White-throated sparrow (Zonotrichia albicollis) liver and pectoralis flight muscle transcriptomic changes in preparation for migration

Migratory songbirds undertake challenging journeys to reach their breeding grounds each spring. They accomplish these nonstop flapping feats of endurance through a suite of physiological changes, including the development of substantial fat stores and flight muscle hypertrophy and an increased capacity for fat catabolism. In addition, migratory birds may show large reductions in organ masses during flight, including the flight muscle and liver, which they must rapidly rebuild during their migratory stopover before replenishing their fat stores. However, the molecular basis of this capacity for rapid tissue remodeling and energetic output has not been thoroughly investigated. We performed RNA-sequencing analysis of the liver and pectoralis flight muscle of captive white-throated sparrows in experimentally photostimulated migratory and nonmigratory condition to explore the mechanisms of seasonal change to metabolism and tissue mass regulation that may facilitate these migratory journeys. Based on transcriptional changes, we propose that tissue-specific adjustments in preparation for migration may alleviate the damaging effects of long-duration activity, including a potential increase to the inflammatory response in the muscle. Furthermore, we hypothesize that seasonal hypertrophy balances satellite cell recruitment and apoptosis, while little evidence appeared in the transcriptome to support myostatin-, insulin-like growth factor 1-, and mammalian target of rapamycin-mediated pathways for muscle growth. These findings can encourage more targeted molecular studies on the unique integration of pathways that we find in the development of the migratory endurance phenotype in songbirds.NEW & NOTEWORTHY Migratory songbirds undergo significant physiological changes to accomplish their impressive migratory journeys. However, we have a limited understanding of the regulatory mechanisms underlying these changes. Here, we explore the transcriptomic changes to the flight muscle and liver of white-throated sparrows as they develop the migratory condition. We use these patterns to develop hypotheses about metabolic flexibility and tissue restructuring in preparation for migration.

Avian adjustments to cold and non-shivering thermogenesis: whats, wheres and hows

Avian cold adaptation is hallmarked by innovative strategies of both heat conservation and thermogenesis. While minimizing heat loss can reduce the thermogenic demands of body temperature maintenance, it cannot eliminate the requirement for thermogenesis. Shivering and non-shivering thermogenesis (NST) are the two synergistic mechanisms contributing to endothermy. Birds are of particular interest in studies of NST as they lack brown adipose tissue (BAT), the major organ of NST in mammals. Critical analysis of the existing literature on avian strategies of cold adaptation suggests that skeletal muscle is the principal site of NST. Despite recent progress, isolating the mechanisms involved in avian muscle NST has been difficult as shivering and NST co-exist with its primary locomotory function. Herein, we re-evaluate various proposed molecular bases of avian skeletal muscle NST. Experimental evidence suggests that sarco(endo)plasmic reticulum Ca²⁺ -ATPase (SERCA) and ryanodine receptor 1 (RyR1) are key in avian muscle NST, through their mediation of futile Ca²⁺ cycling and thermogenesis. More recent studies have shown that SERCA regulation by sarcolipin (SLN) facilitates muscle NST in mammals; however, its role in birds is unclear. Ca²⁺ signalling in the muscle seems to be common to contraction, shivering and NST, but elucidating its roles will require more precise measurement of local Ca²⁺ levels inside avian myofibres. The endocrine control of avian muscle NST is still poorly defined. A better understanding of the mechanistic details of avian muscle NST will provide insights into the roles of these processes in regulatory thermogenesis, which could further inform our understanding of the evolution of endothermy among vertebrates.

Skeletal muscle and metabolic flexibility in response to changing energy demands in wild birds

Phenotypically plastic responses of animals to adjust to environmental variation are pervasive. Reversible plasticity (i.e., phenotypic flexibility), where adult phenotypes can be reversibly altered according to prevailing environmental conditions, allow for better matching of phenotypes to the environment and can generate fitness benefits but may also be associated with costs that trade-off with capacity for flexibility. Here, we review the literature on avian metabolic and muscle plasticity in response to season, temperature, migration and experimental manipulation of flight costs, and employ an integrative approach to explore the phenotypic flexibility of metabolic rates and skeletal muscle in wild birds. Basal (minimum maintenance metabolic rate) and summit (maximum cold-induced metabolic rate) metabolic rates are flexible traits in birds, typically increasing with increasing energy demands. Because skeletal muscles are important for energy use at the organismal level, especially to maximum rates of energy use during exercise or shivering thermogenesis, we consider flexibility of skeletal muscle at the tissue and ultrastructural levels in response to variations in the thermal environment and in workloads due to flight exercise. We also examine two major muscle remodeling regulatory pathways: myostatin and insulin-like growth factor -1 (IGF-1). Changes in myostatin and IGF-1 pathways are sometimes, but not always, regulated in a manner consistent with metabolic rate and muscle mass flexibility in response to changing energy demands in wild birds, but few studies have examined such variation so additional study is needed to fully understand roles for these pathways in regulating metabolic flexibility in birds. Muscle ultrastrutural variation in terms of muscle fiber diameter and associated myonuclear domain (MND) in birds is plastic and highly responsive to thermal variation and increases in workload, however, only a few studies have examined ultrastructural flexibility in avian muscle. Additionally, the relationship between myostatin, IGF-1, and satellite cell (SC) proliferation as it relates to avian muscle flexibility has not been addressed in birds and represents a promising avenue for future study.

How does mitochondrial function relate to thermogenic capacity and basal metabolic rate in small birds?

We investigated the role of mitochondrial function in the avian thermoregulatory response to a cold environment. Using black-capped chickadees (Poecile atricapillus) acclimated to cold (-10°C) and thermoneutral (27°C) temperatures, we expected to observe an upregulation of pectoralis muscle and liver respiratory capacity that would be visible in mitochondrial adjustments in cold-acclimated birds. We also predicted that these adjustments would correlate with thermogenic capacity (Msum) and basal metabolic rate (BMR). Using tissue high-resolution respirometry, mitochondrial performance was measured as respiration rate triggered by proton leak and the activity of complex I (OXPHOSCI) and complex I+II (OXPHOSCI+CII) in the liver and pectoralis muscle. The activity of citrate synthase (CS) and cytochrome c oxidase (CCO) was also used as a marker of mitochondrial density. We found 20% higher total CS activity in the whole pectoralis muscle and 39% higher total CCO activity in the whole liver of cold-acclimated chickadees relative to that of birds kept at thermoneutrality. This indicates that cold acclimation increased overall aerobic capacity of these tissues. Msum correlated positively with mitochondrial proton leak in the muscle of cold-acclimated birds while BMR correlated with OXPHOSCI in the liver with a pattern that differed between treatments. Consequently, this study revealed a divergence in mitochondrial metabolism between thermal acclimation states in birds. Some functions of the mitochondria covary with thermogenic capacity and basal maintenance costs in patterns that are dependent on temperature and body mass.

Understanding how variable thermal environments affect the molecular mechanisms underlying temperature-sensitive phenotypes: lessons from sex determination

The thermal environment that organisms experience can affect many aspects of their phenotype. As global temperatures become more unpredictable, it is imperative that we understand the molecular mechanisms by which organisms respond to variable, and often transient, thermal environments. Beyond deciphering the mechanisms through which organisms respond to temperature, we must also appreciate the underlying variation in temperature-dependent processes, as this variation is essential for understanding the potential to adapt to changing climates. In this Commentary, we use temperature-dependent sex determination as an example to explore the mechanistic processes underlying the development of temperature-sensitive phenotypes. We synthesize the current literature on how variable thermal conditions affect these processes and address factors that may limit or allow organisms to respond to variable environments. From these examples, we posit a framework for how the field might move forward in a more systematic way to address three key questions: (1) which genes directly respond to temperature-sensitive changes in protein function and which genes are downstream, indirect responders?; (2) how long does it take different proteins and genes to respond to temperature?; and (3) are the experimental temperature manipulations relevant to the climate the organism experiences or to predicted climate change scenarios? This approach combines mechanistic questions (questions 1 and 2) with ecologically relevant conditions (question 3), allowing us to explore how organisms respond to transient thermal environments and, thus, cope with climate change.

A high-quality genome assembly and annotation of the dark-eyed junco Junco hyemalis, a recently diversified songbird

The dark-eyed junco (Junco hyemalis) is one of the most common passerines of North America, and has served as a model organism in studies related to ecophysiology, behavior, and evolutionary biology for over a century. It is composed of at least 6 distinct, geographically structured forms of recent evolutionary origin, presenting remarkable variation in phenotypic traits, migratory behavior, and habitat. Here, we report a high-quality genome assembly and annotation of the dark-eyed junco generated using a combination of shotgun libraries and proximity ligation Chicago and Dovetail Hi-C libraries. The final assembly is ∼1.03 Gb in size, with 98.3% of the sequence located in 30 full or nearly full chromosome scaffolds, and with a N50/L50 of 71.3 Mb/5 scaffolds. We identified 19,026 functional genes combining gene prediction and similarity approaches, of which 15,967 were associated to GO terms. The genome assembly and the set of annotated genes yielded 95.4% and 96.2% completeness scores, respectively when compared with the BUSCO avian dataset. This new assembly for J. hyemalis provides a valuable resource for genome evolution analysis, and for identifying functional genes involved in adaptive processes and speciation.

How thermal challenges change gene regulation in the songbird brain and gonad: implications for sexual selection in our changing world

In a rapidly warming world, exposure to high temperatures may impact fitness, but the gene regulatory mechanisms that link sublethal heat to sexually selected traits are not well understood, particularly in endothermic animals. Our experiment used zebra finches (Taeniopygia guttata), songbirds that experience extreme temperature fluctuations in their native Australia. We exposed captive males to an acute thermal challenge (43°C) compared with thermoneutral (35°C) and lower (27°C) temperatures. We found significantly more heat dissipation behaviors at 43°C, a temperature previously shown to reduce song production and fertility, and more heat retention behaviors at 27°C. Next, we characterized transcriptomic responses in tissues important for mating effort - the posterior telencephalon, for its role in song production, and the testis, for its role in fertility and hormone production. Differential expression of hundreds of genes in the testes, but few in the brain, suggest the brain is less responsive to extreme temperatures. Nevertheless, gene network analyses revealed that expression related to dopaminergic signaling in the brain co-varied with heat dissipation behaviors, providing a mechanism by which temporary thermal challenges may alter motivational circuits for song production. In both brain and testis, we observed correlations between thermally sensitive gene networks and individual differences in thermoregulatory behavior. Although we cannot directly relate these gene regulatory changes to mating success, our results suggest that individual variation in response to thermal challenges could impact sexually selected traits in a warming world.

Metabolic Profiling and Integration of Metabolomic and Transcriptomic Data From Pectoralis Muscle Reveal Winter-Adaptive Metabolic Responses of Black-Capped Chickadee and American Goldfinch

Seasonal changes, such as alterations in food availability or type and cold conditions, present challenges to free-living birds living in highly seasonal climates. Small birds respond to such challenges through seasonal metabolic flexibility, which better matches seasonal metabolic phenotypes to environmental conditions and can improve fitness. To better understand the mechanistic basis of this metabolic flexibility, we conducted a large-scale metabolic profiling of pectoralis muscle in black-capped chickadees (Poecile atricapillus) and American goldfinches (Spinus tristis), which are small, year-round bird species of temperate-zones. We analyzed muscle samples using non-biased, global metabolomics profiling technology based on UHLC/MS/MS2 platforms. A total of 582 metabolites was characterized for summer and winter season samples. Chickadees showed greater seasonal separation of global metabolite profiles than goldfinches, which is consistent with previous transcriptomic studies of pectoralis muscle in these two species. Reduced levels of amino acids during winter occurred in both species and might reflect decreasing dietary protein intake, amino acid shuttling to other pathways for thermogenesis and/or elevated rates of protein turnover in the pectoralis muscle. Concomitant decreased abundances in tricarboxylic acid cycle (TCA) metabolites suggest faster cycling of the oxidative phosphorylation pathway in winter to meet the metabolic demands of thermogenesis. Accordingly, chickadees displayed shifts toward lipid oxidation in winter, whereas goldfinches showed winter declines in ketone bodies, which suggests increased energy demand or subtle changes in substrate availability. Beyond the winter-specific changes in metabolite abundances, integration of the metabolomic and the transcriptomic data revealed a landscape of gene–metabolite associations related to the winter-adaptive metabolic response. This landscape of gene–metabolite pairs was overrepresented by pathways associated with transport of small molecules, metabolism of amino acids and derivatives, activation and biosynthesis of fatty acid derivatives, and biosynthesis and metabolism of nicotinate and nicotinamide derivatives. Collectively, our results suggest that increased levels of NADH and its derivatives in the pectoralis muscle are a potential novel mechanism for increasing winter metabolic output, fueled by lipids, for thermogenesis during winter.

Snow Buntings Maintain Winter-Level Cold Endurance While Migrating to the High Arctic

Arctic breeding songbirds migrate early in the spring and can face winter environments requiring cold endurance throughout their journey. One such species, the snow bunting (Plectrophenax nivalis), is known for its significant thermogenic capacity. Empirical studies suggest that buntings can indeed maintain winter cold acclimatization into the migratory and breeding phenotypes when kept captive on their wintering grounds. This capacity could be advantageous not only for migrating in a cold environment, but also for facing unpredictable Arctic weather on arrival and during preparation for breeding. However, migration also typically leads to declines in the sizes of several body components linked to metabolic performance. As such, buntings could also experience some loss of cold endurance as they migrate. Here, we aimed to determine whether free-living snow buntings maintain a cold acclimatized phenotype during spring migration. Using a multi-year dataset, we compared body composition (body mass, fat stores, and pectoralis muscle thickness), oxygen carrying capacity (hematocrit) and metabolic performance (thermogenic capacity – Msum and maintenance energy expenditure – BMR) of birds captured on their wintering grounds (January–February, Rimouski, QC, 48°N) and during pre-breeding (April–May) in the Arctic (Alert, NU, 82°). Our results show that body mass, fat stores and Msum were similar between the two stages, while hematocrit and pectoralis muscle thickness were lower in pre-breeding birds than in wintering individuals. These results suggest that although tissue degradation during migration may affect flight muscle size, buntings are able to maintain cold endurance (i.e., Msum) up to their Arctic breeding grounds. However, BMR was higher during pre-breeding than during winter, suggesting higher maintenance costs in the Arctic.

Temperature heterogeneity correlates with intraspecific variation in physiological flexibility in a small endotherm

Phenotypic flexibility allows individuals to reversibly modify trait values and theory predicts an individual's relative degree of flexibility positively correlates with the environmental heterogeneity it experiences. We test this prediction by integrating surveys of population genetic and physiological variation with thermal acclimation experiments and indices of environmental heterogeneity in the Dark-eyed Junco (Junco hyemalis) and its congeners. We combine field measures of thermogenic capacity for 335 individuals, 22,006 single nucleotide polymorphisms genotyped in 181 individuals, and laboratory acclimations replicated on five populations. We show that Junco populations: (1) differ in their thermogenic responses to temperature variation in the field; (2) harbor allelic variation that also correlates with temperature heterogeneity; and (3) exhibit intra-specific variation in thermogenic flexibility in the laboratory that correlates with the heterogeneity of their native thermal environment. These results provide comprehensive support that phenotypic flexibility corresponds with environmental heterogeneity and highlight its importance for coping with environmental change.

Avian red blood cell mitochondria produce more heat in winter than in autumn

Endotherms in cold regions improve heat-producing capacity when preparing for winter. We know comparatively little about how this change is fueled by seasonal adaptation in cellular respiration. Thus, we studied the changes of mitochondrial function in red blood cells in sympatric Coal (Periparus ater), Blue (Cyanistes caeruleus), and Great (Parus major) tits between autumn and winter. These species differ more than twofold in body mass and in several aspects of their foraging ecology and social dominance, which could require differential seasonal adaptation of energy expenditure. Coal and Great tits in particular upregulated the mitochondrial respiration rate and mitochondrial volume in winter. This was not directed toward ATP synthesis, instead reflecting increased uncoupling of electron transport from ATP production. Because uncoupling is exothermic, this increased heat-producing capacity at the sub-cellular level in winter. This previously unexplored the route of thermogenesis in birds should be addressed in future work.

Metabolic Flexibility in Response to Within-Season Temperature Variability in House Sparrows

The climatic variability hypothesis (CVH) posits that more flexible phenotypes should provide a fitness advantage for organisms experiencing more variable climates. While typically applied across geographically separated populations, whether this principle applies across seasons or other conditions (e.g., open vs. sheltered habitats) which differ in climatic variability remains essentially unstudied. In north-temperate climates, climatic variability in winter usually exceeds that in summer, so extending the CVH to within-population seasonal variation predicts that winter phenotypes should be more flexible than summer phenotypes. We tested this prediction of the within-season extension of the CVH by acclimating summer and winter-collected house sparrows (Passer domesticus) to 24, 5, and -10°C and measuring basal metabolic rate (BMR) and summit metabolic rate (M_sum = maximum cold-induced metabolic rate) before and after acclimation (Accl). To examine mechanistic bases for metabolic variation, we measured flight muscle and heart masses and citrate synthase and β-hydroxyacyl coA-dehydrogenase activities. BMR and M_sum were higher for cold-acclimated than for warm-acclimated birds, and BMR was higher in winter than in summer birds. Contrary to our hypothesis of greater responses to cold Accl in winter birds, metabolic rates generally decreased over the Accl period for winter birds at all temperatures but increased at cold temperatures for summer birds. Flight muscle and heart masses were not significantly correlated with season or Accl treatment, except for supracoracoideus mass, which was lower at -10°C in winter, but flight muscle and heart masses were positively correlated with BMR and flight muscle mass was positively correlated with M_sum. Catabolic enzyme activities were not clearly related to metabolic variation. Thus, our data suggest that predictions of the CVH may not be relevant when extended to seasonal temperature variability at the within-population scale. Indeed, these data suggest that metabolic rates are more prominently upregulated in summer than in winter in response to cold. Metabolic rates tended to decrease during Accl at all temperatures in winter, suggesting that initial metabolic rates at capture (higher in winter) influence metabolic Accl for captive birds.

Structural plasticity of the avian pectoralis: a case for geometry and the forgotten organelle

The avian pectoralis muscle demonstrates incredible plasticity. This muscle is the sole thermogenic organ of small passerine birds, and many temperate small passerines increase pectoralis mass in winter, potentially to increase heat production. Similarly, this organ can double in size prior to migration in migratory birds. In this Commentary, following the August Krogh principle, I argue that the avian pectoralis is the perfect tissue to reveal general features of muscle physiology. For example, in both mammals and birds, skeletal muscle fiber diameter is generally accepted to be within 10–100 µm. This size constraint is assumed to include reaction-diffusion limitations, coupled with metabolic cost savings associated with fiber geometry. However, avian muscle fiber structure has been largely ignored in this field, and the extensive remodeling of the avian pectoralis provides a system with which to investigate this. In addition, fiber diameter has been linked to whole-animal metabolic rates, although this has only been addressed in a handful of bird studies, some of which demonstrate previously unreported levels of plasticity and flexibility. Similarly, myonuclei, which are responsible for protein turnover within the fiber, have been forgotten in the avian literature. The few studies that have addressed myonuclear domain (MND) changes in avian muscle have found rates of change not previously seen in mammals. Both fiber diameter and MND have strong implications for aging rates; most aging mammals demonstrate muscular atrophy (a decrease in fiber diameter) and changes in MND. As I discuss here, these features are likely to differ in birds.

Seasonal and elevational variation in glucose and glycogen in two songbird species

Birds naturally maintain high glucose concentrations in the blood and tissues, even when relying on fat to meet the metabolic demands of flight or thermogenesis. One possibility is that high glucose levels might be needed to deal with these metabolic demands. Thus, we hypothesized that birds chronically exposed to colder temperatures and higher elevations have higher circulating glucose and tissue free glucose and glycogen compared to conspecifics living at warmer temperatures and lower elevations. Adult House Sparrows (Passer domesticus) and House Finches (Haemorhous mexicanus) were captured from Phoenix, AZ (340 m elevation), and Albuquerque, NM (1600 m elevation), during the summer and winter months. We measured plasma glucose, as well as free glucose and glycogen from multiple tissues. In general, high elevation and colder temperatures were associated with higher tissue glycogen and higher free glucose concentrations in the brain. These findings indicate that glucose and glycogen are subject to seasonal phenotypic flexibility as well as geographic variations that may relate to local food availability and abundance.

Seasonal variation in body composition in an Afrotropical passerine bird: increases in pectoral muscle mass are, unexpectedly, associated with lower thermogenic capacity

Phenotypic flexibility in avian metabolic rates and body composition have been well-studied in high-latitude species, which typically increase basal metabolic rate (BMR) and summit metabolism (M_sum) when acclimatized to winter conditions. Patterns of seasonal metabolic acclimatization are more variable in lower-latitude birds that experience milder winters, with fewer studies investigating adjustments in avian organ and muscle masses in the context of metabolic flexibility in these regions. We quantified seasonal variation (summer vs winter) in the masses of organs and muscles frequently associated with changes in BMR (gizzard, intestines and liver) and M_sum (heart and pectoral muscles), in white-browed sparrow-weavers (Plocepasser mahali). We also measured pectoral muscle thickness using a portable ultrasound system to determine whether we could non-lethally estimate muscle size. A concurrent study measured seasonal changes in BMR and M_sum in the same population of sparrow-weavers, but different individuals. There was no seasonal variation in the dry masses of the gizzard, intestines or liver of sparrow-weavers, and during the same period, BMR did not vary seasonally. We found significantly higher heart (~ 18% higher) and pectoral muscle (~ 9% higher) dry mass during winter, although ultrasound measurements did not detect seasonal changes in pectoral muscle size. Despite winter increases in pectoral muscle mass, M_sum was ~ 26% lower in winter compared to summer. To the best of our knowledge, this is the first study to report an increase in avian pectoral muscle mass but a concomitant decrease in thermogenic capacity.

Life history predicts flight muscle phenotype and function in birds

Functional traits are the essential phenotypes that underlie an organism's life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals' ecology, studies of functional variation are often restricted to species-level comparisons, ignoring critical variation within species. In birds, interspecific comparisons have been foundational in connecting flight muscle phenotypes to species-level ecology, but intraspecific variation has remained largely unexplored. We asked how age- and sex-dependent demands on flight muscle function are reconciled in birds. The flight muscle is an essential multifunctional organ, mediating a large range of functions associated with powered flight and thermoregulation. These functions must be balanced over an individual's lifetime. We leveraged within- and between-species comparisons in a clade of small passerines (Tarsiger bush-robins) from the eastern edge of the Qinghai-Tibet Plateau. We integrated measurements of flight muscle physiology, morphology, behaviour, phenology and environmental data, analysing trait data within a context of three widespread, adaptive life-history strategies-sexual dichromatism, age and sex-structured migration, and delayed plumage maturation. This approach provides a framework of the selective forces that shape functional variation within and between species. We found more variation in flight muscle traits within species than has been previously described between species of birds under 20 g. This variation was associated with the discovery of mixed muscle fibre types (i.e. both fast glycolytic and fast oxidative fibres), which differ markedly in their physiological and functional attributes. This result is surprising given that the flight muscles of small birds are generally thought to contain only fast oxidative fibres, suggesting a novel ecological context for glycolytic muscle fibres in small birds. Within each species, flight muscle phenotypes varied by age and sex, reflecting the functional demands at different life-history stages and the pressures that individuals face as a result of their multi-class identity (i.e. species, age and sex). Our findings reveal new links between avian physiology, ecology, behaviour and life history, while demonstrating the importance of demographic-dependent selection in shaping functional phenotypic variation.

Consequences of being phenotypically mismatched with the environment: rapid muscle ultrastructural changes in cold-shocked black-capped chickadees (Poecile atricapillus)

Phenotypic flexibility has received considerable attention in the last decade; however, whereas many studies have reported amplitude of variation in phenotypic traits, much less attention has focused on the rate at which traits can adjust in response to sudden changes in the environment. We investigated whole animal and muscle phenotypic changes occurring in black-capped chickadees (Poecile atricapillus) acclimated to cold (-5°C) and warm (20°C) temperatures in the first 3 h following a 15°C temperature drop (over 3 h). Before the temperature change, cold-acclimated birds were consuming 95% more food, were carrying twice as much body fat, and had 23% larger pectoralis muscle fiber diameters than individuals kept at 20°C. In the 3 h following the temperature drop, these same birds altered their pectoralis muscle ultrastructure by increasing the number of capillaries per fiber area and the number of nuclei per millimeter of fiber by 22%, consequently leading to a 22% decrease in myonuclear domain (amount of cytoplasm serviced per nucleus), whereas no such changes were observed in the warm-acclimated birds. To our knowledge, this is the first demonstration of such a rapid adjustment in muscle fiber ultrastructure in vertebrates. These results support the hypothesis that chickadees maintaining a cold phenotype are better prepared than warm-phenotype individuals to respond to a sudden decline in temperature, such as what may be experienced in their natural wintering environment.

Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows

Known as the ‘third polar region’, the Qinghai-Tibet Plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there. Previous studies of birds, animals and humans have focused on well-differentiated populations in later stages of phenotypic divergence. The adaptive processes during the initial phase of highland adaptation remain poorly understood. We studied a human commensal, the Eurasian Tree Sparrow, which has followed human agriculture to the Qinghai-Tibet Plateau. Despite strong phenotypic differentiation at multiple levels, in particular in muscle-related phenotypes, highland and lowland populations show shallow genomic divergence and the colonization event occurred within the past few thousand years. In a one-month acclimation experiment investigating phenotypic plasticity, we exposed adult lowland tree sparrows to a hypoxic environment and did not observe muscle changes. Through population genetic analyses, we identified a signature of polygenic adaptation, whereby shifts in allele frequencies are spread across multiple loci, many of which are associated with muscle-related processes. Our results reveal a case of positive selection in which polygenic adaptation appears to drive rapid phenotypic evolution, shedding light on early stages of adaptive evolution to a novel environment.

Seasonal muscle ultrastructure plasticity and resistance of muscle structural changes during temperature increases in resident black-capped chickadees and rock pigeons

Resident birds in temperate zones respond to seasonally fluctuating temperatures by adjusting their physiology, such as changes in basal metabolic rate or peak metabolic rate during cold exposure, or altering their organ sizes, so as to match the thermogenic requirements of their current environment. Climate change is predicted to cause increases in the frequency of heat and cold wave events, which could increase the likelihood that birds will face an environmental mismatch. Here, we examined seasonality and the effects of acute and chronic heat shock to 33°C and subsequent recovery from heat shock on the ultrastructure of the superficial pectoralis muscle fiber diameter, myonuclear domain (MND) and capillary density in two temperate bird species of differing body mass, the black-capped chickadee (Poecile atricapillus) and the rock pigeon (Columba livia). We found that muscle fiber ultrastructure did not change with heat treatment. However, in black-capped chickadees, there was a significant increase in fiber diameter in spring phenotype birds compared with summer phenotype birds. In rock pigeons, we saw no differences in fiber diameter across seasons. Capillary density did not change as a function of fiber diameter in black-capped chickadees, but did change seasonally, as did MND. Across seasons, as fiber diameter decreased, capillary density increased in the pectoralis muscle of rock pigeons. For both species in this study, we found that as fiber diameter increased, so did MND. Our findings imply that these two temperate birds employ different muscular growth strategies that may be metabolically beneficial to each.

Within-winter flexibility in muscle and heart lipid transport and catabolism in passerine birds

Small birds in cold climates may show within-winter metabolic flexibility to match metabolic capacities to prevailing weather conditions. This flexibility may occur over periods of days to weeks, but the underlying mechanisms for such flexibility are not well understood. Because lipids are the primary fuel for sustained thermogenesis, we examined whether lipid transport and catabolism can mediate within-winter metabolic flexibility in two small temperate-zone wintering passerine birds, dark-eyed juncos (Junco hyemalis) and house sparrows (Passer domesticus). We used simple and multiple regression analyses to test for correlations of several lipid transporters in pectoralis muscle (plasma membrane-bound and cytosolic fatty acid-binding proteins, FABP; fatty acyl translocase, FAT/CD36) and regulatory enzymes (carnitine acyl transferase, CPT; β-hydroxyacyl CoA dehydrogenase, HOAD) in pectoralis and heart with short-term (ST, 0-7 days), medium-term (MT, 14-30 days) and long-term (LT, 30-year mean daily and extreme minimum temperatures, day of winter season) temperature variables. We hypothesized negative correlations between these regulators and temperature variables. Juncos showed negative correlations for FABPs with ST or MT temperature variables, but other lipid transporters and regulatory enzymes showed positive correlations with ST or MT temperatures for juncos, suggesting no consistent pathway-wide response to within-winter temperatures. LT temperature variables showed several significant associations with lipid transporters and enzymes for juncos, but also not in consistent directions. House sparrows showed the expected negative correlations with LT temperatures for FABPpm, but positive correlations with temperature variables for FABPc, CPT and HOAD. Different species-specific patterns of variation and the absence of consistent pathway-wide responses to temperature suggest that the lipid transport and catabolism pathway is not a uniform mediator of within-winter metabolic flexibility among small birds.

Large muscles are beneficial but not required for improving thermogenic capacity in small birds

It is generally assumed that small birds improve their shivering heat production capacity by developing the size of their pectoralis muscles. However, some studies have reported an enhancement of thermogenic capacity in the absence of muscle mass variation between seasons or thermal treatments. We tested the hypothesis that an increase in muscle mass is not a prerequisite for improving avian thermogenic capacity. We measured basal (BMR) and summit (M_sum) metabolic rates of black capped chickadees (Poecile atricapillus) acclimated to thermoneutral (27 °C) and cold (-10 °C) temperatures and obtained body composition data from dissections. Cold acclimated birds consumed 44% more food, and had 5% and 20% higher BMR and M_sum, respectively, compared to individuals kept at thermoneutrality. However, lean dry pectoralis and total muscle mass did not differ between treatments, confirming that the improvement of thermogenic capacity did not require an increase in skeletal muscle mass. Nevertheless, within temperature treatments, M_sum was positively correlated with the mass of all measured muscles, including the pectoralis. Therefore, for a given acclimation temperature individuals with large muscles do benefit from muscle size in term of heat production but improving thermogenic capacity during cold acclimation likely requires an upregulation of cell functions.

Metabolic Flexibility as an Adaptation to Energy Resources and Requirements in Health and Disease

The ability to efficiently adapt metabolism by substrate sensing, trafficking, storage, and utilization, dependent on availability and requirement, is known as metabolic flexibility. In this review, we discuss the breadth and depth of metabolic flexibility and its impact on health and disease. Metabolic flexibility is essential to maintain energy homeostasis in times of either caloric excess or caloric restriction, and in times of either low or high energy demand, such as during exercise. The liver, adipose tissue, and muscle govern systemic metabolic flexibility and manage nutrient sensing, uptake, transport, storage, and expenditure by communication via endocrine cues. At a molecular level, metabolic flexibility relies on the configuration of metabolic pathways, which are regulated by key metabolic enzymes and transcription factors, many of which interact closely with the mitochondria. Disrupted metabolic flexibility, or metabolic inflexibility, however, is associated with many pathological conditions including metabolic syndrome, type 2 diabetes mellitus, and cancer. Multiple factors such as dietary composition and feeding frequency, exercise training, and use of pharmacological compounds, influence metabolic flexibility and will be discussed here. Last, we outline important advances in metabolic flexibility research and discuss medical horizons and translational aspects.

Understanding Evolutionary Impacts of Seasonality: An Introduction to the Symposium

Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging. Here, we have identified four important research questions with the goal of advancing our understanding of evolutionary impacts of seasonality. First, we ask how characteristics of environments and species will determine which adaptive response occurs. Relevant characteristics include costs and limits of plasticity, predictability, and reliability of cues, and grain of environmental variation relative to generation time. A second important question is how phenological shifts will amplify or ameliorate selection on physiological hardiness. Shifts in phenology can preserve the thermal niche despite shifts in climate, but may fail to completely conserve the niche or may even expose life stages to conditions that cause mortality. Considering distinct environmental sensitivities of life history stages will be key to refining models that forecast susceptibility to climate change. Third, we must identify critical physiological phenotypes that underlie seasonal adaptation and work toward understanding the genetic architectures of these responses. These architectures are key for predicting evolutionary responses. Pleiotropic genes that regulate multiple responses to changing seasons may facilitate coordination among functionally related traits, or conversely may constrain the expression of optimal phenotypes. Finally, we must advance our understanding of how changes in seasonal fluctuations are impacting ecological interaction networks. We should move beyond simple dyadic interactions, such as predator prey dynamics, and understand how these interactions scale up to affect ecological interaction networks. As global climate change alters many aspects of seasonal variability, including extreme events and changes in mean conditions, organisms must respond appropriately or go extinct. The outcome of adaptation to seasonality will determine responses to climate change.

Comparative Transcriptomics of Seasonal Phenotypic Flexibility in Two North American Songbirds

Phenotypic flexibility allows organisms to reversibly alter their phenotypes to match the changing demands of seasonal environments. Because phenotypic flexibility is mediated, at least in part, by changes in gene regulation, comparative transcriptomic studies can provide insights into the mechanistic underpinnings of seasonal phenotypic flexibility, and the extent to which regulatory responses to changing seasons are conserved across species. To begin to address these questions, we sampled individuals of two resident North American songbird species, American goldfinch (Spinus tristis) and black-capped chickadee (Poecile atricapillus) in summer and winter to measure seasonal variation in pectoralis transcriptomic profiles and to identify conserved and species-specific elements of these seasonal profiles. We found that very few genes exhibited divergent responses to changes in season between species, and instead, a core set of over 1200 genes responded to season concordantly in both species. Moreover, several key metabolic pathways, regulatory networks, and gene functional classes were commonly recruited to induce seasonal phenotypic shifts in these species. The seasonal transcriptomic responses mirror winter increases in pectoralis mass and cellular metabolic intensity documented in previous studies of both species, suggesting that these seasonal phenotypic responses are due in part to changes in gene expression. Despite growing evidence of muscle nonshivering thermogenesis (NST) in young precocial birds, we did not find strong evidence of upregulation of genes putatively involved in NST during winter in either species, suggesting that seasonal modification of muscular NST is not a prominent contributor to winter increases in thermogenic capacity for adult passerine birds. Together, these results provide the first comprehensive overview of potential common regulatory mechanisms underlying seasonally flexible phenotypes in wild, free-ranging birds.

Metabolic costs imposed by hydrostatic pressure constrain bathymetric range in the lithodid crab Lithodes maja

The changing climate is shifting the distributions of marine species, yet the potential for shifts in depth distributions is virtually unexplored. Hydrostatic pressure is proposed to contribute to a physiological bottleneck constraining depth range extension in shallow-water taxa. However, bathymetric limitation by hydrostatic pressure remains undemonstrated, and the mechanism limiting hyperbaric tolerance remains hypothetical. Here, we assess the effects of hydrostatic pressure in the lithodid crab Lithodes maja (bathymetric range 4-790 m depth, approximately equivalent to 0.1 to 7.9 MPa hydrostatic pressure). Heart rate decreased with increasing hydrostatic pressure, and was significantly lower at ≥10.0 MPa than at 0.1 MPa. Oxygen consumption increased with increasing hydrostatic pressure to 12.5 MPa, before decreasing as hydrostatic pressure increased to 20.0 MPa; oxygen consumption was significantly higher at 7.5-17.5 MPa than at 0.1 MPa. Increases in expression of genes associated with neurotransmission, metabolism and stress were observed between 7.5 and 12.5 MPa. We suggest that hyperbaric tolerance in Lmaja may be oxygen-limited by hyperbaric effects on heart rate and metabolic rate, but that Lmaja's bathymetric range is limited by metabolic costs imposed by the effects of high hydrostatic pressure. These results advocate including hydrostatic pressure in a complex model of environmental tolerance, where energy limitation constrains biogeographic range, and facilitate the incorporation of hydrostatic pressure into the broader metabolic framework for ecology and evolution. Such an approach is crucial for accurately projecting biogeographic responses to changing climate, and for understanding the ecology and evolution of life at depth.

The performing animal: causes and consequences of body remodeling and metabolic adjustments in red knots facing contrasting thermal environments

Using red knots ( Calidris canutus) as a model, we determined how changes in mass and metabolic activity of organs relate to temperature-induced variation in metabolic performance. In cold-acclimated birds, we expected large muscles and heart as well as improved oxidative capacity and lipid transport, and we predicted that this would explain variation in maximal thermogenic capacity (Msum). We also expected larger digestive and excretory organs in these same birds and predicted that this would explain most of the variation in basal metabolic rate (BMR). Knots kept at 5°C were 20% heavier and maintained 1.5 times more body fat than individuals kept in thermoneutral conditions (25°C). The birds in the cold also had a BMR up to 32% higher and a Msum 16% higher than birds at 25°C. Organs were larger in the cold, with muscles and heart being 9–20% heavier and digestive and excretory organs being 21–36% larger than at thermoneutrality. Rather than the predicted digestive and excretory organs, the cold-induced increase in BMR correlated with changes in mass of the heart, pectoralis, and carcass. Msum varied positively with the mass of the pectoralis, supracoracoideus, and heart, highlighting the importance of muscles and cardiac function in cold endurance. Cold-acclimated knots also expressed upregulated capacity for lipid transport across mitochondrial membranes [carnitine palmitoyl transferase (CPT)] in their pectoralis and leg muscles, higher lipid catabolism capacity in their pectoralis muscles [β-hydroxyacyl CoA-dehydrogenase (HOAD)], and elevated oxidative capacity in their liver and kidney (citrate synthase). These adjustments may have contributed to BMR through changes in metabolic intensity. Positive relationships among Msum, CPT, and HOAD in the heart also suggest indirect constraints on thermogenic capacity through limited cardiac capacity.

Context-dependent regulation of pectoralis myostatin and lipid transporters by temperature and photoperiod in dark-eyed juncos

A prominent example of seasonal phenotypic flexibility is the winter increase in thermogenic capacity (=summit metabolism, [Formula: see text]) in small birds, which is often accompanied by increases in pectoralis muscle mass and lipid catabolic capacity. Temperature or photoperiod may be drivers of the winter phenotype, but their relative impacts on muscle remodeling or lipid transport pathways are little known. We examined photoperiod and temperature effects on pectoralis muscle expression of myostatin, a muscle growth inhibitor, and its tolloid-like protein activators (TLL-1 and TLL-2), and sarcolemmal and intracellular lipid transporters in dark-eyed juncos Junco hyemalis. We acclimated winter juncos to four temperature (3 °C or 24 °C) and photoperiod [short-day (SD) = 8L:16D; long-day (LD) = 16L:8D] treatments. We found that myostatin, TLL-1, TLL-2, and lipid transporter mRNA expression and myostatin protein expression did not differ among treatments, but treatments interacted to influence lipid transporter protein expression. Fatty acid translocase (FAT/CD36) levels were higher for cold SD than for other treatments. Membrane-bound fatty acid binding protein (FABPpm) levels, however, were higher for the cold LD treatment than for cold SD and warm LD treatments. Cytosolic fatty acid binding protein (FABP_c) levels were higher on LD than on SD at 3 °C, but higher on SD than on LD at 24 °C. Cold temperature groups showed upregulation of these lipid transporters, which could contribute to elevated M_sum compared to warm groups on the same photoperiod. However, interactions of temperature or photoperiod effects on muscle remodeling and lipid transport pathways suggest that these effects are context-dependent.

Individual Differences in the Phenotypic Flexibility of Basal Metabolic Rate in Siberian Hamsters Are Consistent on Short- and Long-Term Timescales

Basal metabolic rate (BMR) correlates with the cost of life in endothermic animals. It usually differs consistently among individuals in a population, but it may be adjusted in response to predictable or unpredictable changes in the environment. The phenotypic flexibility of BMR is considered an adaptation to living in a stochastic environment; however, whether it is also repeatable it is still unexplored. Assuming that variations in phenotypic flexibility are evolutionarily important, we hypothesized that they are consistently different among individuals. We predicted that not only BMR but also its flexibility in response to changes in ambient temperature (T_a) are repeatable on short- and long-term timescales. To examine this, we acclimated Siberian hamsters (Phodopus sungorus) for 100 d to winterlike and then to summerlike conditions, and after each acclimation we exposed them interchangeably to 10° and 28°C for 14 d. The difference in BMR measured after each exposure defined an individual's phenotypic flexibility (ΔBMR). BMR was repeatable within and among seasons. It was also flexible in both seasons, but in winter this flexibility was lower in individuals responding to seasonal changes than in nonresponding ones. When we accounted for individual responsiveness, the repeatability of ΔBMR was significant in winter (τ = 0.48, P = 0.01) and in summer (τ = 0.55, P = 0.005). Finally, the flexibility of BMR in response to changes in T_a was also repeatable on a long-term timescale, that is, among seasons (τ = 0.31, P = 0.008). Our results indicate the evolutionary importance of the phenotypic flexibility of energy metabolism and suggest that it may be subject to selection.

Uncoupling Basal and Summit Metabolic Rates in White-Throated Sparrows: Digestive Demand Drives Maintenance Costs, but Changes in Muscle Mass Are Not Needed to Improve Thermogenic Capacity

Avian basal metabolic rate (BMR) and summit metabolic rate (M_sum) vary in parallel during cold acclimation and acclimatization, which implies a functional link between these variables. However, evidence suggests that these parameters may reflect different physiological systems acting independently. We tested this hypothesis in white-throated sparrows (Zonotrichia albicollis) acclimated to two temperatures (-8° and 28°C) and two diets (0% and 30% cellulose). We expected to find an uncoupling of M_sum and BMR where M_sum, a measure of maximal shivering heat production, would reflect muscle and heart mass variation and would respond only to temperature, while BMR would reflect changes in digestive and excretory organs in response to daily food intake, responding to both temperature and diet. We found that the gizzard, liver, kidneys, and intestines responded to treatments through a positive relationship with food intake. BMR was 15% higher in cold-acclimated birds and, as expected, varied with food intake and the mass of digestive and excretory organs. In contrast, although M_sum was 19% higher in cold-acclimated birds, only heart mass responded to temperature (+18% in the cold). Pectoral muscles did not change in mass with temperature but were 8.2% lighter on the cellulose diet. Nevertheless, M_sum varied positively with the mass of heart and skeletal muscles but only in cold-acclimated birds. Our results therefore suggest that an upregulation of muscle metabolic intensity is required for cold acclimation. This study increases support for the hypothesis that BMR and M_sum reflect different physiological systems responding in parallel to constraints associated with cold environments.

Within-Winter Flexibility in Muscle Masses, Myostatin, and Cellular Aerobic Metabolic Intensity in Passerine Birds

Metabolic rates of passerine birds are flexible traits that vary both seasonally and among and within winters. Seasonal variation in summit metabolic rates (M_sum = maximum thermoregulatory metabolism) in birds is consistently correlated with changes in pectoralis muscle and heart masses and sometimes with variation in cellular aerobic metabolic intensity, so these traits might also be associated with shorter-term, within-winter variation in metabolic rates. To determine whether these mechanisms are associated with within-winter variation in M_sum, we examined the effects of short-term (ST; 0-7 d), medium-term (MT; 14-30 d), and long-term (LT; 30-yr means) temperature variables on pectoralis muscle and heart masses, pectoralis expression of the muscle-growth inhibitor myostatin and its metalloproteinase activators TLL-1 and TLL-2, and pectoralis and heart citrate synthase (CS; an indicator of cellular aerobic metabolic intensity) activities for two temperate-zone resident passerines, house sparrows (Passer domesticus) and dark-eyed juncos (Junco hyemalis). For both species, pectoralis mass residuals were positively correlated with ST temperature variables, suggesting that cold temperatures resulted in increased turnover of pectoralis muscle, but heart mass showed little within-winter variation for either species. Pectoralis mRNA and protein expression of myostatin and the TLLs were only weakly correlated with ST and MT temperature variables, which is largely consistent with trends in muscle masses for both species. Pectoralis and heart CS activities showed weak and variable trends with ST temperature variables in both species, suggesting only minor effects of temperature variation on cellular aerobic metabolic intensity. Thus, neither muscle or heart masses, regulation by the myostatin system, nor cellular aerobic metabolic intensity varied consistently with winter temperature, suggesting that other factors regulate within-winter metabolic variation in these birds.

Transcriptomic plasticity in brown adipose tissue contributes to an enhanced capacity for nonshivering thermogenesis in deer mice

For small mammals living at high altitude, aerobic heat generation (thermogenesis) is essential for survival during prolonged periods of cold, but is severely impaired under conditions of hypobaric hypoxia. Recent studies in deer mice (Peromyscus maniculatus) reveal adaptive enhancement of thermogenesis in high- compared to low-altitude populations under hypoxic cold stress, an enhancement that is attributable to modifications in the aerobic metabolism of muscles used in shivering. However, because small mammals rely heavily on nonshivering mechanisms for cold acclimatization, we tested for evidence of adaptive divergence in nonshivering thermogenesis (NST) under hypoxia. To do so, we measured NST and characterized transcriptional profiles of brown adipose tissue (BAT) in high- and low-altitude deer mice that were (i) wild-caught and acclimatized to their native altitude, and (ii) born and reared under common garden conditions at low elevation. We found that NST performance under hypoxia is enhanced in wild-caught, high-altitude deer mice, a difference that is associated with increased expression of coregulated genes that influence several physiological traits. These traits include vascularization and O2 supply to BAT, brown adipocyte proliferation and the uncoupling of oxidative phosphorylation from ATP synthesis in the generation of heat. Our results suggest that acclimatization to hypoxic cold stress is facilitated by enhancement of nonshivering heat production, which is driven by regulatory plasticity in a suite of genes that influence intersecting physiological pathways.

Phenotypic flexibility of energetics in acclimated Siberian hamsters has a narrower scope in winter than in summer

As photoperiod shortens with the approach of winter, small mammals should reduce their energy expenditure to survive periods of food limitation. However, within seasons, animals should balance their energy budgets as abiotic conditions change, sometimes unpredictably; cold spells should increase heat production, while warm spells should do the opposite. Therefore, we addressed specific questions about the possible interactions between seasonal acclimatization and the intra-seasonal phenotypic flexibility of metabolic rate. We hypothesized that phenotypic flexibility in small mammals differs seasonally and is greater in summer than in winter, and predicted that seasonal adjustments in energetics, which are driven by photoperiod, overwhelm the influence of variations in the thermal environment. We measured body mass, basal metabolic rate (BMR), facultative non-shivering thermogenesis (fNST), body temperature, and calculated minimum thermal conductance in Siberian hamsters Phodopus sungorus. Animals were acclimated to winter-like, and then to summer-like conditions and, within each season, were exposed twice, for 3 weeks to 10, 20 or 28 °C. We used differences between values measured after these short acclimation periods as a measure of the scope of phenotypic flexibility. After winter acclimation, hamsters were lighter, had lower whole animal BMR, higher fNST than in summer, and developed heterothermy. After these short acclimations to the above-mentioned temperatures, hamsters showed reversible changes in BMR and fNST; however, these traits were less flexible in winter than in summer. We conclude that seasonal acclimation affects hamster responses to intra-seasonal variations in the thermal environment. We argue that understanding seasonal changes in phenotypic flexibility is crucial for predicting the biological consequences of global climate changes.

Divergence and Functional Degradation of a Sex Chromosome-like Supergene

A major challenge in biology is to understand the genetic basis of adaptation. One compelling idea is that groups of tightly linked genes (i.e., "supergenes" [1, 2]) facilitate adaptation in suites of traits that determine fitness. Despite their likely importance, little is known about how alternate supergene alleles arise and become differentiated, nor their ultimate fate within species. Herein we address these questions by investigating the evolutionary history of a supergene in white-throated sparrows, Zonotrichia albicollis. This species comprises two morphs, tan and white, that differ in pigmentation and components of social behavior [3-5]. Morph is determined by alternative alleles at a balanced >100-Mb inversion-based supergene, providing a unique system for studying gene-behavior relationships. Using over two decades of field data, we document near-perfect disassortative mating among morphs, as well as the fitness consequences of rare assortative mating. We use de novo whole-genome sequencing coupled with population- and phylogenomic data to show that alternate supergene alleles are highly divergent at over 1,000 genes and that these alleles originated prior to the split of Z. albicollis from its sister species and may be polymorphic in Z. albicollis due to a past hybridization event. We provide evidence that the "white" allele may be degrading, similar to neo-Y/W sex chromosomes. We further show that the "tan" allele has surprisingly low levels of genetic diversity yet does not show several canonical signatures of recurrent positive selection. We discuss these results in the context of the origin, molecular evolution, and possible fate of this remarkable polymorphism.

The potential for climate-driven bathymetric range shifts: sustained temperature and pressure exposures on a marine ectotherm, Palaemonetes varians

Range shifts are of great importance as a response for species facing climate change. In the light of current ocean-surface warming, many studies have focused on the capacity of marine ectotherms to shift their ranges latitudinally. Bathymetric range shifts offer an important alternative, and may be the sole option for species already at high latitudes or those within enclosed seas; yet relevant data are scant. Hydrostatic pressure (HP) and temperature have wide ranging effects on physiology, importantly acting in synergy thermodynamically, and therefore represent key environmental constraints to bathymetric migration. We present data on transcriptional regulation in a shallow-water marine crustacean (Palaemonetes varians) at atmospheric and high HP following 168-h exposures at three temperatures across the organisms' thermal scope, to establish the potential physiological limit to bathymetric migration by neritic fauna. We observe changes in gene expression indicative of cellular macromolecular damage, disturbances in metabolic pathways and a lack of acclimation after prolonged exposure to high HP. Importantly, these effects are ameliorated (less deleterious) at higher temperatures, and exacerbated at lower temperatures. These data, alongside previously published behavioural and heat-shock analyses, have important implications for our understanding of the potential for climate-driven bathymetric range shifts.

Adaptive Modifications of Muscle Phenotype in High-Altitude Deer Mice Are Associated with Evolved Changes in Gene Regulation

At high-altitude, small mammals are faced with the energetic challenge of sustaining thermogenesis and aerobic exercise in spite of the reduced O2 availability. Under conditions of hypoxic cold stress, metabolic demands of shivering thermogenesis and locomotion may require enhancements in the oxidative capacity and O2 diffusion capacity of skeletal muscle to compensate for the diminished tissue O2 supply. We used common-garden experiments involving highland and lowland deer mice (Peromyscus maniculatus) to investigate the transcriptional underpinnings of genetically based population differences and plasticity in muscle phenotype. We tested highland and lowland mice that were sampled in their native environments as well as lab-raised F1 progeny of wild-caught mice. Experiments revealed that highland natives had consistently greater oxidative fiber density and capillarity in the gastrocnemius muscle. RNA sequencing analyses revealed population differences in transcript abundance for 68 genes that clustered into two discrete transcriptional modules, and a large suite of transcripts (589 genes) with plastic expression patterns that clustered into five modules. The expression of two transcriptional modules was correlated with the oxidative phenotype and capillarity of the muscle, and these phenotype-associated modules were enriched for genes involved in energy metabolism, muscle plasticity, vascular development, and cell stress response. Although most of the individual transcripts that were differentially expressed between populations were negatively correlated with muscle phenotype, several genes involved in energy metabolism (e.g., Ckmt1, Ehhadh, Acaa1a) and angiogenesis (Notch4) were more highly expressed in highlanders, and the regulators of mitochondrial biogenesis, PGC-1α (Ppargc1a) and mitochondrial transcription factor A (Tfam), were positively correlated with muscle oxidative phenotype. These results suggest that evolved population differences in the oxidative capacity and capillarity of skeletal muscle involved expression changes in a small suite of coregulated genes.