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Title: HIGH-THROUGHPUT PHYLOGENOMICS: FROM ANCIENT DNA TO SIGNATURES OF HUMAN ANIMAL HUSBANDRY

Author
item DECKER, JARED - University Of Missouri
item PIRES, J - University Of Missouri
item CONANT, GAVIN - University Of Missouri
item MCKAY, STEPHANIE - University Of Missouri
item Heaton, Michael - Mike
item VILKKI, JOHANNA - Mtt Agrifood Research Finland
item SEABURY, CHRISTOPHER - Texas A&M University
item CAETANO, ALEXANDRE - Embrapa Genetic Resources
item JOHNSON, GARY - University Of Missouri
item BRENNEMAN, RICK - H Doorly Zoo
item HANOTTE, OLIVIER - International Livestock Research Institute (ILRI) - Kenya
item EGGERT, LORI - University Of Missouri
item WIENER, PAMELA - University Of Edinburgh
item KIM, JONG-JOO - Yeungnam University
item KIM, KWAN - Chungbuk National University
item Sonstegard, Tad
item Van Tassell, Curtis - Curt
item NEIBERGS, HOLLY - Washington State University
item CHEN, KEFEI - Adelaide University
item COOPER, ALAN - Adelaide University
item MCEWAN, JOHN - Agresearch
item BRAUNING, RUDIGER - Agresearch
item COUTINHO, LUIZ - Universidad De Sao Paulo
item BABAR, MASROOR - University Of Veterinary And Animal Sciences
item WILSON, GREGORY - Canadian Wildlife Service
item MCCLURE, MATTHEW - University Of Missouri
item ROLF, MEGAN - University Of Missouri
item KIM, JAEWOO - University Of Missouri
item SCHNABEL, ROBERT - University Of Missouri
item TAYLOR, JEREMY - University Of Missouri

Submitted to: Cold Spring Harbor Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 4/25/2009
Publication Date: 5/7/2009
Citation: Decker, J.E., Pires, J.C., Conant, G.C., Mckay, S.D., Heaton, M.P., Vilkki, J., Seabury, C.M., Caetano, A.R., Johnson, G.S., Brenneman, R.A., Hanotte, O., Eggert, L.S., Wiener, P., Kim, J., Kim, K.S., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., Chen, K., Cooper, A., Mcewan, J.C., Brauning, R., Coutinho, L.L., Babar, M.E., Wilson, G.A., Mcclure, M.C., Rolf, M.M., Kim, J., Schnabel, R.D., Taylor, J.F. 2009. HIGH-THROUGHPUT PHYLOGENOMICS: FROM ANCIENT DNA TO SIGNATURES OF HUMAN ANIMAL HUSBANDRY. Cold Spring Harbor Meeting.

Interpretive Summary:

Technical Abstract: We utilized the Illumina BovineSNP50 BeadChip with 54,693 single nucleotide polymorphism loci developed for Bos taurus taurus to rapidly genotype 677 individuals representing 61 Pecoran (horned ruminant) species diverged by up to 29 million years. We produced a completely bifurcating tree, the first phylogeny with this level of resolution for this rapidly radiated infraorder based upon 40,843 genome-wide SNP. The phylogeny proposes 17 new relationships and increases the support for 16 other nodes within the infraorder. We also successfully genotyped an ancient Bison priscus DNA sample amplified from 20,000 year old remains collected from Siberia and integrated this extinct species into the Bovini phylogeny. To accurately describe relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation we constructed a phylogenomic network that provides strong support for the hypothesis of two independent sites for cattle domestication in the Fertile Crescent and the Indus Valley, while also strongly suggesting that if it occurred, any third large-scale domestication event was more likely in Africa than East Asia. Finally, we genotyped 110 modern Bison bison representing 5 populations and demonstrated that hybridization with cattle ~150 years ago can be detected as introgressed haplotypes which comprise 1-3% of the haploid genome. These haplotypes are not randomly distributed within the genome and strongly suggest selection for cow-specific alleles within several regions of the genome.