UC San Diego

While parasites can alter community structure, comprise a substantial proportion of the diversity in food webs, and also help us resolve trophic links, few studies have incorporated parasites into food webs. One of the main challenges of adequately adding parasites in food webs is accurate identification of parasites to the species level. In addition to having a large, undescribed diversity of species, many parasites have multiple-host complex life cycles, with poorly documented larval stages, infecting a wide range of vertebrate and invertebrate hosts. It is difficult to connect the larval stages to the adult stages, even when adult stages are described. DNA sequencing can inform efforts to document the parasite diversity in food webs and to connect different parasite life stages. This thesis seeks to inform a large effort to put parasites into the food webs for 13 estuaries along the California and Baja California coast. I obtained DNA sequences of the cytochrome oxidase 1 (CO1) gene and/or 18S rDNA for 123 samples of parasitic platyhelminthes (larval cestodes and trematodes), from 15 species of invertebrate hosts (including: bivalves, decapods, arthropods, and gastropods), that were only previously crudely identified based on morphology. Three different phylogenies were created to provide an improved degree of taxonomic resolution compared to the previous working names. I worked to test and develop new degenerate COI primers that had great promise in terms of sequencing efficiency (percentage of samples sequenceable). However, much testing and trouble-shooting revealed the inadequacy of the new primers, and other primers were used to obtain additional sample sequences. On the whole, this work provided sequences for 31 parasite samples, 26 species, corrected 3 misidentifications, and increased the taxonomic resolution for 24 samples. This work sets the stage for continuing efforts to link the larval stages to other parasite life stages, and permits a more accurate depiction of parasite diversity in food webs.