Tracking the origins of an adaptive trait syndrome with ancient DNA

利用古代 DNA 追踪适应性特质综合症的起源

• 批准号: 1640788
• 负责人: Benjamin Blackman
• 金额: $ 61.85万
• 依托单位: University of California-Berkeley
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-01-01 至 2020-09-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1640788&HistoricalAwards=false
• 关键词: Tracking; origins; adaptive; trait; syndrome

This study will trace genetic changes over a 3000 year period to understand the evolution of domestication in sunflower. Understanding how the complex suites of traits associated with domestication are assembled over time is a central but empirically challenging question in evolutionary biology and a topic of critical importance to agriculture, conservation, and human health. Adaptations frequently involve the coordinated change of multiple morphological, physiological, or behavioral characters, and this pattern is especially true with respect to the transformation of wild plants into crops. Domesticated approximately 5000 years ago by Native Americans, this important staple crop has a rich archaeological record and extensive genomic resources. Using cutting-edge DNA sequencing methods, a dataset reflecting the time series covering the domestication period from ancient through contemporary DNA will be developed. The research can provide new perspectives on agriculture and trade by early Native American cultures. Trainees gain international experience at the Centre for GeoGenetics in Copenhagen. A high school genomics curriculum will be developed through a summer internship program at the National Museum of Natural History that directly engages high school students in scientific discovery through initial sequencing of a new plant genome.Genome-wide studies of ancient DNA have been made possible by recent technological advances and provide a unique opportunity to reconstruct the historical genetic sequence of multi-trait adaptation. By following the timing and order with which beneficial genetic changes, and by inference changes in domestication traits, accumulate, the DNA dataset obtained will address a core debate over how fast domestication proceeded and test key predictions from evolutionary theory. Several hundred candidate domestication genes identified through genomic diversity and gene expression studies will be followed over an archaeological time series covering the domestication period. Using cutting-edge solution-based sequence capture methods to vastly enrich recovery of specific sequences, several hundred of these genes will be genotyped over a time series using sunflower archaeological remains covering the domestication period. By combining this genotypic information with knowledge of gene function, the project will determine which traits evolved earlier during domestication than others and whether those traits share common features. Through integrating the ancient DNA data with existing data on effect sizes, the project will test whether variants associated with large differences in phenotype predominantly appear early or late in the adaptation process. Sunflower is an important crop today, is divergent from its wild relative in many traits, and this genetic study provides a unique opportunity to investigate how and under what conditions different evolutionary forces and genetic phenomena influence the timing and order of beneficial substitutions affecting an integrated set of traits

这项研究将追踪3000年来的遗传变化，以了解向日葵驯化的进化。 了解与驯化相关的复杂性状如何随着时间的推移而组装，是进化生物学中一个核心但具有经验挑战性的问题，也是一个对农业，保护和人类健康至关重要的话题。适应常常涉及多种形态、生理或行为特征的协调变化，这种模式在将野生植物转化为作物方面尤其如此。大约5000年前被美洲原住民驯化，这种重要的主食作物有丰富的考古记录和广泛的基因组资源。利用最先进的DNA测序方法，将开发一个反映从古代到当代DNA驯化时期时间序列的数据集。这项研究可以为早期美洲土著文化的农业和贸易提供新的视角。受训人员在哥本哈根地球遗传学中心获得国际经验。将通过在国立自然历史博物馆的暑期实习项目开发高中基因组学课程，通过对新植物基因组的初步测序，直接让高中生参与科学发现。最近的技术进步使对古代DNA的全基因组研究成为可能，并为重建多性状适应的历史遗传序列提供了独特的机会。通过跟踪有益的遗传变化的时间和顺序，以及驯化性状的推断变化，获得的DNA数据集将解决关于驯化进行得有多快的核心争论，并测试进化理论的关键预测。几百个候选驯化基因，通过基因组多样性和基因表达的研究将遵循考古学的时间序列涵盖驯化期。 使用尖端的基于解决方案的序列捕获方法来极大地丰富特定序列的恢复，这些基因中的数百个将使用涵盖驯化时期的向日葵考古遗迹在时间序列上进行基因分型。通过将这些基因型信息与基因功能的知识相结合，该项目将确定哪些性状在驯化过程中比其他性状进化得更早，以及这些性状是否具有共同的特征。通过将古老的DNA数据与现有的效应量数据相结合，该项目将测试与表型差异较大相关的变异是否主要出现在适应过程的早期或晚期。向日葵是当今重要的作物，在许多性状上与其野生近缘种不同，这项遗传研究提供了一个独特的机会，以研究不同的进化力量和遗传现象如何以及在何种条件下影响影响有益替代的时间和顺序，从而影响一套完整的性状

项目成果

Plant Genomics: Evolution and Development of a Major Crop Parasite

植物基因组学：主要农作物寄生虫的进化和发展

• DOI: 10.1016/j.cub.2019.07.067
• 发表时间: 2019
• 期刊: Current Biology
• 影响因子: 9.2
• 作者: Stokes, Peter J.N.;Blackman, Benjamin K.
• 通讯作者: Blackman, Benjamin K.