A Bayesian method for identification of stock mixtures from molecular marker data

Molecular markers have been demonstrated to be useful for the estimation of stock mixture proportions where the origin of individuals is determined from baseline samples. Bayesian statistical methods are widely recognized as providing a preferable strategy for such analyses. In general, Bayesian estimation is based on standard latent class models using data augmentation through Markov chain Monte Carlo techniques. In this study, we introduce a novel approach based on recent developments in the estimation of genetic population structure. Our strategy combines analytical integration with stochastic optimization to identify stock mixtures. An important enhancement over previous methods is the possibility of appropriately handling data where only partial baseline sample information is available. We address the potential use of nonmolecular, auxiliary biological information in our Bayesian model.

Comparing the identification of southern California juvenile rockfishes (genus Sebastes spp.) by restriction site analysis of the mitochondrial ND3/ND4 region and by morphological characteristics

Rockfish (Sebastes spp.) juveniles are often difficult to identify by using morphological characters. This study independently applies morphological characters and a key based on mitochondrial restriction site variation to identify juvenile rockf ishes collected in southern California during juvenile rockfish surveys. Twenty-four specimens of Sebastes were examined genetically without knowledge of the morphological assignment. Seventeen fish were identified genetically as S. semicinctus, S. goodei, S. auriculatus, S. jordani, S. levis, S. rastrelliger, and S. saxicola. Identities for the remaining fish were narrowed to two or three species: 1) three fish were either S. carnatus or S. chrysomelas; 2) one fish was either S. chlorosticus, S. eos, or S. rosenblatti; and 3) three fish could have been either S. hopkinsi or S. ovalis, the latter for which we now have distinguishing mitochondrial markers. The genetic and morphological assignments concurred except for the identity of one fish that could only be narrowed down to S. hopkinsi or S. semicinctus by using morphological characters. Genetics excluded more species from multispecies groupings than did the morphological approach, especially species within the subgenus Sebastomus. Species in the genetically unresolvable groups may be similar because of recent divergence or because of interspecies introgression.

Toward identification of larval sailfish (Istiophorus platypterus), white marlin (Tetrapturus albidus), and blue marlin (Makaira nigricans) in the western North Atlantic Ocean*

The identification of larval istiophorid billfishes from the western North Atlantic Ocean has long been problematic. In the present study, a molecular technique was used to positively identify 27 larval white marlin (Tetrapturus albidus), 96 larval blue marlin (Makaira nigricans), and 591 larval sailfish (Istiophorus platypterus) from the Straits of Florida and the Bahamas. Nine morphometric measurements were taken for a subset of larvae (species known), and lower jaw pigment patterns were recorded on a grid. Canonical variates analysis (CVA) was used to reveal the extent to which the combination of morphometric, pigment pattern, and month of capture information was diagnostic to species level. Linear regression revealed species-specific relationships between the ratio of snout length to eye orbit diameter and standard length (SL). Confidence limits about these relationships served as defining characters for sailfish >10 mm SL and for blue and white marlin >17 mm SL. Pigment pattern analysis indicated that 40% of the preflexion blue marlin examined possessed a characteristic lower jaw pigment pattern and that 62% of sailfish larvae were identifiable by lower jaw pigments alone. An identification key was constructed based on pigment patterns, month of capture, and relationships between SL and the ratio of snout length to eye orbit diameter. The key yielded identifications for 69.4% of 304 (blind sample) larvae used to test it; only one of these identifications was incorrect. Of the 93 larvae that could not be identified by the key, 71 (76.3%) were correctly identified with CVA. Although identif ication of certain larval specimens may always require molecular techniques, it is encouraging that the majority (92.4%) of istiophorid larvae examined were ultimately identifiable from external characteristics alone.