Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant–hominin co-evolution back to the Pliocene (original) (raw)
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As genetic and archaeological evidence has developed over the past few years, it has become apparent that our most basic assumptions about how crops became incorporated into human culture may be in need of fundamental revision. Conventionally, crop origins have been understood through a local founding model in which one or multiple centers of small localized populations are formed through cultivation leading to domesticated forms as plants adapt to local human environments either over short, or more recently, longer time frames. However, the genetic expectations of such models are not being met by archaeogenomic and archaeological data. A key concept to the local
Plants 12(12):2310, 2023
De novo domestication is a novel trend in plant genetics, where traits of wild or semi-wild species are changed by the use of modern precision breeding techniques so that they conform to modern cultivation. Out of more than 300,000 wild plant species, only a few were fully domesticated by humans in prehistory. Moreover, out of these few domesticated species, less than 10 species dominate world agricultural production by more than 80% today. Much of this limited diversity of crop exploitation by modern humans was defined early in prehistory at the emergence of sedentary agro-pastoral cultures that limited the number of crops evolving a favorable domestication syndrome. However, modern plant genetics have revealed the roadmaps of genetic changes that led to these domestication traits. Based on such observations, plant scientists are now taking steps towards using modern breeding technologies to explore the potential of de novo domestication of plant species that were neglected in the past. We suggest here that in this process of de novo domestication, the study of Late Paleolithic/Late Archaic and Early Neolithic/Early Formative exploration of wild plants and identification of neglected species can help identify the barriers towards domestication. Modern breeding technologies may then assist us to break these barriers in order to perform de novo domestication to increase the crop species diversity of modern agriculture.
PNAS
Recent increases in archaeobotanical evidence offer insights into the processes of plant domestication and agricultural origins, which evolved in parallel in several world regions. Many different crop species underwent convergent evolution and acquired domestication syndrome traits. For a growing number of seed crop species, these traits can be quantified by proxy from archaeological evidence, providing measures of the rates of change during domestication. Among domestication traits, nonshattering cereal ears evolved more quickly in general than seed size. Nevertheless, most domestication traits show similarly slow rates of phenotypic change over several centuries to millennia, and these rates were similar across different regions of origin. Crops reproduced vegetatively, including tubers and many fruit trees, are less easily documented in terms of morphological domestication, but multiple lines of evidence outline some patterns in the development of vegecultural systems across the New World and Old World tropics. Pathways to plant domestication can also be compared in terms of the cultural and economic factors occurring at the start of the process. Whereas agricultural societies have tended to converge on higher population densities and sedentism, in some instances cultivation began among sedentary hunter–gatherers whereas more often it was initiated by mobile societies of hunter–gatherers or herder–gatherers."
Ancient Plant DNA as a Window Into the Cultural Heritage and Biodiversity of Our Food System
Frontiers in Ecology and Evolution, 2020
Since the beginning of the ancient DNA revolution in the 1980s, archeological plant remains and herbarium specimens have been analyzed with molecular techniques to probe the evolutionary interface of plants and humans. In tandem with archeobotany, ethnobiology, and other methods, ancient DNA offers tremendous insights into the co-evolution of people and plants, and the modern genomic era offers increasingly nuanced perspectives on plant use through time. Meanwhile, our global food system faces threats linked with declining biodiversity, an uncertain climate future, and vulnerable crop-wild relatives. Ancient plant DNA does not yield easy answers to these complex challenges, but we discuss how it can play an important role in ongoing conversations about resilience, sustainability, and sovereignty in our food system.
Domestication and plant genomes
Current opinion in plant biology, 2010
The techniques of plant improvement have been evolving with the advancement of technology, progressing from crop domestication by Neolithic humans to scientific plant breeding, and now including DNA-based genotyping and genetic engineering. Archeological findings have shown that early human ancestors often unintentionally selected for and finally fixed a few major domestication traits over time. Recent advancement of molecular and genomic tools has enabled scientists to pinpoint changes to specific chromosomal regions and genetic loci that are responsible for dramatic morphological and other transitions that distinguish crops from their wild progenitors. Extensive studies in a multitude of additional crop species, facilitated by rapid progress in sequencing and resequencing(s) of crop genomes, will further our understanding of the genomic impact from both the unusual population history of cultivated plants and millennia of human selection.
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.
2020
The divergent nature of evolution suggests that securing the human benefits that are directly provided by biodiversity may require counting on disparate lineages of the Tree of Life. However, quantitative evidence connecting evolutionary history to human well-being is still surprisingly tenuous. Here, we drew on a global review of plant-use records and the most comprehensive vascular plant phylogeny available demonstrating that, at any sample size, maximum levels of phylogenetic diversity captured significantly greater numbers of plant-use records than random selection, both globally and across the main continental regions of the world. Our study establishes an empirical foundation that links evolutionary history to human well-being, and it will serve as a discussion baseline to promote better-grounded accounts of the services that are directly provided by biodiversity.