Larval Rockfish Dispersal Rates from Oceanography, Genetics and Otolith Marks

Researchers: Maureen Waite (Graduate Student)
Collaborators: Larry LeClair, Ray Buckley, WDFW, Olympia, WA, Mitsuhiro Kawase, School of Oceanography, University of Washington, Seattle, WA.
Funding: Washington Sea Grant, 2007-2009

MPAs are increasingly used to manage exploited stocks and to conserve biodiversity. However, although the effects of MPAs on biomass, age distribution and species richness are well established, the extent of larval exchange between MPAs and surrounding areas is essentially unknown. Therefore, the benefit of areas surrounding MPAs from increased reproductive output of protected stocks and the ability of isolated MPAs to maintain sufficient recruitment without larval influx cannot be evaluated. Such uncertainties in the function of MPAs complicate the scientific design of MPA networks and reduce the acceptance of MPAs by stakeholders such as fishers. Here, we propose to estimate larval dispersal rates of brown rockfish (Sebastes auriculatus) from an artificial reef at Pt. Heyer in Puget Sound by combining oceanographic models with parental identification from genetic markers and induced strontium marking of otoliths. Specifically, we will (i) predict larval dispersal from empirical and simulated drift trajectories; (ii) identify juveniles of resident adults at Pt Heyer and elsewhere, thus estimating realized dispersal; (iii) estimate annual variation in drift trajectories and realized dispersal; (iv) compare predictions and realized dispersal to assess the extent of larval retention and transport in Puget Sound. Our project aims to improve the scientific basis of MPA (marine protected area) design and thus increase the acceptance of MPAs by fishers and the public.

For more information, please see the website, Finding Nemo in Puget Sound.

Adaptation to a Changing World: Molecular Evidence for Selective Mortality in Walleye Pollock Larvae

Researchers: Isadora Jimenez-Hidalgo (Research Scientist)
Collaborators: Mike Canino, Kevin Bailey, Alaska Fisheries Science Center, National Marine Fisheries Service, Seattle, WA
Funding: North Pacific Research Board, 2007-2008

The impacts of climate change are an issue of global concern, especially where ecosystems or species are already stressed due to anthropogenic influences. Exploited fish stocks may be particularly vulnerable to climate change as slight changes in larval and juvenile survival may affect recruitment and subsequent stock biomass. Mortality rates are typically very high during sensitive periods in the early life history stages of many fish species, and may greatly affect the strength of the resulting year class. However, despite a general understanding of environmental effects on year class strength, it is still unknown whether larval and juvenile mortality are entirely random, or whether specific genotypes are favored under certain conditions. Here, we propose to use modern techniques of population genomics to assess the extent of selective mortality during early larval stages of walleye pollock. Specifically, we will assess the relative success of different genotypes by estimating temporal and spatial genetic differentiation in two years with contrasting environmental conditions, in particular temperature. We will identify molecular markers under selection that can be used to (i) estimate selection coefficients, (ii) assess the scope for adaptation to changing climates, and (iii) estimate rates of exchange between pollock populations in different ecosystems.

An Exploratory Investigation to Optimize Genetic Markers for Population Genetic Studies on Pacific Halibut (Hippoglossus stenolepis)

Researcher: James Rhydderch, Lyndsay Newton (Research Scientists)
Collaborator: Timothy Loher, International Pacific Halibut Commission, Seattle, WA
Funding: International Pacific Halibut Commission, 2003 - ongoing

The eastern north Pacific halibut resource is presently managed under the assumption that a single panmictic population exists from California through the eastern Bering Sea. This assumption rests largely upon studies that indicate northeasterly larval drift throughout the Gulf of Alaska and into the Bering Sea, balanced by southwesterly migration of juveniles and adults over broad geographic expanses. In addition, limited genetic studies have failed to demonstrate significant difference between northern and southern stock components. However, there is reason to hypothesize that population structure is more complex, and that the Bering Sea may harbor an isolated stock that could be managed independently. Oceanographic data suggest that larvae spawned in the southeast Bering Sea should remain in the Bering Sea gyre, and the juveniles that migrate from Bristol Bay into the Gulf may simply represent fish that were spawned south of the Alaska Peninsula and were transported into the Bering Sea as larvae. Previous genetic studies have failed to sample the Bering Sea appropriately and have used genetic markers that lacked the resolution required to resolve genetic population structure. No previous research has analyzed fish captured on the spawning grounds, the point in the annual movement cycle that actually defines the genetic stock. During this project, tissue samples collected from halibut from the north-east Pacific were used to optimize genetic markers and obtain preliminary data for a subsequent thorough analysis of the population structure of Pacific halibut. Genetic markers to be tested include microsatellite loci, mitochondrial DNA sequences and genes reported to be under selection.

Biocomplexity, Sustainability and the Role of Small Populations

Researcher: Lyndsay Newton (Research Scientist), Jocelyn Lin (Graduate Student)
Collaborator: co-PI with Ray Hilborn, Tom Quinn, Daniel Schindler (SAFS, UW)
Funding: Pew Foundation, 2005 – ongoing

Small populations are harbingers of range expansion and precursors to extinction. We have a unique opportunity to study a large number of small populations of chinook, chum, pink, coho and sockeye salmon in Bristol Bay Alaska, where the University of Washington has maintained field stations and data series since the late 1940s. These habitats are also quite unique in there has been almost no anthropogenic habitat modification nor are there any introduced exotic species. We propose to explore the dynamics of these small populations to provide insight on (1) how climate change may be affecting the distribution of salmon, (2) how networks of meta populations interact to influence stability and sustainability of populations, (3) how multispecies assemblages differentially use habitats and interact, in particular how rare species interact with a dominant species (sockeye salmon in Bristol Bay), (4) the frequency of colonization and extinction, and (5) the dynamics of very small populations as it relates to the dynamics of extinction. We will augment the existing long term abundance trends for 20 streams with more intense monitoring of abundance for 2 seasons, and use molecular genetic tools to determine the connectedness of individual populations and the importance of sources and sinks in population maintenance.

Evaluation of the Reproductive Success of Wild and Hatchery Steelhead in Natural and Hatchery Environments

Researchers: Todd Seamons (Staff Biologist), Michael Dauer (Graduate Student)
Collaborators: co-PI with Tom Quinn and Kerry Naish, School of Fisheries and Aquatic Sciences, University of Washington
Funding: Bonneville Power Administration, 2003-2009

Complex stochastic and deterministic processes related to breeding dynamics and survival of progeny result in differential reproductive success of adult salmonids with different phenotypic traits. These processes are essential to the long-term health of populations but are markedly different from patterns of mating and subsequent reproductive success in hatcheries. Hatchery populations are on evolutionary trajectories that may reduce their fitness, and their interactions with wild populations are a serious conservation concern. However, it is unclear to what extent hatchery fish can contribute to the stability or recovery of populations. To conserve wild salmonids and wisely manage hatchery populations, we propose to extend a unique study of reproductive success including wild steelhead, hatchery origin fish spawning naturally, and hatchery fish propagated in the hatchery. We have been sampling adults and smolts of the winter steelhead population in Forks Creek, a Willapa River tributary, since winter 1995-96. We are in a rare position – we are able to extend these data to the returning adult F2 within a year and to the F3 within the next four years. Our experiment will allow us to compare the genetic diversity from one generation to the next in natural and hatchery environments for males and females, estimate the reproductive success of the offspring of wild-hatchery matings in the wild, and determine the extent to which a wild population “resists” or “amalgamates” the genetic material from hatchery fish after cessation of hatchery releases over several generations. Specifically, we will document the phenotypic traits of fish used for breeding in the hatchery or migrating to spawn in the river, and will then use parentage analysis from DNA microsatellites to determine the reproductive success of individual fish, link these results to various fitness traits in spawning individuals, and examine the changes in gene frequency over three complete generations. Preliminary results from the returning adult F1 indicate markedly lower survival of hatchery compared to wild fish, with the differences largely in the freshwater rather than marine phases, and hybridization between wild and hatchery fish (despite significant differences in average spawning timing). We have also found great variation in realized reproductive success of hatchery-spawned adults, probably resulting from variation in fertilization success and low but variable marine survival among families. These results leave open the question of whether the population’s long-term health will be affected by the hatchery influence. Our study is poised to address this question within the next few years.

Genetic Stock Structure in Pacific Cod

Graduate Student: Kathryn Cunningham (Graduate Student)
Collaborators: Mike Canino, Alaska Fisheries Science Center, National Marine Fisheries Service, Seattle, WA, Greg Bargmann, Washington Department of Fish and Wildlife, Olympia, WA
Funding: Washington Sea Grant, 2003-2006

Pacific cod (Gadus macrocephalus) form the basis of important commercial fisheries and are a central food item for pinnipeds and many marine animals. Nevertheless, little is known about their population structure, migration patterns and recruitment processes, and the species is currently managed as a single population stock. Tagging studies show limited adult dispersal and spawning site fidelity, though data on genetic population structure are limited to early allozyme work. Here we propose to provide valuable management guidelines by identifying spawning populations of Pacific cod on large and small geographic scales. The study will focus on the Gulf of Alaska and eastern Bering Sea, where Pacific cod are harvested in localized fisheries managed under both state and federal plans. We will also examine the temporal stability of any genetic patterns, and so evaluate the predictive value of our data. We will collect large (N~100) samples of spawning individuals, thereby avoiding complications caused by inclusion of non-spawning migratory fish. Preliminary experiments have demonstrated the applicability of microsatellite markers isolated from walleye pollock for the current project, and we plan to use a minimum of 12 loci for the proposed study. We will further refine our investigation by analysis of the pantophysin locus, which has been shown to be under selection and which is thus more likely to reveal essentially self-recruiting populations in high gene-flow species such as cod. We will evaluate the results in comparison with major fishing areas, oceanography and age structure. The identification of essentially self-recruiting populations as units for management is one of the essential basic requirements for stock assessment. Current management plans for both federal and state Pacific cod fisheries are based upon the assumption of genetic panmixia, though there are few data to support this hypothesis. Our results will produce such data on stock structure and thus falls centrally within one of the goals of the WSGP Fisheries and Living Resources subprogram. Furthermore, the project will provide valuable data for pending experiments on hatchery supplementation of Pacific cod, which require information on the genetic stock structure of cod for broodstock selection.

Long-term Changes in Genetic Diversity and Population Structure in Pacific Herring

Researcher: Danielle Mitchell (Graduate Student), Elizabeth Heeg (Research Scientist)
Collaborators: Greg Bargmann, Washington Department of Fish and Wildlife, Olympia, WA, Pat McAllister, Washington Department of Fish and Wildlife, La Conner, WA
Funding: School of Fisheries and Aquatic Sciences, Washington Sea Grant, 2003-2006

Recent reductions in abundance of herring stocks in the Pacific Northwest have renewed the attention of management agencies, scientists and the public on human effects on marine fish biodiversity. Potentially of great concern are here the fluctuations in abundance of local spawning aggregates, which do not only affect dependent fisheries, but may also have major ecosystem impacts, especially on species relying on herring as food. However, little is known about the mechanisms of such demographic instability, in particular whether they reflect extinctions of locally adapted populations, whether they are local signs of range shifts of a large metapopulation or whether they are merely random fluctuations in a species with high recruitment variability. The ensuing uncertainty in the population concept in herring is exemplified by the variety of management strategies: whereas the Washington Department of Fish and Wildlife (WDFW) attempts to conserve spawning populations at each spawning ground, the management goal in British Columbia is the maintenance of overall abundance in a specific region. For a decision on the appropriate management strategy, the taxonomic, demographic and genetic status of spawning assemblages needs to be established, requiring a thorough assessment of spatial and temporal patterns in demographic and genetic populations structure. Indeed, decisions on recent petitions to list Puget Sound spawning aggregations under the Endangered Species Act (ESA) were complicated by the scarcity of genetic data. Currently, at least 18 herring ‘stocks’ are recognized within the Puget Sound area, which differ in spawning location, age structure, spawning time and pre-spawner behavior. Here, we use scale collections available at WDFW for a long-term study of temporal trends in genetic population structure within Puget Sound, and its dependence on fishing pressure and climate shifts. The investigation of the stock structure of Puget Sound herring will not only facilitate the identification of appropriate units of management and conservation, but will also provide information about the genetic dynamics of the metapopulation of a marine species.

Biocomplexity of Alaskan Sockeye Salmon

Graduate student: Jocelyn Lin (Graduate Student; NOAA – Sea Grant Fellowship in Population Dynamics)
Collaborators: Ray Hilborn, School of Fisheries and Aquatic Sciences, University of Washington, Tom Quinn, School of Fisheries and Aquatic Sciences, University of Washington
Funding: School of Aquatic and Fisheries Sciences, NSF fellowship to JL, NSF biocomplexity program

Recent research has demonstrated the importance of biocomplexity for the maintenance of productivity and fishery yields of Bristol Bay sockeye salmon. Such biocomplexity consists of several hundred populations with very different morphology, life history and genetics, hierarchically structured into lake and creek systems of the Wood River system. Although data on such population differentiation is accumulating, there is still much uncertainty about genetic relationships among populations, the evolution of such biocomplexity and effects of biocomplexity at smaller geographical scales such as specific lakes and rivers. Here, we will investigate genetic relationships among creek and beach spawning salmon populations on Little Togiak Lake, a lake with a manageable number of sockeye populations. Subsequently, we will analyze populations from the adjacent Lake Nerka, and investigate the behavior of individual populations within their nursing lakes by applying Mixed Stock Analyses to salmon juveniles.

Completed Projects

Potential for Sustainable Expansion of the Dogfish (Squalus acanthias) Fishery in the Northeast Pacific

Graduate students: Jim Franks (Graduate Student)
Collaborator: Vincent Gallucci, School of Fisheries and Aquatic Sciences, University of Washington
Funding: NOAA Saltonstall Kennedy (2003-2006)

Dogfish (Squalus acanthias) supports major fisheries in many areas of the world, and has been the basis of considerable economic return to a wide range of fishing communities. Nevertheless, due to slow growth, late maturity and low fecundity, the species is susceptible to overfishing, with a particularly slow rate of population recovery. Indeed, dogfish populations on the Atlantic coast of the US were declared overfished in 1998 (26th Northeast Regional Stock Assessment Workshop), and have since been subject to a fishery management plan (FMP). In the Pacific Northwest, on the other hand, some stocks may be at a critical level (e.g. in North Puget Sound) while in other areas, e.g., the Georgia Strait, an increase in fishing pressure may be sustainable. Such uncertainties confirm the need for management attention in a coordinated effort between the U.S. and Canada since the Puget Sound basin includes both the Canadian Straits of Georgia and the U.S. Puget Sound. Our premise is that as fishing effort within the sheltered Puget Basin reaches sustainable levels and catches decrease, fishing effort will extend to other coastal areas, which are as yet essentially unexploited. The dominant work in coastal populations is from Canadian waters, with relatively little published work about populations off the U.S. coasts, although there are databases for dogfish captured in NMFS surveys. This situation has been recognized by the American Fisheries Society and by a call for research on the "distribution, stock structure and life history characteristics" in the Pacific. Here, we propose to investigate the stock structure of dogfish along the latitudinal gradient from California to Alaska using both molecular genetic markers and demographic characteristics, and to collect population parameters for the estimation of potential yields. This is important information for the management of an expanded fishery along the coastal regions north and south of Washington State and Canada. We will also carry out a preliminary investigation of socioeconomic indicators of the fishermen employed in this fishery. The dogfish fishery is co-managed under the Boldt decision between the State of Washington and the Tulalip and Lumi Tribes. A socio-cultural study of the fishers and the co-management plan is an important precursor to any socioeconomic study.

Species Identity and Life History of Hematodinium, the Causative Agent of Bitter Crab Syndrome in Northeast Pacific Snow, Chionoecetes opilio, and Tanner, C. bairdi, Crab

Researchers: Pam Jensen, Yuichi Saito
Collaborators: Frank Morado, Alaska Fisheries Science Center, National Marine Fisheries Service, Seattle, WA, Dr. Doug Woodby, Alaska Department of Fish & Game, Juneau, AK
Funding: North Pacific Research Board (2003 – 2005)

Population abundance estimates of Chionoecetes opilio have taken a drastic downturn over the last three years. A possible cause for this reduction is poor recruitment. Unpublished data (Morado et al.) suggest that a significant cause of poor recruitment of juvenile C. opilio and poor recovery of C. bairdi is the high disease prevalence of Hematodinium, the causative agent of Bitter Crab Syndrome (BCS). Despite its worldwide emergence as a significant cause of crustacean mortalities, little is known about the pathogen. In this project, we develop molecular tools to elucidate the life history of the parasite outside of its crab hosts and more accurately diagnose and monitor the prevalence of BCS in Bering Sea snow and Tanner crabs. Effort is also directed at determining whether one or more species of Hematodinium exist in North Pacific crabs. All research objectives could have profound management implications and enhance efforts to develop effective stock rebuilding plans for both Chionoecetes species.