Bryan P. White, MS Biology, California State University Fullerton, Masters Thesis, 2014.
DNA barcoding is a method of biological identification that, in most metazoans, involves the use of a single mitochondrial gene, cytochrome oxidase I (COI) as a species level marker. In this thesis, the application of DNA barcoding to biomonitoring and biological identification are reviewed and analyzed. Chapter 1 is a summary and review chapter intended to introduce the topic of DNA barcoding, how it is generally used as a tool for biological identification, and how it might be applied to biomonitoring. Chapter 2 introduces the topic of species delimitation and how DNA barcoding techniques can be used to operatively delimit DNA barcodes into putative (hypothesized) species generally referred to as operational taxonomic units (OTUs). Four different species delimitation methods were compared in order to understand how algorithmic differences might affect richness estimates obtained from DNA barcodes. Chapter 3 introduces the concept of environmental DNA (eDNA), ambient DNA that can be detected using quantitative PCR or next generation sequencing methods. This chapter consists of an experimental effort to understand the persistence and transit of environmental DNA (eDNA) in freshwater streams using New Zealand mudsnails (Potamopyrgus antipodarum) as a test case. Chapter 4 reflects an ongoing barcoding effort and analysis of the shell morphology of two keyhole limpets (Fissurellidae), the giant keyhole limpet (Megathura crenulata) and the rough keyhole limpet (Diodora aspera). Recently, M. crenulata and D. aspera were been shown to be closely related species, and their example represents an opportunity to understand how recently diverged species can exhibit large morphological differences. In this chapter, the presence of static allometry in morphological characters and molecular clock estimates of the divergence times of M. crenulata and D. aspera are explored.
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