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

Maternal effects, either environmental or genetic in origin, are an underappreciated source of phenotypic variance in natural populations. Maternal genetic effects have the potential to constrain or enhance the evolution of offspring traits depending on their magnitude and their genetic correlation with direct genetic effects. We estimated the maternal effect variance and its genetic component for 12 traits expressed over the life history in a pedigreed population of wild red deer (morphology, survival/longevity, breeding success). We only found support for maternal genetic effect variance in the two neonatal morphological traits: birth weight (urn:x-wiley:00143820:media:evo14000:evo14000-math-0001 = 0.31) and birth leg length (urn:x-wiley:00143820:media:evo14000:evo14000-math-0002 = 0.17). For these two traits, the genetic correlation between maternal and direct additive effects was not significantly different from zero, indicating no constraint to evolution from genetic architecture. In contrast, variance in maternal genetic effects enhanced the additive genetic variance available to respond to natural selection. Maternal effect variance was negligible for late‐life traits. We found no evidence for sex differences in either the direct or maternal genetic architecture of offspring traits. Our results suggest that maternal genetic effect variance declines over the lifetime, but also that this additional heritable genetic variation may facilitate evolutionary responses of early‐life traits.The long-term project and this research were funded by the UK Natural Environment Research Council, and most of the SNP genotyping was supported by a European Research Council Advanced Grant to JMP

Inbreeding depression in red deer calves

BACKGROUND Understanding the fitness consequences of inbreeding is of major importance for evolutionary and conservation biology. However, there are few studies using pedigree-based estimates of inbreeding or investigating the influence of environment and age variation on inbreeding depression in natural populations. Here we investigated the consequences of variation in inbreeding coefficient for three juvenile traits, birth date, birth weight and first year survival, in a wild population of red deer, considering both calf and mother's inbreeding coefficient. We also tested whether inbreeding depression varied with environmental conditions and maternal age. RESULTS We detected non-zero inbreeding coefficients for 22% of individuals with both parents and at least one grandparent known (increasing to 42% if the dataset was restricted to those with four known grandparents). Inbreeding depression was evident for birth weight and first year survival but not for birth date: the first year survival of offspring with an inbreeding coefficient of 0.25 was reduced by 77% compared to offspring with an inbreeding coefficient of zero. However, it was independent of measures of environmental variation and maternal age. The effect of inbreeding on birth weight appeared to be driven by highly inbred individuals (F = 0.25). On the other hand first year survival showed strong inbreeding depression that was not solely driven by individuals with the highest inbreeding coefficients, corresponding to an estimate of 4.35 lethal equivalents. CONCLUSIONS These results represent a rare demonstration of inbreeding depression using pedigree-based estimates in a wild mammal population and highlight the potential strength of effects on key components of fitness.This research was supported by a NERC grant to LEBK, JMP and THCB, NERC and BBSRC fellowships to DHN and a Royal Society fellowship to LEBK

Rage against the regime: niche-regime interactions in the societal embedding of plant-based milk

This paper engages with the debate on niche-regime interactions in sustainability transitions, using a study of plant-based milk and its struggles against the entrenched liquid dairy-milk regime, which has various sustainability problems. Plant-based milk is under-studied, so our empirical contribution consists of an exploration of its diffusion in the UK. We make three conceptual contributions. The first calls for a bidirectional analysis that addresses niche-oriented activities by incumbent actors, in addition to the outward-oriented activities by niche advocates presented in most studies of niche-regime interaction. The second contribution nuances Smith and Raven’s fit-and-conform and stretch-and-transform typology: using a societal embedding framework which distinguishes four environments, we suggest that hybrid patterns are possible in which innovations follow a ‘fit’ pattern in one environment but ‘stretch’ in another. The third contribution highlights the potential role of cultural meanings in galvanizing transitions by eroding positive associations that support the regime and stabilise consumer purchasing

Fitness costs of parasites explain multiple life history tradeoffs in a wild mammal

Reproduction in wild animals can divert limited resources away from immune defence, resulting in increased parasite burdens. A longstanding prediction of life history theory states that these parasites can harm the individual, reducing the organism's subsequent fitness and producing reproduction-fitness tradeoffs. Here, we examined associations among reproductive allocation, immunity, parasitism, and subsequent fitness in a wild population of individually identified red deer ( Cervus elaphus ). Using path analysis, we investigated whether costs of lactation for downstream survival and fecundity were mediated by changes in strongyle nematode count and mucosal antibody levels. Lactating females exhibited increased parasite counts, which were in turn associated with substantially decreased fitness in the following year in terms of overwinter survival, fecundity, subsequent calf weight, and parturition date. This study offers observational evidence for parasite regulation of multiple life history tradeoffs, supporting the role of parasites as an important mediating factor in wild mammal populations.The anonymised data files are present in the `DataList.rds` object; the scripts will run the path analysis and generate the figures, using these datasets. Funding provided by: Natural Environment Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000270Award Number: NE/L00688X/1Funding provided by: Natural Environment Research CouncilCrossref Funder Registry ID: http://dx.doi.org/10.13039/501100000270Award Number: NE/L002558/1Noninvasive faecal collection from the Isle of Rum red dee

Utilisation of amber suppression/non-natural amino acid technology for protein engineering and cellular control

The amber suppression technology is an intracellular methodology that allows position specific incorporation of a specific non-natural amino acid (NAA) into proteins using imported NAA-specific machinery during protein translation. The method has been utilised to incorporate over 50 NAAs into proteins (e.g. those that confer unique reactivity (and allow subsequent conjugation of additional factors), installation of post-translational modification mimics, modulation of protein function and those that aid in structural determination). Therefore, the aim of the work presented within this Thesis was to explore the use of this technology in novel applications; namely the installation and study of a reactive moiety within a defined environment and the creation of a ‘biological switch’ to control the production of the protein and subsequently a cellular phenotype. It was demonstrated that incorporation of the NAA, azidophenylalanine, within the hydrophobic pocket of T4 Lysozyme (T4LazF) could provide a protein scaffold to stabilise, shield and thereby allow exploration of the chemical reactivity of the photoreactive aryl azide moiety using various spectroscopic techniques. Specifically, electron paramagnetic spectroscopy of irradiated T4LazF demonstrated that the singlet phenyl nitrene species had been captured. To create a ‘biological switch’ to control the production of a protein and the subsequent cellular phenotype, the duality of the amber suppression method was the basis for the novel application rather than the chemical reactivity of the NAA. E. coli and mammalian cell motility readout systems were successfully created using flagellin (non-flagellate) and Rac1 (GTPase protein involved in lamellipodia production) knockout cell lines respectively in conjunction with specially created plasmid constructs. However, complexities regarding the implementation of amber suppression in order to control this motility via the presence/absence of NAA limited the functionality of these readout systems. The work presented has advanced the field of amber suppression and NAA technology by demonstrating that generating reactive intermediates derived from NAAs within a defined chemical environment of a protein provides a novel technique to generate and study highly reactive intermediates. In addition, it has been shown that the amber suppression technology has potential to act as a biological switch to control cellular responses

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