Genetic variation, simplicity, and evolutionary constraints for function-valued traits.

Understanding the patterns of genetic variation and constraint for continuous reaction norms, growth trajectories, and other function-valued traits is challenging. We describe and illustrate a recent analytical method, simple basis analysis (SBA), that uses the genetic variance-covariance (G) matrix to identify "simple" directions of genetic variation and genetic constraints that have straightforward biological interpretations. We discuss the parallels between the eigenvectors (principal components) identified by principal components analysis (PCA) and the simple basis (SB) vectors identified by SBA. We apply these methods to estimated G matrices obtained from 10 studies of thermal performance curves and growth curves. Our results suggest that variation in overall size across all ages represented most of the genetic variance in growth curves. In contrast, variation in overall performance across all temperatures represented less than one-third of the genetic variance in thermal performance curves in all cases, and genetic trade-offs between performance at higher versus lower temperatures were often important. The analyses also identify potential genetic constraints on patterns of early and later growth in growth curves. We suggest that SBA can be a useful complement or alternative to PCA for identifying biologically interpretable directions of genetic variation and constraint in function-valued traits.

Evolution of the additive genetic variance-covariance matrix under continuous directional selection on a complex behavioural phenotype.

Given the pace at which human-induced environmental changes occur, a pressing challenge is to determine the speed with which selection can drive evolutionary change. A key determinant of adaptive response to multivariate phenotypic selection is the additive genetic variance-covariance matrix ( G: ). Yet knowledge of G: in a population experiencing new or altered selection is not sufficient to predict selection response because G: itself evolves in ways that are poorly understood. We experimentally evaluated changes in G: when closely related behavioural traits experience continuous directional selection. We applied the genetic covariance tensor approach to a large dataset (n = 17 328 individuals) from a replicated, 31-generation artificial selection experiment that bred mice for voluntary wheel running on days 5 and 6 of a 6-day test. Selection on this subset of G: induced proportional changes across the matrix for all 6 days of running behaviour within the first four generations. The changes in G: induced by selection resulted in a fourfold slower-than-predicted rate of response to selection. Thus, selection exacerbated constraints within G: and limited future adaptive response, a phenomenon that could have profound consequences for populations facing rapid environmental change.

Aggressive behavior, brain size and domestication in clonal rainbow trout lines.

Domestication causes behavior and brain size changes in many species. We addressed three questions using clonal rainbow trout lines: What are the mirror-elicited aggressive tendencies in lines with varying degrees of domestication? How does brain size relate to genotype and domestication level? Finally, is there a relationship between aggressive behavior and brain size? Clonal lines, although sampling a limited subset of the species variation, provide us with a reproducible experimental system with which we can develop hypotheses for further research. We performed principal component analyses on 12 continuous behavior and brain/body size variables and one discrete behavioral variable ("yawn") and detected several aggression syndromes. Two behaviors, "freeze" and "escape", associated with high domestication; "display" and "yawn" behavior associated with wild lines and "swim against the mirror" behavior associated with semi-wild and domestic lines. Two brain size traits, total brain and olfactory volume, were significantly related to domestication level when taking total body size into account, with domesticated lines having larger total brain volume and olfactory regions. The aggression syndromes identified indicate that future QTL mapping studies on domestication-related traits would likely be fruitful.

Warped functional analysis of variance.

This article presents an Analysis of Variance model for functional data that explicitly incorporates phase variability through a time-warping component, allowing for a unified approach to estimation and inference in presence of amplitude and time variability. The focus is on single-random-factor models but the approach can be easily generalized to more complex ANOVA models. The behavior of the estimators is studied by simulation, and an application to the analysis of growth curves of flour beetles is presented. Although the model assumes a smooth latent process behind the observed trajectories, smootheness of the observed data is not required; the method can be applied to irregular time grids, which are common in longitudinal studies.

Sclerotinia sclerotiorum populations infecting canola from China and the United States are genetically and phenotypically distinct.

Genetic and phenotypic diversity and population differentiation of Sclerotinia sclerotiorum isolates infecting canola from China and the United States were investigated. Genetic diversity was assessed with eight microsatellite markers and mycelial compatibility groups (MCGs). Phenotypic diversity was assessed with sensitivity to three fungicides, production of oxalate and sclerotia, growth rate, and virulence on two canola cultivars. No shared MCGs or multilocus haplotypes were detected between the two populations, and populations differed significantly (P < 0.001). Recombination was detected in both populations but was greater in the Chinese population. A polymerase chain reaction detection assay showed that ~60% of the isolates were inversion-plus at the mating type locus. The two populations differed significantly (P < 0.05) for all of the phenotypic traits except for sensitivity to fungicide fluazinam and virulence. Isolates in the Chinese population were unique in several aspects. Despite the phenotypic differentiation, heritabilities of the phenotypic traits were similar for both populations. Significant correlations were found among five phenotypic traits. Cross resistance to benomyl and iprodione was detected. Virulence was not significantly correlated with any other phenotypic trait and had the least heritability. However, both populations were equally virulent on either a susceptible or a moderately resistant canola cultivars.

Telomere Length is a Susceptibility Marker for Tasmanian Devil Facial Tumor Disease.

Telomeres protect chromosomes from degradation during cellular replication. In humans, it is well-documented that excessive telomere degradation is one mechanism by which cells can become cancerous. Increasing evidence from wildlife studies suggests that telomere length is positively correlated with survival and health and negatively correlated with disease infection intensity. The recently emerged devil facial tumor disease (DFTD) has led to dramatic and rapid population declines of the Tasmanian devil throughout its geographic range. Here, we tested the hypothesis that susceptibility to DFTD is negatively correlated with telomere length in devils across three populations with different infection histories. Our findings suggest telomere length is correlated with DFTD resistance in three ways. First, devils from a population with the slowest recorded increase in DFTD prevalence (West Pencil Pine) have significantly longer telomeres than those from two populations with rapid and exponential increases in prevalence (Freycinet and Narawantapu). Second, using extensive mark-recapture data obtained from a long-term demographic study, we found that individuals with relatively long telomeres tend to be infected at a significantly later age than those with shorter telomeres. Third, a hazard model showed devils with longer telomeres tended to become infected at a lower rate than those with shorter telomeres. This research provides a rare study of telomere length variation and its association with disease in a wildlife population. Our results suggest that telomere length may be a reliable marker of susceptibility to DFTD and assist with future management of this endangered species.

An integrative modeling approach to the age-performance relationship in mammals at the cellular scale.

Physical and cognitive performances change across lifespan. Studying cohorts of individuals in specific age ranges and athletic abilities remains essential in assessing the underlying physiological mechanisms that result in such a drop in performance. This decline is now viewed as a unique phenotypic biomarker and a hallmark of the aging process. The rates of decline are well documented for sets of traits such as running or swimming but only a limited number of studies have examined the developmental and senescent phases together. Moreover, the few attempts to do so are merely descriptive and do not include any meaningful biological features. Here we propose an averaged and deterministic model, based on cell population dynamics, replicative senescence and functionality loss. It describes the age-related change of performance in 17 time-series phenotypic traits, including human physical and cognitive skills, mouse lemur strength, greyhound and thoroughbred speed, and mouse activity. We demonstrate that the estimated age of peak performance occurs in the early part of life (20.5% ± 6.6% of the estimated lifespan) thus emphasizing the asymmetrical nature of the relationship. This model is an initial attempt to relate performance dynamics to cellular dynamics and will lead to more sophisticated models in the future.

The age-performance relationship in the general population and strategies to delay age related decline in performance.

The age-performance relationship describes changes in the organism's structural and functional capabilities over the course of the lifespan. The typical, empirical pattern is an asymmetrical inverted-U shape association with peak capacity occurring early in life. This process is well described in the literature, with an increasing interest in features that characterize this pattern, such as the rate of growth, age of peak performance, and rate of decline with aging. This is usually examined in cohorts of individuals followed over time with repeat assessments of physical or cognitive abilities. This framework ought to be integrated into public health programs, embedding the beneficial (such as physical or cognitive training) or adverse effects (such as chronic diseases or injuries) that respectively sustain or limit capabilities. The maintenance of physical or cognitive performances at older ages would result in both optimal health and promote resistance to disabling conditions and chronic diseases, such as obesity and type 2 diabetes. The causes of accelerated degeneration of health optima are mainly: sedentary and unhealthy lifestyles -including poor nutrition-, exposure to environmental pollutants, and heterogeneity in aging. Better knowledge of optima, compatible with or required for good health, should also allow for establishing ideal conditions for longevity.

The relative importance of genetics and phenotypic plasticity in dictating bone morphology and mechanics in aged mice: evidence from an artificial selection experiment.

Both genetic and environmental factors are known to influence the structure of bone, contributing to its mechanical behavior during, and adaptive response to, loading. We introduce a novel approach to simultaneously address the genetically mediated, exercise-related effects on bone morphometrics and strength, using mice that had been selectively bred for high levels of voluntary wheel running (16 generations). Female mice from high running and control lines were either allowed (n=12, 12, respectively) or denied (n=11, 12, respectively) access to wheels for 20 months. Femoral shaft, neck, and head were measured with calipers and via micro-computed tomography. Fracture characteristics of the femoral head were assessed in cantilever bending. After adjusting for variation in body mass by two-way analysis of covariance, distal width of the femur increased as a result of selective breeding, and mediolateral femoral diameter was reduced by wheel access. Cross-sectional area of the femoral mid-shaft showed a significant linetype x activity effect, increasing with wheel access in high-running lines but decreasing in control lines. Body mass was significantly positively correlated with many of the morphometric traits studied. Fracture load of the femoral neck was strongly positively predicted by morphometric traits of the femoral neck (r2>0.30), but no significant effects of selective breeding or wheel access were found. The significant correlations of body mass with femoral morphometric traits underscore the importance of controlling for body size when analyzing the response of bone size and shape to experimental treatments. After controlling for body mass, measures of the femoral neck remain significant predictors of femoral neck strength.

Age-Related Changes in Locomotor Performance Reveal a Similar Pattern for Caenorhabditis elegans, Mus domesticus, Canis familiaris, Equus caballus, and Homo sapiens.

Locomotion is one of the major physiological functions for most animals. Previous studies have described aging mechanisms linked to locomotor performance among different species. However, the precise dynamics of these age-related changes, and their interactions with development and senescence, are largely unknown. Here, we use the same conceptual framework to describe locomotor performances in Caenorhabditis elegans, Mus domesticus, Canis familiaris, Equus caballus, and Homo sapiens. We show that locomotion is a consistent biomarker of age-related changes, with an asymmetrical pattern throughout life, regardless of the type of effort or its duration. However, there is variation (i) among species for the same mode of locomotion, (ii) within species for different modes of locomotion, and (iii) among individuals of the same species for the same mode of locomotion. Age-related patterns are modulated by genetic (such as selective breeding) as well as environmental conditions (such as temperature). However, in all cases, the intersection of the rising developmental phase and the declining senescent phase reveals neither a sharp transition nor a plateau, but a smooth transition, emphasizing a crucial moment: the age at peak performance. This transition may define a specific target for future investigations on the dynamics of such biological interactions.

Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops.

Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations-known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available.

Antioxidant gene expression in active and sedentary house mice (Mus domesticus) selected for high voluntary wheel-running behavior.

We present liver mRNA levels of the two antioxidant enzymes catalase (CAT) and Mn-superoxide dismutase (SOD2) in four treatment groups of house mice assayed by RNase protection at 20 months of age. These groups were mice from four replicate selection and four replicate control lines from the sixteenth generation of selective breeding for high voluntary wheel running, housed with or without running wheels from age 3 weeks through 20 months. Exercising control females had induced CAT expression; SOD2 exhibited a similar pattern in females from two of the four control lines. Exercising male mice had induced CAT expression, but not SOD2 expression, irrespective of genetic background. We discuss these results with respect to both evolutionary (genetic) and training (exercise-induced) adaptations and explore predictions of these results in relation to the oxidative-damage theory of senescence.

Different effects of intensity and duration of locomotor activity on circadian period.

An outstanding unresolved issue in chronobiology is how the level of locomotor activity influences length of the free-running, endogenous circadian period (tau). To address this issue, the authors studied a novel model, 4 replicate lines of laboratory house mice (Mus domesticus) that had been selectively bred for high wheel-running activity (S) and their 4 unselected control (C) lines. Previous work indicates that S mice run approximately twice as many revolutions/day and exhibit an altered dopaminergic function as compared with C mice. The authors report that S mice have a tau shorter by about 0.5 h as compared with C mice. The difference in tau was significant both under constant light (control lines: tau = 25.5 h; selected: tau = 24.9 h) and under constant dark (control lines: 23.7 h; selected: 23.4 h). Moreover, the difference remained statistically significant even when the effects of running speed and time spent running were controlled in ANCOVA. Thus, something more fundamental than just intensity or duration of wheel-running activity per se must underlie the difference in tau between the S and C lines. However, despite significant difference in total wheel-running activity between females and males, tau did not differ between the sexes. Similarly, among individuals within lines, tau was not correlated with wheel-running activity measured as total revolutions per day. Instead, tau tended to decrease with average running speed but increase with time spent running. Finally, within individuals, an increase in time spent running resulted in decreased tau in the next few days, but changes in running speed had no statistically significant effect. The distinctions between effects of duration versus intensity of an activity, as well as between the among- versus within-individual correlations, are critical to understanding the relation between locomotor activity and pace of the circadian clock.

Ontogenies in mice selected for high voluntary wheel-running activity. I. Mean ontogenies.

The evolutionary importance of postnatal ontogenies has long been recognized, but most studies of ontogenetic trajectories have focused exclusively on morphological traits. For animals, this represents a major omission because behavioral traits and their ontogenies often have relatively direct relationships to fitness. Here four replicate lines of house mice artificially selected for high early-age wheel running and their four replicate control lines were used to evaluate the effects of early-age directional selection, genetic drift, and activity environment (presence or absence of a running wheel) on variation in the ontogenies of three traits known to be genetically correlated: voluntary wheel running, body mass, and food consumption. Early-age selection significantly changed both the shape and position of the wheel-running and food-consumption ontogenies while influencing the position, but not the shape, of the body mass ontogeny. Genetic drift (as indicated by variation among replicate lines) produced significant changes in both the position and shape of all three ontogenies; however, its effect differed between the selection and control groups. For wheel running and food consumption, genetic drift only influenced the control ontogenies, whereas for body mass, genetic drift had a significant effect in both selection groups. Both body-mass and food-consumption ontogenies were significantly altered by activity environment, with the environment causing significant changes in the shape and position of both ontogenies. Overall the results demonstrate strong effects of early-age selection, genetic drift, and environmental variation on the evolution and expression of behavioral and morphological ontogenies, with selection changing only the position of the morphological ontogeny but both the position and shape of the behavioral ontogenies.

Evolution of a small-muscle polymorphism in lines of house mice selected for high activity levels.

To study the correlated evolution of locomotor behavior and exercise physiology, we conducted an artificial selection experiment. From the outbred Hsd:ICR strain of Mus domesticus, we began eight separate lines, each consisting of 10 breeding pairs. In four of the lines, we used within-family selection to increase voluntary wheel running. The remaining four lines were random-bred (within lines) to serve as controls. Various traits have been monitored to test for correlated responses. Here, we report on organ masses, with emphasis on the triceps surae muscle complex, an important extensor of the ankle. Mice from the selected lines exhibit reduced total body mass, increased relative (mass-corrected) kidney mass, and reduced relative triceps surae mass. In addition, a discrete muscle-mass polymorphism was observed: some individuals had triceps surae that were almost 50% lighter than normal for their body mass. This small-muscle phenotype was observed in only three of the eight lines: in one control line, it has fluctuated in frequency between zero and 10%, whereas in two of the selected lines it has increased in frequency to approximately 50% by generation 22. Data from a set of parents and offspring (generations 23 and 24) are consistent with inheritance as a single autosomal recessive allele. Evidence for the adaptive significance of the small-muscle allele was obtained by fitting multiple-generation data to hierarchical models that include effects of genetic drift and/or selection. The small-muscle allele is estimated to have been present at low frequency (approximately 7%) in the base population, and analysis indicates that strong selection favors the allele in the selected but not control lines. We hypothesize that the small muscles possess functional characteristics and/or that the underlying allele causes pleiotropic effects (e.g., reduced total body mass; increased relative heart, liver, and kidney mass) that facilitate high levels of wheel running. Nevertheless, at generation 22, wheel running of affected individuals did not differ significantly from those with normal-sized muscles, and the magnitude of response to selection has been similar in all four selected lines, indicating that multiple genetic "solutions" are possible in response to selection for high activity levels.

Dominance, plasma testosterone levels, and testis size in house mice artificially selected for high activity levels.

Male house mice (Mus domesticus) from four replicate lines selectively bred for high voluntary wheel-running behavior were compared with four random-bred control lines with respect to dominance, testis size, and plasma testosterone level. Behavior was measured with a tube apparatus in which focal mice encountered a standard opponent from an inbred strain, and positions of mice were scored over a 10-min period; the test was replicated the following day. Blood samples were taken from undisturbed mice 1 week prior to testing (baseline condition) and immediately after the first tube test; plasma testosterone was measured by enzyme immunoassay with chromatography. As compared with control lines, mice from selected lines tended to be smaller in body mass, to have larger testes, and were significantly less likely to advance towards their opponent during the second tube-test encounter. However, no significant differences in either baseline or post-encounter testosterone levels were detected. Significant differences in body mass, relative testis size, position during the first tube-test encounter, and baseline testosterone were found among the replicate lines within linetype, which indicates founder effects, random genetic drift, unique mutations, and/or multiple responses to selection. At the level of individual variation (residuals from nested analysis of covariance models), an inverse relationship between baseline testosterone and advancing in the tube test was observed, and the relationship was stronger during the second test day. This unexpected result may reflect an alternate coping strategy.

Food wasting by house mice: variation among individuals, families, and genetic lines.

Under ad libitum conditions, laboratory house mice (Mus domesticus) fragment considerable amounts of pelleted food and leave it scattered in their cages. The proportion of food thus wasted (in relation to food eaten) varies remarkably among individuals, from 2% to 40%, but is highly consistent in consecutive trials, even when the mice were moved from 22 to -10 degrees C and food consumption doubled. Food wasting did not differ either between the sexes or between genetic lines that had been selected (10 generations) for high voluntary wheel-running behavior (n=4) and their unselected control lines (n=4). However, it varied significantly among replicate lines within the selection groups and among families within the lines (coefficient of intraclass correlation for full sibs, rhof=0.41 in room temperature trials and rhof=0.34 in cold trials). Moreover, the percent of food wasted was negatively correlated with food consumption in the cold trials (males: r=-.36, females: r=-.20) and with total litter mass at weaning (the litters into which they were born; r=-.24), two traits that may affect Darwinian fitness. We conclude that food wastage should not be ignored without justification in calculations of food consumption. In addition, "table manners" can convey reliable information about family origin of an individual and its quality, and therefore could potentially play a role in establishment of social status.

Limits to behavioral evolution: the quantitative genetics of a complex trait under directional selection.

Replicated selection experiments provide a powerful way to study how "multiple adaptive solutions" may lead to differences in the quantitative-genetic architecture of selected traits and whether this may translate into differences in the timing at which evolutionary limits are reached. We analyze data from 31 generations (n=17,988) of selection on voluntary wheel running in house mice. The rate of initial response, timing of selection limit, and height of the plateau varied significantly between sexes and among the four selected lines. Analyses of litter size and realized selection differentials seem to rule out counterposing natural selection as a cause of the selection limits. Animal-model analyses showed that although the additive genetic variance was significantly lower in selected than control lines, both before and after the limits, the decrease was not sufficient to explain the limits. Moreover, directional selection promoted a negative covariance between additive and maternal genetic variance over the first 10 generations. These results stress the importance of replication in selection studies of higher-level traits and highlight the fact that long-term predictions of response to selection are not necessarily expected to be linear because of the variable effects of selection on additive genetic variance and maternal effects.

Oxidative stress among SOD-1 genotypes in rainbow trout (Oncorhynchus mykiss).

Natural variation in the antioxidant-enzyme SOD-1 (superoxide dismutase) is known to alter the impacts of oxidative damage at both the cellular and organismal levels. Using three homozygous clonal lines of rainbow trout [Hot Creek (n=30), Arlee (n=21), and Swanson (n=10)], which differ for single nucleotide polymorphisms (SNPs) and amino acid substitutions at the SOD-1 locus, we investigated the functional effects of this variation on SOD-1 activity during ozone stress and subsequent levels of oxidative damage to DNA and cell membranes. Fish from each line were subjected to either control conditions or 24h of ozone stress, after which tissues were analyzed for antioxidant status and oxidative damage. Liver SOD-1 activity was lower in ozonated vs. control fish in the Hot Creek line, and among ozonated fish, Hot Creek was lower than Arlee. Total erythrocyte SOD activity was not significantly impacted by ozonation; however significant differences in total erythrocyte SOD activity were measured among clonal lines, driven primarily by lower activity in the Hot Creek line. Ozone had a significant treatment effect in all oxidative damage parameters assessed: it increased DNA lesions in erythrocytes and levels of lipid peroxidation in gill tissue and plasma. Among lines, Swanson showed higher lipid peroxidation levels in gill tissue after ozonation than Arlee or Hot Creek. Conversely, Swanson control and treatment fish had significantly lower plasma lipid peroxidation levels than did fish from the other lines. Overall, the among-line differences in SOD and SOD-1 activity and oxidative damage provide evidence that SOD-1 genotypes differ functionally under both oxidative stress and control conditions; however, other genetic differences among lines should be investigated in order to further explain the phenotypic differences in SOD enzyme activity and oxidative damage described here.

Endocrine rhythms in the brown bear (Ursus arctos): Evidence supporting selection for decreased pineal gland size.

Many temperate zone animals adapt to seasonal changes by altering their physiology. This is mediated in large part by endocrine signals that encode day length and regulate energy balance and metabolism. The objectives of this study were to determine if the daily patterns of two important hormones, melatonin and cortisol, varied with day length in captive brown bears (Ursus arctos) under anesthetized and nonanesthetized conditions during the active (March-October) and hibernation periods. Melatonin concentrations varied with time of day and season in nonanesthetized female bears despite exceedingly low nocturnal concentrations (1-4 pg/mL) in the active season. In contrast, melatonin concentrations during hibernation were 7.5-fold greater than those during the summer in anesthetized male bears. Functional assessment of the pineal gland revealed a slight but significant reduction in melatonin following nocturnal light application during hibernation, but no response to beta-adrenergic stimulation was detected in either season. Examination of pineal size in two bear species bears combined with a phylogenetically corrected analysis of pineal glands in 47 other species revealed a strong relationship to brain size. However, pineal gland size of both bear species deviated significantly from the expected pattern. Robust daily plasma cortisol rhythms were observed during the active season but not during hibernation. Cortisol was potently suppressed following injection with a synthetic glucocorticoid. The results suggest that melatonin and cortisol both retain their ability to reflect seasonal changes in day length in brown bears. The exceptionally small pineal gland in bears may be the result of direct or indirect selection.