The genetic architecture of maternal effects across ontogeny in the red deer

Genetic architecture of inbreeding depression may explain its persistence in a population of wild red deer

Inbreeding depression is of major concern in declining populations, but relatively little is known about its genetic architecture in wild populations, such as the degree to which it is composed of large or small effect loci and their distribution throughout the genome. Here, we combine fitness and genomic data from a wild population of red deer to investigate the genomic distribution of inbreeding effects. Based on the runs of homozygosity (ROH)-based inbreeding coefficient, FROH, we use chromosome-specific inbreeding coefficients (FROHChr) to explore whether the effect of inbreeding varies between chromosomes. Under the assumption that within an individual the probability of being identical-by-descent is equal across all chromosomes, we used a multi-membership model to estimate the deviation of FROHChr from the average inbreeding effect. This novel approach ensures effect sizes are not overestimated whilst maximising the power of our available dataset of >3000 individuals genotyped on >35,000 autosomal SNPs. We find that most chromosomes confer a minor reduction in fitness-related traits, which when these effects are summed, results in the observed inbreeding depression in birth weight, survival and lifetime breeding success. However, no chromosomes had a significant detrimental effect compared to the overall effect of inbreeding, indicating no major effect loci. We conclude that in this population, inbreeding depression is likely the result of multiple mildly or moderately deleterious mutations spread across all chromosomes, which are difficult to detect with statistical confidence. Such mutations will be inefficiently purged, which may explain the persistence of inbreeding depression in this population.

Rapid decline of prenatal maternal effects with age is independent of postnatal environment in a precocial bird

Maternal effects are an important source of phenotypic variation with potentially large fitness consequences, but how their importance varies with the quality of the environment across an individual's ontogeny is poorly understood. We bred Japanese quail (Coturnix japonica) of known pedigree and experimentally manipulated the quality of the offspring diet, to estimate the importance of prenatal maternal effects in shaping variation in body mass from hatching to adulthood. Maternal genetic effects on body mass at hatching were strong, and largely caused by variation in egg mass, but their importance rapidly declined with age. Whereas there was a large effect of diet on growth, this did not affect the decline of maternal effects variance. The importance of additive genetic and residual variance increased with age, with the latter being considerably larger in the poor diet treatment. Hence, we found no evidence for prenatal maternal effect by postnatal environment interactions and that prenatal maternal effects are rapidly replaced by direct additive genetic and residual effects when offspring start to develop outside the egg. Thereby these results shed new light on the dynamics of the role of maternal versus offspring genes across ontogeny and environments.

Early-life behavior, survival, and maternal personality in a wild marsupial

Individual behavior varies for many reasons, but how early in life are such differences apparent, and are they under selection? We investigated variation in early-life behavior in a wild eastern gray kangaroo (Macropus giganteus) population, and quantified associations of behavior with early survival. Behavior of young was measured while still in the pouch and as subadults, and survival to weaning was monitored. We found consistent variation between offspring of different mothers in levels of activity at the pouch stage, in flight initiation distance (FID) as subadults, and in subadult survival, indicating similarity between siblings. There was no evidence of covariance between the measures of behavior at the pouch young versus subadult stages, nor of covariance of the early-life behavioral traits with subadult survival. However, there was a strong covariance between FIDs of mothers and those of their offspring tested at different times. Further, of the total repeatability of subadult FID (51.5%), more than half could be attributed to differences between offspring of different mothers. Our results indicate that 1) behavioral variation is apparent at a very early stage of development (still in the pouch in the case of this marsupial); 2) between-mother differences can explain much of the repeatability (or "personality") of juvenile behavior; and 3) mothers and offspring exhibit similar behavioral responses to stimuli. However, 4) we found no evidence of selection via covariance between early-life or maternal behavioral traits and juvenile survival in this wild marsupial.

Sex-specific trait architecture in a spider with sexual size dimorphism

Sexual dimorphism, or sex-specific trait expression, may evolve when selection favours different optima for the same trait between sexes, that is, under antagonistic selection. Intra-locus sexual conflict exists when the sexually dimorphic trait under antagonistic selection is based on genes shared between sexes. A common assumption is that the presence of sexual-size dimorphism (SSD) indicates that sexual conflict has been, at least partly, resolved via decoupling of the trait architecture between sexes. However, whether and how decoupling of the trait architecture between sexes has been realized often remains unknown. We tested for differences in architecture of adult body size between sexes in a species with extreme SSD, the African hermit spider (Nephilingis cruentata), where adult female body size greatly exceeds that of males. Specifically, we estimated the sex-specific importance of genetic and maternal effects on adult body size among individuals that we laboratory-reared for up to eight generations. Quantitative genetic model estimates indicated that size variation in females is to a larger extent explained by direct genetic effects than by maternal effects, but in males to a larger extent by maternal than by genetic effects. We conclude that this sex-specific body-size architecture enables body-size evolution to proceed much more independently than under a common architecture to both sexes.

Genetic variance and indirect genetic effects for affiliative social behavior in a wild primate

Affiliative social behaviors are linked to fitness components in multiple species. However, the role of genetic variance in shaping such behaviors remains largely unknown, limiting our understanding of how affiliative behaviors can respond to natural selection. Here, we employed the "animal model" to estimate environmental and genetic sources of variance and covariance in grooming behavior in the well-studied Amboseli wild baboon population. We found that the tendency for a female baboon to groom others ("grooming given") is heritable (h2 = 0.22 ± 0.048), and that several environmental variables-including dominance rank and the availability of kin as grooming partners-contribute to variance in this grooming behavior. We also detected small but measurable variance due to the indirect genetic effect of partner identity on the amount of grooming given within dyadic grooming partnerships. The indirect and direct genetic effects for grooming given were positively correlated (r = 0.74 ± 0.09). Our results provide insight into the evolvability of affiliative behavior in wild animals, including the possibility for correlations between direct and indirect genetic effects to accelerate the response to selection. As such they provide novel information about the genetic architecture of social behavior in nature, with important implications for the evolution of cooperation and reciprocity.

A polygenic basis for birth weight in a wild population of red deer (Cervus elaphus)

The genetic architecture of traits under selection has important consequences for the response to selection and potentially for population viability. Early QTL mapping studies in wild populations have reported loci with large effect on trait variation. However, these results are contradicted by more recent genome-wide association analyses, which strongly support the idea that most quantitative traits have a polygenic basis. This study aims to re-evaluate the genetic architecture of a key morphological trait, birth weight, in a wild population of red deer (Cervus elaphus), using genomic approaches. A previous study using 93 microsatellite and allozyme markers and linkage mapping on a kindred of 364 deer detected a pronounced QTL on chromosome 21 explaining 29% of the variance in birth weight, suggesting that this trait is partly controlled by genes with large effects. Here, we used data for more than 2,300 calves genotyped at >39,000 SNP markers and two approaches to characterise the genetic architecture of birth weight. First, we performed a genome-wide association (GWA) analysis, using a genomic relatedness matrix to account for population structure. We found no SNPs significantly associated with birth weight. Second, we used genomic prediction to estimate the proportion of variance explained by each SNP and chromosome. This analysis confirmed that most genetic variance in birth weight was explained by loci with very small effect sizes. Third, we found that the proportion of variance explained by each chromosome was slightly positively correlated with its size. These three findings highlight a highly polygenic architecture for birth weight, which contradicts the previous QTL study. These results are probably explained by the differences in how associations are modelled between QTL mapping and GWA. Our study suggests that models of polygenic adaptation are the most appropriate to study the evolutionary trajectory of this trait.

The Unusual Value of Long-Term Studies of Individuals: The Example of the Isle of Rum Red Deer Project

Long-term studies of individuals enable incisive investigations of questions across ecology and evolution. Here, we illustrate this claim by reference to our long-term study of red deer on the Isle of Rum, Scotland. This project has established many of the characteristics of social organization, selection, and population ecology typical of large, polygynous, seasonally breeding mammals, with wider implications for our understanding of sexual selection and the evolution of sex differences, as well as for their population dynamics and population management. As molecular genetic techniques have developed, the project has pivoted to investigate evolutionary genetic questions, also breaking new ground in this field. With ongoing advances in genomics and statistical approaches and the development of increasingly sophisticated ways to assay new phenotypic traits, the questions that long-term studies such as the red deer study can answer become both broader and ever more sophisticated. They also offer powerful means of understanding the effects of ongoing climate change on wild populations.

Maternal effects do not resolve the paradox of stasis in birth weight in a wild red deer populaton

In natural populations, quantitative traits seldom show short-term evolution at the rate predicted by evolutionary models. Resolving this "paradox of stasis" is a key goal in evolutionary biology, as it directly challenges our capacity to predict evolutionary change. One particularly promising hypothesis to explain the lack of evolutionary responses in a key offspring trait, body weight, is that positive selection on juveniles is counterbalanced by selection against maternal investment in offspring growth, given that reproduction is costly for the mothers. Here, we used data from one of the longest individual-based studies of a wild mammal population to test this hypothesis. We first showed that despite positive directional selection on birth weight, and heritable variation for this trait, no genetic change has been observed for birth weight over the past 47 years in the study population. Contrarily to our expectation, we found no evidence of selection against maternal investment in birth weight-if anything, selection favors mothers that produce large calves. Accordingly, we show that genetic change in birth weight over the study period is actually lower than that predicted from models including selection on maternal performance; ultimately our analysis here only deepens rather than resolves the paradox of stasis.

Age-dependent genetic architecture across ontogeny of body size in sticklebacks

Heritable variation in traits under natural selection is a prerequisite for evolutionary response. While it is recognized that trait heritability may vary spatially and temporally depending on which environmental conditions traits are expressed under, less is known about the possibility that genetic variance contributing to the expected selection response in a given trait may vary at different stages of ontogeny. Specifically, whether different loci underlie the expression of a trait throughout development and thus providing an additional source of variation for selection to act on in the wild, is unclear. Here we show that body size, an important life-history trait, is heritable throughout ontogeny in the nine-spined stickleback (Pungitius pungitius). Nevertheless, both analyses of quantitative trait loci and genetic correlations across ages show that different chromosomes/loci contribute to this heritability in different ontogenic time-points. This suggests that body size can respond to selection at different stages of ontogeny but that this response is determined by different loci at different points of development. Hence, our study provides important results regarding our understanding of the genetics of ontogeny and opens an interesting avenue of research for studying age-specific genetic architecture as a source of non-parallel evolution.

The role of maternally transferred antibodies in maternal performance in red deer

Maternal effects are ubiquitous. Yet, the pathways through which maternal effects occur in wild mammals remain largely unknown. We hypothesise that maternal immune transfer is a key mechanism by which mothers can affect their offspring fitness, and that individual variation in maternally derived antibodies mainly depends on a mother's characteristics and the environmental conditions she experiences. To test this, we assayed six colostrum-derived antibodies in the plasma of 1447 neonates in a wild red deer population. Neonatal antibody levels were mainly affected by maternal genes, environmental variation and costs of prior reproductive investment. We found consistent heterogeneity in maternal performance across traits, with mothers producing the heaviest calves also having calves with more antibodies. Unexpectedly, antibody levels were not associated with calf survival. We provide a unique example of how evolutionary theory on maternal effects can be used to gain insight into the causes of maternal effects in wild populations.