Protected Species Research Publications - Methods and Technology

2015-2016

• Ackerman et al. 2016. Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead.  Evolutionary Applications
• Adimey et al. 2016. Twenty-six years of post-release monitoring of Florida manatees (Trichechus manatus latirostris): evaluation of a cooperative rehabilitation program. Aquatic Mammals
• Adams et al. 2016. A century of Chinook salmon consumption by marine mammal predators in the Northeast Pacific Ocean. Ecological Informatics
• Becker et al. 2016. Moving towards dynamic ocean management: how well do modeled ocean products predict species distributions? Remote Sensing
• Bergmann et al. 2016. Line cutter for use when releasing large marine organisms caught on longline gear. Fisheries Research
• Bright et al. 2016. Tracking growth and survival of rescued boulder corals. Restoration Ecology
• Conner et al. 2016. Evaluating impacts using a BACI design, ratios, and a Bayesian approach with a focus on restoration. Environmental Monitoring and Assessment
• Demetras et al. 2016. Development of underwater recorders to quantify predation of juvenile Chinook salmon (Oncorhynchus tshawytscha) in a river environment. Fishery Bulletin
• Durban et al. 2016. Photogrammetry of blue whales with an unmanned hexacopter.  Marine Mammal Science
• Goertler et al. 2016. Estimating common growth patterns in juvenile Chinook salmon from diverse genetic stocks and a large spatial extent. PLos One
• Goshe et al. 2016. Validation of back-calculated body lengths and timing of growth mark deposition in Hawaiian green sea turtles. Ecology and Evolution
• Goulette and Lipsky. 2016. Nonlethal batch identification of Atlantic Salmon using coded wire tags.  North American Journal of Fisheries Management
• Griffiths and Barlow. 2016. Cetacean acoustic detections from free-floating vertical hydrophone arrays in the southern California Current. The Journal of the Acoustical Society of America
• Harris et al. 2016. Validation of ultrasound as a noninvasive tool to measure subcutaneous fat depth in leatherback sea turtles (Dermochelys coriacea). Journal of Zoology and WIldlife Medicine 
• Head et al. 2016. Techniques for improving estimates of maturity ogives in groundfish using double-reads and measurement error models.  Fisheries Research
• Heenehan et al. 2016. Using acoustics to prioritize management decisions to protect coastal dolphins: A case study using Hawaiian spinner dolphins. Marine Policy
• Jorgensen et al. 2016. Assessing spatial covariance among time series of abundance. Ecology and Evolution
• Nadeem et al.  2016. Integrating population dynamics models and distance sampling data: a spatial hierarchical state-space approach. Ecology
• Roch et al. 2016. Management of acoustic metadata for bioacoustics. Ecological Informatics   
• Stanistreet et al. 2016. Effects of duty-cycled passive acoustic recordings on detecting the presence of beaked whales in the northwest Atlantic. Journal of the Acoustical Society of America
• 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
   

2017

• Anderson et al. 2017. Genetic and individual assignment of tetraploid green sturgeon with SNP assay data. Conservation Genetics
• Borggaard et al. 2017. Managing U.S. Atlantic large whale entanglements: Four guiding principles. Marine Policy
• Braun et al. 2017. An R package for improved geolocation of archival-tagged fishes using a hidden Markov method. Methods in Ecology and Evolution
• Corkeron et al. 2017. A right whale pootree: classification trees of fecal hormones identify reproductive states in North Atlantic right whales (Eubalaena glacialis). Conservation Physiology
• Goulette and Hawkes 2017. Altering vertical placement of hydroacoustic receivers for improved efficiency in cold water estuary zones. North American Journal of Fisheries Management
• Jacobson et al. 2017. Using paired visual and passive acoustic surveys to estimate passive acoustic detection parameters for harbor porpoise abundance estimates. Journal of the Acoustical Society of America
• Johnson et al. 2017. Framework for increasing the science and management value of life stage monitoring networks for endangered Sacramento River winter run Chinook salmon in California’s regulated rivers and coastal ocean.  San Francisco Estuary & Watershed Science
• Neely et al. 2017. Skin transcriptomes of common bottlenose dolphins (Tursiops truncatus) from the northern Gulf of Mexico and southeastern U.S. Atlantic coasts. Marine Genomics
• Redfern et al. 2017. Predicting cetacean distributions in data-poor marine ecosystems. Biodiversity Research
• Taylor et al. 2017. Guidelines and quantitative standards to improve consistency in cetacean subspecies and species delimitation relying on molecular genetic data. Marine Mammal Science
• Van Oppen et al. 2017. Shifting paradigms in restoration of the world’s coral reefs. Global Change Biology
• Vetters Bichell et al. 2017. The reliability of pigment pattern-based identification of wild bottlenose dolphins. Marine Mammal Science
   

2018

• Angliss et al. 2018. Comparing manned to unmanned aerial surveys for cetacean monitoring in the Arctic: methods and operational results. Journal of Unmanned Vehicle Systems
• Bogucki et al. 2018. Applying deep learning to right whale photo identification. Conservation Biology
• Caretta, JV. 2018. A machine-learning approach to assign species to 'unidentified' entangled whales. Endangered Species Research
• Emmons et al. 2018. Quantifying variation in killer whale (Orcinus orca) morphology using elliptical Fourier analysis. Marine Mammal Science
• Farmer et al. 2018. Resilience of the endangered sperm whale Physeter macrocephalus to foraging disturbance in the Gulf of Mexico, USA: a bioenergetic approach. Marine Ecology Progress Series
• Ferguson et al. 2018. Performance of manned and unmanned aerial surveys to collect visual data and imagery for estimating arctic cetacean density and associated uncertainty. Journal of Unmanned Vehicle Systems
• Fleming et al. 2018. Combining acoustic and visual detections in habitat models of Dall’s porpoise. Ecological Modelling
• Fleming et al. 2018. The utility of combining stable isotope and hormone analyses for marine megafauna research. Frontiers in Marine Science
• Haver et al. 2018. Monitoring long-term soundscape trends in U.S. waters: The NOAA/NPS Ocean Noise Reference Station Network. Marine Policy
• Hinke et al. 2018. Estimating nest-level phenology and reproductive success of colonial seabirds using time-lapse cameras. Methods in Ecology and Evolution
• Jensen et al. 2018. Environmental warming and feminisation of one of the largest sea turtle populations in the world. Current Biology
• 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
• Miller et al. 2018. Estimating drift of directional sonobuoys from acoustic bearings. The Journal of the Acoustical Society of America
• O’Farrell et al. 2018. Alternative Juvenile Production Estimate (JPE) forecast approaches for Sacramento River winter-run Chinook salmon. San Francisco Estuary and Watershed Science
• Shertzer et al. 2018. Characterizing sex ratios of sea turtle populations: a Bayesian mixture modeling approach applied to juvenile loggerheads (Caretta caretta). Journal of Experimental Marine Biology and Ecology
• Wetzel et al. 2018. The effect of reduced data on the ability to monitor rebuilding of overfished fish stocks. Fishery Bulletin
   

2019

• Avens et al. 2019. Regional comparison of leatherback sea turtle maturation attributes and reproductive longevity.  Marine Biology
• Chabot et al. 2019. Characterizing stable isotope relationships between green turtle (Chelonia mydas) skin and unhatched eggs. Rapid Communications in Mass Spectrometry
• Dudley 2019. Insights from an individual based model of a fish population on a large regulated river. Environmental Biology of Fishes
• Eiler et al. 2019. Tracking the movements of juvenile Chinook salmon using an autonomous underwater vehicle under payload control. Fisheries Acoustics, Applied Sciences and Practical Applications
• Hare et al. 2019. Atlantic salmon recovery informing and informed by Ecosystem-Based Fisheries Management. Fisheries Magazine
• Hildebrand et al. 2019. Assessing seasonality and density from passive acoustic monitoring of signals presumed to be from pygmy and dwarf sperm whales in the Gulf of Mexico. Frontiers in Marine Science
• Mollica et al. 2019. Skeletal records of bleaching reveal different thermal thresholds of Pacific coral reef assemblages.  Coral Reefs
• National Academy of Sciences, Engineering, and Medicine. 2019.  Research Review of Interventions to Increase the Persistence and Resilience of Coral Reefs. The National Academia Press 
• Orben et al. 2019. Comparing imaging, acoustics, and radar to monitor Leach's storm-petrel colonies. PeerJ 
• Ramirez et al. 2019. Reconstructing sea turtle ontogenetic habitat shifts through trace element analysis of bone tissue.  Marine Ecology Progress Series
• Rust et al. 2019. Accuracy and precision of age determination using growth layer groups for California sea lions (Zalophus californianus) with known ages. Marine Mammal Science
• Young et al. 2019. Drift and beaching patterns of sea otter carcasses and car tire dummies. Marine Mammal Science 
• Williams et al. 2019. Leveraging automated image analysis tools to transform our capacity to assess status and trends on coral reefs. Frontiers in Marine Science
• Zollett and Swimmer. 2019. Safe handling practices to increase post-capture survival of cetaceans, sea turtles, seabirds, sharks, and billfish in tuna fisheries. Endangered Species Research