Ancient demographic reconstruction and spat temporal population genomics of European nightjar

The sequenced genomes in this project were used for two sub-projects, detailed below:Ancient Demographic Reconstruction:A species' demographic history provides important context to contemporary population genetics and insights into past responses to climate change. An individual's genome offers a view into the evolutionary history of current populations. Pairwise Sequentially Markovian Coalescent (PSMC) analysis uses information from a single genome to identify changes in effective population size over the last 5 million years. In this study, we applied PSMC analysis to two European nightjar (Caprimulgus europaeus) genomes, sampled from Northwest and Southern Europe, to explore the demographic history of nightjars in Europe. We successfully reconstructed the effective population size over the last 5 million years. Our analysis revealed that the effective population size of nightjars increased during stable warm periods and decreased during cooler spans and prolonged glacial periods, in response to global climate change. PSMC analysis on the pseudo-diploid combination of the two genomes showed fluctuations in gene flow between ancestral populations over time, with gene flow ceasing by the last-glacial period. Our results suggest possible divergence in the European nightjar population, with timings consistent with differentiation driven by isolation in different refugia during glaciation periods. Additionally, our findings indicate that migratory behavior in nightjars likely evolved before the last-glacial period and persisted throughout the Pleistocene. However, further genetic structure analysis of individuals from known breeding sites across the species' contemporary range is necessary to understand the extent and origins of range-wide differentiation in nightjars.Nightjar Spatio-temporal Population Genomics:Migratory birds are inherently mobile, a strategy that may reduce the impacts of habitat loss and fragmentation on genetic structuring and diversity. However, specialist resource requirements and distribution at range edges may counteract these benefits. The European nightjar (Caprimulgus europaeus) is a long-distance migratory bird and a habitat specialist. Like other long-distance migrants, nightjars have experienced a significant demographic decline across the British Isles and much of Northern and Western Europe over the last century. Despite the species' mobility, limited ringing recoveries suggest high site fidelity and little movement between breeding sites in the British Isles, the species' western range limit. With the population decline in nightjars well-documented in the British Isles, there is a need to quantify the extent and genetic impacts. We applied full genome resequencing to 60 historic (1841-1980) and 36 modern individual nightjars from the British population. Our results showed a statistically significant 34.8% loss in heterozygosity over the last ~180 years in this population, indicating a move away from panmixia and demonstrating weak spatial structure in the modern population. Such fine-scale structuring in migratory birds is rare. Our findings provide a case study on the impact of fragmentation on a species with specialist resource requirements at its range limit. Similar negative demographic trends in nightjars and other long-distance migrants in Northern and Western Europe suggest that the genetic signature found in the British population may be representative of other nightjar populations and European avifauna more broadly. While our results indicate no immediate cause for conservation concern for nightjars, they do show a trajectory of declining genetic diversity and increasing structure, potentially shared with other migratory species. Our study underscores the value of applying spatio-temporal population genetics analysis to migratory bird populations, despite their inherent mobility.