknown. We investigated these effects in European whitefish (Coregonus lavaretus) by experimentally manipulating the presence and identity of seminal plasma and by fertilizing the eggs of multiple females with the manipulated and unmanipulated semen of several males in a full-factorial breeding design. The presence of both own seminal plasma and foreign seminal plasma inhibited sperm motility, and the removal of own seminal plasma decreased embryo survival. Embryos hatched significantly earlier after both semen manipulations than in control fertilizations; foreign seminal plasma also increased offspring aerobic swimming performance. Given that our experimental design allowed us to control potentially confounding sperm-mediated (sire) effects and maternal effects, our results indicate that seminal plasma may have direct intergenerational consequences for offspring phenotype and performance. This novel source of offspring phenotypic variance may provide new insights into the evolution of polyandry and mechanisms that maintain heritable variation in fitness and associated female mating preferences.

Developmental and Ecological Benefits of the Maternally Transmitted Microbiota in a Dung Beetle.

To complete their development, diverse animal species rely on the presence of communities of symbiotic microbiota that are vertically transmitted from mother to offspring. In the dung beetle genus Onthophagus, newly hatched larvae acquire maternal gut symbionts by the consumption of a maternal fecal secretion known as the pedestal. Here, we investigate the role of pedestal symbionts in mediating the normal development of Onthophagus gazella. Through the stepwise removal of environmental and maternal sources of microbial inoculation, we find that pedestal microbiota can enhance both overall growth and developmental rate in O. gazella. Further, we find that the beneficial effects of symbionts on developmental outcomes are amplified in the presence of ecologically relevant temperature and desiccation stressors. Collectively, our results suggest that the pedestal may provide an adaptive function by transmitting beneficial microbiota to developing dung beetle larvae and that the importance of microbiota for developmental and fitness outcomes may be context dependent.

Parental effects and the evolution of phenotypic memory.

Despite growing evidence for nongenetic inheritance, the ecological conditions that favour the evolution of heritable parental or grandparental effects remain poorly understood. Here, we systematically explore the evolution of parental effects in a patch-structured population with locally changing environments. When selection favours the production of a mix of offspring types, this mix differs according to the parental phenotype, implying that parental effects are favoured over selection for bet-hedging in which the mixture of offspring phenotypes produced does not depend on the parental phenotype. Positive parental effects (generating a positive correlation between parental and offspring phenotype) are favoured in relatively stable habitats and when different types of local environment are roughly equally abundant, and can give rise to long-term parental inheritance of phenotypes. By contrast, unstable habitats can favour negative parental effects (generating a negative correlation between parental and offspring phenotype), and under these circumstances, even slight asymmetries in the abundance of local environmental states select for marked asymmetries in transmission fidelity.

Paternal condition affects offspring reproduction and life history in a sex-specific manner in Drosophila melanogaster.

Nongenetic parental effects can contribute to the adaptation of species to changing environments by circumventing some of the limitations of genetic inheritance. A clearer understanding of the influence of nongenetic inheritance and its potentially sex-specific responses in daughters and sons is needed to better predict the evolutionary trajectories of species. However, whereas nongenetic maternal effects have long been recognized and widely studied, comparatively little is known about corresponding paternal effects. Here, by following 30 isogenic lines of Drosophila melanogaster across two generations, each reared under two dietary regimes in each generation, we tested how protein restriction during larval development of the fathers affects the fitness and health of their daughters and sons. We then quantified genetic and non-genetic paternal, and direct environmental, effects across multiple axes of offspring fitness. Daughters and sons responded differently to their father's developmental history. While isolines differed in mean trait values, their specific responses to protein restriction generally varied little. The sex- and trait-specific responses to paternal effects emphasize the complexity of inter-generational parental effects, which raise important questions about their mode of transmission and adaptive value, including the potential for conflict between the sexes.

Evolutionary history of sexual selection affects microRNA profiles in Drosophila sperm.

The presence of small RNAs in sperm is a relatively recent discovery and little is currently known about their importance and functions. Environmental changes including social conditions and dietary manipulations are known to affect the composition and expression of some small RNAs in sperm and may elicit a physiological stress response resulting in an associated change in gamete miRNA profiles. Here, we tested how microRNA profiles in sperm are affected by variation in both sexual selection and dietary regimes in Drosophila melanogaster selection lines. The selection lines were exposed to standard versus low yeast diet treatments and three different population sex ratios (male-biased, female-biased, or equal sex) in a full-factorial design. After 38 generations of selection, all males were maintained on their selected diet and in a common garden male-only environment prior to sperm sampling. We performed transcriptome analyses on miRNAs in purified sperm samples. We found 11 differentially expressed miRNAs with the majority showing differences between male- and female-biased lines. Dietary treatment only had a significant effect on miRNA expression levels in interaction with sex ratio. Our findings suggest that long-term adaptation may affect miRNA profiles in sperm and that these may show varied interactions with short-term environmental changes.

Evolutionary consequences of pesticide exposure include transgenerational plasticity and potential terminal investment transgenerational effects.

Transgenerational plasticity, the influence of the environment experienced by parents on the phenotype and fitness of subsequent generations, is being increasingly recognized. Human-altered environments, such as those resulting from the increasing use of pesticides, may be major drivers of such cross-generational influences, which in turn may have profound evolutionary and ecological repercussions. Most of these consequences are, however, unknown. Whether transgenerational plasticity elicited by pesticide exposure is common, and the consequences of its potential carryover effects on fitness and population dynamics, remains to be determined. Here, we investigate whether exposure of parents to a common pesticide elicits intra-, inter-, and transgenerational responses (in F0, F1, and F2 generations) in life history (fecundity, longevity, and lifetime reproductive success), in an insect model system, the seed beetle Callosobruchus maculatus. We also assessed sex specificity of the effects. We found sex-specific and hormetic intergenerational and transgenerational effects on longevity and lifetime reproductive success, manifested both in the form of maternal and paternal effects. In addition, the transgenerational effects via mothers detected in this study are consistent with a new concept: terminal investment transgenerational effects. Such effects could underlie cross-generational responses to environmental perturbation. Our results indicate that pesticide exposure leads to unanticipated effects on population dynamics and have far-reaching ecological and evolutionary implications.

Effects of paternal diet and antioxidant addition to the semen extender on bovine semen characteristics and on the phenotype of the resulting embryo.

The aim of this study was to examine the effects of long-term dietary supplementation of young Nellore bulls with rumen-protected polyunsaturated fatty acids (PUFAs) and of the inclusion of catalase in the semen extender on semen quality, in vitro sperm fertilizing ability, and intracytoplasmic lipid content in the resulting embryos. Twelve Nellore bulls were supplemented with rumen-protected PUFAs or with a basal diet from 14 to 24 months of age. The semen was collected at the end of supplementation. For cryopreservation, the ejaculate was divided into two equal volumes and catalase was added to the extender in one of the fractions. Thus, the experimental design consisted of a 2 × 2 factorial scheme with two diets (control and PUFA) and two extenders (Cat+ and Cat-). Total motility and the percentage of rapid cells in fresh semen were negatively affected by dietary supplementation with PUFAs (P < 0.05), but these effects did not persist after freezing. The frozen/thawed semen of animals fed PUFAs exhibited an increase in the percentages of damaged plasma and acrosomal membranes, as well as an increase in the proportion of lipids ions at m/z 578 and m/z 757 detected by MALDI-MS. Nevertheless, there was no effect of the treatments on in vitro embryo development. However, embryos derived from bulls supplemented with PUFAs exhibited higher lipid accumulation compared to control (P < 0.05). In conclusion, PUFA supplementation promoted worsening of semen quality without affecting the in vitro sperm fertilizing ability; however, the paternal diet affected the intracytoplasmic lipid content in the resulting embryos.

The specificity of sperm-mediated paternal effects in threespine sticklebacks.

Parental effects may help offspring respond to challenging environments, but whether parental exposure to different environmental challenges induces similar responses in offspring is largely unknown. We compared the offspring of threespine stickleback (Gasterosteus aculeatus) fathers who had been exposed to a potentially threatening stimulus (net), a native predator (sculpin), or who had been left unexposed (control). Relative to offspring of control fathers, offspring of sculpin-exposed fathers were more responsive (greater change in activity) to a simulated sculpin predator attack, while offspring of net-exposed fathers were less responsive (fewer antipredator behaviors) and showed altered stress responses compared to the control. To evaluate whether parental exposure primes offspring to respond to specific stimuli (e.g., offspring of net-exposed fathers respond most strongly to a net), we then exposed offspring of each paternal treatment to nets, native sculpin models, or non-native trout models. Paternal treatment did not influence offspring response to different stimuli; instead, offspring were generally more responsive to the native sculpin predator compared to nets or non-native trout predator, suggesting that sticklebacks have innate predator recognition of native predators. Collectively, these results underscore that, while parental exposure to non-ecologically relevant stressors elicits effects in intergenerational studies, these findings may not mirror those produced when parents encounter ecologically relevant stressors. Knowing that parental effects can be predator-specific furthers our understanding of the ways in which parental effects may evolve to be adaptive and suggests the potential for transgenerational plasticity to affect how animals respond to human induced environmental change, including non-native predators.

The interplay between sperm-mediated and care-mediated paternal effects in threespine sticklebacks.

The environment experienced by one generation can influence the phenotypes of future generations. Because parental cues can be conveyed to offspring at multiple points in time, ranging from fertilization to posthatching/parturition, offspring can potentially receive multiple cues from their parents via different mechanisms. We have relatively little information regarding how different mechanisms operate in isolation and in tandem, but it is possible, for example, that offspring phenotypes induced by nongenetic changes to gametes may be amplified by, mitigated by, or depend upon parental care. Here, we manipulated paternal experience with predation risk prior to fertilization in threespine stickleback, Gasterosteus aculeatus, and then examined the potential of paternal care to mitigate and/or amplify sperm-mediated paternal effects. Specifically, we compared (1) offspring of predator-exposed fathers who were reared without paternal care, (2) offspring of predator-exposed fathers who were reared with paternal care, (3) offspring of control (unexposed) fathers who were reared without paternal care and (4) offspring of control fathers who were reared with paternal care. We found that offspring of predator-exposed fathers were less active and had higher cortisol following a simulated predator attack. Although predator-exposed males shifted their paternal care behaviours - reduced fanning early in egg development and increased fanning right before egg hatching compared to control males - this shift in paternal behavior did not appear to affect offspring traits. This suggests that paternal care neither amplifies nor compensates for these phenotypic effects induced by sperm and that nongenetic changes induced by sperm may occur independently of nongenetic changes induced by paternal care. Overall, these results underscore the importance of considering how parents may have multiple nongenetic mechanisms by which they can influence offspring.

Genotypic variation in the persistence of transgenerational responses to seasonal cues.

Phenotypes respond to environments experienced directly by an individual, via phenotypic plasticity, or to the environment experienced by ancestors, via transgenerational environmental effects. The adaptive value of environmental effects depends not only on the strength and direction of the induced response but also on how long the response persists within and across generations, and how stably it is expressed across environments that are encountered subsequently. Little is known about the genetic basis of those distinct components, or even whether they exhibit genetic variation. We tested for genetic differences in the inducibility, temporal persistence, and environmental stability of transgenerational environmental effects in Arabidopsis thaliana. Genetic variation existed in the inducibility of transgenerational effects on traits expressed across the life cycle. Surprisingly, the persistence of transgenerational effects into the third generation was uncorrelated with their induction in the second generation. Although environmental effects for some traits in some genotypes weakened over successive generations, others were stronger or even in the opposite direction in more distant generations. Therefore, transgenerational effects in more distant generations are not merely caused by the retention or dissipation of those expressed in prior generations, but they may be genetically independent traits with the potential to evolve independently.

Diet-Induced Modification of the Sperm Epigenome Programs Metabolism and Behavior.

Globally, obesity has reached epidemic proportions. The rapidly increasing numbers of overweight people can be traced back to overconsumption of energy-dense, poor-quality foods as well as physical inactivity. This development has far-reaching and costly implications. Not only is obesity associated with serious physiological and psychological complications, but mounting evidence also indicates a ripple effect through generations via epigenetic changes. Parental obesity could induce intergenerational and transgenerational changes in metabolic and brain function of the offspring. Most research has focused on maternal epigenetic and gestational effects; however, paternal contributions are likely to be substantial. We focus on the latest advances in understanding the mechanisms of epigenetic inheritance of obesity-evoked metabolic and neurobiological changes through the paternal germline that predict wide-ranging consequences for the following generation(s).

Pregnancy drugs, fetal germline epigenome, and risks for next-generation pathology: A call to action.

Drugs taken during pregnancy can affect three generations at once: the gestating woman (F0), her exposed fetus (F1), and the fetal germ cells that confer heritable information for the grandchildren (F2). Unfortunately, despite growing evidence for connections between F0 drug exposures and F2 pathology, current approaches to risk assessment overlook this important dimension of risk. In this commentary, we argue that the unique molecular vulnerabilities of the fetal germline, particularly with regard to global epigenomic reprogramming, combined with empirical evidence for F2 effects of F1 in utero drug and other exposures, should change the way we consider potential long-term consequences of pregnancy drugs and alter toxicology's standard somatic paradigm. Specifically, we (1) suggest that pregnancy drugs common in the postwar decades should be investigated as potential contributors to the "missing heritability" of many pathologies now surging in prevalence; (2) call for inclusion of fetal germline risks in pregnancy drug safety assessment; and (3) highlight the need for intensified research to ascertain generational impacts of diethylstilbestrol, a vanguard question of human germline toxicity. Only by fully addressing this important dimension of transplacental exposure can we responsibly evaluate safety of drug exposures during pregnancy and convey the full scope of risks, while also retrospectively comprehending the generational legacy of recent history's unprecedented glut of evolutionarily novel intrauterine exposures. Environ. Mol. Mutagen. 60:445-454, 2019. © 2019 Wiley Periodicals, Inc.