Northern and Southern expansions of Atlantic brown trout (Salmo trutta) populations during the Pleistocene MARTÍ CORTEY 1,2 *, MANUEL VERA 1,3 , CARLES PLA 1 and JOSÉ-LOÍS GARCÍA-MARÍN 1 1 Laboratori d’Ictiologia Genètica, Facultat de Ciències-UdG, Campus de Montilivi s/n, 17071 Girona, Spain 2 Centre de Recerca en Sanitat Animal, UAB-IRTA, Edifici CReSA, Campus Bellaterra, Cerdanyola del Vallès (Barcelona), 08193, Spain 3 Departamento de Xenética, Facultad Veterinaria, Campus Lugo USC, Lugo, 27002, Spain Received 6 November 2008; accepted for publication 12 January 2009 The phylogeography of Atlantic brown trout (Salmo trutta) was analysed using mitochondrial DNA control region complete sequences of 774 individuals from 57 locations. Additionally, the available haplotype information from 100 published populations was incorporated in the analysis. Combined information from nested clade analysis, haplotype trees, mismatch distributions, and coalescent simulations was used to characterize population groups in the Atlantic basin. A major clade involved haplotypes assigned to the Atlantic (AT) lineage, but another major clade should be considered as a distinct endemic lineage restricted to the Iberian Peninsula. The phylogeography of the Atlantic populations showed the mixed distribution of several Atlantic clades in glaciated areas of Northern Europe, whereas diverged haplotypes dominated the coastal Iberian rivers. Populations inhabiting the Atlantic rivers of southern France apparently contributed to postglacial colonization of northern basins, but also comprised the source of southern expansions during the Pleistocene. © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 904–917. ADDITIONAL KEYWORDS: glacial refugia – mitochondrial control region – phylogeography. INTRODUCTION Paleoclimate records indicate that the last 700 Kyr have been dominated by major ice ages with a cycle of approximately 100 Kyr interrupted by relatively short warm interglacials, such as those that we experience at present (Hewitt, 1996). The Quaternary cold periods in Europe are thought to have heavily influ- enced the amount and distribution of intraspecific genetic variation in both animals and plants (Taberlet et al., 1998). High genetic richness in southern Europe is common, and is probably the result of refugial persistence and accumulation of variation over several ice ages, whereas the rapid postglacial colonization is probably responsible for the reduced complexity of northern lineages (Hewitt, 1996, 2000, 2001). High-resolution climate records in the North Atlantic and Greenland during the late Pleistocene demonstrate dramatic climate variability over the past 130 Kyr (Bond et al., 1993), which led to abrupt changes in the terrestrial ecosystem across the Atlan- tic basin (Sánchez Goñi et al., 2000). The distribution of genetic diversity in temperate freshwater fish has been deeply modified because of Pleistocene glaciations, even though these modifica- tions have not necessarily implied a reduction, but sometimes rather an extension of their distribution area (Durand et al., 1999a; Yamamoto et al., 2004; Kikko et al., 2008). In several freshwater species, such as the perch (Perca fluviatilis; Nesbø et al., 1999), the grayling (Thymallus thymallus; Koskinen et al., 2000) or the bullhead (Cottus gobio; Kontula & Väinölä, 2001; Volckaert et al., 2002), late North Europe’s recolonization has been achieved from several glacial refugia located around the Scandina- vian ice sheet. In other European fish such as the chub (Squalius cephalus; Durand, Persat & Bouvet, *Correspondence author. Email: marti.cortey@cresa.uab.cat Biological Journal of the Linnean Society, 2009, 97, 904–917. With 3 figures © 2009 The Linnean Society of London, Biological Journal of the Linnean Society, 2009, 97, 904–917 904