Introduction

Climate variability has been significantly affecting diversification and extinction processes and, together with other abiotic and biotic forces, restricting species to specific areas (Peterson, 2009; Quante, 2010). Understanding the role of climate in shaping the genetic structure of species is a major goal in biogeography and evolutionary biology (e.g. Carnaval et al., 2009; Velo‐Antón et al., 2013) and a priority for applying conservation strategies (Ladle & Whittaker, 2011).

Repeated warming–cooling cycles that occurred during the Pleistocene have been suggested to affect the distribution patterns and genetic substructure of taxa world‐wide by forcing species to retract or spread according to their ecological requirements (Avise et al., 1998; Hewitt, 2000, 2004; Peterson & Ammann, 2013). While thermophilic species retreated and lost habitat during glacial periods (e.g. Hewitt, 1999; Garcia‐Porta et al., 2012; Kindler et al., 2013), cold temperate species expanded their distributional ranges, potentially connecting populations with the increase of suitable habitats (e.g. Fedorov et al., 2003; Kropf et al., 2003; Bannikova et al., 2010; Velo‐Antón et al., 2013). Suitable climatic regions (i.e. refugia) allowed the persistence of isolated populations during unfavourable conditions, promoting allopatric differentiation and later acting as centres of expansion (Bennett & Provan, 2008; Stewart et al., 2010; Schmitt & Varga, 2012). In this regard, the Iberian Peninsula has long been recognized as a major glacial refuge for European fauna during Pleistocene (Taberlet et al., 1998). Multiple levels of genetic substructure in both mediterranean (i.e. thermophilic) and Euro‐Siberian (i.e. temperate) species suggest that different areas within Iberia favoured the persistence of isolated populations during these periods (see Gómez & Lunt, 2007). Phylogeographic patterns have been well studied in many Iberian taxa, especially in ectothermal species of low dispersal abilities, such as amphibians and reptiles (see Weiss & Ferrand, 2007). Still, independent inferences with palaeoclimatic models are needed to better understand the role of climatic oscillations in the evolutionary processes occurred in Western Europe (e.g. Garcia‐Porta et al., 2012; Igea et al., 2013).

The combination of genetic and environmental data in spatial frameworks has increased research perspectives in biogeography and evolutionary biology (Kozak et al., 2008; Alvarado‐Serrano & Knowles, 2014). Such approaches have allowed characterizing species environmental preferences (Barata et al., 2012), identifying the potential location of past climatic refugia (Waltari et al., 2007), understanding the role of past climatic changes in spatial and genetic connectivity (Velo‐Antón et al., 2013), or studying the dynamics of hybrid zones (Tarroso et al., 2014). By integrating phylogeographic and ecological niche‐modelling analyses, signals of historical processes can be explicitly related to reconstructions of past distributional ranges, reinforcing interpretations of the probable responses of species to climatic oscillations (Waltari et al., 2007; Alvarado‐Serrano & Knowles, 2014). Ecological niche models are based on the realized ecological niche concept, assuming that the environmental (i.e. the Grinnellian) niche of a species determines its large‐scale distribution (Soberón, 2007), and thus, reconstructions of past distributional ranges are not exempt of assumptions and uncertainties derived from these techniques (Kozak et al., 2008; Wiens et al., 2009; Alvarado‐Serrano & Knowles, 2014). Nevertheless, the combination of phylogeographic and ecological niche‐modelling analyses is promising for unveiling questions related to the restrictiveness distribution of many species (e.g. Beatty & Provan, 2013), especially in taxa with high environmental dependency, such as reptiles (e.g. Edwards et al., 2012; Camargo et al., 2013).

In this work, we combine phylogeographic and ecological niche‐modelling analyses to infer the role of climate in the evolutionary history of the nearly Iberian endemic reptile Vipera seoanei. It is a Euro‐Siberian species restricted to northern Portugal and Spain and entering a few kilometres in south‐western France (Braña, 2002; Brito, 2008). Vipera seoanei is included in the Pelias clade (subfamily Viperinae, subgenus Pelias) and probably diverged from its sister species (Vipera berus) in the late Pliocene (Garrigues et al., 2005; Ursenbacher et al., 2006a). As other European vipers, its ectothermal physiology probably made it susceptible to the environmental niche alterations of the Pleistocene, whereas low dispersal hampered tracking geographic shifts in environmental conditions and strongly affected connectivity and gene flow among populations (e.g. Ursenbacher et al., 2006a,b, 2008; Ferchaud et al., 2012; Velo‐Antón et al., 2012). However, information about genetic variability and structuring is unavailable for this species, and its evolutionary history and intraspecific systematics still rely on morphological variability (Bea et al., 1984; Saint‐Girons et al., 1986; Martínez‐Freiría & Brito, 2013). Previous studies identified two parapatric groups, designated as subspecies (V. s. cantabrica and V. s. seoanei), which morphologically converge in contact zones, and high phenotypic polymorphism of populations, with four coloration patterns and high frequency of melanistic specimens at high altitude (Bea et al., 1984; Saint‐Girons et al., 1986). Environmental factors, such as precipitation or temperature, are likely to be related to geographic variation in pholidotic traits, suggesting the occurrence of adaptive diversification processes (Martínez‐Freiría & Brito, 2013).

Our main goal is to understand the influence of Pleistocene climatic oscillations on V. seoanei genetic structure by integrating phylogeographic and ecological niche‐modelling approaches, and to compare it to currently known phylogeographic patterns described for other taxa across northern Iberia. Specifically, we aim to: (1) assess the intraspecific genetic structure and variability of V. seoanei; (2) identify stable climatic areas for the species in the past; (3) infer a biogeographic scenario for the species; and (4) resolve the systematics within the species. We anticipate a strong response to Pleistocene climatic oscillations of this Euro‐Siberian species restricted to one of the major European glacial refugia.