Journal Article

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle

MacHugh, David E., Donoghue, Mark T., Murphy, Alison, Lohan, Amanda J., Tai, Shuaishuai, Bradley, Daniel G., Braud, Martin, Schroeder, Steven, Liu, Yuan, Spillane, Charles, Teasdale, Matthew D., Rue-Albrecht, Kévin, Magee, David A., Park, Stephen D E, Edwards, Ceiridwen J., Sonstegard, Tad S., Loftus, Brendan J., McGettigan, Paul A., Chamberlain, Andrew T.

2015

Overview

Background Domestication of the now-extinct wild aurochs, Bos primigenius , gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus . While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought.

• Publisher: BioMed Central,Springer Nature B.V
• Subject: Animal Genetics and Genomics / Animal populations / Animals / Bioinformatics / Biomedical and Life Sciences / Bos primigenius / Bos taurus / Bos taurus indicus / Bovidae / Cattle / Cattle - genetics / Chromosomes / Deoxyribonucleic acid / DNA / Domestication / England / Europe / Evolution, Molecular / Evolutionary Biology / Evolutionary genetics / Extinct species / Extinction / Extinction, Biological / Gene flow / Gene loci / Genetic diversity / Genetic Variation / genome / Genomes / Genomics / Human Genetics / Life Sciences / Metabolism / Microbial Genetics and Genomics / MicroRNAs / Mitochondrial DNA / neurophysiology / Nucleotide sequence / nucleotide sequences / Phylogeny / Phylogeography / Plant Genetics and Genomics / Polymorphism / Positive selection / Ruminants - classification / Ruminants - genetics / Sequence Analysis, DNA / Single-nucleotide polymorphism / United Kingdom