Domestication as a process: modeling demography and selection in maize using ancient DNA

驯化过程：利用古代 DNA 对玉米进行人口统计和选择建模

• 批准号: 389693117
• 负责人: Professor Dr. Markus Stetter
• 金额: --
• 依托单位: Department of Plant Sciences
• 依托单位国家: 德国
• 项目类别: Research Fellowships
• 财政年份: 2017
• 资助国家: 德国
• 起止时间: 2016-12-31 至 2018-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/389693117?language=en
• 关键词: Domestication; process; modeling; demography; selection

Over 10,000 years ago humans began to domesticate wild plants, leading to profound changes in human lifestyles and communities referred to as the Neolithic Revolution. Crop domestication is in fact often modeled as a revolutionary event that separated the crop from wild plant: field studies have suggested that under the right conditions domestication could have occurred in a matter of decades, and evolutionary genetic models of crop domestication have followed this suit, treating domestication as an instantaneous event followed by expansion of the domesticated population. Archaeological remains, in contrast, suggest that domestication-related phenotypes took millennia to evolve. Elucidating this discrepancy between archaeological records and population genetic analyses will provide a better understanding of crop domestication and early human civilization.Maize is an ideal model to study crop domestication and adaptation, as its domestication history is well known and there is an enormous base of genomic and phenotypic data available. Archaeological data are also plentiful, including recently available genomic data from dozens of ancient samples. This project proposes to use maize as a model to investigate the timing and mode of selection during domestication. We propose two advances to the study of domestication. First, we will make use of new methodological approaches in quantitative genetics to study phenotypic evolution in ancient samples. While most phenotypes of such historical samples remain unknown, because only small parts of the plants persist, integrating genomic data from ancient samples with mapping data available from studies of extant populations with phenotypes allows us to study changes in the genetic component of phenotypes of interest. This allows us to investigate phenotypes under selection in ancient samples and the timing of phenotypic change. Second, we will take advantage of time series models to study the demographic history of maize during domestication. Until now, time series modeling has been employed for experimental evolution with microorganisms that have short generation times. However, including ancient samples into evolutionary modeling of domestication provides the opportunity to reconstruct the history of crops using time series modeling. Combined, these approaches will help to clarify the discrepancy between archaeology and population genetics on the question of duration of domestication.The proposed project leverages the extensive phenotypic and genotypic resources from modern maize inbreds, traditional maize landraces from the center of domestication, ancient maize samples from across the early extension range of the crop and the wild ancestor of maize to study selection on polygenic traits and maize demography over time. The study introduces the emerging field of paleopopulation genetics into crop research and the results will improve our understanding of crop domestication and selection of complex traits.

一万多年前，人类开始驯化野生植物，导致了人类生活方式和社区的深刻变化，被称为新石器时代革命。事实上，作物驯化通常被建模为将作物从野生植物中分离出来的革命性事件：田间研究表明，在适当的条件下，驯化可能在几十年内发生，作物驯化的进化遗传模型也遵循这一点，将驯化视为一个瞬时事件，随后是驯化种群的扩张。相比之下，考古遗迹表明，驯化相关的表型花了数千年的时间才进化出来。阐明考古记录和群体遗传分析之间的差异将有助于更好地理解作物驯化和早期人类文明。玉米是研究作物驯化和适应的理想模型，因为它的驯化历史众所周知，并且有大量的基因组和表型数据。考古数据也很丰富，包括最近从几十个古代样本中获得的基因组数据。本计画拟以玉米为模式，探讨驯化过程中选择的时机与方式。我们提出两个研究进展的驯化。首先，我们将利用数量遗传学的新方法来研究古代样本的表型进化。虽然这些历史样本的大多数表型仍然未知，因为只有一小部分植物持续存在，但将来自古代样本的基因组数据与从具有表型的现存种群研究中获得的映射数据相结合，使我们能够研究感兴趣的表型的遗传成分的变化。这使我们能够调查古代样本中选择下的表型和表型变化的时间。其次，我们将利用时间序列模型来研究玉米驯化过程中的人口统计历史。到目前为止，时间序列建模已被用于具有短世代时间的微生物的实验进化。然而，将古代样本纳入驯化的进化建模提供了使用时间序列建模重建作物历史的机会。结合起来，这些方法将有助于澄清考古学和群体遗传学在驯化持续时间问题上的差异。拟议的项目利用了来自现代玉米自交系、来自驯化中心的传统玉米地方品种、来自作物早期扩展范围的古代玉米样品和玉米的野生祖先，以研究多基因性状和玉米的选择。随着时间的推移。该研究将古种群遗传学这一新兴领域引入作物研究，其结果将提高我们对作物驯化和复杂性状选择的理解。