Conservation and aquacultural genetics of the Pacific lion-paw scallop (Nodipecten subnodosus)

The Pacific lion-paw scallop (Nodipecten suhnodosus) is uniquely distributed in waters of the Pacific Ocean and Gulf of California, surrounding the Baja California Peninsula, Mexico. Of importance to fisheries and aquaculture companies, little is understood about the biology or ecology of this species. The overall goal of this dissertation was to use molecular techniques to increase our understanding this species in its native range as well as in aquaculture.;Diversity within aquaculture was examined by genotyping progeny from an induced mass spawn of six adults (Chapter 2). As lion-paw scallops are functional hermaphrodites, mtDNA was used along with microsatellite genotyping to assign maternal and paternal parentage of each progeny. A significant skew in parental contribution was found when comparing the type and quantity of gametes each spawner contributed to the progeny. Over half of the progeny were full-siblings and self-fertilization was observed. These data warn against mass spawns in aquaculture in order to maintain population diversity.;To develop a tool for quantitative trait mapping and future marker assisted selection, genetic linkage maps were created using progeny from a single pairwise mating (Chapter 3). The female and male maps had 27 and 20 linkage groups covering 971.8 and 962.1cM, respectively. Combining the data resulted in 23 linkage groups with 63 microsatellite markers and 341 AFLP loci covering 1116.1cM. QTL analyses for size identified two linkage groups in the female and one in the male that are associated with growth phenotypes. Orange shell color was significantly associated with linkage group Nsub8.;Microsatellite genotypes and mtDNA sequences were used to examine the genetic structure and diversity of wild aggregations and samples spawned for aquacultural production (Chapter 1). Significant genetic differentiation was observed comparing samples between the Pacific and Gulf while no structure was evident within either coast. Artificially spawned samples did not reflect the diversity of the wild source populations. A common mtDNA haplotype present in samples from both coasts suggests relatively recent isolation of the aggregations studied. However, while similar to one another with nuclear genotypes, mitochondrial data show two divergent clades in wild aggregations, which raise questions about the taxonomic status of this species. These population level analyses will be valuable for future monitoring of the aggregations.