Maximum likelihood estimation of human craniometric heritabilities

This study presents univariate narrow-sense heritability estimates for 33 common craniometric dimensions, calculated using the maximum likelihood variance components method on a skeletal sample of 298 pedigreed individuals from Hallstatt, Austria. Quantitative genetic studies that use skeletal cranial measurements as a basis for inferring microevolutionary processes in human populations usually employ heritability estimates to represent the genetic variance of the population. The heritabilities used are often problematic: most come from studies of living humans, and/or they were calculated using statistical techniques or assumptions violated by human groups. Most bilateral breadth measures in the current study show low heritability estimates, while cranial length and height measures have heritability values ranging between 0.102-0.729. There appear to be differences between the heritabilities calculated from crania and those from anthropometric studies of living humans, suggesting that the use of the latter in quantitative genetic models of skeletal data may be inappropriate. The univariate skeletal heritability estimates seem to group into distinct regions of the cranium, based on their relative values. The most salient group of measurements is for the midfacial/orbital region, with a number of measures showing heritabilities less than 0.30. Several possible reasons behind this pattern are examined. Given the fact that heritabilities calculated on one population should not be applied to others, suggestions are made for the use of the data presented.     

Heritability of phenotypic udder traits to improve resilience to mastitis in Texel ewes

There are no estimates of the heritability of phenotypic udder traits in suckler sheep, which produce meat lambs, and whether these are associated with resilience to mastitis. Mastitis is a common disease which damages the mammary gland and reduces productivity. The aims of this study were to investigate the feasibility of collecting udder phenotypes, their heritability and their association with mastitis in suckler ewes. Udder and teat conformation, teat lesions, intramammary masses (IMM) and litter size were recorded from 10 Texel flocks in Great Britain between 2012 and 2014; 968 records were collected. Pedigree data were obtained from an online pedigree recording system. Univariate quantitative genetic parameters were estimated using animal and sire models. Linear mixed models were used to analyse continuous traits and generalised linear mixed models were used to analyse binary traits. Continuous traits had higher heritabilities than binary with teat placement and teat length heritability (h²) highest at 0.35 (SD 0.04) and 0.42 (SD 0.04), respectively. Udder width, drop and separation heritabilities were lower and varied with udder volume. The heritabilities of IMM and teat lesions (sire model) were 0.18 (SD 0.12) and 0.17 (SD 0.11), respectively. All heritabilities were sufficiently high to be in a selection programme to increase resilience to mastitis in the population of Texel sheep. Further studies are required to investigate genetic relationships between traits and to determine whether udder traits predict IMM, and the potential benefits from including traits in a selection programme to increase resilience to chronic mastitis.     

Power studies in the estimation of genetic parameters and the localization of quantitative trait loci for backcross and doubled haploid populations

A statistical model for doubled haploids and backcrosses based on the interval-mapping methodology has been used to carry out power studies to investigate the effects of different experimental designs, heritabilities of the quantitative trait, and types of gene action, using two test statistics, the F of Fisher-Snedecor and the LOD score. The doubled haploid experimental design is more powerful than backcrosses while keeping actual type I errors similar to nominal ones. For the doubled haploid design, individual QTLs, showing heritabilities as low as 5% were detected in about 90% of the cases using only 250 individuals. The power to detect a given QTL is related to its contribution to the heritability of the trait. For a given nominal type I error, tests using F values are more powerful than with LOD scores. It seems that more conservative levels should be used for the LOD score in order to increase the power and obtain type I errors similar to nominal ones.     

NATURAL HERITABILITIES: CAN THEY BE RELIABLY ESTIMATED IN THE LABORATORY?

The validity of the assumption, that laboratory estimates of heritabilities will tend to overestimate natural heritabilities, due to a reduction in environmental variability and thus the phenotypic variance of traits, is examined. One hundred sixty-five field estimates of narrow sense heritabilities derived from the literature are compared with 189 estimates from laboratory studies on wild, outbred animal populations derived from the data set of Mousseau and Roff. The results indicate that 84% of field heritabilities are significantly different from zero and that for morphological, behavioral, and life-history traits there are no significant differences between laboratory and field estimates of heritability. Unexpectedly, mean heritabilities for morphological and life-history traits are actually higher in the field than in the lab. Twenty-two cases were found for which both laboratory and natural heritabilities had been estimated on the same traits. For this subset of the data, laboratory heritabilities tended to be higher than field estimates, but the difference was not significant. Also, the correlation between lab and field estimates was high (r = 0.6, P < 0.001), and the regression slope did not differ significantly from one. The major implications of this study are that laboratory estimates of heritability should generally provide reasonable estimations of both the magnitude and the significance of heritabilities in nature.     

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.     

Social cues affect quantitative genetic variation and covariation in animal personality traits

The social environment is expected to have substantial effects on behavior, and as a consequence, its heritability and evolvability. We investigated these effects by exposing Australian field crickets (Teleogryllus oceanicus) to either silence or recordings of male acoustic sexual signals. We used a combined pedigree and full‐sib/half‐sib breeding design to estimate the repeatability, heritability, and evolvability of behaviors related to boldness, exploration, and activity. All behaviors measured were significantly repeatable in both social environments. Additionally, most behaviors showed significant heritabilities in the two environments. We found no difference in repeatabilities between the silent and the acoustic environment but did find significant differences in the heritabilities and evolvabilities between these environments. There was a high degree of similarity between the phenotypic covariance matrices across the two environments, while the genotypic covariance matrices were highly dissimilar. Reflecting this, we found significant genotype‐by‐environment interactions for most of the behaviors. Lastly, we found that the repeatable aspect of behavior (“personality”) was significantly heritable for most behaviors, but that these heritabilities were higher in the acoustic than in the silent environment. We conclude that the social environment can have a significant impact on the heritability and evolvability of behavior, and argue that evolutionary inferences from phenotypic studies should be made with caution.     

Group differences in the heritability of items and test scores

It is important to understand potential sources of group differences in the heritability of intelligence test scores. On the basis of a basic item response model we argue that heritabilities which are based on dichotomous item scores normally do not generalize from one sample to the next. If groups differ in mean ability, the functioning of items at different ability levels may result in group differences in the heritability of items, even when these items function equivalently across groups and the heritability of the underlying ability is equal across groups. We illustrate this graphically, by computer simulation, and by focusing on several problems associated with a recent study by Rushton et al. who argued that the heritability estimates of items of Raven''s Progressive Matrices test in North-American twin samples generalized to other population groups, and hence that the population group differences on this test of general mental ability (or intelligence) had a substantial genetic component. Our results show that item heritabilities are strongly dependent on the group on which the heritabilities were based. Rushton et al.''s results were artefactual and do not speak to the nature of population group differences in intelligence test performance.     

SNP-based heritability estimation using a Bayesian approach

Heritability is a central element in quantitative genetics. New molecular markers to assess genetic variance and heritability are continually under development. The availability of molecular single nucleotide polymorphism (SNP) markers can be applied for estimation of variance components and heritability on population, where relationship information is unknown. In this study, we evaluated the capabilities of two Bayesian genomic models to estimate heritability in simulated populations. The populations comprised different family structures of either no or a limited number of relatives, a single quantitative trait, and with one of two densities of SNP markers. All individuals were both genotyped and phenotyped. Results illustrated that the two models were capable of estimating heritability, when true heritability was 0.15 or higher and populations had a sample size of 400 or higher. For heritabilities of 0.05, all models had difficulties in estimating the true heritability. The two Bayesian models were compared with a restricted maximum likelihood (REML) approach using a genomic relationship matrix. The comparison showed that the Bayesian approaches performed equally well as the REML approach. Differences in family structure were in general not found to influence the estimation of the heritability. For the sample sizes used in this study, a 10-fold increase of SNP density did not improve precision estimates compared with set-ups with a less dense distribution of SNPs. The methods used in this study showed that it was possible to estimate heritabilities on the basis of SNPs in animals with direct measurements. This conclusion is valuable in cases when quantitative traits are either difficult or expensive to measure.     

Quantitative genetics of skeletal nonmetric traits in the rhesus macaques of Cayo Santiago. III. Relative heritability of skeletal nonmetric and metric traits

This study addresses the long-standing controversy in skeletal biology concerning the relative utility of skeletal metric and nonmetric traits for studies of biological relationship. This controversy centers on the relative heritability of these two trait sets. This paper presents heritabilities for a series of skeletal metric and nonmetric traits measured with the same sample of mother-offspring pairs from the Cayo Santiago skeletal collection of rhesus macaques. Skeletal nonmetric traits display significantly greater heritability estimates than metric traits. This difference is due primarily to the high heritability estimates of hyperostotic nonmetric traits. Foraminal traits are not significantly more heritable than skeletal metric traits. The generality of this pattern of heritability values, in which hyperostotic nonmetric traits are more highly heritable than foraminal nonmetric and metric traits, depends on future empirical study of the correlation of heritability values in populations and theoretical work.     

The quantitative genetics of sexually selected traits,preferred traits and preference: a review and analysis of the data

The maintenance of variation in sexually selected traits is a puzzle that has received increasing attention in the past several decades. Traits that are related to fitness, such as life‐history or sexually selected traits, are expected to have low additive genetic variance (and hence, heritability) due to the rapid fixation of advantageous alleles. However, previous analyses have suggested that the heritabilities of sexually selected traits are on average higher than nonsexually selected traits. We show that the heritabilities of sexually selected traits are not significantly different from those of nonsexually selected traits overall or when separated into the three trait categories: behavioural, morphological and physiological. In contrast with previous findings, the heritability of preference is quite low (h² = 0.25 ± 0.06) and is in the same range as life‐history traits. We distinguish preferred traits as a category of sexually selected traits and find that the heritability of the former is not significantly different than sexually selected traits overall (0.48 ± 0.04 vs. 0.46 ± 0.03). We test the hypothesis that the heritability of sexually selected traits is negatively correlated with the strength of sexual selection. As predicted, there is a significant negative correlation between the heritabilities of sexually selected traits and the strength of selection. This suggests that heritabilities do indeed decrease as sexual selection increases but sexual selection is not strong enough to cause heritabilities of sexually selected traits to deviate from the same type of nonsexually selected traits.     

A distribution model for heritability.

A regression model to predict quantiles of narrow sense individual and family mean heritabilities is developed and used to predict confidence intervals either directly or via a generalized beta distribution model. Extensive simulations of balanced sib analysis trials in randomized complete block designs and normal distributed environmental and additive genetic effects confirmed that heritabilities follow a beta distribution even in cases with up to 10% of the data missing at random. The new model is both more accurate and more precise than commonly used alternatives based on "exact" chi 2 distributions and Satterthwaites approximations to the degrees of freedom. Estimates of the expected heritability and a Taylor approximation of the standard error of the heritability are needed as input to the quantile model. Applications of the presented models for estimating confidence intervals and as an aid in the design of experiments are provided.     

Maximum-likelihood variance components analysis of heritabilities of cranial nonmetric traits

Nonmetric traits of the cranium are often used to support hypotheses of the history and divergence of human populations. These studies rely on the assumption that nonmetric traits are heritable, yet few skeletal series exist with associated pedigree information that allow for the calculation of additive genetic variance, or heritability. In addition, traits for which heritabilities have been published represent dichotomous present/absent forms instead of the range of expression that can be observed for many nonmetric characters. In the present study I use a maximum-likelihood variance components analysis to calculate univariate narrow-sense heritability estimates on the skeletal series from Hallstatt, Austria, for 9 sutural bones, 27 multilevel traits, and dichotomized present/absent forms for 19 of these multilevel characters. Most of the trait heritabilities do not differ significantly from a model of h2 = 0, and they have large standard errors. In a heuristic comparison of multilevel versus dichotomous trait forms, most of the nonmetric characters showed no differences in heritability between the two methods used for parsing the phenotypic variation, although where differences were noted, the presence-absence version had higher heritabilities. These results have implications not only for the use of particular nonmetric traits in population studies but also for the practice of character dichotomization in data collection.     

Heritability and evolvability of fitness and nonfitness traits: Lessons from livestock

Data from natural populations have suggested a disconnection between trait heritability (variance standardized additive genetic variance, V_A) and evolvability (mean standardized V_A) and emphasized the importance of environmental variation as a determinant of trait heritability but not evolvability. However, these inferences are based on heterogeneous and often small datasets across species from different environments. We surveyed the relationship between evolvability and heritability in >100 traits in farmed cattle, taking advantage of large sample sizes and consistent genetic approaches. Heritability and evolvability estimates were positively correlated (r = 0.37/0.54 on untransformed/log scales) reflecting a substantial impact of V_A on both measures. Furthermore, heritabilities and residual variances were uncorrelated. The differences between this and previously described patterns may reflect lower environmental variation experienced in farmed systems, but also low and heterogeneous quality of data from natural populations. Similar to studies on wild populations, heritabilities for life‐history and behavioral traits were lower than for other traits. Traits having extremely low heritabilities and evolvabilities (17% of the studied traits) were almost exclusively life‐history or behavioral traits, suggesting that evolutionary constraints stemming from lack of genetic variability are likely to be most common for classical “fitness” (cf. life‐history) rather than for “nonfitness” (cf. morphological) traits.     

EVOLUTIONARY PREDICTABILITY IN NATURAL POPULATIONS: DO MATING SYSTEM AND NONADDITIVE GENETIC VARIANCE INTERACT TO AFFECT HERITABILITIES IN PLANTAGO LANCEOLATA?

Quantitative genetics has been an immensely powerful tool in manipulating the phenotypes of domesticated plants and animals. Much of the predictive power of quantitative genetics depends on the breeder's control over the context in which phenotype and mating are being expressed. In the natural world, these contexts are often difficult to describe, let alone control. We are left, therefore, with a poor understanding of the limits of quantitative genetics in natural populations. One of the crucial contextual elements for assessing breeding value is the genetic background in which an individual's genes are being assessed. When interacting genes are polymorphic within a population, the degree of mating among relatives can influence the correlations among mates and the predictions of a response to selection. Population structure can strongly influence the degree to which dominance and epistasis influences additive genetic variance and heritability. The extent of inbreeding can also influence heritabilities through its effect on the environmental component of phenotypic variance. The applicability of standard quantitative genetic breeding designs to the measurement of heritabilities in natural populations therefore depends in part on: (1) the mating system of the population; and (2) the importance of gene interactions in determining phenotypic variation. We tested for an effect of mating structure on the partitioning of phenotypic variance and heritability by comparing two breeding designs in a common environment. Both breeding designs used 139 pollen parents taken from mapped locations in a population of Plantago lanceolata L., and crossed to 280 seed parents from the same population. One design was random-mating, the second was biased toward near-neighbor matings to an extent determined by field measure of pollen-mediated gene flow distances. The offspring were grown randomly mixed in a common garden. Nine traits were measured: central corm diameter, number of leaves, area of the most recently fully expanded leaf, density of hairs (cm^-2) on the leaves, dry weight per unit leaf area, photosynthetic capacity, transpiration rates, water use efficiency, and reproductive dry weight. Heritabilities and variance components from the two designs were compared using randomization tests. None of the variance components or the heritabilities differed significantly between breeding designs at the 0.05 level. The test could distinguish differences between the heritabilities measured in the two breeding designs as small as 0.11, on average. Thus, for the degree of inbreeding normally exhibited in P. lanceolata there is insufficient gene interaction present within populations to influence the partitioning of variance between additive and nonadditive components or to influence heritability estimates to a meaningful extent. We suggest that for Plantago other sources of variation in heritability estimates, such as maternal effects and genotype × environment interactions, are more important influences than the interaction between inbreeding and gene interactions, and standard heritability estimate based on random breeding is as accurate as one taking the natural mating structure into account.     

Genetics of Callous-Unemotional Behavior in Children

Callous-unemotional behavior (CU) is currently under consideration as a subtyping index for conduct disorder diagnosis. Twin studies routinely estimate the heritability of CU as greater than 50%. It is now possible to estimate genetic influence using DNA alone from samples of unrelated individuals, not relying on the assumptions of the twin method. Here we use this new DNA method (implemented in a software package called Genome-wide Complex Trait Analysis, GCTA) for the first time to estimate genetic influence on CU. We also report the first genome-wide association (GWA) study of CU as a quantitative trait. We compare these DNA results to those from twin analyses using the same measure and the same community sample of 2,930 children rated by their teachers at ages 7, 9 and 12. GCTA estimates of heritability were near zero, even though twin analysis of CU in this sample confirmed the high heritability of CU reported in the literature, and even though GCTA estimates of heritability were substantial for cognitive and anthropological traits in this sample. No significant associations were found in GWA analysis, which, like GCTA, only detects additive effects of common DNA variants. The phrase ‘missing heritability’ was coined to refer to the gap between variance associated with DNA variants identified in GWA studies versus twin study heritability. However, GCTA heritability, not twin study heritability, is the ceiling for GWA studies because both GCTA and GWA are limited to the overall additive effects of common DNA variants, whereas twin studies are not. This GCTA ceiling is very low for CU in our study, despite its high twin study heritability estimate. The gap between GCTA and twin study heritabilities will make it challenging to identify genes responsible for the heritability of CU.     

HERITABILITIES OF DOMINANCE-RELATED TRAITS IN MALE BANK VOLES (CLETHRIONOMYS GLAREOLUS)

A number of studies have shown that in several animal species females prefer dominant males as mating partners, but fewer attempts have been made to measure possible indirect benefits of this choice. One reason for this may be that, even though dominance is a widely used concept, the definition of dominance still remains controversial Furthermore, defining and measuring the heritability of social behaviors is problematic because they are not individual traits but, by definition, involve interactions between at least two individuals. In this study we estimated heritabilities and coefficients of additive genetic variances (CV_A) for male traits that are closely associated with dominance and female mating preferences in bank voles (Clethrionomys glareolus). The heritability values were estimated using father-offspring regression. All heritability estimates were relatively high ranging from 0.531 (urine marking) to 0.767 (preputial glands). The CV_A-values indicated high levels of additive genetic variance especially in the characters most closely related to dominance: the weight of preputial glands and urine marking behavior. All phenotypic correlations among the traits measured were significantly positive and the genetic correlations were of similar magnitude as the corresponding phenotypic counterparts. Even though heritabilities may be lower in the natural environment than under controlled laboratory conditions, our results suggest that characters closely related to dominance may be at least partly genetically determined.     

Impact of reconstructed pedigrees on progeny-test breeding values in red spruce

Pedigrees reconstructed through DNA marker assigned paternities in polymix (PMX) and open pollinated (OP) progeny tests were analyzed using mixed models to test the effect of unequal male reproductive success and pedigree errors on quantitative genetic parameters. The reconstructed pedigree increased heritabilities in the larger PMX test. Increased heritability resulted from adding the paternities to the pedigree per se, not by correcting the male reproductive bias by specifying the exact pedigree. Removing hypothesized pedigree errors had no effect on quantitative parameters, either because the magnitude of the errors was too small (PMX) or the progeny test was too small to detect variance components reliably (OP). Although there was no advantage in backwards selection, the increased additive variance, heritabilities and accuracy of progeny with assigned paternities in the pedigree, should permit forward selection of offspring with greater genetic gain and complete control of coancestry for future breeding decisions. Some possible breeding population structures with the new genetic information are discussed.     

Impact of reconstructed pedigrees on progeny-test breeding values in red spruce

Pedigrees reconstructed through DNA marker assigned paternities in polymix (PMX) and open pollinated (OP) progeny tests were analyzed using mixed models to test the effect of unequal male reproductive success and pedigree errors on quantitative genetic parameters. The reconstructed pedigree increased heritabilities in the larger PMX test. Increased heritability resulted from adding the paternities to the pedigree per se, not by correcting the male reproductive bias by specifying the exact pedigree. Removing hypothesized pedigree errors had no effect on quantitative parameters, either because the magnitude of the errors was too small (PMX) or the progeny test was too small to detect variance components reliably (OP). Although there was no advantage in backwards selection, the increased additive variance, heritabilities and accuracy of progeny with assigned paternities in the pedigree, should permit forward selection of offspring with greater genetic gain and complete control of coancestry for future breeding decisions. Some possible breeding population structures with the new genetic information are discussed.     

Canine behavioral genetics — A review

A chronological review of the history of research in canine behavioral genetics is presented. Prior to the work of Scott and Fuller, many studies attempted to describe observed results in simple Mendelian terms. More recently, a quantitative mode of inheritance has been ascribed to many behavioral traits, and heritabilities have been calculated in different populations. Studies of behavioral traits are complicated by the effects of learning, which may well explain the reports of low heritability of behavioral traits measured on adults. Both genotype and environment have been shown to play major roles in the expression of behavioral traits. Maternal effects and the sex of an individual have important effects on behavior scores. Breeders usually select for both physical and behavioral traits in the same individuals, and this review includes a summary of reported research on the relationships between physical and mental traits.     

Realized Sampling Variances of Estimates of Genetic Parameters and the Difference between Genetic and Phenotypic Correlations

A data set of 1572 heritability estimates and 1015 pairs of genetic and phenotypic correlation estimates, constructed from a survey of published beef cattle genetic parameter estimates, provided a rare opportunity to study realized sampling variances of genetic parameter estimates. The distribution of both heritability estimates and genetic correlation estimates, when plotted against estimated accuracy, was consistent with random error variance being some three times the sampling variance predicted from standard formulae. This result was consistent with the observation that the variance of estimates of heritabilities and genetic correlations between populations were about four times the predicted sampling variance, suggesting few real differences in genetic parameters between populations. Except where there was a strong biological or statistical expectation of a difference, there was little evidence for differences between genetic and phenotypic correlations for most trait combinations or for differences in genetic correlations between populations. These results suggest that, even for controlled populations, estimating genetic parameters specific to a given population is less useful than commonly believed. A serendipitous discovery was that, in the standard formula for theoretical standard error of a genetic correlation estimate, the heritabilities refer to the estimated values and not, as seems generally assumed, the true population values.