Extensive gene flow over Europe and possible speciation over Eurasia in the ectomycorrhizal basidiomycete Laccaria amethystina complex LUCIE VINCENOT,* 1 KAZUHIDE NARA,† CHRISTOPHER STHULTZ,* JESSY LABBE ´ ,‡§ MARIE-PIERRE DUBOIS,* LEHO TEDERSOO, – FRANCIS MARTIN‡ and MARC-ANDRE ´ SELOSSE* *UMR5175, Centre d’Ecologie Fonctionnelle et Evolutive, 1919 route de Mende, 34293 Montpellier Cedex 5, France, †Department of Natural Environmental Studies, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8563, Japan, ‡UMR1136, Interactions Arbres ⁄ Microorganismes, INRA-Nancy, 54280 Champenoux, France, §Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6034, USA, –Institute Ecology and Earth Sciences and The Natural History Museum, University of Tartu, 40 Lai Str., 51005 Tartu, Estonia Abstract Biogeographical patterns and large-scale genetic structure have been little studied in ectomycorrhizal (EM) fungi, despite the ecological and economic importance of EM symbioses. We coupled population genetics and phylogenetic approaches to understand spatial structure in fungal populations on a continental scale. Using nine microsatellite markers, we characterized gene flow among 16 populations of the widespread EM basidiomycete Laccaria amethystina over Europe (i.e. over 2900 km). We also widened our scope to two additional populations from Japan (10 4 km away) and compared them with European populations through microsatellite markers and multilocus phylogenies, using three nuclear genes (NAR, G6PD and ribosomal DNA) and two mitochondrial ribosomal genes. European L. amethystina populations displayed limited differentiation (average F ST = 0.041) and very weak isolation by distance (IBD). This panmictic European pattern may result from effective aerial dispersal of spores, high genetic diversity in populations and mutualistic interactions with multiple hosts that all facilitate migration. The multilocus phylogeny based on nuclear genes confirmed that Japanese and European specimens were closely related but clustered on a geographical basis. By using microsatellite markers, we found that Japanese populations were strongly differentiated from the European populations (F ST = 0.416), more than expected by extrapolating the European pattern of IBD. Population structure analyses clearly separated the populations into two clusters, i.e. European and Japanese clusters. We discuss the possibility of IBD in a continuous population (considering some evidence for a ring species over the Northern Hemisphere) vs. an allopatric speciation over Eurasia, making L. amethystina a promising model of intercontinental species for future studies. Keywords: cryptic speciation, ectomycorrhizal fungi, gene flow, inbreeding, isolation by distance, microsatellite markers, phylogeography, population structure Received 11 July 2011; revision received 27 October 2011; accepted 1 November 2011 Introduction Many fungal species extend over a whole continent, or even over several continents (Douhan et al. 2007; Queloz et al. 2011), and a comparative analysis of regional inventories revealed that 28–63% of macrofungal spe- cies are shared by at least two continental regions (Mueller et al. 2007). Hence, they seem to follow the Correspondence: Lucie Vincenot, Fax: (+39 0461650872); E-mail: lucie.vincenot@cefe.cnrs.fr 1 Present address: Sustainable Agro-Ecosystems and Bioresources, Fondazione Edmund Mach-IASMA, via Edmund Mach 1, 38100 San Michele all’Adige, Italy Ó 2011 Blackwell Publishing Ltd Molecular Ecology (2011) doi: 10.1111/j.1365-294X.2011.05392.x