Tracking the origins of an adaptive trait syndrome with ancient DNA

这项研究将追踪3000年的遗传变化，以了解向日葵驯化的演变。了解与驯化相关的复杂性状是如何随着时间的推移而组装起来的，是进化生物学中的一个核心但具有经验挑战性的问题，也是对农业、保护和人类健康至关重要的话题。适应通常涉及多种形态、生理或行为特征的协调变化，这种模式在野生植物向作物的转化方面尤其如此。大约5000年前由美洲原住民驯化，这种重要的主要作物具有丰富的考古记录和广泛的基因组资源。利用尖端的DNA测序方法，将开发一个反映从古代到当代DNA驯化时期的时间序列的数据集。这项研究可以为早期美洲原住民文化的农业和贸易提供新的视角。受训人员在哥本哈根的地球遗传学中心获得国际经验。高中基因组学课程将通过在国立自然历史博物馆的暑期实习项目来开发，该项目将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。最近的技术进步使古DNA的全基因组研究成为可能，并为重建多性状适应的历史基因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，以及驯化特征的推断变化，所获得的DNA数据集将解决驯化进行速度有多快的核心争论，并测试进化论的关键预测。通过基因组多样性和基因表达研究确定的数百个候选驯化基因将在涵盖驯化时期的考古时间序列中进行跟踪。使用尖端的基于解决方案的序列捕获方法，极大地丰富了特定序列的恢复，数百个这些基因将在一个时间序列中使用向日葵考古遗迹覆盖驯化时期进行基因分型。通过将基因型信息与基因功能知识相结合，该项目将确定哪些特征在驯化过程中进化得比其他特征早，以及这些特征是否具有共同特征。通过整合古代DNA数据和现有的效应量数据，该项目将测试与表型大差异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亲缘植物不同，这项遗传研究提供了一个独特的机会来研究不同的进化力量和遗传现象如何以及在什么条件下影响有益替代的时间和顺序，从而影响一整套性状

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