National Protected Species Toolbox Initiative Publications

Through the National Protected Species Toolbox Initiative, NOAA Fisheries is developing quantitative analytical tools that will improve protected species assessments and better analyze impacts from human activities, research and development capabilities, and address critical management concerns. Below are publications associated with this initiative.

2025 Publications

Pausch, R. E., Hale, J. R., Kiffney, P., Sanderson, B., Azat, S., Barnas, K., … & Marx, S. 2025. Review of ecological valuation and equivalency analysis methods for assessing temperate nearshore submerged aquatic vegetation. Conservation Biology, 39(1), e14380. https://doi.org/10.1111/cobi.14380

2024 Publications

Rider, M. J., Avens, L., Haas, H. L., Hatch, J. M., Patel, S. H., & Sasso, C. R. 2024. Where the leatherbacks roam: movement behavior analyses reveal novel foraging locations along the Northwest Atlantic shelf. Frontiers in Marine Science, 11. https://doi.org/10.3389/fmars.2024.1325139

Rider, M. J., Avens, L., Haas, H. L., Harms, C. A., Patel, S. H., Snodgrass, D., & Sasso, C. R. 2024. Regional variation in leatherback dive behavior in the northwest Atlantic. Endangered Species Research 55: 169-185. DOI: https://doi.org/10.3354/esr01365

Taras, B.D., Conn, P.B., Bravington, M.V., Kilian, A., Lang, A.R., Bryan, A., Stimmelmayr, R. and Quakenbush, L. 2024. Estimating demographic parameters for bearded seals, Erignathus barbatus, in Alaska using close‐kin mark‐recapture methods. Evolutionary Applications, 17(11), p.e70035. https://doi.org/10.1111/eva.70035

Veggerby, K., MD Scheuerell, BL Sanderson, P Kiffney and B Ferriss. 2024. Shellfish aquaculture farms as foraging habitat for nearshore fishes and crabs. Marine and Coastal Fisheries 16:e10282. https://doi.org/10.1002/mcf2.10282

Veggerby, K. B., Scheuerell, M. D., Sanderson, B. L., & Kiffney, P. M. 2024. Stable isotopes reveal intertidal fish and crabs use bivalve farms as foraging habitat in Puget Sound, Washington. Frontiers in Marine Science, 10, 1282225. https://doi.org/10.3389/fmars.2023.1282225

Ver Hoef, J.M., Blagg, E., Dumelle, M., Dixon, P.M., Zimmerman, D.L. and Conn, P.B. 2024. Marginal inference for hierarchical generalized linear mixed models with patterned covariance matrices using the Laplace approximation. Environmetrics, 35(7), p.e2872. https://doi.org/10.1002/env.2872

2023 Publications

Hatch, J. M., Murray, K. T., Patel, S., Smolowitz, R., & Haas, H. L. (2023). Evaluating simple measures of spatial-temporal overlap as a proxy for encounter risk between a protected species and commercial fishery. Frontiers in Conservation Science, 4, 1118418. https://doi.org/10.3389/fcosc.2023.1118418

Khan CB, Goetz KT, Cubaynes HC, Robinson C, Murnane E, Aldrich T, Sackett M, Clarke PJ, LaRue MA, White T, et al. 2023. A Biologist’s Guide to the Galaxy: Leveraging Artificial Intelligence and Very High-Resolution Satellite Imagery to Monitor Marine Mammals from Space. Journal of Marine Science and Engineering. 11(3):595. https://doi.org/10.3390/jmse11030595

Munsch, S. H., Walter, R. K., Sanderson, B. L., Reshitnyk, L., O’Leary, J. K., Kiffney, P. M., … & Beaty, F. L. 2023. Decades of eelgrass meadow dynamics across the northeast Pacific support seascape-scale conservation. ICES Journal of Marine Science, 80(10), 2520-2529. https://doi.org/10.1093/icesjms/fsad162

Munsch SH, Beaty FL, Beheshti KM, Chesney WB and others. 2023. Northeast Pacific eelgrass dynamics: interannual expansion distances and meadow area variation over time. Mar Ecol Prog Ser 705:61-75. https://doi.org/10.3354/meps14248

Sigourney, D. B., DeAngelis, A., Cholewiak, D., & Palka, D. 2023. Combining passive acoustic data from a towed hydrophone array with visual line transect data to estimate abundance and availability bias of sperm whales (Physeter macrocephalus). PeerJ, 11, e15850. https://doi.org/10.7717/peerj.15850

Szesciorka, A. R., Demer, D. A., Santora, J. A., Forney, K. A., & Moore, J. E. 2023. Multiscale relationships between humpback whales and forage species hotspots within a large marine ecosystem. Ecological Applications, 33(2), e2794. https://doi.org/10.1002/eap.2794

2022 Publications

Carretta, J. V., & Henry, A. G. 2022. Risk assessment of whale entanglement and vessel strike injuries from case narratives and classification trees. Frontiers in Marine Science, 9, 863070. https://doi.org/10.3389/fmars.2022.863070

Conn, P. B., Ver Hoef, J.M., McClintock, B.T., Johnson, D.S., & Brost, B. 2022. A GLMM approach for combining multiple relative abundance surfaces. Methods in Ecology and Evolution, 13, 2236-2247. https://doi.org/10.1111/2041-210X.13948

Curtis, K. A., Calambokidis, J., Audley, K., De Weerdt, J., Garita, F., Martínez‐Loustalot, P., & Palacios, J. D. 2022. “Abundance of Humpback Whales (Megaptera novaeangliae) Wintering in Central America and Southern Mexico from a One‐Dimensional Spatial Capture‐Recapture Model.” US Department of Commerce, NOAA Technical Memorandum NMFS‐SWFSC‐661. 27 pp. https://repository.library.noaa.gov/view/noaa/40459

Hatch, J.M., Haas, H.L., Sasso, C.R., Patel, S.H. and Smolowitz, R.J., 2022. Estimating the complex patterns of survey availability for loggerhead turtles. The Journal of Wildlife Management, 86(4), p.e22208. https://doi.org/10.1002/jwmg.22208

Johnson, D. S., Brost, B. M., & Hooten, M. B. 2022. Greater than the sum of its parts: Computationally flexible Bayesian hierarchical modeling. Journal of Agricultural, Biological and Environmental Statistics, 27(2), 382-400. https://doi.org/10.1007/s13253-021-00485-9

McClintock, B. T., Abrahms, B., Chandler, R. B., Conn, P. B., Converse, S. J., Emmet, R. L., … & Johnson, D. S. 2022. An integrated path for spatial capture–recapture and animal movement modeling. Ecology, 103(10), e3473. https://doi.org/10.1002/ecy.3473

2021 Publications

Egan, K. E., Viehman, T. S., Holstein, D. M., Poti, M., Groves, S. H., & Smith, T. B. 2021. Predicting the distribution of threatened orbicellid corals in shallow and mesophotic reef ecosystems. Marine Ecology Progress Series, 667, 61-81. DOI: https://doi.org/10.3354/meps13698

Patel, S. H., Winton, M. V., Hatch, J. M., Haas, H. L., Saba, V. S., Fay, G., & Smolowitz, R. J. 2021. Projected shifts in loggerhead sea turtle thermal habitat in the Northwest Atlantic Ocean due to climate change. Scientific Reports, 11(1), 8850. https://doi.org/10.1038/s41598-021-88290-9

Shelton, A.O., G.H. Sullaway, E.J. Ward, B.E. Feist, K.A. Somers, V.J. Tuttle, J.T. Watson, W.H. Satterthwaite. 2021. Redistribution of salmon populations in the Northeast Pacific Ocean in response to climate. Fish and Fisheries 22:503-517 https://doi.org/10.1111/faf.12530

Sullaway, G. H., Shelton, A. O., & Samhouri, J. F. 2021. Synchrony erodes spatial portfolios of an anadromous fish and alters availability for resource users. Journal of Animal Ecology, 90(11), 2692-2703. https://doi.org/10.1111/1365-2656.13575

Ver Hoef, J. M., Johnson, D., Angliss, R., & Higham, M. 2021. Species density models from opportunistic citizen science data. Methods in Ecology and Evolution, 12(10), 1911-1925. https://doi.org/10.1111/2041-210X.13679

2020 Publications

Chasco, B., J.T. Thorson, S. Heppell, L. Avens, J. Braun-McNeill, A.B. Bolten, K.A. Bjorndal, and E.J. Ward. 2020. Integrated mixed-effect growth models for species with incomplete ageing histories: a case study for loggerhead sea turtle Caretta caretta. Marine Ecology Progress Series 636:221-234. https://doi.org/10.3354/meps13222

Chen, Y-H., K. Shertzer, and T. Shay Viehman. 2020. Spatio-temporal dynamics of the threatened elkhorn coral Acropora palmata: Implications for conservation. Diversity and Distributions 26:1582- 1597. https://doi.org/10.1111/ddi.13143

Conn, P. B., Bravington, M. V., Baylis, S., & Ver Hoef, J. M. 2020. Robustness of close‐kin mark–recapture estimators to dispersal limitation and spatially varying sampling probabilities. Ecology and Evolution, 10(12), 5558-5569. https://doi.org/10.1002/ece3.6296

Curtis, K.A., and J.V. Carretta. 2020. ObsCovgTools: Assessing observer coverage needed to document and estimate rare event bycatch. Fisheries Research 225. https://doi.org/10.1016/j.fishres.2020.105493

Solsona-Berga A, Frasier KE, Baumann-Pickering S, Wiggins SM, Hildebrand JA. 2020. DetEdit: A graphical user interface for annotating and editing events detected in long-term acoustic monitoring data. PLoS Comput Biol 16(1):e1007598. https://doi.org/10.1371/journal.pcbi.1007598

Stock, B. C., Ward, E. J., Eguchi, T., Jannot, J. E., Thorson, J. T., Feist, B. E., & Semmens, B. X. 2020. Comparing predictions of fisheries bycatch using multiple spatiotemporal species distribution model frameworks. Canadian Journal of Fisheries and Aquatic Sciences, 77(1), 146-163. https://doi.org/10.1139/cjfas-2018-0281

Viehman, T.S., M. Nemeth, S.H. Groves, C.A. Buckel, S. Griffin, D. Field, T.D. Moore, J. Moore. 2020. Coral assessment and restoration in the U.S. Caribbean after 2017 hurricanes. NOAA National Ocean Service, National Centers for Coastal Ocean Science. NOAA Technical Memorandum 278. Silver Spring, MD. 64 pp. https://doi.org/10.25923/7r0b-wc52.

2019 Publications

Hatch, J.M., H.L. Haas, P.M. Richards, and K.A. Rose. 2019. Life-history constraints on maximum population growth for loggerhead turtles in the northwest Atlantic. Ecol Evol 9:9442-9452. https://doi.org/10.1002/ece3.5398

Shelton, A.O., W.H. Satterthwaite, E.J. Ward, B.E. Feist, and B. Burke. 2019. Using hierarchical models to estimate stock-specific and seasonal variation in ocean distribution, survivorship, and aggregate abundance of fall run Chinook salmon. Canadian Journal of Fisheries and Aquatic Science 76:95-108. https://doi.org/10.1139/cjfas-2017-0204

Stock, B.C., E.J. Ward, J.T. Thorson, J.E. Jannot, and B.X. Semmens. 2019. The utility of spatial model-based estimators of unobserved bycatch. ICES J Marine Science 76:255–267. https://doi.org/10.1093/icesjms/fsy153

Woodman, S. M., Forney, K. A., Becker, E. A., DeAngelis, M. L., Hazen, E. L., Palacios, D. M., & Redfern, J. V. 2019. eSDM: a tool for creating and exploring ensembles of predictions from species distribution and abundance models. Methods in Ecology and Evolution, 10(11), 1923-1933.https://doi.org/10.1111/2041-210X.13283

2018 Publications

Sharf, H.R, M.B. Hooten, D.S. Johnson, and J.W. Durban. 2018. Process convolution approaches for modeling interacting trajectories. Environmetrics 29. https://doi.org/10.1002/env.2487

Wilson, K., E. Hanks, and D. Johnson. 2018. Estimating animal utilization densities using continuous-time Markov chain models. Methods in Ecol Evol 9:1232-1240. https://doi.org/10.1111/2041-210X.12967

2017 Publications

Tolimieri, N., Holmes, E. E., Williams, G. D., Pacunski, R., & Lowry, D. 2017. Population assessment using multivariate time‐series analysis: A case study of rockfishes in Puget Sound. Ecology and evolution, 7(8), 2846-2860. https://doi.org/10.1002/ece3.2901

Viehman TS. 2017 Coral decline and habitat loss in the Caribbean: Modeling abiotic limitations on coral populations and communities. PhD dissertation. Duke University. https://dukespace.lib.duke.edu/server/api/core/bitstreams/7ce2481c-6099-43b2-9aec-f5f4a3748ad9/content

Warden, M.L., H.L. Haas, P.M. Richards, K.A. Rose, and J.M Hatch. 2017. Monitoring trends in sea turtle populations: walk or fly? Endang Species Res 34:323-337. https://doi.org/10.3354/esr00855

Wilson, K., Littnan, C., & Read, A. J. 2017. Movements and home ranges of monk seals in the main Hawaiian Islands. Marine Mammal Science, 33(4), 1080-1096. https://doi.org/10.1111/mms.12429

2016 Publications

Ascani, F., Van Houtan, K. S., Di Lorenzo, E., Polovina, J. J., & Jones, T. T. 2016. Juvenile recruitment in loggerhead sea turtles linked to decadal changes in ocean circulation. Global Change Biology, 22(11), 3529-3538. https://doi.org/10.1111/gcb.13331

Scharf, H.R., M.B. Hooten, B.K. Fosdick, D.S. Johnson, J.M. London, and J.W. Durban. 2016. Dynamic social networks based on movement. Annals of Applied Statistics 10:2182-2202. https://doi.org/10.1214/16-AOAS970

2015 Publications

Curtis, K.A., J.E. Moore, C. Boyd, P.W. Dillingham, R.L. Lewison, B.L. Taylor, and K. James. 2015. Managing catch of marine megafauna: Guidelines for setting limit reference points. Marine Policy 61:249-263. https://doi.org/10.1016/j.marpol.2015.07.002

Curtis, K.A., J.E. Moore, and S.R. Benson. 2015. Estimating limit reference point for western Pacific leatherback turtle (Dermochelys coriacea) in the U.S. West Coast. PLoS One 10. https://doi.org/10.1016/j.marpol.2015.07.002

Lamont, M. M., Putman, N. F., Fujisaki, I., & Hart, K. M. 2015. Spatial requirements of different life-stages of the loggerhead turtle (Caretta caretta) from a distinct population segment in the northern Gulf of Mexico. Herpetological Conservation and Biology, 10(1), 26-43. http://www.herpconbio.org/Volume_10/Issue_1/Lamont_etal_2015.pdf

Putnam, N.F., P. Verley, C.S. Endres, and K.J. Lohmann. 2015. Magnetic navigation behavior and the oceanic ecology of young loggerhead turtles. J Experimental Biology 218:1044-1050. https://doi.org/10.1242/jeb.109975

Putman, N.F., and K.L. Mansfield. 2015. Direct evidence of swimming demonstrates active dispersal in the sea turtle “lost years.” Current Biology 25:1-7. https://doi.org/10.1016/j.cub.2015.03.014

Putman, N. F., Abreu-Grobois, F. A., Iturbe-Darkistade, I., Putman, E. M., Richards, P. M., & Verley, P. 2015. Deepwater Horizon oil spill impacts on sea turtles could span the Atlantic. Biology Letters, 11(12), 20150596. https://doi.org/10.1098/rsbl.2015.0596

Warden, M.L., H.L. Haas, K.A. Rose, and P.M. Richards. 2015. A spatially explicit population model of simulated fisheries impact on loggerhead turtles (Caretta caretta) in the Northwest Atlantic Ocean. Ecological Modeling 299:23-39. https://doi.org/10.1016/j.ecolmodel.2014.11.025

2013 Publications

Moore, J. E., Curtis, K. A., Lewison, R. L., Dillingham, P. W., Cope, J. M., Fordham, S. V., … & Zhou, S. 2013. Evaluating sustainability of fisheries bycatch mortality for marine megafauna: a review of conservation reference points for data-limited populations. Environmental Conservation, 40(4), 329-344. https://doi.org/10.1017/S037689291300012X

Curtis, K. A., & Moore, J. E. 2013. Calculating reference points for anthropogenic mortality of marine turtles. Aquatic Conservation: Marine and Freshwater Ecosystems, 23(3), 441-459. https://doi.org/10.1002/aqc.2308