Manual for starch gel electrophoresis: A method for the detection of genetic variation

The procedure to conduct horizontal starch gel electrophoresis on enzymes is described in detail. Areas covered are (I) collection and storage of specimens, (2) preparation of tissues, (3) preparation of a starch gel, (4) application of enzyme extracts to a gel, (5) setting up a gel for electrophoresis, (6) slicing a gel, and (7) staining a gel. Recipes are also included for 47 enzyme stains and 3 selected gel buffers. (PDF file contains 26 pages.

Population Genetic Structure and Life History Variability in \u3ci\u3eOncorhynchus nerka\u3c/i\u3e from the Snake River Basin

We used the variation at 64 allozyme loci to examine genetic relationships among 32 samples of sockeye salmon Oncorhynchus nerka and kokanee (resident sockeye salmon) from the Snake River basin and other North American locations. The genetic differentiation among populations was pronounced: Wright’s FST was higher (0.244) than has been reported in any other study of Pacific salmon. A detailed examination of the O. nerka from lakes in the Sawtooth Valley of Idaho was undertaken to help guide recovery planning for the endangered Redfish Lake population and to help resolve the relationships between the resident and anadromous forms. In Redfish Lake, adult sockeye salmon that returned in 1991–1993 were genetically distinct from local kokanee but similar to a small group of “residual” sockeye salmon discovered in the lake in 1992. This result is consistent with the hypothesis that the original sockeye salmon population was not extirpated by Sunbeam Dam early in this century. Populations of O. nerka that appear to be native to the Snake River were also found in Alturas Lake, Stanley Lake, and Warm Lake, although the latter two lakes also showed evidence of nonnative gene pools. Kokanee sampled from Pettit Lake are clearly the result of an introduction of late-spawning kokanee from northern Idaho, and we found evidence of two O. nerka gene pools in Wallowa Lake, both traceable to introductions of nonnative kokanee

A Genetic Survey of English Sole Populations in the Salish Sea

This summer I interned at the Northwest Fisheries Science Center in Seattle, WA and participated in NOAA’s Salish Sea Project. The Salish Sea Project’s goal is to identify genetically distinctive groups of species in the Salish Sea that may have unique evolutionary and/or adaptive backgrounds. These findings will allow NOAA to promote and monitor the natural production of species in the Salish Sea, to select representative populations for experimental work regarding pollution, ocean acidification and climate change, to contribute to managing the ecosystem for intra- and inter-species diversity, and to help make informed decisions about adaptive management and marine protected areas (MPA). Our focus for the summer was English Sole (Parophrys vetulus). We performed microsatellite analysis on 480 individuals over ten populations and used factoid correspondence analysis to summarize the variation across five loci. Significant differences were seen among only three of the ten populations. These results are preliminary; up to fifteen loci should be analyzed before a conclusion is reached on the genetic variability of these populations. We would also like to include English Sole populations north of the Strait of Georgia, and along the Oregon coast

Assembling a multi species view of population level differentiation of marine life in the Salish Sea.

Our goal is to understand the Salish Sea ecosystem more completely by studying the population genetics of multiple species, plants and animals, covering a variety of habitats, trophic, and taxonomic groups. We believe these data will help inform ecosystem based management, e.g., the practical design of a network of marine protected areas or reservoirs (MPA). We present results of a population genetic study of English sole collected within the Salish Sea and from offshore as far north as Haida Gwaii, a study done in cooperation with NOAA Teacher in the Laboratory, Canadian Department of Fisheries and Oceans (CDFO), and Washington Department of Fish and Wildlife (WDFW). We also illustrate a sample design and the cooperative nature of this type of work by presenting the status of a new genetic and phenetic study of spot prawn that has been initiated with funds from The Suquamish Tribe and in cooperation with CDFO; WDFW; The Lummi, Muckleshoot, Nisqually, and Swinomish tribes; Vancouver Aquarium; and Mariner High School, Everett, WA. Patterns of population variability demonstrated from work in other research laboratories for Olympia oysters, Pacific herring and hake, and yellow eye rockfish are discussed. The ecosystem is experiencing change, including climate change, ocean acidification, and urban growth, and identifying the geographic nature of population variability for a variety of species will help us establish better tools for monitoring and protecting species, species groups, and habitats. In the process, we will learn what abiotic and biotic factors affect the patterns genetic connectivity for different marine taxonomic groups, and therefore be in a better position to understand, model, and track population responses to environmental change. Collaborative and cooperative work like this highlights the diversity of animal and plant life that is found but rarely recognized in our marine backyards

Genetic Characterization of <i>Oncorhynchus mykiss</i> Prior to Dam Removal with Implications for Recolonization of the Elwha River Watershed, Washington

<p>For more than 100 years, two dams blocked upstream migration of steelhead <i>Oncorhynchus mykiss</i> (anadromous Rainbow Trout) on the Elwha River, Washington. Prior to the removal of both dams (completed in 2015), 30 spatiotemporal collections of resident Rainbow Trout, steelhead, hatchery steelhead, and hatchery-derived Rainbow Trout (1,949 individuals) were made from 17 sites in the river, and the pattern of genetic diversity and connectivity were evaluated using 13 microsatellite loci. Wild-origin steelhead spawned below the downstream dam and were genetically distinguishable from upriver (above dam) resident Rainbow Trout (<i>F</i>_ST = 0.034), and the resident Rainbow Trout segregated into two distinct groups (<i>F</i>_ST = 0.056). Nonnative-origin hatchery steelhead varied from the indigenous steelhead (<i>F</i>_ST = 0.029), and the hatchery trout differed from the resident trout (<i>F</i>_ST = 0.163). Collections of resident Rainbow Trout from the upper portion of the basin were distinguished by lower estimates of genetic variability (<i>H_e, A</i>_R, and A/L) and effective population size compared with resident Rainbow Trout in the middle reaches of the Elwha River. The break between the two trout groups coincided with Rica Canyon, 8 river kilometers upstream from the Glines Canyon Dam (the upstream dam), suggesting that the upper and middle trout groups represent historic <i>O. mykiss</i> groups separated by flow conditions in the canyon prior to dam construction. Anticipating the potential for genetic exchange between steelhead and resident Rainbow Trout following dam removal, we evaluated the ability of the microsatellite baseline to distinguish F₁ crosses between the life history groups with computer simulations. These results demonstrate how a genetic baseline can be used as a conservation management tool to measure potential genetic introgression among resident populations and recolonizing anadromous populations.</p> <p>Received June 17, 2016; accepted October 10, 2016 Published online December 12, 2016 </p

Dam trout: Genetic variability in <i>Oncorhynchus mykiss</i> above and below barriers in three Columbia River systems prior to restoring migrational access

<div><p>Restoration of access to lost habitat for threatened and endangered fishes above currently impassable dams represents a major undertaking. Biological monitoring is critical to understand the dynamics and success of anadromous recolonization as, in the case of <i>Oncorhynchus mykiss</i>, anadromous steelhead populations are reconnected with their conspecific resident rainbow trout counterparts. We evaluate three river systems in the Lower Columbia River basin: the White Salmon, Sandy, and Lewis rivers that are in the process of removing and/or providing passage around existing human-made barriers in <i>O</i>. <i>mykiss</i> riverine habitat. In these instances, now isolated resident rainbow trout populations will be exposed to competition and/or genetic introgression with steelhead and vice versa. Our genetic analyses of 2,158 fish using 13 DNA microsatellite (mSAT) loci indicated that within each basin anadromous <i>O</i>. <i>mykiss</i> were genetically distinct from and significantly more diverse than their resident above-dam trout counterparts. Above long-standing natural impassable barriers, each of these watersheds also harbors unique rainbow trout gene pools with reduced levels of genetic diversity. Despite frequent releases of non-native steelhead and rainbow trout in each river, hatchery releases do not appear to have had a significant genetic effect on the population structure of <i>O</i>. <i>mykiss</i> in any of these watersheds. Simulation results suggest there is a high likelihood of identifying anadromous x resident individuals in the Lewis and White Salmon rivers, and slightly less so in the Sandy River. These genetic data are a prerequisite for informed monitoring, managing, and conserving the different life history forms during upstream recolonization when sympatry of life history forms of <i>O</i>. <i>mykiss</i> is restored.</p></div

Effective population size.

<p>Effective population size <i>N</i>_e by watershed, where steelhead collections are in crosshatch pattern. * indicates the <i>N</i>_E estimate was infinity.</p

Collection sites in the Sandy River watershed.

<p>Bar indicates Little Sandy River Diversion Dam (1912–2008) at Rkm 2.7. Collections No. 1 and 2 were taken at Rkm 16, No. 3 was taken at Rkm 6.44 near Arrow Creek, and No.4-8 were taken at or just upstream of the site of the Little Sandy River Diversion Dam. A complete barrier is illustrated at Rkm 11.78 (3.2 m) and partial barrier falls are found at Rkm 9.14 (2.7 m) and Rkm 13.37 (2.5 m). The Bull Run trap collections were made at Rkm 0.5 on the Bull Run River. The Sandy River enters the Columbia River at Rkm 190.</p

Collections information for the White Salmon River.

<p>Life stages are juvenile (J) and adult (A). Wright’s <i>F</i>_<i>IS</i> value and indicative adjusted nominal level (5%) is 0.0001 based on 351,000 randomizations (significant <i>P</i> values are bolded); LD number of loci in linkage disequilibrium over a 106 pair-wise comparisons; heterozygosity expected and observed; allele richness <i>A</i>_R based on 20 fish; estimate of effective population size <i>Ne</i> and associated 95% confidence interval CI. Collections above an impassable natural barrier are noted.</p

STRUCTURE results.

<p>Estimates of percent ancestry of each individual fish to a hypothetical color-coded population (Y axis) grouped by collection site numbers (X axis) as provided in Tables <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197571#pone.0197571.t001" target="_blank">1</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197571#pone.0197571.t002" target="_blank">2</a>. A. White Salmon River for K = 7 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197571#pone.0197571.s010" target="_blank">S10</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197571#pone.0197571.s012" target="_blank">S12</a> Figs); B. Sandy River watershed for K = 5, where the resident rainbow trout are from Little Sandy River (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197571#pone.0197571.s013" target="_blank">S13</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197571#pone.0197571.s015" target="_blank">S15</a> Figs).</p