Epigenomics as a paradigm to understand the nuances of phenotypes

Quantifying the relative importance of genomic and epigenomic modulators of phenotype is a focal challenge in comparative physiology, but progress is constrained by availability of data and analytic methods. Previous studies have linked physiological features to coding DNA sequence, regulatory DNA sequence, and epigenetic state, but few have disentangled their relative contributions or unambiguously distinguished causative effects ('drivers') from correlations. Progress has been limited by several factors, including the classical approach of treating continuous and fluid phenotypes as discrete and static across time and environment, and difficulty in considering the full diversity of mechanisms that can modulate phenotype, such as gene accessibility, transcription, mRNA processing and translation. We argue that attention to phenotype nuance, progressing to association with epigenetic marks and then causal analyses of the epigenetic mechanism, will enable clearer evaluation of the evolutionary path. This would underlie an essential paradigm shift, and power the search for links between genomic and epigenomic features and physiology. Here, we review the growing knowledge base of gene-regulatory mechanisms and describe their links to phenotype, proposing strategies to address widely recognized challenges.

How can we fully realize the potential of mathematical and biological models to reintegrate biology?

Both mathematical models and biological model systems stand as tractable representations of complex biological systems or behaviors. They facilitate research and provide insights, and they can describe general rules. Models that represent biological processes or formalize general hypotheses are essential to any broad understanding. Mathematical or biological models necessarily omit details of the natural systems and thus may ultimately be "incorrect" representations. A key challenge is that tractability requires relatively simple models but simplification can result in models that are incorrect in their qualitative, broad implications if the abstracted details matter. Our paper discusses this tension, and how we can improve our inferences from models. We advocate for further efforts dedicated to model development, improvement, and acceptance by the scientific community, all of which may necessitate a more explicit discussion of the purpose and power of models. We argue that models should play a central role in reintegrating biology as a way to test our integrated understanding of how molecules, cells, organs, organisms, populations, and ecosystems function.

Shifts in the relative fitness contributions of fecundity and survival in variable and changing environments

Organisms respond to shifts in climate means and variability via distinct mechanisms. Accounting for these differential responses and appropriately aggregating them is central to understanding and predicting responses to climate variability and change. Separately considering fitness components can clarify organismal responses: fecundity is primarily an integrated, additive response to chronic environmental conditions over time via mechanisms such as energy use and acquisition, whereas survival can be strongly influenced by short-term, extreme environmental conditions. In many systems, the relative importance of fecundity and survival constraints changes systematically along climate gradients, with fecundity constraints dominating at high latitudes or altitudes (i.e. leading range edges as climate warms), and survival constraints dominating at trailing range edges. Incorporating these systematic differences in models may improve predictions of responses to recent climate change over models that assume similar processes along environmental gradients. We explore how detecting and predicting shifts in fitness constraints can improve our ability to forecast responses to climate gradients and change.

Drivers of Infectious Disease Seasonality: Potential Implications for COVID-19

Not 1 year has passed since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19). Since its emergence, great uncertainty has surrounded the potential for COVID-19 to establish as a seasonally recurrent disease. Many infectious diseases, including endemic human coronaviruses, vary across the year. They show a wide range of seasonal waveforms, timing (phase), and amplitudes, which differ depending on the geographical region. Drivers of such patterns are predominantly studied from an epidemiological perspective with a focus on weather and behavior, but complementary insights emerge from physiological studies of seasonality in animals, including humans. Thus, we take a multidisciplinary approach to integrate knowledge from usually distinct fields. First, we review epidemiological evidence of environmental and behavioral drivers of infectious disease seasonality. Subsequently, we take a chronobiological perspective and discuss within-host changes that may affect susceptibility, morbidity, and mortality from infectious diseases. Based on photoperiodic, circannual, and comparative human data, we not only identify promising future avenues but also highlight the need for further studies in animal models. Our preliminary assessment is that host immune seasonality warrants evaluation alongside weather and human behavior as factors that may contribute to COVID-19 seasonality, and that the relative importance of these drivers requires further investigation. A major challenge to predicting seasonality of infectious diseases are rapid, human-induced changes in the hitherto predictable seasonality of our planet, whose influence we review in a final outlook section. We conclude that a proactive multidisciplinary approach is warranted to predict, mitigate, and prevent seasonal infectious diseases in our complex, changing human-earth system.

Ambient Temperature Cycles Affect Daily Torpor and Hibernation Patterns in Malagasy Tenrecs

Hibernation and daily torpor (heterothermy) allow endotherms to cope with demanding environmental conditions. The depth and duration of torpor bouts vary considerably between tropical and temperate climates, and tropical hibernators manage to cope with a wider spectrum of ambient temperature (T_a) regimes during heterothermy. As cycles in T_a can have profound effects on activity and torpor patterns as well as energy expenditure, we examined how these characteristics are affected by daily fluctuating versus constant T_a in a tropical hibernator, the lesser hedgehog tenrec (Echinops telfairi). Throughout the study, regardless of season, the tenrecs became torpid every day. In summer, E. telfairi used daily fluctuations in T_a to passively rewarm from daily torpor, which led to synchrony in the activity phases and torpor bouts between individuals and generally decreased energy expenditure. In contrast, animals housed at constant T_a showed considerable variation in timing and they had to invest more energy through endogenous heat production. During the hibernation season (winter) E. telfairi hibernated for several months in constant, as well as in fluctuating T_a and, as in summer, under fluctuating T_a arousals were much more uniform and showed less variation in timing compared to constant temperature regimes. The timing of torpor is not only important for its effective use, but synchronization of activity patterns could also be essential for social interactions, and successful foraging bouts. Our results highlight that T_a cycles can be an effective zeitgeber for activity and thermoregulatory rhythms throughout the year and that consideration should be given to the choice of temperature regime when studying heterothermy under laboratory conditions.

Does sex really matter? Explaining intraspecies variation in ocean acidification responses

Ocean acidification (OA) poses a major threat to marine ecosystems globally, having significant ecological and economic importance. The number and complexity of experiments examining the effects of OA has substantially increased over the past decade, in an attempt to address multi-stressor interactions and long-term responses in an increasing range of aquatic organisms. However, differences in the response of males and females to elevated pCO₂ have been investigated in fewer than 4% of studies to date, often being precluded by the difficulty of determining sex non-destructively, particularly in early life stages. Here we highlight that sex can significantly impact organism responses to OA, differentially affecting physiology, reproduction, biochemistry and ultimately survival. What is more, these impacts do not always conform to ecological theory based on differential resource allocation towards reproduction, which would predict females to be more sensitive to OA owing to the higher production cost of eggs compared with sperm. Therefore, non-sex-specific studies may overlook subtle but ecologically significant differences in the responses of males and females to OA, with consequences for forecasting the fate of natural populations in a near-future ocean.

Daily temperature variation and extreme high temperatures drive performance and biotic interactions in a warming world

We review the major patterns on the effects of daily temperature variation (DTV) and extreme high temperatures (EXT) on performance traits and the resulting outcome of biotic interactions in insects. EXT profoundly affects the outcome of all types of biotic interactions: competitive, predator-prey, herbivore-plant, host-pathogen/parasitoid and symbiotic interactions. Studies investigating effects of DTV on biotic interactions are few but also show strong effects on competitive and host-pathogen/parasitoid interactions. EXT typically reduces predation, and is expected to reduce parasitoid success. The effects of EXT and DTV on the outcome of the other interaction types are highly variable, yet can be predicted based on comparisons of the TPCs of the interacting species, and challenges the formulation of general predictions about the change in biotic interactions in a warming world.

The fallacy of the average: on the ubiquity, utility and continuing novelty of Jensen's inequality

Biologists often cope with variation in physiological, environmental and ecological processes by measuring how living systems perform under average conditions. However, performance at average conditions is seldom equal to average performance across a range of conditions. This basic property of nonlinear averaging - known as 'Jensen's inequality' or 'the fallacy of the average' - has important implications for all of biology. For instance, a burgeoning awareness of Jensen's inequality has improved our ability to predict how plants and animals will respond to a warmer and more variable future climate. But for many biologists, the fallacy of the average is still a novel concept. Here, I highlight the importance of Jensen's inequality, provide a simple graphical approach to understanding its effects, and explore its consequences at atomic, molecular, organismal and ecological levels.