Interpreting Polygenic Score Effects in Sibling Analysis

Researchers often claim that sibling analysis can be used to separate causal genetic effects from the assortment of biases that contaminate most downstream genetic studies. Indeed, typical results from sibling models show large (>50%) attenuations in the associations between polygenic scores and phenotypes compared to non-sibling models, consistent with researchers' expectations about bias reduction. This paper explores these expectations by using family (quad) data and simulations that include indirect genetic effect processes and evaluates the ability of sibling models to uncover direct genetic effects. We find that sibling models, in general, fail to uncover direct genetic effects; indeed, these models have both upward and downward biases that are difficult to sign in typical data. When genetic nurture effects exist, sibling models create 'measurement error' that attenuate associations between polygenic scores and phenotypes. As the correlation between direct and indirect effect changes, this bias can increase or decrease. Our findings suggest that interpreting results from sibling analysis aimed at uncovering direct genetic effects should be treated with caution.

Sibling rivalry versus mother's curse: can kin competition facilitate a response to selection on male mitochondria?

Assuming that fathers never transmit mitochondrial DNA (mtDNA) to their offspring, mitochondrial mutations that affect male fitness are invisible to direct selection on males, leading to an accumulation of male-harming alleles in the mitochondrial genome (mother's curse). However, male phenotypes encoded by mtDNA can still undergo adaptation via kin selection provided that males interact with females carrying related mtDNA, such as their sisters. Here, using experiments with Drosophila melanogaster carrying standardized nuclear DNA but distinct mitochondrial DNA, we test whether the mitochondrial haplotype carried by interacting pairs of larvae affects survival to adulthood, as well as the fitness of the adults. Although mtDNA had no detectable direct or indirect genetic effect on larva-to-adult survival, the fitness of male and female adults was significantly affected by their own mtDNA and the mtDNA carried by their social partner in the larval stage. Thus, mtDNA mutations that alter the effect of male larvae on nearby female larvae (which often carry the same mutation, due to kinship) could theoretically respond to kin selection. We discuss the implications of our findings for the evolution of mitochondria and other maternally inherited endosymbionts.

The Price equation as a bridge between animal breeding and evolutionary biology

The genetic response to selection is central to both evolutionary biology and animal and plant breeding. While Price's theorem (PT) is well-known in evolutionary biology, most breeders are unaware of it. Rather than using PT, breeders express response to selection as the product of the intensity of selection ( i ), the accuracy of selection ( ρ ) and the additive genetic standard deviation ( σ A ); R = iρσ A . In contrast to the univariate ‘breeder's equation’, this expression holds for multivariate selection on Gaussian traits. Here, I relate R = iρσ A to PT, and present a generalized version, R = i w ρ A , w σ A , valid irrespective of the trait distribution. Next, I consider genotype–environment covariance in relation to the breeder's equation and PT, showing that the breeder's equation may remain valid depending on whether the genotype–environment covariance works across generations. Finally, I consider the response to selection in the prevalence of an endemic infectious disease, as an example of an emergent trait. The result shows that disease prevalence has much greater heritable variation than currently believed. The example also illustrates that the indirect genetic effect approach moves elements of response to selection from the second to the first term of PT, so that changes acting via the social environment come within the reach of quantitative genetics. This article is part of the theme issue ‘Fifty years of the Price equation’.

Individual selection leads to collective efficiency through coordination

Social interactions involving coordination between individuals are subject to an “evolutionary trap.” Once a suboptimal strategy has evolved, mutants playing an alternative strategy are counterselected because they fail to coordinate with the majority. This creates a detrimental situation from which evolution cannot escape, preventing the evolution of efficient collective behaviours. Here, we study this problem using the framework of evolutionary robotics. We first confirm the existence of an evolutionary trap in a simple setting. We then, however, reveal that evolution can solve this problem in a more realistic setting where individuals need to coordinate with one another. In this setting, robots evolve an ability to adapt plastically their behaviour to one another, as this improves the efficiency of their interaction. This ability has an unintended evolutionary consequence: a genetic mutation affecting one individual’s behaviour also indirectly alters their partner’s behaviour because the two individuals influence one another. As a consequence of this indirect genetic effect, pairs of partners can virtually change strategy together with a single mutation, and the evolutionary barrier between alternative strategies disappears. This finding reveals a general principle that could play a role in nature to smoothen the transition to efficient collective behaviours in all games with multiple equilibriums.

Heritable spouse effects increase evolutionary potential of human reproductive timing

Sexual reproduction is inherently interactive, especially in animal species such as humans that exhibit extended pair bonding. Yet we have little knowledge of the role of male characteristics and their evolutionary impact on reproductive behavioural phenotypes, to the extent that biologists typically consider component traits (e.g. reproductive timing) as female-specific. Based on extensive genealogical data detailing the life histories of 6435 human mothers born across four centuries of modern history, we use an animal modelling approach to estimate the indirect genetic effect of men on the reproductive phenotype of their partners. These analyses show that a woman's reproductive timing (age at first birth) is influenced by her partner's genotype. This indirect genetic effect is positively correlated with the direct genetic effect expressed in women, such that total heritable variance in this trait is doubled when heritable partner effects are considered. Our study thus suggests that much of the heritable variation in women's reproductive timing is mediated via partner effects, and that the evolutionary potential of this trait is far greater than previously appreciated.

Parasitoid wasps influence where aphids die via an interspecific indirect genetic effect

Host–parasite interactions are a key paradigm for understanding the process of coevolution. Central to coevolution is how genetic variation in interacting species allows parasites to evolve manipulative strategies. However, genetic variation in the parasite may also be associated with host phenotype changes, thereby changing the selection on both species. For instance, parasites often induce changes in the behaviour of their host to maximize their own fitness, yet the quantitative genetic basis for behavioural manipulation has not been fully demonstrated. Here, we show that the genotype of the parasitoid wasp Aphidius ervi has a significant effect on where its aphid host Acyrthosiphon pisum moves to die following parasitism, including the likelihood that the aphid abandons the plant. These results provide a clear example of an interspecific indirect genetic effect whereby the genetics of one species influences the expression of a specific behavioural trait in another.

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, r 2 =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.