[97] Acta Theriologica 55 (2): 97–108, 2010. PL ISSN 0001-7051 doi: 10.4098/j.at.0001-7051.002.2010 Phylogenetic relationships among the European and American bison and seven cattle breeds reconstructed using the BovineSNP50 Illumina Genotyping BeadChip Cino PERTOLDI, Ma³gorzata TOKARSKA, Jan M. WÓJCIK, Agata KAWA£KO, Ettore RANDI, Torsten N. KRISTENSEN, Volker LOESCHCKE, David COLTMAN, Gregory A. WILSON, Vivi R. GREGERSEN and Christian BENDIXEN Pertoldi C., Tokarska M., Wójcik J. M., Kawa³ko A., Randi E., Kristensen T. N., Loeschcke V., Coltman D., Wilson G. A., Gregersen V. R. and Bendixen C. 2010. Phylogenetic relationships among the European and American bison and seven cattle breeds reconstructed using the BovineSNP50 Illumina Genotyping BeadChip. Acta Theriologica 55: 97–108. Here we present the first attempt to use the BovineSNP50 Illumina Genotyping BeadChip for genome-wide screening of European bison Bison bonasus bonasus (EB), two subspecies of American bison: the plains bison Bison bison bison (PB), the wood bison Bison bison athabascae (WB) and seven cattle Bos taurus breeds. Our aims were to (1) reconstruct their evolutionary relationships, (2) detect any genetic signature of past bottlenecks and to quantify the consequences of bottlenecks on the genetic distances amongst bison sub- species and cattle, and (3) detect loci under positive or stabilizing selection. A Bayesian clustering procedure (STRUCTURE) detected ten genetically distinct clusters, with separation among all seven cattle breeds and European and American bison, but no separation between plain and wood bison. A linkage disequilibrium based program (LDNE) was used to estimate the effective population size (N e ) for the cattle breeds; N e was generally low, relative to the census size of the breeds (cattle breeds: mean N e = 299.5, min N e = 18.1, max N e = 755.0). BOTTLENECK 1.2 detected signs of population bottlenecks in EB, PB and WB populations (sign test and standardized sign test: p = 0.0001). Evidence for loci under selection was found in cattle but not in bison. All extant wild populations of bison have shown to have survived severe bottle- necks, which has likely had large effects on genetic diversity within and differentiation among groups. Mammal Research Institute, Polish Academy of Sciences, Waszkiewicza 1c, 17-230 Bia³owie¿a, Poland, email: biocp@nf.au.dk (CP, MT, JMW, AK); Department of Biological Sciences, Ecology and Genetics, Institute of Biological Sciences, Aarhus University, Ny Munkegade, Building 1540, 8000 Crhus C, Denmark (CP, VL); Istituto Superiore per la Protezione e la Ricerca Ambientale, via Cá Fornacetta 9, I-40064, Ozzano Emilia (BO), Italy (ER); Department of Genetics and Biotechnology, Faculty of Agricultural Sciences, Aarhus University, P.O. Box 50, DK-8830 Tjele, Denmark (TNK, VRG, CB); Department of Biological Science, University of Alberta, Center of Biological Sciences, Edmonton, AB T6G 2E9, Canada (DC, GAW); Canadian Wildlife Service 200, 4999 – 98 Ave, Edmonton, AB T6B 2X3, Canada (GAW) Key words: SNPs, haplotypes, bottleneck, founder effect, breed comparison