The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated episodes of introgression. Genomes of archaeological crops have the potential to reveal these dynamics without being obscured by recent breeding or introgression. We report a temporal series of archaeogenomes of the crop sorghum (Sorghum bicolor) from a single locality in Egyptian Nubia. These data indicate no evidence for the effects of a domestication bottleneck, but instead reveal a steady decline in genetic diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially to shape architectural and nutritional domestication traits and to facilitate adaptation to the local environment. Later introgression between sorghum races allowed the exchange of adaptive traits and achieved mutual genomic rescue through an ameliorated mutation load. These results reveal a model of domestication in which genomic adaptation and deterioration were not focused on the initial stages of domestication but occurred throughout the history of cultivation.
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Sequence data were deposited in the European Molecular Biology Laboratory European Bioinformatics Institute (project code PRJEB24962).
The serial founder event simulation was executed using the program founderv6.pl available for download at: https://warwick.ac.uk/fac/sci/lifesci/research/archaeobotany/downloads/founderv6.
Journal peer review information: Nature Plants thanks Terence Brown, Xuehui Huang and other anonymous reviewer(s) for their contribution to the peer review of this work.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
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The authors thank M. Nesbitt for permitting the use of herbaria material from Kew Gardens. O.S., W.V.N., G.B. and R.G.A. were supported by the NERC (NE/L006847/1), and L.K. was also supported by NERC (NE/L012030/1). The work by C.S. and D.Q.F. with archaeobotanical materials was supported by a European Research Council grant (no. 323842).
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Nature Plants (2019)