Identification of harbor porpoise (Phocoena phocoena) prey species using PCR based molecular techniques

• Main Author: Francis Joseph Oliaro
• Other Authors: Jose de la Torre, Karen Crow, Frances Gulland
• Format: Master Thesis
• Language: English
• Published: San Francisco State University 2013
• Subjects: Pacific; Phocoena phocoena
• Online Access: http://hdl.handle.net/10211.3/130150

For reasons that are presently unclear, Pacific harbor porpoises (Phocoena phocoena) have recently re-established their range inside San Francisco Bay. To create an inventory of primary prey species consumed, DNA was extracted from stomach contents of stranded harbor porpoises found in central California and the San Francisco Bay area. DNA extracts were used as templates in Polymerase Chain Reactions (PCR) with group-specific primer sets that selectively amplify DNA of fishes, cephalopods and crustaceans as well as prevent amplification of porpoise DNA. Extracts that were positive in group-specific PCR's were tested again using more specific primer sets that only amplify particular local fishes and cephalopods. All of the amplicons from both sets of PCR's were purified and direct sequenced. DNA sequences of prey species' were identified by BLAST searches of the GenBank nucleotide database using the Megablast algorithm for highly similar sequences.