Assessing adaptive genetic variation for conservation and management of the European grayling (Thymallus thymallus)

Huml, Jana Vanessa (2017) Assessing adaptive genetic variation for conservation and management of the European grayling (Thymallus thymallus). Doctoral thesis (PhD), Manchester Metropolitan University.

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Abstract

In this PhD, functional genetic variation of European grayling (Thymallus thymallus) is assessed to inform conservation and management of the species. This study is the first to characterize immune variation at the Major Histocompatibility complex (MHC) in grayling. The MHC is a marker of high ecological relevance, because of the strong association between immunity and fitness. Taking advantage of advances in sequencing technology, an analytical pipeline optimized for high-throughput, efficient and accurate genotyping of multi-gene families in non-model species is presented. Immune genetic variation is compared to neutral marker data. Results confirm the hypothesis that neutral marker variation does not predict immune genetic variation. Further, the possible effect of supplementing wild populations with hatchery-reared fish on immune genetic variation is evaluated. Significantly lower estimates of heterozygosity were found in stocked than purely native populations. Lower differentiation at immune genes than at neutral markers are indicative of the effects of balancing selection acting upon the MHC, within purely native, but not stocked populations. Furthermore species distribution modelling is used to identify environmental parameters shaping the distribution of grayling. To evaluate risks imposed by climate change, the sensitivity of grayling to climatic variables and range changes under predicted future scenarios are assessed. Locally-optimised mitigation strategies are shown to increase habitat suitability estimates under conditions of climate change. Evolutionary dynamics between hosts and pathogens are important factors in determining an individual’s susceptibility to disease. Studying the microbiome is therefore a promising tool to investigate the risk of disease-mediated extinctions, in relation to environmental conditions and host genetics. This study presents a preliminary analysis on the microbiome of grayling to inform experimental design for future large-scale studies. Altogether, data presented here contribute to improve the management of European grayling. More broadly, it informs conservation research in general, demonstrating the value of taking multiple approaches.