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The phylogeographic studies of unrelated species that share overlapping distributions lead to new perspectives. Indeed, if different species with similar distributions shared the same phylogeographic pattern, then a common extrinsic cause could be proposed, involving some important issues for species conservation. Considering different mitochondrial studies of European freshwater fishes (threatened or not), it will be possible to perform such a comparative phylogeographic analyses. However, we illustrated how similar mitochondrial patterns can be due to different demographic models or evolutionary scenarios inducing numerous pitfalls. In this review, we present some major theoretical and practical challenges on phylogeography that need to be overcome before the inference of a global scenario. More than the evolution of the phylogeography discipline, estimation of the history of populations/species and their relationships is one of the most important challenges for conservation managers.

Quaternary Pattern of Freshwater Fishes in Europe: Comparative Phylogeography and Conservation Perspective