Environmental Variance Components Research Articles

347 Quantifying phenotypic and genetic variation for cow fertility phenotypes in American Simmentals using total herd reporting data

Abstract Inefficiencies in reproduction are the largest drivers of loss in United States beef production. Nearly all reproductive traits are at least modestly heritable, making genetic selection and improvement possible over the long term. Cow-centric reproductive traits present unique challenges, as they are not expressed in male animals and will not be observed until later in the productive life of a female, if at all. This makes cow-centric fertility traits ideal candidates for selection with Expected Progeny Differences (EPDs). We used a commercially generated dataset from the American Simmental Association (ASA) to explore the phenotypic and genetic variation in these traits. The dataset comprised Total Herd Enrollment (THE) records, which required unbiased reporting of enrollment, calving, and disposal for 303,158 females (132,403 cows and 170,755 heifers). Using the THE data, we calculated three continuous and two discrete traits that are indicators of heifer and cow fertility and rebreeding ability. These traits were: 1) calving date (calving date of the cow relative to the start of the calving season), 2) calving interval (days between calves), 3) first calving interval (calving interval observation between the first and second calving record for a female), 4) heifer pregnancy (did the animal calve as 2-yr-old?), and 5) discrete early calving (did animal calve in the first 30 d of the calving season?). We observed a significant difference in calving date in mature cows that calved in the first 30 d of the calving season of their contemporary group as heifers compared with those that calved later (Table 1). Early calving heifers averaged a nearly 10 d sooner calving date throughout their productive lives compared with those that calved after 30 d as heifers (29.9 d vs. 40.2 d, P-value < 0.01). We used a combined pedigree and genomic approach, implemented in GIBBSF90+, to estimate genetic, environmental, and permanent environmental variance components. We estimated heritabilities of 0.24 (± 0.037215) for heifer pregnancy, 0.06 (± 0.009265) for calving date, 0.07 (± 0.015451) for discrete early calving, 0.04 (± 0.003954) for calving interval, and 0.04 (± 0.009604) for first calving interval. We observed positive phenotypic and genetic correlations between these traits, ranging from 0.01 to 0.96 (Table 2). This work provides an extensive population survey of phenotypic trends in reproductive performance and management in a large seedstock population. The heritable nature of the inspected traits motivates further work in understanding their genetic architectures and how they are affected by heterosis in crossbreeding programs.

Cohort Effects on Tobacco Consumption and Its Genetic and Environmental Variance Among Finnish Adults Born Between 1880 and 1957

Abstract Introduction Population research indicates that smoking behaviors in Finland have varied over time by sex and birth cohort. Smoking behaviors are influenced by genes and the environment; like the behaviors themselves, these underlying influences are not necessarily stable over time and may be modifiable by national drug policy. Aims and Methods We utilized longitudinal mixed-effects models and causal–common–contingent twin models to evaluate sex and cohort effects on tobacco consumption and the underlying genetic and environmental variance components in a birth cohort sample of same-sex twins born in Finland between 1880 and 1957, assessed in 1975, 1981, 1990, and 2011. Results We identified significant main effects of age, sex, and cohort on quantity of cigarette consumption, as well as significant age × cohort and sex × cohort interactions. We also identified sex and cohort effects on the liability to initiate regular smoking and the magnitude of variation underlying quantity of cigarette consumption. That said, heritability and environmental contributions to both traits were not different between the four sex × cohort groups. Conclusions Our results indicate sex and cohort effects on the prevalence of smoking and its underlying variation. Our results on changing prevalence mirror existing population-level research in Finnish samples, but we did not identify differences in heritability found in other studies of cohort effects in tobacco use, potentially due to power issues. These results highlight the importance of considering age, cohort, and timing of policy changes when evaluating changes in substance consumption across time. Implications This study identifies sex and cohort effects influencing tobacco consumption in a sample of Finnish adult twins born between 1880 and 1957. Our results are in line with other population-level research in Finland and research on cohort effects influencing alcohol use in the same sample. Our results highlight the intertwining effects of age, cohort, sex, and substance policies on substance use.

A Genetically Informed Study of the Association Between Perceived Stress and Loneliness

Although research shows a strong positive association between perceived stress and loneliness, the genetic and environmental etiology underlying their association remains unknown. People with a genetic predisposition to perceived stress, for example, may be more prone to feeling lonely and vice versa. Conversely, unique factors in people’s lives may explain differences in perceived stress levels that, in turn, affect feelings of loneliness. We tested whether genetic factors, environmental factors, or both account for the association between perceived stress and loneliness. Participants were 3,066 individual twins (nFemale = 2,154, 70.3%) from the Washington State Twin Registry who completed a survey during April–May, 2020. Structural equation modeling was used to analyze the item-level perceived stress and loneliness measures. The correlation between latent perceived stress and latent loneliness was .68. Genetic and nonshared environmental variance components underlying perceived stress accounted for 3.71% and 23.26% of the total variance in loneliness, respectively. The genetic correlation between loneliness and perceived stress was .45 and did not differ significantly between men and women. The nonshared environmental correlation was .54 and also did not differ between men and women. Findings suggest that holding constant the strong genetic association between perceived stress and loneliness, unique life experiences underlying people’s perceived stress account for individual differences in loneliness.

Genetic mapping reveals new loci and alleles for flowering time and plant height using the double round-robin population of barley.

Flowering time and plant height are two critical determinants of yield potential in barley (Hordeum vulgare). Despite their role in plant physiological regulation, a complete overview of the genetic complexity of flowering time and plant height regulation in barley is still lacking. Using a double round-robin population originated from the crossings of 23 diverse parental inbred lines, we aimed to determine the variance components in the regulation of flowering time and plant height in barley as well as to identify new genetic variants by single and multi-population QTL analyses and allele mining. Despite similar genotypic variance, we observed higher environmental variance components for plant height than flowering time. Furthermore, we detected new QTLs for flowering time and plant height. Finally, we identified a new functional allelic variant of the main regulatory gene Ppd-H1. Our results show that the genetic architecture of flowering time and plant height might be more complex than reported earlier and that a number of undetected, small effect, or low-frequency genetic variants underlie the control of these two traits.

Diurnal variation in genetic parameters for locomotor activity in Drosophila melanogaster assessed under natural thermal conditions.

In nature, organisms are exposed to variable and occasionally stressful environmental conditions. Responses to diurnal and seasonal fluctuations, such as temperature and food accessibility, involve adaptive behavioural and physiological changes. While much work has been done on understanding the genetic architecture and evolutionary potential of stress tolerance traits under constant thermal conditions, there has been less focus on the quantitative genetic background in variable environments. In this study, we use the Drosophila Genetic Reference Panel (DGRP) to investigate the locomotor activity, a key behavioural trait, under variable natural thermal conditions during the summer in a temperate environment. Male flies from 100 DGRP lines were exposed to natural thermal and light conditions in Drosophila activity monitors across three experimental days. We found that activity was highly temperature and time dependent and varied between lines both within and between days. Furthermore, we observed variation in genetic and environmental variance components, with low to moderate estimates of the heritability for locomotor activity, consistently peaking in the afternoons. Moreover, we showed that the estimated genetic correlations of locomotor activity between two time points decreased, as the absolute differences in ambient temperature increased. In conclusion, we find that the genetic background for locomotor activity is environment specific, and we conclude that more variable and unpredictable future temperatures will likely have a strong impact on the evolutionary trajectories of behavioural traits in ectotherms.

Genetic and environmental impact on mandibular growth in mono- and dizygotic twins during adolescence: A retrospective cohort study

This study aimed to discover the genetic and environmental factors that contribute to the mandibular development of untreated monozygotic and dizygotic twins. The sample, taken from the Forsyth Moorrees Twin Study, included 52 untreated monozygotic twins (36 male, 16 female) and 46 untreated dizygotic twins (23 male, 23 female). At the ages of 12 and 17, lateral cephalograms were collected and traced to assess total mandibular length, mandibular ramus length, mandibular corpus length, gonial angle, SNB, and bony chin prominence. The genetic and environmental components of variation were assessed using multilevel mixed-effects structural equation modelling. At 12 years of age, high additive genetic influences were observed for total mandibular length (74%), gonial angle (76%), SNB (41%), and bony chin prominence (64%), whereas strong dominant genetic components were observed for corpus length (72%), and mandibular ramus length was under unique environment influence (54%). At 17 years of age, only total mandibular length (45%), ramus length (53%), gonial angle (76%), and bony chin prominence (68%) were under strong additive genetic control, while the remainder were under strong dominant genetic control. Although monozygotic and dizygotic twins share at least a portion of their DNA, additive, dominant, or environmental components were discovered during adolescence. Nonetheless, by the age of 17, the majority of the mandibular traits are under either additive or dominant genetic impact.

Behavioral genetics of temporal framing: Heritability of time perspective and its common genetic bases with major personality traits.

The present study aimed to provide a seminal behavioral genetic analysis of time perspectives (TPs). Moreover, we intended to investigate the magnitude of genetic vs. environmental components of the well-established assocations between TPs and personality features. Individual differences in temporal framing processes, referred to as TPs, are vital psychological and behavioral outcomes. Although proponents of TP theory emphasize mainly environmental origins of the tendencies to adopt certain TPs, research provides evidence for marked associations between the temporal dimensions and major personality traits that are known to be heritable. Hence, it was essential to empirically verify these claims. The article reports an analysis of genetic and environmental components of variance in TPs based on a study adopting a twin design, conducted on a sample of 393 pairs of twins (135 monozygotic and 258 dizygotic). Multivariate Cholesky decomposition supported an EA model assuming impacts of both unshared environmental factors (E) and additive genetic factors (A) across all TP dimensions, suggesting that the effects of shared environment on TPs are plausibly negligible. Heritability indices of TPs ranged between 0.51 for Present-Fatalistic and 0.62 for Present-Hedonistic, suggesting that the majority of the variance in TPs stems from genetic influences. Substantial genetic correlations were found between TPs and the Big Five personality traits. The findings provide further evidence for conceptualizing TPs as biologically based personality traits and challenge the claims that TP is mainly a product of culture, education, and personal experiences.

Additive genetic and environmental variation interact to shape the dynamics of seasonal migration in a wild bird population.

Dissecting joint micro-evolutionary and plastic responses to environmental perturbations requires quantifying interacting components of genetic and environmental variation underlying expression of key traits. This ambition is particularly challenging for phenotypically discrete traits where multiscale decompositions are required to reveal non-linear transformations of underlying genetic and environmental variation into phenotypic variation, and when effects must be estimated from incomplete field observations. We devised a joint multistate capture-recapture and quantitative genetic animal model, and fitted this model to full-annual-cycle resighting data from partially-migratory European shags (Gulosus aristotelis) to estimate key components of genetic, environmental and phenotypic variance in the ecologically critical discrete trait of seasonal migration versus residence. We demonstrate non-negligible additive genetic variance in latent liability for migration, resulting in detectable micro-evolutionary responses following two episodes of strong survival selection. Further, liability-scale additive genetic effects interacted with substantial permanent individual and temporary environmental effects to generate complex non-additive effects on expressed phenotypes, causing substantial intrinsic gene-by-environment interaction variance on the phenotypic scale. Our analyses therefore reveal how temporal dynamics of partial seasonal migration arise from combinations of instantaneous micro-evolution and within-individual phenotypic consistency, and highlight how intrinsic phenotypic plasticity could expose genetic variation underlying discrete traits to complex forms of selection.

GENETIC ARCHITECTURE OF SUBJECTIVE HEALTH: RELATIONSHIP WITH PHYSICAL HEALTH, COGNITION, AND DEPRESSION

Abstract The fact that self-rated health (SH) predicts mortality and a variety of other health outcomes independent of objective health measures generates questions about mechanisms and etiologies. SH can be considered an indicator of physical health, per se, resulting from active cognitive processing of explicit information about one’s own health and intuitive knowledge of symptoms and physical sensations. The extent to which SH taps shared cultural ideas about health should be reflected in estimates of the shared environmental component of variance (C). SH has also been associated with emotional health measures, such as neuroticism and depression. Previous analyses have been limited by sex (only women), sample size, age (range = 63-76), and failure to include cognitive function. The current analysis used data from 8291 adults ranging in age from 22 to 102 from the international Interplay of Genes and Environment Across Multiple Studies (IGEMS) consortium to investigate the genetic architecture of SH. Genetic influences on self-rated health (SRH) were investigated in the context of CIRS (Cumulative Illness Rating Scale), MMSE (Mini-Mental Status Exam), and depression (CES-D or CAMDEX). Independent pathways modeling indicated that all genetic variance for SRH was shared with CIRS, MMSE, and depression. Comparison of groups older and younger than 74 indicated age differences in genetic architecture of SRH. Evidence suggests that the discordance between objective and subjective health increases in late adulthood, possibly as a result of greater emphasis on psychological rather than physical components of subjective health assessments by older adults.

Genetic Parameters of Reproductive Performances in Hungarian Large White, Landrace, and Their Crossbred F1 Pigs from 2010 to 2018

Genetic parameters, breeding values, and aggregate breeding values of number of piglets born alive (NBA), number of weaned piglets (NWE), and litter weight at weaning (LWWE) were predicted in the Hungarian Large White, Hungarian Landrace breeds, and in their cross (F1). Seven repeatability animal models were used. BLUP and REML methodology were used to estimate breeding values and variance–covariance components. PEST and VCE 6 software were used for estimating breeding values and variance components. Heritability for NBA and NWE was the same for all seven models. On the contrary, heritability estimates for LWWE were higher in comparison with NBA and NWE. The permanent environmental variance component was small for all traits. The large White breed had positive and significant genetic trends for all seven models and for all three traits. Landrace breed had significant trends for NBA, which was negative, and for NWE, the results were positive. The constructed indices result in one number (i.e., aggregate genetic merit); thus, the animals can be selected based on their overall performance considering the various aspects.

Longitudinal genetic analysis for Pacific abalone growth-related traits in sea-based culture system

Pedigreed family-based selective breeding is an appealing approach in genetic improvement of aquaculture species as the benefits can be cumulative and permanent. To determine the longitudinal growth characteristics of Pacific abalone (Haliotis discus hannai), shell colour rings were manipulated by feeding alternative algae, and shell length (SL) identification was performed at different ages. Eight SL records were obtained from 3147 individuals in 192 full-sib families at 6, 7, 9, 13, 18, 24, 28, and 32 months after hatching. To estimate the additive genetic and environmental variance components, longitudinal genetic analysis of repeated SL measurements was conducted using multivariate, auto-regressive, antedependence and random regression models with restricted maximum likelihood method. The results showed that the multivariate model with common full-sib family variance and residual heterogeneity of variance was the best model for the given dataset. Heritability estimates showed a decreasing trend with age, which is similar to the results obtained from the quadratic polynomial random regression model, and ranged from 0.629 at 9 months to 0.259 at 32 months. The separate rearing and tagging of single abalone at 6 months may have led to significant common environment family bias and overestimation of heritability. The antedependence model did not achieve a better fit for the obtained dataset. Estimates of genetic correlation between contiguous ages were high, ranging from 0.622 between 6 and 32 months to 0.987 between 28 and 32 months. The results demonstrated that genetic gain can be obtained in selection for Pacific abalone growth and outlined information regarding the age at which selection should be performed. This study can provide data and guidelines to a Pacific abalone selection program for growth related-traits.

A Note on Jöreskog’s ACDE Twin Model: A Solution, Not the Solution

The classical twin design is used to decompose phenotypic variance into genetic and environmental variance components. In practice, for reasons of identification, either an ADE or an ACE twin model is fitted, i.e., models with three variance components. Jöreskog proposed to use the Moore-Penrose inverse to estimate the four genetic and environmental variance components in the ACDE twin model. We demonstrate that the variance components thus obtained do not equal the true genetic and environmental variance components. Given a ACDE model, resorting to an ADE or ACE model or applying Jöreskog’s method will not produce correct results. However, it is possible that Jöreskog’s method will produce a better approximation to the true variance components under certain configurations of A, D, C, and E variance components.

Self-rated health when population health is challenged by the COVID-19 pandemic; a longitudinal study

RationaleThe coronavirus disease 2019 (COVID-19) pandemic and consequent lockdown measures have had a large impact on people's lives. Recent evidence suggests that self-rated health (SRH) scores remained relatively stable or increased during the pandemic. ObjectiveFor the current project, we examine potential changes in the variance decomposition of SRH before and during the COVID-19 pandemic in the Netherlands. MethodsWe analyse data from the Netherlands Twin Register to examine pre-pandemic SRH scores (N = 16,127), pandemic SRH scores (N = 17,451), and SRH difference scores (N = 7464). Additionally, we perform bivariate genetic analyses to estimate genetic and environmental variance components in pre-pandemic and pandemic SRH, and estimate the genetic correlation to assess potential gene-environment interaction. ResultsThe majority of the sample (66.7%) reported the same SRH before and during the pandemic, while 10.8% reported a decrease, and 22.5% an increase. Individuals who reported good/excellent SRH before the pandemic were most likely to report unchanged SRH during the pandemic, and individuals with bad/mediocre/reasonable SRH more often reported increased SRH. The bivariate longitudinal genetic model reveals no significant change in variance decomposition of SRH from before to during the pandemic, with a heritability estimate of 45% (CI 36%–52%). We found that the genetic correlation could be constrained to 1, and a moderate unique environmental correlation (rE = 0.49, CI = 0.37 to 0.60). ConclusionsWe theorize that the increases in SRH are explained by uninfected individuals evaluating their health more positively than under normal circumstances (partly through social comparison with infected individuals), rather than actual improvements. As the same genes are expressed under different environmental exposures, these results imply no evidence for gene-environment interaction. While different environmental factors might influence SRH at the two time-points, the influence of environmental factors does not become relatively more important during the pandemic.

Genetic Analysis of Water Stress Tolerance Attributes in F1 Maize Diallel Crosses

A half diallel set of crosses involving 10 inbred lines of maize along with commercial hybrid ARCGH 128 were evaluated at two different irrigation treatment during two season 2019 and 2020 using RCBD design with three replications at two locations (Minia and Assuit governorates), to determine combining ability and gene action for grain yield and its components. the most superior crosses for the economic traits were detected in L1 X L2 for leaf proline content, ear weight and number of rows/ear, L1 X L8 for number of ear /plot and number of rows/ear, L4 X L9 for Days to tasseling and Days to silking, L3 X L8 for Leaf angle, leaf rolling, number of kernels/ear, number of rows/ear and number of kernels/row and L3 X L10 for days to tasseling, days to silking,leaf rolling, relative water content (RWC %), kernel fresh weight, number of rows/ear and yield. Highly significant and larger in magnitude values of dominance (H1 and H2) components were found to be at the significant level at (5%) for all studied characters which confirmed their importance in the expression of these characters. However (D) dominance component was reached to the significant level only for the normal irrigation treatment for the leaf angel at both locations, all irrigation treatment for leaf proline content at both locations, normal irrigation treatment for number of kernel/row at Assuit location and all irrigation treatment for 100 kernel weight and number of ear/plot at both locations. The (F) component was significant and positive for all irrigation treatment for leaf proline content at both location, normal irrigation treatment for number of kernel/row at Assuit location, all irrigation treatments for 100 kernel weight at both location, stress irrigation treatment for number of ear/plot at Minia location. Significant differences of environmental variance (E) components were recorded for all irrigation treatment for leaf rolling at Assuit location, all irrigation treatment for ear weight at Minia location and all irrigation treatment for number of rows/ear and number of ear/plot at both locations. Dominance component of variance (H1 and H2) were significant and/or highly significant for all studied traits and (H1) was greater than (H2) in F1 indicating that positive and negative alleles at loci of these trait were not in proportional equal for parents. The estimator (h2) were refers to the dominance effect overall heterozygous loci was significant for all studied traits except days to tasseling for normal irrigation treatment at both locations, stress irrigation treatment for leaf angel at Minia location, all irrigation treatment for leaf rolling at both locations, normal irrigation treatment for ear weight/kg/plot at both locations and for stress irrigation treatment for number of rows/ear at Minia location. Average degree of dominance (H1/D) 0.5 was more than unity for all traits, these finding indicated the involved of an over dominance expression for all characters. However the over dominance observed in such character may not be an index of true over dominance could be based due to linkage epistasis or both together. Since the ratio of dominance (KD) recessive (KR) alleles was more than one for all the studied characters, these indicates a preponderance of dominant gene in the parents for the characters. The value of K (h2/H2, which stands for the number of groups of genes that exhibit dominance for each character) was <1 for all the studied characters for normal irrigation treatment at Assuit location and all irrigation treatment at Minia location and all irrigation treatment at Minia location for number of rows/ear and 100 kernel weight/gm. This suggested that just one group of genes showed dominance governed all of them while this parameter could be underestimated, when the dominance effects of all genes was not concerned with equivalent, size and distribution, where the distribution of genes was correlated, or complementary gene interactions occur. Heritability values in bored sense (h2b) were relatively low for all characters. However, heritability in narrow sense (h2n) was high scored values more 50% except leaf rolling for stress irrigation treatment at Minia location (0.48%) these results confirmed that the environmental effects constitute a major portion of the total phenotypic variation in these characters.

Heritability of facial soft tissue growth in mono- and dizygotic twins at 12 and 17 years of age: A retrospective cohort study.

The purpose of this investigation of untreated monozygotic and dizygotic twins was to identify the genetic and environmental components to the facial soft tissue growth. The sample consisted of 52 untreated monozygotic twins (36 male and 16 female) and 46 untreated dizygotic twins (23 male and 23 female) from the Forsyth Moorrees Twin Study (1959-1975). Lateral cephalograms were taken at 12 and 17years of age and traced to analyse facial convexity, nasolabial angle, upper and lower lip thickness, upper and lower lip profile and nose prominence. The genetic and environmental components of variance were analysed with structural equation modelling for multilevel mixed-effects model. At 12years of age, strong additive genetic influence was seen for facial convexity (70%), upper lip profile (66%) and nose prominence (65%), whereas strong dominant genetic components were found for upper lip thickness (56%). Nevertheless, under unique environment influence were nasolabial angle (58%), lower lip profile (51%) and lower lip thickness (64%). At 17years of age, only upper lip thickness (55%) and nose prominence (84%) were under strong additive genetic control, while the rest of the variables were under strong dominant genetic control. The only exception was lower lip thickness (61%), which is still influenced by the unique environment. Although monozygotic/dizygotic twins share at least part of their genome, at both times either additive, dominant or environmental components were found. Nevertheless, at 17years of age most of the variables are either under additive or dominant genetic influence.

How genetic and environmental variance in personality traits shift across the life span: Evidence from a cross-national twin study.

Decades of research have shown that about half of individual differences in personality traits is heritable. Recent studies have reported that heritability is not fixed, but instead decreases across the life span. However, findings are inconsistent and it is yet unclear whether these trends are because of a waning importance of heritable tendencies, attributable to cumulative experiential influences with age, or because of nonlinear patterns suggesting Gene × Environment interplay. We combined four twin samples (N = 7,026) from Croatia, Finland, Germany, and the United Kingdom, and we examined age trends in genetic and environmental variance in the six HEXACO personality traits: Honesty-Humility, Emotionality, Extraversion, Agreeableness, Conscientiousness, and Openness. The cross-national sample ranges in age from 14 to 90 years, allowing analyses of linear and nonlinear age differences in genetic and environmental components of trait variance, after controlling for gender and national differences. The amount of genetic variance in Extraversion, Agreeableness, and Openness followed a reversed U-shaped pattern across age, showed a declining trend for Honesty-Humility and Conscientiousness, and was stable for Emotionality. For most traits, findings provided evidence for an increasing relative importance of life experiences contributing to personality differences across the life span. The findings are discussed against the background of Gene × Environment transactions and interactions. (PsycInfo Database Record (c) 2021 APA, all rights reserved).

Familial Risk and Heritability of Hematologic Malignancies in the Nordic Twin Study of Cancer.

Simple SummaryHematologic malignancies account for 8–9% of all incident cancers. Both genetic and environmental risk factors contribute to cancer development, but it is unclear if there is shared heritability between hematologic malignancies. This study aimed to investigate familial predisposition to hematologic malignancies using the largest twin study of cancer in the world. We compared individual risk in the general population and the risk of cancer in one twin before some age given that the other twin had (another) cancer before that age. Furthermore, by analyzing information about whether the twins were identical or fraternal, we could estimate the relative importance of genetic and environmental influences on the risk for developing hematologic cancers. This study confirmed previous findings of familial predisposition to hematologic malignancies and provides novel evidence that familial predisposition decreases with increasing age. The latter points to the importance of taking age into account in the surveillance of hematological cancers.We aimed to explore the genetic and environmental contributions to variation in the risk of hematologic malignancies and characterize familial dependence within and across hematologic malignancies. The study base included 316,397 individual twins from the Nordic Twin Study of Cancer with a median of 41 years of follow-up: 88,618 (28%) of the twins were monozygotic, and 3459 hematologic malignancies were reported. We estimated the cumulative incidence by age, familial risk, and genetic and environmental variance components of hematologic malignancies accounting for competing risk of death. The lifetime risk of any hematologic malignancy was 2.5% (95% CI 2.4–2.6%), as in the background population. This risk was elevated to 4.5% (95% CI 3.1–6.5%) conditional on hematologic malignancy in a dizygotic co-twin and was even greater at 7.6% (95% CI 4.8–11.8%) if a monozygotic co-twin had a hematologic malignancy. Heritability of the liability to develop any hematologic malignancy was 24% (95% CI 14–33%). This estimate decreased across age, from approximately 55% at age 40 to about 20–25% after age 55, when it seems to stabilize. In this largest ever studied twin cohort with the longest follow-up, we found evidence for familial risk of hematologic malignancies. The discovery of decreasing familial predisposition with increasing age underscores the importance of cancer surveillance in families with hematological malignancies.

Analysis of (co) variance components and estimation of breeding value of growth and production traits in Dahlem Red chicken using pedigree relationship in an animal model.

Variance and covariance components of growth and production traits were analyzed employing REML animal model to assess the Dahlem Red (PD-3) chicken population for direct additive genetic, maternal effects and to estimate the estimated breeding value (EBV), genetic parameters, genetic trends and rate of inbreeding (ΔF) utilizing seven generation’s data. The generation and hatch had significant (P≤0.01) effect on the body weight at 0 day (BW0), 2 (BW2), 4 (BW4) and 6 weeks (BW6) and shank length at six weeks of age (SL6). The average least squares means (LSM) for BW6 and SL6 were 273.93±0.62 g and 53.97±0.05 mm, respectively. All the production traits were significantly (P≤0.01) influenced by generation and hatch. The average LSM for age at sexual maturity (ASM), egg production up to 40 weeks (EP40) and egg mass up to 40 weeks (EM40) were 168.82±0.25 d, 72.60±0.41 eggs and 4.21±0.07 kg, respectively. Model 5 with additive direct, maternal genetic, maternal permanent environmental and residual variance components was the best for BW0, BW2 and BW4 based on the AIC values obtained in WOMBAT. Model 4 was the best model for BW6, SL6, ASM, EP40 and EM40 with additive direct, maternal permanent environmental and residual variance components. Maternal effects were higher during early age, decreased with age, and remained present until 20 weeks of age. The heritability (h2) estimates were low to moderate in magnitude for all the growth traits and ranged from 0.02±0.03 to 0.19±0.03. The maternal heritability was high at hatch (0.35±0.06), decreased gradually until 4th week (0.02±0.01) and ceased afterwards. The heritabilities of EP40 (0.11±0.03) and EM40 (0.12±0.04) were low. The direct additive genetic correlations (ra) between BW2, BW4, BW6 and SL6 were high and positive (P≤ 0.05). The additive genetic and maternal permanent environmental correlation between EP40 and EM40 were high and positive (P≤ 0.05). The EBV of EM40 was significant (P≤ 0.05) with 0.48 kg/generation in PD-3 chicken at the end of the seventh generation. The EBV of EP40 showed an increasing trend with a genetic gain of 1.87 eggs per generation. The average inbreeding coefficient of the population was 0.019 and average ΔF was 0.007 over the last seven generations of selection. The EBV trends for primary and associated traits showed linear trends in the desired direction and negligible inbreeding.

Multilevel Twin Models: Geographical Region as a Third Level Variable

The classical twin model can be reparametrized as an equivalent multilevel model. The multilevel parameterization has underexplored advantages, such as the possibility to include higher-level clustering variables in which lower levels are nested. When this higher-level clustering is not modeled, its variance is captured by the common environmental variance component. In this paper we illustrate the application of a 3-level multilevel model to twin data by analyzing the regional clustering of 7-year-old children’s height in the Netherlands. Our findings show that 1.8%, of the phenotypic variance in children’s height is attributable to regional clustering, which is 7% of the variance explained by between-family or common environmental components. Since regional clustering may represent ancestry, we also investigate the effect of region after correcting for genetic principal components, in a subsample of participants with genome-wide SNP data. After correction, region no longer explained variation in height. Our results suggest that the phenotypic variance explained by region might represent ancestry effects on height.

The Augmented Classical Twin Design: Incorporating Genome-Wide Identity by Descent Sharing Into Twin Studies in Order to Model Violations of the Equal Environments Assumption.

The Classical Twin Method (CTM) compares the similarity of monozygotic (MZ) twins with that of dizygotic (DZ) twins to make inferences about the relative importance of genes and environment in the etiology of individual differences. The design has been applied to thousands of traits across the biomedical, behavioral and social sciences and is arguably the most widely used natural experiment known to science. The fundamental assumption of the CTM is that trait relevant environmental covariation within MZ pairs is the same as that found within DZ pairs, so that zygosity differences in within-pair variance must be due to genetic factors uncontaminated by the environment. This equal environments assumption (EEA) has been, and still is hotly contested, and has been mentioned as a possible contributing factor to the missing heritability conundrum. In this manuscript, we introduce a new model for testing the EEA, which we call the Augmented Classical Twin Design which uses identity by descent (IBD) sharing between DZ twin pairs to estimate separate environmental variance components for MZ and DZ twin pairs, and provides a test of whether these are equal. We show through simulation that given large samples of DZ twin pairs, the model provides unbiased estimates of variance components and valid tests of the EEA under strong assumptions (e.g. no epistatic variance, IBD sharing in DZ twins estimated accurately etc.) which may not hold in reality. Sample sizes in excess of 50,000 DZ twin pairs with genome-wide genetic data are likely to be required in order to detect substantial violations of the EEA with moderate power. Consequently, we recommend that the Augmented Classical Twin Design only be applied to datasets with very large numbers of DZ twin pairs (> 50,000 DZ twin pairs), and given the strong assumptions relating to the absence of epistatic variance, appropriate caution be exercised regarding interpretation of the results.