DISSERTATION RESEARCH: Extending anchored phylogenomics into plants with a case study of beaksedge (tribe Rhynchosporeae; Cyperaceae) diversification in the New World

喙莎草属（约375种，属Cyperaceae， Rhynchosporeae）是了解美洲三个亚热带/热带草原和稀树草原中心的多样性和多样化模式的理想物种，因为它们是每个地区最多样化的类群之一。例如，Rhynchospora是北美东南沿海平原特有的植物属中分类群最多的（49个）。本研究将使用“锚定系统基因组学”（鉴定和测序100或1000个高度保守的锚定区域，两侧分散在整个基因组中的更多可变区域）来产生大约100个喙莎草物种的强大系统发育，该系统发育将用于该群体多样化的时间和果实形态、栖息地特异性和C3/C4光合作用的进化。该项目将生成一个“工具包”，用于固定单子科植物的系统基因组学，单子科植物有65,000个物种，为人类提供了绝大多数食物（如水稻、玉米和小麦）。更好地了解这些作物及其野生近缘种之间的关系有助于作物改良。该项目还将使喙莎草的物种得到更精确的鉴定。在生态和保护研究中，由于鉴定困难，喙莎草通常只被鉴定为属。这一点尤其重要，因为在美国，81种喙莎草被认为是湿地指标，而且对该部落多样性的代表性不足，降低了保护评估的准确性，并使一些生态相互作用的研究变得不可能。该项目还将培养一名系统基因组学研究生，系统基因组学正在成为系统分类学、生物地理学、生态学和进化领域日益重要的技能。

The beaksedges (ca. 375 spp. in tribe Rhynchosporeae; Cyperaceae) are ideal for understanding patterns of diversity and diversification in the three American centers of subtropical/tropical grasslands and savanna because they are one of the most diverse groups in each area. For example, Rhynchospora has the greatest number of taxa (49) endemic to the SE North American Coastal Plain of any plant genus. This study will use 'anchored phylogenomics' (identifying and sequencing 100s or 1000s of highly conserved anchor regions flanked by more variable regions scattered throughout the genome) to produce a robust phylogeny for ca. 100 beaksedge species that will be used to the timing of diversification of the group and the evolution of fruit morphology, habitat specificity, and C3/C4 photosynthesis.The project will generate a 'toolkit' for anchored phylogenomics in the monocots, a group of 65,000 species that provides the great majority of the human diet (e.g., rice, maize, and wheat). Better knowledge of the relationships among these crop plants and their wild relatives is useful in crop improvement. The project will also enable more precise identifications of beaksedge species, which are often only identified to genus in ecological and conservation studies because of difficulties in identification. This is especially significant because 81 beaksedge species are recognized as wetland indicators in the United States and under-representation of the tribe's diversity reduces the accuracy of conservation assessments and makes the study of some ecological interactions impossible. The project will also train a graduate student in phylogenomics, which is emerging as an increasingly important skill set in systematics, biogeography, ecology, and evolution.