Molecular Ecology (2008) 17, 2245–2257 doi: 10.1111/j.1365-294X.2008.03739.x © 2008 Natural History Museum, London Journal compilation © 2008 Blackwell Publishing Ltd Blackwell Publishing Ltd Genetic discontinuity, breeding-system change and population history of Arabis alpina in the Italian Peninsula and adjacent Alps S. W. ANSELL, M. GRUNDMANN, S. J. RUSSELL, H. SCHNEIDER and J. C. VOGEL Department of Botany, The Natural History Museum, London SW7 5BD, UK Abstract Arabis alpina is a widespread plant of European arctic and alpine environments and belongs to the same family as Arabidopsis thaliana. It grows in all major mountain ranges within the Italian glacial refugia and populations were sampled over a 1300 km transect from Sicily to the Alps. Diversity was studied in nuclear and chloroplast genome markers, combining phylogeographical and population genetic approaches. Alpine populations had significantly lower levels of nuclear genetic variation compared to those in the Italian Peninsula, and this is associated with a pronounced change in within-population inbreeding. Alpine populations were significantly inbred (F IS = 0.553), possibly reflecting a change to the self-incompatibility system during leading edge colonization. The Italian Peninsula populations were approaching Hardy–Weinberg equilibrium (outbreeding, F IS = 0.076) and genetic variation was highly structured, consistent with independent local ‘refugia within refugia’ and the fragmentation of an established population by Quaternary climate oscillations. There is very little evidence of genetic exchange between the Alps and the Italian Peninsula main distribution ranges. The Alps functioned as a glacial sink for A. alpina, while the Italian Peninsula remains a distinct and separate long-term refugium. Comparative analysis indicated that inbreeding populations probably recolonized the Alps twice: (i) during a recent postglacial colonization of the western Alps from a Maritime Alps refugium; and (ii) separately into the central Alps from a source outside the sampling range. The pronounced geographical structure and inbreeding discontinuities are significant for the future development of A. alpina as a model species. Keywords: allozyme electrophoresis, Arabis alpina, breeding system, chloroplast DNA, multiple refugia, recolonization Received 20 November 2007; revision accepted 13 January 2008 Introduction The Italian Peninsula is considered to be one of the three principle glacial refugia in Europe (Hewitt 2000, 2004). Like other areas in Europe, its landscape and flora was shaped by the Quaternary climatic events over the last 2.5 Myr (Huntley 1990; Taberlet 1998; Petit et al. 2003; Hewitt 2004). Fossil pollen records indicate that the lowlands had relatively equitable conditions for temperate vegetation to survive during glaciations (Huntley & Birks 1983), while the high mountains may have been suitable for alpine species (Schönswetter et al. 2005). With the Apennines creating a more or less continuous mountain crest (with altitudes above 1000 m) along the length of Italy, cold- adapted taxa may have survived in situ over consecutive Quaternary glacial cycles. At present, Italy’s role in the long-term survival of arctic- alpine taxa is poorly understood, despite its proximity to the Alps, one of Europe’s major centres of alpine biodiversity (Vare et al. 2003). In general, alpine species have poor fossil records, with few having woody parts, and most are insect pollinated, resulting in low microfossil (pollen) densities (Svendsen et al. 2004). Alpine biogeographical hypotheses have therefore been largely developed from extant distri- bution and, lately, from genetic data. The distribution of arctic-alpine elements within the alpine flora appears to be nonrandom (Tribsch & Schönswetter 2003), and levels of Correspondence: Stephen W. Ansell, Fax: +44 207 9425529; E-mail: s.ansell@nhm.ac.uk