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Decoding Domesticate DNA in Archaeological Bone and Manuscripts

Final Report Summary - CODEX (Decoding Domesticate DNA in Archaeological Bone and Manuscripts)

The genetics of cattle, sheep and goat tell us about the past of these animals and their intimately shared history with humans. As this story fills out it will be a compelling one with elements of migrations, human selection of livestock genomes, population fluctuations due to disease, hybridisation with wild relatives and the pivotal process of domestication over 10,000 years ago. However, extrapolating to the past from modern genetic variation is imprecise as it is impossible to decipher these myriad overlaid influences. The project overcame this by obtaining livestock genomes from the past using ultra high throughput sequencing and a discovery that the petrous bone, the densest bone in the mammalian skeleton, is an efficient time capsule, preserving domestic animal DNA. We have gathered data from >325 genomes sampled over a stretch of over 13000 years of prehistory in these species, giving the first spatiotemporal reference grid of variation in each. For example analysis of these tell us that domestication was a mosaic process in goats with very different lineages of wild goat incorporated in the east, west and south of the Fertile Crescent. Early signals of genes under selection have emerged including for pigmentation, stature, reproduction, milking and response to dietary change, providing evidence for an 8,000 year old human agency in moulding genome variation within a partner species. In ancient Fertile Crescent cattle genomes secondary input from local wild aurochsen into cattle migrating from the core region is clear in the southern Levant and Early Balkans herds, implying input from the wild is an ongoing, but granular process. In Near Eastern ancient cattle, Bos indicus secondary introgression from the east is profound and widespread, coinciding with the abrupt 4,200 BP climate event, a multi-century drought causing the collapse of empires and which defines the onset of our current geological age. This influx was a rapid, likely male-driven process suggesting active breeding with arid-adapted zebu bulls. A strong sampling of genomes through time in Northwest Europe shows the genome changes at key production genes that give rise to the breeds that populate the bulk of the worlds cattle herds today. Sheep genomes also illustrate the complexity of domestic origins across the Fertile Crescent and show migration patterns in later periods. We have also established that precisely dated historical genomes may be accessed using a different substrate, that of parchment sampled from manuscripts. The major difficulty, that these are often invaluable cultural treasures with no possibility of destructive sampling, has been circumvented by our discovery that whole livestock genome sequences may be recovered from DNA adhering to the rubbings of an eraser used only on the surface of a document. We have published the first genomic data from parchments and show the utility of this approach for genetic postcoding of artifacts; placing them in grids of modern genetic landscapes. Interestingly, we see a genome shift between 17th and 18th century British sheep, in part of our thousand year intensive survey of genetic change in a species that was the driver of that island’s wool-centred economy. Parchment rubbings also give genomic information from human manuscript users and their microbiome.