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

History and environment shape crop biodiversity, particularly in areas with vulnerable human 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 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 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 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 Conquest 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 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 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 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 trajectories.

历史与环境共同塑造作物生物多样性，在人类社区与生态系统均较为脆弱的区域尤为如此。对作物生物多样性进行历时追踪，有助于理解乡土社会如何应对人为活动或气候变化带来的挑战。本次研究从阿根廷寒冷干旱的安第斯山区获取了保存状态极佳的藜麦（Chenopodium quinoa Willd.）古DNA，通过使用24个SSR（Simple Sequence Repeat）分子标记对157份古、现代藜麦种子进行基因分型，并结合聚类分析与溯祖分析，得以追踪1800年间藜麦多样性的变化与延续特征。聚类分析结果显示，现代藜麦与古代藜麦之间存在清晰的种群分化模式。溯祖分析结果表明，单一种群内的遗传漂变无法解释古、现代藜麦之间的遗传分化。与西班牙征服时期相关的遗传瓶颈假说，在局域尺度上似乎也不成立。相较之下，最合理的情景是：原有藜麦基因库被遗传多样性更低的新型基因库所替代。这一基因库更替过程在过去1800年间至少发生过两次：第一次发生于6世纪至12世纪，彼时农业集约化程度已显著提升，早于印加与西班牙征服事件；第二次则始于13世纪并延续至今，其中19世纪后期的农业边缘化现象，大概率由持续数十年的严重干旱所引发。尽管这类局域基因库更替过程并不意味着集合种群（metapopulation）尺度上的遗传多样性损失，但它们佐证了一个观点：与社会及环境变化相关的基因库更替，可由截然相反的农业发展轨迹所驱动。