Revealing the Demographic History of the European nightjar (Caprimulgus europaeus).

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. Revealing the Demographic History of the European nightjar ( Caprimulgus europaeus ). Abstract 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