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 wellsupported 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.ancient DNA ͉ Pecorans ͉ domestication

Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)

“…Previous studies have demonstrated that robust phylogenetic signal can be obtained by querying domestic animal SNP arrays with DNA from related species of the same genus, family, or order, despite having diverged tens of millions of years from the array reference genome (Decker et al 2009;McCue et al 2012). Here, we generated genome-wide SNP data from 38 cat species and analyzed these separately and together with Y-linked variation and whole mitogenomes, allowing us to disentangle different maternal, paternal, and biparental histories within a diverse family of mammals.…”

“…To demonstrate that a potential bias of nucleotide identification caused by the two-dye Illumina genotyping system on nondomestic cat species did not influence phylogenetic accuracy, we also performed a second phylogenetic analysis in which the nuclear SNP matrix was translated into a binary matrix ("0" representing G or C; "1" representing A or T), following Decker et al (2009).…”

Genetic parameters for carcass weight, conformation and fat in five beef cattle breeds

“…Moreover, the five studied beef breeds have diverged genetically during their phylogenetic history. Charolais and Limousin are continental French breeds, Hereford and Angus are of British origin, and Simmental originated from Switzerland (Decker et al, 2009). In breeds with low muscularity and high fat deposition (especially Hereford), high fat levels are more strongly genetically connected to heavier carcasses and high muscularity.…”

New World cattle show ancestry from multiple independent domestication events

“…Given the close interaction of humans with domesticated species and the economic importance of domesticated organisms, it is not surprising that humans have developed many of these species as model organisms. Over the last few years, genomic data have been used to reconstruct the domestication history of many of these species, including dogs (1, 2), horses (3), sheep (4), and cattle (5,6). The global economic importance of cattle, in combination with the anthropological interest in the shared history of cattle and humans over the last 10,000 y, makes cattle an ideal target for spatial genetic research.…”