Hood, G.W., Blauvelt, K., Bottom, D.L., Castro, J.M., Johnson, G.E., Jones, K.K., Krueger, K.L., Thom, R.M., and A. Wilson. 2021. Using landscape ecology principles to prioritize habitat restoration projects across the Columbia River Estuary. Restoration Ecology. Available at http://doi.org/10.1111/rec.13519.

Jones, K.K., Cornwell, T.J., Bottom, D.L., Stein, S., and S. Starcevich. 2021. Interannual variability in life-stage specific survival and life history diversity of coho salmon in a coastal Oregon basin. Can. J. Fish. Aquat. Sci. 78: 1887-1899. Available at https://dx.doi.org/10.1139/cjfas-2020-0306.

Jones, K.K., T.J. Cornwell, D.L. Bottom, S. Stein, and K.J. Anlauf-Dunn. 2018. Population viability improves following termination of Coho Salmon hatchery releases. North American Journal of Fisheries Management 38: 39-55. Available at https://doi.org/10.1002/nafm.10029.

Krueger, K.L., D.L. Bottom, W.G. Hood, G.E. Johnson, K.K. Jones, and R.M. Thom. 2017. An expert panel process to evaluate habitat restoration actions in the Columbia River estuary. Journal of Environmental Management 188: 337-350. Available at http://dx.doi.org/10.1016/j.jenvman.2016.11.028.

Flitcroft, R.L., D.L. Bottom, K.L. Haberman, K.F. Bierly, K.K. Jones, C.A. Simenstad, A. Gray, K.S. Ellingson, E. Baumgartner, T.J. Cornwell, and L.A. Campbell. 2016. Expect the unexpected: place-based protections can lead to unforseen benefits. Aquatic Conservation: Marine and Freshwater Ecosystems 26 (Suppl.1): 39-59. DOI:10.1002/aqc.2660.

Fleming, I.A., D.L. Bottom, K.K. Jones, and C.A. Simenstad. 2014. Resilience of anadromous and resident salmonid populations. Journal of Fish Biology 85(1): 1-7.

Jones, K.K., T.J. Cornwell, D.L. Bottom, L.A. Campbell, and S. Stein. 2014. The contribution of esuary-resident life histories to the return of adult Oncorhynchus kisutch. Journal of Fish Biology 85(1): 52-80. Available at http://onlinelibrary.wiley.com/doi/10.1111/jfb.12380/full.

Stein, S., T.J. Cornwell, and K.K. Jones. 2012. Life history variability, habitat use, and migratory behavior of coastal cutthroat trout in the Salmon River, Oregon. Monitoring Report Number OPSW-ODFW-2012-10, Oregon Department of Fish and Wildlife, Salem.

Jones, K.K., T.J. Cornwell, D. L. Bottom, S. Stein, H. Wellard Kelly, and L.A. Campbell. 2011. Recovery of Wild Coho Salmon in Salmon River Basin, 2008-10. Monitoring Program Report Number OPSW-ODFW-2011-10, Oregon Department of Fish and Wildlife, Salem, OR.

Cornwell, T.J., K.K. Jones, and S. Stein. 2010. Life history variability, habitat use, and migratory behavior of coastal cutthroat trout in the Salmon River, Oregon. Oregon Department of Fish and Wildlife, Fish Research Project 13420-8-J810, Annual Progress Report, Corvallis.

Hering, D.K., D.L. Bottom, E.F. Prentice, K.K. Jones, and I.A. Fleming. 2010. Tidal movements and residency of subyearling Chinook salmon (Oncorhynchus tshawytscha) in an Oregon salt marsh channel. Canadian Journal of Fisheries and Aquatic Sciences 67: 524–533.

Hering, D.K. 2010. Growth, Residence, and Movement of Juvenile Chinook Salmon within Restored and Reference Estuarine Marsh Channels in Salmon River, Oregon. Oregon State University, MS Thesis, Corvallis.

Volk, E.C., D.L. Bottom, K.K. Jones, and C.A. Simenstad. 2010. Reconstructing Juvenile Chinook Salmon Life History in the Salmon River Estuary, Oregon, Using Otolith Microchemistry and Microstructure. Transactions of the American Fisheries Society 139:535–549.

Bottom, D.L., K.K. Jones, C. Simenstad, and C. Smith, editors. 2009. Pathways to Resilient Salmon Ecosystems. Ecology and Society [online] URL - http://www.ecologyandsociety.org/viewissue.php?sf=34.

Bottom, D.L., K.K. Jones, C.A. Simenstad, and C.L. Smith. 2009. Reconnecting social and ecological resilience in salmon ecosystems. Ecology and Society 14(1): 5. [online] URL: http://www.ecologyandsociety.org/vol14/iss1/art5/.

Hering, D.K., T.J. Cornwell, and K.K. Jones. 2009. Abundance, distribution, and migratory behavior of coastal cutthroat trout in two lower Columbia River tributaries. Oregon Department of Fish and Wildlife, Fish Research Project, Progress Report, Corvallis.

Jones, K. K., T.J. Cornwell, D.L. Bottom, D.K. Hering, and S. Stein. 2009. Recovery of Wild Coho Salmon in Salmon River Basin, 2008. Monitoring Program Report Number OPSW-ODFW-2009-10, Oregon Department of Fish and Wildlife, Salem, OR.

Jones, D.S., I.A. Fleming, L.K. McLaughlin, and K.K. Jones. 2008. Feeding ecology of cutthroat trout in the Salmon River estuary, Oregon. Pages 144-151 in P.J. Connolly, T.H. Williams, and R.E. Gresswell, editors. The 2005 coastal cutthroat trout symposium: status, management, biology, and conservation. Oregon Chapter, American Fisheries Society, Portland.

Krentz, L.K. 2007. Habitat Use, Movement, and Life History Variation of Coastal Cutthroat Trout Oncorhynchus clarkii clarkii in the Salmon River Estuary, Oregon. Oregon State University, MS Thesis, Corvallis.

Bieber, A. 2005. Variability in Juvenile Chinook Foraging and Growth Potential in Oregon Estuaries: Implications for Habitat Restoration. M.S. Thesis, School of Aquatic and Fishery Sciences, University of Washington, Seattle.

Bottom, D.L., and 7 co-authors. 2005. Salmon at river’s end: the role of the estuary in the decline and recovery of Columbia River salmon. U.S. Dept. Commerce, NOAA Technical Memorandum NMFS-NWFSC-68.  246p. (see http://www.nwfsc.noaa.gov)

Bottom, D.L., K.K. Jones, T.J. Cornwell, A. Gray, C.A. Simenstad. 2005. Patterns of Chinook salmon migration and residency in the Salmon River estuary (Oregon). Estuarine, Coastal and Shelf Science 64:79-93.

Gray, A.  2005.  The Salmon River estuary: restoring tidal inundation and tracking ecosystem response. Ph.D Thesis, School of Aquatic and Fishery Sciences, University of Washington, Seattle. 208p.

Burke, J.L. 2004. Life histories of juvenile Chinook salmon in the Columbia River Estuary, 1916 to the present. Oregon State University, MS Thesis, Corvallis.

Gray, A., C.A. Simenstad, D.L. Bottom, T.J. Cornwell. 2002. Contrasting functional performance of juvenile salmon habitat in recovering wetlands in the Salmon River estuary, Oregon, U.S.A. Restoration Ecology 10(3): 514-526.

Cornwell, T.J., D.L. Bottom, and K.K. Jones. 2001. Rearing of juvenile salmon in recovering wetlands of the Salmon River Estuary. Oregon Department of Fish and Wildlife, Information Reports 2001-05, Salem.

Bottom, D.L. and K.K. Jones. 1990. Species composition, distribution, and invertebrate prey of fish assemblages in the Columbia River estuary. Progress in Oceanography 25: 243-270.

Jones, K.K., C.A. Simenstad, D.L. Higley, and D.L. Bottom. 1990. Community structure, distribution, and standing stock of benthos, epibenthos, and plankton in the Columbia River estuary. Progress in Oceanography 25: 211-241.

Oregon Estuary Inventory Reports

Bottom, D.,B. Kreag, F. Ratti, C. Roye, and R. Starr.1979. Habitat Classification and inventory methods for the management of Oregon estuaries. Estuary Inventory Report, Volume 1. Oregon Department of Fish and Wildlife, Salem.

Kreag, R.A. 1979. Natural resources of Netarts estuary. Estuary Inventory Report, Volume, No. 1. Oregon Department of Fish and Wildlife, Salem.

Kreag, R.A. 1979. Natural resources of Sand Lake estuary. Estuary Inventory Report, Volume 2, No. 2. Oregon Department of Fish and Wildlife, Salem.

Starr, R.M. 1979. Natural resources of Nestucca estuary. Estuary Inventory Report, Volume 2, No. 3. Oregon Department of Fish and Wildlife, Salem.

Starr, R.M. 1979. Natural resources of Siletz estuary. Estuary Inventory Report, Volume 2, No. 4. Oregon Department of Fish and Wildlife, Salem.

Ratti, F. 1979. Natural resources of Umpqua estuary. Estuary Inventory Report, Volume 2, No. 5. Oregon Department of Fish and Wildlife, Salem.

Roye, C. 1979. Natural resources of Coos estuary. Estuary Inventory Report, Volume 2, No. 6. Oregon Department of Fish and Wildlife, Salem.

Kreag, R.A. 1979. Natural resources of Coquille estuary. Estuary Inventory Report, Volume 2, No. 7. Oregon Department of Fish and Wildlife, Salem.

Ratti, F. 1979. Natural resources of Rogue estuary. Estuary Inventory Report, Volume 2, No. 8. Oregon Department of Fish and Wildlife, Salem.

Ratti, F. 1979. Natural resources of Chetco estuary. Estuary Inventory Report, Volume 2, No. 9. Oregon Department of Fish and Wildlife, Salem.

Oregon Estuary Information and Progress Reports and Gray Literature (selected)

Bottom, D.L., B.A. Miller, and K.K. Jones. 1985. A baseline survey of fish and invertebrates in the lower Umpqua River estuary, Oregon. Oregon Department of Fish and Wildlife, Research and Development Section, Corvallis.

Bottom, D.L., K.K. Jones, and J.D. Rodgers. 1988. Fish community structure, standing crop, and production in upper South Slough (Coos Bay), Oregon. NOAA Technical Report Series OCRM/SPD.

Bottom, D.L., K.K. Jones, J.D. Rodgers, and R.F. Brown. 1989. Management of living marine resources: a research plan for the Washington and Oregon Continental Margin. National Coastal Resources Research and Development Institute NCRI-T-89-004 and Oregon Department of Fish and Wildlife. Newport, Oregon.

Cornwell, T.J., D.L. Bottom, and K.K. Jones. 2001. Rearing of Juvenile salmon in recovering wetlands of the Salmon River Estuary. Information Report 2001-5, Oregon Department of Fish and Wildlife, Salem.

Hancock, D.R., T.F. Gaumer, G.B. Willeke, G.P. Robart, and J. Flynn. 1979. Subtidal Clam Populations: Distribution, Abundance, and Ecology. ORESU-T-79-002, Sea Grant College Program, Oregon State University.

Higley, D.L., and R.L. Holton. 1981. A study of the invertebrates and fishes of salt marshes in two Oregon estuaries. Miscellaneous Report No. 81-5, Oregon State University, prepared for U.S. Army Corps of Engineers.

Johnson, J.A., D.P. Liscia, and D.M. Anderson. 1986. The seasonal occurrence and distribution of fish in the Umpqua estuary, April 1977 through January 1986. Oregon Department of Fish and Wildlife, Salem.

Miller, B.A., D.L. Bottom, and K.K. Jones. 1984. Disposal of seafood waste to enhance recreational fisheries on the Umpqua River estuary. Progress Report, Fish Research Project, Oregon Department of Fish and Wildlife, Salem.

Mullen, R.E. 1977. The occurrence and distribution of Fish in the Umpqua River Estuary, June through October 1972. Information Report 77-3, Oregon Department of Fish and Wildlife, Salem.

Mullen, R.E. 1978. Fishes of the Salmon River Estuary, Oregon. Information Report 79-5, Oregon Department of Fish and Wildlife, Salem.

Reimers, P.E., and K.J. Baxter. 1976. Fishes of the Sixes River, Oregon. Information Report 76-4, Oregon Department of Fish and Wildlife, Salem.