Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.
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.
IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland. sdepark@gmail.com.
Stephen D E
SD
Park
Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. david.magee@ucd.ie.|Department of Animal Science, University of Connecticut, Storrs, CT, 06029, USA. david.magee@ucd.ie.
David A
DA
Magee
Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. paul.mcgettigan@ucd.ie.
Paul A
PA
McGettigan
Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland. teasdalm@tcd.ie.
Matthew D
MD
Teasdale
Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Rd, Oxford, OX1 3QY, UK. ceiridwen.edwards@gmail.com.
Ceiridwen J
CJ
Edwards
UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland. amanda.lohan@ucd.ie.
Amanda J
AJ
Lohan
UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland. alison.murphy@ucd.ie.
Alison
A
Murphy
Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland. braud.martin@gmail.com.
Martin
M
Braud
Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland. mta.donoghue@gmail.com.
Mark T
MT
Donoghue
BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China. liuyuan@genomics.cn.
Yuan
Y
Liu
Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK. andrew.chamberlain@manchester.ac.uk.
Andrew T
AT
Chamberlain
Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. kevin.rue@ucdconnect.ie.
Kévin
K
Rue-Albrecht
Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA. steven.schroeder@ars.usda.gov.
Steven
S
Schroeder
Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland. charles.spillane@nuigalway.ie.
Charles
C
Spillane
BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China. shuaishuai.tai@genomics.cn.
Shuaishuai
S
Tai
Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland. dbradley@tcd.ie.
Daniel G
DG
Bradley
Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA. tad.sonstegard@ars.usda.gov.|Recombinetics Inc., St. Paul, MN, 55104, USA. tad.sonstegard@ars.usda.gov.
Tad S
TS
Sonstegard
UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland. brendan.loftus@ucd.ie.|UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland. brendan.loftus@ucd.ie.
Brendan J
BJ
Loftus
Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. david.machugh@ucd.ie.|UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland. david.machugh@ucd.ie.
David E
DE
MacHugh
D000818:Animals; D002417:Cattle / Q000235:genetics*; D004739:England; D005060:Europe; D019143:Evolution, Molecular; D053476:Extinction, Biological; D014644:Genetic Variation; D023281:Genomics; D058974:Phylogeography; D012418:Ruminants / Q000145:classification / Q000235:genetics; D017422:Sequence Analysis, DNA