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

一万多年前，人类开始驯化野生植物，导致人类生活方式和社区发生深刻变化，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：实地研究表明，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了这一规律，将驯化视为瞬时事件，随后是驯化种群的扩张。相比之下，考古遗迹表明，与驯化相关的表型需要数千年的进化。阐明考古记录与种群遗传分析之间的这种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，因为它的驯化历史是众所周知的，并且有大量的基因组和表型数据基础。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。本项目拟以玉米为模型，研究驯化过程中的选择时机和选择方式。我们提出了驯化研究的两个进展。首先，我们将利用定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保留下来，但将古代样本的基因组数据与具有表型的现存种群研究中可用的制图数据相结合，使我们能够研究感兴趣的表型遗传成分的变化。这使我们能够研究在古代样本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研究玉米驯化过程中的人口统计学历史。到目前为止，时间序列模型已被用于具有较短世代的微生物的实验进化。然而，将古代样本纳入驯化的进化模型提供了使用时间序列模型重建作物历史的机会。这些方法结合起来，将有助于澄清考古学和种群遗传学在驯化时间问题上的差异。该项目利用来自现代玉米自交系、来自驯化中心的传统玉米地方品种、来自玉米早期推广范围的古玉米样本和玉米野生祖先的广泛表型和基因型资源，研究玉米多基因性状的选择和玉米人口统计学随时间的变化。该研究将古人类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认识。

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.