Expanding the application of haplotype-based genomic predictions to the wild: A case of antibody response against Teladorsagia circumcincta in Soay sheep.

BACKGROUND: Genomic prediction of breeding values (GP) has been adopted in evolutionary genomic studies to uncover microevolutionary processes of wild populations or improve captive breeding strategies. While recent evolutionary studies applied GP with individual single nucleotide polymorphism (SNP), haplotype-based GP could outperform individual SNP predictions through better capturing the linkage disequilibrium (LD) between the SNP and quantitative trait loci (QTL). This study aimed to evaluate the accuracy and bias of haplotype-based GP of immunoglobulin (Ig) A (IgA), IgE, and IgG against Teladorsagia circumcincta in lambs of an unmanaged sheep population (Soay breed) based on Genomic Best Linear Unbiased Prediction (GBLUP) and five Bayesian [BayesA, BayesB, BayesCπ, Bayesian Lasso (BayesL), and BayesR] methods. RESULTS: The accuracy and bias of GPs using SNP, haplotypic pseudo-SNP from blocks with different LD thresholds (0.15, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9, and 1.00), or the combinations of pseudo-SNPs and non-LD clustered SNPs were obtained. Across methods and marker sets, higher ranges of genomic estimated breeding values (GEBV) accuracies were observed for IgA (0.20 to 0.49), followed by IgE (0.08 to 0.20) and IgG (0.05 to 0.14). Considering the methods evaluated, up to 8% gains in GP accuracy of IgG were achieved using pseudo-SNPs compared to SNPs. Up to 3% gain in GP accuracy for IgA was also obtained using the combinations of the pseudo-SNPs with non-clustered SNPs in comparison to fitting individual SNP. No improvement in GP accuracy of IgE was observed using haplotypic pseudo-SNPs or their combination with non-clustered SNPs compared to individual SNP. Bayesian methods outperformed GBLUP for all traits. Most scenarios yielded lower accuracies for all traits with an increased LD threshold. GP models using haplotypic pseudo-SNPs predicted less-biased GEBVs mainly for IgG. For this trait, lower bias was observed with higher LD thresholds, whereas no distinct trend was observed for other traits with changes in LD. CONCLUSIONS: Haplotype information improves GP performance of anti-helminthic antibody traits of IgA and IgG compared to fitting individual SNP. The observed gains in the predictive performances indicate that haplotype-based methods could benefit GP of some traits in wild animal populations.

Age-specific impacts of vegetation functional traits on gastrointestinal nematode parasite burdens in a large herbivore.

Gastrointestinal nematode (GIN) parasites play an important role in the ecological dynamics of many animal populations. Recent studies suggest that fine-scale spatial variation in GIN infection dynamics is important in wildlife systems, but the environmental drivers underlying this variation remain poorly understood. We used data from over two decades of GIN parasite egg counts, host space use, and spatial vegetation data from a long-term study of Soay sheep on St Kilda to test how spatial autocorrelation and vegetation in an individual's home range predict parasite burden across three age groups. We developed a novel approach to quantify the plant functional traits present in a home range to describe the quality of vegetation present. Effects of vegetation and space varied between age classes. In immature lambs, strongyle parasite faecal egg counts (FEC) were spatially structured, being highest in the north and south of our study area. Independent of host body weight and spatial autocorrelation, plant functional traits predicted parasite egg counts. Higher egg counts were associated with more digestible and preferred plant functional traits, suggesting the association could be driven by host density and habitat preference. In contrast, we found no evidence that parasite FEC were related to plant functional traits in the host home range in yearlings or adult sheep. Adult FEC were spatially structured, with highest burdens in the north-east of our study area, while yearling FEC showed no evidence of spatial structuring. Parasite burdens in immature individuals appear more readily influenced by fine-scale spatial variation in the environment, highlighting the importance of such heterogeneity for our understanding of wildlife epidemiology and health. Our findings support the importance of fine-scale environmental variation for wildlife disease ecology and provides new evidence that such effects may vary across demographic groups within a population.

Trait-dependent associations between early- and late-life reproduction in a wild mammal.

Early- versus late-life trade-offs are a central prediction of life-history theory that are expected to shape the evolution of ageing. While ageing is widely observed in wild vertebrates, evidence that early-late trade-offs influence ageing rates remains limited. Vertebrate reproduction is a complex, multi-stage process, yet few studies have examined how different aspects of early-life reproductive allocation shape late-life performance and ageing. Here, we use longitudinal data from a 36-year study of wild Soay sheep to show that early-life reproduction predicts late-life reproductive performance in a trait-dependent manner. Females that started breeding earlier showed more rapid declines in annual breeding probability with age, consistent with a trade-off. However, age-related declines in offspring first-year survival and birth weight were not associated with early-life reproduction. Selective disappearance was evident in all three late-life reproductive measures, with longer-lived females having higher average performance. Our results provide mixed support for early-late reproductive trade-offs and show that the way early-life reproduction shapes late-life performance and ageing can differ among reproductive traits.

Contemporary selection on MHC genes in a free-living ruminant population.

Genes within the major histocompatibility complex (MHC) are the most variable identified in vertebrates. Pathogen-mediated selection is believed to be the main force maintaining MHC diversity. However, relatively few studies have demonstrated contemporary selection on MHC genes. Here, we examine associations between MHC variation and several fitness measurements including total fitness and five fitness components, in 3400 wild Soay sheep (Ovis aries) monitored between 1989 and 2012. In terms of total fitness, measured as lifetime breeding success of all individuals born, we found haplotypes named C and D were associated with decreased and increased male total fitness respectively. In terms of fitness components, juvenile survival was associated with haplotype divergence while individual haplotypes (C, D and F) were associated with adult fitness components. Consistent with the increased male total fitness, the rarest haplotype D has increased in frequency throughout the study period more than expected under neutral expectations. Our results demonstrate that contemporary natural selection is acting on MHC class II genes in Soay sheep and that the mode of selection on specific fitness components can be different mode from selection on total fitness.

Using genomic prediction to detect microevolutionary change of a quantitative trait.

Detecting microevolutionary responses to natural selection by observing temporal changes in individual breeding values is challenging. The collection of suitable datasets can take many years and disentangling the contributions of the environment and genetics to phenotypic change is not trivial. Furthermore, pedigree-based methods of obtaining individual breeding values have known biases. Here, we apply a genomic prediction approach to estimate breeding values of adult weight in a 35-year dataset of Soay sheep (Ovis aries). Comparisons are made with a traditional pedigree-based approach. During the study period, adult body weight decreased, but the underlying genetic component of body weight increased, at a rate that is unlikely to be attributable to genetic drift. Thus cryptic microevolution of greater adult body weight has probably occurred. Genomic and pedigree-based approaches gave largely consistent results. Thus, using genomic prediction to study microevolution in wild populations can remove the requirement for pedigree data, potentially opening up new study systems for similar research.

Vitamin D status is heritable and under environment-dependent selection in the wild.

Vitamin D has a well-established role in skeletal health and is increasingly linked to chronic disease and mortality in humans and companion animals. Despite the clear significance of vitamin D for health and obvious implications for fitness under natural conditions, no longitudinal study has tested whether the circulating concentration of vitamin D is under natural selection in the wild. Here, we show that concentrations of dietary-derived vitamin D2 and endogenously produced vitamin D3  metabolites are heritable and largely polygenic in a wild population of Soay sheep (Ovis aries). Vitamin D2  status was positively associated with female adult survival, and vitamin D3  status predicted female fecundity in particular, good environment years when sheep density and competition for resources was low. Our study provides evidence that vitamin D status has the potential to respond to selection, and also provides new insights into how vitamin D metabolism is associated with fitness in the wild.

Associations between MHC class II variation and phenotypic traits in a free-living sheep population.

Pathogen-mediated selection (PMS) is thought to maintain the high level of allelic diversity observed in the major histocompatibility complex (MHC) class II genes. A comprehensive way to demonstrate contemporary selection is to examine associations between MHC variation and individual fitness. As individual fitness is hard to measure, many studies examine associations between MHC variation and phenotypic traits, including direct or indirect measures of adaptive immunity thought to contribute to fitness. Here, we tested associations between MHC class II variation and five phenotypic traits measured in free-living sheep captured in August: weight, strongyle faecal egg count, and plasma IgA, IgE and IgG immunoglobulin titres against the gastrointestinal nematode parasite Teladorsagia circumcincta. We found no association between MHC class II variation and weight or strongyle faecal egg count. We did, however, find associations between MHC class II variation and immunoglobulin levels which varied with isotype, age and sex. Our results suggest associations between MHC and phenotypic traits are more likely to be found for traits more closely associated with pathogen defence than integrative traits such as bodyweight and highlight the association between MHC variation and antibodies in wild populations.

Having a better home range does not reduce the cost of reproduction in Soay sheep.

A cost of reproduction may not be observable in the presence of environmental or individual heterogeneity because they affect the resources available to individuals. Individual space use is critical in determining both the resources available to individuals and the exposure to factors that mediate the value of these resources (e.g. competition and parasitism). Despite this, there has, to our knowledge, been little research to understand how between-individual differences in resource acquisition, caused by variation in space use, interact with environmental variation occurring at the population scale to influence estimates of the cost of reproduction in natural populations. We used long-term data from the St. Kilda Soay sheep population to understand how differences in age, relative home range quality, and average adult body mass, interacted with annual variation in population density and winter North Atlantic Oscillation index to influence over-winter survival and reproduction in the subsequent year, for females that had invested into reproduction to varying degrees. Our results suggest that Soay sheep females experience costs both in terms of future survival and future reproduction. However, we found little evidence that estimated costs of reproduction vary depending on relative home range quality. There are several possible causes for the lack of a relationship between relative home range quality and our estimate of the costs experienced by females. These include the potential for a correlation between relative home range quality and reproductive allocation to mask a relationship between home range quality and reproductive costs, as well as the potential for the benefit of higher quality home ranges being offset by higher densities. Nevertheless, our results raise questions regarding the presence or context-dependence of relationships between resource access and the estimated cost of reproduction.

Within-trio tests provide little support for post-copulatory selection on major histocompatibility complex haplotypes in a free-living population.

Sexual selection has been proposed as a force that could help maintain the diversity of major histocompatibility complex (MHC) genes in vertebrates. Potential selective mechanisms can be divided into pre-copulatory and post-copulatory, and in both cases, the evidence for occurrence is mixed, especially in natural populations. In this study, we used a large number of parent-offspring trios that were diplotyped for MHC class II genes in a wild population of Soay sheep (Ovis aries) to examine whether there was within-trio post-copulatory selection on MHC class II genes at both the haplotype and diplotype levels. We found there was transmission ratio distortion of one of the eight MHC class II haplotypes (E) which was transmitted less than expected by fathers, and transmission ratio distortion of another haplotype (A) which was transmitted more than expected by chance to male offspring. However, in both cases, these deviations were not significant after correction for multiple tests. In addition, we did not find any evidence of post-copulatory selection at the diplotype level. These results imply that, given known parents, there is no strong post-copulatory selection on MHC class II genes in this population.

Patterns of MHC-dependent sexual selection in a free-living population of sheep.

The MHC is one of the most polymorphic gene clusters in vertebrates and play an essential role in adaptive immunity. Apart from pathogen-mediated selection, sexual selection can also contribute to the maintenance of MHC diversity. MHC-dependent sexual selection could occur via several mechanisms but at present there is no consensus as to which of these mechanisms are involved and their importance. Previous studies have often suffered from limited genetic and behavioural data and small sample size, and were rarely able to examine all the mechanisms together, determine whether signatures of MHC-based non-random mating are independent of genomic effects or differentiate whether MHC-dependent sexual selection takes place at the pre- or post-copulatory stage. In this study, we use Monte Carlo simulation to investigate evidence for non-random MHC-dependent mating patterns by all three mechanisms in a free-living population of Soay sheep. Using 1710 sheep diplotyped at the MHC class IIa region and genome-wide SNPs, together with field observations of consorts, we found sexual selection against a particular haplotype in males at the pre-copulatory stage and sexual selection against female MHC heterozygosity during the rut. We also found MHC-dependent disassortative mating at the post-copulatory stage, along with strong evidence of inbreeding avoidance at both stages. However, results from generalized linear mixed models suggest that the pattern of MHC-dependent disassortative mating could be a by-product of inbreeding avoidance. Our results therefore suggest that while multiple apparent mechanisms of non-random mating with respect to the MHC may occur, some of them have alternative explanations.

Detangling the mechanisms and timing of MHC-dependent sexual selection using Soay sheep.

Immune defence is a key component of fitness, and individuals are expected to have evolved preferences for mates that ensure immunocompetent offspring. Potential preferences include those for mates with specific heritable immune gene profiles ("good genes") or for immunogenetically dissimilar mates to increase offspring immune gene diversity. The major histocompatibility complex (MHC) is by far the most investigated immune gene in mate choice studies, but we still know very little about its role in sexual selection for genetic benefits. In this issue of Molecular Ecology, Huang et al. capitalize on the extraordinary wealth of behavioural, life history and genetic/genomic data from the free-living Soay sheep population on the Island of Hirta to address this problem. While the authors find evidence of both pre- and postcopulatory MHC-based sexual selection, postcopulatory MHC-dissimilar mate choice is indistinguishable from genome-wide effects, suggesting it is a byproduct of inbreeding avoidance in Soay sheep. The study's comprehensive sampling ensures that inferences are generalizable to the entire population and provides a gold standard for studies investigating immune gene-based sexual selection.

Life-history strategy varies with the strength of competition in a food-limited ungulate population.

Fluctuating population density in stochastic environments can contribute to maintain life-history variation within populations via density-dependent selection. We used individual-based data from a population of Soay sheep to examine variation in life-history strategies at high and low population density. We incorporated life-history trade-offs among survival, reproduction and body mass growth into structured population models and found support for the prediction that different life-history strategies are optimal at low and high population densities. Shorter generation times and lower asymptotic body mass were selected for in high-density environments even though heavier individuals had higher probabilities to survive and reproduce. In contrast, greater asymptotic body mass and longer generation times were optimal at low population density. If populations fluctuate between high density when resources are scarce, and low densities when they are abundant, the variation in density will generate fluctuating selection for different life-history strategies, that could act to maintain life-history variation.

Maternally derived anti-helminth antibodies predict offspring survival in a wild mammal.

The transfer of antibodies from mother to offspring provides crucial protection against infection to offspring during early life in humans and domestic and laboratory animals. However, few studies have tested the consequences of variation in maternal antibody transfer for offspring fitness in the wild. Further, separating the immunoprotective effects of antibodies from their association with nutritional resources provided by mothers is difficult. Here, we measured plasma levels of total and parasite-specific antibodies in neonatal (less than 10 days old) wild Soay sheep over 25 years to quantify variation in maternal antibody transfer and test its association with offspring survival. Maternal antibody transfer was predicted by maternal age and previous antibody responses, and was consistent within mothers across years. Neonatal total IgG antibody levels were positively related to early growth, suggesting they reflected nutritional transfer. Neonatal parasite-specific IgG levels positively predicted first-year survival, independent of lamb weight, total IgG levels and subsequent lamb parasite-specific antibody levels. This relationship was partly mediated via an indirect negative association with parasite burden. We show that among-female variation in maternal antibody transfer can have long-term effects on offspring growth, parasite burden and fitness in the wild, and is likely to impact naturally occurring host-parasite dynamics.

Characterisation of major histocompatibility complex class IIa haplotypes in an island sheep population.

The ovine MHC class IIa is known to consist of six to eight loci located in close proximity on chromosome 20, forming haplotypes that are typically inherited without recombination. Here, we characterise the class IIa haplotypes within the Soay sheep (Ovis aries) on St. Kilda to assess the diversity present within this unmanaged island population. We used a stepwise sequence-based genotyping strategy to identify alleles at seven polymorphic MHC class IIa loci in a sample of 118 Soay sheep from four cohorts spanning 15 years of the long-term study on St. Kilda. DRB1, the most polymorphic MHC class II locus, was characterised first in all 118 sheep and identified six alleles. Using DRB1 homozygous animals, the DQA (DQA1, DQA2 and DQA2-like) and DQB (DQB1, DQB2 and DQB2-like) loci were sequenced, revealing eight haplotypes. Both DQ1/DQ2 and DQ2/DQ2-like haplotype configurations were identified and a single haplotype carrying three DQB alleles. A test sample of 94 further individuals typed at the DRB1 and DQA loci found no exceptions to the eight identified haplotypes and a haplotype homozygosity of 21.3%. We found evidence of historic positive selection at DRB1, DQA and DQB. The limited variation at MHC class IIa loci in Soay sheep enabled haplotype characterisation but showed that no single locus could capture the full extent of the expressed variation in the region.

Characterisation of the effect of day length, and associated differences in dietary intake, on the gut microbiota of Soay sheep.

Differences in the rumen bacterial community have been previously reported for Soay sheep housed under different day length conditions. This study extends this previous investigation to other organs of the digestive tract, as well as the analysis of ciliated protozoa and anaerobic fungi. The detectable concentrations of ciliated protozoa and anaerobic fungi decreased with increased day length in both the rumen and large colon, unlike those of bacteria where no effect was observed. Conversely, bacterial community composition was affected by day length in both the rumen and large colon, but the community composition of the detectable ciliated protozoa and anaerobic fungi was not affected. Day length-associated differences in the bacterial community composition extended to all of the organs examined, with the exception of the duodenum and the jejunum. It is proposed that differences in rumen fill and ruminal 'by-pass' nutrients together with endocrinological changes cause the observed effects of day length on the different gut microbial communities.

Pedigree-Based Estimation of Reproductive Value.

How successful an individual or cohort is, in terms of their genetic contribution to the future population, is encapsulated in the concept of reproductive value, and is crucial for understanding selection and evolution. Long-term studies of pedigreed populations offer the opportunity to estimate reproductive values directly. However, the degree to which genetic contributions, as defined by a pedigree, may converge on their long-run values within the time frames of available data sets, such that they may be interpreted as estimates of reproductive value, is unclear. We develop a system for pedigree-based calculation of the expected genetic representation that both individuals and cohorts make to the population in the years following their birth. We apply this system to inference of individual and cohort reproductive values in Soay sheep (Ovis aries) from St Kilda, Outer Hebrides. We observe that these genetic contributions appear to become relatively stable within modest time frames. As such, it may be reasonable to consider pedigree-based calculations of genetic contributions to future generations as estimates of reproductive value. This approach and the knowledge that the estimates can stabilize within decades should offer new opportunities to analyze data from pedigreed wild populations, which will be of value to many fields within evolutionary biology and demography.

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.

Natural Selection on Antihelminth Antibodies in a Wild Mammal Population.

An effective immune response is expected to confer fitness benefits through improved resistance to parasites but also incur energetic costs that negatively impact fitness-related traits, such as reproduction. The fitness costs and benefits of an immune response are likely to depend on host age, sex, and levels of parasite exposure. Few studies have examined the full extent to which patterns of natural selection on immune phenotypes vary across demographic groups and environments in the wild. Here, we assessed natural selection on plasma levels of three functionally distinct isotypes (IgA, IgE, and IgG) of antibodies against a prevalent nematode parasite measured in a wild Soay sheep population over 26 years. We found little support for environment-dependent selection or reproductive costs. However, antibody levels were negatively associated with parasite egg counts and positively associated with subsequent survival, albeit in a highly age- and isotype-dependent manner. Raised levels of antiparasite IgA best predicted reduced egg counts, but this did not predict survival in lambs. In adults increased antiparasite IgG predicted reduced egg counts, and in adult females IgG levels also positively predicted overwinter survival. Our results highlight the potential importance of age- and sex-dependent selection on immune phenotypes in nature and show that patterns of selection can vary even among functionally related immune markers.

Estimation of Individual Growth Trajectories When Repeated Measures Are Missing.

Individuals in a population vary in their growth due to hidden and observed factors such as age, genetics, environment, disease, and carryover effects from past environments. Because size affects fitness, growth trajectories scale up to affect population dynamics. However, it can be difficult to estimate growth in data from wild populations with missing observations and observation error. Previous work has shown that linear mixed models (LMMs) underestimate hidden individual heterogeneity when more than 25% of repeated measures are missing. Here we demonstrate a flexible and robust way to model growth trajectories. We show that state-space models (SSMs), fit using R package growmod, are far less biased than LMMs when fit to simulated data sets with missing repeated measures and observation error. This method is much faster than Markov chain Monte Carlo methods, allowing more models to be tested in a shorter time. For the scenarios we simulated, SSMs gave estimates with little bias when up to 87.5% of repeated measures were missing. We use this method to quantify growth of Soay sheep, using data from a long-term mark-recapture study, and demonstrate that growth decreased with age, population density, weather conditions, and when individuals are reproductive. The method improves our ability to quantify how growth varies among individuals in response to their attributes and the environments they experience, with particular relevance for wild populations.

Sex differences in telomeres and lifespan in Soay sheep: From the beginning to the end.

There is tremendous diversity in ageing rates and lifespan not only among taxa but within species, and particularly between the sexes. Women often live longer than men, and considerable research on this topic has revealed some of the potential biological, psychological and cultural causes of sex differences in human ageing and lifespan. However, sex differences in lifespan are widespread in nonhuman animals suggesting biology plays a prominent role in variation in ageing and lifespan. Recently, evolutionary biologists have borrowed techniques from biomedicine to identify whether similar mechanisms causing or contributing to variation in ageing and lifespan in humans and laboratory animals also operate in wild animals. Telomeres are repetitive noncoding DNA sequences capping the ends of chromosomes that are important for chromosomal stability but that can shorten during normal cell division and exposure to stress. Telomere shortening is hypothesized to directly contribute to the ageing process as once telomeres shorten to some length, the cells stop dividing and die. Men tend to have shorter telomeres and faster rates of telomere attrition with age than women, suggesting one possible biological cause of sex differences in lifespan. In this issue of Molecular Ecology, Watson et al. () show that telomere lengths in wild Soay sheep are similar between females and males near the beginning of life but quickly diverge with age because males but not females showed reduced telomere lengths at older ages. The authors further show that some of the observed sex difference in telomere lengths in old age may be due to male investment in horn growth earlier in life, suggesting that sexually dimorphic allocation to traits involved in sexual selection might underlie sex differences in telomere attrition. This study provides a rare example of how biological mechanisms potentially contributing to sex differences in lifespan in humans may also operate in free-living animals. However, future studies using a longitudinal approach are necessary to confirm these observations and identify the ultimate and proximate causes of any sex differences in telomere lengths. Collaborations between evolutionary biologists and gerontologists are especially needed to identify whether telomere lengths have a causal role in ageing, particularly in natural conditions, and whether this directly contributes to sex differences in lifespan.