Freshwater ecosystems are highly biodiverse1 and important for livelihoods and economic development2, but are under substantial stress3. To date, comprehensive global assessments of extinction risk have not included any speciose groups primarily living in freshwaters. Consequently, data from predominantly terrestrial tetrapods4,5 are used to guide environmental policy6 and conservation prioritization7, whereas recent proposals for target setting in freshwaters use abiotic factors8, 9, 10, 11, 12-13. However, there is evidence14, 15, 16-17 that such data are insufficient to represent the needs of freshwater species and achieve biodiversity goals18,19. Here we present the results of a multi-taxon global freshwater fauna assessment for The IUCN Red List of Threatened Species covering 23,496 decapod crustaceans, fishes and odonates, finding that one-quarter are threatened with extinction. Prevalent threats include pollution, dams and water extraction, agriculture and invasive species, with overharvesting also driving extinctions. We also examined the degree of surrogacy of both threatened tetrapods and freshwater abiotic factors (water stress and nitrogen) for threatened freshwater species. Threatened tetrapods are good surrogates when prioritizing sites to maximize rarity-weighted richness, but poorer when prioritizing based on the most range-restricted species. However, they are much better surrogates than abiotic factors, which perform worse than random. Thus, although global priority regions identified for tetrapod conservation are broadly reflective of those for freshwater faunas, given differences in key threats and habitats, meeting the needs of tetrapods cannot be assumed sufficient to conserve freshwater species at local scales.

ABSTRACTMaladapted immigrants may reduce wild population productivity and resilience, depending on the degree of fitness mismatch between dispersers and locals. Thus, domesticated individuals escaping into wild populations is a key conservation concern. In Prince William Sound, Alaska, over 700 million pink salmon (Oncorhynchus gorbuscha) are released annually from hatcheries, providing a natural experiment to characterize the mechanisms underlying impacts to wild populations. Using a dataset of > 200,000 pink salmon sampled from 30 populations over 8 years, we detected significant body size and phenological differences between hatchery‐ and wild‐origin spawners, likely driven by competitive differences during maturation and broodstock selection practices. Variation in traits was reduced in hatchery fish, raising biodiversity concerns. However, phenotypic traits of immigrants and locals were positively correlated. We discuss possible mechanisms that may explain this pattern and how it may reduce adverse impacts associated with reduced trait variation. This study suggests that domestication impacts are likely widespread, but local adaptation may be maintained by phenotypic sorting.

In response to ocean heating and hatchery production, pink salmon (Oncorhynchus gorbuscha) returning from the North Pacific Ocean steadily increased after 1975, leading to concerns about their influence on food webs and competition with other species. Using measurements of distance between scale annuli of 24 584 individual sockeye salmon (O. nerka), we examined growth during their 2 or 3 years at sea from 1977 to 2015 for eight populations in Alaska. We found significant, negative autocorrelations at 1 lag year in annual growth of sockeye salmon, with a consistent pattern of lower growth in odd years, i.e. opposite to the biennial pattern of pink salmon abundance. Peak pink salmon abundances reduced growth of sockeye salmon from 7 to 14% during the second year in the ocean compared with growth when pink salmon abundance was low, while third-year growth was reduced up to 17%. The overall effect of pink salmon abundance on sockeye growth was over two times greater than the effect of sockeye salmon abundance. Production hatcheries and ocean heating contribute to the competitive dominance of pink salmon, underscoring the need to consider this unintended anthropogenic effect on the growth and productivity of sockeye salmon throughout the North Pacific.

1. Describing and explaining patterns of individual animal behaviors in situ, and their repeatability over the annual cycle, is an emerging field in ecology owing largely to advances in tagging technology. 2. We describe individual movements of adult Sakhalin taimen Parahucho perryi, an endangered salmonid fish, in the headwaters of a river in northern Japan during the spring spawning season over two years. 3. Migration timing, separated into stages prior to, during, and following the spawning period, was found to be more consistent and repeatable for females than males. 4. We hypothesized that the observed coordinated movement within seasons, and repeatability in migration timing across seasons, could result from 1) individual-specific responsiveness resulting from endogenous, biological traits that are mediated by environmental factors, or 2) social interactions among comigrating individuals. 5. We found that water temperature and water level experienced by fish near the river mouth approximately a week before arrival at the spawning ground explained variability in run timing between years for females but not males. 6. We found no evidence of conspecific attraction or repulsion resulting from social interactions among the spawners and post-spawners. 7. We conclude that individual-specific responsiveness to environmental cues was the likely mechanism underpinning the observed migration timing and movement patterns. 8. Determining the importance of these environmental and social factors not only during spawning but also during non-breeding life-history stages would contribute to a more comprehensive understanding of migratory connectivity in this species.

The homing behaviour of salmon is a remarkable natural phenomenon, critical for shaping the ecology and evolution of populations yet the spatial scale at which it occurs is poorly understood. This study investigated the spatial scale and mechanisms driving homing as depicted by spawning site-choice behaviour in pink salmon (Oncorhynchus gorbuscha) in Prince William Sound, Alaska. Molecular pedigree analyses of over 30,000 adult spawners in four streams revealed that pink salmon exhibit fine-scale site fidelity within a stream, returning to within <100 m of their parents. Homing behaviours were driven in part by a salinity gradient between intertidal and freshwater environments, with individuals incubated in freshwater environments more than twice as likely to spawn upstream of tidal influence than those incubated in the intertidal. Our findings challenge the traditional view that pink salmon populations are genetically and phenotypically homogenous due to their short freshwater residency as juveniles and high rates of dispersal as returning adults (i.e. straying). This study has important implications for rates of inbreeding, local adaptation and gene flow within populations, and is particularly relevant to the management of salmon hatcheries, given the high incidence of hatchery-origin pink salmon, reared in freshwater hatchery environments, that stray into wild populations of Prince William Sound.

Widespread mortality of Pacific salmon Oncorhynchus spp. returning to spawn in Alaska coincided with record-breaking air temperatures and prolonged drought in summer 2019. Extreme environmental conditions are expected to happen more frequently with rapid climate change and challenge the notion that Alaska could indefinitely provide abundant, cool freshwater habitat for Pacific salmon. A total of 110 geographically widespread opportunistic observations of premature mortality (carcasses) were collected from a variety of sources. Premature mortalities were documented for Pink Salmon Oncorhynchus gorbuscha, Sockeye Salmon O. nerka, Chum Salmon O. keta, Chinook Salmon O. tshawytscha, and Coho Salmon O. kisutch. Additionally, observations of Pink Salmon returning to spawn in Prince William Sound streams in 2019, obtained from systematic aerial surveys conducted annually, revealed low migration success in 87% of rain-driven streams (n = 30), 52% of snow-driven streams (n = 65), and only 18% of glacier-driven streams (n = 11). Salmon mortality observations were consistent with death due to heat stress resulting from high water temperatures or drought caused hypoxia and stranding. Developing a better understanding of how broad-scale climate patterns manifest at the stream scale can help us determine whether a major shift in Pacific salmon productivity is underway and inform fisheries management plans to better mitigate future risks.

The frequency of reproduction and homing success are crucial in determining the lifetime reproductive fitness of iteroparous salmonids. We examined consecutive spawning and homing by Sakhalin taimen (Parahucho perryi), one of the least-studied iteroparous salmonids. The average consecutive return rate was 69.5%, the highest ever reported for an iteroparous salmonid. The consecutive return rates were highest for large spawners, females, and individuals with active inter-tributary movements in the preceding year. We estimated tributary-scale repeat homing rates to be 50–87%, which was significantly higher than expected by chance alone. The repeat homing rates were higher for spawners that entered tributaries with more abundant spawners in the preceding year, which is consistent with the pheromone hypothesis because the abundance of spawners in a tributary is expected to correlate to the concentration of chemical homing cues emanating from offspring in the following year. These extremely high consecutive return and homing rates likely facilitated local adaptation over evolutionary time scales and have contributed to population stability in this river system. These same traits, however, may impede species recovery following habitat restoration efforts within the species historic range (e.g. dam barrier removal or improved passage) due to their limited rate of dispersal.

Pacific salmon hatcheries support important commercial fisheries for Pink Salmon Oncorhynchus gorbuscha and Chum Salmon O. keta in Prince William Sound (PWS), Alaska. State policy mandates that hatchery-produced fish must not negatively impact natural populations, which can occur during mixed fisheries and via ecological and genetic interactions. Therefore, we quantified the spatial and temporal overlap of natural- and hatchery-origin salmon (1) as they migrated into PWS and (2) in PWS spawning streams. Intensive sampling during 2013-2015, combined with ancillary agency harvest and hatchery composition data, also allowed us to estimate the hatchery, natural, and total run sizes. Estimated annual proportions (SE in parentheses) of hatchery fish in the preharvest run ranged from 0.55 (0.01) to 0.86 (0.03) for Pink Salmon and from 0.51 (0.03) to 0.73 (0.02) for Chum Salmon. Proportions of hatchery fish across all sampled PWS spawning streams were much lower, ranging from 0.05 (0.03) to 0.15 (0.07) for Pink Salmon and from 0.03 (0.03) to 0.09 (0.03) for Chum Salmon. In both species, relatively high instream proportions of hatchery fish tended to be geographically localized, while many streams exhibited low proportions. The estimated total PWS runs were 50-142 million Pink Salmon and 2.3-5.4 million Chum Salmon. Commercial fisheries harvested 94-99% of hatchery-origin fish of both species, 27-50% of natural-origin Pink Salmon, and 17-20% of natural-origin Chum Salmon. Despite very high harvest rates on hatchery-produced fish, an estimated 0.8-4.5 million hatchery Pink Salmon and 30,000-90,000 hatchery Chum Salmon strayed into PWS spawning streams. Our findings provide context for further research on the relative productivity of hatchery- and natural-origin salmon spawning in streams, density-dependent survival, improvements in fidelity to hatchery release sites, the influence of hatchery production on escapement management and policy, and refinements in harvest management precision in PWS.

Life-history and life-cycle models of Pink salmon (Oncorhynchus gorbuscha) are developed to provide insight into production dynamics of northern Bering Sea Pink salmon. Arctic ecosystems, including freshwater and marine ecosystems in the northern Bering Sea, are warming at a rapid rate. Due to their short, two-year life cycle, Pink salmon are well known to respond rapidly to ecosystem change and can provide unique insight into ecosystem impacts of warming Arctic conditions. Life-cycle models suggest a lack of density-dependence for adult Pink salmon spawners in the Yukon River and potential for some density-dependence for adult Pink salmon spawners in the Norton Sound region. Life-history models identify a positive and significant relationship between the abundance index for juvenile Pink salmon and average Nome air temperature during their freshwater residency (August to June). This relationship supports the notion that warming air temperatures in this region (as a proxy for river and stream temperatures) are contributing to improved freshwater survival or increased capacity of freshwater habitats to support Pink salmon production. Life-history models also identify the number of adult Pink salmon returning to Norton Sound and the Yukon River is significantly related to the juvenile abundance in the northern Bering Sea. This result indicates that much of the variability in survival for northern Bering Sea Pink salmon occurs during early life-history stages and that juvenile abundance is an informative leading indicator of Pink salmon runs to this region.

Pacific salmon productivity is influenced by ocean conditions and interspecific interactions, yet their combined effects are poorly understood. Using data from 47 North American sockeye salmon (Oncorhynchus nerka) populations, we present evidence that the magnitude and direction of climate and competition effects vary over large spatial scales. In the south, a warm ocean and abundant salmon competitors combined to strongly reduce sockeye productivity, whereas in the north, a warm ocean substantially increased productivity and offset the negative effects of competition at sea. From 2005 to 2015, the approximately 82 million adult pink salmon (Oncorhynchus gorbuscha) produced annually from hatcheries were estimated to have reduced the productivity of southern sockeye salmon by ∼15%, on average. In contrast, for sockeye at the northwestern end of their range, the same level of hatchery production was predicted to have reduced the positive effects of a warming ocean by ∼50% (from a ∼10% to a ∼5% increase in productivity, on average). These findings reveal spatially dependent effects of climate and competition on sockeye productivity and highlight the need for international discussions about large-scale hatchery production.

An in situ method was applied to monitor the responses of adult Pacific herring Clupea pallasi to predators. An autonomous, upward-facing echosounder was deployed on the seabed at 40 m just prior to the peak of the herring spawning season in Port Gravina, Prince William Sound, Alaska, USA. Monitoring took place over a continuous 4 d period (9-12 April 2016), during which herring and predators (seabirds and Steller sea lions Eumetopias jubatus) were tracked. Herring speeds varied (mean = 33.1 cm s(-1), range = 0.02-127.1 cm s(-1)) and were significantly lower than predator speeds (mean = 56.3 cm s(-1), range = 13.7-144.6 cm s(-1)). Swim speeds of herring and predators were positively correlated when regressions were lagged to 2.5 min and indicate a link between activity states of prey and predator. Changes in depth of herring were correlated positively with predator depths over a period of up to 5 min, which corresponds with seabird dive durations. This monitoring method can increase our understanding of sub-lethal effects of predators on Pacific herring and provide a direct method to quantify predation intensity on this critical life history stage.

Hierarchical population structure can result from range-wide geographic subdivision under conditions of environmental heterogeneity and weak gene flow. While a lower level of structure can be formed by local populations within eco-geographic regions, an upper level can be characterized by variation between populations from different regions, and thus, be represented by evolutionarily significant units (ESUs) defined by environmental, ecological and genetic variation. Selection of ESUs may depend on the sequence of using these three sources of variation. We propose to determine ESUs by first using non-genetic, ecological and geographical gradients for defining preliminary population groups (eco-geographic units, EGUs) and then testing whether the boundaries of these units are genetically coherent and thus represent ESUs or warrant their further modification. We evaluate this approach using Sakhalin taimen, an East Asian endangered endemic fish. Forty-one samples (473 fish) were drawn from thirty populations across the species range and genotyped at microsatellite DNA markers. We assign the populations into ESUs based on geographic and life history criteria and subsequent application of genetic diversity analyses. The ESUs appeared to be greatly diverged genetically. Within ESUs, local populations are genetically differentiated, have low effective sizes, show signatures of demographic decline and extremely restricted gene flow. Conservation plans aimed to restore or maintain a specific threatened population should take into account such hierarchical structure, and in particular be based on the genetic resources drawn from each population or using ecologically and genetically similar populations from the same ESU as donors for restoration of the population.

Sakhalin taimen Parahucho perryi, an east Asian fish noted to be one of the largest salmonids in the world, is threatened throughout its range in northern Japan and neighboring Russian Federation. We report here on the first effort to enumerate and characterize the spawning run of a river population. We applied sonar and video methods in a tributary of the Sarufutsu River in Hokkaido, Japan, and evaluated environmental controls on migration. Over two years we estimated the tributary population to range from 335 to 425. We found passage rate by our site to increase with temperature and decrease with river discharge, and migratory cues were reinforced by strong diel fluctuations in environmental conditions. Finally, we report evidence of males arriving early to the spawning grounds in this species. Given our results and data on the recreational fishery, we conclude that a substantial number of individuals in the population are affected by angling, underscoring the need to establish fishing regulations. Further, our study indicates passage success can vary over the migration period, and efforts at modifying or removing impediments, and devoting more research to factors controlling passage, could ultimately improve the status of this species.

1.Ecological interactions between wild and hatchery salmonids: an introduction to the special issue.-2. Mechanisms influencing competition between hatchery and wild juvenile anadromous Pacific salmonids in fresh water and their relative competitive abilities.- 3.Predation by hatchery yearling salmonids on wild subyearling salmonids in the freshwater environment: A review of studies, two case histories, and implications for management,- 4.Development of natural growth regimes for hatchery-reared steelhead to reduce residualism, fitness loss, and negative ecological interactions.- 5.PCD Risk 1: A tool for assessing and reducing ecological risks of hatchery operations in freshwater.- 6. Risk management of non-target fish taxa in the Yakima River Watershed associated with hatchery salmon supplementation.- 7. Ecological risk assessment of multiple hatchery programs in the upper Columbia watershed using Delphi and modeling approaches.- 8. Lack of trophic competition among wild and hatchery juvenile chum salmon during early marine residence in Taku Inlet, Southeast Alaska.- 9. Spatial and trophic overlap of marked and unmarked Columbia River Basin spring Chinook salmon during early marine residence with implications for competition between hatchery and naturally produced fish10. - Wild chinook salmon survive better than hatchery salmon in a period of poor production.

Abstract An international effort carried out during 2011-2012 culminated in three completed IUCN status assessments of Hucho spp., thus completing assessments for all species in this and a related genus Parahucho. These species hold great ecological and evolutionary significance in the salmonid family, and are recognized as the largest salmonids in the world. Specialists have long recognized their precarious status. The reports conclude that all species of taimen are now listed as threatened or Data Deficient on The IUCN Red List of Threatened Species™, and point to a host of ongoing and emerging threats, including habitat loss and overharvest. I summarize the key data used to arrive at the status categories, and emphasize some key conservation measures that must be taken to avoid extinction at both the local population scale and at the species level. I provide some cautionary advice on the use of hatcheries to recover depressed populations and emphasize the need to undertake new research expeditions to assess the uncertain current status of Hucho bleekeri Kimura and Hucho ishikawae Mori.

The optimism of early salmon hatchery practitioners toincrease abundance (Lichatowich 1999) has been tem-pered in recent decades by theoretical and empiricalstudiesindicatingunintendednegativeeffectshatcheriescanhaveonwildPacificsalmonandsteelhead(Naishetal. 2008; Pearsons and Temple 2010). Unintendedeffects of hatcheries are much more difficult and costlyto assess than evaluating the benefits of hatchery pro-duction to provide harvest opportunities. Holisticallyevaluating the relative costs and benefits of past andcurrent hatchery practices requires an understanding andestimation of the unintended effects (Pearsons 2010). Inrecent years, national and local governments, indigenous(e.g. First Nations or tribal) resource agencies, privateindustry and NGO conservation groups have begunefforts to reform public salmon and steelhead hatcherysystems in North America, which include critically eval-uating societal and biological risks and benefits.A significant number of national and internationalpolicy concernsandactions aredirectlyrelevantto thisissue. In the US Pacific Northwest, for example, theNational Oceanic and Atmospheric Administration(NOAA) is currently evaluating the environmentalimpact of salmon and steelhead hatcheries throughfederal mandates such as the Endangered Species Actand the Mitchell Act. The US State of Alaska is facedwith ongoing challenges of adhering to the State’sfisheries policies regarding sustainability, geneticsand escapement goals in the face of a growing privatesalmon hatchery industry in the State. In Canada, theDepartment of Fisheries and Oceans (DFO) is in theprocessofimplementinganambitiousnewWildSalmonPolicythatmustaddressimpactshatcherieshaveonwildsalmon. There is fresh thinking and emerging newinitiativesinbothJapanandRussiatoidentifyandseparately manage wild salmon in these nations.The growing demand for sustainable seafood hasput the global spotlight on salmon, which is near thetop of the list of most desired seafood, buoyed byreports of health benefits of eating salmon. Third partysustainability certifications of wild capture fisheries isrequired in many global markets, and Pacific salmon

Background: Concern about the decline of wild salmon has attracted the attention of the International Union for the Conservation of Nature (IUCN). The IUCN applies quantitative criteria to assess risk of extinction and publishes its results on the Red List of Threatened Species. However, the focus is on the species level and thus may fail to show the risk to populations. The IUCN has adapted their criteria to apply to populations but there exist few examples of this type of assessment. We assessed the status of sockeye salmon Oncorhynchus nerka as a model for application of the IUCN population-level assessments and to provide the first global assessment of the status of an anadromous Pacific salmon.Methods/Principal Findings: We found from demographic data that the sockeye salmon species is not presently at risk of extinction. We identified 98 independent populations with varying levels of risk within the species' range. Of these, 5 (5%) are already extinct. We analyzed the risk for 62 out of 93 extant populations (67%) and found that 17 of these (27%) are at risk of extinction. The greatest number and concentration of extinct and threatened populations is in the southern part of the North American range, primarily due to overfishing, freshwater habitat loss, dams, hatcheries, and changing ocean conditions.Conclusions/Significance: Although sockeye salmon are not at risk at the species-level, about one-third of the populations that we analyzed are at risk or already extinct. Without an understanding of risk to biodiversity at the level of populations, the biodiversity loss in salmon would be greatly underrepresented on the Red List. We urge government, conservation organizations, scientists and the public to recognize this limitation of the Red List. We also urge recognition that about one-third of sockeye salmon global population diversity is at risk of extinction or already extinct.

Advances in salmon culture practices during the latter part of the 20th century provided the opportunity for mass production of juvenile salmon. Hatchery-produced salmon currently outnumber wild salmon in some regions around the Pacific Rim, raising concerns about their ecological impacts on wild salmon. We convened five regional sessions at an international conference to identify and discuss issues related to ecological interactions between wild and hatchery salmon. Session participants were charged with identifying key interaction types by salmon life stage. Each group was asked to summarize key research needs and identify management actions that might be needed to reduce risks from hatchery programs. Some common themes emerged in all the sessions, including the importance of predation and competition interactions in freshwater environments during juvenile life stages and breeding interactions among adults. Much less is understood about interactions in estuarine and marine ecosystems, even though these environments may be critical in determining recruitment success. Some groups identified a need for field experiments to test hypotheses related to ecological interactions and the need to understand and, where possible, control hatchery straying. Some groups also discussed the importance of carrying capacity in different environments and how hatchery programs may be contributing to density-dependent effects. There is a lack of focused studies on ecological interactions between wild and hatchery salmon in the Western Pacific. The authors of this paper hope to encourage new research efforts to better understand ecological interactions to help inform management efforts aimed at reducing hatchery risks to wild salmon.