Parallelism and divergence in immune responses: a comparison of expression levels in two lakes

Question: How do immune phenotypes differ between infected and uninfected wild individuals, and is the effect the same in different populations? Organisms: Threespine stickleback (Gasterosteus aculeatus) from two lake populations on the island of North Uist, Scotland, sampled in May 2015. Methods: For each fish, we recorded length, sex, reproductive status, condition, and parasitic infection. We measured the expression levels of eight genes that act as key markers of immune system function using qPCR, and then examined the relationship between measured factors and immune gene expression profiles within each population. Conclusions: Populations differed significantly in their immune gene expression profiles. Within each population, multiple factors, including condition, reproductive status, and Schistocephalus solidus infection levels, were found to correlate with expression levels of different arms of the immune system

Measuring the immune system of the three-spined stickleback: investigating natural variation by quantifying immune expression in the laboratory and the wild

Current understanding of the immune system comes primarily from lab-based studies. There has been substantial interest in examining how it functions in the wild, but studies have been limited by a lack of appropriate assays and study species. The three-spined stickleback (Gasterosteus aculeatus L.) provides an ideal system in which to advance the study of wild immunology, but requires the development of suitable immune assays. We demonstrate that meaningful variation in the immune response of stickleback can be measured using real-time PCR to quantify the expression of eight genes, representing the innate response and Th1, Th2 and Treg type adaptive responses. Assays are validated by comparing the immune expression profiles of wild and laboratory raised stickleback, and by examining variation across populations on North Uist, Scotland. We also compare the immune response potential of laboratory raised individuals from two Icelandic populations by stimulating cells in culture. Immune profiles of wild fish differed from laboratory-raised fish from the same parental population, with immune expression patterns in the wild converging relative to those in the laboratory. Innate measures differed between wild populations, whilst the adaptive response was associated with variation in age, relative size of fish, reproductive status and S. solidus infection levels. Laboratory-raised individuals from different populations showed markedly different innate immune response potential. The ability to combine studies in the laboratory and in the wild underline the potential of this toolkit to advance our understanding of the ecological and evolutionary relevance of immune system variation in a natural setting

No evidence of local adaptation of immune responses to Gyrodactylus in three-spined stickleback (Gasterosteus aculeatus)

Parasitism represents one of the most widespread lifestyles in the animal kingdom, with the potential to drive coevolutionary dynamics with their host population. Where hosts and parasites evolve together, we may find local adaptation. As one of the main host defences against infection, there is the potential for the immune response to be adapted to local parasites. In this study, we used the three-spined stickleback and its Gyrodactylus parasites to examine the extent of local adaptation of parasite infection dynamics and the immune response to infection. We took two geographically isolated host populations infected with two distinct Gyrodactylus species and performed a reciprocal cross-infection experiment in controlled laboratory conditions. Parasite burdens were monitored over the course of the infection, and individuals were sampled at multiple time points for immune gene expression analysis. We found large differences in virulence between parasite species, irrespective of host, and maladaptation of parasites to their sympatric host. The immune system responded to infection, with a decrease in expression of innate and Th1-type adaptive response genes in fish infected with the less virulent parasite, representing a marker of a possible resistance mechanism. There was no evidence of local adaptation in immune gene expression levels. Our results add to the growing understanding of the extent of host-parasite local adaptation, and demonstrate a systemic immune response during infection with a common ectoparasite. Further immunological studies using the stickleback-Gyrodactylus system can continue to contribute to our understanding of the function of the immune response in natural populations

Measuring the immune system of the three-spined stickleback: investigating natural variation by quantifying immune expression in the laboratory and the wild

Current understanding of the immune system comes primarily from lab-based studies. There has been substantial interest in examining how it functions in the wild, but studies have been limited by a lack of appropriate assays and study species. The three-spined stickleback (Gasterosteus aculeatus L.) provides an ideal system in which to advance the study of wild immunology, but requires the development of suitable immune assays. We demonstrate that meaningful variation in the immune response of stickleback can be measured using real-time PCR to quantify the expression of eight genes, representing the innate response and Th1, Th2 and Treg type adaptive responses. Assays are validated by comparing the immune expression profiles of wild and laboratory raised stickleback, and by examining variation across populations on North Uist, Scotland. We also compare the immune response potential of laboratory raised individuals from two Icelandic populations by stimulating cells in culture. Immune profiles of wild fish differed from laboratory-raised fish from the same parental population, with immune expression patterns in the wild converging relative to those in the laboratory. Innate measures differed between wild populations, whilst the adaptive response was associated with variation in age, relative size of fish, reproductive status and S. solidus infection levels. Laboratory-raised individuals from different populations showed markedly different innate immune response potential. The ability to combine studies in the laboratory and in the wild underline the potential of this toolkit to advance our understanding of the ecological and evolutionary relevance of immune system variation in a natural setting

Admixture between ancient lineages, selection, and the formation of sympatric stickleback species-pairs

Ecological speciation has become a popular model for the development and maintenance of reproductive isolation in closely related sympatric pairs of species or ecotypes. An implicit assumption has been that such pairs originate (possibly with gene flow) from a recent, genetically homogeneous ancestor. However, recent genomic data have revealed that currently sympatric taxa are often a result of secondary contact between ancestrally allopatric lineages. This has sparked an interest in the importance of initial hybridization upon secondary contact, with genomic reanalysis of classic examples of ecological speciation often implicating admixture in speciation. We describe a novel occurrence of unusually well-developed reproductive isolation in a model system for ecological speciation: the three-spined stickleback (Gasterosteus aculeatus), breeding sympatrically in multiple lagoons on the Scottish island of North Uist. Using morphological data, targeted genotyping, and genome-wide single-nucleotide polymorphism data, we show that lagoon resident and anadromous ecotypes are strongly reproductively isolated with an estimated hybridization rate of only ∼1%. We use palaeoecological and genetic data to test three hypotheses to explain the existence of these species-pairs. Our results suggest that recent, purely ecological speciation from a genetically homogeneous ancestor is probably not solely responsible for the evolution of species-pairs. Instead, we reveal a complex colonization history with multiple ancestral lineages contributing to the genetic composition of species-pairs, alongside strong disruptive selection. Our results imply a role for admixture upon secondary contact and are consistent with the recent suggestion that the genomic underpinning of ecological speciation often has an older, allopatric origin

Abiotic environmental variation drives virulence evolution in a fish host-parasite geographic mosaic

1. Parasite virulence varies greatly. Theory predicts that this arises from parasites optimising a trade-off between the mortality they inflict on current hosts, and their transmission to future hosts. The effect of the environment on this coevolution is rarely considered. 2. Geographic mosaics are fertile systems for studying coevolution, but again, the diversity of outcomes is often assumed to result from co-evolutionary dynamism, rather than being moulded by the environment. 3. Here we quantify variation in virulence among lakes in a geographic mosaic of coevolution between a trematode ectoparasite (Gyrodactylus arcuatus) and its three-spined stickleback(Gasterosteus aculeatus) host. 4. Virulence varies greatly in this system, and parasites are generally locally adapted to their hosts. 5. Parasites are also locally adapted to the water in their own lake, and virulence is strongly related to lake pH, the dominant axis of abiotic environmental variation in this system. 6. These results suggest that the evolution of virulence can be substantially affected by the abiotic environment, which has important implications for understanding coevolution. There are also implications for the evolutionary management of disease e.g. ectoparasites in aquaculture, the impacts of which might be expected to reduce given ongoing acidification of aquatic ecosystems

The maintenance of standing genetic variation: Gene flow vs. selective neutrality in Atlantic stickleback fish

Adaptation to derived habitats often occurs from standing genetic variation. The maintenance within ancestral populations of genetic variants favourable in derived habitats is commonly ascribed to long-term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favoured in derived habitats are neutral in ancestral populations when their frequency is relatively low. To explore the latter, we first identify genetic variants important to the adaptation of threespine stickleback fish (Gasterosteus aculeatus) to a rare derived habitat-nutrient-depleted acidic lakes-based on whole-genome sequence data. Sequencing marine stickleback from six locations across the Atlantic Ocean then allows us to infer that the frequency of these derived variants in the ancestral habitat is unrelated to the likely opportunity for gene flow of these variants from acidic-adapted populations. This result is consistent with the selective neutrality of derived variants within the ancestor. Our study thus supports an underappreciated explanation for the maintenance of standing genetic variation, and calls for a better understanding of the fitness consequences of adaptive variation across habitats and genomic backgrounds

Temporal variation in fitness pay-offs promotes cooperative breeding in long-tailed tits Aegithalos caudatus

abstract: Cooperative breeding is paradoxical because some individuals forego independent reproduction and instead help others to reproduce. The ecological constraints model states that such behavior arises because of constraints on independent reproduction. Spatial variation in constraints has been shown to co-vary with the incidence of cooperative breeding in correlational and experimental studies. Here, we examine whether temporally variable ecological constraints can act in a similar way to promote cooperative breeding in the atypical system of long-tailed tits Aegithalos caudatus. In this species, individuals may switch reproductive tactics from breeding to helping within the same breeding season. Using 7 yr of field data, we show that reproductive success declined seasonally because of declines in brood size, nestling weight, and juvenile survival. The survival to breeding age of chicks from nests with helpers was higher than for chicks from nests without helpers, and since helpers usually helped at the nest of a close relative, they accrued inclusive fitness benefits. We used these data to model the expected fitness payoffs of breeding and helping at different times during the season. The model shows that late in the breeding season, the fitness payoff from a kin-directed helping tactic becomes greater than that from independent breeding. The behavioral switch predicted by the model is consistent with the observed switch from breeding to helping, which shows that cooperative breeding may evolve as a way of making the best of a bad job at the end of a temporally constrained breeding season

Case study: The Edinburgh Research Archive

This chapter discusses the many real-life issues encountered during the development process of a combined e-theses and e-print repository which ultimately became the Edinburgh Research Archive

The institutional repository in the digital library

We begin by looking at the concept of institutional repositories within the broader context of digital libraries. ‘Digital libraries’ can mean many things, but we consider them to be libraries first and foremost, and built upon the enduring principles of information management which have lain at the heart of the practice of librarianship for hundreds of years. We look also at the significance of the qualification which defines the scope of this book – the institutional repository. Libraries are themselves repositories, and have always dealt in the management of repositories for their users. With libraries now routinely managing repositories of various types in digital format, what does it mean to qualify ‘repository’ with ‘institutional’