Power of a dual-use SNP panel for pedigree reconstruction and population assignment

The use of high-throughput, low-density sequencing approaches has dramatically increased in recent years in studies of eco-evolutionary processes in wild populations and domestication in commercial aquaculture. Most of these studies focus on identifying panels of SNP loci for a single downstream application, whereas there have been few studies examining the trade-offs for selecting panels of markers for use in multiple applications. Here, we detail the use of a bioinformatic workflow for the development of a dual-purpose SNP panel for parentage and population assignment, which included identifying putative SNP loci, filtering for the most informative loci for the two tasks, designing effective multiplex PCR primers, optimizing the SNP panel for performance, and performing quality control steps for downstream applications. We applied this workflow to two adjacent Alaskan Sockeye Salmon populations and identified a GTseq panel of 142 SNP loci for parentage and 35 SNP loci for population assignment. Only 50-75 panel loci were necessary for >95% accurate parentage, whereas population assignment success, with all 172 panel loci, ranged from 93.9% to 96.2%. Finally, we discuss the trade-offs and complexities of the decision-making process that drives SNP panel development, optimization, and testing.

Effects of recombinant salmon type II growth hormone and bovine growth hormone on growth of coho salmon (Oncorhynchus kisutch)

A comparison of the efficacy of salmon and bovine growth hormone to stimulate growth of coho salmon juveniles was performed. Oncorhynchus nerka (sockeye salmon) type II growth hormone (nGH2) was produced using a bacterial expression system, yielding approximately 25 mg of refolded recombinant protein per litre of cells. The purified nGH2 and bovine growth hormone (bGH) were tested in juvenile O. kisutch (coho salmon) over 24 weeks. Weekly intraperitoneal injections of 0.1 and 0.5 μg/g nGH2 resulted in a dose-dependent increase in weight and fork length compared to control fish injected with bovine serum albumin (BSA). Application of 0.5 μg/g bGH resulted in the same stimulation of growth as did 0.5 μg/g nGH2, indicating these proteins were equipotent. Following 6 weeks of treatment and a subsequent rest period of 7 weeks, coho salmon were further treated with bGH at 0.5 μg/g. A prior treatment with bGH did not reduce growth-promoting activity of bGH in subsequent treatments. Throughout the experiment, condition factor decreased at similar rates for all treatment groups. These data show that bGH, which is widely available, can be used to elevate growth rate in juvenile salmon comparably to homologous GH, and validate the use of bGH in physiological or ecological experiments where rapid growth is desired compared to that seen in wild type.

A time-lapse photography method for monitoring salmon (Oncorhynchus spp.) passage and abundance in streams

Accurately estimating population sizes is often a critical component of fisheries research and management. Although there is a growing appreciation of the importance of small-scale salmon population dynamics to the stability of salmon stock-complexes, our understanding of these populations is constrained by a lack of efficient and cost-effective monitoring tools for streams. Weirs are expensive, labor intensive, and can disrupt natural fish movements. While conventional video systems avoid some of these shortcomings, they are expensive and require excessive amounts of labor to review footage for data collection. Here, we present a novel method for quantifying salmon in small streams (<15 m wide, <1 m deep) that uses both time-lapse photography and video in a model-based double sampling scheme. This method produces an escapement estimate nearly as accurate as a video-only approach, but with substantially less labor, money, and effort. It requires servicing only every 14 days, detects salmon 24 h/day, is inexpensive, and produces escapement estimates with confidence intervals. In addition to escapement estimation, we present a method for estimating in-stream salmon abundance across time, data needed by researchers interested in predator--prey interactions or nutrient subsidies. We combined daily salmon passage estimates with stream specific estimates of daily mortality developed using previously published data. To demonstrate proof of concept for these methods, we present results from two streams in southwest Kodiak Island, Alaska in which high densities of sockeye salmon spawn.