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Publications (journals)
Year: 2017

Takata, L, TR Sommer, JL Conrad, and BM Schreier. 2017. Rearing and migration of juvenile Chinook salmon (Oncorhynchus tshawytscha) in a large river floodplain. Environmental Biology of Fishes.  DOI: 10.1007/s10641-017-0631-0

Corline, NJ., Sommer T, Jeffres CA, Katz J (2017) Zooplankton ecology and trophic resources for rearing native fish on an agricultural floodplain in the Yolo Bypass California, USA. Wetlands Ecology and Management. doi:10.1007/s11273-017-9534-2

Mahardja B, Farruggia MJ, Schreier B, Sommer T (2017) Evidence of a Shift in the Littoral Fish Community of the Sacramento-San Joaquin Delta. PLoS ONE 12(1): e0170683. doi:10.1371/journal.pone.0170683

Year: 2016

Mahardja, B., J. L. Conrad, L. Lusher, and B. Schreier. 2016. Abundance trends, distribution, and habitat associations of the invasive Mississippi Silverside (Menidia audens) in the Sacramento-San Joaquin Delta, California, USA. San Francisco Estuary and Watershed Science. 14(1): Article 2.

Brandl SC, BM Schreier, JL Conrad, B May, and MR Baerwald. 2016. Generation of quantitative polymerase chain reaction detectability half-lives and comparison of sampling protocols for genetic diet studies of San Francisco Estuary fishes. Transactions of the American Fisheries Society 145:3, 441-449

Schreier, BM, MR Baerwald, JL Conrad, G Schumer, and B May. 2016. Examination of predation on early life stage Delta Smelt in the San Francisco Estuary using DNA diet analysis. Transactions of the American Fisheries Society 145: 723-733.

Jeffries, KM, Connon, RE, Bjelde, BE, Komoroske, LM, Britton, MT, Sommer, T, Todgham, AE, Fangue, N. 2016. Effects of high temperatures on threatened estuarine fishes during periods of extreme drought. Journal of Experimental Biology 2019: 1705-1716.

Year: 2015

Brandl S, Schumer G, Schreier BM, Conrad JL, May B, Baerwald MR. 2015. Ten real-time PCR assays for detection of fish predation at the community level in the San Francisco Estuary-Delta. Molecular Ecology Resources 15: 278-284.

Frederick Feyrer, Ken Newman, Matthew Nobriga & Ted Sommer. 2015. Delta Smelt Habitat in the San Francisco Estuary: A Reply to Manly, Fullerton, Hendrix, and Burnham’s “Comments on Feyrer et al. Modeling the Effects of Future Outflow on the Abiotic Habitat of an Imperiled Estuarine Fish”. Estuaries and Coasts DOI 10.1007/s12237-015-9987-6.

Mahardja, B., B. May, F. Feyrer, R. Coalter, N. Fangue, T. Foin, and M. Baerwald. 2015. Interannual variation in connectivity and comparison of effective population size between two splittail (Pogonichthys macrolepidotus) populations in the San Francisco Estuary. Conservation Genetics. 16(2): 385-398. DOI: 10.1007/s10592-014-0665-1.

Year: 2014

Ted R. Sommer, William C. Harrell, Frederick Feyrer. 2014.  Large-bodied fish migration and residency in a flood basin of the Sacramento River, California, USA. Ecology of Freshwater Fish 2014: 23: 414–423

Year: 2013

Feyrer F, Portz D, Odum D, Newman KB, Sommer T, et al. (2013) SmeltCam: Underwater Video Codend for Trawled Nets with an Application to the Distribution of the Imperiled Delta Smelt. PLoS ONE 8(7): e67829. doi: 10.1371/journal.pone.0067829

Sommer, Ted, and Francine Mejia, 2013, A place to Call Home: A Synthesis of Delta Smelt Habitat in the Upper San Francisco Estuary,  San Francisco Estuary and Watershed Science 11(2), 27 p.

del Rosario, Rosalie B.; Redler, Yvette J.; Newman, Ken; Brandes, Patricia L.; Sommer, Ted; Reece, Kevin;  Vincik, Robert. 2013.
Migration Patterns of Juvenile Winter-run-sized Chinook Salmon (Oncorhynchus tshawytscha) through the Sacramento–San Joaquin Delta. San Francisco Estuary and Watershed Science, 11(1).1-22.

Ferrari, M.C.O, L. Ranåker, K.L. Weinersmith, M.J. Young, A. Sih, and J.L. Conrad. 2013. Effects of turbidity and an invasive waterweed on predation by introduced largemouth bass. Environmental Biology of Fishes. Published online March 2013

Year: 2012

Loboschefsky, Erik; Benigno, Gina; Sommer, Ted; Rose, Kenneth; Ginn, Timothy; Massoudieh, Arash;  et al.(2012).
Individual-level and Population-level Historical Prey Demand of San Francisco Estuary Striped Bass Using a Bioenergetics Model. San Francisco Estuary and Watershed Science, 10(1).

Year: 2011

Massoudieh, A., E. Loboschefsky, T. Sommer , T. Ginn, K. Rose, F. Loge. 2011. Spatio-temporal modeling of striped bass egg and larval movement and fate in the San Francisco Bay-Delta. Ecological Modeling. (in press)

Sommer, T., F, Mejia, M. Nobriga, F. Feyrer, and L. Grimaldo. The Spawning Migration of Delta Smelt in the Upper San Francisco Estuary (pdf, 470 kb).  San Francisco Estuary and Watershed Science (2011) 9 (2), 16 pages

Sommer, T., F. Mejia, K. Hieb, R. Baxter, E. J. Loboschefsky and F. J. Loge. 2011. Long-term shifts in the lateral distribution of age-0 striped bass Morone saxatilis in the San Francisco estuary (pdf, 425 kb). Transactions of the American Fisheries Society (2011) 140: 1451-1459

Year: 2010

James A. Hobbs., Levi S. Lewis., Naoaki Ikemiyagi., Ted Sommer and Randall D. Baxter. 2010. The use of otolith strontium isotopes (87Sr/86Sr) to identify nursery habitat for a threatened estuarine fish (pdf, 300 kb). Environ Biol Fish (2010) 89:557–569

Henery, Rene E., Ted R. Sommer, and Charles R. Goldman. 2010. Growth and Methylmercury Accumulation in Juvenile Chinook Salmon in the Sacramento river and Its Floodplain, the Yolo Bypass, Transactions of the American Fisheries Society, 139: 550-563.

Feyrer, Fredrick, Newman, Ken, Nobriga, Matthew, Sommer, Ted. (2010). Modeling the Effects of Future Outflow on the Abiotic Habitat of an Imperiled Estuarine Fish. Estuaries and Coasts. DOI 10.1007/s12237-010-9343-9

Feyrer, Frederick, Hobbs, James, & Sommer, Ted. (2010). Salinity Inhabited by Age-0 Splittail (Pogonichthys macrolepidotus) as Determined by Direct Field Observation and Retrospective Analyses with Otolith Chemistry. San Francisco Estuary and Watershed Science, 8(2). http://escholarship.org/uc/item/14j5160h

Year: 2009

Feyrer, F., T. Sommer and S. Slater. 2009. Old School vs. New School: Status of Threadfin Shad Five Decades after its Introduction to the Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science. Vol. 7, Issue 1, Article 3.

Grimaldo, Lenny F., Ted Sommer, Nick Van Ark, Gardner Jones, Erika Holland, Peter Moyle, Bruce Herbold, and Pete Smith. 2009. Factors affecting fish entrainment into massive water diversions in a freshwater tidal estuary: Can fish losses be managed? North American Journal of Fisheries Management 29:1253-1270, 2009.

Lehman, P.W., S.J. Teh, G.L. Boyer, M.L. Nobriga, E. Bass, and C. Hogle. 2009. Initial impacts of Microcystis aeruginosa blooms on the aquatic food web in the San Francisco Estuary. Hydrobiologia (in press) DOI 10.1007/s10750-009-9999-y

Lehman, P.W., S. Mayr, L. Mecum, and C. Enright. 2009. The freshwater tidal wetland Liberty Island, CA was both a source and sink of inorganic and organic material to the San Francisco Estuary. Aquatic Ecology (in press) DOI 10.1007/s10452-009-9295-y.

Year: 2008

Benigno, Gina M. and Ted R. Sommer. 2008. Just add water: sources of chironomid drift in a large river floodplain (pdf, 300 kb). Hydrobiologia DOI 10.1007/s10750-007-9239-2

Kimmerer, Wim J. and Matthew L. Nobriga. 2008. Investigating Particle Transport and Fate in the Sacramento-San Joaquin Delta Using a Particle Tracking Model. San Francisco Estuary and Watershed Science. Vol. 6, Issue 1 (February), Article 4.

Lehman, P. W., T. Sommer & L. Rivard, 2008. The influence of floodplain habitat on the quantity of riverine phytoplankton carbon produced during the flood season in San Francisco Estuary. Aquatic Ecology 42: 363-378.

Nobriga, M., T. Sommer, F. Feyrer, and K. Fleming. 2008. Long-term trends in summertime habitat suitability for delta smelt, Hypomesus transpacificus. San Francisco Estuary and Watershed Science.

Sommer, T., W.C. Harrell, and T. R. Swift, 2008. Extreme hydrologic banding in a large-river Floodplain, California, U.S.A. Hydrobiologia 598:409-415.

Sommer, T., B. Harrell, Z. Matica, and F. Feyrer. 2008. Habitat associations and behavior of adult and juvenile splittail (Cyprinidae: Pogonichthys macrolepidotus) in a managed floodplain wetland. San Francisco Estuary and Watershed Science. Vol. 6, Issue 2 (June), Article 3.

Year: 2007
Baerwald, M., V. Bien, F. Feyrer, and B. May. 2007. Microsatellite analysis reveals two genetically8 distinct splittail (Pogonichthys macrolepidotus) populations in the San Francisco Estuary.9 Conservation Genetics. 8:159-167.

Sommer, T., C. Armor, R. Baxter, R. Breuer, L. Brown, M. Chotkowski, S. Culberson, F. Feyrer, M. Gingras, B. Herbold, W. Kimmerer, A. Mueller-Solger, M. Nobriga, and K. Souza. 2007. The collapse of pelagic fishes in the upper San Francisco Estuary. Fisheries 32:270-277.

Feyrer, F., T. Sommer, and J. Hobbs, 2007. Living in a dynamic environment: variability in life history traits of age-0 splittail in tributaries of San Francisco Bay. Transactions of the American Fisheries Society 136:1393-1405.

Feyrer, F., M. Nobriga, and T. Sommer. 2007. Multi-decadal trends for three declining fish species: habitat patterns and mechanisms in the San Francisco Estuary, California, U.S.A. Canadian Journal of Fisheries and Aquatic Sciences 64:723-734.

Nobriga, M., and F. Feyrer. 2007. Shallow-water piscivore-prey dynamics in the Sacramento-San Joaquin Delta. San Francisco Estuary and Watershed Science Vol5 (Article4), Iss2 May 2007

Sommer, T., R. Baxter, and F. Feyrer. 2007. Splittail revisited: how recent population trends and restoration activities led to the "delisting" of this native minnow. Pages 25-38 in M.J. Brouder and J.A. Scheuer, editors. Status, distribution, and conservation of freshwater fishes of western North America. American Fisheries Society Symposium 53. Bethesda, Maryland.

Cranston, P.S., G.M. Benigno, and M.C. Domingeuz. 2007. Hydrobaenus saetheri Cranston, new species, an aestivating, winter-emerging chironomid (Diptera: Chironomidae) from California. Pages 73-79 in Contributions to the Systematics and Ecology of Aquatic Diptera-A tribute to Ole A. Saether. T. Andersen, editor. The Caddis Press

Feyrer, F., J.A. Hobbs, M. Baerwald, T. Sommer, Q. Yin, K. Clark, B.P. May, and W.A. Bennett. 2007. Otolith microchemistry provides information complimentary to microsatellite DNA for a migratory fish. Transactions of the American Fisheries Society 136:469-476.

Year: 2006
Feyrer, F, T. Sommer, and W. Harrell. 2006. Managing floodplain inundation for native fish: production dynamics of age-0 splittail in California's Yolo Bypass. Hydrobiologia 573:213-226.

Feyrer, F, T. Sommer, and W. Harrell. 2006. Importance of flood dynamics versus intrinsic physical habitat in structuring fish communities: evidence from two adjacent engineered floodplains on the Sacramento River, California. North American Journal of Fisheries Management 26:408-417.

Nobriga, M., F. Feyrer, and R. Baxter. 2006. Aspects of Sacramento pikeminnow biology in nearshore habitats of the Sacramento-San Joaquin Delta. Western North American Naturalist 66:106-114.

Year: 2005
Sommer, T, W. Harrell, and M. Nobriga. 2005. Habitat use and stranding risk of juvenile Chinook slamon on a seasonal floodplain. North American Journal of Fisheries Management 25:1493-1504.

Nobriga, M., F. Feyrer, R. Baxter, and M. Chotkowski. 2005. Fish community ecology in an altered river delta: spatial patterns in species composition, life history strategies, and biomass. Estuaries 28:776-785

Feyrer, F., T.R. Sommer, and R. Baxter. 2005. Spatial-temporal distribution and habitat associations of age-0 splittail in the lower San Francisco Estuary Watershed. Copeia 2005:159-168.

Kimmerer, W., S. Avent, S. Bollens, F. Feyrer, L. Grimaldo, P. Moyle, M. Nobriga, and T. Visintainer. 2005. Variability in length-weight relationships used to estimate biomass of estuarine fishes from survey data. Transactions of the American Fisheries Society 134:481-495.

Year: 2004
Sommer, T.R., W.C. Harrell, A. Mueller-Solger, B. Tom, and W. Kimmerer. 2004. Effects of flow variation on channel and floodplain biota and habitats of the Sacramento River, California, USA. Aquatic Conservation: Marine and Freshwater Ecosystems 14:247-261.

Moyle, P.B., R.D. Baxter, T.R. Sommer, T.C. Foin, and S.A. Matern. 2004. Biology and population dynamics of Sacramento splittail (Pogonichthys macrolepidotus) in the San Francisco Estuary: a review. San Francisco Estuary and Watershed Science 2:2(May 2004), Article 3. Available from SFEWS

Feyrer, F., T.R Sommer, S.C. Zeug, G. O'Leary, and W. Harrell. 2004. Fish assemblages of perennial floodplain ponds of the Sacramento River, California (USA), with implications for the conservation of natives fishes. Fisheries Management and Ecology 11:335-344.

Schemel, L.E., T.R. Sommer, A.B. Muller-Solger, and W.C. Harrell. 2004. Hydrologic variability, water chemistry, and phytoplankton biomass in a large floodplain of the Sacramento River, CA, USA. Hydrobiologia 513:129-139.

Feyrer, F., L.R Brown, R.L Brown, and J.J Orsi, editors. 2004. Early Life History of Fishes in the San Francisco Estuary and Watershed. American Fisheries Society, Symposium 39, Bethesda, Maryland. Available from AFS

Feyrer, F. 2004. Ecological segregation of native and alien larval fish assemblages in the southern Sacramento-San Joaquin Delta. Pages 67-79 in F. Feyrer, L.R. Brown, R.L. Brown, and J.J. Orsi, editors. Early Life History of Fishes in the San Francisco Estuary and Watershed. American Fisheries Society, Symposium 39, Bethesda, Maryland.

Grimaldo, L.F, R.E. Miller, C.M. Peregrin, and Z.P Hymanson. 2004. Spatial and temporal distribution of ichthyoplankton in three habitat types of the Sacramento-San Joaquin Delta. Pages 81-96 in F. Feyrer, L.R. Brown, R.L. Brown, and J.J. Orsi, editors. Early Life History of Fishes in the San Francisco Estuary and Watershed. American Fisheries Society, Symposium 39, Bethesda, Maryland.

Culberson, S.D., C.B. Harrison, C. Enright, and M.L. Nobriga. 2004. Sensitivity of larval fish transport to location, timing, and behavior using a particle tracking model in Suisun Marsh, California. Pages 257-267 in F. Feyrer, L.R. Brown, R.L. Brown, and J.J. Orsi, editors. Early Life History of Fishes in the San Francisco Estuary and Watershed. American Fisheries Society, Symposium 39, Bethesda, Maryland.

Nobriga, M.L, Z. Matica, and Z.P Hymanson. 2004. Evaluating entrainment vulnerability to agricultural irrigation diversions: A comparison among open-water fishes. Pages 281-295 in F. Feyrer, L.R. Brown, R.L. Brown, and J.J. Orsi, editors. Early Life History of Fishes in the San Francisco Estuary and Watershed. American Fisheries Society, Symposium 39, Bethesda, Maryland.

Sommer, T.R., W.C. Harrell, R. Kurth, F. Feyrer, S.C. Zeug, and G. O'Leary. 2004. Ecological patterns of early life stages of fishes in a river-floodplain of the San Francisco Estuary. Pages 111-123 in F. Feyrer, L.R. Brown, R.L. Brown, and J.J. Orsi, editors. Early Life History of Fishes in the San Francisco Estuary and Watershed. American Fisheries Society, Symposium 39, Bethesda, Maryland.

Year: 2003
Feyrer, F. and M. Healey. 2003. Fish community structure and environmental correlates in the highly altered southern Sacramento-San Joaquin Delta. Environmental Biology of Fishes 66:123-132.

Feyrer, F., B. Herbold, S.A. Matern, and P.B. Moyle. 2003. Dietary shifts in a stressed fish assemblage: Consequences of a bivalve invasion in the San Francisco Estuary. Environmental Biology of Fishes 67:277-288.

Harrell, W.C. and T.R. Sommer. 2003. Patterns of Adult Fish Use on California's Yolo Bypass Floodplain. Pages 88-93 in P.M. Faber, editor. California riparian systems: Processes and floodplain management, ecology, and restoration. 2001 Riparian Habitat and Floodplains Conference Proceedings, Riparian Habitat Joint Venture, Sacramento, California.

Sommer, T.R., W.C. Harrell, M.L. Nobriga and R. Kurth. 2003. Floodplain as habitat for native fish: Lessons from California's Yolo Bypass. Pages 81-87 in P.M. Faber, editor. California riparian systems: Processes and floodplain management, ecology, and restoration. 2001 Riparian Habitat and Floodplains Conference Proceedings, Riparian Habitat Joint Venture, Sacramento, California.

Toft, J.D., C.A. Simenstad, J.A. Cordell, and L.F. Grimaldo. 2003. The effects of introduced water hyacinth on habitat structure, invertebrate assemblages, and fish diets. Estuaries 26:746-758.

Year: 2002
Feyrer, F. and M. Healey. 2002. Structure, sampling gear and environmental associations, and historical changes in the fish assemblage of the southern Sacramento-San Joaquin Delta. California Fish and Game 88:126-138.

Nobriga, M.L. 2002. Larval delta smelt diet composition and feeding incidence: environmental and ontogenetic influences. California Fish and Game 88:149-164.

Sommer, T., L. Conrad, G. O'Leary, F. Feyrer, and W. Harrell. 2002. Spawning and rearing of splittail in a model floodplain wetland. Transactions of the American Fisheries Society 131:966-974.

Year: 2001
Uriu-Adams, J.Y., C.K. Reece, L.K. Nguyen, B.J. Horvath, R. Nair, R.A. Barter, & C.L. Keen. 2001. Effect of butyl benzyl phthalate on reproduction and zinc metabolism. Toxicology 159:55-68.

Veldhuizen, T. 2001. Life history, distribution, and impacts of the Chinese mitten crab, Eriocheir sinensis. Aquatic Invaders 12:1-9.

Sommer, T.R., D. McEwan and R. Brown. 2001. Factors affecting chinook salmon spawning in the lower Feather River. California Department of Fish and Game Fish Bulletin 179:269-297.

Sommer, T., M. L. Nobriga, B. Harrell, W. Batham, & W. J. Kimmerer. 2001. Floodplain rearing of juvenile chinook salmon: evidence of enhanced growth and survival. Canadian Journal of Fisheries and Aquatic Sciences 58:325-333.

Sommer, T., B. Harrell, M. Nobriga, R. Brown, P. Moyle, W. Kimmerer, and L. Schemel. 2001. California's Yolo Bypass: evidence that flood control can be compatible with fisheries, wetlands, wildlife, and agriculture. Fisheries 26:6-16.

Year: 1998
Feyrer, F. and R. Baxter. 1998. Splittail fecundity and egg size. California Fish and Game 84:119-126.

Year: 1998
Sommer, T., R. Baxter, and B. Herbold. 1997. Resilience of splittail the the Sacramento-San Joaquin Estuary. Transactions of the American Fisheries Society 126:961-976.