Protected Species Research Publications - Ecology and Climate Change

2015-2016

• Armstrong et al. 2016. Adaptive capacity at the northern front: sockeye salmon behaviorally thermoregulate during novel exposure to warm temperatures. Conservation Physiology
• Becker et al. 2016. Moving towards dynamic ocean management: how well do modeled ocean products predict species distributions? Remote Sensing
• Bouwes et al. 2016. Ecosystem experiment reveals benefits of beaver assisted restoration to a population of ESA listed steelhead (Oncorhynchus mykiss).  Scientific Reports
• Brown et al. 2016. Coupled downscaled climate models and ecophysiological metrics forecast habitat compression for an endangered estuarine fish. PLos One
• Burke et al. 2016. Estimating behavior in a black box: how coastal oceanographic dynamics influence yearling Chinook salmon marine growth and migration behaviors. Environmental Biology of Fishes
• Busch and McElhany 2016. Estimates of the direct effect of seawater pH on the survival rate of species groups in the California Current ecosystem. PLoS One
• Conner et al. 2016. Evaluating impacts using a BACI design, ratios, and a Bayesian approach with a focus on restoration. Environmental Monitoring and Assessment
• Dale et al. 2016. Interannual variability in the feeding and condition of subyearling Chinook salmon off Oregon and Washington.  Fisheries Oceanography
• Demetras et al. 2016. Development of underwater recorders to quantify predation of juvenile Chinook salmon (Oncorhynchus tshawytscha) in a river environment. Fishery Bulletin
• Hare et al. 2015. A vulnerability assessment of fish and invertebrates to climate forcing on the Northeast U.S. Continental Shelf. PLos One 
• Hayes et al. 2016. Observations of steelhead in the California Current lead to a marine-based hypothesis for the half-pounder life history, with climate change implications for anadromy. North Pacific Anadromous Fish Commission Bulletin
• Jeffries et al. 2016. Effects of high temperatures on threatened estuarine fishes during periods of extreme drought. Journal of Experimental Biology
• Jorgensen et al. 2016. Assessing spatial covariance among time series of abundance. Ecology and Evolution
• Komoroske et al. 2016. Sublethal salinity stress contributes to habitat limitation in an endangered estuarine fish. Evolutionary Applications
• Leitwein et al. 2016. Ancestry and adaptive evolution of anadromous, resident, and adfluvial rainbow trout (Oncorhynchus mykiss) in the San Francisco Bay Area: application of adaptive genomic variation to conservation in a highly impacted landscape. Evolutionary Applications
• Lehman et al. 2016. Relationships between Chinook Salmon swimming performance and water quality in the San Joaquin River, California. Transactions of the American Fisheries Society
• Martin et al. 2016. An ecosystem services perspective for the oceanic eastern tropical Pacific: commercial fisheries, carbon storage, recreational fishing, and biodiversity.  Frontiers in Marine Science
• Miller et al. 2016. Detecting sedimentation impacts to coral reefs resulting from dredging the Port of Miami, Florida USA. PeerJ
• Miller et al. 2016. Reef-scale trends in Florida Acropora spp. abundance and the effects of population enhancement. PeerJ
• Morley et al. 2016. Seasonal variation exceeds effects of salmon carcass additions on benthic food webs in the Elwha River. Ecosphere
• Moser et al. 2016. Biology and life history of green sturgeon (Acipenser medirostris): state of the science. Journal of Applied Ichthyology
• Ohlberger et al. 2016. Population coherence and environmental impacts across spatial scales: a case study of Chinook salmon. Ecosphere
• Okuyama et al. 2016. Fine-scale monitoring of routine deep dives by gravid leatherback turtles during the internesting interval indicate a capital breeding strategy. Frontiers in Marine Science
• Patel et al. 2016. Climate impacts on sea turtle breeding phenology in Greece and associated foraging habitats in the wider Mediterranean Region. PLoS One
• Peters et al. 2016. Changes in streambed composition in salmonid spawning habitat of the Elwha River during dam removal. Journal of the American Water Resources Association
• Roberts et al. 2016. Habitat-based cetacean density models for the U.S. Atlantic and Gulf of Mexico. Scientific Reports
• Ruzicka et al. 2016. Evidence that summer jellyfish blooms impact Pacific Northwest salmon production. Ecosphere 
• Sabal et al. 2016. Contrasting patterns in growth and survival of Central Valley fall run Chinook salmon related to hatchery and ocean conditions. Environmental Biology of Fishes
• Sather et al. 2016. Shallow tidal freshwater habitats of the Columbia River: spatial and temporal variability of fish communities and density, size, and genetic stock composition of juvenile Chinook Salmon. Transactions of the American Fisheries Society
• Urban et al. 2016.  Improving the forecast for biodiversity under climate change. Science
• Vargas-Angel et al. 2015. Baseline assessment of net calcium carbonate accretion rates on U.S. Pacific Reefs. PLoS One      
• Wall et al. 2016. Design and monitoring of woody structures and their benefits to juvenile steelhead trout (Oncorhynchus mykiss) using a net rate of energy intake model. Canadian Journal of Fisheries and Aquatic Sciences
• Wells et al. 2016. Marine ecosystem perspectives on Chinook salmon recruitment: A synthesis of empirical and modeling studies from the California upwelling system. Marine Ecology Progress Series
• Yan Jiao and Browder. 2015. Modeling spatially-varying ecological relationships using geographically weighted Generalized Linear Model: a simulation study based on longline seabird bycatch. Fisheries Research
• Yasumiishi et al. 2016. Trends and factors influencing the length, compensatory growth, and size-selective mortality of juvenile Bristol Bay, Alaska, sockeye salmon (Oncorhynchus nerka) at sea. Marine and Coastal Fisheries 
   

2017

• Abrahms et al. 2017. Climate mediates the success of migration strategies in a marine predator. Ecology Letters
• Arthur et al. 2017. Winter habitat predictions of a key Southern Ocean predator, the Antarctic fur seal (Arctocephalus gazella). Deep Sea Research Part II: Topical Studies in Oceanography
• Becker et al. 2017. Habitat-based density models for three cetacean species off Southern California illustrate pronounced seasonal differences.  Frontiers in Marine Science
• Boyd et al. 2017. Estimation of population size and trends for highly mobile species with dynamic spatial distributions. Diversity and Distributions
• Braun et al. 2017. An R package for improved geolocation of archival-tagged fishes using a hidden Markov method. Methods in Ecology and Evolution
• Brewitt et al. 2017. Hot eats and cool creeks: juvenile Pacific salmonids use maintstem prey while in thermal refuge. Canadian Journal of Fisheries and Aquatic Sciences
• Cordoleani et al. 2017. Movement and survival of wild Chinook salmon smolts from Butte Creek during their out-migration to the ocean: comparison of a dry versus wet year. Transactions of the American Fishery Society
• Daly et al. 2017. Anomalous ocean conditions in 2015: impacts on spring Chinook salmon and their prey field. Marine Ecology Progress Series
• Fullerton et al. 2017. Stream network shape influences the strength of growth and phenological responses to climate change in juvenile salmon. Ecosphere
• Goertler et al. 2017. Seasonal floodplain-tidal slough complex supports size variation for juvenile Chinook salmon (Oncorhynchus tshawytscha).  Ecology of Freshwater Fish
• Grieve et al. 2017. Projecting the effects of climate change on Calanus finmarchicus distribution within the U.S. Northeast Continental Shelf. Scientific Reports
• Hawkes et al. 2017. Assessment of early migration dynamics of river-specific hatchery Atlantic Salmon smolts. Transactions of the American Fisheries Society
• Hervieux et al. 2017. More reliable coastal SST forecasts from the North American multimodel ensemble. Climate Dynamics
• Hines et al. 2017. Diel shifts in salmonid fry micro-habitat selection. North American Journal of Fisheries Management
• Hornsby et al. 2017. Using salinity to identify common bottlenose dolphin habitat in Barataria Bay, Louisiana, USA. Endangered Species Research
• Hovel et al. 2017. Within-lake heterogeneity mediates community response to warming trends. Ecology
• Huntington et al. 2017. Facilitation in Caribbean coral reefs: high densities of staghorn coral foster greater coral condition and reef fish composition. Oecologia
• Joyce et al. 2017. Physiological, morphological, and ecological tradeoffs influence vertical habitat use of deep-diving toothed-whales in the Bahamas. PLoS One
• Lehman et al. 2017. Relationships between Chinook salmon swimming performance and water quality in the San Joaquin River, California.  Transactions of the American Fisheries Society
• MacAvoy et al. 2017. Sources of stable isotope variation among stranded Western Atlantic dolphins (Tursiops truncatus) in North Carolina. Marine Mammal Science
• Mansfield et al. 2017. First satellite tracks of South Atlantic sea turtle ‘lost years’: seasonal variation in trans-equatorial movement. Proceedings of the Royal Society B: Biological Sciences
• McHugh et al. 2017. Linking models across scales to assess the viability and restoration potential of a threatened population of steelhead (Oncorhynchus mykiss) in the Middle Fork John Day River, Oregon, USA. Ecological Modelling
• Sampson et al. 2017. Trophic ecology of green turtle Chelonia mydas juveniles in the Colombian Pacific. Journal of the Marine Biological Association of the United Kingdom
• Scales et al. 2017. Should I stay or should I go? Modelling year-round habitat suitability and drivers of residency for fin whales in the California Current. Diversity and Distributions
• Siegelman-Charbit et al. 2017. Physical forcing on fish abundance in the southern California Current System. Fisheries Oceanography 
• Silber et al. 2017. Projecting marine mammal distribution in a changing climate. Frontiers in Marine Science 
• Van Oppen et al. 2017. Shifting paradigms in restoration of the world’s coral reefs. Global Change Biology
• Vizza et al. 2017. Evaluating the consequences of salmon nutrients for riparian organisms: linking condition metrics to stable isotopes. Ecology and Evolution
• Ward et al. 2017. 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. PLoS One
• Weijerman et al. 2017. A comparative application of trophic ecosystem models to evaluate drivers of endangered Hawaiian monk seal populations. Marine Ecology Progress Series
• Wells et al. 2017. Environmental conditions and prey-switching by a seabird predator impact juvenile salmon survival. Journal of Marine Systems
• Williams et al. 2017. Thermal stress exposure, bleaching response, and mortality in the threatened coral Acropora palmata. Marine Pollution Bulletin
   

2018

• Abrahms et al. 2018. Mesoscale activity facilitates energy gain in a top predator. Proceedings of the Royal Society B: Biological Sciences
• Amaya et al. 2018. Large-scale sea turtle mortality events in El Salvador attributed to paralytic shellfish toxin-producing algae blooms. Frontiers in Marine Science
• Becker et al. 2018. Predicting cetacean abundance and distribution in a changing climate. Diversity and Distributions
• Caretta, JV. 2018. A machine-learning approach to assign species to 'unidentified' entangled whales. Endangered Species Research
• Chittaro et al. 2018. Variability in the performance of juvenile Chinook salmon is explained primarily by when and where they resided in estuarine habitats. Ecology of Fresh Water Fish
• Fleming et al. 2018. The utility of combining stable isotope and hormone analyses for marine megafauna research. Frontiers in Marine Science
• Friedman et al. 2018. Environmental and geographic relationships among salmon forage assemblages along the continental shelf of the California Current. Marine Ecology Progress Series
• Gorospe et al. 2018. Local biomass baselines and the recovery potential for Hawaiian coral reef fish communities.  Frontiers in Marine Science 
• Halley et al. 2018. How survival curves affect populations' vulnerability to climate change. PLoS One
• Harborne et al. 2018. Modelling and mapping regional‐scale patterns of fishing impact and fish stocks to support coral‐reef management in Micronesia. Diversity and Distributions
• Hardy et al. 2018. Characterizing a sea turtle developmental habitat using Landsat observations of surface-pelagic drift communities in the eastern Gulf of Mexico. IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing
• Henderson et al. 2018. Spatial variability in ocean‐mediated growth potential is linked to Chinook salmon survival. Fisheries Oceanography
• Herbold et al. 2018. Managing for salmon resilience in California’s variable and changing climate. San Francisco Estuary and Watershed Science
• Jensen et al. 2018. Environmental warming and feminisation of one of the largest sea turtle populations in the world. Current Biology
• Jones et al. 2018. Massive mortality of a planktivorous seabird in response to a marine heatwave. Geophysical Research Letters
• Keogan et al. 2018. Global phenological insensitivity to shifting ocean temperatures among seabirds. Nature Climate Change
• Michel. 2018. Decoupling outmigration from marine survival indicates outsized influence of streamflow on cohort success for California’s Chinook salmon populations. Canadian Journal of Fisheries and Aquatic Sciences
• Olsen et al. 2018. Ocean futures under ocean acidification, marine protection, and changing fishing pressures explored using a worldwide suite of ecosystem models.  Frontiers in Marine Science
• Patel et al. 2018. Loggerhead turtles are good ocean-observers in stratified mid-latitude regions. Estuarine Coastal and Shelf Science
• Phillips et al. 2018. Selective occupancy of a persistent yet variable coastal river plume by two seabird species. Marine Ecology Progress Series
• Robinson et al. 2018. Environmental conditions and herbivore biomass determine coral reef benthic community composition: implications for quantitative baselines. Coral Reefs
• Scales et al. 2018. Fisheries bycatch risk to marine megafauna is intensified in Lagrangian coherent structures. Proceedings of the National Academy of Sciences  
• Shelby Walker et al. 2018. Brevetoxin exposure in sea turtles in south Texas (USA) during Karenia brevis red tide. Diseases of Aquatic Organisms
• Tolimieri et al. 2018. Oceanographic drivers of sablefish recruitment in the California Current. Fisheries Oceanography

2019

• Abrahms et al. 2019. Memory and resource tracking drive blue whale migrations. Proceedings of the National Academy of Sciences
• Brame et al. 2019. Biology, ecology, and status of the smalltooth sawfish, Pristis pectinata, in the USA. Endangered Species Research 
• Crozier et al. 2019. Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem. PLoS One
• Dudley 2019. Insights from an individual based model of a fish population on a large regulated river. Environmental Biology of Fishes
• Foley et al. 2019. Assessing Karenia brevis red tide as a mortality factor of sea turtles in Florida, USA. Diseases of Aquatic Organisms
• Hare et al. 2019. Atlantic salmon recovery informing and informed by Ecosystem-Based Fisheries Management. Fisheries Magazine
• Heenan et al. 2019. Natural variation in coral reef trophic structure across environmental gradients.  Frontiers in Ecology and the Environment
• Henderson et al. 2019. Estimating spatial–temporal differences in Chinook salmon outmigration survival with habitat- and predation-related covariates. Canadian Journal of Fisheries and Aquatic Sciences
• Hetherington et al. 2019. Re-examining trophic dead ends: stable isotope values link gelatinous zooplankton to leatherback turtles in the California Current. Marine Ecology Progress Series
• McHenry et al. 2019. Projecting marine species range shifts from only temperature can mask climate vulnerability. Global Change Biology
• Mollica et al. 2019. Skeletal records of bleaching reveal different thermal thresholds of Pacific coral reef assemblages.  Coral Reefs
• Ryan et al. 2019. Humpback whale song occurrence reflects ecosystem variability in feeding and migratory habitat of the northeast Pacific. PLoS One
• Van Cise et al. 2019. Oceanographic barriers, divergence, and admixture: phylogeography and taxonomy of two putative subspecies of short-finned pilot whale. Molecular Ecology
• Venegas et al. 2019. The rarity of depth refugia from coral bleaching heat stress in the western and central Pacific Islands. Scientific Reports
• Woodworth-Jefcoats et al. 2019. Relative impacts of simultaneous stressors on a pelagic marine ecosystem. Frontiers in Marine Science 
• Wren et al. 2019. Variations in black-footed albatross sightings in a North Pacific transitional area due to changes in fleet dynamics and oceanography 2006 - 2017.  Deep Sea Research Part II: Topical Studies in Oceanography