• Identification and application of molecular markers to chum salmon population genetics

      Garvin, Michael R.; Gharrett, A. J.; Tallmon, David; Smoker, William (2008-08)
      I developed a new technique, DEco-TILLING (an adaptation of Eco-TILLING), to discover useful single nucleotide polymorphisms (SNPs) rapidly and inexpensively. Some chum salmon (Oncorhynchus keta) populations have declined in Western Alaska and in other areas of their geographic range. Possible reasons include climate shifts, by- catch in fisheries, and other perturbations. Genetics offers powerful tools that can be used to monitor this species on the high seas in stock mixtures aiding management of by- catch identification and other contributors to declines. Single nucleotide polymorphisms are a genetic marker that can be easily and rapidly surveyed on many individuals. Tools like SNPs offer advantages in discriminating stocks in mixtures. However, tens or hundreds of informative SNPs must be discovered from among the millions in the chum salmon genome. Available discovery methods introduce ascertainment bias into this process, which can result in uninformative SNPs or the failure to identify useful ones. I incorporated and improved a genotyping assay to screen SNPs in thousands of individuals for a tenth of the cost of the standard available assay, and improved an assay to resolve the phase of linked SNPs. I show that the SNPs that I discovered are informative and can be use for mixed stock analysis.
    • The influence of decomposing salmon on water chemistry

      Brickell, David C.; Goering, John J. (University of Alaska, Institute of Water Resources, 1971)
      To increase our knowledge of the biological and chemical effects of the decomposition of seafood material, we have initiated a study of the decomposition of salmon carcasses in a natural system in southeastern Alaska (i.e. Little Port Walter estuary). The Pacific salmon migrates through this estuary when returning to its natal stream to spawn. Following spawning the fish die and the carcasses are eventually carried to the estuary where they sink to the bottom. During periods of low stream flow, the dead carcasses may remain in the stream itself until higher stream flows transport them to the estuary. In years of large escapements, the density of fish in the spawning stream can be very high. In the system chosen for our work, spawning densities greater than six fish per m2 have been recorded although at the time the current study was conducted the spawning density was slightly more than two fish per m2. Since our system involves primarily pink salmon (O. gorbuscha), the average weight of the fish can be assumed to be 2-3 kilograms. Thus, our study is concerned with the fate and distribution of some 75 metric tons of organic matter in the form of salmon carcasses in one small estuary in Southeastern Alaska. We are particularly interested in determining: (1) the effects of the salmon carcass decomposition on the nitrogen chemistry of the water in which the decomposition occurs; (2) the form and distribution of the organic matter which is returned to the marine system; and (3) the rate at which remineralization occurs. This paper presents the results of our initial investigations.