Phylogenetic relationships among the European and American bison and seven cattle breeds reconstructed using the BovineSNP50 Illumina Genotyping BeadChip

• Autorzy: Pertoldi C. , Tokarska M. , Wojcik J.M. , Kawalko A. , Randi E. , Kristensen T.N. , Loeschcke V. , Coltman D. , Wilson G.A. , Gregersen V.R. , Bendixen C.
• Języki publikacji: EN

Abstrakty

EN

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 subspecies 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 bottlenecks, which has likely had large effects on genetic diversity within and differentiation among groups.

Słowa kluczowe

EN

phylogenetic relationship; European bison; American bison; bison; cattle; animal breed; reconstruction; haplotype; bottleneck; founder effect; breed comparison; BeadChip technology; genotyping

• Wydawca: -
• Czasopismo: Acta Theriologica
• Rocznik: 2010
• Tom: 55
• Numer: 2
• Opis fizyczny: p.97-108,fig.,ref.

Twórcy

autor

Pertoldi C.

• Polish Academy of Sciences, Waszkiewicza 1c, 17-230 Bialowieza, Poland

autor

Tokarska M.

autor

Wojcik J.M.

autor

Kawalko A.

autor

Randi E.

autor

Kristensen T.N.

autor

Loeschcke V.

autor

Coltman D.

autor

Wilson G.A.

autor

Gregersen V.R.

autor

Bendixen C.

Bibliografia

• Antao T., Lopes A., Lopes R. J., Beja-Pereira A. and Luikart G. 2008. LOSITAN: A workbench to detect molecular adaptation based on a F st-outlier method. BMC Bioinformatics 9: 323.
• Beaumont M. A. and Nichols R. A. 1996. Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society London B 263: 1619–1626.
• Bradley D. G., MacHugh D. E., Cunningham P. and Loftus R. T. 1996. Mitochondrial diversity and the origins of African and European cattle. Proceedings of the National Academy of Science, USA 96: 5131–5135.
• Caballero A. and Toro M. A. 2000. Interrelations between effective population size and other pedigree tools for the management of conserved populations. Genetical Research 75: 331–343.
• Clutton Brock J. 1999. A natural history of domesticated mammals. Cambridge University Press, Cambridge.
• Cornuet J. M. and Luikart G. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144: 2001–2014.
• Felsenstein J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
• Fernández H. M. and Vrba E. S. 2005. A complete estimate of the phylogenetic relationships in Ruminantia: a dated species-level supertree of the extant ruminants. Biological Reviews of the Cambridge Philosophical Society (London) 80: 269–302.
• Freese C. H., Aune K. E., Boyd D. P., Derr J. N., Forrest S. C., Gates C. C., Gogan P. J. P., Grassel S. M., Halbert N. D., Kunkel K. and Redford K. H. 2007. Second chance for the plains bison. Biological Conservation 136: 175–184.
• Goodnight C. 1914. My experience with bison hybrids. Journal of Heredity 5: 197–199.
• Halbert N. D. 2003. The utilization of genetic markers to resolve modern management issues in historic bison populations: Implications for species conservation. PhD thesis, Texas A&M University, Galveston: 1–199.
• Halbert N. D. and Derr J. N. 2007. A comprehensive evaluation of cattle introgression into US Federal bison herds. Journal of Heredity 98: 1–12.
• Halbert N. D., Raudsepp T., Chowdhary B. P. and Derr J. N. 2004. Conservation genetic analysis of the Texas state bison herd. Journal of Mammalogy 85: 924–931.
• Halbert N. D., Ward T. J., Schnabel R. D., Taylor J. F. and Derr J. N. 2005. Conservation genomics: disequilibrium mapping of domestic cattle chromosomal segments in North American bison populations. Molecular Ecology 10: 2343–2362.
• Hammer Ř., Harper D. A. T. and Ryan P. D. 2001. PAST: Palaeontological Statistics software package for education and data analysis. Palaeontologia Electronica 4: 1–9. www.earthsci.carleton.ca/paleo/toc.htm
• Hartl G. B. and Pucek Z. 1994. Genetic depletion in the European bison (Bison bonasus) and the significance of electrophoretic heterozygosity for conservation. Conservation Biology 8: 167–174.
• Heptner V. G., Nasimovic A. A. and Bannikov A. G. 1966. Die Säugetiere der Sovietunion. 1. Paarhufer und Unpaarhufer. G. Fischer Verlag, Jena: 1–939.
• Janecek L. L., Honeycutt R. L., Adkins R. M. and Davis S. K. 1996. Mitochondrial gene sequences and the molecular systematics of the artiodactyl subfamily Bovinae. Molecular Phylogenetics and Evolution 6: 107–119.
• Kim K. I., Lee J. H., Lee S. S. and Yang Y. H. 2003. Phylogenetic relationships of northeast Asian cattle to other cattle populations determined using mitochondrial DNA D-loop sequence polymorphism. Biochemical Genetics 41: 91–98.
• Krasińska M., Szuma E., Kobryńczuk F. and Szara T. 2008. Morphometric variation of the skull during postnatal development in the Lowland European bison Bison bonasus bonasus. Acta Theriologica 53: 193–216.
• Lenstra J. A. and Bradley D. G. 1999. Systematics and phylogeny of cattle. [In: The genetics of cattle. R. Fries and A. Ruvinsky, eds]. AB Int, Wallingford: 1–14.
• Loftus R. T., MacHugh D. E., Bradley D. G., Sharp P. M. and Cunningham E. P. 1994. Evidence for two independent domestications of cattle. Proceedings of the National Academy of Science, USA 91: 2757–2761.
• Luenser K., Fickel J., Lehnen A., Speck S. and Ludwig A. 2005. Low level of genetic variability in European bisons (Bison bonasus) from the Białowieża National Park in Poland. European Journal of Wildlife Research 51: 84–87.
• MacEachern S., McEwan J. and Goddard M. 2009. Phylogenetic reconstruction and the identification of ancient polymorphism in the Bovini tribe (Bovidae, Bovinae). BMC Genomics 10: 177.
• McDonald J. N. 1980. The north American bison: Their classification and evolution. University of California Press, Berkeley, California.
• Myrdal J. 1994. [Food and breeding from the 1500 to the 1800]. [In: Svenska husdjur frín medeltid till víra dagar. J. Myrdal and S. Sten, eds]. Nordiska Museet, Stockholm: 14–31. [In Swedish]
• Nielsen R. K., Pertoldi C. and Loeschcke V. 2007. Genetic evaluation of the captive breeding program of the Asiatic wild ass, onager (Equus hemionus onager). Journal of Zoology 272: 349–357.
• Peakall R. and Smouse P. E. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288–295.
• Pertoldi C., Bach L. A., Barker J. S. F., Lundberg P. and Loeschcke V. 2007a. The consequences of the variance-mean rescaling effect on effective population size. Oikos 5: 769–774.
• Pertoldi C., Bach L. A. and Loeschcke V. 2008. On the brink between extinction and persistence. Biology Direct 3: 47. doi: 10.1186/1745-6150-3-47
• Pertoldi C., Bijlsma R. and Loeschcke V. 2007b. Conservation genetics in a globally changing environment: present problems, paradoxes and future challenges. Biodiversity and Conservation 16: 4147–4163.
• Pertoldi C., Tokarska M., Wójcik J. M., Demontis D., Loeschcke V., Gregersen V. R., Coltman D., Wilson G. A., Randi E., Hansen M. M. and Bendixen C. 2009. Depauperate genetic variability detected in the American and European bison using genomic techniques. Biology Direct 4: 48. doi: 10.1186/1745-6150-4-48.
• Pertoldi C., Wójcik J. M., Tokarska M., Kawałko A., Kristensen T. N., Loeschcke V., Gregersen V. R., Coltman D., Wilson G. A., Randi E., Henryon M. and Bendixen C. 2010. Genome variability in European and American bison detected using the BovineSNP50 BeadChip. Conservation Genetics 11: 627–634. doi: 10.1007/s10592-009-9977-y
• Pritchard J. K., Stephens M. and Donelly P. 2000. STRUCTURE 2. Available at http://​/​www.​stats.​ox.​ac.​uk/​~pritch/​ home.html
• Pucek Z., Belousova I. P., Krasińska M., Krasiński Z. and Olech W. 2004. European Bison Status Survey and Conservation Action Plan IUCN/SSC Bison Specialist Group. Gland and Cambridge, IUCN.
• Radwan J., Kawałko A., Wójcik J. M. and Babik W. 2007. MHC-DRB3 variation in a free-living population of European bison Bison bonasus. Molecular Ecology 16: 531–540. doi: 10.1111./j.1365-294X.2006.03179.x
• Saitou N. and Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4: 406–25.
• Sambrook J., Fritsch E. F. and Maniatis T. 1989. Molecular cloning: A laboratory manual. Second edition. Cold Spring Harbor Laboratory Press, New York.
• Schneider S., Kueffer J. M., Roessli D. and Excoffier L. 2000. ARLEQUIN: a software package for population genetics. Geneve: Genetics and Biometry Lab, Department of Anthropology, University of Geneve. http://​anthropologie.​ unige.ch/arlequin
• Shapiro B., Drummond A. J., Rambaut A. A., Wilson M., Sher A., Pybus O. G., Gilbert M. T. P., Barnes I., Binladen J., Willerslev E., Hansen A., Baryshnikov G. F., Burns J., Davydov S., Driver J., Gubin S. V., Harington C. R., Keddie G., Kosintsev P., Kunz M. L., Martin L. D., Stephenson R., Storer J., Tedford R., Vorobiev A., Zimov S. and Cooper A. 2004. Rise and fall of the Beringian steppe bison. Science 306: 1561–1565.
• Sneath P. H. A. and Sokal R. R. 1973. Numerical Taxonomy. W. H. Freeman and Company, San Francisco. Soper J. D. 1941. History, range and home life of the northern bison. Ecological Monographs 11: 347–412.
• Sørensen A. C., Sørensen M. K. and Berg P. 2005. Inbreeding in Danish dairy cattle breeds. Journal of Dairy Science 88: 1865–1872.
• Tokarska M., Kawałko A., Wójcik J. M. and Pertoldi C. 2009a. Genetic variability in the European bison (Bison bonasus) population from Białowieża forest over fifty years. Biological Journal of the Linnean Society 97: 801–809.
• Tokarska M., Marshall T., Kowalczyk R., Wójcik J. M., Pertoldi C., Kristensen T. N., Loeschcke V., Gregersen V. R. and Bendixen C. 2009b. Effectiveness of microsatellite and SNP markers for parentage and identity analysis in species with low genetic diversity: the case of European bison. Heredity 103: 326–332. doi:10.1038/hdy. 2009.73
• Van Zyll de Jong C. G. 1986. A systematic study of recent bison, with particular consideration of the wood bison (Bison bison athabascae, Rhoads, 1898). National Museum of Canada, Publications in Natural Sciences 6: 1–69 + VIII.
• Van Zyll de Jong C. G., Gates C., Reynolds H. and Olson W. 1995. Phenotypic variation in remnant populations of North American bison. Journal of Mammalogy 76: 391–405.
• Verkaar E. L. C., Nijman I. J., Beeke M., Hanekamp E. and Lenstra J. A. 2004. Maternal and paternal lineages in cross-breeding bovine species has wisent a hybrid origin? Molecular Biology and Evolution 21: 1165–1170.
• Waples R. S. 2006. A bias correction for estimates of effective population size based on linkage disequilibrium at unlinked gene loci. Conservation Genetic 7: 167–184.
• Waples R. S. and Do C. 2008. LDNE: a program for estimating effective population size from data on linkage disequilibrium. Molecular Ecology Resources 8: 753–756.
• Ward T. J., Bielawski J. P., Davis S. K., Templeton J. W. and Derr J. N. 1999. Identification of domestic cattle hybrids in wild cattle and bison species: a general approach using mtDNA markers and the parametric bootstrap. Animal Conservation 2: 51–57.
• Wilson G. A. and Strobeck C. 1999. Genetic variation within and relatedness among wood and plains bison populations. Genome 42: 483–496.
• Wójcik J. M., Kawałko A., Tokarska M., Jaarola M., Vallenback P. and Pertoldi C. 2009. Post-bottleneck mtDNA diversity in a free-living population of European bison: implications for conservation. Journal of Zoology 277: 81–87. doi: 10.1111/j.1469-7998.2008.00515.x
• Yeh F. C. and Boyle T. J. 1997. Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belgian Journal of Botany 129: 157