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Background  Understanding how past climatic oscillations have affected organismic evolution will help predict the impact that current climate change has on living organisms. The European turtle dove,  Streptopelia turtur , is a warm-temperature adapted species and a long distance migrant that uses multiple flyways to move between Europe and Africa. Despite being abundant, it is categorized as vulnerable because of a long-term demographic decline. We studied the demographic history and population genetic structure of the European turtle dove using genomic data and mitochondrial DNA sequences from individuals sampled across Europe, and performing paleoclimatic niche modelling simulations.    Results  Overall our data suggest that this species is panmictic across Europe, and is not genetically structured across flyways. We found the genetic signatures of demographic fluctuations, inferring an effective population size ( Ne ) expansion that occurred between the late Pleistocene and early Holocene, followed by a decrease in the  Ne  that started between the mid Holocene and the present. Our niche modelling analyses suggest that the variations in the  Ne  are coincident with recent changes in the availability of suitable habitat.    Conclusions  We argue that the European turtle dove is prone to undergo demographic fluctuations, a trait that makes it sensitive to anthropogenic impacts, especially when its numbers are decreasing. Also, considering the lack of genetic structure, we suggest all populations across Europe are equally relevant for conservation.    Electronic supplementary material  The online version of this article (doi:10.1186/s12862-016-0817-7) contains supplementary material, which is available to authorized users.

Genomic evidence of demographic fluctuations and lack of genetic structure across flyways in a long distance migrant, the European turtle dove