DISSERTATION RESEARCH: Genomic architecture as a species delimitation tool: validating a novel approach using rDNA variation for discovering species boundaries in ground beetles.

由于估计有数以百万计的未被发现或未被描述的物种，迫切需要新的技术来提高科学家发现物种的能力。认识到生物多样性不仅对比较生物学很重要，而且还因为它为与生物学有关的各种应用学科提供了一个重要的决策框架，如农业、生物修复、生物物理学、生物医学(等等)。这项研究建议开发一种新的、广泛适用的方法，以地面甲虫(Bembidion属)为模型来鉴定物种。初步数据显示，这一组中的物种在基因组结构的某些方面可能会有很大的差异，尽管它们之间的关系非常密切。这些基因组结构的差异是通过用现代测序技术检查一组基因(核糖体DNA(RDNA)基因)来揭示的。这种对“rDNA指纹”的分析成本很低，并有可能比传统方法更有效地帮助发现新物种。这项研究的结果将用于本科生的培训机会，以及一个涉及高中生的社区推广项目。将验证rDNA指纹作为物种划界工具的使用，方法是通过低覆盖率的Illumina测序对更多标本进行概况分析，并将rDNA指纹中的模式与建立在五个基因树上的现有物种概念和形态分析进行比较。将使用实时聚合酶链式反应分析，然后对相关标本进行额外的测序，来探索更大范围的步甲虫rDNA指纹的变异程度。最后，将通过比较荧光原位杂交(FISH)来探索rDNA顺反子内拷贝数膨胀的机制，以检验rDNA片段的许多拷贝已经转移到其与常染色质边界附近的异染色质DNA的假设。

With millions of undiscovered or undescribed species estimated, new techniques that increase scientists' ability to discover species is urgently needed. Recognizing biodiversity is important not only for comparative biology, but also because it provides an important decision-making framework for very diverse applied disciplines related to biology, such as agriculture, bioremediation, biophysics, biomedicine (among others). This research proposes to develop a new, widely applicable approach to identifying species using ground beetles (genus Bembidion) as a model. Preliminary data show that species in this group can have large differences in some aspects of the structure of their genomes despite being very closely related. These differences in genome structure are revealed by examining a set of genes (ribosomal DNA (rDNA) genes) with modern sequencing techniques. This analysis of 'rDNA fingerprints' costs little to obtain and has potential to help discover new species more efficiently than more traditionally used methods. Results from this research will be used for training opportunities for undergraduate students, as well as a community outreach project involving high school students. The use of rDNA fingerprints as a species delimitation tool will be validated by profiling additional specimens through low-coverage Illumina sequencing and comparing patterns in rDNA fingerprints to existing species concepts that are built on five gene trees and morphological analysis. The extent of variation in rDNA fingerprints across a wider group of carabid beetles will be explored using a real-time PCR assay followed by additional sequencing of relevant specimens. Finally, the mechanism of copy number inflation within the rDNA cistron will be explored through comparative fluorescent in situ hybridization (FISH), to test the hypothesis that many copies of fragments of rDNA have been transferred to heterochromatic DNA near its boundary with euchromatin.