Heritability of cardiovascular and personality traits in 6,148 Sardinians

In family studies, phenotypic similarities between relatives yield information on the overall contribution of genes to trait variation. Large samples are important for these family studies, especially when comparing heritability between subgroups such as young and old, or males and females. We recruited a cohort of 6,148 participants, aged 14–102 y, from four clustered towns in Sardinia. The cohort includes 34,469 relative pairs. To extract genetic information, we implemented software for variance components heritability analysis, designed to handle large pedigrees, analyze multiple traits simultaneously, and model heterogeneity. Here, we report heritability analyses for 98 quantitative traits, focusing on facets of personality and cardiovascular function. We also summarize results of bivariate analyses for all pairs of traits and of heterogeneity analyses for each trait. We found a significant genetic component for every trait. On average, genetic effects explained 40% of the variance for 38 blood tests, 51% for five anthropometric measures, 25% for 20 measures of cardiovascular function, and 19% for 35 personality traits. Four traits showed significant evidence for an X-linked component. Bivariate analyses suggested overlapping genetic determinants for many traits, including multiple personality facets and several traits related to the metabolic syndrome; but we found no evidence for shared genetic determinants that might underlie the reported association of some personality traits and cardiovascular risk factors. Models allowing for heterogeneity suggested that, in this cohort, the genetic variance was typically larger in females and in younger individuals, but interesting exceptions were observed. For example, narrow heritability of blood pressure was approximately 26% in individuals more than 42 y old, but only approximately 8% in younger individuals. Despite the heterogeneity in effect sizes, the same loci appear to contribute to variance in young and old, and in males and females. In summary, we find significant evidence for heritability of many medically important traits, including cardiovascular function and personality. Evidence for heterogeneity by age and sex suggests that models allowing for these differences will be important in mapping quantitative traits.     

Shared spatial effects on quantitative genetic parameters: accounting for spatial autocorrelation and home range overlap reduces estimates of heritability in wild red deer

Social structure, limited dispersal, and spatial heterogeneity in resources are ubiquitous in wild vertebrate populations. As a result, relatives share environments as well as genes, and environmental and genetic sources of similarity between individuals are potentially confounded. Quantitative genetic studies in the wild therefore typically account for easily captured shared environmental effects (e.g., parent, nest, or region). Fine-scale spatial effects are likely to be just as important in wild vertebrates, but have been largely ignored. We used data from wild red deer to build "animal models" to estimate additive genetic variance and heritability in four female traits (spring and rut home range size, offspring birth weight, and lifetime breeding success). We then, separately, incorporated spatial autocorrelation and a matrix of home range overlap into these models to estimate the effect of location or shared habitat on phenotypic variation. These terms explained a substantial amount of variation in all traits and their inclusion resulted in reductions in heritability estimates, up to an order of magnitude up for home range size. Our results highlight the potential of multiple covariance matrices to dissect environmental, social, and genetic contributions to phenotypic variation, and the importance of considering fine-scale spatial processes in quantitative genetic studies.     

Within- and between-zygosity variance in oral traits among US and Punjabi twins

Cross-cultural comparison of twin variances reveals widespread heterogeneity among zygosities for dental occlusal traits, implying various biases in calculation of genetic variance or heritability estimates. These estimates are fairly robust for dental size traits, however. Differences in pattern between Punjabi (Northwest Indian) and American twins highlight the environmental differences that affect heritability determinations.     

Assumptions and Properties of Limiting Pathway Models for Analysis of Epistasis in Complex Traits

For most complex traits, results from genome-wide association studies show that the proportion of the phenotypic variance attributable to the additive effects of individual SNPs, that is, the heritability explained by the SNPs, is substantially less than the estimate of heritability obtained by standard methods using correlations between relatives. This difference has been called the “missing heritability”. One explanation is that heritability estimates from family (including twin) studies are biased upwards. Zuk et al. revisited overestimation of narrow sense heritability from twin studies as a result of confounding with non-additive genetic variance. They propose a limiting pathway (LP) model that generates significant epistatic variation and its simple parametrization provides a convenient way to explore implications of epistasis. They conclude that over-estimation of narrow sense heritability from family data (‘phantom heritability’) may explain an important proportion of missing heritability. We show that for highly heritable quantitative traits large phantom heritability estimates from twin studies are possible only if a large contribution of common environment is assumed. The LP model is underpinned by strong assumptions that are unlikely to hold, including that all contributing pathways have the same mean and variance and are uncorrelated. Here, we relax the assumptions that underlie the LP model to be more biologically plausible. Together with theoretical, empirical, and pragmatic arguments we conclude that in outbred populations the contribution of additive genetic variance is likely to be much more important than the contribution of non-additive variance.     

Accounting for female space sharing in St. Kilda Soay sheep (Ovis aries) results in little change in heritability estimates

When estimating heritability in free‐living populations, it is common practice to account for common environment effects, because of their potential to generate phenotypic covariance among relatives thereby biasing heritability estimates. In quantitative genetic studies of natural populations, however, philopatry, which results in relatives being clustered in space, is rarely accounted for. The two studies that have been carried out so far suggest absolute declines in heritability estimates of up to 43% when accounting for space sharing by relatives. However, due to methodological limitations these estimates may not be representative. We used data from the St. Kilda Soay sheep population to estimate heritabilities with and without accounting for space sharing for five traits for which there is evidence for additive genetic variance (birthweight, birth date, lamb August weight, and female post‐mortem jaw and metacarpal length). We accounted for space sharing by related females by separately incorporating spatial autocorrelation, and a home range similarity matrix. Although these terms accounted for up to 18% of the variance in these traits, heritability estimates were only reduced by up to 7%. Our results suggest that the bias caused by not accounting for space sharing may be lower than previously thought. This suggests that philopatry does not inevitably lead to a large bias if space sharing by relatives is not accounted for. We hope our work stimulates researchers to model shared space when relatives in their study population share space, as doing so will enable us to better understand when bias may be of particular concern.     

Patterns of genotype-by-environment interaction in diameter at breast height at age 3 for eucalypt hybrid clones grown for reafforestation of lands affected by salinity

The commercial viability of plantations established for the recovery of saline lands may be supported by the deployment of improved genetic material matched to these particularly challenging environments. Patterns of genotype-by-environment interaction were investigated in a highly unbalanced data set of diameter at breast height at approximately 3 years for a total of 841 genotypes from ten Eucalyptus camaldulensis × Eucalyptus globulus and Eucalyptus camaldulensis × Eucalyptus grandis hybrid families assessed across 21 trials grown on a range of saline and non-saline low rainfall sites from southeast Queensland through central NSW, Victoria, Tasmania and southeast South Australia to southwest Western Australia using factor-analytic mixed-model methods. There was significant heterogeneity among trials in estimates of family variance, genotype-within-family variance, the ratio of family variance to total genetic variance and individual broad-sense heritability. Cluster analyses indicated that family effects were highly correlated across a main group of 19 trials and that most trials fell into two major groups for genotype-within-family effects, with an average correlation among trials within these groups of 0.55. There was, however, no obvious geographical or other explanation for the patterns, suggesting that genotypes should be deployed on the basis of broad-scale adaptation.     

Prediction of breeding values and selection responses with genetic heterogeneity of environmental variance

There is empirical evidence that genotypes differ not only in mean, but also in environmental variance of the traits they affect. Genetic heterogeneity of environmental variance may indicate genetic differences in environmental sensitivity. The aim of this study was to develop a general framework for prediction of breeding values and selection responses in mean and environmental variance with genetic heterogeneity of environmental variance. Both means and environmental variances were treated as heritable traits. Breeding values and selection responses were predicted with little bias using linear, quadratic, and cubic regression on individual phenotype or using linear regression on the mean and within-family variance of a group of relatives. A measure of heritability was proposed for environmental variance to standardize results in the literature and to facilitate comparisons to "conventional" traits. Genetic heterogeneity of environmental variance can be considered as a trait with a low heritability. Although a large amount of information is necessary to accurately estimate breeding values for environmental variance, response in environmental variance can be substantial, even with mass selection. The methods developed allow use of the well-known selection index framework to evaluate breeding strategies and effects of natural selection that simultaneously change the mean and the variance.     

(Co)Variance components and genetic parameter estimates for growth traits in Moghani sheep

Genetic parameters were estimated for birth weight (BW), weaning weight (WW), yearling weight (YW), average daily gain from birth to weaning (ADG1) and average daily gain from weaning to yearling (ADG2) in Moghani sheep. Maximum number of data was 4237 at birth, but only 1389 records at yearling were investigated. The data was collected from 1995 to 2007 at the Breeding Station of Moghani sheep in Jafarabad, Moghan, Iran. (Co)Variance components and genetic parameters were estimated with different models which including direct effects, with and without maternal additive genetic effects as well as maternal permanent environmental effects using restricted maximum likelihood (REML) method. The most appropriate model for each trait was determined based on likelihood ratio tests and Akaike's Information Criterion (AIC). Maternal effects were important only for pre-weaning traits. Direct heritability estimates for BW, ADG1, WW, ADG2 and YW were 0.07, 0.08, 0.09, 0.09 and 0.17, respectively. Fractions of variance due to maternal permanent environmental effects on phenotypic variance were 0.08 for ADG1. Maternal heritability estimates for BW and WW were 0.18 and 0.06, respectively. Multivariate analysis was performed using the most appropriate models obtained in univariate analysis. Direct genetic correlations among studied traits were positive and ranged from 0.37 for BW–ADG2 to 0.85 for ADG1–YW. Maternal genetic correlation estimate between BW and WW was 0.33. Phenotypic and environmental correlation estimates were generally lower than those of genetic correlation. Low direct heritability estimates imply that mass selection for these traits results in slow genetic gain.     

How does selfing affect the genetic variance of quantitative traits? An updated meta‐analysis on empirical results in angiosperm species

Most theoretical works predict that selfing should reduce the level of additive genetic variance available for quantitative traits within natural populations. Despite a growing number of quantitative genetic studies undertaken during the last two decades, this prediction is still not well supported empirically. To resolve this issue and confirm or reject theoretical predictions, we reviewed quantitative trait heritability estimates from natural plant populations with different rates of self‐fertilization and carried out a meta‐analysis. In accordance with models of polygenic traits under stabilizing selection, we found that the fraction of additive genetic variance is negatively correlated with the selfing rate. Although the mating system explains a moderate fraction of the variance, the mean reduction of narrow‐sense heritability values between strictly allogamous and predominantly selfing populations is strong, around 60%. Because some nonadditive components of genetic variance become selectable under inbreeding, we determine whether self‐fertilization affects the relative contribution of these components to genetic variance by comparing narrow‐sense heritability estimates from outcrossing populations with broad‐sense heritability estimated in autogamous populations. Results suggest that these nonadditive components of variance may restore some genetic variance in predominantly selfing populations; it remains, however, uncertain how these nonadditive components will contribute to adaptation.     

Effects of spatial autocorrelation,natal philopatry and phenotypic plasticity on the heritability of laying date

We investigated the effect of spatial autocorrelation on heritability (h²) estimates of laying date and clutch size in a population of great tits Parus major. We found that h² of laying date, but not clutch size, declined significantly with increasing distance between the nestbox of mothers and daughters. This decline was caused by a decreasing effect of spatial autocorrelation in laying date, rather than by the existence of genotype–environment interactions (GEI). After correcting for the effect of spatial autocorrelation, h² of laying date was low (0.16 ± 0.07), but significant, and surprisingly consistent with increasing distance between parental and offspring environments. The h² of clutch size was not much affected by spatial autocorrelation. Most previously published estimates of the heritability of laying date include various degrees of common environment effects, which can bias estimates both upwards and downwards. We suggest that using techniques that take spatial autocorrelation into account might be a fruitful approach to estimate h² of traits that show a high degree of plasticity.     

Quantitative genetic parameters for wild stream‐living brown trout: heritability and parental effects

Adaptability depends on the presence of additive genetic variance for important traits. Yet few estimates of additive genetic variance and heritability are available for wild populations, particularly so for fishes. Here, we estimate heritability of length‐at‐age for wild‐living brown trout (Salmo trutta), based on long‐term mark‐recapture data and pedigree reconstruction based on large‐scale genotyping at 15 microsatellite loci. We also tested for the presence of maternal and paternal effects using a Bayesian version of the Animal model. Heritability varied between 0.16 and 0.31, with reasonable narrow confidence bands, and the total phenotypic variance increased with age. When introducing dam as an additional random effect (accounting for c. 7% of total phenotypic variance), the level of additive genetic variance and heritability decreased (0.12–0.21). Parental size (both for sires and for dams) positively influenced length‐at‐age for juvenile trout – either through direct parental effects or through genotype‐environment correlations. Length‐at‐age is a complex trait reflecting the effects of a number of physiological, behavioural and ecological processes. Our data show that fitness‐related traits such as length‐at‐age can retain high levels of additive genetic variance even when total phenotypic variance is high.     

Genetic parameters for growth, wood density and pulp yield in Eucalyptus globulus

Genetic variation and co-variation among the key pulpwood selection traits for Eucalyptus globulus were estimated for a range of sites in Portugal, with the aim of improving genetic parameters used to predict breeding values and correlated response to selection. The trials comprised clonally replicated full-sib families (eight trials) and unrelated clones (17 trials), and exhibited varying levels of pedigree connectivity. The traits studied were stem diameter at breast height, Pilodyn penetration (an indirect measure of wood basic density) and near infrared reflectance predicted pulp yield. Univariate and multivariate linear mixed models were fitted within and across sites, and estimates of additive genetic, total genetic, environmental and phenotypic variances and covariances were obtained. All traits studied exhibited significant levels of additive genetic variation. The average estimated within-site narrow-sense heritability was 0.19 ± 0.03 for diameter and 0.29 ± 0.03 for Pilodyn penetration, and the pooled estimate for predicted pulp yield was 0.42 ± 0.14. When they could be tested, dominance and epistatic effects were generally not statistically significant, although broad-sense heritability estimates were slightly higher than narrow-sense heritability estimates. Averaged across trials, positive additive (0.64 ± 0.08), total genetic (0.58 ± 0.04), environmental (0.38 ± 0.03) and phenotypic (0.43 ± 0.02) correlation estimates were consistently obtained between diameter and Pilodyn penetration. This data argues for at least some form of pleiotropic relationship between these two traits and that selection for fast growth will adversely affect wood density in this population. Estimates of the across-site genetic correlations for diameter and Pilodyn penetration were high, indicating that the genotype by environment interaction is low across the range of sites tested. This result supports the use of single aggregated selection criteria for growth and wood density across planting environments in Portugal, as opposed to having to select for performance in different environments.     

Genetic and environmental variations in quantitative characters in fishes: a comparative analysis of monoclonal triploid and bisexual tetraploid spined loaches (<Emphasis Type="Italic">Cobitis</Emphasis>, Cobitidae)

The heritability estimates of 25 external morphometric characters and 23 craniometric indices are obtained by use of variances in monoclonal all-female triploids and bisexual tetraploids of spined loaches (genus Cobitis, Cobitidae) collected from the same breeding biotope. Most of studied traits demonstrate low heritability confirming previous conclusion on the similarity between external morphometric characters and craniological indices in relative effects of genetic and environmental components in their total phenotypic variation. Low heritability estimates in most of external morphological traits correspond to their low diagnostic value in Cobitis species. As a whole, in spite of certain deviations, studies on clonal forms do not refute the concept on higher heritability estimates in diagnostically significant traits in comparison with traits without diagnostic values in the same taxonomic group. Low heritability in most morphometric traits more probably is resulted from their low additive genetic variation caused by strong selection of evolutionary developed specific body shape in spined loaches, because strong selection should reduce the genetic variance in body proportions to minimal size. Sex differences observed in heritability estimates should be interpreted as a result of linkage of several additive genes controlling these traits to sex chromosomes. A few characters demonstrating high heritability estimates up to 0.492–0.580 are of great interest for taxonomic and phylogenetic studies in genus Cobitis and related taxa.     

On methodological aspects of ecological experiments (comments on M. V. Kozlov publication)

The meaning of conception of pseudoreplication in ecological experiments is discussed. The replications are found to be pseudo if factors causing random variation act on such replications as on one unit. For example, preudoreplications could appear if a single flipped coin would be split up. The absence of random spatial distribution of experimental and control fields could be considered as a mistake because the experimental results could interfere with spatial heterogeneity. However, there are no pseudoreplications in this case, because the variations of ecological systems are produced by factors that are different in different places and each organism responds to these factors individually. The pseudoreplication should be created by multiple determination of a response of an individual organism. Also recommendations for applications of randomized block design and analysis of covariance for field trials in plant communities are proposed. Randomized blocks unite the experimental and control fields occupying the identical place in the series of spatial heterogeneity. The influence of such heterogeneity on random variation of determined parameters could be excluded by this approach. The heterogeneity considered only at the scale of used blocks. As far as control and experimental fields belongs to a single set, the series of heterogeneities, that comprises the range of their parameters, is identical. The random sorting of the large amount of experimental and control samples consisting of the same number of replications will produces replications in the same place of the series of general heterogeneity of investigated set. The replications occupying the same places of the sorted series form "virtual block". The population of such blocks includes the majority of random variation and allows one to reveal even very weak experimental effects by variance analysis.     

Spatial autocorrelation of allozyme and quantitative markers within a natural population of Centaurea jacea (Asteraceae)

This paper compares the fine‐scale genetic structure of quantitative traits and allozyme markers within a natural population of Centaurea jacea s.l. To that end, a spatial autocorrelation approach is developed based on pairwise correlation coefficients between individuals and using sib families. Statistical properties of the proposed statistics are investigated with numerical simulations. Our results show that most quantitative traits have a significant spatial structure for their genetic component. On average, allozyme markers and the genetic component of quantitative traits have similar patterns of spatial autocorrelation that are consistent with a neutral model of isolation by distance. We also show evidence that environmental heterogeneity generates a spatial structure for the environmental component of quantitative traits. Results are discussed in terms of mechanisms generating spatial structure and are compared with those obtained on a large geographical scale.     

Quantitative conservation genetics of wild and managed bees

Quantitative genetic traits provide insights into the evolutionary potential of populations, as heritability estimates measure the population’s ability to respond to global changes. Although wild and managed bees are increasingly threatened by the degradation of natural habitats and climate change, risking plant biodiversity and agriculture production, no study has yet performed a systematic review of heritability estimates across the group. Here we help fill this knowledge gap, gathering all available heritability estimates for ants, bees, and wasps, evaluating which factors affect these estimates and assessing the reported genetic correlations between traits. Using a model selection approach to analyze a dataset of more than 800 heritability estimates, we found that heritability is influenced by trait type, with morphological traits exhibiting the highest heritability estimates, and defense and metabolism-related traits showing the lowest estimates. Study system, sociality degree, experimental design, estimation type (narrow or broad-sense heritability), and sample size were not found to affect heritability estimates. Results remained unaltered when correcting for phylogenetic inertia, and when analyzing social bees separately. Genetic correlations between honeybee traits revealed both positive coefficients, usually for traits in the same category, and negative coefficients, suggesting trade-offs among other traits. We discuss these findings and highlight the importance of maintaining genetic variance in fitness-related traits. Our study shows the importance of considering heritability estimates and genetic correlations when designing breeding and conservation programs. We hope this meta-analysis helps identify sustainable breeding approaches and conservation strategies that help safeguard the evolutionary potential of wild and managed bees.     

Broad and narrow heritabilities of quantitative traits in a founder population

Estimation of the components of variance for a quantitative trait allows one to evaluate both the degree to which genetics influences the trait and the trait's underlying genetic architecture. For particular traits, the estimates also may have implications for discriminating between potential models of selection and for choosing an appropriate model for linkage analysis. Using a recently developed method, we estimate the additive and dominance components of variance--or, equivalently, the narrow and broad sense heritabilities--of several traits in the Hutterites, a founder population with extensive genealogical records. As a result of inbreeding and because Hutterite individuals are typically related through multiple lines of descent, we expect that power to detect dominance variance will be increased relative to that in outbred studies. Furthermore, the communal lifestyle of the Hutterites allows us to evaluate the genetic influences in a relatively homogeneous environment. Four phenotypes had a significant dominance variance, resulting in a relatively high broad heritability. We estimated the narrow and broad heritabilities as being, respectively,.36 and.96 for LDL,.51 and 1.0 for serotonin levels, and.45 and.76 for fat free mass (FFM). There was no significant additive component for systolic blood pressure (SBP), resulting in a narrow heritability of 0 and a broad heritability of.45. There were several traits for which we found no significant dominance component, resulting in equal broad and narrow heritability estimates. These traits and their heritabilities are as follows: HDL,.63; triglycerides,.37; diastolic blood pressure,.21; immunoglobulin E,.63; lipoprotein(a),.77; and body-mass index,.54. The large difference between broad and narrow heritabilities for LDL, serotonin, FFM, and SBP are indicative of strong dominance effects in these phenotypes. To our knowledge, this is the first study to report an estimate of heritability for serotonin and to detect a dominance variance for LDL, FFM, and SBP.     

Testing marker-based estimates of heritability in the wild

Marker-based estimates of heritability are an attractive alternative to pedigree-based methods for estimating quantitative genetic parameters in field studies where it is difficult or impossible to determine relationships and pedigrees. Here I test the ability of the marker-based method to estimate heritability of a suite of traits in a wild population of bighorn sheep (Ovis canadensis) using marker data from 32 microsatellite loci. I compared marker-based estimates with estimates obtained using a pedigree and the animal model. Marker-based estimates of heritability were imprecise and downwardly biased. The high degree of uncertainty in marker-based estimates suggests that the method may be sufficient to detect the presence of genetic variance for highly heritable traits, but not sufficiently reliable to estimate genetic parameters.     

Quantitative Genetic Analysis of Temperature Regulation in MUS MUSCULUS. I. Partitioning of Variance

Heritabilities (from parent-offspring regression) and intraclass correlations of full sibs for a variety of traits were estimated from 225 litters of a heterogeneous stock (HS/Ibg) of laboratory mice. Initial variance partitioning suggested different adaptive functions for physiological, morphological and behavioral adjustments with respect to their thermoregulatory significance. Metabolic heat-production mechanisms appear to have reached their genetic limits, with little additive genetic variance remaining. This study provided no genetic evidence that body size has a close directional association with fitness in cold environments, since heritability estimates for weight gain and adult weight were similar and high, whether or not the animals were exposed to cold. Behavioral heat conservation mechanisms also displayed considerable amounts of genetic variability. However, due to strong evidence from numerous other studies that behavior serves an important adaptive role for temperature regulation in small mammals, we suggest that fluctuating selection pressures may have acted to maintain heritable variation in these traits.     

Genetic parameters for direct and maternal effects on body weights of Draa goats

Genetic parameters and (co)variance components were estimated for weights at birth and at 30, 90 and 180 days of age for Draa goat maintained at Ouarzazate station over a period of 18 years (1988–2005). Records of 1498 kids, the progeny of 46 sires and 404 dams were used in the study. Analyses were carried out by restricted maximum likelihood. Six different animal models including or ignoring maternal genetic or permanent environmental effects were fitted for all traits. The Model 2 with only permanent environmental maternal effects seemed most suitable. Estimates of direct heritability from this model were 0.16 for birth weight and 0.07, 0.11 and 0.11 for weights at 30, 90 and 180 days, respectively. Maternal heritability estimates varied from 0.00 to 0.24 for all traits according to the model used (Models 4–6). Bivariate analysis by Model 2 was also used to estimate genetic correlations between traits. The estimates of genetic and phenotypic correlations among weights were positive and intermediate to high in value. Despite the low estimated heritabilities of body weight traits of Draa goat, there is a small genetic variability that may be exploited to improve growth performance.