Exploring the efficacy, utility, and limitations of DNA barcoding within the class Aves.

摘要

This thesis investigates the efficacy of a recently proposed molecular bioidentifcation system known as "DNA barcoding". This system employs a short, standardized gene region (648bp of the mitochondrial gene cytochrome c oxidase I, in the case of animals) as a unique species identifier. To test species-level resolution, I constructed a library of DNA barcode sequences for birds from three regions: the Nearctic (North America), the southern Neotropics (Argentina), and the eastern Palearctic (Russia, Mongolia, and Kazakhstan). The accuracy of barcode-based species identification was assessed using the currently accepted avian taxonomy, which is the most robust of any taxonomic group. I also tested the use of DNA barcodes for species discovery via detection of large intraspecific divergences. Common intraspecific and interspecific trends in phylogeography were compared within and between biogeographical realms. Using the avian barcode library, I also compared the performance of several different methods for species delimitation, including distance-based thresholds, tree-based methods, and character-based methods (wherein each nucleotide of the sequence is treated as a unique character). Finally, I used the abundance of sequence data to test for signs of selection in cytochrome c oxidase I. Whole mitochondrial genomes available from GenBank were used to review the consistency of selective pressure throughout the genome. This largely confirmed the role of purifying selection in the evolution of the mitochondrial genome in birds. Overall, this study substantiates the utility of DNA barcoding as a reliable tool for the purposes of species identification and for highlighting taxa in need of further taxonomic review.