Ecological and population genomics of the wild yellow-necked mouse, Apodemus flavicollis

Species belonging to the genus Apodemus are one of the most common and broadly distributed small mammals in the Palearctic, making them ideal for studying ecological and evolutionary processes in natural systems. Although much research has focused on the ecology of Apodemus sp., relatively little is known about the evolutionary processes which govern their natural variation in the wild. This is, in part, due to the limitations of de novo genomic research in traditionally non-model organisms. However, recent advances in high-throughput library preparation techniques such as RADseq, have made non-model organisms more accessible for genome wide analyses. This thesis shows how a modified RADseq protocol (quaddRAD) can be used to conduct ecological and evolutionary genomics research in a large population of wild yellow-necked mice, Apodemus flavicollis, that is subject to highly seasonal conditions.

I show how a high quality genomic dataset of 21,011 SNPs can be generated using quaddRAD, and discuss the rationale behind the methodology in detail. I then use the genotypes to construct a multi-generational pedigree, and describe the population’s demography, fitness and allele frequency dynamics over time. I find significant variation in the genetic contributions of mice to each generation, where by the end of the study, 53.6% of the sampled population was descended from a single individual. Contrary to the expected high levels of inbreeding and low genetic diversity in such a population, I find it is largely panmictic, which suggests a large degree of connectivity to nearby populations allowing genetic rescue through high levels of migration and gene flow.

Finally, I show how heterothermic responses, which reduce an individuals energy budget by up to 65% under harsh conditions, are not only highly variable in the population, but also highly heritable. This suggests heterothermy could be subject to natural selection. I show that heterothermic responses form two distinct thermal strategies in the morphospace, which may be the result of different modes of selection acting on the population to maintain significant natural variation. This thesis shows the viability of quaddRAD for large scale genomics research in wild Apodemus sp., to cement their role as a model organism for ecological and evolutionary genomics research.