Molecular Ecology (2007) 16, 4972–4983 doi: 10.1111/j.1365-294X.2007.03585.x © 2007 The Authors Journal compilation © 2007 Blackwell Publishing Ltd Blackwell Publishing Ltd Nuclear and chloroplast microsatellites reveal extreme population differentiation and limited gene flow in the Aegean endemic Brassica cretica (Brassicaceae) KRISTINA EDH,* BJÖRN WIDÉN† and ALF CEPLITIS* *Department of Cell and Organism Biology, Lund University, Sölvegatan 29, SE-22362, Lund, Sweden, †Department of Ecology, Section of Plant Ecology and Systematics, Lund University, Sölvegatan 37, SE-22362, Lund, Sweden Abstract Nuclear and chloroplast microsatellite markers were used to study population structure and gene flow among seven Cretan populations of the Aegean endemic plant species Brassica cretica (Brassicaceae). Both nuclear and chloroplast markers revealed exceptionally high levels of population differentiation (overall F ST = 0.628 and 1.000, respectively) and relatively little within-population diversity (overall H S = 0.211 and 0.000, respectively). Maximum-likelihood estimates of directional migration rates were low among all pairs of populations (average Nm = 0.286). There was no evidence that differences in flower colour between populations had any influence on historical levels of gene flow. In addition, a haplotype network showed that all five chloroplast haplotypes found in the sample were closely related. Together, these results suggest that current patterns of diversification in B. cretica are mainly a result of genetic drift during the last half million years. The main conclusions from the present study are consistent with the prevailing hypothesis that plant diversification in the Aegean region is driven by random rather than adaptive differentiation among isolated populations. Keywords: Aegean flora, Brassica cretica, differentiation, gene flow, microsatellites, population structure Received 24 June 2007; revision accepted 14 September 2007 Introduction Fragmentation of species into genetically isolated popu- lations has important consequences for diversification, adaptation and speciation (Dobzhansky 1937; Mayr 1942; Rieseberg & Burke 2001; Coyne & Orr 2004; Morjan & Rieseberg 2004). This is evident in the flora of the Aegean region, encompassing the Aegean archipelago and the adjacent Greek and Turkish mainland areas, which has among the highest levels of plant diversity and endemism on earth (Médail & Quézel 1997). The diversity of the Aegean flora has been primarily attributed to the region’s complex geological history, which has resulted in a highly fragmented insular landscape with many plant species in this area showing scattered distributions in small, geographically isolated populations (Snogerup 1985; Thompson 2005). According to the prevailing hypothesis for the evolution of the Aegean flora, geographical isolation of plant populations and a concomitantly reduced gene flow followed by random differentiation — ‘nonadaptive radiation’ (sensu Strid 1970) — has caused the mosaic of variation typically displayed by Aegean plant taxa (Runemark 1969; Strid 1970; Snogerup et al. 1990; Bittkau & Comes 2005; see also Thompson 2005). Among the islands of the Aegean, Crete is by far the largest and also floristically the most diverse: well over two-thirds of all Greek plant species are found in Crete and it has the greatest proportion of endemic species in the Aegean area (Greuter 1971; Webb 1978). Crete has also experi- enced a much longer history of isolation compared to the smaller Aegean islands of the Cyclades and the Dodecanese, which did not disconnect from the continental landmass of Asia Minor until late Pleistocence some 0.5 million years ago (see, e.g. Schilthuizen et al. 2004; Simaiakis & Mylonas 2006). By contrast, Crete had become separated from the Greek mainland and subsequently split up into smaller islands (palaeo-islands) already around 8 million years ago Correspondence: Alf Ceplitis, Fax: +46-46-147478, E-mail: alf.ceplitis@cob.lu.se