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Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops
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Allaby, Robin G., Gutaker, Rafał M., Clarke, Andrew C., Pearson, Neil, Ware, Roselyn, Palmer, Sarah A., Kitchen, James and Smith, Oliver (2014) Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops. Philosophical Transactions of the Royal Society B: Biological Sciences, Volume 370 (Number 1660). Article number 20130377. doi:10.1098/rstb.2013.0377 ISSN 0962-8436.
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Official URL: http://dx.doi.org/10.1098/rstb.2013.0377
Abstract
Our understanding of the evolution of domestication has changed radically in the past 10 years, from a relatively simplistic rapid origin scenario to a protracted complex process in which plants adapted to the human environment. The adaptation of plants continued as the human environment changed with the expansion of agriculture from its centres of origin. Using archaeogenomics and computational models, we can observe genome evolution directly and understand how plants adapted to the human environment and the regional conditions to which agriculture expanded. We have applied various archaeogenomics approaches as exemplars to study local adaptation of barley to drought resistance at Qasr Ibrim, Egypt. We show the utility of DNA capture, ancient RNA, methylation patterns and DNA from charred remains of archaeobotanical samples from low latitudes where preservation conditions restrict ancient DNA research to within a Holocene timescale. The genomic level of analyses that is now possible, and the complexity of the evolutionary process of local adaptation means that plant studies are set to move to the genome level, and account for the interaction of genes under selection in systems-level approaches. This way we can understand how plants adapted during the expansion of agriculture across many latitudes with rapidity.
| Item Type: | Journal Article | ||||
|---|---|---|---|---|---|
| Subjects: | S Agriculture > SB Plant culture | ||||
| Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) | ||||
| Library of Congress Subject Headings (LCSH): | Crops -- Adaptation, Evolutionary genetics | ||||
| Journal or Publication Title: | Philosophical Transactions of the Royal Society B: Biological Sciences | ||||
| Publisher: | The Royal Society Publishing | ||||
| ISSN: | 0962-8436 | ||||
| Official Date: | 8 December 2014 | ||||
| Dates: |
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| Volume: | Volume 370 | ||||
| Number: | Number 1660 | ||||
| Article Number: | Article number 20130377 | ||||
| DOI: | 10.1098/rstb.2013.0377 | ||||
| Status: | Peer Reviewed | ||||
| Publication Status: | Published | ||||
| Access rights to Published version: | Restricted or Subscription Access | ||||
| Date of first compliant deposit: | 28 December 2015 | ||||
| Date of first compliant Open Access: | 28 December 2015 | ||||
| Funder: | Natural Environment Research Council (Great Britain) (NERC), Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Leverhulme Trust (LT) | ||||
| Grant number: | NE/F000391/1 (NERC), NE/G005974/1 (NERC), BB/G0177941 (BBSRC), F/00 215/BC (LT) |
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