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Alaska Ecosystems Program

AFSC Molecular Ecology Research Laboratory

The AFSC’s Molecular Ecology Research Laboratory (MERL) was established in 2002 by Rolf Ream of the AFSC’s National Marine Mammal Laboratory (NMML) and Mike Canino of the AFSC’s Resource Assessment and Conservation Engineering (RACE) Division. There are a myriad of applications for molecular work at the Center, from the more obvious population structure studies to identification of cryptic forms (e.g., larvae, partially digested stomach contents, and parasites), repeated identification of individuals, elucidation of family lines, and diet assessment from fecal matter. While the technology is constantly expanding, techniques and protocols frequently are simplified, and there are a number of analyses that can be done via molecular methods that are easier, faster, more efficient, and more reliable than traditional methods. MERL researchers have experience in project development, proposal writing, equipment use, laboratory protocols, and data analysis, and can assist other AFSC researchers who are beginning or continuing molecular-based projects at MERL.

Several projects have been completed by MERL researchers, and there are many interesting ongoing investigations. Mike Canino and his team have developed microsatellite markers for Atka mackerel and Pacific cod and, in collaboration with Lorenz Hauser at the University of Washington School of Aquatic and Fisheries Sciences (UW SAFS), have used these markers in population genetics studies of both species. They also used microsatellite fingerprinting to examine the mating system (parentage) and patterns of egg cannibalism in Atka mackerel. Recently, Mike’s team collaborated with Stew Grant, at the University of Alaska, Anchorage (UAA), to complete a population genetics structure study of walleye pollock based on mitochondrial DNA (mtDNA) cytochrome oxidase I (COI) sequence variation. Mike’s team has also used DNA to identify, or “barcode” (identify species based on comparisons of COI sequences), 13 species of skates.

Pam Jensen (RACE) and her team, in collaboration with Lorenz Hauser (UW SAFS), have developed a PCR-(polymerase chain reaction) based assay to detect a dinoflagellate parasite of crustaceans that causes Bitter Crab Syndrome in Tanner and snow crabs in the Pacific. Compared to the traditional histological method of reading individual blood smears, this assay allows large numbers of samples to be assessed very quickly. In collaboration with the Alaska Department of Fish and Game (ADF&G), this assay is currently being used to monitor the prevalence of Bitter Crab Syndrome in the Bering Sea, Gulf of Alaska, and Southeast Alaska, and, in collaboration with the Department of Fisheries and Oceans Canada, in selected sites in Newfoundland. Similar infections are found in over 40 other crustacean species in the Northern Hemisphere. While the dinoflagellates infecting these hosts are morphologically indistinguishable from each other, based on a comparison of ribosomal DNA sequences, Pam’s team determined that the dinoflagellates infecting lobster and crabs resolve into at least two species.

Using mtDNA, Bobette Dickerson (NMML) recently completed a project looking for population structure in northern fur seals across their entire range, from the Beaufort Sea to British Columbia, and compared these results to Rolf Ream’s work examining the population structure using microsatellites. She is collaborating with Malin Pinsky (Stanford University) to look for changes in population composition over time by comparing the mtDNA sequences used for the northern fur seal population work to sequences obtained from ancient northern fur seal bones (500-2,500 years before present) found in native American middens throughout their range. In addition, Bobette regularly uses mtDNA sequences to identify (to species) samples from unknown pinnipeds, which are collected by North Pacific groundfish fisheries observers. Another NMML researcher, Harriet Huber, has completed an investigation of the population structure of harbor seals in the Washington, Oregon, and British Columbia areas using mtDNA. She found high degrees of structure, particularly for such a small geographic scale. To determine if the mixing that is occurring is sex-linked, she will be expanding the study to include microsatellites in the near future.

Other exciting projects are under way at MERL. A quantitative polymerase chain reaction (QPCR) assay for red king crab larvae in plankton samples will be developed, in collaboration with the University of Alaska Southeast (UAS), to allow us to determine the presence or absence, as well as approximate numbers, of larvae in a given sample without examining the sample microscopically. The QPCR assay will facilitate large-scale plankton studies by allowing rapid processing of plankton samples. Universal primers are being used to investigate the species identity of an egg parasite in shrimp.

Plans are under way, in collaboration with the ADF&G and the UAS, to use DNA barcoding to examine the diet of newly settled and juvenile Tanner crabs. The small size of young crabs and their prey, which is often shredded prior to consumption, makes identification of prey items tedious and uncertain; molecular techniques will speed the process. Paternity of Steller sea lions on a rookery in Russia is being examined using microsatellite fingerprinting to elucidate familial relationships, mating success of individual sea lions, survivorship, and ultimately the mating success of offspring. Historical demographic patterns of population expansion in both pollock and Pacific cod are being examined, in collaboration with Stew Grant (UAA), by using selection on the pantophysin gene in Pacific cod, in collaboration with Lorenz Hauser (UW SAFS), and mtDNA in pollock.

If you are interested in learning more about the molecular research conducted at MERL, please feel free to contact any of the researchers currently working at the lab.

By Bobette Dickerson and Pam Jensen

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