Thomas L, Jaramillo-Legorreta A, Cardenas-Hinojosa G, Nieto-Garcia E, Rojas-Bracho L, Ver Hoef JM, Moore J, Taylor B, Barlow J, Tregenza N. Last call: passive acoustic monitoring shows continued rapid decline of critically endangered vaquita. Journal of Acoustical Society of America Express Letters. Submitted.

Lennert-Cody C, Buckland ST, Gerrodette T, Webb A, Barlow J, Fretwell PT, Maunder MN, Kitakado T, Moore JE, Scott MD, Skaug HJ. Review of potential line-transect methodologies for estimating abundance of dolphin stocks in the eastern tropical Pacific. Journal of Cetacean Research and Management. Submitted.

44. Boyd C, Barlow J, Becker EA, Forney KA, Gerrodette T, Moore JE, Punt AE. 2017. Estimation of population size and trends for highly mobile species with dynamic spatial distributions. Diversity and Distributions. In press.


43. Williams R, Ashe E, Gaut K, Gryba R, Moore JE, Rexstad E, Sandilands D, Steventon J, Reeves R. 2017. Animal counting toolkit: a practical guide to small-boat surveys for estimating abundance of coastal marine mammals. Endangered Species Research 34:149-165.

42. Taylor BL, Rojas-Bracho L, Moore J, Jaramillo-Legorreta A, Ver Hoef J.M., Cardenas-Hinojosa G, Nieto-Garcia E, Barlow J, Gerrodette T, Tregenza N, Thomas L, Hammond P.S.  2016. Extinction is imminent for Mexico’s endemic porpoise unless fishery bycatch is eliminated.  Conservation Letters DOI: 10.1111/conl.12331


41. Jaramillo-Legorreta A, Cardenas-Hinojosa G, Nieto-Garcia E, Rojas-Bracho L, Ver Hoef J, Moore J, Tregenza N, Barlow J, Gerrodette T, Thomas L, Taylor B. 2016. Acoustic monitoring reveals a catastrophic decline in Mexico’s vaquita, the world’s most endangered marine mammal. Conservation Biology 31:183-191

40. Nadeem K, Moore JE, Zhang Y, Chipman H. 2016. Integrating Population Dynamics Models and Distance Sampling Data: A Spatial Hierarchical State-Space Approach. Ecology. In press.


39. Williams R, Moore JE, Gomez-Salazar C, Trujillo F, Burt L. 2016. Searching for trends in river dolphin abundance: Designing surveys for looming threats, and evidence for opposing trends of two species in the Colombian Amazon. Biological Conservation 195: 136 - 145


38. Curtis KA, Moore JE, Benson SR. 2015. Estimating limit reference points for western Pacific leatherback turtles (Dermochelys coriacea) in the U.S. West Coast EEZ. PLoS ONE 10(9): e0136452. doi:10.1371/journal.pone.0136452. Link to article.


37. Curtis KA, Moore JE, Boyd C, Dillingham PW, Lewison RL, Taylor BL, James KC. 2015. Managing catch of marine megafauna: guidelines for setting limit reference point. Marine Policy 61: 249-263


36. Dillingham P, Moore JE, Fletcher D, Cortes E, James K, Curtis KA, Lewison RL. In press. Improved estimation of intrinsic growth rmax for long-lived species: integrating matrix models and allometry. Ecological Applications.  Link to Preprint.


35. James K, Lewison RL, Dillingham P, Curtis KA, Moore JE. 2015. Drivers of retention and discards of elasmobranch non-target catch.  Environmental Conservation. Link to First View of article.


34. Martin SL, Stohs SM, Moore JE. 2015. Bayesian inference and assessment for rare-event bycatch in marine fisheries: a drift gillnet fishery case study.  Ecological Applications 25:416-429.


33. Moore JE, Barlow JP. 2014. Improved abundance and trend estimates for sperm whales in the eastern North Pacific from Bayesian hierarchical modeling. Endangered Species Research 25:141-150. Link to article  


32. Lewison RL, Crowder LB, Wallace BP, Moore JE, Cox TM, Zydelis R, McDonald S, DiMatteo A, Dunn D, Kot CY, Bjorkland R, Kelez S, Soykan C, Stewart KR, Sims M, Boustany A, Read AJ, Halpin P, Nichols WJ, Safina C. 2014. Global patterns of marine mammal, seabird and sea turtle bycatch reveal taxa-specific and cumulative megafauna hotspots. Proceedings of the National Academy of Sciences of the United States 111:5271-5276


31. Moore, JE, Curtis KA, Dillingham PW, Cope JM, Fordham S, Heppell S, Pardo SA, Simpfendorfer CA, Tuck G, Zhou S. 2013. Evaluating sustainability of fisheries bycatch mortality for marine megafauna: conservation reference points for data-limited populations. Environmental Conservation 40:329-344.


30. Moore JE, Barlow J. 2013. Declining abundance of beaked whales (family Ziphiidae) in the California Current large marine ecosystem. PLOS ONE 8(1): e52770. Link to article


29. Curtis KA, Moore JE. 2013. Calculating reference points for sustainable take of marine turtles. Aquatic Conservation: Marine and Freshwater Ecosystems 23:441-459.


28. Turvey ST, CL Risley, JE Moore, LA Barrett, H Yujiang, Z Xiujiang, Z Kaiya, W Ding. 2013. Can local ecological knowledge be used to assess status and extinction drivers in a threatened freshwater cetacean? Biological Conservation 157:352-360


27. Moore, J.E. 2012. Management reference points to account for direct and indirect impacts of fishing on marine mammals. Marine Mammal Science 29:446-473.


26. Finkbeiner, E.M., B.P. Wallace, J.E. Moore, R.L. Lewison, L.B. Crowder. 2011. Cumulative estimates of sea turtle bycatch and mortality in U.S.A. fisheries between 1990-2007. Biological Conservation 144:2719-2727


25. Moore, J.E., and J. Barlow. 2011. Bayesian hierarchical estimation of fin whale abundance trends from a 1991-2008 time series of line-transect surveys in the California Current. Journal of Applied Ecology 48:1195-1205. 


24. Zydelis, R., R.L. Lewison, S.A. Shaffer, J.E. Moore, et al (14 authors). 2011. Dynamic habitat models: Using telemetry data to project fisheries bycatch. Proceedings of the Royal Society B 278(1722):3191-3200. 


23. Lewison, R.L., C.U. Soykan, T. Cox, H. Peckham, N. Pilcher, N. LeBoeuf, S. McDonald, J. Moore, C. Safina, L. Crowder. 2011. Ingredients for addressing the challenges of fisheries bycatch. Bulletin of Marine Science 87:235-250.


22. Moore, J. E., T.M. Cox, R.L. Lewison, A.J. Read, R. Bjorkland, S.L. McDonald, L.B. Crowder, E. Aruna, I. Ayissi, P. Espeut, C. Joynson-Hicks, N. Pilcher, C. Poonian, B. Solarin, and J. Kiszka. 2010. An interview-based approach to assess marine mammal and sea turtle captures in artisanal fisheries. Biological Conservation 143:795-805.


21. Moore, J.E., B. Wallace, R. Lewison, R. Zydelis, T. Cox, L. Crowder. 2009. A review of marine mammal, sea turtle and seabird bycatch in USA fisheries and the role of policy in shaping management. Marine Policy 33:435-451.


20. Bryant, J.P., T.P. Clausen, R.K. Swihart ... J.E. Moore, et al. (21 authors). 2009. Fire drives transcontinental variation in tree birch defense against browsing by snowshoe hares. American Naturalist 174:13-23.


19. Poonian, C.N.S., M.D. Hauzer, A.B. Allaoui, T.M. Cox, J.E. Moore, A.J. Read, R.L. Lewison, and L. B. Crowder. 2008. Rapid assessment of sea turtle and marine mammal bycatch in the Union of the Comoros.WIOMSA Journal 7:207-216.


18. Moore, J.E., and A.J. Read. 2008. A Bayesian uncertainty analysis of cetacean demography and bycatch mortality using age-at-death data. Ecological Applications 18:1914-1931.


17. Soykan, C.U., J.E. Moore, R.Zydelis, R. L.Lewison, L.B. Crowder, and C. Safina. 2008. Why study bycatch? An introduction to the Theme Section on fisheries bycatch. Endangered Species Research 5:91-102.


16. Moore, J.E., and R. Zydelis. 2008. Quantifying seabird bycatch: where do we go from here? Animal Conservation 11:257-259.


15. Eckert, S.A, J.E. Moore, D.D. Dunn, R. Sagarminaga, K.L. Eckert, P.N. Halpin. 2008. Hierarchical state-space models of loggerhead turtle movement behavior in relation to turtle size and oceanographic features. Ecological Applications 18:290-308.


Related to disseration work at Purdue University (forest fragmentation ecology)


14. Rizkalla, C., J.E. Moore, and R.K. Swihart. 2009. Modeling patch occupancy: relative performance of ecologically scaled landscape indices. Landscape Ecology 24:77-88.


13. Moore, J.E., and R.K. Swihart. 2008. Factors affecting the relationship between seed removal and seed mortality. Canadian Journal of Zoology 86:378-385.


12. Moore, J.E., A.B. McEuen, R.K. Swihart, T.A. Contreras, and M.A. Steele. 2007. Determinants of seed-removal distance by scatter-hoarding rodents in deciduous forests. Ecology 88:2529-2540.


11. Moore, J.E., and R.K. Swihart. 2007. Toward ecologically explicit null models of nestedness. Oecologia152:763-777.


10. Moore, J. E., and R. K. Swihart. 2007. Importance of fragmentation-tolerant species as seed dispersers in disturbed landscapes. Oecologia 151:663-674.


9. Moore, J.E. and R.K. Swihart. 2006. Diet choice of captive Blue Jays: implications for tree dispersal. Condor108:377-388.


8. Swihart, R.K., J.J. Lusk, J.E. Duchamp, C.E. Rizkalla, and J.E. Moore. 2006. The roles of landscape context, niche breadth, and range boundaries in predicting species responses to habitat alteration. Diversity and Distributions 12:277-287. 


7. Moore, J.E., and R.K. Swihart. 2005. Modeling patch occupancy by forest rodents: incorporating detectability and spatial autocorrelation with hierarchically structured data. Journal of Wildlife Management 69:933-949.


6. Moore, J.E., Scheiman, D. M. and R. K. Swihart 2004. Field comparison of removal and modified double-observer modeling for estimating detectability and abundance of birds. Auk 121:865-876.


Related to Master's research at Humboldt State University on foraging ecology of black brant


5. Lee, D.E., J.M. Black, J.E. Moore, and J.S. Sedinger. 2007. Age-specific stopover ecology of black brant at Humboldt Bay, California. Wilson Journal of Ornithology 119:9-22.


4. Moore, J.E. and J.M. Black. 2006. Slave to the tides: spatio-temporal foraging dynamics of spring staging black brant. Condor 108:661-677.


3. Moore, J.E., and J.M. Black. 2006. Historical changes in black brant use on Humboldt Bay, California.Wildlife Biology 12:151-162.


2. Moore, J.E., M.A. Colwell, R.M. Mathis, and J.M. Black. 2004. Staging of Pacific flyway brant in relation to eelgrass abundance and site isolation, with special consideration of Humboldt Bay, California. Biological Conservation 115:475-486.


Undergraduate work at U.C. Davis


1. Moore, J.E. and P.V. Switzer. 1998. Pre-roosting aggregations in the American Crow Corvus brachyrhyncos.Canadian Journal of Zoology 76:508-512.


NOAA Technical Memoranda and Other Selected Reports 

Moore JE, Barlow J. 2017. Population abundance and trend estimates for beaked whales and sperm whales in the California Current from ship-based visual line-transect survey data, 1991 – 2014.  NOAA Tech Memo NOAA-TM-NMFS-SWFSC-585.

Carretta JV, Moore JE, Forney KA. 2017. Regression tree and ratio estimates of marine mammal, sea turtle and seabird bycatch in the California drift gillnet fishery: 1990-2015. NOAA Tech Memo NOAA-TM-NMFS-SWFSC-568.

Moore JE. 2015. Intrinsic growth (rmax) and generation time (T) estimates for the cetacean genera Sousa, Orcaella, and Neophocaena, in support of IUCN Red List assessments. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-550.


Jaramillo-Legorreta A, Rojas-Bracho L, Ver Hoef J, Moore J, Thomas L, Barlow J, Cooke J, Gerrodette T, Taylor B. 2014. Report on vaquita rate of change between 2011 and 2013 using passive acoustic data by the Expert Panel on spatial models. June 24 - 26, 2014, Meeting held at Southwest Fisheries Science Center, La Jolla, CA, USA.


Carretta JV, Moore JE. 2014. Recommendations for pooling annual bycatch estimates when events are rare. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-528.


Dewar, H., T. Eguchi, J. Hyde, D. Kinzey, S. Kohin, J. Moore, B.L. Taylor, and R. Vetter. 2014. Status review of the northeastern Pacific population of white sharks (Carcharodon carcharias) under the Endangered Species Act. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-523.


Punt A.E., and J.E. Moore. 2013. Seasonal gray whales in the Pacific Northwest: An assessment of optimum sustainable population level for the Pacific Coast Feeding Group. U.S. Department of Commerce, NOAA Technical Memorandum NMFS, NOAA-TM-NMFS-SWFSC-518.  Link to report


Weller D.W., Bettridge S., Brownell R.L., Laake J.L., Moore J.E., Rosel P.E., Taylor B.L., Wade P.R. 2013. Report of the National Marine Fisheries Service Gray Whale Stock Identification Workshop. U.S. Department of Commerce, NOAA Technical Memorandum NMFS, NOAA-TM-NMFS-SWFSC-507. Link to report


Moore, J.E., and D.W. Weller. 2013. Probability of taking a western North Pacific gray whale during the proposed Makah hunt. U.S. Department of Commerce, NOAA Technical Memorandum NMFS, NOAA-TM-NMFS-SWFSC-506, 13 p. Link to report


Lewison R.L., Moore J.E. 2012. Improving interview-based assessments of sea turtle and marine mammal bycatch in West Africa: putting fishing activity into a socio-economic context. Project Report prepared for NOAA Office of International Affairs, September 2012.


Moore, J.E. and R. Merrick (eds). 2011. Guidelines for Assessing Marine Mammal Stocks: Report of the GAMMS III Workshop, February 15-18, 2011, La Jolla, California. NOAA Technical Memorandum NMFS-OPR-47. U.S. Department of Commerce. Link to report

Books and book chapters 

Moore JE, Forney KA, Weller DW. Surveys. Chapter 17 in Encyclopedia of Marine Mammals, 2nd ed.

Moore JE, Curtis KA. 2016. Developing control rules for threatened bycatch species. Chapter 14 in Management Science in Fisheries: An Introduction to Simulation-Based Methods. Taylor and Francis.


Moore, J. E. and R. E. Russell. 2004. Empirical considerations for modeling animal movements in human-dominated landscapes. Pages 165-180 in R.K. Swihart and J.E. Moore, editors. Conserving Biodiversity in Agricultural Landscapes: Model-Based Planning Tools. Purdue University Press, West Lafayette, IN.


Russell, R. E., J. E. Moore, M. S. Miller, T. M. Sutton, and S. M. Knapp. 2004. Selecting surrogate species for ecological assessments in land-use planning: a case study in the Upper Wabash River Basin. Pages 181-213 in R.K. Swihart and J.E. Moore, editors. Conserving Biodiversity in Agricultural Landscapes: Model-Based Planning Tools. Purdue University Press, West Lafayette, IN.


Swihart, R. K. and J. E. Moore. 2004. Conserving Biodiversity in Agricultural Landscapes: Model-Based Planning Tools. Purdue University Press, West Lafayette, IN. 


Peer-reviewed journal articles