To obtain copies of my publications please visit my Google Scholar cite

Selected Publications


*indicates student coauthor  **indicates postdoc coauthor in the Nye lab

O’Leary C*, TJ Miller, J Thorson, JA Nye (accepted). Understanding historical Summer Flounder (Paralichthys dentatus) abundance patterns through the incorporation of oceanography-dependent vital rates in Bayesian hierarchical models. Canadian Journal of Fisheries and Aquatic Sciences.

J Grear, O’Leary, C**, JA Nye, S Tettelbach, CJ Gobler, (in review). Effects of coastal acidification on North Atlantic bivalves: Scaling up laboratory experiments to in situ populations using matrix modelling approaches. Marine Ecology Progress Series

Nye, J. A., M. G. Frisk, R. M. Cerrato, M. Sclafani, C. N. Flagg, S. R. Sagarese and J. A. Olin. (2018). Effects of a storm-induced barrier breach on community assemblages and ecosystem structure within a temperate lagoonal estuary: A post Hurricane Sandy analysis. Natural Resource Report NPS/NER/NRR—2018/1702. National Park Service, Fort Collins, Colorado.

Thomas, A, A Pershing, KD Friedland, JA Nye, KE Mills, MA Alexander, NR Record, R Weatherbee, ME Henderson (2017) Seasonal trends in phenology shifts in sea surface temperature on the North American northeast shelf. Elementa: Science of the Anthropocene

Alexander, MA, JD Scott, KD Friedland, KE Mills, JA Nye, AJ Pershing and AC Thomas. (2018). Projected sea surface temperatures over the 21st century: changes in the mean, variability and extremes. Elementa: Science of the Anthropocene

Xu, H**, TJ Miller, S Hameed, L Alade, JA Nye. (2018) Evaluating model fit and forecast performance after incorporating the Gulf Stream Index into Southern New England yellowtail flounder state-space age-structured assessment model. Fisheries Oceanography

Henderson, ME**, A Thomas, K Mills, A Pershing and JA Nye (2018). Effects of spring temperature phenology on fish species distribution and biomass along the Northeast United States Continental Shelf Reviews in Fish Biology and Fisheries

Morse, RE*, K Friedland, D Tommasi, C Stock, JA Nye (2017). Distinct zooplankton regime shift patterns across ecoregions of the U.S. Northeast continental shelf Large Marine Ecosystem. Journal of Marine Systems 165: 77-91.

Pershing, AJ, MA Alexander, CM Hernandez, LA Kerr, A Le Bris, KE Mills, JA Nye, GD Sherwood. (2016). Response to Comments on “Slow adaptation in the face of rapid warming leads to collapse of the Gulf of Maine cod fishery”. Science352(6284), 423-423

Friedland KD, NR Record, RG Asch, T Kristiansen, VS Saba, KF Drinkwater, S Henson, RT Leaf, RE Morse, DG Johns, SI Large, S Hjollo, JA Nye, MA Alexander, R Ji. (2016) Seasonal phytoplankton blooms in the North Atlantic linked to the overwintering strategies of copepods. Elementa: Science of the Anthropocene 4:000099

Pershing,  A. J., M. A. Alexander, C. M. Hernandez, L. A. Kerr, A. Le Bris, K. E. Mills, J. A. Nye, N. R. Record, H. A. Scannell, J. D. Scott, G. D. Sherwood,  A. C. Thomas (2015). Slow adaptation in the face of rapid warming leads to the collapse of an iconic fishery. Science 350 (6262): 809-812.

Xu, H.*, Hye-Mi Kim, JA Nye, and S Hameed  (2015) Impacts of North Atlantic Oscillation on Sea Surface Temperature on the Northeast US Continental Shelf.  Continental Shelf Research 105: 60-66.

Lynch PD**, Nye JA, Hare JA, Stock CA, Alexander MA, Scott JD, Curti KL, Drew K (2015) Projected ocean warming poses a challenge to anadramous river herring populations. ICES Journal of Marine Science

Tommasi, D.**, J.A. Nye, C. Stock, J. Hare, M. Alexander, K. Drew (2015).  Effect of environmental conditions on river herring freshwater survival: a coastwide perspective.  Canadian Journal of Fisheries and Aquatic Sciences 72(7): 1037-1047.

Nye, J.A., M. Baker, R. Bell, A. Kenny, K.H. Kilbourne, K.D. Friedland, E. Martino, M. Stachura, K.S. Van Houtan, and R. Wood. 2014. Ecosystem effects of the Atlantic Multidecadal Oscillation.  Journal of Marine Systems 133: 103-116

Alexander, M., J.A. Nye, and K. Kilbourne. 2014.  AMO: Measurement, Mechanisms and Relations to other Climate Patterns.  Journal of Marine Systems 133: 14-26.

K.H. Kilbourne, M.A. Alexander, and J.A. Nye. 2014. A low latitude paleoclimate perspective on Atlantic multidecadal variability. Journal of Marine Systems 133: 4-13

Friedland, K.D., B. V. Shank, C. D. Todd, P. McGinnity, J.A. Nye. 2014.  Differential response of continental stock complexes of Atlantic salmon (Salmo salar) to the Atlantic Multi-decadal Oscillation. Journal of Marine Systems 133: 77-87

Alheit, J., Drinkwater, K.F. and J.A. Nye.  2014. Introduction to Special Issue: Atlantic Multidecadal Oscillation-mechanism and impact on marine ecosystems. Journal of Marine Systems 133: 1-3.

Friedland, K.D., J. Kane, J.A. Hare, R.G. Lough, P.S. Fratantoni, M.J. Fogarty, and J.A. Nye. 2013. Thermal habitat constraints on zooplankton species associated with Atlantic cod (Gadus morhua) on the US Northeast Continental Shelf. Progress in Oceanography 113: 1-13

Mills K, Pershing A, Brown C, Chen Y, Chiang F, Holland D, Lehuta S, Nye J, Sun J, Thomas A. 2013. Fisheries management in a changing climate: Lessons from the 2012 ocean heat wave in the Northwest Atlantic. Oceanography 26(2): 191-195.

Nye, J.A., R. Gamble, and J.S. Link. 2013. Relative impact of warming and removing top predators on the Northeast US large marine ecosystem. Ecological Modelling 264: 157-168.

McClure MM, Alexander M, Borggaard D, Boughton D, Crozier L, Griffis R, Jorgensen JC, Lindley ST, Nye J, Rowland MJ. 2013. Incorporating climate science in applications of the US Endangered Species Act for aquatic species. Conservation Biology 27:1222-1233

Snover AK, Mantua NJ, Littell JS, Alexander MA, Mcclure MM, Nye J.  2013. Choosing and Using Climate‐Change Scenarios for Ecological‐Impact Assessments and Conservation Decisions. Conservation Biology 27:1147-1157

Fogarty, M.J. and 13 others. 2012  Status of the Northeast U.S. Continental Shelf Large Marine Ecosystem: An Indicator-Based Approach (In: Advancing an Ecosystem Approach in the Gulf of Maine. American Fisheries Society Symposium 79)

Hare, J., J. Manderson, J. A. Nye,  M. Alexander, P. Auster, D. Borggaard, A. Capatondi, K. Damon-Randall, E. Huepel, I. Mateo, L. O’Brien, D. Richardson, C. Stock, S. T. Biegel.  2012.  Cusk (Brosme brosme) and climate change: assessing the threat to a data poor candidate species under the Endangered Species Act. ICES Journal of Marine Science 69(10): 1753-1768.

Shackell, N., A. Bundy, J.A. Nye, and J.S. Link. 2012.  Coherent responses to climate and fishing across large marine ecosystems of the Northwest Atlantic ICES Journal of Marine Science 69(2): 151-162.

Nye, J.A. T.M. Joyce, Y. Kwon, and J.S. Link. 2011.  Silver hake tracks changes in Northwest Atlantic circulation.  Nature communications 2: 412 doi: 10.1038/ncomms1420

Nye, J.A.., D. Loewensteiner, and T.J. Miller 2011.  Annual, seasonal and regional variability in the diet of Atlantic croaker Micropogonias undulatus in Chesapeake Bay.  Estuaries and Coasts 34: 691-700.

Link, J.S., J.A. Nye, and J.A. Hare. 2010.  Guidelines for incorporating fish distribution shifts into a fisheries management context. Fish and Fisheries 12(4): 461-469.

Lucey, S. and J.A. Nye. 2010.  Changes in community structure within the Northeast US continental shelf ecosystem.  Marine Ecology Progress Series 415: 23-33

Moustahfid, H., M.C. Tyrell, J.S. Link, J.A. Nye, B.E. Smith, and R.J. Gamble. 2010.  Functional feeding responses of piscivorous fishes from the northeast US continental shelf Oecologia 163 (4): 1059-1067.

Nye, J.A., A. Bundy, N. Shackell, K.D. Friedland, and J.S. Link. 2010. Synchrony in the abundance trends of major commercial and ecologically important fishes in the Gulf of Maine ecosystem.  ICES Journal of Marine Science 67(1): 26-40.

Nye, J.A., J.S. Link, J.A. Hare, and W.J. Overholtz. 2009.  Changing spatial distribution of fish stocks in relation to climate and population size on the Northeast US continental shelf. Marine Ecology Progress Series 393:111-129

Nye, J.A., T.E. Helser, and T.E. Targett. 2008.  Reproductive characteristics of weakfish in Delaware Bay: implications for management.  North American Journal of Fisheries Management 28(1): 1-11.

Nye, J.A., D.D. Davis, and T.J. Miller. 2007.  The effect of maternal exposure to contaminated sediment on the growth and condition of larval Fundulus heteroclitus.  Aquatic Toxicology 82: 242-250.