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.

Genetic architecture and lifetime dynamics of inbreeding depression in a wild mammal

Inbreeding depression is ubiquitous, but we still know little about its genetic architecture and precise effects in wild populations. Here, we combine long-term life-history data with 417 K imputed SNP genotypes for 5952 wild Soay sheep to explore inbreeding depression on a key fitness component, annual survival. Inbreeding manifests in long runs of homozygosity (ROH), which make up nearly half of the genome in the most inbred individuals. The ROH landscape varies widely across the genome, with islands where up to 87% and deserts where only 4% of individuals have ROH. The fitness consequences of inbreeding are severe; a 10% increase in individual inbreeding FROH is associated with a 60% reduction in the odds of survival in lambs, though inbreeding depression decreases with age. Finally, a genome-wide association scan on ROH shows that many loci with small effects and five loci with larger effects contribute to inbreeding depression in survival.

Senescence in immunity against helminth parasites predicts adult mortality in a wild mammal

Our understanding of the deterioration in immune function in old age-immunosenescence-derives principally from studies of modern human populations and laboratory animals. The generality and significance of this process for systems experiencing complex, natural infections and environmental challenges are unknown. Here, we show that late-life declines in an important immune marker of resistance to helminth parasites in wild Soay sheep predict overwinter mortality. We found senescence in circulating antibody levels against a highly prevalent nematode worm, which was associated with reduced adult survival probability, independent of changes in body weight. These findings establish a role for immunosenescence in the ecology and evolution of natural populations.

No evidence for parental age effects on offspring leukocyte telomere length in free-living Soay sheep

In humans, the effect of paternal age at conception (PAC) on offspring leukocyte telomere length (LTL) is well established, with older fathers thought to pass on longer telomeres to their offspring in their sperm. Few studies have looked for PAC effects in other species, but it has been hypothesised that the effect will be exacerbated in polygamous species with higher levels of sperm competition and production. We test for maternal (MAC) and paternal age at conception effects on offspring LTL in Soay sheep, a primitive breed experiencing strong sperm competition. We use qPCR to measure relative telomere length in 389 blood samples (n = 318 individuals) collected from an unmanaged population of sheep on St Kilda, where individual age and parentage are known. We find no evidence that either MAC or PAC are associated with LTL in offspring across the age range, or when considering only young lambs (n = 164). This is the first study to test for parental age effects on offspring LTL in a wild mammal population, and the results contrast with the findings of numerous human studies that find a PAC effect, as well as predictions of a stronger PAC effect in polygamous species.

Robust extraction of quantitative structural information from high-variance histological images of livers from necropsied Soay sheep

Quantitative information is essential to the empirical analysis of biological systems. In many such systems, spatial relations between anatomical structures is of interest, making imaging a valuable data acquisition tool. However, image data can be difficult to analyse quantitatively. Many image processing algorithms are highly sensitive to variations in the image, limiting their current application to fields where sample and image quality may be very high. Here, we develop robust image processing algorithms for extracting structural information from a dataset of high-variance histological images of inflamed liver tissue obtained during necropsies of wild Soay sheep. We demonstrate that features of the data can be measured in a fully automated manner, providing quantitative information which can be readily used in statistical analysis. We show that these methods provide measures that correlate well with a manual, expert operator-led analysis of the same images, that they provide advantages in terms of sampling a wider range of information and that information can be extracted far more quickly than in manual analysis.

Accounting for female space sharing in St. Kilda Soay sheep (Ovis aries) results in little change in heritability estimates

When estimating heritability in free-living populations, it is common practice to account for common environment effects, because of their potential to generate phenotypic covariance among relatives thereby biasing heritability estimates. In quantitative genetic studies of natural populations, however, philopatry, which results in relatives being clustered in space, is rarely accounted for. The two studies that have been carried out so far suggest absolute declines in heritability estimates of up to 43% when accounting for space sharing by relatives. However, due to methodological limitations these estimates may not be representative. We used data from the St. Kilda Soay sheep population to estimate heritabilities with and without accounting for space sharing for five traits for which there is evidence for additive genetic variance (birthweight, birth date, lamb August weight, and female post-mortem jaw and metacarpal length). We accounted for space sharing by related females by separately incorporating spatial autocorrelation, and a home range similarity matrix. Although these terms accounted for up to 18% of the variance in these traits, heritability estimates were only reduced by up to 7%. Our results suggest that the bias caused by not accounting for space sharing may be lower than previously thought. This suggests that philopatry does not inevitably lead to a large bias if space sharing by relatives is not accounted for. We hope our work stimulates researchers to model shared space when relatives in their study population share space, as doing so will enable us to better understand when bias may be of particular concern.

Detecting genes for variation in parasite burden and immunological traits in a wild population: testing the candidate gene approach

Identifying the genes underlying phenotypic variation in natural populations can provide novel insight into the evolutionary process. The candidate gene approach has been applied to studies of a number of traits in various species, in an attempt to elucidate their genetic basis. Here, we test the application of the candidate gene approach to identify the loci involved in variation in gastrointestinal parasite burden, a complex trait likely to be controlled by many loci, in a wild population of Soay sheep. A comprehensive literature review, Gene Ontology databases, and comparative genomics resources between cattle and sheep were used to generate a list of candidate genes. In a pilot study, these candidates, along with 50 random genes, were then sequenced in two pools of Soay sheep; one with low gastrointestinal nematode burden and the other high, using a NimbleGen sequence capture experiment. Further candidates were identified from single nucleotide polymorphisms (SNPs) that were highly differentiated between high- and low-resistance sheep breeds. A panel of 192 candidate and control SNPs were then typed in 960 individual Soay sheep to examine whether they individually explained variation in parasite burden, as measured as faecal egg count, as well as two immune measures (Teladorsagia circumcincta-specific antibodies and antinuclear antibodies). The cumulative effect of the candidate and control SNPs were estimated by fitting genetic relationship matrices (GRMs) as random effects in animal models of the three traits. No more significant SNPs were identified in the pilot sequencing experiment and association study than expected by chance. Furthermore, no significant difference was found between the proportions of candidate or control SNPs that were found to be significantly associated with parasite burden/immune measures. No significant effect of the candidate or control gene GRMs was found. There is thus little support for the candidate gene approach to the identification of loci explaining variation in parasitological and immunological traits in this population. However, a number of SNPs explained significant variation in multiple traits and significant correlations were found between the proportions of variance explained by individual SNPs across multiple traits. The significant SNPs identified in this study may still, therefore, merit further investigation.

Selection and microevolution of coat pattern are cryptic in a wild population of sheep

Understanding the maintenance of genetic variation in natural populations is a core aim of evolutionary genetics. Insight can be gained by quantifying selection at the level of the genotype, as opposed to the phenotype. Here, we show that in a natural population of Soay sheep which is polymorphic for coat pattern, recessive genetic variants at the causal gene, agouti signalling protein (ASIP) are associated with reduced lifetime fitness. This was due primarily to a reduction in juvenile survival of uniformly coloured (self-type) sheep, which are homozygous recessive, and occurs despite significantly higher reproductive success in surviving self-type adults. Consistent with their relatively low fitness, we show that the frequency of self-type individuals has declined from 1985 to 2008. Remarkably though, the frequency of the underlying self-allele has increased, because the frequency of heterozygous individuals (who harbour the majority of all self-alleles) has increased. Indeed, the ratio of observed/expected heterozygous individuals has increased during the study, such that there is now a significant excess of heterozygotyes. By employing gene-dropping simulations, we show that microevolutionary trends in the frequency and excess of ASIP heterozygotes are too pronounced to be caused by genetic drift. Studying this polymorphism at the level of phenotype rather than underlying genotype would have failed to detect cryptic fitness differences. We would also have been unable to rule out genetic drift as an evolutionary force driving genetic change. This highlights the importance of resolving the underlying genetic basis of phenotypic variation in explaining evolutionary dynamics.

Environmental coupling of selection and heritability limits evolution

There has recently been great interest in applying theoretical quantitative genetic models to empirical studies of evolution in wild populations. However, while classical models assume environmental constancy, most natural populations exist in variable environments. Here, we applied a novel analytical technique to a long-term study of birthweight in wild sheep and examined, for the first time, how variation in environmental quality simultaneously influences the strength of natural selection and the genetic basis of trait variability. In addition to demonstrating that selection and genetic variance vary dramatically across environments, our results show that environmental heterogeneity induces a negative correlation between these two parameters. Harsh environmental conditions were associated with strong selection for increased birthweight but low genetic variance, and vice versa. Consequently, the potential for microevolution in this population is constrained by either a lack of heritable variation (in poor environments) or by a reduced strength of selection (in good environments). More generally, environmental dependence of this nature may act to limit rates of evolution, maintain genetic variance, and favour phenotypic stasis in many natural systems. Assumptions of environmental constancy are likely to be violated in natural systems, and failure to acknowledge this may generate highly misleading expectations for phenotypic microevolution.

Epidemiology of parasitic protozoan infections in Soay sheep (Ovis aries L.) on St Kilda

The feral Soay sheep (Ovis aries L.) population on Hirta, St Kilda, is host to a diverse component parasite community, but previous parasitological studies of the population have only focussed on the metazoan species. This paper reports the first epidemiological study of the protozoan species comprising Cryptosporidium parvum, Giardia duodenalis and 11 species of Eimeria in Soay sheep across 3 years of varying host population density. Prevalence and intensity of almost all species of protozoa significantly decreased with host age, with the exception of E. granulosa, which increased in prevalence with host age. The prevalence of C. parvum appeared to vary positively with host population density but that of G. duodenalis did not vary significantly with density. Most species of Eimeria showed a distinct lag in infection level following the host population crash of 2002, taking up to 2 years to decrease. Mixed Eimeria species intensity and diversity were highest in 2002, a year of low host density. Parasite diversity decreased with host age and was higher in males. There were 5 positive pair-wise associations between protozoa species in terms of prevalence. The results of this study highlight the potential for protozoal infection to shape the evolution of parasite resistance in wild host populations harbouring diverse parasite species.

Gastrointestinal nematode species burdens and host mortality in a feral sheep population

Every few years a large proportion of the feral sheep on Hirta, St Kilda die due to food shortage. The effects of malnutrition are exacerbated by gastrointestinal nematodes. As found in sheep flocks in mainland Britain, Teladorsagia circumcincta has long been considered the predominant and most pathogenic nematode species in all age classes of Soay sheep. Previous research indicated that intensity of this species showed a negative association with host age and comprised 75% of the entire gastrointestinal burden. Here we present new data that show Trichostrongylus axei and Trichostrongylus vitrinus to be the predominant worm pathogens in young Soay sheep. In the present study, Trichostrongylus spp. burdens declined with host age whereas T. circumcincta actually increased in burden over the first few age classes. Also, male hosts had significantly higher burdens of Trichostrongylus spp. than females, with this genus making up a higher proportion of the strongyle egg producing community in male hosts than female hosts. These new findings raise questions concerning our previous interpretation of the main nematode species contributing to strongyle egg count in the population, and the contrasting infection patterns of these nematode species in unmanaged St Kilda Soay sheep compared with domestic sheep in mainland Britain.

Low-level parasitic worm burdens may reduce body condition in free-ranging red deer (Cervus elaphus)

Regulation of ungulate populations by parasites relies on establishing a density-dependent relationship between infection and vital demographic rates which may act through the effect of parasites on body condition. We examine evidence for parasite impacts in 285 red deer (Cervus elaphus) harvested during 1991 and 1992 on the Isle of Rum. In the abomasa, prevalence of nematodes was 100% and the most abundant genus observed were Ostertagia species, however, mean intensity of infection was low (less than 1000) relative to other studies. Additional species, also present in low numbers, included Nematodirus spp., Capillaria spp., Cooperia spp., Monieza expanza, Oesophagostomum venulosum and Trichuris ovis. Lungworm (Dictyocaulus spp.) and tissue worm (Elaphostronygylus cervi) larvae were also observed in faecal samples. There was no evidence for acquired immunity to abomasal nematodes. Despite low levels of infection, both adult male and female deer showed significant negative correlation between indices of condition (kidney fat index, dressed carcass weight and larder weight) and intensity of Ostertagia spp. infection. However, there was no evidence that pregnancy rate in females was related to intensity of infection. For calves, there was no relationship between body condition and intensity of infection. The apparent subclinical effects of low-level parasite infection on red deer performance could alternatively be due to animals in poorer nutritional state being more susceptible to infection. Either way the results suggest that further studies of wild populations are justified, in particular where high local host densities exist or alternative ungulate hosts are present, and, where experimental treatments are tractable.

Heterozygosity, inbreeding and neonatal traits in Soay sheep on St Kilda

We investigated whether birth weight and neonatal survival, a period within which 24% of all mortalities occur, were correlated with levels of inbreeding in St Kilda Soay sheep, using pedigree inbreeding coefficients and four marker-based estimators of inbreeding. None of the inbreeding estimators, either of the offspring, or of their mothers, explained significant variation in a lamb's birth weight or probability of surviving the neonatal period, suggesting low inbreeding depression for these traits. We evaluated the correlation between the marker-based measures of inbreeding and inbreeding coefficients obtained from the Soay pedigree, where paternal links were inferred using the same panel of microsatellite markers. Even when using a relatively complete portion of the pedigree, in which all individuals had known maternal and paternal grandparents, the correlation was found to be weak (r = -0.207, where mean f = 0.0168). These results add support to the recent prediction that when the mean and variance in inbreeding are low in a population, heterozygosity-fitness correlations can be very weak or even undetectable. The pursuit of more detailed pedigrees offers the best prospect for identifying inbreeding depression within this study population.

Why large-scale climate indices seem to predict ecological processes better than local weather

Large-scale climatic indices such as the North Atlantic Oscillation are associated with population dynamics, variation in demographic rates and values of phenotypic traits in many species. Paradoxically, these large-scale indices can seem to be better predictors of ecological processes than local climate. Using detailed data from a population of Soay sheep, we show that high rainfall, high winds or low temperatures at any time during a 3-month period can cause mortality either immediately or lagged by a few days. Most measures of local climate used by ecologists fail to capture such complex associations between weather and ecological process, and this may help to explain why large-scale, seasonal indices of climate spanning several months can outperform local climatic factors. Furthermore, we show why an understanding of the mechanism by which climate influences population ecology is important. Through simulation we demonstrate that the timing of bad weather within a period of mortality can have an important modifying influence on intraspecific competition for food, revealing an interaction between climate and density dependence that the use of large-scale climatic indices or inappropriate local weather variables might obscure.

Non-invasive assessment of parasitic nematode species diversity in wild Soay sheep using molecular markers

Considerable effort has been put into detecting and identifying parasitic nematodes in live ruminants, but to date most studies are limited to a small group of nematodes and/or to experimentally infected sheep. In this study, a PCR-based assay using species-specific primer pairs, located in the second internal transcribed spacer ribosomal DNA, was developed to identify nine different species from six different families of parasitic nematodes in a wild, unmanaged and naturally infected population of sheep. Each primer pair was tested for its specificity and sensitivity and it exclusively amplified the species it was designed for and exhibited a high degree of sensitivity. The method was applied to eggs and cultured larvae to identify the parasitic nematodes present in a pooled faecal sample from several host individuals with unknown parasite burden. To test detection reliability, a faecal sample from an individual with known parasite burden (through post-mortem analysis) was also examined. All species present could be correctly identified by PCR, but detecting very low levels and/or early stages of infection proved to be difficult. The method was also tested for its applicability to high through-put screening of faecal samples.

Fine-scale genetic structure in a free-living ungulate population

The fine-scale genetic structure of wild animal populations has rarely been analysed, yet is potentially important as a confounding factor in quantitative genetic and allelic association studies, as well as having implications for population dynamics, inbreeding and kin selection. In this study, we examined the extent to which the three spatial subunits, or hefts, of the Village Bay population of Soay sheep (Ovis aries) on St Kilda, Scotland, are genetically structured using data from 20 microsatellite and protein loci. Allele frequencies differed significantly among three hefts in all the study years we considered (1987-2000 inclusive). Small but significantly positive F(ST) and negative F(IS) values were observed in most years, indicating that the hefts are genetically differentiated, and that within each heft there is more observed heterozygosity than would be expected if each were an isolated breeding population. Males showed less fidelity to their natal heft, and as a consequence higher levels of relatedness within hefts were observed among females than among males. There was a significant negative relationship between geographical proximity and relatedness in pairwise comparisons involving females, and on average pairs of females located within 50 m of each other were related at the equivalent level of second cousins. Structure is therefore largely driven by incomplete postnatal dispersal by females. Mating appears to be random with respect to the spatial-genetic substructure of the hefts, and therefore genetic structure does not contribute to the overall rate of inbreeding in the population. However, genetic substructure can lead to allelic associations and generate environmental effects within lineages that have the potential to confound heritability analyses and allelic association studies.

Estimating the prevalence of inbreeding from incomplete pedigrees

A previous review of inbreeding in natural populations suggested that close inbreeding (inbreeding coefficient f = 0.25) is generally rare in wild birds and mammals. However, the review did not assess rates of moderate inbreeding (f = 0.125), which may make a rather larger contribution to overall inbreeding in a population. Furthermore, previous studies may have underestimated the prevalence of inbreeding in wild populations with incomplete pedigrees. By categorizing inbreeding events by the relationship of the parental pair, we suggest a simple method for estimating rates of close and moderate inbreeding from incomplete pedigree data. We applied this method to three wild populations of ruminants: red deer on Rum, Scotland, Soay sheep on Hirta, Scotland and reintroduced Arabian oryx on the Jiddat-al-Harasis, Oman. Although paternal half-sib pairs were the most common category of inbreeding in all three populations, there was considerable variation among populations in the frequencies of the various categories of inbreeding. This variation may be largely explained by differences in population size and dynamics, in maternal and paternal sibship size and in the overlap of reproductive lifespan of consecutive generations. Close and moderate inbreeding appear to be a routine part of breeding behaviour in these ruminant populations.

A microsatellite polymorphism in the gamma interferon gene is associated with resistance to gastrointestinal nematodes in a naturally-parasitized population of Soay sheep

Free-living Soay sheep (Ovis aries) on the island of Hirta, St Kilda, Scotland, are naturally parasitized by gastrointestinal nematodes, predominantly Teladorsagia circumcincta. In this paper we show that reduced faecal egg counts (FEC) are associated with an allele at a microsatellite locus located in the first intron of the interferon gamma gene (o(IFN)-gamma) in Soay sheep lambs and yearlings, measured at approximately 4 and 16 months of age, respectively. The same allele was also associated with increased T. circumcincta-specific antibody (IgA) in lambs, but not associated significantly in yearlings. Flanking control markers failed to show a significant association with either FEC or IgA. These results suggest that a polymorphic gene conferring increased resistance to gastrointestinal nematode parasites is located at or near the interferon gamma gene, and support previous reports which have mapped a quantitative trait locus (QTL) for resistance to this region in domestic sheep. Our data are consistent with the idea that a functional polymorphism leading to reduced expression or efficacy of (IFN)-gamma could enhance the immune response to gastrointestinal nematodes by favouring the activity of the Th2 cell subset and antibody associated immune mechanisms.

Heritable variation in resistance to gastro-intestinal nematodes in an unmanaged mammal population

The impact of parasites on natural populations has received considerable attention from evolutionary biologists in recent years. Central to a number of theoretical developments during this period is the assumption of additive genetic variation in resistance to parasites. However, very few studies have estimated the heritability of parasite resistance under field conditions, and those that have are mainly restricted to birds and their ectoparasites. In this paper, to our knowledge, we show for the first time in a free-ranging mammal population, Soay sheep (Ovis aries) living on the islands of St Kilda, that there is significant heritable variation in resistance to gastrointestinal nematodes. This result is consistent with earlier studies on this population which have indicated locus-specific associations with parasite resistance. We discuss our results in the context of current studies examining heritable resistance to parasites in domestic sheep and the possible mechanisms of selective maintenance of genetic variation for resistance to gastrointestinal nematodes in the St Kilda Soay sheep population.

Effect of sub-lethal doses of albendazole on the fecundity of Dictyocaulus viviparus

During an evaluation of the efficacy of prolonged low-dose albendazole therapy on nematode infections in calves, it was observed that a dose-rate of 2 mg kg-1 given daily for 10 days was highly effective at expelling Dictyocaulus viviparus, but smaller doses suppressed the faecal output of larvae without killing the lungworms. A more detailed study with four experimentally infected calves given 1 mg kg-1 day-1 for 10 days showed that faecal output of larvae ceased after six to eight days but resumed four to six days after the withdrawal of the drug. The albendazole-induced sterility was therefore reversible. A subsidiary study showed that the strain of parasite used was fully susceptible to albendazole.

Chemoprophylaxis and immunity to parasitic bronchitis in cattle--a field experiment comparing topical ivermectin and an oxfendazole intraruminal device

Seeder calves infected with Dictyocaulus viviparus were used to contaminate a field divided into three similar paddocks. Twenty-four autumn-born calves were allocated to three matched groups; one group was given topical ivermectin treatments (0.5 mg/kg) at 3, 8 and 13 weeks after turnout (Day 0); each member of a second group was given an oxfendazole pulse-release intraruminal device (OPRB) at turnout; while a third group was kept as untreated controls to monitor the natural epidemiological pattern of events. Severe pasteurella pneumonia exacerbated by lungworm infection occurred in the controls after Day 24. Two died and repeated doses of antibiotic and anthelmintic therapy were necessary to save the remainder. Clinical signs were much milder in the ivermectin and OPRB groups and resolved with only a single dose of antibiotic. The OPRB group excreted some lungworm larvae at this time, but none was detected in the faeces of the ivermectin group during the grazing season. At housing, five calves from each group and four lungworm-naive calves were challenged with D. viviparus larvae. The infection became patent in all challenge-control calves, but no larvae were passed by any of the trial animals. Post-mortem worm-counts revealed percentage takes for the challenge controls, trial controls, ivermectin and OPRB groups of 16.7, 0.01, 0.9 and 0.2, respectively. All trial groups had therefore developed a substantial immunity.

Comparative study of early-season prophylaxis using ivermectin with lungworm vaccination in the control of parasitic bronchitis and gastroenteritis in cattle

Twenty-four first-season calves were randomly allocated to three similar groups (1-non-treated controls; 2 - vaccinated against lungworm; 3 - treated with ivermectin 21, 56 and 91 days after turnout) and set-stocked on separate pastures. Parasitic bronchitis became evident in the controls and signs of parasitic gastroenteritis were seen later in the vaccinates, but the ivermectin-treated calves remained healthy. After autumn housing, all were kept as a single group for the winter. The following summer, six of the ivermectin-treated animals and their matching vaccinates were grazed together, without further prophylaxis, along with six first-season calves. The latter displayed evidence of mild but debilitating pulmonary and gastrointestinal parasitic disease while both groups of yearlings remained healthy (with the exception of one diarrhoeic vaccinate). Thus, the immune status of the ivermectin-treated animals appeared to be comparable to that of the vaccinates. This conclusion was supported by parasitological observations and by artificial challenge at the end of the second grazing season.

Netobimin in drinking water for treatment of bovine parasitic bronchitis: a field experiment

Lungworm-infected seeder calves were used on four 1.41 ha paddocks to ensure that groups of 11 calves would be exposed to a heavy challenge with Dictyocaulus viviparus. By the 39th day after turnout there was a serious episode of respiratory disease and a diagnosis of parasitic bronchitis was confirmed by post mortem and faecal examination. One group of trial calves was treated with netobimin administered in the drinking water at 2.8 mg/kg/day for seven consecutive days; another group received the same treatment supplemented with flunixin meglumine at 2.2 mg/kg/day for three days; a third group was given a single oral dose of 7.5 mg netobimin/kg; only emergency treatments were given to calves in the control group. The clinical response to the drinking water treatments was highly satisfactory and better than the response to the single oral treatment.