| Summary: | Doctor of Philosophy === Department of Statistics === Suzanne Dubnicka === DNA barcodes are short strands of nucleotide bases taken from the cytochrome c oxidase
subunit 1 (COI) of the mitochondrial DNA (mtDNA). A single barcode may have the form C
C G G C A T A G T A G G C A C T G . . . and typically ranges in length from 255 to around
700 nucleotide bases. Unlike nuclear DNA (nDNA), mtDNA remains largely unchanged as
it is passed from mother to offspring. It has been proposed that these barcodes may be
used as a method of differentiating between biological species (Hebert, Ratnasingham, and
deWaard 2003). While this proposal is sharply debated among some taxonomists (Will
and Rubinoff 2004), it has gained momentum and attention from biologists. One issue
at the heart of the controversy is the use of genetic distance measures as a tool for species differentiation. Current methods of species classification utilize these distance measures that are heavily dependent on both evolutionary model assumptions as well as a clearly defined "gap" between intra- and interspecies variation (Meyer and Paulay 2005). We point out the limitations of such distance measures and propose a character-based method of species classification which utilizes an application of Bayes' rule to overcome these deficiencies. The proposed method is shown to provide accurate species-level classification. The proposed methods also provide answers to important questions not addressable with current methods.
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