Francis Juanes

Infectious disease, shifting climates, and opportunistic predators: cumulative factors potentially impacting wild salmon declines

Emerging diseases are impacting animals under high‐density culture, yet few studies assess their importance to wild populations. Microparasites selected for enhanced virulence in culture settings should be less successful maintaining infectivity in wild populations, as once the host dies, there are limited opportunities to infect new individuals. Instead, moderately virulent microparasites persisting for long periods across multiple environments are of greatest concern. Evolved resistance to endemic microparasites may reduce susceptibilities, but as barriers to microparasite distributions are weakened, and environments become more stressful, unexposed populations may be impacted and pathogenicity enhanced. We provide an overview of the evolutionary and ecological impacts of infectious diseases in wild salmon and suggest ways in which modern technologies can elucidate the microparasites of greatest potential import. We present four case studies that resolve microparasite impacts on adult salmon migration success, impact of river warming on microparasite replication, and infection status on susceptibility to predation. Future health of wild salmon must be considered in a holistic context that includes the cumulative or synergistic impacts of multiple stressors. These approaches will identify populations at greatest risk, critically needed to manage and potentially ameliorate the shifts in current or future trajectories of wild populations.

Capture severity, infectious disease processes and sex influence post-release mortality of sockeye salmon bycatch

Among Pacific salmon released from gillnets on their way to spawning grounds, those entangled for the longest amount of time, especially females, were very likely to die before spawning. Fish that died earliest were in poorer health than survivors and showed greater activity of several infectious disease causing microbes.

Validation of daily increments and a marine‐entry check in the otoliths of sockeye salmon Oncorhynchus nerka post‐smolts

Juvenile sockeye salmon Oncorhynchus nerka that were reared and smolted in laboratory conditions were found to produce otolith daily increments, as well as a consistently visible marine-entry check formed during their transition to salt water. Field-collected O. nerka post-smolts of an equivalent age also displayed visible checks; however, microchemistry estimates of marine-entry date using Sr:Ca ratios differed from visual estimates by c. 9 days suggesting that microstructural and microchemical processes occur on different time scales.

Aquaculture and the spread of introduced mussel genes in British Columbia

Aquaculture can promote the introduction of non-indigenous species (NIS) into wild marine environments. In addition, NIS aquaculture escapees may hybridize with closely-related native species introducing foreign alleles to their gene pool. To quantify the influence of mussel aquaculture on the native community in British Columbia we sampled mussels from fourteen locations on Vancouver Island. There are two native species in this region, M. trossulus and M. californianus, and two farmed NIS, Mytilus edulis and M. galloprovincialis, both originally from Europe. DNA was extracted from mussel tissue and the mitochondrial cytochrome c oxydase subunit 1 (COI) gene was sequenced. One nuclear locus that exhibits different alleles for M. edulis, M. galloprovincialis and M. trossulus (Glu-5′) was also characterized, using PCR, in order to identify heterozygotes. We found the proportion of NIS introgression depended primarily on farm density. Other habitat traits such as the degree of exposure to the open sea and, to a minor extent, salinity, contributed significantly to explain the distribution of introgressed individuals. Different habitat preference of NIS and native species, and marine currents, provide additional explanations for the distribution of alien and native species along Vancouver Island coasts. As a whole, our results suggest that native M. trossulus populations are more introgressed by M. galloprovincialis genes in open habitats.

Nearshore fish community responses to large scale dam removal: implications for watershed restoration and fish management

The nearshore is a critical zone for northeast Pacific Ocean fish communities, including ecologically and culturally important salmon species. The largest dam removal in the world was recently completed on the Elwha River, with the goal of restoring fisheries and ecosystems to the watershed. The nearshore Elwha fish community was monitored monthly from January 2008 to November 2015 before, during and after dam removal. As of September 2015, approximately 2.6xa0million m3 of sediment material had increased the area of the Elwha delta to over 150xa0ha. Newly formed nearshore habitats were quickly colonized by fish communities during the dam removal period but the communities were similar in total species richness and Shannon diversity before and after dam removal, and were similar to a nearby reference site (Salt Creek estuary). Select fish species, including ESA-listed Pacific salmon and trout Oncorhynchus spp., and eulachon Thaleichthys pacificus, and non-native, American shad (Alosa sapidissima), appeared quickly in these new habitats. Hatchery releases of Chinook, O. tshawytscha, coho, O. kisutch, and steelhead, O. mykiss (over 3xa0million total fish annually to the lower river), dominated the Elwha estuary catch from April through August of each year before, during, and after dam removal. Chum salmon catch rate, size, and duration of estuary occupancy declined during and after dam removal. Overall catches of chum salmon fry prior to, during, and after dam removal were significantly negatively correlated with Chinook salmon catches but significantly, and positively, correlated with coho salmon. When assessed at the Elwha estuary separately, chum abundance was significantly positively correlated with Chinook, coho, and steelhead abundance. These patterns indicate overlap, and likely interaction between these respective groups of hatchery and wild fish. Continued hatchery releases may therefore further challenge chum salmon recovery and should be considered when planning for watershed recovery.

A global perspective on the trophic geography of sharks

Sharks are a diverse group of mobile predators that forage across varied spatial scales and have the potential to influence food web dynamics. The ecological consequences of recent declines in shark biomass may extend across broader geographic ranges if shark taxa display common behavioural traits. By tracking the original site of photosynthetic fixation of carbon atoms that were ultimately assimilated into muscle tissues of 5,394 sharks from 114 species, we identify globally consistent biogeographic traits in trophic interactions between sharks found in different habitats. We show that populations of shelf-dwelling sharks derive a substantial proportion of their carbon from regional pelagic sources, but contain individuals that forage within additional isotopically diverse local food webs, such as those supported by terrestrial plant sources, benthic production and macrophytes. In contrast, oceanic sharks seem to use carbon derived from between 30° and 50° of latitude. Global-scale compilations of stable isotope data combined with biogeochemical modelling generate hypotheses regarding animal behaviours that can be tested with other methodological approaches.Carbon isotopic analysis reveals global biogeographic traits in shark trophic interactions, and sheds light on the diverse foraging behaviour of sharks.

Interoceanic Sex-Biased Migration in Bluefish

AbstractThe Bluefish Pomatomus saltatrix is a highly migratory species that is composed of different stocks and populations along its nearly cosmopolitan distribution. The Bluefish is the only member of its genus and family, and high migration rates could prevent vicariant speciation across its wide geographical distribution. However, the extent of gene flow between distant populations is unknown. We employed two mitochondrial genes (cytochrome-c oxidase subunit I and cytochrome b) and eight nuclear microsatellite loci to study population structure and infer dispersal of this important commercial and recreational fish across its Northern Hemisphere distribution. Higher gene flow estimates for nuclear loci (of biparental inheritance) than for mitochondrial loci (of maternal inheritance) suggested sex-biased dispersal, which could be explained by greater female homing or fidelity to spawning sites and greater dispersal of males. Males could contribute more to transoceanic connectivity of Bluefish population...

Large-scale Dam Removals and Nearshore Ecological Restoration: Lessons Learned from the Elwha Dam Removals

Large dam removals are emerging as an important ecosystem restoration tool, and they often have direct influence on the marine nearshore zone, but dam removal plans give little consideration to nearshore restoration. We provide an overview of the relationship between large-scale dam removals and nearshore restoration, using the Elwha dam removal project, in Washington State, United States, as a basis. The following steps are essential for incorporating nearshore restoration planning into future dam removals: 1) Conceptual and technical modeling of nearshore physical and ecological processes at the drift cell scale to define nearshore priorities and geographic areas to be conserved or restored; 2) Acquiring seasonal field data to inform models, including: water quality; sediment delivery volumes, timing, trajectory and composition; and basic fish community data such as abundance, size, species composition, and trophic components; 3) Mapping nearshore habitat areal extent and ecological function prior to, during, and after dam removal, including vegetation composition and invertebrate community composition; 4) Defining and addressing the implications of habitat barriers and fish management actions for nearshore ecosystem function prior to dam removal. Structures and hatchery practices that conflict with nearshore ecosystem function for wild species prior to, during, and after dam removal should be identified and eliminated; 5) Anticipating nearshore invasive species colonization as a result of dam removal; 6) Developing and implementing long-term adaptive management plans to ensure nearshore restoration goals are identified and met. These steps must begin as early as possible in the planning process.

Potential of passive acoustic recording for monitoring invasive species: freshwater drum invasion of the Hudson River via the New York canal system

We conducted a preliminary passive acoustic survey of the occurrence of freshwater drum, Aplodinotus grunniens, in the New York State Canal System (NYSCS) to demonstrate the usefulness of underwater sound monitoring in invasive species studies. Data from known populations of freshwater drum in Dale Hollow Reservoir and J. Percy Priest Lake in Tennessee and Lake Champlain in New York were used to validate freshwater drum call characteristics. Similar to more well studied marine members of the Sciaenidae, freshwater drum calls are composed of highly variable trains of 1–119 knocks call−1 (meanxa0=xa025 knocks call−1), a mean knock period of 33 knocks s−1, mean peak frequency of 400xa0Hz, and mean duration of 0.8xa0s. The occurrence of drum chorus calls at many locations within the NYSCS indicates likely spawning throughout the system, and suggests the possibility that individuals have invaded the Hudson River from native populations of Lake Champlain, Lake Erie, and Lake Ontario. We point out that the species has been excluded from the east coast of North America throughout history by geographic barriers, and it would have been impossible for the species to gain entrance to the Hudson without the NYSCS, or direct introduction, and thus it is a true invasive which will likely have a dramatic impact on the Hudson River ecosystem. We suggest that freshwater drum most likely also invaded Lakes Oneida, Onondaga, Cayuga and Seneca through the NYSCS. We conclude that passive acoustic surveys are a highly effective non-invasive tool to monitor the distribution of soniferous invasive organisms in aquatic systems, and promise to be especially useful in documenting the future spread of freshwater drum in the Hudson River system.

Effects of temperature and ration on the otolith-to-somatic size relationship in juvenile Chinook salmon (Oncorhynchus tshawytscha): a test of the direct proportionality assumption

Fish otoliths are commonly used to estimate somatic growth rate, but this depends on the assumption that the otolith and body grow in direct proportion. Environmental conditions contribute to variability in somatic growth and can result in deviations from direct proportionality in the otolith-to-somatic size relationship. In the present study we examined the otolith-to-body size relationship for juvenile Chinook salmon (Oncorhynchus tshawytscha) subjected to simulated seasonal (summer, autumn and winter) water temperatures and feeding rations. The otolith-to-somatic size relationship became uncoupled during summer between fish subjected to the cool (15°C) and hot (21°C) water temperatures. A food ration effect was also observed during the summer, such that fish fed an unlimited ration had smaller otoliths than equivalently sized fish fed a limited ration. The effects of water temperature and ration disappeared by the end of autumn, indicating that a seasonal compensatory response occurred in the otolith-to-somatic size relationship after the extreme temperatures and food limitations were alleviated. In winter, this relationship became uncoupled again, but only between fish that were fed throughout the winter and fish that were starved during the 3-month experimental period. The effects of water temperature and rations on the otolith-to-somatic size relationship of juvenile Chinook salmon could have implications for accurately estimating somatic growth from otolith growth in natural populations and should be incorporated into back-calculation techniques.