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Ancient British Aurochs Genome Provides Glimpse Into Complex Cattle Domestication

NEW YORK (GenomeWeb) – Researchers from University College Dublin have sequenced the whole genome of an ancient wild aurochs from Britain, providing insight into the domestication of cattle and their complex relationship to their wild progenitors.

Domestication of the now-extinct aurochs Bos primigenius led to the development of the two major cattle taxa, B. taurus and B. indicus, though the researchers noted that whether there was additional gene flow from aurochs into cattle has been unclear.

As the researchers led by UCD's David MacHugh reported yesterday in Genome Biology, they sequenced the genome of a 6,750-year-old wild British aurochs and compared it to genomic data from more than 80 domesticated B. taurus and B. indicus as well as genetic marker data from a further 1,200 cattle. From this, they found that traditional British and Irish cattle breeds share more genetic material with this wild aurochs than other European breeds, suggesting that localized gene flow occurred from aurochs into cattle.

"Our results show the ancestors of modern British and Irish breeds share more genetic similarities with this ancient specimen than other European cattle," MacHugh said in a statement. "This suggests that early British farmers may have restocked their domesticated herds with wild aurochs."

MacHugh and his colleagues isolated and sequenced DNA obtained from the bone of a 6,750-year-old wild British aurochs that had been found in a cave in Derbyshire, England. They aligned these B. primigenius reads to a B. taurus reference genome, finding some 470 million uniquely mapped reads that spanned 16.62 gigabases of aurochs nuclear and mitochondrial DNA sequence with a mean sequencing depth of 6.23X.

The researchers found more than 5.2 million sequence variants differentiated the ancient British aurochs and the modern cattle reference genomes. Still, many of the SNPs and indels present in the aurochs sample could be found in dbSNP build 140. Further, some 85 percent of aurochs SNPs and 81 percent of aurochs indels were present in re-sequencing data from 81 modern taurine and zebu samples from Europe, Africa, and India.

MacHugh and his colleagues also compiled a large reference SNP dataset consisting of 1,228 cattle samples: 1,225 samples from 73 modern cattle populations representing European and African B. taurus, Asian B. indicus, B. taurus and B. indicus crossbreeds, African B. taurus and European B. taurus crossbreeds, as well as two yaks and the ancient aurochs sample.

Using this dataset, the researchers constructed a maximum likelihood phylogenetic tree. This tree showed complete separation of the taurine and zebu populations, the researchers noted, which they said underscored the evolutionary divergence between the taxa and supporting the separate domestic origins of B. taurus and B. indicus.

The tree also indicated that the ancient British aurochs sample is an outgroup to the entire modern B. taurus clade. In a principal components analysis plot, the ancient British aurochs sample was also peripheral to the European B. taurus samples. MacHugh and his colleagues said that this supports the hypothesis that North European aurochs are an evolutionary outgroup to all domesticated taurine cattle.

By turning to the STRUCTURE admixture tool, the researchers dove deeper into the genetic structure and admixture history of cattle and aurochs, and found that the aurochs specimen included contributions from all three of the European taurine, African taurine, and zebu components.

The zebu components found in three of the four Italian populations and in two East Asian taurine populations had been thought to be due to historical admixture from B. indicus. However, the researchers noted that the three-part genetic structure found in the aurochs specimen suggests that alleles that are now found only in African or Asian cattle may have been more widespread prior to domestication and then lost from most of the domesticated European B. taurus lineages.

Using the ABBA/BABA test of genomic admixture, MacHugh and his colleagues also searched for evidence of post-domestication admixture between domesticated cattle and the wild aurochs. They found that the British aurochs made a significant genetic contribution to modern domestic cattle populations in Britain and Ireland. In particular, they noted that this genetic legacy is most apparent in traditional cattle breeds, such as the Highland, Dexter, Kerry, Welsh Black, and White Park breeds.

Through functional genomic analyses, the researchers explored how domestication shaped the genomes of modern cattle and reported that some 263 variants became fixed in European B. taurus after domestication. The genes associated with these variants were enriched for neurobiological, immune signaling, and growth and metabolism functions. In addition, genomic regions linked to these functions also appeared to be under selection in the cattle genome.

"[Our] study contradicts earlier simple models of cattle domestication and evolution that we and others proposed based on mitochondrial DNA or Y chromosomes," MacHugh added. "What now emerges from high-resolution studies of the nuclear genome is a more nuanced picture of crossbreeding and gene flow between domestic cattle and wild aurochs as early European farmers moved into new habitats such as Britain during the Neolithic."

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