The role of pathogens in shaping genetic variation within and among populations in an island bird

This thesis aimed to investigate the role of pathogen-mediated selection in shaping patterns of genetic variation in Berthelot’s pipit Anthus berthelotii, a passerine endemic to the Macaronesian archipelagos of the Canary Islands, Madeira, and Selvagens. I used restriction-site associated DNA sequencing (RAD-seq) to investigate patterns of neutral diversity among Berthelot’s pipit populations, and in its sister species, the tawny pipit Anthus campestris, finding a loss of genome-wide diversity associated with colonisation history and genetic bottlenecks. I performed genome-wide association studies (GWAS) to identify genomic regions associated with malaria infection and bill length. I detected signatures of divergent selection around potential candidate genes related to immunity and metabolism, suggesting that these traits play oles in divergence and adaptation in this species. I then characterised genetic variation in Berthelot’s and tawny pipits at avian β-defensins (AvBDs), a key gene family of the innate immune system. Allelic richness decreased with increasing numbers of bottlenecks. However, some AvBDs showed elevated nucleotide diversity compared with genome-wide trends. We found no evidence of local adaptation or balancing selection in Berthelot’s pipits, suggesting that AvBD variation in this species is predominantly driven by genetic drift. Finally, I investigated whether malaria was driving fine-scale patterns of variation at SNPs identified in the earlier GWAS, and at the toll-like receptor 4 (TLR4) locus, a pathogen recognition receptor of the innate immune system, in two island populations. Both islands showed potential associations between malaria infection and TLR4 variation. In contrast, there was no association between a GWAS SNP and malaria risk in Tenerife, whereas in Porto Santo, the opposite trend to the original GWAS was found, potentially indicating local adaptation and population divergence. Overall, the evidence suggests that although functional variation in Berthelot’s pipits is strongly influenced by demographic history, adaptation to pathogens may be occurring within and between populations.