Bruce MacFarlane

Research Interests:

Physiological Ecology of Marine, Estuarine, and Anadromous Fishes

My research focuses on the functional relationships of fishes to their environment. Animals are adapted to the environmental conditions in which they have evolved and now live, yet for a variety of natural and anthropogenic reasons these conditions change. Projects seek to understand the environmental requirements of fish and the consequences of changing conditions. Results from these studies not only improve knowledge of the animal’s biology, but also improve their management and conservation.

Research focuses on juvenile salmonids in streams, estuaries, and the coastal ocean of California. Declines in the abundance of Chinook salmon, coho salmon, and steelhead in California have resulted in most stocks being listed by the U.S. Endangered Species Act. Although many aspects of salmon biology have been well studied, surprisingly little is known about their estuarine and early ocean life history phases. My research addresses key issues such as survival, energy metabolism, growth, trophic interactions, migratory patterns, and interspecies competition to learn more about their effects on survival and fitness. Salmonid responses to environmental conditions existing in California, the southern end of the species’ ranges, are likely to differ from those of stocks in the middle of their distributions in the Pacific Northwest where most information on salmonid biology originated previously. Thus, knowledge of salmonid adaptations to conditions in California will expand understanding of the range of biological variability and provide guidance for resource managers in salmon conservation and recovery.

More information: Salmon Ocean Ecology Team

Additional Information:

Selected Publications:

Wells, B.K., J.A. Santora, J.C. Field, R.B. MacFarlane, B.B. Marinovic, and W.J. Sydeman. An ecosystem perspective for quantifying the dynamics of juvenile Chinook salmon (Oncorhynchus tshawytscha) and prey in the central California coastal region. (In review, Marine Ecology Progress Series)

Hayes, S.A., C.V. Hanson, D.E. Pearse, M.H. Bond, J.C. Garza, and R.B. MacFarlane. Should I stay or should I go? The influence of genetic origin on emigration behavior and physiology of resident and anadromous juvenile Oncorhynchus mykiss. (In review, Transactions of the American Fisheries Society)

Sandstrom, P.T., A.J. Ammann, C. Michel, G. Singer, E.D. Chapman, S. Lindley, R.B. MacFarlane, and A.P. Klimley. Tag retention by steelhead trout (Oncorhynchus mykiss) and its application to survival estimates and behavioral assessments. (In review, Environmental Biology of Fishes)

Klimley, A.P., P.T. Sandstrom, S.T. Lindley, and R.B. MacFarlane. Insights into salmon migration from innovations in electronic tagging: past, present, and future. (In review, Environmental Biology of Fishes)

Weber, P.K., R. Barnett-Johnson, J.D. Wikert, M. Workman, C.P. Philis, R.B. MacFarlane, A.K. Schmitt, and M.J. Grove. Hatchery or natural origin: comparison of methods to determine success of integrated hatchery management. (In review, Canadian Journal of Fisheries and Aquatic Sciences)

Perry, R.W., P.L. Brandes, J.R. Burau, A.P. Klimley, B. MacFarlane, C. Michel, and J.R. Skalski. Sensitivity of survival to migration routes used by juvenile Chinooks salmon to negotiate the Sacramento-San Joaquin River Delta. (In press, Environmental Biology of Fishes)

Ammann, A.J., N.J. Delaney, C.J. Michel, and R.B. MacFarlane. The effects of surgically implanted acoustic tags on laboratory growth, survival and swimming performance of hatchery yearling Chinook salmon. (In press, Environmental Biology of Fishes)

Michel, C.J., A.J. Ammann, E.D. Chapman, P.T. Sandstrom, H.E. Fish, M.J. Thomas, G.P. Singer, S.T. Lindley, A.P. Klimley, and R.B. MacFarlane. The effects of environmental factors on the migratory movement patterns of Sacramento River yearling late-fall run Chinook salmon (Oncorhynchus tshawytscha). (In press, Environmental Biology of Fishes)

Chapman, E.D., A.R. Hearn, C. Michel, A.J. Ammann, S.T. Lindley, M.J. Thomas, P.T. Sandstrom, G.P. Singer, M.L. Peterson, R.B. MacFarlane, and A.P. Klimley. Diel movements of outmigrating Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) smolts in the Sacramento/San Joaquin watershed. (In press, Environmental Biology of Fishes)

Johnson, R.C., P.K. Weber, J.D. Wikert, M.L. Workman, R.B. MacFarlane, M.J. Grove, and A.K. Schmitt. 2012. Managed Metapopulations: Do Salmon Hatchery ‘Sources’ Lead to In-River ‘Sinks’ in Conservation? PLoS ONE 7(2): e28880. doi:10.1371/journal.pone.0028880.

Hayes, S.A., N.M. Teutschel, C.J. Michel, C. Champagne, P.W. Robinson, T. Yack, D. Mellinger, S. Simmons, D.P. Costa, and R.B. MacFarlane. Mobile receivers: releasing the mooring to ‘see’ where fish go. Environmental Biology of Fishes DOI 10.1007/s10641-011-9940-x.

Ammann, A., C. Michel, and R.B. MacFarlane. 2011. The effects of surgically implanted acoustic transmitters on laboratory growth, survival, and tag retention in hatchery yearling Chinook salmon. Environmental Biology of Fishes DOI 10.1007/s10641-011-9941-9

Harding, J.A., A.J. Ammann, and R.B. MacFarlane. 2011. Regional and seasonal patterns of epipelagic fish assemblages from the central California Current. Fishery Bulletin 109:261-281.

Hayes, S.A., M.H. Bond, C.V. Hanson, A.W. Jones, A.J. Ammann, J.A. Harding, A.L. Collins, J. Perez, and R.B. MacFarlane. Down, Up, Down and "smolting" twice? 2011. Seasonal movement patterns by juvenile steelhead in a coastal watershed with a bar closing estuary. Canadian Journal of Fisheries and Aquatic Sciences 68:1341-1350.

Hayes, S.A., M.H. Bond, B.K. Wells, C.V. Hanson, A.W. Jones, and R.B. MacFarlane. 2011. Using archival tagging to infer habitat use of central California steelhead and coho salmon. American Fisheries Society Symposium 76:1-22.

MacFarlane, R.B. 2010. Energy dynamics and growth of juvenile Chinook salmon (Oncorhynchus tshawytscha) from the Central Valley of California during the estuarine phase and first ocean year. Canadian Journal of Fisheries and Aquatic Sciences 67:1549-1565.

Ralston, S. and R.B. MacFarlane. 2010. Population estimation of bocaccio (Sebastes paucispinis) based on larval production in the Southern California Bight. Canadian Journal of Fisheries and Aquatic Sciences 67:1005-1020.

Lindley, S.T., C.B. Grimes, M.S. Mohr, W. Peterson, J. Stein, J. Anderson, C. Busack, L. Botsford, T. Collier, D. Bottom, A. Grover, D. Hankin, R. Kope, P. Lawson, A. Low, J. Ferguson, B. MacFarlane, M. Palmer-Swahlen, F. Schwing, J. Smith, C. Tracy, R. Webb, and B. Wells. 2010. What caused the Sacramento River fall Chinook salmon stock collapse? NOAA Technical Memorandum NMFS-SWFSC-447. 121 p.

Perry, R.W., P.L. Brandes, P.T. Sandstrom, A. Ammann, B. MacFarlane, A.P. Klimley, and J.R. Skalski. 2010. Estimating survival and migration route probabilities of juvenile Chinook salmon in the Sacramento-San Joaquin River Delta. North American Journal of Fisheries Management 30:142-156.

Pearse, D.E., S.A. Hayes, M.H. Bond, C.V. Hanson, E.C. Anderson, R. B. MacFarlane, and J.C. Garza. 2009. Over the falls? Rapid evolution of ecotypic differentiation in steelhead/rainbow trout (Oncorhynchus mykiss). Journal of Heredity 100:515-525.

Sturm, E.A., E.A. Gilbert-Horvath, J.C. Garza, and R.B. MacFarlane. 2009. Creation of a captive broodstock for southern coho salmon (Oncorhynchus kisutch): results from the initial rearing and spawning of the first brood year. NOAA Tech Memorandum NMFS-SWFSC-436. 61p.

Bond, M.H., S.A. Hayes, C.V. Hanson, and R.B. MacFarlane. 2008. Marine survival of steelhead (Oncorhynchus mykiss) enhanced by a seasonally closed estuary. Canadian Journal of Fisheries and Aquatic Sciences 65:2242-2252.

Barnett-Johnson, R., T.E. Pearson, F.C. Ramos, C.B. Grimes, and R. B. MacFarlane. 2008. Tracking natal origins of salmon using isotopes, otoliths, and landscape geology. Limnology & Oceanography 53(4): 1633-1642.

Hayes, S.A., M. H. Bond, C.V. Hanson, E.V. Freund, J.J. Smith, E. Anderson, A. Ammann, and R. B. MacFarlane. 2008. Steelhead growth in a small central California watershed: upstream and estuarine rearing patterns. Transactions of the American Fisheries Society 137:114-128.

Williams, J.G., J.J. Anderson, S. Greene, C. Hanson, S.T. Lindley, A. Low, B.P. May, E. McEwan, M.S. Mohr, R.B. MacFarlane, and C. Swanson. 2007. Monitoring and research needed to manage the recovery of threatened and endangered Chinook and steelhead in the Sacramento-San Joaquin basin. NOAA Tech. Memo. NMFS-SWFSC-399.

Bond, M.H., C.V. Hanson, R. Baertsch, S.A. Hayes, and R.B. MacFarlane. 2007. A new low-cost instream antenna system for tracking passive integrated transponder (PIT) tagged fish in small streams. Transactions of the American Fisheries Society 136:562-566.

Lindley, S.T., R.S. Schick, E. Mora, P.B. Adams, J.J. Anderson, S. Greene, C. Hanson, B.P. May, D.R. McEwan, R.B. MacFarlane, C. Swanson, and J.G. Williams. 2007. Framework for assessing viability of threatened and endangered Chinook salmon and steelhead in the Sacramento-San Joaquin basin. San Francisco Estuary and Watershed Science 5(1) http://repositories.cdlib.org/jmie/sfews/vol5/iss1/art4

Trudel, M., M.E. Theiss, C. Bucher, E.V. Farley, Jr., R.B. MacFarlane, E. Casillas, J. P. Fisher, J.F.T. Morris, J.M. Murphy, and D.W. Welch. 2007. Regional variation in marine growth and energy accumulation of juvenile Chinook salmon and coho salmon along the west coast of North America. American Fisheries Society Special Symposium 57:205-232.

Fisher, J., M. Trudel, A. Ammann, J. Orsi, J. Piccolo, C. Bucher, E. Casillas, J. Harding, R.B. MacFarlane, R. Brodeur, J. Morris, and D.W. Welch. 2007. Comparisons of the coastal distributions and abundances of juvenile Pacific salmon from central California to the northern Gulf of Alaska. American Fisheries Society Special Symposium 57:31-80.

Lindley, S.T., R.S. Schick, A. Agrawal, M. Goslin, T. Pearson, E. Mora, J.J. Anderson, B. May, S. Greene, C. Hanson, A. Low, D. McEwan, R.B. MacFarlane, C. Swanson, and J.G. Williams. 2006. Historical population structure of Central Valley steelhead and its alteration by dams. San Francisco Estuary and Watershed Science 4(1): http://repositories.cdlib.org/cgi/viewcontent.cgi?article=1041&context=jmie/sfews

Barnett-Johnson, R., F.C. Ramos, C.B. Grimes, and R.B. MacFarlane. 2005. Validation of Sr isotopes in otoliths by laser ablation multicollector inductively coupled plasma mass spectrometry (LA-MC-ICPMS): opening avenues in fisheries science applications. Canadian Journal of Fisheries and Aquatic Sciences 62:2425-2430.

MacFarlane, R.B., S. Ralston, C. Royer, and E.C. Norton. 2005. Juvenile chinook salmon (Oncorhynchus tshawytscha) growth on the central California coast during the 1998 El Niño and 1999 La Niña. Fisheries Oceanography 14:321-332.

Hayes, S.A., M.H. Bond, C.V. Hanson, and R.B. MacFarlane. 2004. Interactions between endangered wild and hatchery salmonids; can the pitfalls of artificial propagation be avoided in a small coastal stream? Journal of Fish Biology 65 (Supplement A):101-121.

Lindley, S.T., R. Schick, B.P. May, J.J. Anderson, S. Greene, C. Hanson, A. Low, D. McEwan, R.B. MacFarlane, C. Swanson, and J.G. Williams. 2004. Population structure of threatened and endangered Chinook salmon ESUs in California’s Central Valley basin. NOAA Technical Memorandum NOAA-TM-NMFS-SWFSC-360, 66p.

Barnett-Johnson, R., F.C. Ramos, C.B. Grimes, and R.B. MacFarlane. 2004. Determining production sources and spatial structure of Chinook salmon using otolith geochemical markers. In Third International Symposium and Fish Otolith Research and Application Abstracts. Townsville, Australia, p. 83.

Eldridge, M.B., E.C. Norton, B.M. Jarvis, and R.B. MacFarlane. 2002. Energetics of early development in the viviparous yellowtail rockfish. Journal of Fish Biology 61:1122-1134.

MacFarlane, R.B., S. Ralston, C. Royer, and E.C. Norton. 2002. Influences of the 1997-1998 El Niño and 1999 La Niña on juvenile chinook salmon in the Gulf of the Farallones. PICES Scientific Report No. 20:25-29.

MacFarlane, R.B. and E.C. Norton. 2002. Physiological ecology of juvenile chinook salmon (Oncorhynchus tshawytscha) at the southern end of their distribution, the San Francisco Estuary and the Gulf of the Farallones, California. Fishery Bulletin 100:244-257.