Application of molecular genetic methods to rockfish predation and habitat association research efforts in Central California
- Devon Pearse
- John Field
- Kevin Stierhoff
End Date: December 31, 2007
The Sanctuary Integrated Monitoring Network (SIMoN) supported efforts to use previously developed genetic methods to enhance ongoing research projects in the Monterey Bay National Marine Sanctuary by identifying unknown rockfish (Sebastes spp.) samples to the species level.
The approach compares the genotype of an unknown individual at six nuclear microsatellite loci to a reference data set of genotypes from 33 Sebastes species commonly found in Central California. This method was applied to both newly-settled rockfish juveniles as part of a habitat association study and to rockfish remains recovered from the stomachs of jumbo squid (aka Humboldt squid) off the Central California coast.
In the California Current, jumbo squid (Dosidicus gigas) have been shown to feed on juvenile and adult groundfish, including rockfish (Sebastes spp.), Pacific hake, and small flatfish. However, many of the rockfish prey items cannot be identified to the species level, as squid often do not consume the heads, and consequently the otoliths ('ear' bones), of larger prey. As the continued presence of jumbo squid has the potential to alter linkages within California Current food webs, identification of those species most vulnerable to predation will improve the estimation of the impacts of this predator on the ecosystem.
Although degradation prevented identification of all recovered samples, the genetic data provided increased taxonomic resolution of rockfish prey in jumbo squid diets, thus enhancing the information content of ongoing food habits and ecosystem modeling efforts to better understand the consequences of the ongoing presence of these predators.
Summary to DateWidespread concerns by both commercial and recreational fishermen over the potential impacts of jumbo squid (Dosidicus gigas, aka Humboldt squid) on fisheries resources in California prompted the initiation of food habits studies by workers at the Fisheries Ecology Division of the Southwest Fisheries Science Center in Santa Cruz. Results demonstrate that D. gigas commonly feeds on adult groundfish; Sebastes species, Pacific hake, and several species of small flatfish account for ~25% of individual prey items, and a greater proportion of their diet by volume (Field et al. 2007).
Typically, identification of most prey items is done using hard parts (otoliths, beaks, scales) and is relatively straightforward. However, jumbo squid often do not consume the heads of larger prey (Dawe et al. 1997). Consequently, many of the larger individual rockfish (Sebastes spp.) cannot be identified to the species level. The application of molecular genetic approaches to complement traditional food habits studies provides a means to better understand trophic interactions of jumbo squid in the California Current ecosystem.
Genotypic assignment tests, typically used to identify the population-of-origin in within-species studies (Pearse & Crandall 2004), can be applied to between-species identification when suitable markers can be identified. Pearse et al. (2007) evaluated more than 50 microsatellite loci for cross-species amplification and variation, and chose six loci to create a reference data set for 33 Sebastes species commonly found off of Central California. Using these data, unknown samples of Sebastes spp. can be assigned to the species from which their genotype most likely originated based on the allele frequencies in the reference data set. The method has been demonstrated to accurately assign individuals to the species level, and provides a simple and cost effective approach to identify early life history stages, archived, or forensic samples of Sebastes spp. (Pearse et al. 2007).
- Trophic association
- Habitat association
Study MethodsGenotypic assignment tests, typically used to identify the population-of-origin within species, can also be applied to between-species identification when suitable markers can be identified. Pearse et al. (2007) evaluated more than 50 microsatellite loci for amplification and variation, and chose six loci to create a reference data set for 33 Sebastes species commonly found off of Central California. In Sebastes, cross-species amplification of microsatellite loci makes this technique possible, such that samples are assigned to the species from which their genotype most likely originated based on the allele frequencies in the reference data set.
In this study, unknown Sebastes samples were obtained from vertebrae and some skin tissue (generally from the same stomachs as the vertebrae) collected from jumbo squid stomach samples. Squid were collected off of Cordell Bank (CB), Half Moon Bay (HMB), Monterey Bay (MB), and Nine Mile Bank off of San Diego (SD). DNA was extracted from crushed bone or tissue, and used for polymerase chain reaction (PCR) amplification of the six microsatellite loci. All samples were amplified and scored three times with varying reaction conditions. Genotyped scores from the three attempts were then compared for consistency, and individuals which amplified three or more loci in at least one attempted PCR were assigned to species using the reference data set.
Figures and Images
Figure 1. Factorial correspondence analysis of the 33 reference rockfish species using the six-locus panel. Clusters of individual points represent groups of individuals from a single species.
Figure 2. Allele frequencies in the 33 reference rockfish species at the locusSeb 9. Diagnostic alleles for single species are shown in yellow. Many alleles have substantial frequency differences among species. When combined with information from other loci, these data allow unique identification of the species of a given sample.
- Pearse et al. (2008)The link above is for the final report entitled "Application of molecular genetic methods to rockfish predation and habitat association research efforts in Central California" by Devon Pearse and John C. Field, Fisheries Ecology Division, Southwest Fisheries Science Center, NOAA Fisheries.