DISSERTATION RESEARCH: Hybridization and polyploidy as drivers of species diversification and niche evolution during rapid radiations

南美洲的安第斯山脉是地球上物种最丰富、最濒危的生物多样性热点地区之一。鉴于该地区物种的高度特有性，保护该地区尤为重要;在热带安第斯山脉的45，000种植物中，近一半在世界其他地方都找不到。为了有效地保护这种多样性，了解物种之间的关系以及这些物种如何在时间和空间上形成至关重要。然而，这一地区的许多植物群缺乏这样的认识。这项研究旨在提高我们的理解的多样性，在属马尾杉，一个广泛的组的古老的陆地植物，代表了约100种在安第斯山脉的高山，通过确定如何杂交和基因组加倍导致新物种的形成组。这项研究为研究人员在哥伦比亚和厄瓜多尔的森林和高山草原中收集这些植物提供了资金，并使用新开发的DNA测序技术来解决这一古老而生态突出的植物群的进化历史。此外，这笔资金将使研究人员能够通过国家和国际会议以及同行评议的科学出版物传播他们的成果，并对本科生进行尖端分子生物学技术的培训。物种关系和热带美洲马尾杉杂交的进化特征将使用结合DNA测序和通过流式细胞术估计基因组大小的方法进行推断。为了补充以前在中美洲收集的材料，研究人员将从哥伦比亚和厄瓜多尔的安第斯山脉收集植物的叶子材料。干燥的叶材料将用于提取DNA用于测序和使用流式细胞术推断基因组大小。四个核编码基因，可用于推断一个物种是否是杂交起源，将使用太平洋生物科学公司下一代DNA测序平台上最近开发的测序方法进行测序。通过将这种方法与通过流式细胞术进行的基因组大小估计相结合，研究人员将能够确定来自物种间杂交和随后的基因组加倍（多倍化）的物种数量。使用计算系统发育方法，研究人员将推断属中谱系的年龄，组中物种之间的进化关系，以及杂交对物种多样化率的影响。这些结果不仅将提供深入了解美洲马尾杉属物种之间的进化关系，但提高我们的理解的机制，形成和维持物种多样性的安第斯保护热点。

The South American Andes are among the most species-rich and imperiled hotspots of biodiversity on Earth. Conservation of this region is especially important given its high level of species endemism; of the 45,000 species of plants native to the tropical Andes, nearly half are found nowhere else in the world. In order to effectively conserve this diversity, it is critical to understand the relationships among species as well as how those species form with respect to time and space. However, such an understanding is lacking for many plant groups in this region. This research aims to improve our understanding of diversity in the genus Phlegmariurus, a widespread group of ancient land plants that are represented by approximately 100 species in the high mountains of the Andes, by identifying how hybridization and genome doubling led to the formation of new species in the group. This research provides funding for the researchers to collect these plants in forests and alpine grasslands in Colombia and Ecuador and to use newly developed DNA sequencing technologies to resolve the evolutionary history of this ancient and ecologically prominent group of plants. Further, this funding will allow the researchers to disseminate their results through national and international meetings and peer-reviewed scientific publications, and to train undergraduate students in cutting-edge molecular biology techniques.Species relationships and the evolutionary signature of hybridization in tropical American Phlegmariurus will be inferred using an approach that combines DNA sequencing and genome size estimation via flow cytometry. To supplement materials previously collected in Central America, the researchers will collect leaf material from plants in the Andes of Colombia and Ecuador. Dried leaf material will be used both to extract DNA for sequencing and to infer genome size using flow cytometry. Four nuclear-encoded genes, which can be used to infer if a species is of hybrid origin, will be sequenced using the recently developed sequencing approach on the Pacific Biosciences next-generation DNA sequencing platform. By combining this approach with genome size estimation via flow cytometry, the researchers will be able to identify the number of species in the group that originated from inter-species hybridization and subsequent genome doubling (polyploidization). Using computational phylogenetic methods, the researchers will infer the age of lineages in the genus, the evolutionary relationships among species in the group, and the impact of hybridization on rates of species diversification. These results will not only provide insight into the evolutionary relationships among American species of Phlegmariurus, but improve our understanding of the mechanisms underlying the formation and maintenance of species diversity in the Andean conservation hotspot.