A species’ demographic history provides important context to contemporary population genetics and a possible insight into past responses to climate change. An individual’s genome provides a window into the evolutionary history of contemporary populations. Pairwise Sequentially Markovian Coalescent (PSMC) analysis uses information from a single genome to derive fluctuations in effective population size change over the last ~5 million years. Here we apply PSMC analysis to two European nightjar (Caprimulgus europaeus) genomes, sampled in Northwest and Southern Europe, with the aim of revealing the demographic history of nightjar in Europe. We successfully reconstructed effective population size over the last 5 million years for two contemporary nightjar populations. Our analysis shows that nightjar are responsive to global climate change, with effective population size broadly increasing under stable warm periods and decreasing during cooler spans and prolonged glacial periods. PSMC analysis on the pseudo-diploid combination of the two genomes revealed fluctuations in gene flow between the populations over time, with gene flow ceasing by the last-glacial maximum. This pattern of differentiation is in line with the species utilising different refugia during glacial maxima. We suggest that nightjar in Europe may show latitudinal (East-West) genetic structuring as a result of reduced gene flow between different glacial refugia. Finally, our results suggest that migratory behaviour in nightjar likely evolved prior to the last-glacial maximum, with long-distance migration seemingly persisting throughout the Pleistocene. However, further genetic structure analysis of nightjar from known breeding sites across the species’ contemporary range is needed to fully understand the extent and origins of range-wide differentiation in the species.

Understanding the frequency, spatiotemporal dynamics and impacts of parasite coinfections is fundamental to developing control measures and predicting disease impacts. The European turtle dove (Streptopelia turtur) is one of Europe’s most threatened bird species. High prevalence of infection by the protozoan parasite Trichomonas gallinae has previously been identified, but the role of this and other coinfecting parasites in turtle dove declines remains unclear. Using a high-throughput sequencing approach, we identified seven strains of T. gallinae, including two novel strains, from ITS1/5.8S/ITS2 ribosomal sequences in turtle doves on breeding and wintering grounds, with further intra-strain variation and four novel sub-types revealed by the iron-hydrogenase gene. High spatiotemporal turnover was observed in T. gallinae strain composition, and infection was prevalent in all populations (89–100%). Coinfection by multiple Trichomonas strains was rarer than expected (1% observed compared to 38.6% expected), suggesting either within-host competition, or high mortality of coinfected individuals. In contrast, coinfection by multiple haemosporidians was common (43%), as was coinfection by haemosporidians and T. gallinae (90%), with positive associations between strains of T. gallinae and Leucocytozoon suggesting a mechanism such as parasite-induced immune modulation. We found no evidence for negative associations between coinfections and host body condition. We suggest that longitudinal studies involving the recapture and investigation of infection status of individuals over their lifespan are crucial to understand the epidemiology of coinfections in natural populations.