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

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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.