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United States Department of Agriculture

Agricultural Research Service

Title: Resolving the Evolution of Extant and Extinct Ruminants With High-Throughput Phylogenomics

item Decker, Jared
item Pires, J
item Conant, Gavin
item Mckay, Stephanie
item Heaton, Michael - Mike
item Chen, Kefei
item Cooper, Alan
item Vilkki, Johanna
item Seabury, Christopher
item Caetano, Alexandre
item Johnson, Gary
item Brenneman, Rick
item Hanotte, Olivier
item Eggert, Lori
item Wiener, Pamela
item Kim, Jong-joo
item Kim, Kwan
item Sonstegard, Tad
item Van Tassell, Curtis - Curt
item Neibergs, Holly
item Mcewan, John
item Brauning, Rudiger
item Coutinho, Luiz
item Babar, Masroor
item Wilson, Gregory
item Mcclure, Matthew
item Rolf, Megan
item Kim, Jaewoo
item Schnabel, Robert
item Taylor, Jeremy

Submitted to: Proceedings of the National Academy of Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/16/2009
Publication Date: 11/3/2009
Publication URL:
Citation: Decker, J.E., Pires, J.C., Conant, G.C., McKay, S.D., Heaton, M.P., Chen, K., Cooper, A., Vilkki, J., Seabury, C.M., Caetano, A.R., Johnson, G.S., Brenneman, R.A., Hanotte, O., Eggert, L.S., Wiener, P., Kim, J.J., Kim, K.S., Sonstegard, T.S., Van Tassell, C.P., Neibergs, H.L., 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. Resolving the Evolution of Extant and Extinct Ruminants With High-Throughput Phylogenomics. Proceedings of the National Academy of Sciences. 106(44):18644-18649.

Interpretive Summary: This is the first report demonstrating that high-throughput DNA technology designed for one species can be used to genotype ancient DNA from a related extinct species that diverged up to 29 million years ago. The results from a 20,000 year-old DNA sample placed an extinct Bison species close to modern bison within the family of antelopes, cattle, gazelles, goats, and sheep. The DNA technology was also used to resolve the evolutionary relationships for many of the horned ruminant species that currently exist around the world. The report provides insights into the history of domestication and breed formation in cattle and is of broad scientific interest to the research community. These findings also introduce the era of high-throughput phylogenomics in which highly-resolved evolutionary relationships are rapidly and inexpensively constructed for species that are in existence or have become extinct.

Technical Abstract: The Pecorans (higher ruminants) are believed to have rapidly speciated in the Mid-Eocene, resulting in five distinct extant families; Antilocapridae, Giraffidae, Moschidae, Cervidae, and Bovidae. Due to the rapid radiation, the Pecoran phylogeny has proven difficult to resolve and eleven of the fifteen possible rooted phylogenies describing ancestral relationships among the Antilocapridae, Giraffidae, Cervidae, and Bovidae have each been argued as representations of the true phylogeny. Here we demonstrate that a genome-wide single nucleotide polymorphism (SNP) genotyping platform designed for one species can be used to genotype ancient DNA from an extinct species and DNA from species diverged by up to 29 million years and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We utilized a high-throughput assay with 54,693 SNP loci developed for Bos taurus taurus to rapidly genotype 678 individuals representing 61 Pecoran species. We produced a highly resolved phylogeny for this diverse group based upon 40,843 genome-wide SNP, which is five times as many informative characters as have previously been analyzed. We also establish a new method to amplify and screen genomic information from extinct species, and place Bison priscus within the Bovidae. Examining the produced genotypes and placement of samples within a well-supported phylogeny should be an important step in validating the fidelity and integrity of ancient samples. Finally, we constructed a phylogenomic network to accurately describe the relationships between 48 cattle breeds and facilitate inferences concerning the history of domestication and breed formation.

Last Modified: 10/18/2017
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