Phenotypic and Evolutionary Consequences of Social Behaviours: Interactions among Individuals Affect Direct Genetic Effects

Traditional quantitative genetics assumes that an individual''s phenotype is determined by both genetic and environmental factors. For many animals, part of the environment is social and provided by parents and other interacting partners. When expression of genes in social partners affects trait expression in a focal individual, indirect genetic effects occur. In this study, we explore the effects of indirect genetic effects on the magnitude and range of phenotypic values in a focal individual in a multi-member model analyzing three possible classes of interactions between individuals. We show that social interactions may not only cause indirect genetic effects but can also modify direct genetic effects. Furthermore, we demonstrate that both direct and indirect genetic effects substantially alter the range of phenotypic values, particularly when a focal trait can influence its own expression via interactions with traits in other individuals. We derive a function predicting the relative importance of direct versus indirect genetic effects. Our model reveals that both direct and indirect genetic effects can depend to a large extent on both group size and interaction strength, altering group mean phenotype and variance. This may lead to scenarios where between group variation is much higher than within group variation despite similar underlying genetic properties, potentially affecting the level of selection. Our analysis highlights key properties of indirect genetic effects with important consequences for trait evolution, the level of selection and potentially speciation.     

Phenotypic Consequences of Aneuploidy in Arabidopsis thaliana

Aneuploid cells are characterized by incomplete chromosome sets. The resulting imbalance in gene dosage has phenotypic consequences that are specific to each karyotype. Even in the case of Down syndrome, the most viable and studied form of human aneuploidy, the mechanisms underlying the connected phenotypes remain mostly unclear. Because of their tolerance to aneuploidy, plants provide a powerful system for a genome-wide investigation of aneuploid syndromes, an approach that is not feasible in animal systems. Indeed, in many plant species, populations of aneuploid individuals can be easily obtained from triploid individuals. We phenotyped a population of Arabidopsis thaliana aneuploid individuals containing 25 different karyotypes. Even in this highly heterogeneous population, we demonstrate that certain traits are strongly associated with the dosage of specific chromosome types and that chromosomal effects can be additive. Further, we identified subtle developmental phenotypes expressed in the diploid progeny of aneuploid parent(s) but not in euploid controls from diploid lineages. These results indicate long-term phenotypic consequences of aneuploidy that can persist after chromosomal balance has been restored. We verified the diploid nature of these individuals by whole-genome sequencing and discuss the possibility that trans-generational phenotypic effects stem from epigenetic modifications passed from aneuploid parents to their diploid progeny.THE genome of aneuploid individuals contains incomplete chromosome sets. The balance between chromosome types, and the genes they encode, is compromised, resulting in altered expression of many genes, including genes with dosage-sensitive effects on phenotypes. In humans, only a few types of aneuploid karyotypes are viable (Hassold and Hunt 2001), highlighting the deleterious effect of chromosome imbalance. The most commonly known viable form of aneuploidy in humans is Down syndrome, which results from a trisomy of chromosome 21 in an otherwise diploid background. Down syndrome patients exhibit many specific phenotypes, sometimes visible only in a subset of patients (Antonarakis et al. 2004). For phenotypes found in all Down syndrome patients, the penetrance of each phenotype varies between patients (Antonarakis et al. 2004). Despite the increasing amount of information available about the human genome and the availability of a mouse model for Down syndrome (O''Doherty et al. 2005), the genes responsible for most of the phenotypes associated with Down syndrome are still unknown (Patterson 2007; Korbel et al. 2009; Patterson 2009). Recently, detailed phenotypic analyses of as many as 30 aneuploid patients have allowed the identification of susceptibility regions for several specific phenotypes (Patterson 2007, 2009; Korbel et al. 2009; Lyle et al. 2009), but the specific genes remain to be identified. Understanding the physiology of aneuploidy is not only relevant to those individuals with aneuploid genomes but also to understanding cancer since most cancerous cells are aneuploid (Matzke et al. 2003; Pihan and Doxsey 2003; Storchova and Pellman 2004; Holland and Cleveland 2009; Williams and Amon 2009) or the consequences of copy number variation and dosage sensitivity (Dear 2009; Henrichsen et al. 2009).Plants are more tolerant of aneuploidy than animals (Matzke et al. 2003) for reasons that remain unclear. Since the discovery of the Datura trisomic “chromosome mutants” by Blakeslee (1921, 1922), viable trisomics of each chromosome type have been described in numerous species. Trisomics exhibit phenotypes specific to the identity of the triplicated chromosome (Blakeslee 1922; Khush 1973; Koornneef and Van der Veen 1983; Singh 2003). More complex aneuploids, i.e., individuals carrying more than one additional chromosome, can be viable as well and have been observed in many plants species, especially among the progeny of triploid individuals (McClintock 1929; Levan 1942; Johnsson 1945; Khush 1973). Some species appear to be more tolerant of complex aneuploidies than others, suggesting a genetic basis for aneuploidy tolerance (Satina and Blakeslee 1938; Khush 1973; Ramsey and Schemske 2002; Henry et al. 2009). Aneuploid individuals frequently appear spontaneously within polyploid plant populations, presumably due to a failure to equally partition the multiple chromosome sets at meiosis (Randolph 1935; Doyle 1986). These aneuploids exhibit few or subtle phenotypic abnormalities and can often compete with their euploid progenitors (Ramsey and Schemske 1998). Plants therefore provide an excellent opportunity for a genome-wide investigation of aneuploid syndromes: sample size is not limited, phenotypes can be described and assessed in detail, and plant aneuploid populations provide a complex mixture of viable karyotypes.In this article, we report our investigation of the relationship between phenotype and karyotype in populations of aneuploid Arabidopsis thaliana plants. All simple trisomics of A. thaliana have been previously isolated and phenotypically characterized (Steinitz-Sears 1962; Lee-Chen and Steinitz-Sears 1967; Steinitz-Sears and Lee-Chen 1970; Koornneef and Van der Veen 1983), demonstrating that they are tolerated in A. thaliana. We previously reported that aneuploid swarms—populations of aneuploid individuals of varying aneuploid karyotypes—could be obtained from the progeny of triploid A. thaliana individuals (Henry et al. 2005, 2009). Using a combination of a quantitative PCR-based method and flow cytometry, we were able to derive the full aneuploid karyotype of each of these individuals (Henry et al. 2006). We further crossed triploid A. thaliana to diploid or tetraploid individuals and demonstrated that at least 44 of the 60 possible aneuploid karyotypes that could result from these crosses (aneuploid individuals carrying between 11 and 19 chromosomes) were viable and successfully produced adult plants. Taken together, these populations and methods make it possible to explore the basis of aneuploid syndromes in A. thaliana. In this study, we were able to phenotypically characterize at least one individual from 25 different aneuploid karyotypes falling between diploidy and tetraploidy. We demonstrated that specific phenotypes are affected by the dosage of specific chromosome types. The effect of the dosage of specific chromosome types on traits was additive and could be used to predict the observed phenotype. The availability of multiple generations of aneuploid and euploid individuals allowed us to investigate potential long-term effects of aneuploidy as well as parent-of-origin effects on aneuploid phenotypes.     

Functional Consequences of Oxidative Membrane Damage

The interaction of reactive oxygen species with biological membranes is known to produce a great variety of different functional modifications. Part of these modifications may be classified as direct effects. They are due to direct interaction of the reactive species with the molecular machinery under study with a subsequent chemical and functional modification of these molecules. An important part of the observed functional modifications are, however, indirect effects. They are the consequence of an oxidative modification of the environment of biological macromolecules. Lipid peroxidation—via its generation of chemically reactive products—contributes to the loss of cellular functions through the inactivation of membrane enzymes and even of cytoplasmic (i.e., water soluble) proteins. Oxidation of membrane lipids may, however, also increase the efficiency of membrane functions. This was observed for a series of transport systems. Lipid peroxidation was accompanied by activation of certain types of ion channels and ion carriers. The effect is due to an increase of the polarity of the membrane interior by accumulation of polar oxidation products. The concomitant change of the dielectric constant, which may be detected via the increase of the membrane capacitance, facilitates the opening of membrane channels and lowers the inner membrane barrier for the movement of ions across the membrane. The predominant effect, however, at least at a greater extent of lipid peroxidation, is the inhibition of membrane functions. The strong increase of the leak conductance contributes to the depolarization of the membrane potential, it destroys the barrier properties of the membrane and it may finally lead, via an increase of cytoplasmic Ca²⁺ concentration, to cell death. The conclusions were derived from experiments performed with different systems: model systems in planar lipid membranes, native ion channels either reconstituted in lipid membranes or investigated in their natural environment by the patch-clamp method, and two important ion pumps, the Na/K-ATPase and the sarcoplasmic reticulum (SR) Ca-ATPase.     

Causes and Consequences of the DNA Damage Response

A prerequisite for maintaining genome stability in all cell types is the accurate repair and efficient signaling of DNA double strand breaks (DSBs). It is believed that DSBs are initially detected by damage sensors that trigger the activation of transducing kinases. These transducers amplify the damage signal, which is then relayed to effector proteins, which regulate the progression of the cell cycle, DNA repair and apoptosis. Errors in the execution of the repair and/or signaling of DSBs can give rise to multi-systemic disorders characterized by tissue degeneration, infertility, immune system dysfunction, age-related pathologies and cancer. This special Spotlight issue of Cell Cycle highlights recent advances in our understanding of the biology and significance of the DNA damage response. A range of issues are addressed including mechanistic ones: what is the aberrant DNA structure that triggers the activation of the checkpoint - how does chromatin structure influence the recruitment of repair and checkpoint proteins- how does chromosomal instability contribute to the evolution of cancer. In addition, questions related to the physiology of the DNA damage response in normal and abnormal cells is explored: what is the in vivo consequence of altering specific amino acids in a DNA damage sensor- does DNA damage accumulation in stem cells cause aging- how is neurodegeneration linked to deficiencies in specific DNA repair pathways, and finally, what is the biological basis for selection of aberrant DNA damage responses in cancer cells?     

Meta一种群结构及其遗传后果

Ｍｅｔａｐｏｐｕｌａｔｉｏｎ最初是由Ｌｅｖｉｎｓ[1 ] 提出 ,用于表示种群的种群 ,他的这个概念得到广泛接受。由于该词的多义以及在植物种群生态学中也用于表示构件种群 ,因此国内对该词的译法差别较大 ,叶万辉等人对此作了探讨[2 ] 。为防止概念的混淆 ,笔者在本文中采用ｍｅｔａ 种群。Ｍｅｔａ 种群概念被广泛接受的原因之一是它将景观生态学中时空尺度的观点应用于经典种群生态学 ,使其从局域扩展到一定的区域 ,因而更适合于物种的保护和管理 ,徐宏发等人[3] 对此也作了比较详细的论述。ｍｅｔａ 种群结构不仅在种群数量方面 ,对经…     

Destabilizing Protein Polymorphisms in the Genetic Background Direct Phenotypic Expression of Mutant SOD1 Toxicity

Genetic background exerts a strong modulatory effect on the toxicity of aggregation-prone proteins in conformational diseases. In addition to influencing the misfolding and aggregation behavior of the mutant proteins, polymorphisms in putative modifier genes may affect the molecular processes leading to the disease phenotype. Mutations in SOD1 in a subset of familial amyotrophic lateral sclerosis (ALS) cases confer dominant but clinically variable toxicity, thought to be mediated by misfolding and aggregation of mutant SOD1 protein. While the mechanism of toxicity remains unknown, both the nature of the SOD1 mutation and the genetic background in which it is expressed appear important. To address this, we established a Caenorhabditis elegans model to systematically examine the aggregation behavior and genetic interactions of mutant forms of SOD1. Expression of three structurally distinct SOD1 mutants in C. elegans muscle cells resulted in the appearance of heterogeneous populations of aggregates and was associated with only mild cellular dysfunction. However, introduction of destabilizing temperature-sensitive mutations into the genetic background strongly enhanced the toxicity of SOD1 mutants, resulting in exposure of several deleterious phenotypes at permissive conditions in a manner dependent on the specific SOD1 mutation. The nature of the observed phenotype was dependent on the temperature-sensitive mutation present, while its penetrance reflected the specific combination of temperature-sensitive and SOD1 mutations. Thus, the specific toxic phenotypes of conformational disease may not be simply due to misfolding/aggregation toxicity of the causative mutant proteins, but may be defined by their genetic interactions with cellular pathways harboring mildly destabilizing missense alleles.     

Natural and Genetic Engineering of the Heat-Shock Protein Hsp70 in Drosophila melanogaster: Consequences for Thermotolerance

SYNOPSIS. Larvae of the fruit fly, Drosophila melanogaster,live within necrotic fruit, a challenging environment in whichlarvae can experience severe thermal stress. One response tothermal stress, the expression of heat-shock proteins (Hsps),has evolved distinctively in this species; the gene encodingHsp70 has undergone extensive duplication and accounts for thebulk of Hsps that are expressed upon heat shock. Genetic engineeringof hsp70 copy number is sufficient to affect thermotoleranceat some (but not all) life stages. Increases in Hsp70, moreover,can protect intact larvae against thermal inactivation of theenzyme alcohol dehydrogenase and thermal inhibition of feeding.Deleterious consequences of high levels of Hsp70, however, maylimit further evolutionary proliferation of hsp70 genes. Thesefindings illustrate how the perspectives of integrative andcomparative biology, if applied to even well-studied model organisms,can lead to novel findings.     

Vocal Dialect Recognition and Population Genetic Consequences

SYNOPSIS. On the basis of male territorial song, a system ofdiscrete dialects is described in a population of White-crownedSparrows in central, coastal California. Four of these dialectsare genetically differentiated from one another. Inbreedingcoefficients calculated from electrophoretic alleles indicatethat individuals in a dialect are inbred due to isolation ofthe dialect not because of inbreeding with close relatives.Males react more aggressively to male song from an adjacentdialect than to song from another member of their own dialectbut react only weakly to song from a distant dialect. This indicatesthat male-male interactions may have a role in maintaining dialectpopulations. Females of the Mountain White-crowned Sparrow havebeen tested in dialect experiments in the laboratory and foundto respond with precopulatory sexual posturing almost exclusivelyto song from the home dialect in comparison to song from analien dialect. This indicates that female choice of mate mayalso play a role in maintaining dialect populations.     

水蚤滞育的数量遗传学研究:遗传与环境控制及遗传作用

在单性生殖循环水蚤群体中,滞育卵由有性生殖产生．在一系列实验中用到了不同种群和种类的水蚤,通过这些实验来观察：1)有性生殖和滞育卵复苏的遗传和环境控制;2)生活在相同区域中,但有不同生存微环境的近缘种类的有性生殖的光周期反应;3)在群体遗传结构上有性生殖的遗传效应(基因型均值和生活史性状遗传方差)．结果发现：1)遗传作用和环境作用,以及两者的相互作用都对有性生殖和滞育卵的孵化有显著的影响．GE显著的相互作用对环境中观察到的有性生殖来说,有助于维持其较高的遗传方差;2)在相同区域中,不同生存微环境的近缘种类的有性生殖的光周期反应有所不同．这有助于进一步区别近缘的水蚤种类,这也可能是一个水环境中同素异形的物种形成的例子;3)在有性生殖上,生活史性状平均值和遗传方差变化与前代选择造成的均值和遗传方差相反(遗传滑阻),这会造成暂时的适应不良(遗传滑阻和隐藏的遗传变异的表达),应对它补偿滞育的进化优势．     

湖羊出生类型与产活羔数表型及遗传参数估计

收集了26只湖羊种公羊115个女儿共计458窝产羔记录。统计分析表明,湖羊母羊胎产活羔数为1－5羔的比例分别为21．18％、49．78％、25．76％、3．06％和0．22％;公羊对母羊出生类型和产活羔数具有显著影响,胎次对母羊出生类型和产活羔数没有显著影响;母羊出生类型对其产活羔数没有显著影响;湖羊母羊出生类型与产活羔数的遗传力分别为0．251和0．097,它们之间的遗传、表型和环境相关分别为0．241、0．008和0．181,它们之间的协遗传力为0．038。这些参数表明：母羊出生类型与产活羔数是遗传联系不紧密的两个不同性状;根据母羊出生类型来早期选择产活羔数是无效的。     

Genetic and Phenotypic Characterization of Roller Mutants of CAENORHABDITIS ELEGANS

Eighty-eight mutants of C. elegans that display a roller phenotype (a helically twisted body) have been isolated and characterized genetically and phenotypically. The mutations are located in 14 different genes. Most genes contain a number of alleles. Their distribution among the chromosomes appears nonrandom, with seven of the genes being located on linkage group II, some very closely linked. The phenotypes of the mutants suggest that there are five different classes of genes, each class representing a set of similar phenotypic effects: Left Roller (four genes), Right Roller (one gene), Left Squat (one gene), Right Squat (two genes) and Left Dumpy Roller (six genes). The classes of mutants differ with respect to a number of characteristics that include the developmental stages affected and the types of aberrations observed in cuticle structure. A variety of gene interactions were found, arguing that these genes are involved in a common developmental process. The presence of alterations in cuticle morphology strongly suggests that these genes are active in the formation of the nematode cuticle.     

Improving Phenotypic Prediction by Combining Genetic and Epigenetic Associations

We tested whether DNA-methylation profiles account for inter-individual variation in body mass index (BMI) and height and whether they predict these phenotypes over and above genetic factors. Genetic predictors were derived from published summary results from the largest genome-wide association studies on BMI (n ∼ 350,000) and height (n ∼ 250,000) to date. We derived methylation predictors by estimating probe-trait effects in discovery samples and tested them in external samples. Methylation profiles associated with BMI in older individuals from the Lothian Birth Cohorts (LBCs, n = 1,366) explained 4.9% of the variation in BMI in Dutch adults from the LifeLines DEEP study (n = 750) but did not account for any BMI variation in adolescents from the Brisbane Systems Genetic Study (BSGS, n = 403). Methylation profiles based on the Dutch sample explained 4.9% and 3.6% of the variation in BMI in the LBCs and BSGS, respectively. Methylation profiles predicted BMI independently of genetic profiles in an additive manner: 7%, 8%, and 14% of variance of BMI in the LBCs were explained by the methylation predictor, the genetic predictor, and a model containing both, respectively. The corresponding percentages for LifeLines DEEP were 5%, 9%, and 13%, respectively, suggesting that the methylation profiles represent environmental effects. The differential effects of the BMI methylation profiles by age support previous observations of age modulation of genetic contributions. In contrast, methylation profiles accounted for almost no variation in height, consistent with a mainly genetic contribution to inter-individual variation. The BMI results suggest that combining genetic and epigenetic information might have greater utility for complex-trait prediction.