Resolving the evolution of extant and extinct ruminants with high-throughput phylogenomics.
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.
Divisions of Animal Sciences, Biological Sciences, and Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA.
Jared E
JE
Decker
J Chris
JC
Pires
Gavin C
GC
Conant
Stephanie D
SD
McKay
Michael P
MP
Heaton
Kefei
K
Chen
Alan
A
Cooper
Johanna
J
Vilkki
Christopher M
CM
Seabury
Alexandre R
AR
Caetano
Gary S
GS
Johnson
Rick A
RA
Brenneman
Olivier
O
Hanotte
Lori S
LS
Eggert
Pamela
P
Wiener
Jong-Joo
JJ
Kim
Kwan Suk
KS
Kim
Tad S
TS
Sonstegard
Curt P
CP
Van Tassell
Holly L
HL
Neibergs
John C
JC
McEwan
Rudiger
R
Brauning
Luiz L
LL
Coutinho
Masroor E
ME
Babar
Gregory A
GA
Wilson
Matthew C
MC
McClure
Megan M
MM
Rolf
Jaewoo
J
Kim
Robert D
RD
Schnabel
Jeremy F
JF
Taylor
D000818:Animals; D005075:Biological Evolution; D001947:Breeding; D002417:Cattle; D004247:DNA / Q000032:analysis / Q000235:genetics; D053476:Extinction, Biological; D005580:Fossils; D023281:Genomics / Q000379:methods*; D005838:Genotype; D010802:Phylogeny; D012418:Ruminants / Q000235:genetics*
D004247:DNA