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Background  Comparative broad-scale phylogeographic studies of aquatic organisms provide insights on biotic responses to the paleohydrological dynamics associated with climatic oscillations. These insights can be used to formulate a framework for understanding the evolutionary history of a species or closely related taxa as well as aid in predictive modeling of further responses to climate change. Anadromous fishes constitute interesting models for understanding the relative importance of environmental versus biological factors in shaping intraspecific genetic substructure on the interface between marine and freshwater realms. European shads,  Alosa alosa  and  A. fallax  are anadromous species that have persisted through historical large-scale environmental perturbations and now additionally face an array of anthropogenic challenges. A comprehensive phylogeographic investigation of these species is needed to provide insights on both the historical processes that have shaped their extant genetic structure and diversity, and the prospects for their future management and conservation.    Results  Despite introgressive hybridization,  A. alosa  and  A. fallax  are genetically divergent, congruent with previous studies. Three similarly divergent mtDNA clades were recognized within both  A. fallax  and  A. alosa , most likely originating during common periods of isolation during the Pleistocene among the studied oceanographic regions. Periods of basin isolation apparently extended to the Black Sea as additional  Alosa  clades occur there. The present day geographic distribution of genetic diversity within European  Alosa  sp. suggests the existence of a strong but permeable barrier between the Atlantic and Mediterranean seas, as shown for a number of other aquatic species .  Overall mtDNA diversity is considerably lower for  A. alosa  compared to  A. fallax , suggesting that the former species is more sensitive to climatic as well as anthropogenic changes. For  A. fallax , migration from the Mediterranean to the Atlantic was detected but not in the opposite direction, with colonization of the North Atlantic probably occurring after last glacial maximum.    Conclusion  The similar haplotype network topologies between the two species support a common intraspecific history of isolation. Despite these similarities,  A. alosa  and  A. fallax  have clearly responded differently to the hydrological dynamics of the Pleistocene, as reflected in their distinct demographic histories. As the species additionally occupy different ecological niches it should not be surprising that they differ in resilience to natural or human-mediated climatic changes. For  A. fallax , it is further clear that its demographic response to large-scale hydrological events is not synchronized between the Atlantic and Mediterranean basins. These regional and species-specific differences should be incorporated into future predictive modeling of biological response to climate change as well as current management concepts.

Comparative phylogeography and demographic history of European shads (Alosa alosa and A. fallax) inferred from mitochondrial DNA