DISSERTATION RESEARCH: Phylogenomics and biogeography of Vochysia, unraveling its tempo and mode of evolution

现代生物地理学中最耐人寻味的问题之一与新热带植物多样性有关。该地区物种数量的增加一度被认为是由于雨林生境的古老所致；然而，最近的研究表明，在过去的10-20年里，许多新热带开花植物群一直在多样化。新热带地区最近发生的植物多样化事件提出了一些问题，例如为什么最近发生了这么多物种形成事件，什么是促成生物和非生物因素。这项研究的目的是调查Vochysia的生物地理和起源，这是一个严格意义上的新热带类群，高度多样化，分布广泛，相对年轻。通过有助于更好地了解一组植物最近多样化的驱动因素，它将导致一般保护战略的改进，因为它将提高关于物种分布和多样化的知识。这项研究将对研究生和本科生在生物信息学、数据分析、实验室和植物标本库协议方面获得经验的学术进步有价值。该项目旨在通过研究Vochysia多样化的速度和模式来提高对新热带植物历史生物地理学的了解。将使用下一代测序和计算分析工具对该种群进行系统发育重建，为研究血吸虫的进化史提供系统发育树。进化模式的分析将使用系统发育树测年校准、生物地理重建和生态位建模软件进行。这些分析的结果将使人们能够推断出替代与分散以及生态位保守性与分化的相对重要性，重点是当地特有的和稀有的Vochysia物种。Vochysia多样化的速度将涉及使用现代基于贝叶斯的软件来比较该属内以及来自不同生物群的亚门之间的净多样化比率，该软件对物种多样化的复杂动态进行建模。

One of the most intriguing questions in modern biogeography relates to Neotropical plant diversity. The high number of species in this region was once thought to be due to the antiquity of rainforest habitats; however, recent studies suggest that many Neotropical flowering plant groups have been diversifying in the last 10-20 my. Recent episodes of plant diversification in the neotropics raise questions such as why have there been so many recent speciation events and what were the contributing biotic and abiotic factors. This study aims to investigate the biogeography and origin of Vochysia, a strictly Neotropical group that is hyper-diverse, widely distributed and relatively young. By contributing to a better understanding about the drivers of recent diversification in a group of plants, it will lead to an improvement in general conservation strategies since it will improve knowledge about species distribution and diversification. This research will be valuable for the academic progress of a graduate student and an undergraduate student that is gaining experience in bioinformatics, data analysis, laboratory, and herbarium protocols. This project seeks to improve the knowledge of the historical biogeography of plants of the neotropics by investigating the tempo and mode of Vochysia diversification. A phylogenetic reconstruction of the group will be done using next generation sequencing and computational analytical tools to provide a phylogenetic tree for investigating the evolutionary history of Vochysia. The analysis of the mode of evolution will be done using software for phylogenetic tree dating calibration, biogeographical reconstruction, and niche modeling. Results from these analyses will allow inferences to be made about the relative importance of vicariance versus dispersal and niche conservatism versus divergence with an emphasis on endemic and rare species of Vochysia. The tempo of Vochysia diversification will involve comparing the net diversification rates within the genus and between sub-clades from different biomes using a modern Bayesian-based software that models the complex dynamics of species diversification.