Publication Date

Fall 2016

Degree Type


Degree Name

Master of Science (MS)


Moss Landing Marine Laboratories


James T. Harvey


Diet analysis, next-generation sequencing, Sebastes, sexual segregation, Zalophus californianus

Subject Areas

Ecology; Molecular biology; Zoology


Molecular diet analysis has the potential to overcome the limitations of traditional methods. I used prey hard parts and molecular methods to examine sex-specific diet trends and rockfish consumption of California sea lions (Zalophus californianus, CSL). Fresh scat samples (n=219) were collected from Año Nuevo Island, CA (ANI), during the summers of 2013 and 2014. Prey taxa were identified from fish otoliths and cephalopod beaks recovered from cleaned scats. Sex of the CSL depositing the scat was assigned via multiplex PCR of a CSL microsatellite and a carnivore Y chromosome marker. Prey species also were identified using multiple loci in a Next Generation Sequencing framework. Twenty-two fish and 4 cephalopod taxa were identified from hard parts; additionally, 38 fish and 7 invertebrate taxa were identified from molecular data including 16 rockfish species. Hard parts data overestimated the occurrence of prey with robust hard parts whereas molecular data identified additional taxa that lacked diagnostic hard parts. More scats were assigned to females than males in both years, which may be indicative of greater female use of ANI or an increased presence of non-reproductive females within the Monterey Bay region during summer. Estimates of rockfish consumption in 2013 were similar to previous studies, but fewer rockfish were eaten in 2014 than previously reported. The increased presence of benthic and midwater prey indicated a greater prey base in Monterey Bay compared with previous studies.