Tick population genomics and viral diversity in Finland: Implications for emerging tick-borne diseases Publication abstract: Tick-borne diseases are rapidly emerging as major vector-borne health threats across temperate and boreal regions, driven by environmental and ecological change. Tick populations are spreading into areas that were previously unsuitable, creating an urgent need for research in these regions. Ixodes ricinus and I. persulcatus increasingly overlap in sympatric areas in Finland, where they transmit multiple pathogens, including tick-borne encephalitis and Lyme borreliosis, alongside diverse viral, bacterial, and protozoan lineages. Understanding population structure, hybridization, and viral diversity in these vectors is essential for anticipating disease risks. This thesis integrates population genomics, long-term epidemiological synthesis, and single-tick metatranscriptomics to investigate genetic differentiation, hybridization, and RNA virome diversity in Finnish ticks.Genome-wide SNP data generated using ddRADseq from 192 ticks revealed strong genetic differentiation between the two species, with clear separation in multivariate and Bayesian clustering analyses. A total of 11 hybrid individuals (~5.7%) were detected, including both likely F1 hybrids and introgressed individuals, indicating ongoing but limited gene flow in sympatric regions. Genetic diversity was higher in I. ricinus, whereas I. persulcatus showed reduced diversity consistent with recent expansion.A synthesis of over six decades of surveillance data demonstrated a marked increase in the incidence and geographic spread of tick-borne encephalitis in Finland, alongside northward and westward expansion of tick populations and increasing species overlap. This growing public health burden has led to changes in TBE risk areas maintained by the Finnish Institute for Health and Welfare.Metatranscriptomic analysis of 96 individual ticks identified 49 RNA viruses across 12 families, including several novel lineages. Tick species strongly structured viral communities: I. persulcatus was enriched with bunyavirus-like taxa, whereas I. ricinus exhibited higher viral diversity and variability. Together, these findings provide a comprehensive framework for understanding vector-pathogen dynamics and improving disease risk prediction under ongoing environmental change.