Lab PUBLICATIONS

LAB PUBLICATIONS

*author was an OSU graduate student; †author was a student at another institution; **author was an undergraduate

*Blaisdell, J., *Thalmann, H. L., *Klajbor, W., Zhang, Y., Miller, J. A., Laurel, B. J., Kavanaugh, M. 2021. A Dynamic stress-scape framework to evaluate potential effects of multiple environmental stressors on Gulf of Alaska juvenile Pacific Cod. Frontiers in Marine Science.

Claiborne, A. M., Losee, J. P., Miller, J. A. 2020. Estimating migratory behavior and age for anadromous Coastal Cutthroat Trout Oncorhynchus clarkii clarkii in South Puget Sound: evaluation of approaches based on fish scales versus otoliths. North American Journal of Fisheries Management.

†Cavole, L.M., Miller, J.A., Salinas-de-Leon, P., Aburto-Oropeza, O., Marin Jarrin, J.R., Johnson, A. F. 2020. The role of extrinsic variation: cohabiting juvenile fish species exhibit similar otolith elemental signatures. Marine Ecology Progress Series.

Miller, J. A. and Hurst, T. P. 2020. Growth rate, ration, and temperature effects on otolith elemental incorporation. Frontiers in Marine Science.

*Ramirez, M.D, Miller, J. A., **Parks, E., Avens, L., Goshe, L. R. Seminoff, J. A., Snover, M. L., and Heppell, S. S. Accepted. Reconstructing sea turtle ontogenetic habitat shifts through trace element analysis of bone tissue. Marine Ecology Process Series.

*Litz, M. N. C., Miller, J. A., Brodeur, R. D., Daly, E. A., Weitkamp, L. A., and Hansen, A. G. 2018. Energy dynamics of subyearling Chinook salmon reveal the importance of piscivory to short-term growth during early marine residence. Fisheries Oceanography.

*Andrade, J. F., Hurst, T. P., and Miller. J. A. 2018. Behavioral responses of a coastal flatfish to predation-associated cues and elevated CO₂. J. of Sea Research.

Pearcy, W. and Miller, J. A. 2018. Otolith microchemistry of coastal cutthroat trout from Marys and Willamette Rivers. Northwestern Naturalist.

Hurst, T. P., Miller, J. A., Ferm, N., Heintz, R. A., and Farley, E. V. 2018. Spatial variation in potential and realized growth of juvenile Pacific cod in the Bering Sea. Marine Ecology Progress Series.

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. 2018. Biological and ecological studies of Japanese Tsunami Marine Debris (JTMD). Aquatic Invasions.

Wilson, M. T., Dougherty, A., Matta, M. E., Mier, K. L., and Miller, J. A. 2018. Geographic variation in otolith chemistry of age-0 juvenile walleye pollock (Gadus chalcogrammus) in relation to regional hydrography. Marine Ecology Progress Series. 588:163-178.

**Ta, N., Miller, J. A., Chapman, J. C., Pleus, A. E., Calvanese, T., Miller-Morgan, T., Burke, J., and Carlton, J. T. C. 2018. 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.

Elvin, D. W., Carlton, J. T., Geller, J. B., Chapman, J. W., Miller, J. A. 2018. Porifera (Sponges) from Japanese Tsunami Marine Debris arriving in the Hawaiian Islands and on the Pacific coast of North America. Aquatic Invasions 13(1):31-41.

Choong, H. C., Calder, D. R., Chapman, J. W., Miller, J. A., Geller, J. B., Carlton, J. T. 2018. Hydroids (Cnidaria: Hydrozoa: Leptothecata and Limnomedusae) on 2011 Japanese tsunami marine debris landing in North America and Hawai‘i, with revisory notes on Hydrodendron Hincks, 1874 and a diagnosis of Plumaleciidae, new family. Aquatic Invasions 13(1):43-70

Miller, J. A., Carlton, J.T., Chapman, J.W., Geller, J. B., Ruiz, G.M. 2018 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. 2018. Trait-based characterization of species transported on JTMD: Effect of invasion prior invasion history on trait distribution. Marine Pollution Bulletin.

Carlton, J.T., Chapman, J.W., Geller, J.G., Miller, J. A., Carlton, D.A., McCuller, M.I., Treneman, N., Steves, B. P., Ruiz, G.M. 2017. Tsunami-driven rafting: Transoceanic species dispersal and implications for marine biogeography. Science. 357:1402-1406 [Highlighted on Cover].

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 II.

*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.

*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.

Miller, J. A., Peterson, W. T., Du, X., 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.

*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. 2016. 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. 2016. Spatial variability of the surf zone fish and macroinvertebrate community within Oregon dissipative sandy beaches, U.S.A. Marine Ecology.

Miller, J. A.,*DiMaria, R. A., Hurst, T.P. 2016. 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.

†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 98:1633-1643.

†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(6):1899-1910.

†Liberoff, A. L., Quiroga, A. P., Riva-Rossi, C. M., Miller, J. A., Pascual, M. A. 2015. Influence of maternal habitat choice, environment and spatial distribution of juveniles in a partially anadromous rainbow trout (Oncorhynchus mykiss) for adoption of alternative migratory tactics. Ecology of Freshwater Fish. 24(3):424-434.

*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 515:187-202.

*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.

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. Biological Invasions 9(4).

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 an endangered salmon population. PLOS ONE.

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.

†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.

*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.

*Smith, W. D., Miller, J. A., and Heppell, S.S. 2013. Elemental markers in elasmobranchs: effects of environmental history and growth on vertebral chemistry. PLoS ONE. 8(10): e62423.

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.

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

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.

*Tomaro, L., Teel, D. A., 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.

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 4^th 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. (IC, EA, A, F, W)

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.

Miller, J. A., M. A. Banks, D. Gomez-Uchida, 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.

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.