Journal article
Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics
Proceedings of the National Academy of Sciences - PNAS, Vol.106(44), pp.18644-18649
11/03/2009
Handle:
https://hdl.handle.net/2376/104284
PMCID: PMC2765454
PMID: 19846765
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 11 of the 15 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 up to 29 million years ago and that the produced genotypes can be used to resolve the phylogeny for this rapidly radiated infraorder. We used 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 method to amplify and screen genomic information from extinct species, and place
Bison priscus
within the Bovidae. The quality of genotype calls and the placement of samples within a well-supported phylogeny may provide an important test for 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.
Metrics
11 Record Views
Details
- Title
- Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics
- Creators
- Jared E Decker - Divisions ofJ. Chris Pires - Biological Sciences, andGavin C Conant - Divisions ofStephanie D McKay - Divisions ofMichael P Heaton - United States Department of Agriculture, Agricultural Research Service, Meat Animal Research Center, Clay Center NE 68933Kefei Chen - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide SA 5005, AustraliaAlan Cooper - Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide SA 5005, AustraliaJohanna Vilkki - Agrifood Research Finland MTT, FIN-31600, Jokioinen, FinlandChristopher M Seabury - Veterinary Pathobiology, Texas A&M University, College Station TX 77843Alexandre R Caetano - Embrapa Recursos Geneticos e Biotecnologia, Brasilia-DF, C.P. 02372, 70770-900, BrasilGary S Johnson - Department of Veterinary Pathobiology, University of Missouri, Columbia MO 65211Rick A Brenneman - Henry Doorly Zoo, Omaha NE 68107Olivier Hanotte - International Livestock Research Institute, P.O. Box 30709, Nairobi 00100, KenyaLori S Eggert - Biological Sciences, andPamela Wiener - The Roslin Institute, and R(D)SVS, University of Edinburgh, Roslin, Midlothian EH25 9PS, United KingdomJong-Joo Kim - School of Biotechnology, Yeungnam University, Gyeongsan, Republic of KoreaKwan Suk Kim - Department of Animal Science, Chungbuk National University, Cheongju, Republic of KoreaTad S Sonstegard - United States Department of Agriculture, Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville MD 20705Curt P Van Tassell - United States Department of Agriculture, Agricultural Research Service, Bovine Functional Genomics Laboratory, Beltsville MD 20705Holly L Neibergs - Department of Animal Sciences, Washington State University, Pullman WA 99164John C McEwan - Animal Genomics, AgResearch, Invermay, PB 50034, Mosgiel, New ZealandRudiger Brauning - Animal Genomics, AgResearch, Invermay, PB 50034, Mosgiel, New ZealandLuiz L Coutinho - Departamento de Zootecnia, ESALQ-USP, Av. Padua Dias, 11, Piracicaba, SP 13418-900, BrasilMasroor E Babar - Department of Livestock Production, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan; andGregory A Wilson - Canadian Wildlife Service, 200 4999 98th Avenue Northwest, Edmonton AB, Canada T6B 2X3Matthew C McClure - Divisions ofMegan M Rolf - Divisions ofJaeWoo Kim - Divisions ofRobert D Schnabel - Divisions ofJeremy F Taylor - Divisions of
- Publication Details
- Proceedings of the National Academy of Sciences - PNAS, Vol.106(44), pp.18644-18649
- Academic Unit
- Animal Sciences, Department of
- Publisher
- National Academy of Sciences
- Identifiers
- 99900546603001842
- Language
- English
- Resource Type
- Journal article