Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics Export

@article{citeulike:6065136, abstract = {10.1073/pnas.0904691106 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 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 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.}, author = {Decker, Jared E. and Pires, J. Chris and Conant, Gavin C. and McKay, Stephanie D. and Heaton, Michael P. and Chen, Kefei and Cooper, Alan and Vilkki, Johanna and Seabury, Christopher M. and Caetano, Alexandre R. and Johnson, Gary S. and Brenneman, Rick A. and Hanotte, Olivier and Eggert, Lori S. and Wiener, Pamela and Kim, Jong-Joo and Kim, Kwan S. and Sonstegard, Tad S. and Van Tassell, Curt P. and Neibergs, Holly L. and McEwan, John C. and Brauning, Rudiger and Coutinho, Luiz L. and Babar, Masroor E. and Wilson, Gregory A. and McClure, Matthew C. and Rolf, Megan M. and Kim, JaeWoo and Schnabel, Robert D. and Taylor, Jeremy F.}, citeulike-article-id = {6065136}, citeulike-linkout-0 = {http://dx.doi.org/10.1073/pnas.0904691106}, citeulike-linkout-1 = {http://www.pnas.org/content/106/44/18644.abstract}, citeulike-linkout-2 = {http://www.pnas.org/content/106/44/18644.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19846765}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19846765}, day = {3}, doi = {10.1073/pnas.0904691106}, journal = {Proceedings of the National Academy of Sciences}, keywords = {molecular-phylogenetics, phylogenomics, phylogeny}, month = {November}, number = {44}, pages = {18644--18649}, posted-at = {2009-11-03 22:50:55}, priority = {2}, title = {Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics}, url = {http://dx.doi.org/10.1073/pnas.0904691106}, volume = {106}, year = {2009} }

TY - JOUR ID - citeulike:6065136 L3 - citeulike-article-id:6065136 N2 - 10.1073/pnas.0904691106 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 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 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. IS - 44 JF - Proceedings of the National Academy of Sciences EP - 18649 TI - Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics VL - 106 SP - 18644 KW - molecular-phylogenetics KW - phylogenomics KW - phylogeny AU - Decker, Jared AU - Pires, Chris AU - Conant, Gavin AU - McKay, Stephanie AU - Heaton, Michael AU - Chen, Kefei AU - Cooper, Alan AU - Vilkki, Johanna AU - Seabury, Christopher AU - Caetano, Alexandre AU - Johnson, Gary AU - Brenneman, Rick AU - Hanotte, Olivier AU - Eggert, Lori AU - Wiener, Pamela AU - Kim, Jong-Joo AU - Kim, Kwan AU - Sonstegard, Tad AU - Van Tassell, Curt AU - Neibergs, Holly AU - McEwan, John AU - Brauning, Rudiger AU - Coutinho, Luiz AU - Babar, Masroor AU - Wilson, Gregory AU - McClure, Matthew AU - Rolf, Megan AU - Kim, JaeWoo AU - Schnabel, Robert AU - Taylor, Jeremy PY - 2009/11/03/ UR - http://dx.doi.org/10.1073/pnas.0904691106 ER -