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: 1354622
• 负责人: Benjamin Blackman
• 金额: $ 78万
• 依托单位: University of Virginia Main Campus
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-06-01 至 2016-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1354622&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

这项研究将在3000年内追踪遗传变化，以了解葵花籽中驯化的演变。 了解随着时间的推移，了解与驯化相关的复杂套房是如何组装的，这是进化生物学中的一个核心但具有挑战性的问题，并且对农业，保护和人类健康至关重要。适应经常涉及多种形态，生理或行为特征的协调变化，而对于野生植物转化为农作物，这种模式尤其如此。大约5000年前，美国原住民驯化了这种重要的主食，具有丰富的考古记录和广泛的基因组资源。使用尖端的DNA测序方法，将开发反映涵盖从古代到当代DNA的驯化期的时间序列的数据集。这项研究可以通过美洲原住民文化提供有关农业和贸易的新观点。受训人员在哥本哈根的地球估计中心获得国际经验。高中基因组学课程将通过国家自然历史博物馆的暑期实习计划开发，该课程通过对新植物基因组的初步测序直接吸引了高中生的科学发现。近期对古代DNA的基因组进行了研究，并提供了一个独特的机会，并提供了一个独特的机会，可以构建历史遗传学的多种特征适应历史遗传序列。通过遵循有益的遗传变化以及通过推断驯化性状的变化的定时和顺序，所获得的DNA数据集将解决有关驯化如何进行的核心辩论，并从进化论中测试了关键预测。通过基因组多样性鉴定出的数百个候选驯化基因和基因表达研究将在涵盖驯化期的考古时间序列中进行。 使用尖端溶液的序列捕获方法极大地丰富了特定序列的恢复，其中几百个基因将在时间序列中使用向日葵考古学遗体进行基因型，从而涵盖驯化周期。通过将这些基因型信息与基因功能的知识相结合，该项目将确定在驯化过程中比其他特征更早地演变的特征，以及这些特征是否具有共同特征。通过将古代DNA数据与现有效应大小的现有数据相结合，该项目将测试与表型相关的变体是否主要出现在适应过程中。向日葵是当今重要的农作物，在许多特征中与其野生亲戚有所不同，这项遗传研究提供了一个独特的机会，可以调查如何和在什么条件下如何以及如何不同进化力和遗传现象影响影响一组特征集的有益替代的时机和顺序