Here we present the first at tempt 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 (EB), two sub species of American bison: the plains bison Bison bison bison (PB), the wood bison Bi on bison athabascae (WB) and seven ( PB), the wood bison (WB) and seven cattle Bostaurus breeds. Our aims were to (1) re construct their evolutionary relationships, (2) detect any genetic signature of past bottlenecks and to quantify the con sequences of bottle necks 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 disequi librium based program (LDNE) was used to estimate the effective population size ( Ne ) for the cattle breeds; Ne was generally low, relative to the census size of the breeds (cattle breeds: mean Ne = 299.5, min Ne = 18.1, max Ne = 755.0). BOTTLENECK 1.2 de tected signs of pop u la tion bot tle necks in = 755.0). BOTTLENECK 1.2 detected signs of population bottle necks in EB, PB and WB populations (sign test and stan dard ized 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 sur vived severe bottlenecks, which has likely had large effects on genetic diversity within and differentiation among groups. ; Here we present the first at tempt 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 (EB), two sub species of American bison: the plains bison Bison bison bison (PB), the wood bison Bi on bison athabascae (WB) and seven ( PB), the wood bison (WB) and seven cattle Bostaurus breeds. Our aims were to (1) reconstruct their evolutionary relationships, (2) detect any genetic signature of past bottlenecks and to quantify the con sequences of bottle necks on the genetic distances amongst bison subspecies and cattle, and (3) de tect 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 be tween plain and wood bison. A linkage disequi librium based program (LDNE) was used to estimate the effective population size ( Ne ) for the cattle breeds; Ne was generally low, relative to the census size of the breeds (cattle breeds: mean Ne = 299.5, min Ne = 18.1, max Ne = 755.0). BOTTLENECK 1.2 de tected signs of pop u la tion bot tle necks in = 755.0). BOTTLENECK 1.2 detected signs of population bottle necks 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 sur vived se vere bottlenecks, which has likely had large effects on genetic diversity within and differentiation among groups.