The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.
Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics
Open accessAbstract
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.
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Cites
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Cited by
Worldwide Patterns of Ancestry, Divergence, and Admixture in Domesticated Cattle
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Self-citationLarge-scale ruminant genome sequencing provides insights into their evolution and distinct traits
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New World Cattle Show Ancestry from Multiple Independent Domestication Events
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Self-citationDomestication of Cattle: Two or Three Events?
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On the History of Cattle Genetic Resources
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Genomic clues of the evolutionary history of Bos indicus cattle
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Species Composition and Environmental Adaptation of Indigenous Chinese Cattle
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Demography and Rapid Local Adaptation Shape Creole Cattle Genome Diversity in the Tropics
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Metadata
- Authors
- 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.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2009-11-03
- Volume
- 106
- Issue
- 44
- Pages
- 18644-18649
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2101732512
- Cited by
- 223
- References
- 5
- FWCI
- 11.26
- Type
- journal article
- Language
- en
- Open access
- green
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