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.

The role of selection and evolution in changing parturition date in a red deer population.

Changing environmental conditions cause changes in the distributions of phenotypic traits in natural populations. However, determining the mechanisms responsible for these changes-and, in particular, the relative contributions of phenotypic plasticity versus evolutionary responses-is difficult. To our knowledge, no study has yet reported evidence that evolutionary change underlies the most widely reported phenotypic response to climate change: the advancement of breeding times. In a wild population of red deer, average parturition date has advanced by nearly 2 weeks in 4 decades. Here, we quantify the contribution of plastic, demographic, and genetic components to this change. In particular, we quantify the role of direct phenotypic plasticity in response to increasing temperatures and the role of changes in the population structure. Importantly, we show that adaptive evolution likely played a role in the shift towards earlier parturition dates. The observed rate of evolution was consistent with a response to selection and was less likely to be due to genetic drift. Our study provides a rare example of observed rates of genetic change being consistent with theoretical predictions, although the consistency would not have been detected with a solely phenotypic analysis. It also provides, to our knowledge, the first evidence of both evolution and phenotypic plasticity contributing to advances in phenology in a changing climate.

Helminth parasites are associated with reduced survival probability in young red deer.

Helminths are common parasites of wild ungulates that can have substantial costs for growth, mortality and reproduction. Whilst these costs are relatively well documented for mature animals, knowledge of helminths' impacts on juveniles is more limited. Identifying these effects is important because young individuals are often heavily infected, and juvenile mortality is a key process regulating wild populations. Here, we investigated associations between helminth infection and overwinter survival in juvenile wild red deer (Cervus elaphus) on the Isle of Rum, Scotland. We collected fecal samples non-invasively from known individuals and used them to count propagules of 3 helminth taxa (strongyle nematodes, Fasciola hepatica and Elaphostrongylus cervi). Using generalized linear models, we investigated associations between parasite counts and overwinter survival for calves and yearlings. Strongyles were associated with reduced survival in both age classes, and F. hepatica was associated with reduced survival in yearlings, whilst E. cervi infection showed no association with survival in either age class. This study provides observational evidence for fitness costs of helminth infection in juveniles of a wild mammal, and suggests that these parasites could play a role in regulating population dynamics.

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.

Multiple spatial behaviours govern social network positions in a wild ungulate.

The structure of wild animal social systems depends on a complex combination of intrinsic and extrinsic drivers. Population structuring and spatial behaviour are key determinants of individuals' observed social behaviour, but quantifying these spatial components alongside multiple other drivers remains difficult due to data scarcity and analytical complexity. We used a 43-year dataset detailing a wild red deer population to investigate how individuals' spatial behaviours drive social network positioning, while simultaneously assessing other potential contributing factors. Using Integrated Nested Laplace Approximation (INLA) multi-matrix animal models, we demonstrate that social network positions are shaped by two-dimensional landscape locations, pairwise space sharing, individual range size, and spatial and temporal variation in population density, alongside smaller but detectable impacts of a selection of individual-level phenotypic traits. These results indicate strong, multifaceted spatiotemporal structuring in this society, emphasising the importance of considering multiple spatial components when investigating the causes and consequences of sociality.

Fitness Costs of Parasites Explain Multiple Life-History Trade-Offs in a Wild Mammal.

AbstractReproduction in wild animals can divert limited resources away from immune defense, resulting in increased parasite burdens. A long-standing prediction of life-history theory states that these parasites can harm the reproductive individual, reducing its subsequent survival and fecundity, producing reproduction-fitness trade-offs. Here, we examined associations among reproductive allocation, immunity, parasitism, and subsequent survival and fecundity in a wild population of individually identified red deer (Cervus elaphus). Using path analysis, we investigated whether costs of lactation in terms of 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 trade-offs, supporting the role of parasites as an important mediating factor in wild mammal populations.

Consistent within-individual plasticity is sufficient to explain temperature responses in red deer reproductive traits.

Warming global temperatures are affecting a range of aspects of wild populations, but the exact mechanisms driving associations between temperature and phenotypic traits may be difficult to identify. Here, we use a 36-year data set on a wild population of red deer to investigate the causes of associations between temperature and two important components of female reproduction: timing of breeding and offspring size. By separating within- versus between-individual associations with temperature for each trait, we show that within-individual phenotypic plasticity (changes within a female's lifetime) was entirely sufficient to generate the observed population-level association with temperature at key times of year. However, despite apparently adequate statistical power, we found no evidence of any variation between females in their responses (i.e. no "IxE" interactions). Our results suggest that female deer show plasticity in reproductive traits in response to temperatures in the year leading up to calving and that this response is consistent across individuals, implying no potential for either selection or heritability of plasticity. We estimate that the plastic response to rising temperatures explained 24% of the observed advance in mean calving date over the study period. We highlight the need for comparable analyses of other systems to determine the contribution of within-individual plasticity to population-level responses to climate change.

Declining home range area predicts reduced late-life survival in two wild ungulate populations.

Demographic senescence is increasingly recognised as an important force shaping the dynamics of wild vertebrate populations. However, our understanding of the processes that underpin these declines in survival and fertility in old age remains limited. Evidence for age-related changes in foraging behaviour and habitat use is emerging from wild vertebrate studies, but the extent to which these are driven by within-individual changes, and the consequences for fitness, remain unclear. Using longitudinal census observations collected over four decades from two long-term individual-based studies of unmanaged ungulates, we demonstrate consistent within-individual declines in home range area with age in adult females. In both systems, we found that within-individual decreases in home range area were associated with increased risk of mortality the following year. Our results provide the first evidence from the wild that age-related changes in space use are predictive of adult mortality.

Seasonality of helminth infection in wild red deer varies between individuals and between parasite taxa.

Parasitism in wild mammals can vary according to myriad intrinsic and extrinsic factors, many of which vary seasonally. However, seasonal variation in parasitism is rarely studied using repeated samples from known individuals. Here we used a wild population of individually recognized red deer (Cervus elaphus) on the Isle of Rum to quantify seasonality and intrinsic factors affecting gastrointestinal helminth parasitism over the course of a year. We collected 1020 non-invasive faecal samples from 328 known individuals which we then analysed for propagules of three helminth taxa: strongyle nematodes, the common liver fluke Fasciola hepatica and the tissue nematode Elaphostrongylus cervi. Zero-inflated Poisson models were used to investigate how season, age and sex were associated with parasite prevalence and count intensity, while Poisson models were used to quantify individual repeatability within and between sampling seasons. Parasite intensity and prevalence varied according to all investigated factors, with opposing seasonality, age profiles and sex biases between parasite taxa. Repeatability was moderate, decreased between seasons and varied between parasites; both F. hepatica and E. cervi showed significant between-season repeatability, while strongyle nematode counts were only repeatable within-season and showed no repeatability within individuals across the year.

Does Cuff Design Impact Insertion and Removal Force of Tracheostomy Tubes? A Bench Model.

INTRODUCTION: Percutaneous dilatational tracheostomy is a commonly performed procedure in intensive care units. Unrecognized tracheal ring fracture has been suggested as a possible factor for tracheal stenosis. The degree of tracheal compression relates to the amount of force required to cannulate the trachea. The objective of this study was to determine the force required to insert two types of tracheostomy tubes with different cuff designs. MATERIALS AND METHODS: This bench model measured the insertion and removal force of two tracheostomy tubes; one with a barrel-shaped, high-volume, low-pressure cuff (traditional Shiley tracheostomy tube) and another with a taper-shaped, low-volume, low-pressure cuff (Shiley flexible tracheostomy tube). Three sizes of tracheostomy tubes either with a barrel- or taper-shaped cuff were tested (Jackson sizes 4, 6, and 10, corresponding to 6.5-, 7.5-, and 10-mm ISO sizes, respectively). A model representing the tissue that the tube traverses to enter the tracheal lumen was designed, and the tracheostomy tube was mounted on a universal testing machine to measure the force necessary to insert and remove the tube. RESULTS: Across all tracheostomy tubes' sizes tested, significantly less force was required to insert the Shiley flexible tracheostomy tube compared to the traditional Shiley tracheostomy tube. Significantly less force was also required to remove the flexible tracheostomy tube compared to the traditional tracheostomy tube. CONCLUSIONS: This model suggests that less force is required to insert the Shiley flexible tracheostomy tube, which could result in less tracheal compression. This may be because of the smaller taper-shaped cuff that, when deflated, occupies less volume compared to the barrel-shaped cuff. As a result, less tracheal injury may occur when using the Shiley flexible tracheostomy tube during percutaneous tracheostomy procedures.

Cirrhosis and non-hepatic surgery in 2023 - a precision medicine approach.

INTRODUCTION: Patients with liver disease and portal hypertension frequently require surgery carrying high morbidity and mortality. Accurately estimating surgical risk remains challenging despite improved medical and surgical management. AREAS COVERED: This review aims to outline a comprehensive approach to preoperative assessment, appraise methods used to predict surgical risk, and provide an up-to-date overview of outcomes for patients with cirrhosis undergoing non-hepatic surgery. EXPERT OPINION: Robust preoperative, individually tailored, and precise risk assessment can reduce peri- and postoperative complications in patients with cirrhosis. Established prognostic scores aid stratification, providing an estimation of postoperative mortality, albeit with limitations. VOCAL-Penn Risk Score may provide greater precision than established liver severity scores. Amelioration of portal hypertension in advance of surgery may be considered, with prospective data demonstrating hepatic venous pressure gradient as a promising surrogate marker of postoperative outcomes. Morbidity and mortality vary between types of surgery with further studies required in patients with more advanced liver disease. Patient-specific considerations and practicing precision medicine may allow for improved postoperative outcomes.

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 role of platelet mediated thromboinflammation in acute liver injury.

Acute liver injuries have wide and varied etiologies and they occur both in patients with and without pre-existent chronic liver disease. Whilst the pathophysiological mechanisms remain distinct, both acute and acute-on-chronic liver injury is typified by deranged serum transaminase levels and if severe or persistent can result in liver failure manifest by a combination of jaundice, coagulopathy and encephalopathy. It is well established that platelets exhibit diverse functions as immune cells and are active participants in inflammation through processes including immunothrombosis or thromboinflammation. Growing evidence suggests platelets play a dualistic role in liver inflammation, shaping the immune response through direct interactions and release of soluble mediators modulating function of liver sinusoidal endothelial cells, stromal cells as well as migrating and tissue-resident leucocytes. Elucidating the pathways involved in initiation, propagation and resolution of the immune response are of interest to identify therapeutic targets. In this review the provocative role of platelets is outlined, highlighting beneficial and detrimental effects in a spatial, temporal and disease-specific manner.

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.

Ageing red deer alter their spatial behaviour and become less social.

Social relationships are important to many aspects of animals' lives, and an individual's connections may change over the course of their lifespan. Currently, it is unclear whether social connectedness declines within individuals as they age, and what the underlying mechanisms might be, so the role of age in structuring animal social systems remains unresolved, particularly in non-primates. Here we describe senescent declines in social connectedness using 46 years of data in a wild, individually monitored population of a long-lived mammal (European red deer, Cervus elaphus). Applying a series of spatial and social network analyses, we demonstrate that these declines occur because of within-individual changes in social behaviour, with correlated changes in spatial behaviour (smaller home ranges and movements to lower-density, lower-quality areas). These findings demonstrate that within-individual socio-spatial behavioural changes can lead older animals in fission-fusion societies to become less socially connected, shedding light on the ecological and evolutionary processes structuring wild animal populations.

Outcomes of incoming and outgoing second opinions from a UK liver transplant centre.

OBJECTIVE: Second transplant centre opinions (STCOs) for patients declined for liver transplantation are infrequent. We aimed to identify STCOs outcomes from a tertiary transplant centre. DESIGN: Referrals between 2012 and 2020 to Birmingham Unit were reviewed. Incoming: all referrals from out-of-region centres were collated. Outgoing: patients not listed in Birmingham were reviewed to identify referrals for STCOs to the other UK centres (A-F). RESULTS: 2535 patients were assessed for liver transplantation during the study period. Incoming: among 1751 referrals, 23 STCOs (17 unit A, 3 unit B, 1 unit C, 1 unit D and 1 unit E) were provided by Birmingham. Of the STCOs, 13/23 (57%) patients remained unsuitable for transplantation. Therefore, 10/23 (43%) underwent a second liver transplant assessment, of whom five (50%) were still deemed unsuitable, three (30%) listed (one transplanted) and two (20%) died preassessment. Outgoing: among 426 patients not listed, eight (1.8%) patients were referred for STCO (4 unit E, 2 unit B, 1 unit D, 1 unit A). Three (38%) were listed, two (25%) were assessed and declined, two (25%) were unsuitable for assessment and one (12.5%) died while waiting. Combining incoming and outgoing Birmingham STCOs (n=31), six (19%) of STCOs were listed in a second centre. CONCLUSION: Second transplant centre opinions are rare with the majority still deemed unsuitable for liver transplantation. This highlights potential resource implications especially when undergoing a full second formal assessment. A streamlined STCO process with sharing of investigations and use of telemedicine in appropriate patients may allow for greater transparency, quicker decision making and less use of labour-intensive resources.

Individual differences in reproductive costs examined using multi-state methods.

1. Trade-offs among life-history traits are common because individuals have to partition limited resources between multiple traits. Reproductive costs are generally assumed to be high, resulting in reduced survival and fecundity in the following year. However, it is common to find positive rather than negative correlations between life-history traits. 2. Here, we use a data set from the individual-based study of red deer on the Isle of Rum to examine how these costs vary between individuals and at different ages, using multi-state mark-recapture methodology. 3. Females that had reproduced frequently in the past incurred lower costs of reproduction in terms of survival in the following year and were more likely to reproduce in two consecutive years. Older individuals and those that had not reproduced frequently exhibited higher costs. 4. These results highlight the importance of considering heterogeneity and individual quality when examining trade-offs and demonstrate the effectiveness of using detailed long-term data sets to explore life-history strategies using multi-state mark-recapture models.

Exploring socio-demographic and geospatial variation in human papillomavirus vaccination uptake in Virginia.

Significant variation in human papillomavirus (HPV) vaccine coverage exists across the United States. A closer look at state and region-specific coverage is necessary to identify potentially modifiable disparities. Using ArcGIS software, we identify geospatial variation in HPV vaccine coverage in the state of Virginia and examine the relationship between various socio-demographic indicators and HPV vaccination uptake. HPV vaccination rates among adolescents 11 to 17 years as of 07/01/2018 were retrieved at the zip-code level from the Virginia Immunization Information System and chloropleth maps produced. The ArcGIS Hot Spot Analysis tool identified spatial clusters of zip codes with high and low vaccination rates. Population characteristics and socioeconomic indicators were retrieved from the 2010 United States Census and compared between statistically significant clusters of higher or lower than expected vaccination rates. Regions with significantly lower initiation rates were less populated, less educated, and had a lower median household income (MHI) with higher rates of poverty and unemployment. Among male adolescents, these areas had a significantly lower density of primary care providers and smaller African American and Hispanic populations. In contrast, regions with significantly lower series completion were more populated and had a higher MHI, but there was no difference in provider density or minority population. Ultimately, regional socioeconomic indicators are significant predictors of HPV vaccination, but have contrasting implications for series initiation and completion. Targeted interventions and safety net programs have traditionally focused on the socioeconomically disadvantaged, however it is the more affluent communities that may be struggling with series completion.

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 ( hMg2 = 0.31) and birth leg length ( hMg2 = 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.