Discontinuities in quinoa biodiversity in the dry Andes: an 18-century perspective based on allelic genotyping

Abstract

History and environment shape crop biodiversity, particularly in areas with vulnerable human 36 communities and ecosystems. Tracing crop biodiversity over time helps understand how rural societies cope with anthropogenic or climatic changes. Exceptionally well preserved ancient DNA of 38 quinoa (Chenopodium quinoa Willd.) from the cold and arid Andes of Argentina has allowed us to track changes and continuities in quinoa diversity over 18 centuries, by coupling genotyping of 157 40 ancient and modern seeds by 24 SSR markers with cluster and coalescence analyses. Cluster analyses revealed clear population patterns separating modern and ancient quinoas. Coalescence-based 42 analyses revealed that genetic drift within a single population cannot explain genetic differentiation among ancient and modern quinoas. The hypothesis of a genetic bottleneck related to the Spanish 44Conquest also does not seem to apply at a local scale. Instead, the most likely scenario is the replacement of preexisting quinoa gene pools with new ones of lower genetic diversity. This process 46 occurred at least twice in the last 18 centuries: first, between the 6th and 12th centuries-a time of agricultural intensification well before the Inka and Spanish conquests-and then between the 13th 48 century and today-a period marked by farming marginalization in the late 19th century likely due to a severe multidecadal drought. While these processes of local gene pool replacement do not imply 50 losses of genetic diversity at the metapopulation scale, they support the view that gene pool replacement linked to social and environmental changes can result from opposite agricultural 52 trajectories. 54

Ancient Plant Genomics in Archaeology, Herbaria, and the Environment

“…Desiccated and waterlogged archaeobotanical macrofossils, however, have proven to be excellent reservoirs for DNA survival over at least ten thousand years and in diverse environments. Dry caves and rockshelters (68,82,145,152), arid Andean (65,161) and Egyptian (139) sites, and the desert southwestern U.S. (29) have all shown excellent DNA preservation in plant remains, and all complete genome sequences from archaeological plants to date have been from dry-preserved remains. Waterlogged remains are less frequent, since they rely on serendipitous deposition in bodies of water where decomposition is impeded.…”

“…This experiment, showing changes in transposable element composition through archaeological time, suggested a punctuated equilibrium-like model for recent cotton evolution where massive genomic compositional events accompanied domestication with implications for diversity and biology. Other archaeological DNA studies have focused on domestication biogeography in barley (82), the mutation load and adaptive hybridization in sorghum through an Egyptian time-series (139), historical biogeography and biodiversity in North and South American Chenopodium species (68,161), evolutionary ecology and domestication in squashes (67) and bottle gourds (34, 66), the evolution and long-term management of domesticated grapevines (111), and the domestication gene pool of sunflowers (152).…”