Phylogeography, historical demography and habitat suitability modelling of freshwater fishes inhabiting seasonally fluctuating Mediterranean river systems: a case study using the Iberian cyprinid Squalius valentinus S. PEREA and I. DOADRIO Museo Nacional de Ciencias Naturales, CSIC, Biodiversity and Evolutionary Biology Department, C/Jos  e Guti  errez Abascal, 2. 28006, Madrid, Spain Abstract The Mediterranean freshwater fish fauna has evolved under constraints imposed by the seasonal weather/hydrological patterns that define the Mediterranean climate. These conditions have influenced the genetic and demographic structure of aquatic communities since their origins in the Mid-Pliocene. Freshwater species in Mediterra- nean-type climates will likely constitute genetically well-differentiated populations, to varying extents depending on basin size, as a consequence of fragmentation resulting from drought/flood cycles. We developed an integrative framework to study the spatial patterns in genetic diversity, demographic trends, habitat suitability modelling and landscape genetics, to evaluate the evolutionary response of Mediterranean-type fresh- water fish to seasonal fluctuations in weather. To test this evolutionary response, the model species used was Squalius valentinus, an endemic cyprinid of the Spanish Lev- antine area, where seasonal weather fluctuations are extreme, although our findings may be extrapolated to other Mediterranean-type species. Our results underscore the significant role of the Mediterranean climate, along with Pleistocene glaciations, in diversification of S. valentinus. We found higher nuclear diversity in larger drainage basins, but higher mitochondrial diversity correlated to habitat suitability rather than basin size. We also found strong correlation between genetic structure and climatic fac- tors associated with Mediterranean seasonality. Demographic and migration analyses suggested population expansion during glacial periods that also contributed to the cur- rent genetic structure of S. valentinus populations. The inferred models support the significant contribution of precipitation and temperature to S. valentinus habitat suit- ability and allow recognizing areas of habitat stability. We highlight the importance of stable habitat conditions, fostered by typical karstic springs found on the Mediterra- nean littoral coasts, for the preservation of freshwater species inhabiting seasonally fluctuating river systems. Keywords: distribution modelling, freshwater fishes, historical demography, Mediterranean climate, phylogeography, seasonally fluctuating rivers Received 14 May 2014; revision received 8 June 2015; accepted 12 June 2015 Introduction In the Mediterranean basin, the southern European pen- insulas have been recognized as the primary refugia for many species during the Late Cenozoic, most showing high genetic diversity resulting from isolation of geno- types and gain or loss of alleles (Hewitt 2004). The importance of the peninsulas in this respect has been widely debated for flora and terrestrial fauna (Hewitt 2004; Provan & Bennet 2008; Sommer et al. 2009; Fuen- tes-Utrilla et al. 2014), while there has been little interest Correspondence: Silvia Perea, Fax: +34 91 5645078; E-mail: sperea2@gmail.com © 2015 John Wiley & Sons Ltd Molecular Ecology (2015) 24, 3706–3722 doi: 10.1111/mec.13274