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A domestication history of dynamic adaptation and genomic deterioration in sorghum

Oliver Smith, William V Nicholson, Logan Kistler, Emma Mace, Alan Clapham, Pamela Rose, Chris Stevens, Roselyn Ware, Siva Samavedam, Guy Barker, David Jordan, Dorian Q Fuller, Robin G Allaby
doi: https://doi.org/10.1101/336503
Oliver Smith
1School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
2Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 København K, Denmark
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William V Nicholson
1School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
3Warwick Medical School, University of Warwick, Coventry, CV4 7AL, United Kingdom
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Logan Kistler
1School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
4Department of Anthropology, Smithsonian Institution, National Museum of Natural History, Washington, D.C. 20506, USA
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Emma Mace
5Department of Agriculture, Fisheries and Forestry Queensland (DAFFQ), Warwick, Queensland 4370, Australia
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Alan Clapham
1School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
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Pamela Rose
6The Austrian Archaeological Institute, Cairo Branch, Zamalek, Cairo, Egypt
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Chris Stevens
7Institute of Archaeology, UCL, London, United Kingdom
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Roselyn Ware
1School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
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Siva Samavedam
1School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
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Guy Barker
1School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
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David Jordan
8Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Warwick, Queensland 4370, Australia
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Dorian Q Fuller
7Institute of Archaeology, UCL, London, United Kingdom
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Robin G Allaby
1School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
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Abstract

The evolution of domesticated cereals was a complex interaction of shifting selection pressures and repeated introgressions. 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 suggest a steady decline in genetic diversity over time coupled with an accumulating mutation load. Dynamic selection pressures acted sequentially on architectural and nutritional domestication traits, and adaptation to the local environment. Later introgression between sorghum races allowed 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 was not focused on the initial stages of domestication but occurred throughout the history of cultivation.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted June 03, 2018.
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A domestication history of dynamic adaptation and genomic deterioration in sorghum
Oliver Smith, William V Nicholson, Logan Kistler, Emma Mace, Alan Clapham, Pamela Rose, Chris Stevens, Roselyn Ware, Siva Samavedam, Guy Barker, David Jordan, Dorian Q Fuller, Robin G Allaby
bioRxiv 336503; doi: https://doi.org/10.1101/336503
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A domestication history of dynamic adaptation and genomic deterioration in sorghum
Oliver Smith, William V Nicholson, Logan Kistler, Emma Mace, Alan Clapham, Pamela Rose, Chris Stevens, Roselyn Ware, Siva Samavedam, Guy Barker, David Jordan, Dorian Q Fuller, Robin G Allaby
bioRxiv 336503; doi: https://doi.org/10.1101/336503

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