The incidence of bilateral nonmetric skeletal traits: A reanalysis of sampling procedures

For reporting the incidence of bilateral skeletal traits, the choice between sampling statistics depends upon more than their relative efficiencies. Of overreaching importance are the fundamentally different assumptions about the genetic significance of bilateral asymmetry represented by the two principal sampling approaches. Sampling by side is consistent with the premise that trait expression on each side reflects an additive component of genetic variation. Implicit in sampling by individual, by contrast, is the proposition that asymmetries of expression result chiefly from developmental noise. The pattern of age-regression indicated for many of these traits, suggesting a transient developmental role for unilateral expression, supports both this latter view and the thesis of stress asymmetry. Given this pattern, furthermore, incorporating unadjusted trait frequencies into divergence statistics would seem injudicious.     

Why are rare traits unilaterally expressed?: Trait frequency and unilateral expression for cranial nonmetric traits in humans

Based on an analysis of nonmetric trait databases from several large skeletal series in Northern Europe and South America, representing 27 bilateral traits, we report a predictable relationship between the frequency of nonmetric traits and the probability that they are expressed bilaterally. In a wider sampling of traits and populations, this study thus confirms the findings of an earlier study by Ossenberg ([1981] Am. J. Phys. Anthropol. 54:471-479), which reported the same relationship for two mandibular traits. This trend was previously explained by extending the multifactorial threshold model for discontinuous traits to incorporate either separate thresholds for unilateral or bilateral expression, or by a fuzzy threshold in which the probability of bilateral expression increases away from the median threshold value. We show that the trend is produced under the standard multifactorial threshold model for discontinuous traits simply if the within-individual or developmental instability variance remains relatively constant across the range of liability. Under this assumption, the number of individuals in which one side but not the other is pushed over the threshold for trait formation will be a larger proportion of the number of individuals expressing the trait when the trait frequency is low. As trait frequency increases, the significance of within-individual variance as a determinant of trait formation decreases relative to the genetic and among-individual environmental variance. These results have implications for interpreting nonmetric trait data as well as for understanding the prevalence of unilateral vs. bilateral expression of a wide variety of discontinuous traits, including dysmorphologies in humans.     

Genetic correlations between sides and heritability of asymmetry for nonmetric traits in rhesus macaques on Cayo Santiago

The use of nonmetric traits for estimation of biological distance is a long-standing practice in biological anthropology. Nonmetric traits can be scored using either the individual or the side of the individual as the unit of measure. If sides of the individual are genetically correlated the use of sides would produce redundant genetic information. For this reason, Korey (Am. J. Phys. Anthropol. 53:19-23, 1980) argues for the use of individuals as the unit of measure for nonmetric traits. Ossenberg (Am. J. Phys, Anthropol. 54:471-479, 1981), however, argues that bilateral occurrence of nonmetric traits indicates greater genetic liability for the trait and that therefore the sides are the more biologically correct unit of measure. Genetic correlations for 13 cranial nonmetric traits are estimated for a sample of rhesus macaque skeletons from Cayo Santiago. In addition, heritability of asymmetry is estimated for these 13 traits as a test of Ossenberg's contention that asymmetry is genetically influenced. Significant genetic correlations between sides support Korey's contention that nonmetric traits should be scored by individual. Only two asymmetry heritabilities were significantly different from zero, providing no significant support for Ossenberg's contention that asymmetry is genetically determined. Our results support the theory that asymmetry represents a measure of the ability of an organism to buffer stresses. Therefore, a measure of the heritability of asymmetry is a measure of the heritability of the ability to buffer stresses. This ability does not appear to be heritable in this sample.     

Unilateral and bilateral expression of a quantitative trait: asymmetry and symmetry in coronal craniosynostosis

Bilateral symmetry in vertebrates is imperfect and mild asymmetries are found in normal growth and development. However, abnormal development is often characterized by strong asymmetries. Coronal craniosynostosis, defined here as consisting of premature suture closure and a characteristic skull shape, is a complex trait. The premature fusion of the coronal suture can occur unilaterally associated with skull asymmetry (anterior plagiocephaly) or bilaterally associated with a symmetric but brachycephalic skull. We investigated the relationship between coronal craniosynostosis and skull bilateral symmetry. Three-dimensional landmark coordinates were recorded on preoperative computed tomography images of children diagnosed with coronal nonsyndromic craniosynostosis (N = 40) and that of unaffected individuals (N = 20) and analyzed by geometric morphometrics. Our results showed that the fusion pattern of the coronal suture is similar across individuals and types of coronal craniosynostosis. Shape analysis showed that skulls of bilateral coronal craniosynostosis (BCS) and unaffected individuals display low degrees of asymmetry, whereas right and left unilateral coronal craniosynostosis (UCS) skulls are asymmetric and mirror images of one another. When premature fusion of the coronal suture (without taking into account cranial dysmorphology) is scored as a qualitative trait, the expected relationship between trait frequency and trait unilateral expression (i.e. negative correlation) is confirmed. Overall, we interpret our results as evidence that the same biological processes operate on the two sides in BCS skulls and on the affected side in UCS skulls, and that coronal craniosynostosis is a quantitative trait exhibiting a phenotypic continuum with BCS displaying more intense shape changes than UCS.     

Jugular foramen and mylohyoid bridging in an Asian Indian population

The incidence of jugular foramen and mylohyoid groove bridging was studied in a population of East Asian Indian skulls (125 males and 109 females). The criteria of Dodo (J. Anat. 144:153-165, 1986) was used in the identification of a jugular bridge. There was an overall incidence of 8.1% in jugular foramen bridging, with males showing a higher rate, though the difference did not reach statistical significance. The right side showed a statistically significant greater occurrence than the left, and the trait tended to be associated between sides. The overall incidence of mylohyoid bridging was found to be 2.6%, with no difference observed between the sexes. This frequency is less than the values reported for other Asian Indian studies. Studies concerned with the incidences of nonmetric traits such as bony bridging may be useful in population studies especially when utilized in combination, thereby enhancing the value of each trait as an anthropological tool.     

Mylohyoid and jugular foramen bridging in pre-Columbian Chileans

The occurrence of mylohyoid groove bridging and jugular foramen bridging was determined in a population of adult Pre-Columbian Chileans. Two hundred forty-one crania (110 males, 131 females) were examined for jugular foramen bridging and 464 mandibles (252 males and 212 females) were observed for mylohyoid groove bridging. The overall incidence of jugular foramen bridging was 14.94%, with females showing a higher occurrence (18.32%) than males (10.91%); however, no statistical significance was found between the sexes. The right side showed a greater incidence than the left, but again no statistical difference was noted and the occurrence of this trait was found to be associated between the sides. This frequency of jugular foramen bridging is higher than that found in other studies and approaches that reported in North American Eskimo populations. In the case of mylohyoid groove bridging, the incidence was 4.09% with no difference found between the sexes. This frequency of occurrence is less than the values reported previously for the other American populations of Mongoloid ancestry including the Pre-Columbian Peruvian population. The importance of nonmetric skeletal traits for defining population groups and their usefulness as anthropological tools is discussed. It is concluded that hard tissue variations such as bony bridging may be reliable markers to aid in discretely identifying population groups, but their importance can be significantly enhanced by coupling as many traits as possible in future studies.     

Genetic and environmental influence on the asymmetry of dermatoglyphic traits

Fluctuating asymmetry (FA) is defined as random deviations from bilateral symmetry of the body. Thus, its magnitude is often used to evaluate developmental homeostasis. In this study we evaluate the following hypotheses: 1) FA of dermatoglyphic traits has a significant genetic component; 2) prenatal maternal environment (PME) has a significant effect on the FA of dermatoglyphic traits in developmentally healthy individuals; and 3) genetic or environmental factors affect FA on organismal or systemic levels. Therefore, their effect is better seen in composite scores of FA rather than in FA indices for single traits. We analyzed 15 dermatoglyphic traits from 140 pairs of monozygous twins, 120 pairs of dizygous twins, and 106 pairs of mothers and daughters. All individuals were developmentally healthy. The influence of genetic and environmental factors on FA was evaluated by analysis of variance and regression analysis. For a majority of the traits in our study, FA showed significant but weak heritabilities, with values falling within the 0.20-0.35 range. None of the traits taken separately demonstrated the effect of PME on FA to be significantly greater than zero. The composite score of FA tended to have greater heritability values than individual traits. One of them, obtained in principal components analysis, showed a significant PME effect, supporting the hypothesis that FA is a systemic property.     

Inbreeding and developmental stability in three-spined sticklebacks (Gasterosteus aculeatus L.)

Fluctuating asymmetry, small non-directional departures from perfect symmetry in bilateral traits, results from the inability of individuals to buffer development against genetic and environmental perturbations. Fluctuating asymmetry is a widely used measure of developmental stability, and developmental stability has been hypothesised to be inversely related to heterozygosity. We compared male three-spined sticklebacks (Gasterosteus aculeatus L.) that had been inbred for one generation to outbred control males with respect to the asymmetry of a set of bilateral morphometric traits. Inbred fish developed significantly more asymmetric pectoral fins than their outbred counterparts, whereas neither the magnitude of asymmetry for pelvic spines nor for gill covers significantly responded to the treatment. Our results conform to a pattern of heterogeneity amongst traits in their tendency to develop asymmetrically in response to stress.     

THE EVOLUTION OF THRESHOLD TRAITS: A QUANTITATIVE GENETIC ANALYSIS OF THE PHYSIOLOGICAL AND LIFE-HISTORY CORRELATES OF WING DIMORPHISM IN THE SAND CRICKET

Many traits are phenotypically discrete but polygenically determined. Such traits can be understood using the threshold model of quantitative genetics that posits a continuously distributed underlying trait, called the liability, and a threshold of response, individuals above the threshold displaying one morph and individuals below the threshold displaying the alternate morph. For many threshold traits the liability probably consists of a hormone or a suite of hormones. Previous experiments have implicated juvenile hormone esterase (JHE), a degratory enzyme of juvenile hormone, as a physiological determinant of wing dimorphism in the crickets Gryllus rubens and G. firmus. The present study uses a half-sib experiment to measure the heritability of JHE in the last nymphal stadium of G. firmus and its genetic correlation with fecundity, a trait that is itself genetically correlated with wing morph. The phenotypic and genetic parameters are consistent with the hypothesis that JHE is a significant component of the liability. Comparison of sire and dam estimates suggest that nonadditive effects may be important. Two models have been proposed to account for the fitness differences between morphs: the dichotomy model, which assumes that each morph can be characterized by a particular suite of traits, and the continuous model, which assumes that the associated fitness traits are correlated with the liability rather than the morphs themselves. The latter model predicts that the fitness differences will not be constant but change with the morph frequencies. Variation in fecundity and flight muscle histolysis are shown to be more consistent with the continuous model. Data from the present experiment on JHE are inconclusive, but results from a previous selection experiment also suggest that variation in JHE is consistent only with the continuous model.     

Prediction of breeding values for group-recorded traits including genomic information and an individually recorded correlated trait

Records on groups of individuals could be valuable for predicting breeding values when a trait is difficult or costly to measure on single individuals, such as feed intake and egg production. Adding genomic information has shown improvement in the accuracy of genetic evaluation of quantitative traits with individual records. Here, we investigated the value of genomic information for traits with group records. Besides, we investigated the improvement in accuracy of genetic evaluation for group-recorded traits when including information on a correlated trait with individual records. The study was based on a simulated pig population, including three scenarios of group structure and size. The results showed that both the genomic information and a correlated trait increased the accuracy of estimated breeding values (EBVs) for traits with group records. The accuracies of EBV obtained from group records with a size 24 were much lower than those with a size 12. Random assignment of animals to pens led to lower accuracy due to the weaker relationship between individuals within each group. It suggests that group records are valuable for genetic evaluation of a trait that is difficult to record on individuals, and the accuracy of genetic evaluation can be considerably increased using genomic information. Moreover, the genetic evaluation for a trait with group records can be greatly improved using a bivariate model, including correlated traits that are recorded individually. For efficient use of group records in genetic evaluation, relatively small group size and close relationships between individuals within one group are recommended.Subject terms: Genetic markers, Animal breeding     

Statistical Power to Detect Genetic (Co)Variance of Complex Traits Using SNP Data in Unrelated Samples

We have recently developed analysis methods (GREML) to estimate the genetic variance of a complex trait/disease and the genetic correlation between two complex traits/diseases using genome-wide single nucleotide polymorphism (SNP) data in unrelated individuals. Here we use analytical derivations and simulations to quantify the sampling variance of the estimate of the proportion of phenotypic variance captured by all SNPs for quantitative traits and case-control studies. We also derive the approximate sampling variance of the estimate of a genetic correlation in a bivariate analysis, when two complex traits are either measured on the same or different individuals. We show that the sampling variance is inversely proportional to the number of pairwise contrasts in the analysis and to the variance in SNP-derived genetic relationships. For bivariate analysis, the sampling variance of the genetic correlation additionally depends on the harmonic mean of the proportion of variance explained by the SNPs for the two traits and the genetic correlation between the traits, and depends on the phenotypic correlation when the traits are measured on the same individuals. We provide an online tool for calculating the power of detecting genetic (co)variation using genome-wide SNP data. The new theory and online tool will be helpful to plan experimental designs to estimate the missing heritability that has not yet been fully revealed through genome-wide association studies, and to estimate the genetic overlap between complex traits (diseases) in particular when the traits (diseases) are not measured on the same samples.     

REDUCED GENETIC VARIANCE AMONG HIGH FITNESS INDIVIDUALS: INFERRING STABILIZING SELECTION ON MALE SEXUAL DISPLAYS IN DROSOPHILA SERRATA

Directional selection is prevalent in nature, yet phenotypes tend to remain relatively constant, suggesting a limit to trait evolution. However, the genetic basis of this limit is unresolved. Given widespread pleiotropy, opposing selection on a trait may arise from the effects of the underlying alleles on other traits under selection, generating net stabilizing selection on trait genetic variance. These pleiotropic costs of trait exaggeration may arise through any number of other traits, making them hard to detect in phenotypic analyses. Stabilizing selection can be inferred, however, if genetic variance is greater among low‐ compared to high‐fitness individuals. We extend a recently suggested approach to provide a direct test of a difference in genetic variance for a suite of cuticular hydrocarbons (CHCs) in Drosophila serrata. Despite strong directional sexual selection on these traits, genetic variance differed between high‐ and low‐fitness individuals and was greater among the low‐fitness males for seven of eight CHCs, significantly more than expected by chance. Univariate tests of a difference in genetic variance were nonsignificant but likely have low power. Our results suggest that further CHC exaggeration in D. serrata in response to sexual selection is limited by pleiotropic costs mediated through other traits.     

Assessing the Importance of Intraspecific Variability in Dung Beetle Functional Traits

Functional diversity indices are used to facilitate a mechanistic understanding of many theoretical and applied questions in current ecological research. The use of mean trait values in functional indices assumes that traits are robust, in that greater variability exists between than within species. While the assertion of robust traits has been explored in plants, there exists little information on the source and extent of variability in the functional traits of higher trophic level organisms. Here we investigated variability in two functionally relevant dung beetle traits, measured from individuals collected from three primary forest sites containing distinct beetle communities: body mass and back leg length. In doing so we too addressed the following questions: (i) what is the contribution of intra vs. interspecific differences in trait values; (ii) what sample size is needed to provide representative species mean trait values; and (iii) what impact does omission of intraspecific trait information have on the calculation of functional diversity (FD) indices from naturally assembled communities? At the population level, interspecific differences explained the majority of variability in measured traits (between 94% and 96%). In accordance with this, the error associated with calculating FD without inclusion of intraspecific variability was low, less than 20% in all cases. This suggests that complete sampling to capture intraspecific variance in traits is not necessary even when investigating the FD of small and/or naturally formed communities. To gain an accurate estimation of species mean trait values we encourage the measurement of 30–60 individuals and, where possible, these should be taken from specimens collected from the site of study.     

Selection strategies for linkage studies using twins.

Genetic linkage analysis for complex diseases offers a major challenge to geneticists. In these complex diseases multiple genetic loci are responsible for the disease and they may vary in the size of their contribution; the effect of any single one of them is likely to be small. In many situations, like in extensive twin registries, trait values have been recorded for a large number of individuals, and preliminary studies have revealed summary measures for those traits, like mean, variance and components of variance, including heritability. Given the small effect size, a random sample of twins will require a prohibitively large sample size. It is well known that selective sampling is far more efficient in terms of genotyping effort. In this paper we derive easy expressions for the information contributed by sib pairs for the detection of linkage to a quantitative trait locus (QTL). We consider random samples as well as samples of sib pairs selected on the basis of their trait values. These expressions can be rapidly computed and do not involve simulation. We extend our results for quantitative traits to dichotomous traits using the concept of a liability threshold model. We present tables with required sample sizes for height, insulin levels and migraine, three of the traits studied in the GenomEUtwin project.     

Methods for genetic linkage analysis using trisomies.

Certain genetic disorders are rare in the general population, but more common in individuals with specific trisomies. Examples of this include leukemia and duodenal atresia in trisomy 21. This paper presents a linkage analysis method for using trisomic individuals to map genes for such traits. It is based on a very general gene-specific dosage model that posits that the trait is caused by specific effects of different alleles at one or a few loci and that duplicate copies of "susceptibility" alleles inherited from the nondisjoining parent give increased likelihood of having the trait. Our mapping method is similar to identity-by-descent-based mapping methods using affected relative pairs and also to methods for mapping recessive traits using inbred individuals by looking for markers with greater than expected homozygosity by descent. In the trisomy case, one would take trisomic individuals and look for markers with greater than expected homozygosity in the chromosomes inherited from the nondisjoining parent. We present statistical methods for performing such a linkage analysis, including a test for linkage to a marker, a method for estimating the distance from the marker to the trait gene, a confidence interval for that distance, and methods for computing power and sample sizes. We also resolve some practical issues involved in implementing the methods, including how to use partially informative markers and how to test candidate genes.     

Epistatic pleiotropy and the genetic architecture of covariation within early and late-developing skull trait complexes in mice

The role of epistasis as a source of trait variation is well established, but its role as a source of covariation among traits (i.e., as a source of "epistatic pleiotropy") is rarely considered. In this study we examine the relative importance of epistatic pleiotropy in producing covariation within early and late-developing skull trait complexes in a population of mice derived from an intercross of the Large and Small inbred strains. Significant epistasis was found for several pairwise combinations of the 21 quantitative trait loci (QTL) affecting early developing traits and among the 20 QTL affecting late-developing traits. The majority of the epistatic effects were restricted to single traits but epistatic pleiotropy still contributed significantly to covariances. Because of their proportionally larger effects on variances than on covariances, epistatic effects tended to reduce within-group correlations of traits and reduce their overall degree of integration. The expected contributions of single-locus and two-locus epistatic pleiotropic QTL effects to the genetic covariance between traits were analyzed using a two-locus population genetic model. The model demonstrates that, for single-locus or epistatic pleiotropy to contribute to trait covariances in the study population, both traits must show the same pattern of single-locus or epistatic effects. As a result, a large number of the cases where loci show pleiotropic effects do not contribute to the covariance between traits in this population because the loci show a different pattern of effect on the different traits. In general, covariance patterns produced by single-locus and epistatic pleiotropy predicted by the model agreed well with actual values calculated from the QTL analysis. Nearly all single-locus and epistatic pleiotropic effects contributed positive components to covariances between traits, suggesting that genetic integration in the skull is achieved by a complex combination of pleiotropic effects.     

Changes in the expression of genetic characteristics across cohorts in skeletal deformations of farmed salmonids

Genetic analysis of disorder incidence in farmed animals is challenged by two factors. Disorders in different cohorts and environments could be caused by different factors, leading to changes in heritability and to less than unity genetic correlations across cohorts. Moreover, due to computational limitations, liability scale heritabilities at very low incidence may differ from those estimated at higher incidence. We tested whether these two dilemmas occur in skeletal deformations of farmed salmonids using multigeneration data from the Finnish rainbow trout breeding programme and previous salmonid studies. The results showed that heritability was close to zero in cohorts in which management practices maintained incidence at a low level. When there was a management failure and incidence was unusually high, heritability was elevated. This may be due to computational limitations at very low incidence and/or because deformations are induced by different factors in different cohorts. Most genetic correlations between deformations recorded in different generations were weakly to strongly positive. However, also negative correlations between generations were present, showing that high liability at one time can be genetically connected to low liability at another time. The results emphasise that genetic architecture of binary traits can be influenced by trait expression.     

水稻轮回选择群体XTBG-HP1表型遗传多样性分析

该研究基于4个陆稻群体及172个水稻品种或杂交组合,构建了水稻多亲本隐性核不育轮回选择群体XTBG-HP1,并经过4次轮回重组,采用16个表型性状对其进行了遗传多样性分析。结果表明:(1)该群体14个数量性状符合正态分布,各表型均存在极端性状个体。(2)数量性状变异系数范围为0.08～0.41,均值为0.20; Shannon-Wiener多样性指数范围为0.72～1.92,均值为1.50。(3)群体在株型与产量构成因子性状方面有显著的相关性,对株型的选择可以实现产量性状的改良。(4)剑叶长、每穗粒总数、千粒重、穗长、粒长、一次枝梗数、有效穗数、剑叶宽、二次枝梗数、抽穗期10个性状可作为群体综合评价指标。(5)剑叶长、二次枝梗数、每穗粒总数3个表型性状具有较高的遗传变异、丰富的遗传多样性及与综合得分F值相关系数较高。综合以上结果发现,后期群体进行基因挖掘、品种改良以及优良育种材料的选育可以基于剑叶长、二次枝梗数及每穗粒总数3个表型性状,同时要充分利用群体株型与产量构成因子性状间的显著相关性。此外,该研究群体中极端单性状或综合得分F值较高的个体,可进一步用于品种选育。     

Sexual selection, stabilizing selection and fluctuating asymmetry in two populations of pupfish (Cyprinodon pecosensis)

Fluctuating asymmetry of morphological traits is thought to reflect the capacity of a genotype to produce an integrated, functional phenotype. I tested three predictions. (1) In a polygynous breeding system, under intense sexual selection on males, breeding males should show greater symmetry in bilaterally symmetrical traits than non-breeding males or females. (2) If these traits are under stabilizing selection, highly symmetrical individuals also should be modal phenotypes, thus near the mean value for that trait, whereas individuals with increased asymmetry should represent marginal phenotypes, near the extremes of the distribution for that trait. (3) Differences in the intensity of sexual selection should be reflected in differences in the degree of fluctuating asymmetry between sexes among populations. I examined the relationship between male breeding status and the degree of fluctuating asymmetry of four bilaterally symmetrical- traits, preorbital and preopercular pores and pectoral and pelvic fin rays, in two populations of Pecos pupfish which differed in the intensity of sexual selection. These traits do not function in male-male competition or female choice, thus are not directly affected by sexual selection. In Mirror Lake breeding males, as a group, were most symmetrical for all four traits, while non-breeding males and females showed higher levels of fluctuating asymmetry. Similarly, symmetrical individuals also represented modal phenotypes for four traits (breeding males), and for three traits (non-breeding males and females). These patterns were not seen in the Lake Francis population, where breeding males were as asymmetrical as non-breeding males and females, and the degree of fluctuating symmetry did not differ between modal and marginal phenotypes for any of the four traits. When ecological conditions favour intense sexual selection, either through female choice, male-male competition, or both, breeding males represent the most fit phenotypes. Thus sexual selection reinforces the effects of stabilizing selection on characters that do not function as secondary sexual traits. However, when sexual selection is relaxed, differences between sexes disappear.     

The statistical treatment of correlated bilateral traits in the analysis of cranial material.

At present there is no standardized method to derive frequencies from bilateral non-metric traits. In this paper the commonly used methods are evaluated in light of statistical considerations and degree of sample preservation. In particular, we explore the question of dependence between sides for the bilateral traits. Several workers have tested for bilateral trait correlation in incorrect ways, confusing tests for differences in side frequencies with tests for independence. An easy method to test for independence, using the chi-squared test, is recommended. This test is used on 16 bilateral traits in a large sample of prehistoric carnia from Central California and significant dependence is found for all 16 of these traits. We suggest the traditional method of deriving frequencies be used. Both sides of the cranium should be considered, dividing the number of times the trait occurs by the number of sides available for observation. This method can be used even in poorly preserved samples. Side to side correlation may be compensated for by modifying the constants subtracted in the mean measure of divergence and in the expression for the approximate variance of the mean measure of divergence when the samples are drawn from identical populations.