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.
Highlights
During the closing phases of the last glacial stage that had predominated the climate system for previous 100 000 years or so, a number of plant species became adapted to an emergent human environment independently at different centres around the globe
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
That this was an adaptation to the human environment by plants is emphasized by the fact that a number of non-food plants such as small-seeded grasses and legumes adapted to this environment under the same regime of cultivation and became commensals, and display traits of the domestication syndrome [4,5,6]
Summary
During the closing phases of the last glacial stage that had predominated the climate system for previous 100 000 years or so, a number of plant species became adapted to an emergent human environment independently at different centres around the globe. The potential to observe selection and adaptation to the human environment directly through aDNA was first achieved with desiccated remains of maize, in which three biologically significant genes were surveyed over time and space in a handful of samples [28] While these incremental advances using aDNA offered tantalizing glimpses of the evolutionary process, the relatively small datasets generated meant that progress was prohibitively slow until the advent of next-generation sequencing a few years later. While the evidence of TE change over time would appear to support the expectation of large amounts of small change (assuming most transpositions had little effect on the genome functionality), they tell us little about the adaptive value of such change but hint at the potential pace of change and so capability of adaptation that could be possible In this particular study, we considered fragments of retrieved DNA that fell in gene regions as a possible source of information about adaptive change. 0 200 400 600 actual value arrival of BMSV virus adjusted native barley type alien types
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