Dataset Information

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

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.

SUBMITTER: Decker JE

PROVIDER: S-EPMC2765454 | biostudies-literature | 2009 Nov

REPOSITORIES: biostudies-literature

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

Decker Jared E JE Pires J Chris JC Conant Gavin C GC McKay Stephanie D SD Heaton Michael P MP Chen Kefei K Cooper Alan A Vilkki Johanna J Seabury Christopher M CM Caetano Alexandre R AR Johnson Gary S GS Brenneman Rick A RA Hanotte Olivier O Eggert Lori S LS Wiener Pamela P Kim Jong-Joo JJ Kim Kwan Suk KS Sonstegard Tad S TS Van Tassell Curt P CP Neibergs Holly L HL McEwan John C JC Brauning Rudiger R Coutinho Luiz L LL Babar Masroor E ME Wilson Gregory A GA McClure Matthew C MC Rolf Megan M MM Kim Jaewoo J Schnabel Robert D RD Taylor Jeremy F JF

Proceedings of the National Academy of Sciences of the United States of America 20091021 44

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 demonstra ...[more]

PMID: 19846765

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Project description:Snout shape is a prominent aspect of herbivore feeding ecology, interacting with both forage selectivity and intake rate. Previous investigations have suggested ruminant feeding styles can be discriminated via snout shape, with grazing and browsing species characterised by 'blunt' and 'pointed' snouts respectively, often with specification of an 'intermediate' sub-grouping to represent ambiguous feeding styles and/or morphologies. Snout shape morphology is analysed here using a geometric morphometric approach to compare the two-dimensional profiles of the premaxilla in ventral aspect for a large sample of modern ruminant species, for which feeding modes are known from secondary criteria. Results suggest that, when browsing and grazing ruminants are classified ecologically based on a range of feeding style indicators, they cannot be discriminated unambiguously on the basis of snout profile shape alone. Profile shapes in our sample form a continuum with substantial overlap between groupings and a diverse range of morphologies. Nevertheless, we obtained an 83.8 percent ratio of correct post hoc feeding style categorisations based on the proximity of projected profile shapes to group centroids in the discriminant space. Accordingly, this procedure for identifying species whose feeding strategy is 'unknown' can be used with a reasonable degree of confidence, especially if backed-up by additional information. Based on these results we also refine the definitions of snout shape varieties, taking advantage of the descriptive power that geometric morphometrics offers to characterize the morphological disparities observed. The shape variance exhibited by both browsing and grazing ruminants corresponds strongly to body mass, providing further evidence for an interaction between snout shape, feeding style, and body size evolution. Finally, by exploring the role of phylogenetic similarity in snout shape, we find a slight increase in successful categorisation when repeating the analysis with phylogenetic control on the geometric profiles.

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Dataset Information

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

Publications

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

Similar Datasets

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