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Kiffney PM, Lisi PJ, Liermann M, Naman SM, Anderson JH, Bond MH, Pess GR, Koehler ME, Buhle ER, Buehrens TW, Klett RS, Cram JM, Quinn TP. Colonization of a temperate river by mobile fish following habitat reconnection. Ecosphere 2023. [DOI: 10.1002/ecs2.4336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Affiliation(s)
- P. M. Kiffney
- Fish Ecology, Northwest Fisheries Science Center National Marine Fisheries Service, NOAA Seattle Washington USA
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - P. J. Lisi
- Washington Department of Fish and Wildlife Olympia Washington USA
| | - M. Liermann
- Fish Ecology, Northwest Fisheries Science Center National Marine Fisheries Service, NOAA Seattle Washington USA
| | - S. M. Naman
- Department of Zoology University of British Columbia Vancouver British Columbia Canada
- Fisheries and Oceans Canada Freshwaer Ecosystems Section Cultus Lake British Columbia Canada
| | - J. H. Anderson
- Washington Department of Fish and Wildlife Olympia Washington USA
| | - M. H. Bond
- Fish Ecology, Northwest Fisheries Science Center National Marine Fisheries Service, NOAA Seattle Washington USA
| | - G. R. Pess
- Fish Ecology, Northwest Fisheries Science Center National Marine Fisheries Service, NOAA Seattle Washington USA
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | | | - E. R. Buhle
- Affiliate, Northwest Fisheries Science Center National Marine Fisheries Service, NOAA Seattle Washington USA
- Mount Hood Environmental Sandy Oregon USA
| | - T. W. Buehrens
- Washington Department of Fish and Wildlife Ridgefield Washington USA
| | - R. S. Klett
- Colville Indian Tribes Nespelem Washington USA
| | - J. M. Cram
- Washington Department of Fish and Wildlife Wenatchee Washington USA
| | - T. P. Quinn
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
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Lehnert SJ, Kess T, Bentzen P, Kent MP, Lien S, Gilbey J, Clément M, Jeffery NW, Waples RS, Bradbury IR. Genomic signatures and correlates of widespread population declines in salmon. Nat Commun 2019; 10:2996. [PMID: 31278264 PMCID: PMC6611788 DOI: 10.1038/s41467-019-10972-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 06/11/2019] [Indexed: 12/27/2022] Open
Abstract
Global losses of biodiversity are occurring at an unprecedented rate, but causes are often unidentified. Genomic data provide an opportunity to isolate drivers of change and even predict future vulnerabilities. Atlantic salmon (Salmo salar) populations have declined range-wide, but factors responsible are poorly understood. Here, we reconstruct changes in effective population size (Ne) in recent decades for 172 range-wide populations using a linkage-based method. Across the North Atlantic, Ne has significantly declined in >60% of populations and declines are consistently temperature-associated. We identify significant polygenic associations with decline, involving genomic regions related to metabolic, developmental, and physiological processes. These regions exhibit changes in presumably adaptive diversity in declining populations consistent with contemporary shifts in body size and phenology. Genomic signatures of widespread population decline and associated risk scores allow direct and potentially predictive links between population fitness and genotype, highlighting the power of genomic resources to assess population vulnerability.
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Affiliation(s)
- S J Lehnert
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada.
| | - T Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada
| | - P Bentzen
- Biology Department, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
| | - M P Kent
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - S Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, 1430, Norway
| | - J Gilbey
- Marine Scotland Science, Freshwater Fisheries Laboratory, Faskally, Pitlochry, PH16 5LB, UK
| | - M Clément
- Centre for Fisheries Ecosystems Research, Fisheries and Marine Institute of Memorial University of Newfoundland, 155 Ridge Rd, St. John's, NL, A1C 5R3, Canada
- Labrador Institute, Memorial University of Newfoundland, 219 Hamilton River Rd, Happy Valley-Goose Bay, NL, A0P 1E0, Canada
| | - N W Jeffery
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, 1 Challenger Dr, Dartmouth, NS, B2Y 4A2, Canada
| | - R S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, 98112, USA
| | - I R Bradbury
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries Centre, 80 E White Hills Rd, St. John's, Newfoundland, A1C 5X1, Canada
- Biology Department, Dalhousie University, 6050 University Avenue, Halifax, NS, B3H 4R2, Canada
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Fullerton AH, Anzalone S, Moran P, Van Doornik DM, Copeland T, Zabel RW. Setting spatial conservation priorities despite incomplete data for characterizing metapopulations. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2016; 26:2558-2578. [PMID: 27865061 DOI: 10.1002/eap.1411] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 06/13/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Management of spatially structured species poses unique challenges. Despite a strong theoretical foundation, practitioners rarely have sufficient empirical data to evaluate how populations interact. Rather, assumptions about connectivity and source-sink dynamics are often based on incomplete, extrapolated, or modeled data, if such interactions are even considered at all. Therefore, it has been difficult to evaluate whether spatially structured species are meeting conservation goals. We evaluated how estimated metapopulation structure responded to estimates of population sizes and dispersal probabilities and to the set of populations included. We then compared outcomes of alternative management strategies that target conservation of metapopulation processes. We illustrated these concepts for Chinook salmon (Oncorhynchus tshawytscha) in the Snake River, USA. Our description of spatial structure for this metapopulation was consistent with previous characterizations. We found substantial differences in estimated metapopulation structure when we had incomplete information about all populations and when we used different sources of data (three empirical, two modeled) to estimate dispersal, whereas responses to population size estimates were more consistent. Together, these findings suggest that monitoring efforts should target all populations occasionally and populations that play key roles frequently and that multiple types of data should be collected when feasible. When empirical data are incomplete or of uneven quality, analyses using estimates produced from an ensemble of available datasets can help conservation planners and managers weigh near-term options. Doing so, we found trade-offs in connectivity and source dominance in metapopulation-level responses to alternative management strategies that suggest which types of approaches may be inherently less risky.
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Affiliation(s)
- A H Fullerton
- Fish Ecology and Conservation Biology Divisions, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Boulevard E, Seattle, Washington, 98125, USA
| | - S Anzalone
- University of Western Washington, 516 High Street, Bellingham, Washington, 98225, USA
| | - P Moran
- Fish Ecology and Conservation Biology Divisions, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Boulevard E, Seattle, Washington, 98125, USA
| | - D M Van Doornik
- Fish Ecology and Conservation Biology Divisions, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Boulevard E, Seattle, Washington, 98125, USA
| | - T Copeland
- Idaho Department of Fish and Game, Southwest Region, 1414 E Locust Lane, Nampa, Idaho, 83686, USA
| | - R W Zabel
- Fish Ecology and Conservation Biology Divisions, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, 2725 Montlake Boulevard E, Seattle, Washington, 98125, USA
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Ohlberger J, Langangen Ø. Population resilience to catastrophic mortality events during early life stages. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2015; 25:1348-1356. [PMID: 26485960 DOI: 10.1890/14-1534.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Catastrophic mortality events that drastically reduce the abundance of a population or a particular life stage can have long-term ecological and economic effects, and are of great concern in species conservation and management. Severe die-offs may be caused by natural catastrophes such as disease outbreaks and extreme climates, or human-caused disturbances such as toxic spills. Forecasting potential impacts of such disturbances is difficult and highly uncertain due to unknown future conditions, including population status and environmental conditions at the time of impact. Here, we present a framework for quantifying the range of potential, population-level effects of catastrophic events based on a hindcasting approach. A dynamic population model with Bayesian parameter estimation is used to simulate the impact of severe (50-99%) mortality events during the early life stages of Northeast Arctic cod (Gadus morhua), an abundant marine fish population of high economic value. We quantify the impact of such die-offs in terms of subsequent changes in population biomass and harvest through direct comparison of simulated and historical trends, and estimate the duration of the impact as a measure of population resilience. Our results demonstrate strong resilience to catastrophic events that affect early life stages owing to density dependence in survival and a broad population age structure. Yet, while population recovery is. relatively fast, losses in harvest and economic value can be substantial. Future research efforts should focus on long-term and indirect effects via food web interactions in order to better understand the ecological and economic ramifications of catastrophic mortality events.
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Hart EM, Avilés L. Reconstructing local population dynamics in noisy metapopulations--the role of random catastrophes and Allee effects. PLoS One 2014; 9:e110049. [PMID: 25360620 PMCID: PMC4216000 DOI: 10.1371/journal.pone.0110049] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 09/16/2014] [Indexed: 11/23/2022] Open
Abstract
Reconstructing the dynamics of populations is complicated by the different types of stochasticity experienced by populations, in particular if some forms of stochasticity introduce bias in parameter estimation in addition to error. Identification of systematic biases is critical when determining whether the intrinsic dynamics of populations are stable or unstable and whether or not populations exhibit an Allee effect, i.e., a minimum size below which deterministic extinction should follow. Using a simulation model that allows for Allee effects and a range of intrinsic dynamics, we investigated how three types of stochasticity—demographic, environmental, and random catastrophes— affect our ability to reconstruct the intrinsic dynamics of populations. Demographic stochasticity aside, which is only problematic in small populations, we find that environmental stochasticity—positive and negative environmental fluctuations—caused increased error in parameter estimation, but bias was rarely problematic, except at the highest levels of noise. Random catastrophes, events causing large-scale mortality and likely to be more common than usually recognized, caused immediate bias in parameter estimates, in particular when Allee effects were large. In the latter case, population stability was predicted when endogenous dynamics were actually unstable and the minimum viable population size was overestimated in populations with small or non-existent Allee effects. Catastrophes also generally increased extinction risk, in particular when endogenous Allee effects were large. We propose a method for identifying data points likely resulting from catastrophic events when such events have not been recorded. Using social spider colonies (Anelosimus spp.) as models for populations, we show that after known or suspected catastrophes are accounted for, reconstructed growth parameters are consistent with intrinsic dynamical instability and substantial Allee effects. Our results are applicable to metapopulation or time series data and are relevant for predicting extinction in conservation applications or the management of invasive species.
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Affiliation(s)
- Edmund M. Hart
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
| | - Leticia Avilés
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
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Fullerton AH, Lindley ST, Pess GR, Feist BE, Steel EA, McElhany P. Human influence on the spatial structure of threatened Pacific salmon metapopulations. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2011; 25:932-944. [PMID: 21797926 DOI: 10.1111/j.1523-1739.2011.01718.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
To remain viable, populations must be resilient to both natural and human-caused environmental changes. We evaluated anthropogenic effects on spatial connections among populations of Chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) (designated as threatened under the U.S. Endangered Species Act) in the lower Columbia and Willamette rivers. For several anthropogenic-effects scenarios, we used graph theory to characterize the spatial relation among populations. We plotted variance in population size against connectivity among populations. In our scenarios, reduced habitat quality decreased the size of populations and hydropower dams on rivers led to the extirpation of several populations, both of which decreased connectivity. Operation of fish hatcheries increased connectivity among populations and led to patchy or panmictic populations. On the basis of our results, we believe recolonization of the upper Cowlitz River by fall and spring Chinook and winter steelhead would best restore metapopulation structure to near-historical conditions. Extant populations that would best conserve connectivity would be those inhabiting the Molalla (spring Chinook), lower Cowlitz, or Clackamas (fall Chinook) rivers and the south Santiam (winter steelhead) and north fork Lewis rivers (summer steelhead). Populations in these rivers were putative sources; however, they were not always the most abundant or centrally located populations. This result would not have been obvious if we had not considered relations among populations in a metapopulation context. Our results suggest that dispersal rate strongly controls interactions among the populations that comprise salmon metapopulations. Thus, monitoring efforts could lead to understanding of the true rates at which wild and hatchery fish disperse. Our application of graph theory allowed us to visualize how metapopulation structure might respond to human activity. The method could be easily extended to evaluations of anthropogenic effects on other stream-dwelling populations and communities and could help prioritize among competing conservation measures.
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Affiliation(s)
- Aimee H Fullerton
- NOAA Fisheries, Northwest Fisheries Science Center, Seattle, WA 98112, USA.
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Lin BB, Morefield PE. The vulnerability cube: a multi-dimensional framework for assessing relative vulnerability. ENVIRONMENTAL MANAGEMENT 2011; 48:631-643. [PMID: 21638079 PMCID: PMC3150662 DOI: 10.1007/s00267-011-9690-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 04/25/2011] [Indexed: 05/30/2023]
Abstract
The diversity and abundance of information available for vulnerability assessments can present a challenge to decision-makers. Here we propose a framework to aggregate and present socioeconomic and environmental data in a visual vulnerability assessment that will help prioritize management options for communities vulnerable to environmental change. Socioeconomic and environmental data are aggregated into distinct categorical indices across three dimensions and arranged in a cube, so that individual communities can be plotted in a three-dimensional space to assess the type and relative magnitude of the communities' vulnerabilities based on their position in the cube. We present an example assessment using a subset of the USEPA National Estuary Program (NEP) estuaries: coastal communities vulnerable to the effects of environmental change on ecosystem health and water quality. Using three categorical indices created from a pool of publicly available data (socioeconomic index, land use index, estuary condition index), the estuaries were ranked based on their normalized averaged scores and then plotted along the three axes to form a vulnerability cube. The position of each community within the three-dimensional space communicates both the types of vulnerability endemic to each estuary and allows for the clustering of estuaries with like-vulnerabilities to be classified into typologies. The typologies highlight specific vulnerability descriptions that may be helpful in creating specific management strategies. The data used to create the categorical indices are flexible depending on the goals of the decision makers, as different data should be chosen based on availability or importance to the system. Therefore, the analysis can be tailored to specific types of communities, allowing a data rich process to inform decision-making.
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Affiliation(s)
- Brenda B Lin
- Office of Research and Development, U.S. Environmental Protection Agency (8601P), 1200 Pennsylvania Avenue, NW Washington, DC 20460, USA.
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Fausch KD, Rieman BE, Dunham JB, Young MK, Peterson DP. Invasion versus isolation: trade-offs in managing native salmonids with barriers to upstream movement. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2009; 23:859-70. [PMID: 19210302 DOI: 10.1111/j.1523-1739.2008.01159.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Conservation biologists often face the trade-off that increasing connectivity in fragmented landscapes to reduce extinction risk of native species can foster invasion by non-native species that enter via the corridors created, which can then increase extinction risk. This dilemma is acute for stream fishes, especially native salmonids, because their populations are frequently relegated to fragments of headwater habitat threatened by invasion from downstream by 3 cosmopolitan non-native salmonids. Managers often block these upstream invasions with movement barriers, but isolation of native salmonids in small headwater streams can increase the threat of local extinction. We propose a conceptual framework to address this worldwide problem that focuses on 4 main questions. First, are populations of conservation value present (considering evolutionary legacies, ecological functions, and socioeconomic benefits as distinct values)? Second, are populations vulnerable to invasion and displacement by non-native salmonids? Third, would these populations be threatened with local extinction if isolated with barriers? And, fourth, how should management be prioritized among multiple populations? We also developed a conceptual model of the joint trade-off of invasion and isolation threats that considers the opportunities for managers to make strategic decisions. We illustrated use of this framework in an analysis of the invasion-isolation trade-off for native cutthroat trout (Oncorhynchus clarkii) in 2 contrasting basins in western North America where invasion and isolation are either present and strong or farther away and apparently weak. These cases demonstrate that decisions to install or remove barriers to conserve native salmonids are often complex and depend on conservation values, environmental context (which influences the threat of invasion and isolation), and additional socioeconomic factors. Explicit analysis with tools such as those we propose can help managers make sound decisions in such complex circumstances.
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Affiliation(s)
- Kurt D Fausch
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO 80523, USA.
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