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

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

doi:10.1186/s13059-015-0790-2

Abstract

BackgroundDomestication 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.ResultsPhylogenomic 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0790-2) contains supplementary material, which is available to authorized users.

Highlights

Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus
To date, comparative analyses of aurochs and modern cattle DNA sequences have relied on non-recombining uniparental loci that are not representative of ancestry across the whole genome
It is important that information obtained from mitochondrial DNA (mtDNA) and Y-chromosomal DNA is complemented with data from autosomal polymorphisms

Summary

Introduction

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. 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. In contrast to mtDNA studies, analyses of paternally inherited Y chromosome haplotypes remain equivocal as to whether local wild male aurochs contributed to European B. taurus populations [15,16,17]

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Results

Conclusion