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.
Decker
Jared E
JE
Divisions of Animal Sciences, Biological Sciences, and Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA.
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
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