Molecular Ecology (2009) 18, 1523–1536 doi: 10.1111/j.1365-294X.2009.04106.x © 2009 Blackwell Publishing Ltd Blackwell Publishing Ltd Strong correlation of wild barley ( Hordeum spontaneum) population structure with temperature and precipitation variation S. HÜBNER,* M. HÖFFKEN,† E. OREN,* G. HASENEYER,† N. STEIN,† A. GRANER,† K. SCHMID‡ and E. FRIDMAN* *The R.H. Smith Institute of Plant Sciences and Genetics in Agriculture, The R.H. Smith Faculty of Agricultural, Food and Environment, The Hebrew University of Jerusalem, PO Box 12, Rehovot 76100, Israel, †Institute of Plant Genetics and Crop Plant Research (IPK), Correnstrasse 3, 06466 Gatersleben, Germany, ‡Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, PO Box 7080, SE-75007 Uppsala, Sweden Abstract In this study, we present the genetic analysis of a new collection of wild barley (Hordeum spontaneum) using 42 simple sequence repeat (SSR) markers that represent the seven chromosomes. The Barley1K (B1K) infrastructure consists of 1020 accessions collected in a hierarchical sampling mode (HSM) from 51 sites across Israel and represents the wide adaptive niche of the modern barley’s ancestor. According to the genetic structure analysis, the sampled sites can be divided into seven groups, and sampled microsites located on opposing slopes or in different soil types did not show significant genetic differentiation. Although the genetic analysis indicates a simple isolation-by-distance model among the populations, examination of the genetic populations’ structure with abiotic parameters in an ordination analysis revealed that the combination of elevation, mid-day temperature and rainfall explains a high proportion of the variance in the principal components analysis. Our findings demonstrate that the current populations have therefore been shaped and distinguished by non-selective forces such as migration; however, we suggest that aridity and temperature gradients played major roles as selective forces in the adaptation of wild barley in this part of the Fertile Crescent. This unique collection is a prelude for the investigation of the molecular basis underlying plant adaptation and responsiveness to harsh environments. Keywords: adaptation, barley, climate change, conservation, Hordeum spontaneum, microsatellites, population genetics Received 23 September 2008; revision revised 10 December 2008; accepted 19 December 2008 ‘... there is no doubt that the wild forms, ancestral to the presently cultivated species, deserve the same research efforts as given the cultivated species.’ Nicolai I. Vavilov (1887–1943) Many plant species exhibit a high level of genetic and phenotypic variation within their distribution range. This variation is created by population–genetic processes such as mutation, recombination and introgression, and by processes such as genetic drift and natural selection that determine its evolutionary fate. One of the central challenges in current evolutionary research is to disentangle the effects of genetic drift and natural selection on temporal and spatial patterns of genetic variation in order to elucidate the role of adaptive evolution in generating phenotypic diversity (Mitchell-Olds et al. 2007; Ellegren & Sheldon 2008). Since demographic processes, such as rapid population growth or admixture, may produce patterns of genetic var- iation that resemble or confound the outcome of natural selection (Nielsen 2001; Przeworski 2002), the detection of selection on a molecular level remains a challenging task despite the existence of numerous selection tests (Nielsen 2005). However, recent progress in genome technologies has enabled large-scale analyses of genetic variation and Correspondence: Eyal Fridman, Fax: +972-8-9468265; E-mail fridmane@agri.huji.ac.il