Dissertation Research: Phylogeny of Helianthus Including New Methods to Detect Reticulate Evolution

面向普通读者的项目摘要 尽管向日葵属（向日葵）在农艺学和研究上具有重要意义，但物种之间的进化关系在很大程度上仍然没有得到解决。除H. annuus，向日葵的栽培品种，该属包含分布在北美的另外48种。一年生物种是研究二倍体杂交物种形成的模型系统-两个物种之间正常的有性杂交导致的物种形成-因此它们的关系已经被密切研究。但是其他物种之间的关系，特别是多年生植物，还没有很好的了解。这种缺乏分辨率主要是由于最近的快速物种形成和混合物种形成。解决这些关系沿着测试现有的亲本假设的多年生杂交向日葵将解决使用（1）一个相对更快的进化标记;（2）工具重建网状进化（进化的历史，已经演变成一个网状的方式，由于杂交，而不是树状模式）;和（3）多个核标记。目前，可用于推断系统发育历史的核标记数量非常有限。我们的目标是在这个项目结束时，提供一套通用的核引物的植物系统学社区的植物。与计算机科学系的同事合作，对两种完整植物基因组（水稻和拟南芥）进行了比较分析，产生了一系列在这些基因组之间保守的引物对。使用这些引物对18植物被筛选在一个广泛的分类抽样：向日葵，6种蝴蝶兰（兰花），6个跨越其他开花植物群。从这些标记收集的数据将被用于重建网状进化的新算法，这些方法将一起进行测试，对已知的父母的一年生杂交向日葵。如果这些方法正确地推断出这些关系，那么它们将更广泛地应用于研究较少的多年生向日葵。 科学意义：该项目所取得的进展将是当地和全球重建生命之树的关键。向日葵的解析完成了生命之树上的一个谱系，而这些新方法和标记将更广泛地关注树的准确构建。虽然正在收集的标记将专门用于本项目下的方法，但将其用于其他开花植物的能力将带来巨大的好处。此外，在这项研究中使用的计算工作导致了计算机科学家和生物学家之间的新合作，大大提高了未来研究问题的创造力。一个直接的教育影响也被认为是：目前，五名本科生已经在宝贵的分子技术，可以在他们未来的研究中应用的培训。

Project summary for general readers Despite the agronomic and research importance of the genus Helianthus (sunflowers), the evolutionary relationships among the species are still largely unresolved. In addition to H. annuus, the cultivated species of sunflower, the genus contains an additional 48 species that are distributed across North America. The annual species are a model system for studying diploid hybrid speciation - speciation caused by normal sexual hybridization between two species - so their relationships have been closely researched. But relationships among the rest of the species, especially the perennials, are not well understood. This lack of resolution is mostly due mostly to recent rapid speciation and hybrid speciation. Resolving these relationships along with testing the existing parental hypotheses of the perennial hybrid sunflowers will be addressed using (1) a comparatively faster evolving marker; (2) tools for reconstructing reticulate evolution (an evolutionary history that has evolved in a net-like fashion, due to hybridization, instead of a tree-like pattern); and (3) multiple nuclear markers. Currently the number of nuclear markers that are accessible for inferring phylogenetic history is very limited. Our goal at the end of this project is to provide the plant systematic community with a set of universal nuclear primers for plants. In conjunction with colleagues in The Department of Computer Sciences, a comparative analysis of two entire plant genomes (Oryza and Arabidopsis) has produced a series of primer pairs that are conserved between these genomes. Using these primer pairs 18 plants are being screened across a wide taxonomic sampling: six species in Helianthus, six in Phalaenopsis (an orchid), and six that span other flowering plant groups. Data collected from these markers will be used with the new algorithms for reconstructing reticulate evolution and together these methods will be tested on the known parentage of the annual hybrid sunflowers. If these methods correctly infer these relationships then they will be applied more broadly to the less-studied perennial sunflowers. Scientific significance: The advancements made by project will be key in the reconstruction of the Tree of Life, both locally and globally. The resolution of sunflowers completes one lineage on the Tree of Life, while these new methods and markers will focus more widely on the accurate construction of the tree. Although the markers being collected will be used specifically for methods under this project, the capability for their use in other flowering plants will be of tremendous benefit. Additionally, the computational efforts used in this research have resulted in a new collaboration between computer scientists and biologists that has greatly enhanced the creativity of future research questions. An immediate educational impact has also been felt: at present, five undergraduates have been trained in valuable molecular techniques that can be applied in their future research.