Time series of total run and escapement (or spawning biomass, herring).

<p>Total population size and escapement (salmon, in numbers of fish) or total population biomass and spawning stock biomass (spawning herring, in metric tons) for the six populations and four species in our analysis. Harvest for each population can be interpreted as the difference between total (black) and spawning (grey) lines. Red vertical lines are used to indicate 1989 (corresponding to the year of the EVOS event).</p

Evaluating signals of oil spill impacts, climate, and species interactions in Pacific herring and Pacific salmon populations in Prince William Sound and Copper River, Alaska

<div><p>The <i>Exxon Valdez</i> oil spill occurred in March 1989 in Prince William Sound, Alaska, and was one of the worst environmental disasters on record in the United States. Despite long-term data collection over the nearly three decades since the spill, tremendous uncertainty remains as to how significantly the spill affected fishery resources. Pacific herring (<i>Clupea pallasii</i>) and some wild Pacific salmon populations (<i>Oncorhynchus spp</i>.) in Prince William Sound declined in the early 1990s, and have not returned to the population sizes observed in the 1980s. Discerning if, or how much of, this decline resulted from the oil spill has been difficult because a number of other physical and ecological drivers are confounded temporally with the spill; some of these drivers include environmental variability or changing climate regimes, increased production of hatchery salmon in the region, and increases in populations of potential predators. Using data pre- and post-spill, we applied time-series methods to evaluate support for whether and how herring and salmon productivity has been affected by each of five drivers: (1) density dependence, (2) the EVOS event, (3) changing environmental conditions, (4) interspecific competition on juvenile fish, and (5) predation and competition from adult fish or, in the case of herring, humpback whales. Our results showed support for intraspecific density-dependent effects in herring, sockeye, and Chinook salmon, with little overall support for an oil spill effect. Of the salmon species, the largest driver was the negative impact of adult pink salmon returns on sockeye salmon productivity. Herring productivity was most strongly affected by changing environmental conditions; specifically, freshwater discharge into the Gulf of Alaska was linked to a series of recruitment failures—before, during, and after EVOS. These results highlight the need to better understand long terms impacts of pink salmon on food webs, as well as the interactions between nearshore species and freshwater inputs, particularly as they relate to climate change and increasing water temperatures.</p></div

Relationships between spawners (salmon) or spawning stock biomass (herring, in metric tons) and recruits-per-spawner.

<p>Raw data are shown for the years included in our analysis, with each year assigned a unique color. R = recruits, S = spawners, SSB = spawning stock biomass, age-3 recruits = millions of mature and immature age-3 herring, and PWS.</p

Gulf of Alaska freshwater discharge (Royer 1982, IMS 2016) as a driver of Pacific herring productivity.

<p>Shown are (a) the total freshwater discharge (m³ s^-1) and (b) log of observed age-3 recruits per spawning biomass (mt)—log(recruits/SSB)—in grey circles, and the model predicted log(recruits/SSB) using freshwater discharge as a covariate (R² = 0.55). High discharge events correspond to reduced productivity (fewer recruits to the population as three year olds). For historical reference, the discharge time series starting in 1931 is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172898#pone.0172898.s002" target="_blank">S2 Fig</a>. R = millions of mature and immature age-3 herring, SSB = spawning stock biomass in metric tons.</p

Map of Prince William Sound, and the adjacent Copper River Alaska.

<p>Triangles indicate the location of wild salmon stocks included in our analyses, circles show towns, and the asterisk shows where the <i>Exxon Valdez</i> ran aground in 1989.</p

Table of delta-AIC values used for model selection (S1–S5 Tables include raw values).

<p>Table of delta-AIC values used for model selection (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172898#pone.0172898.s006" target="_blank">S1</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0172898#pone.0172898.s010" target="_blank">S5</a> Tables include raw values).</p

Source-Sink Estimates of Genetic Introgression Show Influence of Hatchery Strays on Wild Chum Salmon Populations in Prince William Sound, Alaska

<div><p>The extent to which stray, hatchery-reared salmon affect wild populations is much debated. Although experiments show that artificial breeding and culture influence the genetics of hatchery salmon, little is known about the interaction between hatchery and wild salmon in a natural setting. Here, we estimated historical and contemporary genetic population structures of chum salmon (<i>Oncorhynchus keta</i>) in Prince William Sound (PWS), Alaska, with 135 single nucleotide polymorphism (SNP) markers. Historical population structure was inferred from the analysis of DNA from fish scales, which had been archived since the late 1960’s for several populations in PWS. Parallel analyses with microsatellites and a test based on Hardy-Weinberg proportions showed that about 50% of the fish-scale DNA was cross-contaminated with DNA from other fish. These samples were removed from the analysis. We used a novel application of the classical source-sink model to compare SNP allele frequencies in these archived fish-scales (1964–1982) with frequencies in contemporary samples (2008–2010) and found a temporal shift toward hatchery allele frequencies in some wild populations. Other populations showed markedly less introgression, despite moderate amounts of hatchery straying. The extent of introgression may reflect similarities in spawning time and life-history traits between hatchery and wild fish, or the degree that hybrids return to a natal spawning area. The source-sink model is a powerful means of detecting low levels of introgression over several generations.</p></div

Models of potential impacts (pulse, press, and pulse/recovery) associated with the <i>Exxon Valdez</i> oil spill.

<p>Impacts here are shown for a time lag of 0, however lag-1 and lag-2 equivalents were also considered as predictors in our models.</p

Diagram of a model of genetic introgression based on the classic source-sink model of migration.

<p>Explanation of variables: <i>q_l</i> is the allele frequency at a locus in a source population and is assumed to be unchanging over <i>n</i> generations of introgression. <i>q_n,i,l</i> is the allele frequency at locus, <i>l,</i> in a wild sink population, <i>i</i> after <i>n</i> generations.</p

Chum salmon production in Prince William Sound, Alaska hatcheries.

<p>^a Last used as brood stock in 1986.</p><p>^b Includes releases at Armin F. Koernig Hatchery and Port Chalmers remote release site.</p