Supplementary Methods Sampling and DNA extraction: A total of 348 individuals of U. minor and 92 individuals of U. glabra were used for the analysis of chloroplast diversity. Most of these samples come from ex situ collections from France (Cemagref, Eric Collin), Italy (CNR, Alberto Santini) and Spain (DGB, Salustiano Iglesias). Additional field samples were collected from France (provided by E. Collin), Greece (Stephanos Diamandis), Italy (A. Santini), Spain (Miguel A. Cogolludo) and Britain (Max Coleman), sampled trees were at least 50 m apart, in order to minimise relatedness and clonal origin. Twenty-three of those U. minor samples (from Spain, England and Central Italy) were genotyped using nuclear microsatellites and AFLPs. Total DNA was isolated from leaves as described1. Chloroplast DNA analysis: Chloroplast DNA polymorphism was studied by PCR-RFLP procedure. A set of five primer pairs (DT, SfM, HK, K1K2 and VL) were amplified as described2,3. PCR products were digested with restriction enzymes TaqI (fragments DT, K1K2), MvaI (SfM), HaeIII (HK) and HinfI (VL) following manufacturer’s (Boehringer Mannheim) instructions. The digested fragments were separated on 8% polyacrylamide, 1xTBE gels, and visualised using silver staining. For each polymorphic fragment in the digestion profiles, length variants were numbered by decreasing molecular weight. Haplotypes were defined according to combination of different variants observed in fourteen polymorphic digestion fragments, considering the five amplification fragments together. Arlequin 2.000 software4 was used to calculate the Minimum Spanning Tree (MST) of the haplotypes. Nuclear microsatellites: Seven nuclear microsatellites (Ulmi1-11 (AY520826), Ulmi1-21 (AY520827), Ulmi198 (AY520829), Ulmi1-165 (AY520830), Ulmi1-177 (AY520832), Ulmi2-16 (AY520835), Ulmi2-20 (AY520837))5 were analysed. PCR amplification, fragment visualisation and score were carried out as described5. AFLP analysis: AFLP analysis was performed as described6 with slight modifications7. Preamplification was carried out using EcoRI + A / MseI + C primers. Two primer combinations were used for selective amplification: EcoRI + ACT / MseI + CAG and EcoRI + ACT / MseI + CCA. EcoRI + ACT primer was labelled in its 5’ end with IRDye800 (MWG Biotech AG, Germany). Amplified fragments up to 500 bp were resolved in 8% acrylamide, 7M urea, 0.8xTBE gels on a 4200 Li-Cor automated DNA sequencer (Li-Cor Biosciences, Lincoln, NE, USA). Only polymorphic scorable bands were considered in this analysis. The presence / absence of these bands were visually scored by two persons independently and binary coded (as 1 or 0). TREECON software8 was used to calculate the distance matrix among samples (Nei and Li genetic distance option), which was subjected to cluster analysis by UPGMA. 1. Dellaporta, S. L., Wood, J. & Hicks, J. B. A plant DNA minipreparation: Version II. Plant Mol. Biol. Report 1, 19-21 (1983). 2. Demesure, B., Sodzi, N. & Petit, R. J. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Mol. Ecol. 4, 129-131 (1995). 3. Dumolin-Lapègue, S., Pemonge, M. H., Petit, R. J. An enlarged set of consensus primers for the study of organelle DNA in plants. Mol. Ecol. 6, 393-397 (1997). 4. Schneider, S., Roessli, D. & Excoffier, L. ARLEQUIN Ver. 2.000: a Software for Population Genetics Data Analysis (Department of Anthropology, University of Geneva, Switzeland, 1999). 5. Collada, C., Fuentes-Utrilla, P., Gil, L & Cervera, M. T. Characterization of microsatellite loci in Ulmus minor Miller and cross-amplification in U. glabra Hudson and U. laevis Pall. Mol. Ecol. Notes (in press). 6. Vos, P. et al. AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res. 23, 4407-4414 (1995). 7. Cervera, M. T. et al. Improved AFLP analysis of tree species. Can. J. For. Res. 30(10), 1608-1616 (2000). 8. Van de Peer, Y. & De Wachter, R. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Applic. Biosci. 10, 569-570 (1994).