Multi-omics reveals largely distinct transcript- and protein-level responses to the environment in an intertidal mussel.

Organismal responses to stressful environments are influenced by numerous transcript- and protein-level mechanisms, and the relationships between expression changes at these levels are not always straightforward. Here, we used paired transcriptomic and proteomic datasets from two previous studies from gill of the California mussel, Mytilus californianus, to explore how simultaneous transcript and protein abundance patterns may diverge under different environmental scenarios. Field-acclimatized mussels were sampled from two disparate intertidal sites; individuals from one site were subjected to three further treatments (common garden, low-intertidal or high-intertidal outplant) that vary in temperature and feeding time. Assessing 1519 genes shared between the two datasets revealed that both transcript and protein expression patterns differentiated the treatments at a global level, despite numerous underlying discrepancies. There were far more instances of differential expression between treatments in transcript only (1451) or protein only (226) than of the two levels shifting expression concordantly (68 instances). Upregulated expression of cilium-associated transcripts (likely related to feeding) was associated with relatively benign field treatments. In the most stressful treatment, transcripts, but not proteins, for several molecular chaperones (including heat shock proteins and endoplasmic reticulum chaperones) were more abundant, consistent with a threshold model for induction of translation of constitutively available mRNAs. Overall, these results suggest that the relative importance of transcript- and protein-level regulation (translation and/or turnover) differs among cellular functions and across specific microhabitats or environmental contexts. Furthermore, the degree of concordance between transcript and protein expression can vary across benign versus acutely stressful environmental conditions.

Open Source Solutions in Experimental Design: An Introduction to the Symposium.

The Open Science movement has increased dramatically in popularity with deserved calls to action around transparency, access to resources, and inclusion in our field. However, its practical applications within experimental design have been slow to uptake, with researchers unsure where to even start with the dizzying array of open source hardware and software solutions available. The perceived time investment and unknown cost, especially in implementing open source hardware, has stagnated the implementation of inexpensive experimental solutions, but we sought to increase awareness to lower the barrier to participation in this space. While there are countless technical and financial advantages to integrating open source solutions into every biologist's experimental design, we put an emphasis on the "people" part of the equation in our symposium. This symposium championed innovative experimental designs by early career Society for Integrative and Comparative Biology researchers across all fields of biology, from plants to animals, in the lab or in the field, or even virtually engaging with the public and students. The Open Science movement operates within community norms that champion transparency, continuous development, and collaboration. These values are congruent with the priorities of reducing barriers to participation in science, and we hope our symposium's collection of open source solutions encourages readers to adopt these or other innovative designs into their own experimentation.

Virtual Expeditions Facilitated by Open Source Solutions Broaden Student Participation in Natural History Research.

From its genesis in the Victorian era as an activity for the elite to today's emphasis on "Big Data" and continuous monitoring, natural history has a prominent role in scientific discoveries for many fields. However, participation in field expeditions is limited by funding, space, accessibility, and safety constraints. Others have detailed the active exclusion of minoritized groups from field expeditions and harm/discrimination faced by the few who do participate, but we provide one solution to broaden opportunities for participation in natural history: Virtual Expeditions. Virtual Expeditions are broadly defined as open source, web-facilitated research activities designed to analyze bulk-collected digital data from field expeditions that require visual human interpretation. We show two examples here of their use: an independent research-based analysis of snake behavior and a course-based identification of invertebrate species. We present a guide to their appropriate design, facilitation, and evaluation to result in research grade data. We highlight the importance of open source technology to allow for longevity in methodology and appropriate quality control measures necessary for projects that include dozens of researchers over multiple years. In this perspective, we specifically emphasize the prominent role that open source technology plays in making these experiences feasible and scalable. Even without explicit design as broadening participation endeavors, Virtual Expeditions allow for more inclusive participation of early career researchers with specific participatory limitations. Not only are Virtual Expeditions integral to the large-scale analysis necessary for field expeditions that generate impossibly enormous datasets, but they can also be effective facilitators of inclusivity in natural history research.

Open Hardware in Science: The Benefits of Open Electronics.

Openly shared low-cost electronic hardware applications, known as open electronics, have sparked a new open-source movement, with much untapped potential to advance scientific research. Initially designed to appeal to electronic hobbyists, open electronics have formed a global "maker" community and are increasingly used in science and industry. In this perspective article, we review the current costs and benefits of open electronics for use in scientific research ranging from the experimental to the theoretical sciences. We discuss how user-made electronic applications can help (I) individual researchers, by increasing the customization, efficiency, and scalability of experiments, while improving data quantity and quality; (II) scientific institutions, by improving access to customizable high-end technologies, sustainability, visibility, and interdisciplinary collaboration potential; and (III) the scientific community, by improving transparency and reproducibility, helping decouple research capacity from funding, increasing innovation, and improving collaboration potential among researchers and the public. We further discuss how current barriers like poor awareness, knowledge access, and time investments can be resolved by increased documentation and collaboration, and provide guidelines for academics to enter this emerging field. We highlight that open electronics are a promising and powerful tool to help scientific research to become more innovative and reproducible and offer a key practical solution to improve democratic access to science.

Environment-driven shifts in interindividual variation and phenotypic integration within subnetworks of the mussel transcriptome and proteome.

The environment can alter the magnitude of phenotypic variation among individuals, potentially influencing evolutionary trajectories. However, environmental influences on variation are complex and remain understudied. Populations in heterogeneous environments might exhibit more variation, the amount of variation could differ between benign and stressful conditions, and/or variation might manifest in different ways among stages of the gene-to-protein expression cascade or among physiological functions. Here, we explore these three issues by quantifying patterns of inter-individual variation in both transcript and protein expression levels among California mussels, Mytilus californianus Conrad. Mussels were exposed to five ecologically relevant treatments that varied in the mean and interindividual heterogeneity of body temperature. To target a diverse set of physiological functions, we assessed variation within 19 expression subnetworks, including canonical stress-response pathways and empirically derived coexpression clusters that represent a diffuse set of cellular processes. Variation in expression was particularly pronounced in the treatments with high mean and heterogeneous body temperatures. However, with few exceptions, environment-dependent shifts of variation in the transcriptome were not reflected in the proteome. A metric of phenotypic integration provided evidence for a greater degree of constraint on relative expression levels (i.e., stronger correlation) within expression subnetworks in benign, homogeneous environments. Our results suggest that environments that are more stressful on average - and which also tend to be more heterogeneous - can relax these expression constraints and reduce phenotypic integration within biochemical subnetworks. Context-dependent "unmasking" of functional variation may contribute to interindividual differences in physiological phenotype and performance in stressful environments.

A push for inclusive data collection in STEM organizations.

Professional societies could better survey, and thus better serve, underrepresented groups.

Examining Cultural Structures and Functions in Biology.

Scientific culture and structure organize biological sciences in many ways. We make choices concerning the systems and questions we study. Our research then amplifies these choices into factors that influence the directions of future research by shaping our hypotheses, data analyses, interpretation, publication venues, and dissemination via other methods. But our choices are shaped by more than objective curiosity-we are influenced by cultural paradigms reinforced by societal upbringing and scientific indoctrination during training. This extends to the systems and data that we consider to be ethically obtainable or available for study, and who is considered qualified to do research, ask questions, and communicate about research. It is also influenced by the profitability of concepts like open-access-a system designed to improve equity, but which enacts gatekeeping in unintended but foreseeable ways. Creating truly integrative biology programs will require more than intentionally developing departments or institutes that allow overlapping expertise in two or more subfields of biology. Interdisciplinary work requires the expertise of large and diverse teams of scientists working together-this is impossible without an authentic commitment to addressing, not denying, racism when practiced by individuals, institutions, and cultural aspects of academic science. We have identified starting points for remedying how our field has discouraged and caused harm, but we acknowledge there is a long path forward. This path must be paved with field-wide solutions and institutional buy-in: our solutions must match the scale of the problem. Together, we can integrate-not reintegrate-the nuances of biology into our field.

Kelp Morphology and Herbivory Are Maintained Across Latitude Despite Geographic Shift in Kelp-Wounding Herbivores.

AbstractHerbivores can drastically alter the morphology of macroalgae by directly consuming tissue and by inflicting structural wounds. Wounds can result in large amounts of tissue breaking away from macroalgae, amplifying the damage initially caused by herbivores. Herbivores that commonly wound macroalgae often occur over only a portion of a macroalga's lifespan or geographic range. However, we know little about the influence of these periodic or regional occurrences of herbivores on the large-scale seasonal and geographical patterns of macroalgal morphology. We used the intertidal kelp Egregia menziesii to investigate how the kelp's morphology and the prevalence of two prominent kelp-wounding herbivores (limpets and amphipods) changed over two seasons (spring and summer) and over the northern extent of the kelp's geographic range (six sites from central California to northern Washington). Wounds from limpets and amphipods often result in the kelp's fronds being pruned (intercalary meristem broken away), so we quantified kelp size (combined length of all fronds) and pruning (proportion of broken fronds). We found similar results in each season: herbivores were most likely to occur on large, pruned kelp regardless of site; and limpets were the dominant herbivore at southern sites, while amphipods were dominant at northern sites. Despite the geographic shift in the dominant herbivore, kelp had similar levels of total herbivore prevalence (limpets and/or amphipods) and similar morphologies across sites. Our results suggest that large-scale geographic similarities in macroalgal wounding, despite regional variation in the herbivore community, can maintain similar macroalgal morphologies over large geographic areas.

Acclimation to Future Climate Exposes Vulnerability to Cold Extremes in Intertidal Sea Hares.

Highly dynamic environments like estuaries will undergo unpredictable shifts in thermal and salinity regimes with ongoing climate change. These interactive stressors fluctuate predictably and seasonally over historical periods, which has facilitated the evolution of wide environmental tolerance in some estuarine inhabitants. However, physiological and behavioral acclimatization is seasonally based for many estuarine species, meaning that a shift in the unpredictability of climate events and trends will disrupt the effectiveness of evolved tolerance mechanisms. Of particular concern are extreme cold events and high-volume precipitation events, which will acutely and unpredictably alter an estuarine habitat. The eelgrass sea hare, Phyllaplysia taylori, has documented euryhaline and eurythermal tolerance to summer conditions, but the winter environment may pose a greater challenge to seasonally relevant acclimatization scenarios. Here, we characterized lower critical thermal limits, and behavioral responses to stimuli leading up to these limits, in two central California P. taylori populations under four temperature-salinity scenarios in a laboratory acclimation experiment. Acclimation to warmer conditions significantly increased critical thermal minima, while fresher conditions resulted in high mortality. However, the surviving individuals in the fresher conditions were able to respond to stimuli more quickly overall, despite their shortest response time being at a higher temperature than the saltier-acclimated individuals. Within the environmental context of their natural habitats, we find that acclimation to climate change-induced warming will hinder sea hares' ability to weather existing and future cold extremes and precipitation events.

Inter-individual physiological variation in responses to environmental variation and environmental change: Integrating across traits and time.

Greater understanding of physiological responses to climate change demands deeper comprehension of the causes and consequences of physiological variation. Increasingly, population trait means are being deconstructed into variable signals at the level of individuals. We advocate for greater consideration of such inter-individual physiological variation and how it both depends on and interacts with environmental variability. First, we review several studies on the intertidal mussel Mytilus californianus to illustrate how the magnitude of inter-individual variation may depend on the environmental context analyzed (i.e., is the mean condition benign or stressful?) and/or on the specific physiological metric investigated. Stressful conditions may reveal or mask variation in disparate ways at different levels of analysis (e.g., transcriptome vs. proteome), but we often lack crucial information regarding the relationships among these different physiological metrics and their consequences for fitness. We then reanalyze several published datasets to ask whether individuals employ divergent strategies over time in response to acute heat stress; such time-dependence would further complicate interpretation of physiological variation. However, definitive conclusions are precluded by limited sample sizes and short timescales in extant datasets. A key remaining challenge is to extend these analytical frameworks to longer periods over which individuals in a population experience repeated, but spatially variable, episodic stress events. We conclude that variation at multiple levels of analysis should be investigated over longer periods and, where possible, within individuals (or genotypes) experiencing repeated environmental challenges. Although difficult in practice, such studies will facilitate improved understanding of potential population-level physiological responses to climate change.

High Heat Tolerance Is Negatively Correlated with Heat Tolerance Plasticity in Nudibranch Mollusks.

Rapid ocean warming may alter habitat suitability and population fitness for marine ectotherms. Susceptibility to thermal perturbations will depend in part on plasticity of a species' upper thermal limits of performance (CTmax). However, we currently lack data regarding CTmax plasticity for several major marine taxa, including nudibranch mollusks, thus limiting predictive responses to habitat warming for these species. In order to determine relative sensitivity to future warming, we investigated heat tolerance limits (CTmax), heat tolerance plasticity (acclimation response ratio), thermal safety margins, temperature sensitivity of metabolism, and metabolic cost of heat shock in nine species of nudibranchs collected across a thermal gradient along the northeastern Pacific coast of California and held at ambient and elevated temperature for thermal acclimation. Heat tolerance differed significantly among species, ranging from 25.4°±0.5°C to 32.2°±1.8°C ( x¯±SD ), but did not vary with collection site within species. Thermal plasticity was generally high ( 0.52±0.06 , x¯±SE ) and was strongly negatively correlated with CTmax in accordance with the trade-off hypothesis of thermal adaptation. Metabolic costs of thermal challenge were low, with no significant alteration in respiration rate of any species 1 h after exposure to acute heat shock. Thermal safety margins, calculated against maximum habitat temperatures, were negative for nearly all species examined ( -8.5°±5.3°C , x¯±CI [confidence interval]). From these data, we conclude that warm adaptation in intertidal nudibranchs constrains plastic responses to acute thermal challenge and that southern warm-adapted species are likely most vulnerable to future warming.