Divergence along a steep ecological gradient in Lake whitefish (Coregonus sp.) P. VONLANTHEN, *,  D. ROY,  A. G. HUDSON,*,  C. R. LARGIADE ` R, à D. BITTNER§ & O. SEEHAUSEN*   *Division of Aquatic Ecology & Evolution, Institute of Ecology & Evolution, University of Bern, Bern, Switzerland  Department of Fish Ecology & Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland àInstitute of Clinical Chemistry, Inselspital, University Hospital, and University of Bern, Inselspital, Bern, Switzerland §Computational and Molecular Population Genetics Lab (CMPG), Institute of Ecology & Evolution, University of Bern, Bern, Switzerland Introduction Adaptive radiations often occur with little apparent opportunity for geographical isolation of diverging pop- ulations (Schluter, 2000). A large number of studies have addressed the genetic differences between phenotypes in adaptive radiation but they mostly focus on pheno- typically defined ‘ecotypes’, and often demonstrate that ‘ecotypes’ are genetically differentiated despite geographical proximity (McKinnon & Rundle, 2002; Bernatchez, 2004; Kocher, 2004). Such work has been used to invoke sympatric speciation. However, in many classical radiations, such as the cichlid fish of the African Great Lakes, populations are structured both ecologically and geographically, raising the possibility that genetic divergence, even when currently maintained by ecolog- ical gradients, may have arisen during periods of geo- graphical isolation in the past (Sturmbauer et al., 2003; Koblmu ¨ ller et al., 2007). The prevalence of ecological speciation and adaptive radiation varies considerably among groups of organisms, and the reasons for this remain largely unknown (Kassen et al., 2004; Seehausen, 2006b). Two competing hypotheses are (i) lineage- specific propensity for populations to become spatially isolated, i.e. related to stenotopy and dispersal ability and (ii) lineage-specific propensity to undergo evolutionary divergence despite gene flow, i.e. related to the genetic architecture of adaptive traits. However, few studies have sampled ecological species pairs or multi-species com- plexes in a taxonomically, ecologically and spatially unbiased fashion at the appropriate scale. Despite recent theoretical advances, the relative importance of spatial and ecological factors and their interaction in adaptive Correspondence: Pascal Vonlanthen, Division of Aquatic Ecology & Evolution, Institute of Ecology & Evolution, University of Bern, Baltzerstrasse 6, CH-3012 Bern, Switzerland. Tel.: +41 (0)41 349 22 02; fax: +41 (0)41 349 21 68; e-mail: pascal.vonlanthen@eawag.ch ª 2008 THE AUTHORS. J. EVOL. BIOL. JOURNAL COMPILATION ª 2008 EUROPEAN SOCIETY FOR EVOLUTIONARY BIOLOGY 1 Keywords: clinal speciation; Coregonus; divergent selection; ecological speciation; introgression; microsatellites; species continuum; whitefish. Abstract To understand mechanisms structuring diversity in young adaptive radiations, quantitative and unbiased information about genetic and phenotypic diversity is much needed. Here, we present the first in-depth investigation of whitefish diversity in a Swiss lake, with continuous spawning habitat sampling in both time and space. Our results show a clear cline like pattern in genetics and morphology of populations sampled along an ecological depth gradient in Lake Neucha ˆ tel. Divergent natural selection appears to be involved in shaping this cline given that trait specific P ST -values are significantly higher than F ST -values when comparing populations caught at different depths. These differences also tend to increase with increasing differences in depth, indicating adaptive divergence along a depth gradient, which persists despite considerable gene flow between adjacent demes. It however remains unclear, whether the observed pattern is a result of currently stable selection-gene flow balance, incipient speciation, or reverse speciation due to anthropogenic habitat alteration causing two formerly divergent species to collapse into a single gene pool. doi:10.1111/j.1420-9101.2008.01670.x