Impact of high predation risk on genome-wide hippocampal gene expression in snowshoe hares

Intersexual differences in the number of genes differentially expressed in wild mammals in response to predation risk

Predation is a psychological stressor in prey animals. Besides direct killing and consumption by predators, the perception of predation risk indirectly influence prey population behavior, dynamics and physiology. Few studies identified the transcriptomic response associated with predator presence/abundance in natural populations and uncontrolled settings. However, to our knowledge, intersexual differences in the number of genes whose expression change in response to high predation risk have not been previously reported in wild mammals. Here, by using publicly available gene expression data in wild yellow-bellied marmots (Marmota flaviventer), we found that the number of differentially expressed genes in response to predator stress is higher in female marmots (n = 516) than males (n = 387). Only a small percentage of these differentially expressed genes (n = 36) are shared between the sexes, and that the most of the differentially expressed genes are expressed in a sex-specific manner in response to predation stress. Overall, our results provide new insight into sex-specific variation in gene expression changes in wild mammals under high predation risk.

The impact of variable predation risk on stress in snowshoe hares over the cycle in North America's boreal forest: adjusting to change

The boreal forest is one of the world's ecosystems most affected by global climate warming. The snowshoe hare, its predators, and their population dynamics dominate the mammalian component of the North American boreal forest. Our past research has shown the 9-11-year hare cycle to be predator driven, both directly as virtually all hares that die are killed by their predators, and indirectly through sublethal risk effects on hare stress physiology, behavior, and reproduction. We replicated this research over the entire cycle by measuring changes in predation risk expected to drive changes in chronic stress. We examined changes in hare condition and stress axis function using a hormonal challenge protocol in the late winter of 7 years-spanning all phases of the cycle from the increase through to the low (2014-2020). We simultaneously monitored changes in hare abundance as well as those of their primary predators, lynx and coyotes. Despite observing the expected changes in hare-predator numbers over the cycle, we did not see the predicted changes in chronic stress metrics in the peak and decline phases. Thus, the comprehensive physiological signature indicative of chronic predator-induced stress seen from our previous work was not present in this current cycle. We postulate that hares may now be increasingly showing behavior-mediated rather than stress-mediated responses to their predators. We present evidence that increases in primary productivity have affected boreal community structure and function. We speculate that climate change has caused this major shift in the indirect effects of predation on hares.

Individual variation and the challenge hypothesis

In this paper I discuss how the challenge hypothesis (Wingfield et al., 1990) influenced the development of ideas about animal personality, and describe particularly promising areas for future study at the intersection of these two topics. I argue that the challenge hypothesis influenced the study of animal personality in at least three specific ways. First, the challenge hypothesis drew attention to the ways in which the environment experienced by an organism - including the social environment - can influence biological processes internal to the organism, e.g. changes to physiology, gene expression, neuroendocrine state and epigenetic modifications. That is, the challenge hypothesis illustrated the bidirectional, dynamic relationship between hormones and (social) environments, thereby helping us to understand how behavioral variation among individuals can emerge over time. Because the paper was inspired by data collected on free living animals in natural populations, it drew behavioral ecologists' attention to this phenomenon. Second, the challenge hypothesis highlighted what became a paradigmatic example of a hormonal mechanism for a behavioral spillover, i.e. testosterone's pleiotropic effects on both territorial aggression and parental care causes aggression to "spillover" to influence parenting behavior, thereby limiting behavioral plasticity. Third, the challenge hypothesis contributed to what is now a cottage industry examining individual differences in hormone titres and their relationship with behavioral variation. I argue that one particularly promising future research direction in this area is to consider the active role of behavior and behavioral types in eliciting social interactions, including territorial challenges.

Developmental programming of the HPA axis and related behaviours: epigenetic mechanisms

It has been approximately 30 years since the seminal discoveries of David Barker and his colleagues, and research is beginning to unravel the mechanisms that underlie developmental programming. The early environment of the embryo, foetus and newborn have been clearly linked to altered hypothalamic-pituitary-adrenal (HPA) function and related behaviours through the juvenile period and into adulthood. A number of recent studies have shown that these effects can pass across multiple generations. The HPA axis is highly responsive to the environment, impacts both central and peripheral systems and is critical to health in a wide variety of contexts. Mechanistic studies in animals are linking early exposures to adversity with changes in gene regulatory mechanisms, including modifications of DNA methylation and altered levels of miRNA. Similar associations are emerging from recent human studies. These findings suggest that epigenetic mechanisms represent a fundamental link between adverse early environments and developmental programming of later disease. The underlying biological mechanisms that connect the perinatal environment with modified long-term health outcomes represent an intensive area of research. Indeed, opportunities for early interventions must identify the relevant environmental factors and their molecular targets. This new knowledge will likely assist in the identification of individuals who are at risk of developing poor outcomes and for whom early intervention is most effective.

Population cycles: generalities, exceptions and remaining mysteries

Population cycles are one of nature's great mysteries. For almost a hundred years, innumerable studies have probed the causes of cyclic dynamics in snowshoe hares, voles and lemmings, forest Lepidoptera and grouse. Even though cyclic species have very different life histories, similarities in mechanisms related to their dynamics are apparent. In addition to high reproductive rates and density-related mortality from predators, pathogens or parasitoids, other characteristics include transgenerational reduced reproduction and dispersal with increasing-peak densities, and genetic similarity among populations. Experiments to stop cyclic dynamics and comparisons of cyclic and noncyclic populations provide some understanding but both reproduction and mortality must be considered. What determines variation in amplitude and periodicity of population outbreaks remains a mystery.

Maternal predator odour exposure programs metabolic responses in adult offspring

A cardinal feature of the reaction to stress is the promotion of energy mobilization, enabling appropriate behavioural responses. Predator odours are naturalistic and ecologically relevant stressors present over evolutionary timescales. In this study, we asked whether maternal predator odour exposure could program long-term energy mobilization in C57BL/6 mice offspring. To test this hypothesis, we measured rates of oxygen consumption in prenatally predator odour exposed mice in adulthood while controlling for levels of locomotor activity at baseline and under stress. Circulating thyroid hormone levels and the transcript abundance of key regulators of the hypothalamic-pituitary-thyroid axis within the periventricular nucleus (PVN) of the hypothalamus and in the liver, including carriers and receptors and thyrotropin-releasing hormone, were measured as endocrine mediators facilitating energy availability. Prenatally predator odour exposed mice of both sexes mobilized more energy during lower energy demand periods of the day and under stressful conditions. Further, prenatally predator odour exposed mice displayed modifications of their hypothalamic-pituitary-thyroid axis through increased circulating thyroxine and thyroid hormone receptor α within the PVN and decreased transthyretin in the liver. Overall, these results suggest that maternal exposure to predator odour is sufficient to increase long-term energy mobilization in adult offspring.

Genomic tools for behavioural ecologists to understand repeatable individual differences in behaviour

Behaviour is a key interface between an animal's genome and its environment. Repeatable individual differences in behaviour have been extensively documented in animals, but the molecular underpinnings of behavioural variation among individuals within natural populations remain largely unknown. Here, we offer a critical review of when molecular techniques may yield new insights, and we provide specific guidance on how and whether the latest tools available are appropriate given different resources, system and organismal constraints, and experimental designs. Integrating molecular genetic techniques with other strategies to study the proximal causes of behaviour provides opportunities to expand rapidly into new avenues of exploration. Such endeavours will enable us to better understand how repeatable individual differences in behaviour have evolved, how they are expressed and how they can be maintained within natural populations of animals.

Prenatal stress effects in a wild, long-lived primate: predictive adaptive responses in an unpredictable environment

Prenatal maternal stress affects offspring phenotype in numerous species including humans, but it is debated whether these effects are evolutionarily adaptive. Relating stress to adverse conditions, current explanations invoke either short-term developmental constraints on offspring phenotype resulting in decelerated growth to avoid starvation, or long-term predictive adaptive responses (PARs) resulting in accelerated growth and reproduction in response to reduced life expectancies. Two PAR subtypes were proposed, acting either on predicted internal somatic states or predicted external environmental conditions, but because both affect phenotypes similarly, they are largely indistinguishable. Only external (not internal) PARs rely on high environmental stability particularly in long-lived species. We report on a crucial test case in a wild long-lived mammal, the Assamese macaque (Macaca assamensis), which evolved and lives in an unpredictable environment where external PARs are probably not advantageous. We quantified food availability, growth, motor skills, maternal caretaking style and maternal physiological stress from faecal glucocorticoid measures. Prenatal maternal stress was negatively correlated to prenatal food availability and led to accelerated offspring growth accompanied by decelerated motor skill acquisition and reduced immune function. These results support the ‘internal PAR’ theory, which stresses the role of stable adverse internal somatic states rather than stable external environments.

Temporal dynamics of neurogenomic plasticity in response to social interactions in male threespined sticklebacks

Animals exhibit dramatic immediate behavioral plasticity in response to social interactions, and brief social interactions can shape the future social landscape. However, the molecular mechanisms contributing to behavioral plasticity are unclear. Here, we show that the genome dynamically responds to social interactions with multiple waves of transcription associated with distinct molecular functions in the brain of male threespined sticklebacks, a species famous for its behavioral repertoire and evolution. Some biological functions (e.g., hormone activity) peaked soon after a brief territorial challenge and then declined, while others (e.g., immune response) peaked hours afterwards. We identify transcription factors that are predicted to coordinate waves of transcription associated with different components of behavioral plasticity. Next, using H3K27Ac as a marker of chromatin accessibility, we show that a brief territorial intrusion was sufficient to cause rapid and dramatic changes in the epigenome. Finally, we integrate the time course brain gene expression data with a transcriptional regulatory network, and link gene expression to changes in chromatin accessibility. This study reveals rapid and dramatic epigenomic plasticity in response to a brief, highly consequential social interaction.

Social interactions provoke changes in the brain and behavior but their underlying molecular mechanisms remain obscure. Male sticklebacks are small fish whose fitness depends on their ability to defend a territory. Here, by measuring the time course of gene expression in response to a territorial challenge in two brain regions, we show that a single brief territorial intrusion provoked waves of gene expression that persisted for hours afterwards, with waves of transcription associated with distinct biological processes. Moreover, a single territorial challenge caused dramatic changes to the epigenome. Changes in chromatin accessibility corresponded to changes in gene expression, and to the activity of transcription factors operating within gene regulatory networks. This study reveals rapid and dramatic epigenomic plasticity in response to a brief, highly consequential social interaction. These results suggest that meaningful social interactions (even brief ones) can provoke waves of transcription and changes to the epigenome which lead to changes in neural functioning, and those changes are a mechanism by which animals update their assessment of their social world.

Coping with pregnancy after 9months in the dark: Post-hibernation buffering of high maternal stress in arctic ground squirrels

Pregnancy and lactation are key times in the life of female mammals when energetic resources must be brought to bear to produce and nurture offspring. Changes in glucocorticoid (GC) levels are central to this objective, due to their roles in modulating development and physiology and in mediating energetic tradeoffs. We examined GC changes over reproduction in a species living in a harsh seasonal environment: the arctic ground squirrel (Urocitellus parryii). Females become pregnant immediately after emerging from a ∼9month hibernation, and then must begin this pregnancy during an additional month of freezing temperatures and limited food availability. We measured plasma levels of total cortisol, corticosteroid-binding globulin (CBG), and free cortisol in unstressed females at three stages: not-visibly pregnant, visibly pregnant, and lactating. Total cortisol levels were similar in all stages, but CBG levels increased 4-fold from the not-visibly pregnant stage to visibly pregnant and lactating stage. As a result, the free cortisol fraction declined from 51% of total cortisol when females were not-visibly pregnant to only 5% when they were visibly pregnant (remaining low and stable throughout pregnancy) and 10% when they were lactating. This pattern is markedly different from that seen in other mammals, where 10% or less of GCs are free and these tend to increase during gestation. We postulate that the high free cortisol just prior to visible pregnancy is a seasonal adaptation relating either to the pronounced physiological changes the female must undergo after emerging from hibernation and immediately getting pregnant, or to the mobilization of body reserves for energy to permit pregnancy, or both. Thereafter, high CBG levels may shield the developing offspring from the negative effects of cortisol overexposure.

LaGomiCs-Lagomorph Genomics Consortium: An International Collaborative Effort for Sequencing the Genomes of an Entire Mammalian Order

The order Lagomorpha comprises about 90 living species, divided in 2 families: the pikas (Family Ochotonidae), and the rabbits, hares, and jackrabbits (Family Leporidae). Lagomorphs are important economically and scientifically as major human food resources, valued game species, pests of agricultural significance, model laboratory animals, and key elements in food webs. A quarter of the lagomorph species are listed as threatened. They are native to all continents except Antarctica, and occur up to 5000 m above sea level, from the equator to the Arctic, spanning a wide range of environmental conditions. The order has notable taxonomic problems presenting significant difficulties for defining a species due to broad phenotypic variation, overlap of morphological characteristics, and relatively recent speciation events. At present, only the genomes of 2 species, the European rabbit (Oryctolagus cuniculus) and American pika (Ochotona princeps) have been sequenced and assembled. Starting from a paucity of genome information, the main scientific aim of the Lagomorph Genomics Consortium (LaGomiCs), born from a cooperative initiative of the European COST Action "A Collaborative European Network on Rabbit Genome Biology-RGB-Net" and the World Lagomorph Society (WLS), is to provide an international framework for the sequencing of the genome of all extant and selected extinct lagomorphs. Sequencing the genomes of an entire order will provide a large amount of information to address biological problems not only related to lagomorphs but also to all mammals. We present current and planned sequencing programs and outline the final objective of LaGomiCs possible through broad international collaboration.

Integrating molecular mechanisms into quantitative genetics to understand consistent individual differences in behavior

It is now well appreciated that individual animals behave differently from one another and that individual differences in behaviors-personality differences-are maintained through time and across situations. Quantitative genetics has emerged as a conceptual basis for understanding the key ingredients of personality: (co)variation and plasticity. However, the results from quantitative genetic analyses are often divorced from underlying molecular or other proximate mechanisms. This disconnect has the potential to impede an integrated understanding of behavior and is a disconnect present throughout evolutionary ecology. Here we discuss some of the main conceptual connections between personality and quantitative genetics, the relationship of both with genomic tools, and areas that require integration. With its consideration of both trait variation and plasticity, the study of animal personality offers new opportunities to incorporate molecular mechanisms into both the trait partitioning and reaction norm frameworks provided by quantitative genetics.

Mammalian cycles: internally defined periods and interaction-driven amplitudes

The cause of mammalian cycles—the rise and fall of populations over a predictable period of time—has remained controversial since these patterns were first observed over a century ago. In spite of extensive work on observable mammalian cycles, the field has remained divided upon what the true cause is, with a majority of opinions attributing it to either predation or to intra-species mechanisms. Here we unite the eigenperiod hypothesis, which describes an internal, maternal effect-based mechanism to explain the cycles’ periods with a recent generalization explaining the amplitude of snowshoe hare cycles in northwestern North America based on initial predator abundance. By explaining the period and the amplitude of the cycle with separate mechanisms, a unified and consistent view of the causation of cycles is reached. Based on our suggested theory, we forecast the next snowshoe hare cycle (predicted peak in 2016) to be of extraordinarily low amplitude.

Muscle transcriptome response to ACTH administration in a free-ranging marine mammal

While much of our understanding of stress physiology is derived from biomedical studies, little is known about the downstream molecular consequences of adaptive stress responses in free-living animals. We examined molecular effectors of the stress hormones cortisol and aldosterone in the northern elephant seal, a free-ranging study system in which extreme physiological challenges and cortisol fluctuations are a routine part of life history. We stimulated the neuroendocrine stress axis by administering exogenous adrenocorticotropic hormone (ACTH) and examined the resultant effects by measuring corticosteroid hormones, metabolites, and gene expression before, during, and following administration. ACTH induced an elevation in cortisol, aldosterone, glucose, and fatty acids within 2 h, with complete recovery observed within 24 h of administration. The global transcriptional response of elephant seal muscle tissue to ACTH was evaluated by transcriptomics and involved upregulation of a highly coordinated network of conserved glucocorticoid (GC) target genes predicted to promote metabolic substrate availability without causing deleterious effects seen in laboratory animals. Transcriptional recovery from ACTH was characterized by downregulation of GC target genes and restoration of cell proliferation, metabolism, and tissue maintenance pathways within 24 h. Differentially expressed genes included several adipokines not previously described in muscle, reflecting unique metabolic physiology in fasting-adapted animals. This study represents one of the first transcriptome analyses of cellular responses to hypothalamic-pituitary-adrenal axis stimulation in a free-living marine mammal and suggests that compensatory, tissue-sparing mechanisms may enable marine mammals to maintain cortisol and aldosterone sensitivity while avoiding deleterious long-term consequences of stress.