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Results for “indirect genetic effects”

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At least 19 recordsLinked to original sources

PubMed2002

The genetics of maternal care: direct and indirect genetic effects on phenotype in the dung beetle Onthophagus taurus.

While theoretical models of the evolution of parental care are based on the assumption of underlying genetic variance, surprisingly few quantitative genetic studies of this life-history trait exist. Estimation of the degree of genetic variance in parental care is important because it can be a significant source of maternal effects, which, if genetically based, represent indirect genetic effects. A major prediction of indirect genetic effect theory is that traits without heritable variation can evolve because of the heritable environmental variation that indirect genetic effects provide. In the dung beetle, Onthophagus taurus, females provide care to offspring by provisioning a brood mass. The size of the brood mass has pronounced effects on offspring phenotype. Using a half-sib breeding design we show that the weight of the brood mass females produce exhibits significant levels of additive genetic variance due to sires. However, variance caused by dams is considerably larger, demonstrating that maternal effects are also important. Body size exhibited low additive genetic variance. However, body size exerts a strong maternal influence on the weight of brood masses produced, accounting for 22% of the nongenetic variance in offspring body size. Maternal body size also influenced the number of offspring produced but there was no genetic variance for this trait. Offspring body size and brood mass weight exhibited positive genetic and phenotypic correlations. We conclude that both indirect genetic effects, via maternal care, and nongenetic maternal effects, via female size, play important roles in the evolution of phenotype in this species.

Analysis of Variance↗

PubMed2007

Paternal indirect genetic effects on offspring viability and the benefits of polyandry.

Although females are expected to maximize their reproductive success with only one or a few matings, the females of many species mate with multiple partners. Experimental studies have found evidence for an increase in egg or embryo viability when females mate polyandrously. These studies have been interpreted in the context of genetic-benefit models that propose that multiple mating increases offspring viability because it allows females to select male genotypes that influence viability directly or because it allows females to avoid genetic incompatibility. However, no studies have examined directly the precise mechanisms by which parents influence embryo viability. Using a morphological marker that enabled us to determine paternity and survival of embryos sired by individual male crickets in both sperm-competitive and -noncompetitive situations, we show that males inducing high embryo viability enhance the viability of embryos sired by inferior males. These results indicate that paternal effects and interacting phenotypes determine embryo viability. They show that a male's reproductive success is modified by the interaction between indirect genetic effects of sperm competitors. Importantly, our findings show that the benefits accruing to offspring of multiply mated females need not be transmitted genetically.

Animals↗

PubMed2006

Community heritability measures the evolutionary consequences of indirect genetic effects on community structure.

The evolutionary analysis of community organization is considered a major frontier in biology. Nevertheless, current explanations for community structure exclude the effects of genes and selection at levels above the individual. Here, we demonstrate a genetic basis for community structure, arising from the fitness consequences of genetic interactions among species (i.e., interspecific indirect genetic effects or IIGEs). Using simulated and natural communities of arthropods inhabiting North American cottonwoods (Populus), we show that when species comprising ecological communities are summarized using a multivariate statistical method, nonmetric multidimensional scaling (NMDS), the resulting univariate scores can be analyzed using standard techniques for estimating the heritability of quantitative traits. Our estimates of the broad-sense heritability of arthropod communities on known genotypes of cottonwood trees in common gardens explained 56-63% of the total variation in community phenotype. To justify and help interpret our empirical approach, we modeled synthetic communities in which the number, intensity, and fitness consequences of the genetic interactions among species comprising the community were explicitly known. Results from the model suggest that our empirical estimates of broad-sense community heritability arise from heritable variation in a host tree trait and the fitness consequences of IGEs that extend from tree trait to arthropods. When arthropod traits are heritable, interspecific IGEs cause species interactions to change, and community evolution occurs. Our results have implications for establishing the genetic foundations of communities and ecosystems.

Animals↗

PubMed2005

The evolutionary origin and elaboration of sociality in the aculeate Hymenoptera: maternal effects, sib-social effects, and heterochrony.

We discuss the evolutionary origin and elaboration of sociality using an indirect genetic effects perspective. Indirect genetic effects models simultaneously consider zygotic genes, genes expressed in social partners (especially mothers and siblings), and the interactions between them. Incorporation of these diverse genetic effects should lead to more realistic models of social evolution. We first review haplodiploidy as a factor that promotes the evolution of eusociality. Social insect biologists have doubted the importance of relatedness asymmetry caused by haplodiploidy and focused on other predisposing factors such as maternal care. However; indirect effects theory shows that maternal care evolves more readily in haplodiploids, especially with inbreeding and despite multiple mating. Because extended maternal care is believed to be a precondition for the evolution of eusociality, the evolutionary bias towards maternal care in haplodiploids may result in a further bias towards eusociality in these groups. Next, we compare kin selection and parental manipulation and then briefly review additional hypotheses for the evolutionary origin of eusociality. We present a verbal model for the evolutionary origin and elaboration of sib-social care from maternal care based on the modification of the timing of expression of maternal care behaviors. Specifically, heterochrony genes cause maternal care behaviors to be expressed prereproductively towards siblings instead of postreproductively towards offspring. Our review demonstrates that both maternal effect genes (expressed in a parental manipulation manner) and direct effect zygotic genes (expressed in an offspring control manner) are likely involved in the evolution of eusociality. We conclude by describing theoretical and empirical advances with indirect genetic effects and sociogenomics, and we provide specific quantitative genetic and genomic predictions from our heterochrony model for the evolutionary origin and elaboration of eusociality.

Animals↗

PubMed1985

Genetics of mandible form in the mouse.

The underlying determination of phenotypic variability and covariability is described for 14 traits that define the morphological size and shape of the mature mouse mandible. Variability is partitioned into components due to direct additive and dominance genetic effects, indirect maternal additive genetic effects, genetic covariance between direct additive and indirect maternal additive effects and common and residual environmental effects. Multivariate analyses of the dimensionality of genetic variability indicate several complex and independent genetic components underlie the morphological form of the mandible. The multidimensional nature of the genetic components suggests a complex picture with regard to the consequences of selection on mandibular form.

Analysis of Variance↗

PubMed2025

Measurement and classification of bold-shy behaviours in medaka fish.

MOTIVATION: Boldness-shyness is considered a fundamental axis of behavioural variation in humans and other species, with obvious adaptive causes and evolutionary implications. Besides an individual's own genetics, this phenotype is also affected by the genetic make-up of peers in the individual's social environment. To identify genetic determinants of variation along the bold-shy behavioural axis, a reliable experimental and analytical set-up able to highlight direct and indirect genetic effects is needed. RESULTS: We describe a custom assay designed to detect bold-shy behaviours in medaka fish, combining an open-field and novel-object component. We use this assay to explore direct and social genetic effects on the behaviours of 307 pairs of fish from five inbred medaka strains. Applying a hidden Markov model (HMM) to classify behavioural modes, we find that direct genetic effects influence the proportions of time the five strains spent in slow-moving states, explaining up to 29.7% of the variance in time spent in those states. We also found that an individual's behaviour is influenced by the genetics of its tank partner, explaining up to 8.64% of the variance in the time spent in slow-moving states. Our behavioural assay in combination with the HMM analysis is applicable to follow-up genetic linkage studies of genetic variants involved in direct behavioural effects and indirect social genetic effects. A suitable genetic resource for such studies, the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel has recently been established. AVAILABILITY AND IMPLEMENTATION: The code associated with this work is available on GitHub (https://github.com/birneylab/medaka_behaviour_pilot) and Software Heritage (swh: 1: dir: c9abec1c5d62d22e43c9e97d995c56261784d9ab). Experimental data have been uploaded to the EBI Bioimage Archive (https://doi.org/10.6019/S-BIAD1421).

Animals↗

PubMed2005

Correlated evolution of maternally derived yolk testosterone and early developmental traits in passerine birds.

Recent studies on hormone-mediated maternal effects in birds have highlighted the influence of variable maternal yolk androgen concentration on offspring phenotype, particularly in terms of early development. If genetic differences between laying females regulate variation in yolk hormone concentration, then this physiological maternal effect is an indirect genetic effect which can provide a basis for the co-evolution of maternal and offspring phenotypes. Thus, we investigated the evolutionary associations between maternally derived yolk testosterone (T) and early developmental traits in passerine birds via a comparative, phylogenetic analysis. Our results from species-correlation and independent contrasts analyses provide convergent evidence for the correlated evolution of maternal yolk T concentration and length of the prenatal developmental period in passerines. Here, we show these traits are significantly negatively associated (species-correlation: p<0.001, r2=0.85; independent contrasts: p=0.005). Our results highlight the need for more studies investigating the role of yolk hormones in evolutionary processes concerning maternal effects.

Animals↗

PubMed2002

Quantitative genetics of growth and development time in the burying beetle Nicrophorus pustulatus in the presence and absence of post-hatching parental care.

Despite a growing interest in the evolutionary aspects of maternal effects, few studies have examined the genetic consequences of maternal effects associated with parental care. To begin to provide data on nonlaboratory or nondomestic animals, we compared the effect of presence and absence of parental care on phenotype expression of larval mass and development time at different life-history stages in the burying beetle Nicrophorus pustulatus. This beetle has facultative care; parents can feed their larvae through regurgitation of digested carrion or offspring can feed by themselves from previously prepared carrion. To investigate larval responses to these two levels of care, including estimates of additive genetic effects, maternal effects, and genotype-by-environment interactions, we used a half-sibling split-family breeding experiment-raising half of the offspring of a family in the presence of their mother and the other half without their mother present. Larvae reared with their mother present were on average heavier and developed faster, although some of the differences in development decreased or were eliminated by the adult stage. These results suggest that presence or absence of post-hatching maternal care plays an important role in phenotype expression early in life, whereas later the phenotype of the offspring is determined mainly by the genotype and/or unshared environmental effects. Our study also permitted us to examine the differences in genetic effects between the two care environments. Heritabilities, maternal/common environment effect, and most genetic correlations did not differ between the care treatments. Genetic analyses revealed substantial additive genetic effects for development time but small effects for measures of body mass. Maternal plus common environment effects were high for measures of mass but low for development time, suggesting that indirect genetic effects of maternal and/or common environment are less important for the evolution of development time than for mass. Estimates of genetic correlations revealed a trade-off between the duration of the two development stages after the offspring left the carrion. There was also a negative genetic correlation between the time spent on carrion and the mass at 72 h, when mothers usually stop feeding. The analysis of genotype-by-environment interactions indicates substantial variation among maternal families in response to care. Presence or absence of parental care may therefore contribute to the additive genetic variance through its interaction with the maternal component of the additive genetic variance. The presence of this interaction further suggests that parents may vary in care strategies, with some parents dispersing after preparation of the carrion and some parents staying with the larvae. This interaction may help maintain genetic variation in growth, development time, and parental care behavior. Additional work is needed, however, to quantify indirect genetic effects and genetic variation in parental care behavior itself.

Animals↗

PubMed2025

Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats.

The intestinal microbiome influences health and disease. Its composition is affected by host genetics and environmental exposures. Understanding host genetic effects is critical but challenging in humans, due to the difficulty of detecting, mapping and interpreting them. To address this, we analysed host genetic effects in four cohorts of outbred laboratory rats exposed to distinct but controlled environments. We found that polygenic host genetic effects were consistent across environments. We identified three replicated microbiome-associated loci, one of which involved a sialyltransferase gene and Paraprevotella. We found a similar association in a human cohort, between ST6GAL1 and Paraprevotella, both of which have been linked with immune and infectious diseases. Moreover, we found evidence of indirect genetic effects on microbiome phenotypes, which substantially increased their total genetic variance. Finally, we identified a novel mechanism whereby indirect genetic effects can contribute to "missing heritability".

Journal Article↗

PubMed2000

Maternal and paternal effects on offspring phenotype in the dung beetle Onthophagus taurus.

Parents often have important influences on the development of traits in their offspring. One mechanism by which parents are able to influence offspring phenotype is through the level of care they provide. In onthophagine dung beetles, parents typically provision their offspring by packing dung fragments into a brood mass. Onthophagus taurus males can be separated into two discrete morphs: Large, "major" males have head horns, whereas "minor" males are hornless. Here we show that a switch in parental provisioning strategies adopted by males coincides with the switch in male morphology. Male provisioning results in the production of heavier brood masses than females will produce alone. However, unlike females in which the level of provisioning increases with body size in a continuous manner, the level of provisioning provided by males represents an "all-or-none" tactic with all major males providing a fixed level of provisioning irrespective of their body size. Offspring size is determined largely by the quantity of dung provided to the developing larvae so that paternal and maternal provisioning affects the body size and horn size of offspring produced. The levels of provisioning by individual parents are significantly repeatable, suggesting paternal and maternal effects as candidate indirect genetic effects in the evolution of horn size in the genus Onthophagus.

Animals↗

PubMed2004

Mapping quantitative trait Loci interactions from the maternal and offspring genomes.

The expression of most developmental or behavioral traits involves complex interactions between quantitative trait loci (QTL) from the maternal and offspring genomes. The maternal-offspring interactions play a pivotal role in shaping the direction and rate of evolution in terms of their substantial contribution to quantitative genetic (co)variation. To study the genetics and evolution of maternal-offspring interactions, a unifying statistical framework that embraces both the direct and indirect genetic effects of maternal and offspring QTL on any complex trait is developed. This model is derived for a simple backcross design within the maximum-likelihood context, implemented with the EM algorithm. Results from extensive simulations suggest that this model can provide reasonable estimation of additive and dominant effects of the QTL at different generations and their interaction effects derived from the maternal and offspring genomes. Although our model is framed to characterize the actions and interactions of maternal and offspring QTL affecting offspring traits, the idea can be readily extended to decipher the genetic machinery of maternal traits, such as maternal care. Our model provides a powerful means for studying the evolutionary significance of indirect genetic effects in any sexually reproductive organisms.

Animals↗

PubMed2005

Genetic variance in female condition predicts indirect genetic variance in male sexual display traits.

During sexual encounters, individuals often use signals, such as display traits, to attract mates. If individuals alter their display traits with respect to the genotype of potential mates, indirect genetic effects (IGEs) may occur in which the genes of one individual influence the phenotype of another. Although IGEs between related individuals have received much attention, their occurrence between unrelated individuals during sexual encounters has not. Here, we demonstrate that in the Australian fruit fly Drosophila serrata, males assess females by using both visual and olfactory cues, resulting in a rapid plastic response (within minutes) in male cuticular hydrocarbons (CHCs), a display trait that is an important target of mate choice. Several CHCs in males exhibited significant IGEs, and IGEs were inducible on both males reared in the laboratory and on field-caught individuals. A vector describing genetic variance in multiple CHCs in females was found to be almost identical to a vector describing indirect genetic variance in male CHCs, suggesting that males might assess female CHCs during courtship. This vector displayed contributions from all female CHCs in the same direction and of similar magnitude, suggesting that female condition may be the underlying casual trait that males are assessing. Consistent with this interpretation, when measured directly in a separate experiment, genetic variance in female condition accounted for 19.8% of the indirect genetic variance in male CHCs. These indirect genetic effects have the potential to alter the response to selection of male sexual display traits.

Animals↗

PubMed2025

Separating direct, indirect and parent-of-origin genetic effects in the human population.

Here, we present a novel approach to estimate the degree to which the phenotypic effect of a DNA locus is attributable to four components: alleles in the child (direct genetic effects), alleles in the mother and the father (indirect genetic effects), or is dependent upon the parent from which it is inherited (parent-of-origin, PofO effects). Applying our model, JODIE, to 30,000 child-mother-father trios with phased DNA information from the Estonian Biobank (EstBB) and the Norwegian Mother, Father, Child Cohort (MoBa), we jointly estimate the phenotypic variance attributable to these four effects unbiased of assortative mating (AM) for height, body mass index (BMI) and childhood educational test score (EA). For all three traits, direct effects make the largest contribution to the genetic effect variance. But we find that parental indirect genetic effects make an equivalent combined contribution, and that there is a non-zero PofO effect variance for all traits. We calculate the heritability that would be obtained at the population-level in the absence of AM for common DNA loci, and show that the proportional contribution of direct effects to these heritability values can be calculated as 64.0% for EA in MoBa, 77.1% and 63.4% for height in MoBa and EstBB, and 81.2% and 88.0% for BMI in MoBa and EstBB. Additionally, using within-family genome-wide association testing, we identify 276 independently associated DNA regions that replicate across two additional biobanks, which all show a genotype-phenotype relationship that reflects an interplay of direct, indirect and PofO effects. Determining how direct, parental and PofO genetic effects combine across loci genome-wide to influence human phenotypic variation requires joint modeling of parental and child genotypes alongside the parental origin of loci and here, we make the first attempt to do this in the human population.

EstBB↗

PubMed1977

Estimates of genetic parameters of body weight in descendants of X-irradiated rat spermatogonia.

Effects of nine generations of 450r per generation of ancestral spermatogonial X irradiation of inbred rats on genetic parameters of body weight at 3, 6, and 10 weeks of age and of weight gains between these periods were studied. Covariances among relatives were estimated by mixed model and regression techniques in randomly selected lines with (R) and without (C) radiation history. Analyses of the data were based on five linear genetic models combining additive direct, additive indirect (maternal), dominance and environmental effects. Parameters in these models were estimated by generalized least-squares. A model including direct and indirect genetic effects fit more closely to the data in both R and C lines. Overdominance of induced mutations did not seem to be present. Ancestral irradiation increased maternal additive genetic variances of body weights and gains but not direct genetic variances. Theoretically, due to a negative direct-maternal genetic correlation, within full-sib family selection would be ineffective in increasing body weight at six weeks in both R and C lines. However, progress from mass selection would be expected to be faster in the R lines.

Aging↗

PubMed2025

No More Free Lunch: Challenges to Mendelian Randomization Due to Sample Selection and Complex Methods.

Mendelian randomization (MR) is increasingly used in epidemiological studies to investigate causal relationships. MR depends on 3 fundamental instrumental variable assumptions: relevance, independence, and exclusion restriction. Studies often assume that MR mitigates bias from confounding due to the random allocation of genetic variants at conception. In this perspective, using causal directed acyclic graphs, we discuss several scenarios where biases in MR analyses may arise due to the nature of the data or methods being used. These include (1) collider bias due to the nonrandom selection of participants into study populations used for conducting genome-wide association studies (GWAS), (2) indirect genetic effects arising from population-based GWAS rather than within-family studies, and (3) collider bias due to gene-environment interaction effects on the exposure in nonlinear MR analyses. We provide practical considerations for examining and reducing these biases in MR analyses.

Humans↗

PubMed2001

Theoretical perspectives on language and communication problems in mental retardation and developmental disabilities.

We argue that researchers interested in language and communication problems in mental retardation or any other developmental disorder should view such problems as emerging within the broader context of the behavioral profile, or phenotype, associated with a particular genetic condition. This will require understanding the direct and indirect effects of genes on the development of language and communication and thereby an understanding of the complex relations that exist between language and other dimensions of psychological and behavioral functioning as well as an understanding of the environments in which the developing person acts and is acted upon. We believe that the dominant model for understanding language and communication problems--the nativist approach, which emphasizes the child's innate capacity for acquiring language and characterizes language as consisting of a set of context-free deterministic rules that operate on abstract representations--is inconsistent with an emphasis on indirect genetic effects. We review recent evidence that undermines the nativist approach--evidence concerning the initial state of the language-learning child, the role of environmental input, the competence-performance distinction, and modularity. In place of nativism, we argue for Emergentism, which is a model in which language is seen to emerge from the interaction between the child's biological abilities to map statistical properties of the language input into a distributed representation and the characteristics of the language learning environment and for the purpose of engaging in real-time, meaningful language use.

Child↗

PubMed1997

Apoptosis, haemopoiesis and leukaemogenesis.

Apoptosis, or physiological cell death, is the way in which unwanted cells are removed. The majority of cells formed during haemopoiesis are destined to die by apoptosis before they are fully differentiated, and homeostasis of cell number is maintained by a balance between mitosis and apoptosis. Many haematological malignancies are associated with changes in the number of cells undergoing apoptosis, which may be a direct or an indirect effect. Genetic mutations that prevent cell death cause cells to accumulate and can eventually lead to malignancy. Alternatively, oncogenic mutations that lead to increased cell production can indirectly cause a decrease in apoptosis in some populations and an increase in others. Chemotherapeutic drugs may kill cells directly, or indirectly by inducing apoptosis as a stress response. Therapeutic strategies are evolving to increase the propensity of malignant cells to die by either means and to mitigate side effects by reducing apoptosis in non-malignant cells.

Animals↗

PubMed2005

The evolution of polyandry: intrinsic sire effects contribute to embryo viability.

Females typically mate with more than one male despite the costs incurred, thus questioning Bateman's principle. A series of genetic benefits have been proposed to account for the evolution of polyandry, including the acquisition of viability genes for offspring. The 'intrinsic male quality' hypothesis suggests that polyandry increases the probability that females produce offspring sired by males that bestow high viability on their offspring. Heritable variation in viability is the basic requirement for the occurrence of this genetic benefit. By using a half-sib breeding design with a species of cricket in which polyandry is known to increase hatching success, we present clear experimental evidence that intrinsic male quality contributes to embryo viability. Despite recent support for the evolution of polyandry based on compatibility of genotypes between males and females, we show that hatching success is not determined by an interaction between paternal and maternal genotypes but rather that sons inherit paternal genes that influence the viability of eggs laid by their mates. Moreover, our data implicate a potential role for indirect genetic effects of male accessory gland products on embryo viability. Additive genetic contributions to embryo viability may be an important factor underlying the frequently observed benefits of polyandrous behaviour.

Analysis of Variance↗