Best practices for building and curating databases for comparative analyses.

Comparative analyses have a long history of macro-ecological and -evolutionary approaches to understand structure, function, mechanism and constraint. As the pace of science accelerates, there is ever-increasing access to diverse types of data and open access databases that are enabling and inspiring new research. Whether conducting a species-level trait-based analysis or a formal meta-analysis of study effect sizes, comparative approaches share a common reliance on reliable, carefully curated databases. Unlike many scientific endeavors, building a database is a process that many researchers undertake infrequently and in which we are not formally trained. This Commentary provides an introduction to building databases for comparative analyses and highlights challenges and solutions that the authors of this Commentary have faced in their own experiences. We focus on four major tips: (1) carefully strategizing the literature search; (2) structuring databases for multiple use; (3) establishing version control within (and beyond) your study; and (4) the importance of making databases accessible. We highlight how one's approach to these tasks often depends on the goal of the study and the nature of the data. Finally, we assert that the curation of single-question databases has several disadvantages: it limits the possibility of using databases for multiple purposes and decreases efficiency due to independent researchers repeatedly sifting through large volumes of raw information. We argue that curating databases that are broader than one research question can provide a large return on investment, and that research fields could increase efficiency if community curation of databases was established.

Effect of valine on myotube insulin sensitivity and metabolism with and without insulin resistance.

Population data have consistently demonstrated a correlation between circulating branched-chain amino acids (BCAA) and insulin resistance. Most recently valine catabolite, 3-hydroxyisobutyrate, has emerged as a potential cause of BCAA-mediated insulin resistance; however, it is unclear if valine independently promotes insulin resistance. It is also unclear if excess valine influences the ability of cells to degrade BCAA. Therefore, this study investigated the effect of valine on muscle insulin signaling and related metabolism in vitro. C2C12 myotubes were treated with varying concentrations (0.5 mM-2 mM) of valine for up to 48 h. qRT-PCR and western blot were used to measure metabolic gene and protein expression, respectively. Insulin sensitivity (indicated by pAkt:Akt), metabolic gene and protein expression, and cell metabolism were also measured following valine treatment both with and without varying levels of insulin resistance. Mitochondrial and glycolytic metabolism were measured via oxygen consumption and extracellular acidification rate, respectively. Valine did not alter regulators of mitochondrial biogenesis or glycolysis; however, valine reduced branched-chain alpha-keto acid dehydrogenase a (Bckdha) mRNA (but not protein) expression which was exacerbated by insulin resistance. Valine treatment had no effect on pAkt:Akt following either acute or 48-h treatment, regardless of insulin stimulation or varying levels of insulin resistance. In conclusion, despite consistent population data demonstrating a relationship between circulating BCAA (and related metabolites) and insulin resistance, valine does not appear to independently alter insulin sensitivity or worsen insulin resistance in the myotube model of skeletal muscle.

Macroevolutionary Patterning in Glucocorticoids Suggests Different Selective Pressures Shape Baseline and Stress-Induced Levels.

Glucocorticoid (GC) hormones are important phenotypic mediators across vertebrates, but their circulating concentrations can vary markedly. Here we investigate macroevolutionary patterning in GC levels across tetrapods by testing seven specific hypotheses about GC variation and evaluating whether the supported hypotheses reveal consistent patterns in GC evolution. If selection generally favors the "supportive" role of GCs in responding effectively to challenges, then baseline and/or stress-induced GCs may be higher in challenging contexts. Alternatively, if selection generally favors "protection" from GC-induced costs, GCs may be lower in environments where challenges are more common or severe. The predictors of baseline GCs were all consistent with supportive effects: levels were higher in smaller organisms and in those inhabiting more energetically demanding environments. During breeding, baseline GCs were also higher in populations and species with fewer lifetime opportunities to reproduce. The predictors of stress-induced GCs were instead more consistent with the protection hypothesis: during breeding, levels were lower in organisms with fewer lifetime reproductive opportunities. Overall, these patterns indicate a surprising degree of consistency in how some selective pressures shape GCs across broad taxonomic scales; at the same time, in challenging environments selection appears to operate on baseline and stress-induced GCs in distinct ways.

Rapid evolution of testis size relative to sperm morphology suggests that post-copulatory selection targets sperm number in Anolis lizards.

Post-copulatory sexual selection is thought to be responsible for much of the extraordinary diversity in sperm morphology across metazoans. However, the extent to which post-copulatory selection targets sperm morphology versus sperm production is generally unknown. To address this issue, we simultaneously characterized the evolution of sperm morphology (length of the sperm head, midpiece and flagellum) and testis size (a proxy for sperm production) across 26 species of Anolis lizards, a group in which sperm competition is likely. We found that the length of the sperm midpiece has evolved 2-3 times faster than that of the sperm head or flagellum, suggesting that midpiece size may be the most important aspect of sperm morphology with respect to post-copulatory sexual selection. However, testis size has evolved faster than any aspect of sperm morphology or body size, supporting the hypothesis that post-copulatory sexual selection acts more strongly upon sperm production than upon sperm morphology. Likewise, evolutionary increases in testis size, which typically indicate increased sperm competition, are not associated with predictable changes in sperm morphology, suggesting that any effects of post-copulatory selection on sperm morphology are either weak or variable in direction across anoles. Collectively, our results suggest that sperm production is the primary target of post-copulatory sexual selection in this lineage.

The evolution of androgen receptor expression and behavior in Anolis lizard forelimb muscles.

The motor systems that produce behavioral movements are among the primary targets for the action of steroid hormones, including androgens. Androgens such as testosterone bind to androgen receptors (AR) to induce physiological changes in the size, strength, and energetic capacity of skeletal muscles, which can directly influence the performance of behaviors in which those muscles are used. Because tissues differentially express AR, resulting in tissue-specific sensitivity to androgens, AR expression may be a major target of selection for the evolution of behavior. Anolis lizards (i.e., anoles) provide a robust system for the study of androgen-regulated traits, including the behavioral traits that facilitate social display and locomotion. In this study, we examined six anole species that demonstrate significant variation in the behavioral use of the forelimbs to measure the proportion of myonuclei in the bicep muscles that express AR. Using phylogenetic comparative analyses, we found that species with a greater proportion of nuclei positive for AR expression in the biceps exhibited greater frequencies of locomotor movements and pushup displays. These results suggest that AR expression in skeletal muscles may influence the evolution of androgen-regulated behaviors in this group.

Migration and the evolution of sexual dichromatism: evolutionary loss of female coloration with migration among wood-warblers.

The mechanisms underlying evolutionary changes in sexual dimorphism have long been of interest to biologists. A striking gradient in sexual dichromatism exists among songbirds in North America, including the wood-warblers (Parulidae): males are generally more colourful than females at northern latitudes, while the sexes are similarly ornamented at lower latitudes. We use phylogenetically controlled comparative analysis to test three non-mutually exclusive hypotheses for the evolution of sexual dichromatism among wood-warblers. The first two hypotheses focus on the loss of female coloration with the evolution of migration, either owing to the costs imposed by visual predators during migration, or owing to the relaxation of selection for female social signalling at higher latitudes. The third hypothesis focuses on whether sexual dichromatism evolved owing to changes in male ornamentation as the strength of sexual selection increases with breeding latitude. To test these hypotheses, we compared sexual dichromatism to three variables: the presence of migration, migration distance, and breeding latitude. We found that the presence of migration and migration distance were both positively correlated with sexual dichromatism, but models including breeding latitude alone were not strongly supported. Ancestral state reconstruction supports the hypothesis that the ancestral wood-warblers were monochromatic, with both colourful males and females. Combined, these results are consistent with the hypotheses that the evolution of migration is associated with the relaxation of selection for social signalling among females and that there are increased predatory costs along longer migratory routes for colourful females. These results suggest that loss of female ornamentation can be a driver of sexual dichromatism and that social or natural selection may be a stronger contributor to variation in dichromatism than sexual selection.

Colorful displays signal male quality in a tropical anole lizard.

Parasites influence colorful ornaments and their behavioral display in many animal hosts. Because coloration and display behavior are often critical components of communication, variation in these traits may have important implications for individual fitness, yet it remains unclear whether such traits are signals of quality in many taxa. We investigated the association between ectoparasitic mite load and the color and behavioral use of the throat fan (dewlap) by male Anolis brevirostris lizards. We found that heavily parasitized lizards exhibited lower body condition, duller dewlaps, and less frequent dewlap displays than less parasitized individuals. Our results thus suggest that highly parasitized individuals invest less in both ornamental color and behavioral display of that color. Because the two components of the signal simultaneously provide information on male quality, this study provides novel support for the long-standing hypothesis that colorful traits may function as social or sexual signals in reptiles.

Artificial light at night alters diurnal and nocturnal behavior and physiology in green anole lizards.

Artificial light at night (ALAN) disrupts biological rhythms across widely diverse organisms. To determine how energy is allocated by animals in different light environments, we investigated the impacts of ALAN on behavior and physiology of diurnal green anole lizards (Anolis carolinensis). Two groups of 24 adult lizards (half males, half females) were maintained in a controlled lab setting for six weeks. One group was exposed to a simulated natural summer light-dark cycle; the other was exposed to ALAN that simulated urban, nocturnal light exposure. After an acclimation period, we conducted four behavioral trials. One trial examined behavioral time allocation over two 24 h periods, and three others were conducted during mid-day and mid-night: open field tests, to examine exploratory behavior; foraging trials, to examine prey consumption; and social interaction trials, to examine same-sex interactions. We then measured each lizard's snout-vent length and mass of its body, abdominal fat pads, liver, and, for males, testes. Lizards exposed to ALAN were more likely to be awake at night, using nocturnal light to explore, forage, and display to conspecifics. However, during the day, ALAN lizards were less likely to be awake, slower to move, and females displayed less frequently. ALAN lizards had heavier fat pads and testes, but ALAN did not impact body mass, liver mass, or snout-vent length. In sum, ALAN appears to cause a broad shift towards increased nocturnal activity and may alter metabolic and reproductive processes. Future work should examine the fitness consequences of these behavioral and physiological changes.

Understanding Drivers of Variation and Predicting Variability Across Levels of Biological Organization.

Differences within a biological system are ubiquitous, creating variation in nature. Variation underlies all evolutionary processes and allows persistence and resilience in changing environments; thus, uncovering the drivers of variation is critical. The growing recognition that variation is central to biology presents a timely opportunity for determining unifying principles that drive variation across biological levels of organization. Currently, most studies that consider variation are focused at a single biological level and not integrated into a broader perspective. Here we explain what variation is and how it can be measured. We then discuss the importance of variation in natural systems, and briefly describe the biological research that has focused on variation. We outline some of the barriers and solutions to studying variation and its drivers in biological systems. Finally, we detail the challenges and opportunities that may arise when studying the drivers of variation due to the multi-level nature of biological systems. Examining the drivers of variation will lead to a reintegration of biology. It will further forge interdisciplinary collaborations and open opportunities for training diverse quantitative biologists. We anticipate that these insights will inspire new questions and new analytic tools to study the fundamental questions of what drives variation in biological systems and how variation has shaped life.

What Determines Paternity in Wild Lizards? A Spatiotemporal Analysis of Behavior and Morphology.

Mating behavior in animals can be understood as a sequence of events that begins with individuals encountering one another and ends with the production of offspring. Behavioral descriptions of animal interactions characterize early elements of this sequence, and genetic descriptions use offspring parentage to characterize the final outcome, with behavioral and physiological assessments of mates and mechanisms of copulation and fertilization comprising intermediate steps. However, behavioral and genetic descriptions of mating systems are often inconsistent with one another, complicating expectations for crucial aspects of mating biology, such as the presence of multiple mating. Here, we use behavioral and genetic data from a wild population of the lizard Anolis cristatellus to characterize female multiple mating and the potential for sexual selection through female mate choice in this species. We find that 48% of sampled females bore offspring sired by multiple males. Moreover, spatiotemporal proximity between males and females was associated with whether a male sired a female's offspring, and if yes, how many offspring he sired. Additionally, male body size, but not display behavior, was associated with reproductive outcomes for male-female pairs. While much remains to be learned about the mechanisms of mating and targets of sexual selection in A. cristatellus, it is clear that female multiple mating is a substantial component of this species' mating system in nature.

Life history and environment predict variation in testosterone across vertebrates.

Endocrine systems act as key intermediaries between organisms and their environments. This interaction leads to high variability in hormone levels, but we know little about the ecological factors that influence this variation within and across major vertebrate groups. We study this topic by assessing how various social and environmental dynamics influence testosterone levels across the entire vertebrate tree of life. Our analyses show that breeding season length and mating system are the strongest predictors of average testosterone concentrations, whereas breeding season length, environmental temperature, and variability in precipitation are the strongest predictors of within-population variation in testosterone. Principles from small-scale comparative studies that stress the importance of mating opportunity and competition on the evolution of species differences in testosterone levels, therefore, likely apply to the entire vertebrate lineage. Meanwhile, climatic factors associated with rainfall and ambient temperature appear to influence variability in plasma testosterone, within a given species. These results, therefore, reveal how unique suites of ecological factors differentially explain scales of variation in circulating testosterone across mammals, birds, reptiles, amphibians, and fishes.

Linking ecomechanical models and functional traits to understand phenotypic diversity.

Physical principles and laws determine the set of possible organismal phenotypes. Constraints arising from development, the environment, and evolutionary history then yield workable, integrated phenotypes. We propose a theoretical and practical framework that considers the role of changing environments. This 'ecomechanical approach' integrates functional organismal traits with the ecological variables. This approach informs our ability to predict species shifts in survival and distribution and provides critical insights into phenotypic diversity. We outline how to use the ecomechanical paradigm using drag-induced bending in trees as an example. Our approach can be incorporated into existing research and help build interdisciplinary bridges. Finally, we identify key factors needed for mass data collection, analysis, and the dissemination of models relevant to this framework.

Behavioural display systems across nine Anolis lizard species: sexual dimorphisms in structure and function.

Relationships between structure and function are a primary focus in biology, yet they are most often considered within individual species. Sexually dimorphic communication behaviours and the morphology of associated structures can vary widely, even among closely related species, and these traits provide an ideal opportunity to investigate the evolution of structure-function patterns. Using nine Anolis lizard species, we addressed a series of questions regarding sex differences in and the evolution of relationships between extension of the throat fan (dewlap) and morphology of the muscles and cartilage controlling it. The main results indicated that within species, males displayed the dewlap more often than females and consistently exhibited larger associated structures. These data are consistent with work in other vertebrates in which corresponding sex differences in reproductive morphology and behaviour have been documented. Across species, however, we found no evidence that the rate of dewlap extension evolved in association with dewlap morphology. Thus, we provide an example of traits that, when considered in a phylogenetic framework, exhibited limited associations between behaviour and morphology, perhaps as the result of constraints imposed by the ecological contexts in which different species occur.

Leucine increases mitochondrial metabolism and lipid content without altering insulin signaling in myotubes.

Elevated circulating branched-chain amino acids (BCAA) such as leucine have been consistently correlated with increasing severity of insulin resistance across numerous populations. BCAA may promote insulin resistance through either mTOR-mediated suppression of insulin receptor substrate-1 or through the accumulation of toxic BCAA catabolites. Although the link between circulating BCAA and insulin resistance has been consistent, it has yet to be concluded if BCAA causally contribute to the development or worsening of insulin resistance. This work investigated the effect of leucine both with and without varying levels of insulin resistance on metabolism, metabolic gene expression, and insulin signaling. C2C12 myotubes were treated with and without varied concentrations of leucine up to 2 mM for 24 h both with and without varied levels of insulin resistance. Gene and protein expression were measured via qRT-PCR and Western blot, respectively. Mitochondrial metabolism was measured via O2 consumption. Leucine at 2 mM increased oxidative metabolism as well as gene expression of mitochondrial biogenesis, which was associated with increased cellular lipid content. Despite increased lipid content of leucine-treated cells, neither acute nor chronic leucine treatment at 2 mM affected insulin signaling in insulin sensitive, mildly insulin resistant, or severely insulin resistant cells. Similarly, leucine at lower concentrations (0.25 mM, 0.5 mM, and 1 mM) did not alter insulin signaling either, regardless of insulin resistance. Leucine appears to improve myotube oxidative metabolism and related metabolic gene expression. And despite increased lipid content of leucine-treated cells, leucine does not appear to alter insulin sensitivity either acutely or chronically, regardless of level of insulin resistance.

Baseline and stress-induced corticosterone levels across birds and reptiles do not reflect urbanization levels.

Rates of human-induced environmental change continue increasing with human population size, potentially altering animal physiology and negatively affecting wildlife. Researchers often use glucocorticoid concentrations (hormones that can be associated with stressors) to gauge the impact of anthropogenic factors (e.g. urbanization, noise and light pollution). Yet, no general relationships between human-induced environmental change and glucocorticoids have emerged. Given the number of recent studies reporting baseline and stress-induced corticosterone (the primary glucocorticoid in birds and reptiles) concentrations worldwide, it is now possible to conduct large-scale comparative analyses to test for general associations between disturbance and baseline and stress-induced corticosterone across species. Additionally, we can control for factors that may influence context, such as life history stage, environmental conditions and urban adaptability of a species. Here, we take a phylogenetically informed approach and use data from HormoneBase to test if baseline and stress-induced corticosterone are valid indicators of exposure to human footprint index, human population density, anthropogenic noise and artificial light at night in birds and reptiles. Our results show a negative relationship between anthropogenic noise and baseline corticosterone for birds characterized as urban avoiders. While our results potentially indicate that urban avoiders are more sensitive to noise than other species, overall our study suggests that the relationship between human-induced environmental change and corticosterone varies across species and contexts; we found no general relationship between human impacts and baseline and stress-induced corticosterone in birds, nor baseline corticosterone in reptiles. Therefore, it should not be assumed that high or low levels of exposure to human-induced environmental change are associated with high or low corticosterone levels, respectively, or that closely related species, or even individuals, will respond similarly. Moving forward, measuring alternative physiological traits alongside reproductive success, health and survival may provide context to better understand the potential negative effects of human-induced environmental change.

Actions of chronic physiological 3-hydroxyisobuterate treatment on mitochondrial metabolism and insulin signaling in myotubes.

Branched-chain amino acids (BCAAs) are essential in the diet and may provide benefit for those who partake in regular physical activity and resistance training, yet circulating BCAAs have been repeatedly shown to correlate with severity of insulin resistance in obese/diseased populations. Recently, the valine catabolite 3-hydroxyisobuterate (3HIB) was shown to promote insulin resistance in skeletal muscle by increasing lipid content in vivo. The purpose of this study was to investigate the mechanistic effects of 3HIB on skeletal muscle insulin signaling, metabolism, and related gene expression in vitro. Given these previous observations, we hypothesized that 3HIB would depress skeletal muscle metabolism and insulin sensitivity. C2C12 myotubes were treated with 3HIB for up to 48 hours using both physiological (25-100 µmol/L) and supraphysiological (5 mmol/L) concentrations. Metabolic gene expression was measured via quantitative real-time polymerase chain reaction, mitochondrial metabolism was measured via O2 consumption, and glycolytic metabolism was quantified using extracellular acidification rate. Western blot was used to assess insulin sensitivity following insulin stimulation (indicated by phospho-AKT expression). 3HIB did not alter expressional indicators of mitochondrial biogenesis, glycolysis, BCAA catabolism, or lipogenesis. Chronic physiological 3HIB treatment significantly increased peak oxygen consumption, whereas supraphysiological 3HIB treatment suppressed basal and peak mitochondrial and glycolytic metabolism. Both physiological and supraphysiological 3HIB reduced pAkt expression during insulin stimulation. These findings suggest that 3HIB may reduce muscle insulin sensitivity in cultured myotubes, supporting a potentially causal role of 3HIB in the development of insulin resistance in highly metabolic cell types.

Illuminating Endocrine Evolution: The Power and Potential of Large-Scale Comparative Analyses.

Hormones are central mediators of genotype-phenotype and organism-environment interactions. Despite these important functions, the role of selection in shaping hormonal mediators of phenotype remains poorly understood. Thanks to decades of work by endocrinologists, circulating hormone levels have been measured in a diversity of organisms. Variation in other endocrine traits and mediators (e.g., receptor expression and binding globulins), and the hormonal response to standardized challenges (e.g., restraint, pharmacological challenges) are also increasingly measured in both captive and free-living populations. Large-scale comparative analyses of the multitude of available endocrine data represent a particularly promising approach to addressing the function and evolution of these key phenotypic mediators, and their potential to serve as indicators of disturbance. Several recent phylogenetic comparative analyses and meta-analyses have begun to reveal the power and potential of these approaches to address key questions in integrative biology. Here we highlight two recent developments that are facilitating such analyses: increasingly powerful and flexible phylogenetic comparative methods, and the release of two endocrine trait databases-HormoneBase (currently 474 species) and the Wildlife Endocrinology Information Network (currently 25 species)-that contain compiled measures of endocrine traits across vertebrates. Increasingly comprehensive comparative analyses of endocrine data could provide insight into many interesting questions, including how rapidly changing environments are impacting phenotypes, why endocrine traits differ so remarkably within and across populations, and the evolution of plasticity. The endocrine system mediates interactions between genotypes and phenotypes, and between organisms and their environment. Environmentally induced hormonal responses regulate phenotypic flexibility across timescales by altering physiological state, gene expression, and epigenetic marks. A staggering diversity of phenotypic traits are mediated by hormones from early development through senescence. Through their actions on behavior, hormones also exert widespread influence over how organisms interact with their biotic and abiotic environments. Because hormones are responsive to the environment, there has long been interest in their use as biomarkers of exposure to challenges. More recently, increasing attention has been paid to the potential for within and among-population variation in endocrine regulation or responsiveness to serve as indicators of resistance or resilience to future challenges, or measures of evolutionary potential.

Leucine, Palmitate, or Leucine/Palmitate Cotreatment Enhances Myotube Lipid Content and Oxidative Preference.

Branched-chain amino acids (BCAA) such as leucine stimulate favorable metabolic processes involved in lean tissue preservation and skeletal muscle metabolism. However, higher levels of circulating BCAA correlate with severity of metabolic disease (including diabetes/insulin resistance), and may result from dysregulated BCAA catabolism. Past observations have demonstrated potential interaction between BCAA and dietary fat; however, much of this relationship remains underexplored. This study investigated the effect of leucine both with and without palmitate on oxidative and glycolytic metabolism, as well as indicators of BCAA catabolism using cultured skeletal muscle cells. Specifically, C2C12 myotubes were treated with or without varying concentrations of leucine both with and without palmitate for 24 h. Leucine treatment significantly elevated mRNA expression of metabolic regulators including peroxisome proliferator-activated receptor-gamma coactivator 1-alpha versus leucine with concurrent palmitate treatment. Interestingly, leucine-only, palmitate-only, and leucine with palmitate all significantly increased cellular lipid content, which translated into significantly increased oxidative capacity under substrate-limited conditions. However, upon the addition of excess substrate and carnitine, discrepancies in peak metabolic capacities between various treatments were no longer observed, suggesting leucine, palmitate, or the combination thereof causes a shift in metabolic preference from glycolytic to oxidative. These data also suggest leucine's effect on mitochondrial metabolism may result in part from increased lipid stores in addition to other previously documented pathways.

Detecting Bias in Large-Scale Comparative Analyses: Methods for Expanding the Scope of Hypothesis-Testing with HormoneBase.

To address large-scale questions in evolutionary biology, the compilation of data from a variety of sources is often required. This is a major challenge in the development of databases in organismal biology. Here, we describe the procedure we used to reconstruct the phylogeny of the 474 species represented in HormoneBase, including fish, amphibians, mammals, birds, and reptiles. We also provide the methodology used to compile vertebrate environmental, life history, and metabolic rate data for use in conjunction with the HormoneBase database to test hypotheses of the evolution of steroid hormone traits. We then report a series of analyses using these data to determine the extent to which field measures of circulating hormones and associated life history data exhibit taxonomic and geographic bias. By providing a detailed description of the approaches used to compile and evaluate these data and identifying potential biases in the collection of these data, we hope to make the HormoneBase database a more broadly useful resource for the scientific community to address a diversity of comparative questions.