*= student author

In review

Carlton, J.T., Chapman, J.W., Geller, J.G., Miller, J.A., Ruiz, G.M., Carlton, D.A., McCuller, M.I., Treneman, N., Lewis, R., Bilderback, D., Harris, L. In review. Biological and ecological studies of Japanese Tsunami Marine Debris (JTMD). Aquatic Invasions.

Hurst, T. P., Miller, J. A., Ferm, N., Heintz, R. A., and Farley, E. V. In review. Spatial variation in potential and realized growth of juvenile Pacific cod in the Bering Sea. Marine Ecology Progress Series.

Pearcy, W. and Miller, J. A. In review. Otolith microchemistry of coastal cutthroat trout from Marys and Willamette Rivers.

*Litz, M. N. C., Miller, J. A., Brodeur, R. D., Daly, E. A., Weitkamp, L. A., and Hansen, A. G. In review. Energy dynamics of subyearling Chinook salmon reveal the importance of piscivory to short-term growth during early marine residence. Fisheries Oceanography.

In revision

Wilson, M. T., Dougherty, A., Matta, M. E., Mier, K. L., and Miller, J. A. In revision. Geographic variation in otolith chemistry of age-0 juvenile walleye pollock (Gadus chalcogrammus) in relation to regional hydrography. Marine Ecology Progress Series.

Miller, J. A., Carlton, J.T., Chapman, J.W., Geller, J. B., Ruiz, G.M. Accepted pending revisions. Transoceanic dispersal of the mussel Mytilus galloprovincialis on Japanese tsunami marine debris: A model for evaluating rafting of a coastal species at sea. Marine Pollution Bulletin.

Miller, J. A., *Gillman, R., Carlton, J.T., Clarke-Murray, C., Nelson, J. C., Otani, M., and Ruiz, G. M. Accepted pending revisions. Trait-based characterization of species transported on JTMD: Effect of prior invasion history on trait distribution. Marine Pollution Bulletin.


Matta, M. E., Miller, J. A., Short, J., Helser, T., Hurst, T. P. Rand, K., Ormseth, O. 2017. Spatial and temporal variation in otolith elemental signatures of age-0 Pacific cod (Gadus macrocephalus) in the Gulf of Alaska. Deep Sea Research Part II: Topical Studies in Oceanography.

**Ta, N., Miller, J. A., Chapman, J. C., Pleus, A. E., Calvanese, T., Miller-Morgan, T., Burke, J., and Carlton, J. T. C. In review. The Western Pacific barred knifejaw, Oplegnathus fasciatus (Temminck & Schlegel, 1844) (Pisces: Oplegnathidae) arriving with tsunami debris on the Pacific coast of North America. Aquatic Invasions.

*Litz, M. C. N., Miller, J. A., Copeman, L. A., and Hurst, T. P. 2017. Effects of dietary fatty acids on juvenile salmon growth, biochemistry, and aerobic performance: a laboratory rearing experiment. Journal of Experimental Marine Biology and Ecology.

Miller, J. A., Peterson, W. T., Du, X. N., Morgan, C. A., and *Litz, M. N. C. 2017. Temporal variation in the biochemical ecology of lower trophic levels in the Northern California Current: implications for mid-level trophic productivity. Progress in Oceanography.

*Fedewa, E. J., Miller, J. A., Hurst, T. P., and Jiang, D. 2017. The potential effects of pre-settlement processes on post-settlement growth and survival of juvenile northern rock sole (Lepidopsetta polyxystra) in Gulf of Alaska nursery habitats. Estuarine, Coastal and Shelf Science.

*Litz, M. N.C., Miller, J. A., Copeman, L. A., Teel, D. J., Weitkamp, L. A., Daly, E. A., and Claiborne, A. M. 2017. Ontogenetic shifts in the diets of juvenile Chinook salmon: new insight from stable isotopes and fatty acids. Environmental Biology of Fishes. 

*Smith, W. D., Miller, J. A., Fernando Márquez-Farías, J., and Heppell, S. S. 2016. Elemental signatures reveal the geographic origins of a highly migratory shark: prospects for measuring population connectivity. Marine Ecology Progress Series.

Burke, B. J., Anderson, J. J., Miller, J. A., *Tomaro, L., Banas, N. S., and Baptista, A. M. 2016. Estimating behavior in a black box: How coastal oceanographic dynamics influence yearling Chinook salmon marine growth and migration behaviors. Environmental Biology of Fishes. 99(8):671-686.

*Marin Jarrin, J. R. Teel, D. J., and Miller, J. A. 2016. Stock-specific movement and distribution of juvenile Chinook salmon, Oncorhynchus tshawytscha, in sandy beach surf zones of Oregon and Washington, USA. Estuaries and Coasts.

*Fedewa, E. J., Miller, J. A., Hurst, T. P. 2015. Pre-settlement processes of northern rock sole (Lepidopsetta polyxystra) in relation to interannual variability in the Gulf of Alaska. Journal of Sea Research.

*Marin Jarrin, J. R. and Miller, J. A. 2015. Spatial variability of the surf zone fish and macroinvertebrate community within Oregon dissipative sandy beaches, U.S.A. Marine Ecology.

Hart, L. M., Bond, M. H., May-McNally, S. L., Miller, J. A., and Quinn, T. P. 2015. Use of otolith microchemistry and stable isotopes to investigate the ecology and anadromous migrations of Northern Dolly Varden from the Egegik River, Bristol Bay, Alaska. Environmental Biology of Fishes. DOI 10.1007/s10641-015-0389-1. [PDF]

Bond, M. H., Miller, J. A., and Quinn, T. P. 2015. Beyond dichotomous life histories in partially migrating populations: Cessation of anadromy in a long-lived salmonid. Ecology 96(7):1899-1910.

Miller, J. A., *DiMaria, R. A., Hurst, T.P. 2014. Patterns of larval source distribution and mixing in early life stages of Pacific cod (Gadus macrocephalus) in the southeastern Bering Sea. Deep-Sea Research II. [PDF]

*Losee, J. P. Miller, J. A., Peterson, W. T., Teel, D. J., and Jacobson, K. C. 2014. Influence of ocean ecosystem variability on trophic interactions and survival of juvenile coho and Chinook salmon. Canadian Journal of Fisheries & Aquatic Sciences 71:1747-1757. [PDF]

*Claiborne, A. M., Miller, J. A, Weitkamp, L. A., Teel, D. J., Emmett, R. L. 2014. Evidence for selective mortality in marine environments: the role of fish migration size, timing, and production type. Marine Ecology Progress Series 515:187-2014. [PDF]

Calder, D. R., Choong, H.H. C., Carlton, J. T., Chapman, J. W., Miller, J. A., Geller, J. 2014. Additional hydroids (Cnidaria: Hydrozoa) from Japanese tsunami debris stranding in the northwestern United States. Aquatic Invasions 9:425-440. [PDF]

*Liberoff, A. L., Quiroga, A. P., Riva-Rossi, C. M., Miller, J. A., Pascual, M. A. 2014. Influence of maternal habitat choice, environment and spatial distribution of juveniles on their propensity for anadromy in a partially anadromous population of rainbow trout (Oncorhynchus mykiss). Ecology of Freshwater Fish. doi:10.1111/eff.12157. [PDF]

Miller, J. A., Teel, D. J., Peterson, W. T., and Baptista, A. 2014. Assessing the relative importance of local and regional processes on the survival of a threatened salmon population. PLOS ONE. [PDF]

Daly, E. A., Scheurer, J. A., Brodeur, R. D., Weitkamp, L. A., Beckman, B. R., and Miller, J. A. 2014. Juvenile steelhead distribution, migration, feeding, and growth in the Columbia River estuary, plume, and coastal waters. Marine and Coastal Fisheries: Dynamics, Management, and Ecosystem Science 6:1, 62-80. [PDF]

*Liberoff, A. L., Miller, J. A., Riva Rossi, C. M., Hidalgo, F. J., Fogel, M. L., and Pascual, M. A. 2014. Transgenerational effects of anadromy on juvenile growth traits in an introduced population of rainbow trout (Oncorhynchus mykiss). Canadian Journal of Fisheries & Aquatic Sciences. 71:398-407. [PDF]

*Marin Jarrin, J. R. and Miller, J. A. 2013. Sandy beach surf zones: an alternative habitat for 0-age Chinook salmon. Estuarine, Coastal and Shelf Science. 135:220-230. [PDF]

*Smith, W. D., J. A. Miller, and Heppell, S. S. 2013. Elemental markers in elasmobranchs: effects of environmental history and growth on vertebral chemistry. PLoS ONE. 8(10): e62423. doi:10.1371/journal.pone.0062423. [PDF]

Miller, J. A., Teel, D. J., Baptista, A., and Morgan, C. A. 2013. Disentangling bottom-up and top-down effects on survival during early ocean residence in a population of Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries & Aquatic Sciences. 70:617-629. [PDF]

Hurst, T. P., *Fernandez, E.R., Mathis, J. T., Miller, J.A., Sintson, C.M., *Ahgeak, E.F. 2012. Resiliency of juvenile walleye pollock to projected levels of ocean acidification. Aquatic Biology 17:247-259. [PDF]

Hurst, T. P., Moss, J. H., and Miller, J. A. 2012. Distributional patterns of 0-group Pacific cod (Gadus macrocephalus) in the eastern Bering Sea under variable recruitment and thermal conditions. ICES Journal of Marine Science 69(2):163-174. [PDF]

*Tomaro, L., Teel, D. J., Peterson, W. P., and Miller, J. A.  2012. Early marine residence of Columbia River spring Chinook salmon: when is bigger better? Marine Ecology Progress Series 452:237-252. [PDF]

Miller, J. A. 2011. Effects of water temperature and barium concentration on otolith composition along a salinity gradient: implications for migratory history. Journal of Experimental Marine Biology and Ecology. 405:42-52.

Miller, J. A., Butler, V. L., Simenstad, C. A., Backus, D. H., and Kent, A. J. R. 2011. Life history variation in Columbia River Chinook salmon (Oncorhynchus tshawytscha): a comparison using modern and ~500 yr-old archaeological otoliths. Canadian Journal of Fisheries and Aquatic Sciences. 68:603-617.

Miller, J. A., Wells, B. K., Sogard, S. M., Grimes, C. B., and Cailliet, G. C. 2010. Introduction to Proceedings of the 4th International Otolith Symposium. Environmental Biology of Fishes. 89:203-207.

Shanks, A. L., Roegner, G. C., and Miller, J. A. 2010. Using megalopae abundance to predict future commercial catches of Dungeness crabs in Oregon. CALCOFI Rep. 51:106-118.

*DiMaria, R. A., Miller, J. A., and Hurst, T. 2010. Temperature and growth effects on otolith elemental chemistry of larval Pacific cod, Gadus macrocephalus. Environmental Biology of Fishes. 89:453-462.

Miller, J. A., Gray, A., and Merz, J. 2010. Quantifying the contribution of juvenile migratory phenotypes in a population of Chinook salmon (Oncorhynchus tshawytscha). Marine Ecology Progress Series. 408:227-240.

Miller, J. A., Bellinger, M. R., Golden J. T., *Gibson, L., and Banks, M. A. 2010. Integration of natural and artificial markers in a mixed stock analysis of Chinook salmon (Oncorhynchus tshawytscha). Fisheries Research 102:152-159.

Miller, J. A. 2009. The effects of temperature and water concentration on the otolith incorporation of barium and manganese in juvenile black rockfish (Sebastes melanops Girard). Journal of Fish Biology. 75:39-60.

Miller, J. A. and Kent, A. J. R. 2009. The determination of maternal run time in Chinook salmon (Oncorhynchus tshawytscha) based on Sr/Ca and 87Sr/86Sr within otolith cores. Fisheries Research. 95:373-378.

Miller, J. A. 2007. Scales of variation in the otolith elemental chemistry of juvenile staghorn sculpin (Leptocottus armatus) in three Pacific Northwest estuaries. Marine Biology 151:483-494.

Miller, J. A. and Shanks, A. L. 2005. Abundance and distribution of larval and juvenile fish in Coos Bay, Oregon: a time-series analysis based on light-trap collections. Marine Ecology Progress Series 305:177-191. [PDF]

Miller, J. A., Banks, M. A., Gomez-Uchida, D., and Shanks A. L. 2005. A comparison of population structure in black rockfish (Sebastes melanops) as determined with otolith microchemistry and microsatellite DNA. Canadian Journal of Fisheries and Aquatic Sciences 62(10):2189-2198.

Miller, J. A. and Shanks, A. L. 2004. Evidence for limited larval dispersal in black rockfish (Sebastes melanops): Implications for population structure and marine reserve design. Canadian Journal of Fisheries and Aquatic Sciences 61:1723-1735.

Miller, J. A. and Shanks, A. L. 2004. Ocean-estuary coupling in the Oregon upwelling region: the abundance and transport of juvenile fish and of crab megalopae. Marine Ecology Progress Series 271:267-279. [PDF]

Shanks, A. L., McCulloch, A., and Miller, J. A. 2003. Topographically generated fronts, very nearshore oceanography and the distribution of larval invertebrates and holoplankters. Journal of Plankton Research 25(10):1251-1277.

Miller, J. A. and Simenstad, C. A. 1997. A comparative assessment of natural and created estuarine sloughs as rearing habitat for juvenile Chinook and coho salmon. Estuaries (20)4:796-806.