SCtool:识别复杂性状和疾病间遗传关联的工具

识别复杂性状和疾病间遗传关联可以提供有用的病因学见解,并有助于确定可能的因果关系的优先级。尽管已有很多工具可以实现复杂性状和疾病间遗传关联,但是某些工具代码可读性差、并且不同工具基于不同的计算机语言、工具间的串联性较差。因此,本研究基于全基因组关联研究(GWAS)数据,提出了SCtool,一个开源、跨平台和用户友好的软件工具。SCtool整合了ldsc, TwosampleMR和MR-BMA三种软件,其主要功能是基于GWAS汇总水平的数据,识别复杂性状和疾病、复杂性状和复杂性状以及疾病与疾病间的遗传相关性并探究其间潜在的因果关联。最后,使用SCtool揭示了全身性铁状态(铁蛋白,血清铁,转铁蛋白,转铁蛋白饱和度)与表观遗传时钟GrimAge之间的遗传关联。     

Evolutionary associations between host traits and parasite load: insights from Lake Tanganyika cichlids

Parasite diversity and abundance (parasite load) vary greatly among host species. However, the influence of host traits on variation in parasitism remains poorly understood. Comparative studies of parasite load have largely examined measures of parasite species richness and are predominantly based on records obtained from published data. Consequently, little is known about the relationships between host traits and other aspects of parasite load, such as parasite abundance, prevalence and aggregation. Meanwhile, understanding of parasite species richness may be clouded by limitations associated with data collation from multiple independent sources. We conducted a field study of Lake Tanganyika cichlid fishes and their helminth parasites. Using a Bayesian phylogenetic comparative framework, we tested evolutionary associations between five key host traits (body size, gut length, diet breadth, habitat complexity and number of sympatric hosts) predicted to influence parasitism, together with multiple measures of parasite load. We find that the number of host species that a particular host may encounter due to its habitat preferences emerges as a factor of general importance for parasite diversity, abundance and prevalence, but not parasite aggregation. In contrast, body size and gut size are positively related to aspects of parasite load within, but not between species. The influence of host phylogeny varies considerably among measures of parasite load, with the greatest influence exerted on parasite diversity. These results reveal that both host morphology and biotic interactions are key determinants of host–parasite associations and that consideration of multiple aspects of parasite load is required to fully understand patterns in parasitism.     

A classical setting for associations between markers and loci affecting quantitative traits

We examine the relationships between a genetic marker and a locus affecting a quantitative trait by decomposing the genetic effects of the marker locus into additive and dominance effects under a classical genetic model. We discuss the structure of the associations between the marker and the trait locus, paying attention to non-random union of gametes, multiple alleles at the marker and trait loci, and non-additivity of allelic effects at the trait locus. We consider that this greater-than-usual level of generality leads to additional insights, in a way reminiscent of Cockerham's decomposition of genetic variance into five terms: three terms in addition to the usual additive and dominance terms. Using our framework, we examine several common tests of association between a marker and a trait.     

Genetic associations between maternal traits and aggressive behaviour in Large White sows

The present study examined the possibilities and consequences of selecting pigs for reduced aggression and desirable maternal behaviour. Data were recorded from 798 purebred Large White gilts, with an age of 217±17.7 (mean±SD) days, which were observed at mixing with unfamiliar conspecifics. The reaction of the sows towards separation from their litter was assessed for 2022 litters from 848 Large White sows. Sows’ performance during their time in the farrowing unit was scored based on the traits farrowing behaviour (i.e. need of birth assistance), rearing performance (i.e. litter quality at day 10 postpartum (pp)), usability (i.e. additional labour input during lactation period e.g. for treatments) and udder quality of the sow (i.e. udder attachment). For agonistic behaviour, traits heritabilities of h²=0.11±0.04 to h²=0.28±0.06 were estimated. For the sow’s reaction towards separation from her litter low heritabilities were found (h²=0.03±0.03 for separation test on day 1 pp and h²=0.02±0.03 for separation test on day 10 pp). Heritabilities for lactating sow’s performance (farrowing behaviour, rearing performance, usability of the sow and udder quality) in the farrowing unit ranged from h²=0.03±0.02 to h²=0.19±0.03. Due to these results it can be assumed that selection for these traits, for example, for udder quality or reduced aggression, is possible. Antagonistic associations were found between separation test on day 1 pp and different measures of aggressiveness (r_g=−0.22±0.26 aggressive attack and r_g=−0.41±0.33 reciprocal fighting). Future studies should determine economic as well as welfare-related values of these traits in order to decide whether selection for these traits will be reasonable.     

Pervasive genetic associations between traits causing reproductive isolation in Heliconius butterflies

Ecological speciation proceeds through the accumulation of divergent traits that contribute to reproductive isolation, but in the face of gene flow traits that characterize incipient species may become disassociated through recombination. Heliconius butterflies are well known for bright mimetic warning patterns that are also used in mate recognition and cause both pre- and post-mating isolation between divergent taxa. Sympatric sister taxa representing the final stages of speciation, such as Heliconius cydno and Heliconius melpomene, also differ in ecology and hybrid fertility. We examine mate preference and sterility among offspring of crosses between these species and demonstrate the clustering of Mendelian colour pattern loci and behavioural loci that contribute to reproductive isolation. In particular, male preference for red patterns is associated with the locus responsible for the red forewing band. Two further colour pattern loci are associated, respectively, with female mating outcome and hybrid sterility. This genetic architecture in which ‘speciation genes’ are clustered in the genome can facilitate two controversial models of speciation, namely divergence in the face of gene flow and hybrid speciation.     

Quantitative traits in plants: beyond the QTL

Phenotypic variation for quantitative traits results from segregation at multiple quantitative trait loci (QTL), the effects of which are modified by the internal and external environments. Because of their favorable genetic attributes (e.g. short generation time, large families and tolerance to inbreeding), plants are often used to test new concepts in quantitative trait analysis. Thus far, the molecular basis underlying allelic variation at QTL is similar to the identified variation for simple mendelian loci; namely, alterations in gene expression or protein function. Further comprehensive dissection of complex phenotypes will depend on our ability to link genetic components of the QTL variation to genomic databases.     

Developmental evolution: going beyond the 'just so'

Two new protocols for infecting non-mammalian embryos with viruses, together with RNA inhibition, have provided evolutionary developmental biologists with the tools to study the effects of manipulating gene activity in a wide range of species, allowing them to test hypotheses rather than rely on inference from similarity.     

Developmental biology: cell intercalation one step beyond

Formation of the primitive streak, the equivalent of the blastopore, is a critical step during the early development of amniote embryos. Medio-lateral cell intercalation and the planar cell polarity pathway play a role during this earliest step of gastrulation in the chick embryo.     

The causes of variation in the presence of genetic covariance between sexual traits and preferences

Mating traits and mate preferences often show patterns of tight correspondence across populations and species. These patterns of apparent coevolution may result from a genetic association between traits and preferences (i.e. trait–preference genetic covariance). We review the literature on trait–preference covariance to determine its prevalence and potential biological relevance. Of the 43 studies we identified, a surprising 63% detected covariance. We test multiple hypotheses for factors that may influence the likelihood of detecting this covariance. The main predictor was the presence of genetic variation in mate preferences, which is one of the three main conditions required for the establishment of covariance. In fact, 89% of the nine studies where heritability of preference was high detected covariance. Variables pertaining to the experimental methods and type of traits involved in different studies did not greatly influence the detection of trait–preference covariance. Trait–preference genetic covariance appears to be widespread and therefore represents an important and currently underappreciated factor in the coevolution of traits and preferences.     

The design of complex sexual traits in male barn swallows: associations between signal attributes

Variation in the expression of sexually selected traits among individuals is widely investigated on the premise that these traits evolved to signal male quality. Significant repeatabilities of sexual signals and their associations with condition, mating success, survivorship and age may be the signatures of sexual selection. However, little is known about the relationship between these sexual attributes. Here we studied 28 acoustic and visual traits in the barn swallow, Hirundo rustica, that may potentially function in sexual selection. Based on effect sizes calculated at the between-individual level, we assessed the relationship between repeatability, condition-dependence, attractiveness, age-dependence and viability indicator value of sexual traits using sexual signals as the units of analyses. Those traits that showed high within-year repeatability also showed high between-year repeatability, indicating that between-individual variation is consistent within and among seasons. In addition, age-dependence of traits, probably causing between-year variation, was negatively related to between-year repeatability. Condition-dependence was negatively correlated with effect sizes for the extent to which traits predicted viability. Therefore, traits that are positively related to immediate condition are those that are negatively related to survival, which may be the signature of a trade-off between current and future reproductive success ultimately reflecting signal reliability. No other significant relationship was found between trait attributes. We conclude that multiple sexual signals reflect different aspects of male quality in the barn swallow.     

Developmental regulation of skull morphology II: ontogenetic dynamics of covariance

Canalization may play a critical role in molding patterns of integration when variability is regulated by the balance between processes that generate and remove variation. Under these conditions, the interaction among those processes may produce a dynamic structure of integration even when the level of variability is constant. To determine whether the constancy of variance in skull shape throughout most of postnatal growth results from a balance between processes generating and removing variation, we compare covariance structures from age to age in two rodent species, cotton rats (Sigmodon fulviventer) and house mice (Mus musculus domesticus). We assess the overall similarity of covariance matrices by the matrix correlation, and compare the structures of covariance matrices using common subspace analysis, a method related to common principal components (PCs) analysis but suited to cases in which variation is so nearly spherical that PCs are ambiguous. We find significant differences from age to age in covariance structure and the more effectively canalized ones tend to be least stable in covariance structure. We find no evidence that canalization gradually and preferentially removes deviations arising early in development as we might expect if canalization results from compensatory differential growth. Our results suggest that (co)variation patterns are continually restructured by processes that equilibrate variance, and thus that canalization plays a critical role in molding patterns of integration.     

Factors affecting the reproductive success of the crab spider Misumenoides formosipes: the covariance between juvenile and adult traits

Summary To examine the importance of covariance between stages in traits related to foraging, we quantified the relationships between reproductive success and sizerelated variability in weight gain in juvenile and adult instars of the crab spider Misumenoides formosipes (Araneae: Thomisidae). Prereproductive weight and fecundity are both highly correlated with carapace width, a linear measure of size which does not change within an instar. In field populations, adult females with larger carapaces gain more weight and are more likely to reproduce than females with smaller carapaces. The growth rate of spiders fed ad libitum in the laboratory is unrelated to size, suggesting that size-related differences in the field are due to variation in prey-capture success. Adult females with a carapace width less than 3.4 mm comprised 22% of the population, but were never found to reproduce. Of the individuals that did reproduce, a 17% increase in carapace width resulted in a 100% increase in fecundity. Juvenile stages must be examined to understand adult foraging and reproductive success, because the net weight gained by juvenile instars determines adult size. The final weight gained by spiders in the antepenultimate and penultimate instars explained nearly all the variation in carapace width in the penultimate and adult instars, respectively. We found that constraints on foraging in late juvenile stages are different from the adult stage. Penultimate foraging behavior differs from that of adults, because of constraints on foraging in the period preceding ecdysis. Additionally, in both late juvenile instars, carapace width had little or no effect on the final weight gained within the instar suggesting that factors that affect foraging are different between the juvenile and adult stages. These analyses stress the fact that to fully understand the effects of foraging on reproductive success, we must examine stage-specific constraints throughout an organism's life history.     

Rapid reversal of a potentially constraining genetic covariance between leaf and flower traits in Silene latifolia

Genetic covariance between two traits generates correlated responses to selection, and may either enhance or constrain adaptation. Silene latifolia exhibits potentially constraining genetic covariance between specific leaf area (SLA) and flower number in males. Flower number is likely to increase via fecundity selection but the correlated increase in SLA increases mortality, and SLA is under selection to decrease in dry habitats. We selected on trait combinations in two selection lines for four generations to test whether genetic covariance could be reduced without significantly altering trait means. In one selection line, the genetic covariance changed sign and eigenstructure changed significantly, while in the other selection line eigenstructure remained similar to the control line. Changes in genetic variance–covariance structure are therefore possible without the introduction of new alleles, and the responses we observed suggest that founder effects and changes in frequency of alleles of major effect may be acting to produce the changes.     

The use of genetic correlations to evaluate associations between SNP markers and quantitative traits

Open-pollinated progeny of Corymbia citriodora established in replicated field trials were assessed for stem diameter, wood density, and pulp yield prior to genotyping single nucleotide polymorphisms (SNP) and testing the significance of associations between markers and assessment traits. Multiple individuals within each family were genotyped and phenotyped, which facilitated a comparison of standard association testing methods and an alternative method developed to relate markers to additive genetic effects. Narrow-sense heritability estimates indicated there was significant additive genetic variance within this population for assessment traits ( $ {\widehat{h}^{{2}}} = 0.{28}\;{\text{to}}\;0.{44} $ ) and genetic correlations between the three traits were negligible to moderate (r _G?=?0.08 to 0.50). The significance of association tests (p values) were compared for four different analyses based on two different approaches: (1) two software packages were used to fit standard univariate mixed models that include SNP-fixed effects, (2) bivariate and multivariate mixed models including each SNP as an additional selection trait were used. Within either the univariate or multivariate approach, correlations between the tests of significance approached +1; however, correspondence between the two approaches was less strong, although between-approach correlations remained significantly positive. Similar SNP markers would be selected using multivariate analyses and standard marker-trait association methods, where the former facilitates integration into the existing genetic analysis systems of applied breeding programs and may be used with either single markers or indices of markers created with genomic selection processes.     

Food and fitness: associations between crop yields and life-history traits in a longitudinally monitored pre-industrial human population

Severe food shortage is associated with increased mortality and reduced reproductive success in contemporary and historical human populations. Studies of wild animal populations have shown that subtle variation in environmental conditions can influence patterns of mortality, fecundity and natural selection, but the fitness implications of such subtle variation on human populations are unclear. Here, we use longitudinal data on local grain production, births, marriages and mortality so as to assess the impact of crop yield variation on individual age-specific mortality and fecundity in two pre-industrial Finnish populations. Although crop yields and fitness traits showed profound year-to-year variation across the 70-year study period, associations between crop yields and mortality or fecundity were generally weak. However, post-reproductive individuals of both sexes, and individuals of lower socio-economic status experienced higher mortality when crop yields were low. This is the first longitudinal, individual-based study of the associations between environmental variation and fitness traits in pre-industrial humans, which emphasizes the importance of a portfolio of mechanisms for coping with low food availability in such populations. The results are consistent with evolutionary ecological predictions that natural selection for resilience to food shortage is likely to weaken with age and be most severe on those with the fewest resources.     

Apolipoprotein A-II: beyond genetic associations with lipid disorders and insulin resistance

PURPOSE OF REVIEW: Apolipoprotein A-II, the second major HDL apolipoprotein, was often considered of minor importance relatively to apolipoprotein A-I and its role was controversial. This picture is now rapidly changing, due to novel polymorphisms and mutations, to the outcome of clinical trials, and to studies with transgenic mice. RECENT FINDINGS: The -265 T/C polymorphism supports a role for apolipoprotein A-II in postprandial very-low-density lipoprotein metabolism. Fibrates, which increase apolipoprotein A-II synthesis, significantly decrease the incidence of major coronary artery disease events, particularly in subjects with low HDL cholesterol, high plasma triglyceride, and high body weight. The comparison of transgenic mice overexpressing human or murine apolipoprotein A-II has highlighted major structural differences between the two proteins; they have opposite effects on HDL size, apolipoprotein A-I content, plasma concentration, and protection from oxidation. Human apolipoprotein A-II is more hydrophobic, displaces apolipoprotein A-I from HDL, accelerates apolipoprotein A-I catabolism, and its plasma concentration is decreased by fasting. Apolipoprotein A-II stimulates ATP binding cassette transporter 1-mediated cholesterol efflux. Human and murine apolipoprotein A-II differently affect glucose metabolism and insulin resistance. A novel beneficial role for apolipoprotein A-II in the pathogenesis of hepatitis C virus has been shown. SUMMARY: The hydrophobicity of human apolipoprotein A-II is a key regulatory factor of HDL metabolism. Due to the lower plasma apolipoprotein A-II concentration during fasting, measurements of apolipoprotein A-II in fed subjects are more relevant. More clinical studies are necessary to clarify the role of apolipoprotein A-II in well-characterized subsets of patients and in the insulin resistance syndrome.     

A semiparametric test to detect associations between quantitative traits and candidate genes in structured populations

MOTIVATION: Although population-based association mapping may be subject to the bias caused by population stratification, alternative methods that are robust to population stratification such as family-based linkage analysis have lower mapping resolution. Recently, various statistical methods robust to population stratification were proposed for association studies, using unrelated individuals to identify associations between candidate genes and traits of interest. The association between a candidate gene and a quantitative trait is often evaluated via a regression model with inferred population structure variables as covariates, where the residual distribution is customarily assumed to be from a symmetric and unimodal parametric family, such as a Gaussian, although this may be inappropriate for the analysis of many real-life datasets. RESULTS: In this article, we proposed a new structured association (SA) test. Our method corrects for continuous population stratification by first deriving population structure and kinship matrices through a set of random genetic markers and then modeling the relationship between trait values, genotypic scores at a candidate marker and genetic background variables through a semiparametric model, where the error distribution is modeled as a mixture of Polya trees centered around a normal family of distributions. We compared our model to the existing SA tests in terms of model fit, type I error rate, power, precision and accuracy by application to a real dataset as well as simulated datasets.     

Developmental traits and life strategy of redlichiid trilobites

The developmental mode of four redlichiid trilobites is summarized, based upon exceptionally well-preserved, articulated specimens from Cambrian Series 2 (stages 3 and 4) strata in southwestern China and South Australia. These relatively complete developmental sequences indicate a balanced rate in segment increase and addition to the thorax during the meraspid phase, which might explain why most redlichiids possess micropygous body patterning during ontogeny. In addition, an analysis of the size distribution, developmental strategy, and distribution of specimen numbers at different growth stages reveals a distinct developmental strategy during the redlichiid life cycle. A relatively short pre-holaspid and a prolonged holaspid phase in these redlichiid taxa offers insight into the developmental control and life strategy in these primitive arthropods.