DISSERTATION RESEARCH: Out of the Bushes and Into the Trees: Alternative Approaches to a Problematic Lamiaceae Phylogeny

薄荷科（唇形科）是开花植物中最多样化和经济上最重要的家族之一，许多物种用于传统药物或作为木材，烹饪草药和香料以及精油的重要来源。唇形科的极端形态复杂性，加上跨越不同生境的大量物种，提出了许多分类学或分类问题;通常很难区分密切相关的物种。最近发表了许多分子研究来帮助修订分类？利用遗传密码（DNA）信息重建物种间系统发育（系谱）关系的研究。然而，这些分析经常产生未解决关系的模式，用于解决遗传问题的标准方法，例如在分析中合理添加物种和基因，在很大程度上是无效的。拟议的研究使用唇形科作为案例研究，以评估新的，替代的方法来解决困难的系统发育问题，并探讨如何进化关系的限制，可以有效地和具有成本效益的大型生物群重建。这些方法涉及大规模DNA（或基因组）测序和系统发育推断的新计算方法。这项研究是解决唇形科系统发育问题的必要一步，将有助于推动薄荷系统学？从灌木丛到树林里？也就是说，从目前尚未解决的进化树中解决清楚？布什？拟议的研究是在系统生物学的前沿，结合实地植物学与计算生物学和分子遗传学的最新进展，它有可能证明新的，跨学科的方法来解决困难的系统发育问题，可以适用于其他有问题的植物和动物群体的功效。这项研究的结果将：产生第一个叶绿体基因组的唇形科;有助于深入了解北美薄荷集团的进化历史和植物地理学;并提供了一个必要的框架，急需的分类修订。此外，由于这项研究需要实地勘探和种群抽样，它将有助于发现和识别新的薄荷物种或重要的遗传多样性来源，这些物种或遗传多样性可能需要政府机构或保护组织的保护。

The mint family (Lamiaceae) is among the most diverse and economically important families of flowering plants, with many species used in traditional medicines or serving as important sources of timber, culinary herbs and spices, and essential oils. The extreme morphological complexity of the Lamiaceae, combined with the large number of species spanning diverse habitats, presents many taxonomic, or classification, problems; it is often difficult to distinguish closely related species. Numerous molecular studies have been published recently to help revise classifications?studies that reconstruct phylogenetic (genealogical) relationships among species using information from the genetic code (DNA). However, these analyses regularly yield patterns of unresolved relationships, and standard approaches used to resolve phylogenies, such as the reasonable addition of species and genes into the analyses, have been largely ineffective. The proposed research uses Lamiaceae as a case study to evaluate new, alternative approaches for resolving difficult phylogenetic problems and explores the limits of how evolutionary relationships can be efficiently and cost-effectively reconstructed for large groups of organisms. These approaches involve large-scale DNA (or genome) sequencing and new computational methods for phylogenetic inference. The research represents a necessary step towards resolving difficult phylogenetic problems in Lamiaceae and will help move mint systematics ?out of the bushes and into the trees??that is, to resolve clear evolutionary trees from the current unresolved ?bush? patterns.The proposed research is at the forefront of systematic biology, combing field botany with recent advances in computational biology and molecular genetics, and it has the potential to demonstrate the efficacy of new, cross-disciplinary approaches to resolving difficult phylogenetic problems that can be applied to other problematic groups of plants and animals. The results of this study will: produce the first chloroplast genomes for Lamiaceae; contribute insights into the evolutionary history and biogeography of North American mint groups; and provide an essential framework for a much-needed taxonomic revision. Moreover, because this study requires field exploration and population sampling, it will facilitate the discovery and recognition of new mint species or important sources of genetic diversity that may warrant protection by government agencies or conservation organizations.