Bayesian Analyses of Genetic Variation and Population Differentiation in Pacific Swordfish (Xiphias gladius L.) and the Development of High Resolution Melting Assays for Species Identification and Potential Sex-Linked Marker Survey in Istiophorid Billfish

Swordfish (Xiphias gladius L.) and istiophorid billfish fisheries in all ocean basins are important commercially and recreationally. Proper assessments of these fisheries are hampered by species misidentification, unknown sex ratios, and unclarified population structure. This dissertation focuses on: 1) genetic assays to identify Pacific billfishes, 2) the characterization of molecular markers potentially linked to gender determination in swordfish and billfishes, and 3) the characterization of the genetic population structure of Pacific swordfish. Unambigous identification of black marlin (Istiompax indica), blue marlin (Makaira nigricans), striped marlin (Kajikia audax) and sailfish (Istiophorus platypterus) was accomplished with two variants of high resolution melting (HRM), including HRM of a 491 bp segment, and melting profiles of a 48 bp unlabeled probe. Both HRM assays target variation in the mitochondrial DNA NADH dehydrogenase subunit 2 (ND2) gene and represent fast and robust alternatives to identify Pacific billfish. Surveys to identify gender-linked molecular markers were conducted using gender-validated samples. The characterization of Randomly Amplified Polymorphic DNA (RAPD) primers suggests a XY chromosomal system in blue marlin, and a ZW chromosomal system in sailfish, and possibly swordfish. Nucleotide sequence analyses of 12 loci known linked to gender determination in other teleosts showed no linkage in blue marlin, sailfish and swordfish. The genetic population structure of Pacific swordfish was surveyed using 16 samples (n=891) with an ample geographic coverage and that included early stages (n=150) and adults (n=741). Bayesian analyses of 20 single nucleotide polymorphisms (SNPs) contained in 10 nuclear loci indicate statistically significant genetic heterogeneity of tropical samples relative to temperate samples, but also with respect to other tropical samples, but no differences among temperate samples. The observed patterns are discussed in light of differences among regions in oceanographic conditions, adult and larval distributions, and tagging experiments