University of Oregon

Alan Shanks – Professor Emeritus

Professor Marine Biology


Ph.D. Marine Biology, 1985. Scripps Institution of Oceanography, University of California, San Diego. Thesis Title: The effects of larval behavior and distribution on the cross shelf dispersal of coastal crabs. Thesis Advisor: Dr. James Enright.
B.A. With Honors, 1977. University of California, Santa Cruz


Mail:   OIMB, P.O. Box 5389,
Charleston OR, 97420
Phone:   (541) 888-2581 x 277
Fax:   (541) 888-3250

Graduate Students

*Alan no longer takes graduate students*


Alumni (recent)

Brittney Dlouhy (MS)
Marley Jarvis (PhD) 

Cate Prtichard (MS)
Laura Garcia Peteiro (Postdoc)
Leif Rasmuson (PhD)
Alexa Romersa (MS)
Carlissa Salant (MS)
Mike Thomas (MS)


BI 390 Animal Behavior
BI 458/558 Biological Oceanography

Selected Publications



Morgan, S.G., A.L. Shanks, A.G. Fujimura, A. J. H. M. Reniers, J. MacMahan, C. D. Griesemer, M. Jarvis, and J. Brown (In Press) Surfzone hydrodynamics as a key determinant of spatial variation in rocky intertidal communities. Royal Society of London, Proc. B.

Shanks, A.L. S.G. Morgan, J. MacMahan, A.J.H.M. Reniers, R. Kudela, M. Jarvis, J. Brown, A. Fujimura, L. Ziccarelli, C. Griesemer (2016) Variation in the Abundance of Pseudo-nitzschia and Domoic Acid with Surf Zone Type. Harmful    Algal Blooms 55:172-178.

Pritchard, C., A.L. Shanks, R. Rimler, M. Oates, and S. Rumrill. (2015). The Olympia oyster Ostrea lurida: Recent advances in natural history ecology and restoration. Journal of Shellfish Research 34:259-271.

Peteiro, L.G. and A.L. Shanks (2015). Up and down or how to stay in the bay: retentive strategies of Olympia oyster larvae in a shallow estuary. Marine Ecology Progress Series. Doi:10.3354/meps11283. 530:103-117.

Shanks, A.L., S. G. Morgan, J. MacMahan, Ad J.H.M Reniers, M. Jarvis, J. Brown, and C. Griesemer (2015). Transport of Larvae and Detritus Across the Surf Zone of a Steep Reflective Pocket Beach. Marine Ecology Progress Series doi 10.3354/meps11223

Brown, J.A., J. H. MacMahan, A.J.H.M. Reniers, E. B. Thornton, A.L. Shanks, S.G.Morgan, and E.L. Gallagher (In Revision). Mixing and Transport on a Steep Beach. Continental Shelf Research.

Rasmuson, L., A.L. Shanks (2014). In situ observations of Dungeness crab, Cancer magister, megalopae used to estimate transport distances by internal waves. Marine Ecology Progress Series. 511:143-152. doi: 10.3354/meps10926.

Fujimura, A., Reniers, A., Claire Paris, C., Shanks, A.L., MacMahan, J., and Morgan, S. (2014). Numerical simulations of larval transport into a rip-channeled surf zone. Limnology and Oceanography 56:1434-1447.

Shanks, A.L., A. Walser, L. Shanks (2014) Population structure, northern           range limit, and recruitment variation in the intertidal limpet Lottia scabra. Marine Biology. DOI 10.1007/s00227-014-2400-3

Shanks, A.L., S. G. Morgan, J. MacMahan, Ad J.H.M Reniers, M. Jarvis, J. Brown, and C. Griesemer (2014). Onshore transport of plankton by internal tides and upwelling-relaxation events. Marine Ecology Progress Series, DOI10.3354/meps10717

Fujimura, A., Reniers, A., Claire Paris, C., Shanks, A.L., MacMahan, J., and Morgan, S. (2013). Slope-dependent biophysical modeling of surf zone larval transport. Coastal Dynamics 2013 pp. 661-670.

Leis, J., Caselle, J., Bradbury, I., Kristiansen, T, Llopiz, J., Miller, M., O’Connor, M., Paris-Limouzy, C., Sogard, S., Shanks, A., Swearer, S., Treml, E., Vetter, R.,Warner, R. (2013) Does fish larval dispersal differ between high and low latitudes? Proceedings of the Royal Society B. 280,20130327

Shanks, A.L. (2013) Atmospheric Forcing Drives Recruitment Variation in the Dungeness Crab (Cancer magister), Revisited. Fishery Oceanography 22: 263-272.

Dunn, P. H. and A.L. Shanks (2012). Mating success of female Dungeness crabs (Cancer magister) in Oregon coastal waters. Journal of Shellfish  Research 31(3): 1–5.

Lord, J.P. and A.L. Shanks (2012). Continuous growth facilitates feeding and reproduction: impact of size on energy allocation patterns for organisms with indeterminate growth. Marine Biology DOI 10.1007/s00227-012-1918-5

Cooper, E.E. and A. L. Shanks (2011). Latitude and coastline shape correlate with age-structure of Chlorostoma (Tegula) funebralis populations. Marine Ecology Progress Series. 424:133-143.

Shanks, A.L. and R.K. Shearman (2011). Thread-drifting juvenile Mytilus spp. in continental shelf waters off Coos Bay, Oregon USA. Marine Ecology Progress Series. 427:105-115.

Marin Jarrin, J.R. and A.L. Shanks (2011). Spatio-temporal dynamics of the surf-zone faunal assemblages at a southern Oregon sandy beach. Marine Ecology. 32: 232-242

Shanks, A.L., S.G. Morgan, J. MacMahan, and A. J.H.M Reniers (2010). Surf zone hydrodynamics as determinants of temporal and spatial  variation in larval recruitment. Journal of Experimental Marine Biology and Ecology.392:140-150.

Shanks, A.L., J. A. Miller, and G.C. Roegner (2010). Predicting the Future Commercial Catch of Dungeness Crabs. California Cooperative Oceanic Fisheries Investigations Reports. 51:1-13.

Davidson, T.M., A.L. Shanks, and S. S. Rumrill (2009) The composition and density of fauna utilizing burrow microhabitats created by a non-native burrowing crustacean (Sphaeroma quoianum). Biol. Invasions DOI 10.1007/s10530-009-9556-7

Shanks, A.L. (2009). Barnacle Settlement vs. Recruitment as Indicators of Larval Delivery: Effects of Post-settlement Mortality and Recruit Density. Marine Ecology Progress Series. 385:205-216

Hodder, J. and A.L. Shanks (2009). Bridging the gap: spanning the distance between high school and college education: Faculty Response. Frontiers in Ecology. 7:221-222

Shanks, A.L. and C.A. Pfister (2009). Annual recruitment of three species of tidepool fishes is driven by variation in springtime coastal hydrodynamics. Limnology and Oceanography. 54:1481-1487.

Shanks, A.L. and R.K. Shearman (2009) Paradigm lost? Cross-shelf distributions of intertidal invertebrate larvae were unaffected by upwelling or downwelling. Marine Ecology Progress Series. 385:189-204.

Shanks, A.L. (2009). Barnacle Settlement vs. Recruitment as Indicators of Larval Delivery: Time series analysis and Hypothesized Delivery Mechanisms. Marine Ecology Progress Series. 385:217-226.

Shanks, A.L. (2009). Pelagic Larval Duration and Dispersal Distance Revisited. Biological Bulletin. 216:373-385.

Emlet, R.B., S.A. Maslakova, A.L. Shanks, and C.M. Young. (2009). Virtual Symposium: Biology of Marine Invertebrate Larvae. Biological Bulletin. 216:201-202

Marin Jarrin, J.R., Shanks, A.L., and Banks, M.A. (2009). Confirmation of the presence and use of sandy beach surf-zones by juvenile Chinook salmon. Environmental Biology of Fishes. DOI 10.1007/s10641-009-9470-y.

Davidson, T.M., Rumrill, S.S., and Shanks, A.L.(2008). Colonization and substratum preference of an introduced burrowing crustacean in a temperate estuary. Journal of Experimental Marine Biology and Ecology 354:144-149.

Marin Jarrin, J.R. Shanks A.L. (2008) Ecology of a population of Lissocrango stylirostris (Caridea: Cragonidae) with notes on the occurrence and biology of its parasite, Argeia pugettensis (Isopoda: Bopyridae). Journal of Crustacean Biology 28:613-621.

Shanks, A.L. and Roegner, G.C., (2007) Recruitment-limitation in Dungeness crab populations is driven by temporal variation in atmospheric forcing. Ecology 88:1726-1737.

Shanks, A.L. and L. Brink (2005, Feature Article). Upwelling, downwelling, and cross-shelf transport of bivalve larvae: test of a hypothesis. Marine Ecology Progress Series. 302:1-12

Miller, J. A., M. A. Banks, D. Gomez-Uchida, and A. L. Shanks. (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, 62:2189-2198.

Miller, J. A. and A. L. Shanks. (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.

Shanks, A.L. and Eckert, G. (2005). Life-History Traits and Population Persistence of California Current Fishes and Benthic Crustaceans; Solution of A Marine Drift Paradox. Ecological Monographs 75:505-524.

Miller, J. A. and A. L. Shanks. (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 larval invertebrates. Marine Ecology Progress Series 271:267-279.

McCulloch, A.A. and Shanks, A.L. (2003). Topographically generated fronts, very nearshore oceanography and the settlement of mussel larvae and barnacle cyprids. Journal of Plankton Research 25:1427-1439.

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

Shanks, A. L., McCulloch, A.A. (2003) Fortnightly Periodicity in the Abundance of Diatom and Dinoflagellate Taxa at a Coastal Study Site. Journal of Experimental Marine Biology and Ecology 296:113-126.

Shanks, A.L. and McCulloch, A.A. (2003). Topographically Generated Fronts, Very Nearshore Oceanography and The Distribution of Chlorophyll, Detritus and Selected Diatom and Dinoflagellate Taxa. Marine Biology 143:969-980.

Roegner, G.C., Armstrong, D.A., Hickey, B.M., and Shanks, A.L. (2003). Ocean distribution and recruitment of Dungeness crab megalopae to estuaries in southern Washington State. Estuaries 26(4b):1058-1070.

Shanks, A.L., Largier, J., and Brubaker, J. (2003). Observations on the distribution of meroplankton during an upwelling event. Journal of Plankton Res. 25: 645-667.

Johnson, K.B. and A.L. Shanks. (2003). Low rates of predation on planktonic marine invertebrate larvae. Marine Ecology Progress Series. 248:125-139.

Shanks, A.L., Grantham, B., and Carr, M. (2003). Propagule Dispersal Distance and the Size and Spacing of Marine Reserves. Ecological Applications 13: S159-S169.

Grantham, B.A., G.L. Eckert, and A.L. Shanks (2003). Dispersal potential of marine invertebrates in diverse habitats Ecological Applications 13: S108-S116.

Sponaugle, S, Cowen, R.K., Shanks, A.L., Morgan, S.G., Leis, J.M., Pineda, J., Boehlert, G.W., Kingsford, M.J., Lindeman, K., Grimes, C., and Munro, J.L. (2002). Predicting self-recruitment in marine populations: Biophysical correlates and mechanisms. Bulletin of Marine Science. 70(1) Suppl.: 341-375.

Johnson, J. and A.L. Shanks (2002). Time series of the Abundance of the Post larvae of the crabs Cancer magister and Cancer spp. on the Southern Oregon Coast and their cross-shelf transport. Estuaries 25: 1138-1142.

Shanks, A. L. (2002) Internal Tides and the Biology of Continental Shelf         Waters. In: The Oceanography and Ecology of the Nearshore and Bays in Chile. Eds. Juan C. Castilla and John L. Largier. Ediciones Universidad Catolica de Chile, Santiago, Chile. pp. 3-27.

Shanks, A.L. (2002). The Abundance, Vertical Flux, and Still Water Gravitational and in situ Sinking Rates of Marine Snow in a Shallow Coastal Water Column. Continental Shelf Research. 22: 2045-2064.

Shanks, A.L., J. Largier, L. Brink, J. Brubaker and R. Hoff. (2002). Observations on the distribution of meroplankton during a downwelling event and associated intrusion of the Chesapeake Bay estuarine plume. Journal of Plankton Res. 24: 391-416.

Kingsford, M. J., J. Leis, A. L. Shanks K. Lindeman, S. Morgan and J. Pineda (2002). Sensory Environments, larval abilities and local self-recruitment. Bulletin of Marine Science. 70(1) Suppl.: 309-340

Roegner, G.C., Hickey, B., Newton, J., Shanks, A.L., and Armstrong, D. (2002). Wind-induced plume and bloom intrusions into Willapa Bay, Washington. Limnology and Oceanography. 47: 1033-1042

Shanks, A.L. (2002). Previous Agonistic Experience Determines the Pattern of Foraging in Territorial and Non-territorial Lottia gigantea  (Sowerby). Behavioral Ecology 13: 467-471.

Roegner, G.C. and A.L. Shanks (2001). Import of coastally-derived chlorophyll a to South Slough, Oregon. Estuaries. 24: 244-256.

Shanks, A.L., J. Largier, L. Brink, J. Brubaker and R. Hoff. (2000). Demonstration of the onshore transport of larval invertebrates by the shoreward movement of an upwelling front. Limnology and Oceanography. 45: 230-236

Amend, M. and A.L. Shanks. 1999. The timing of larval release in the mole crab. Emerita talpoida. Marine Ecology Progress Series. 183: 295-300.

Shanks, A.L. 1998. Abundance of post-larval Callinectes sapidus, Penaeus spp., Uca spp., and Labinia spp. collected at an outer coastal site and their cross-shelf transport. Marine Ecology Progress Series. 168: 57-69.

Shanks, A.L. 1998. Apparent oceanographic triggers to the spawning of the limpet Lottia digitalis. Journal of Experimental Marine Biology and Ecology. 222: 31-42.

Johnson, K.B. and Shanks, A.L. 1997. Predation upon meroplankton: Assessing the risk at near-natural prey densities and in the presence of background plankton. Marine Ecology Progress Series. 158: 293-296.

Shanks, A.L. and K. Walters. 1997. Holoplankton, meroplankton, and meiofauna associated with marine snow. Marine Ecology Progress Series. 156: 75-86.

Shanks, A.L. and K. del Carmen. 1997. Larval polychaetes are strongly associated with marine snow. Marine Ecology Progress Series. 154: 211-221.

Shanks, A.L. and K. Walters. 1996. The feeding of a heterotrophic dinoflagellate (Noctiluca) in marine snow. Limnology and Oceanography 41: 177-181.

Walters, K. and A.L. Shanks. 1996. Complex trophic and nontrophic interactions between meiobenthic copepods and marine snow. Journal of Experimental Marine Biology and Ecology. 198: 131-145.

Larson, E.T. and A.L. Shanks. 1996. The consumption of marine snow by juvenile stripped and white mullet. Marine Ecology Progress Series. 130: 19-28.

Shanks, A.L. 1995. Mechanisms of cross-shelf dispersal of larval invertebrates and fish. In: Ecology of Marine Invertebrate Larvae. Ed. L.R. McEdward. CRC Press Inc. Boca Raton, Florida, pp. 323-368.

Shanks, A.L. 1995. Orientated swimming by megalopae of several eastern North Pacific crab species and its potential role in their onshore migration. Journal of Experimental Marine Biology and Ecology. 186: 1-17

Wright, W.G. and A.L. Shanks. 1995. Interspecific association between bail-out behavior and habitat is geographically and phylogenetically widespread. Journal of Experimental Marine Biology and Ecology.188: 133-143.

Wright, W.G. and A.L. Shanks. 1993. Previous experience determines territorial behavior in Lottia gigantea, an archaeogastropod limpet. Journal of Experimental Marine Biology and Ecology.166: 217-229.

Shanks, A.L. and M. Reeder. 1993. Reducing microzones and sulfide production in marine snow. Marine Ecology Progress Series. 96: 43-47.

Shanks, A.L. and E.W. Edmondson. 1990. Vertical flux of metazoans (holoplankton, meiofauna, and larval invertebrates) due to their association with marine snow. Limnology and Oceanography 35: 455-463.

Shanks, A.L. and E. W. Edmondson. 1989. Laboratory-made marine snow: A biological model of the real thing. Marine Biology 101: 463-470.

Shanks, A.L. 1988. Further support for the hypothesis that internal waves can transport larvae of invertebrates and fish onshore. Fisheries Bulletin 86 (4): 703-714.

Shanks, A.L. and W.M. Graham. 1988. Chemical defense in a scyphomedusa. MarineEcology Progress Series. 45: 81-86.

Shanks, A.L. 1987. Mechanisms of cross-shelf larval transport. p.15-28. In Signposts in the Sea. W.F. Herrnkind (Ed). Dept. of Biological Science, Florida State  University, Tallahassee.

Shanks, A.L. and W. G. Wright. 1987. Internal-wave-mediated shoreward transport of cyprids, megalopae, and gammarids and correlated longshore differences in the settling rate of intertidal barnacles. Journal of Experimental Marine Biology and Ecology. 114: 1-13.

Wells, J.T. and A.L. Shanks. 1987. Observations and geologic significance of marine snow in a shallow-water, partially-enclosed marine embayment. Journal of Geophysical Research 92(C12): 13,185-13,190.

Shanks, A.L. 1987. The onshore transport of an oil spill by internal waves. Science 235: 1198-1200.

Shanks, A.L. and W. M. Graham. 1987. Orientated swimming in the jellyfish Stomolophus meleagris L. Agassiz (Scyphozoan, Rhizostomida). Journal of Experimental Marine Biology and Ecology. 108: 159-169.

Shanks, A.L. 1986. Vertical migration and cross-shelf dispersal of larval Cancer spp. and Randallia ornata (Crustacea, Brachyura) off the coast of southern California. Marine Biology 92: 189-200.

Shanks, A.L. 1986. Tidal periodicity in the daily settlement of intertidal barnacle larvae and an hypothesized mechanism for the cross-shelf transport of   cyprids. Biological Bulletin 170: 429-440.

Shanks, A.L. and W.G. Wright. 1986. Adding teeth to wave action: The destructive effects of wave-borne rocks on intertidal organisms. Oecologia. 69: 420-428.

Shanks, A.L., W.G. Wright, and G. Maltz. 1986. What triggers “bail out” in the  limpet Lottia gigantea. Marine Behavior Physiology 12: 71-79.

Beers, J.R., J.D. Trent, F.M.H. Reid, and A.L. Shanks. 1986. Macroaggregates and their  phytoplanktonic components in the Southern California Bight. Journal of Plankton Research 8: 475-487.

Shanks, A.L. 1985. The behavioral basis of internal wave induced shoreward transport of the megalopae of Pachygrapsus crassipes. Marine Ecology Progress Series. 24: 289-295.

Shanks, A.L. 1983. Surface slicks associated with tidally forced internal waves may transport pelagic larvae of benthic invertebrates and fishes shoreward. Marine Ecology Progress Series. 13: 311-315.

Shanks, A.L. and J.D. Trent. 1980. Marine snow: Sinking rates and role in vertical flux. Deep-Sea Research 27A: 137-143.

Shanks, A.L. and J.D. Trent. 1979. Marine snow: Microscale nutrient patches. Limnology and Oceanography 24: 850-854.

Trent, J.D., A.L. Shanks, and M.W. Silver. 1978. In Situ and laboratory measurements on macroscopic aggregates in Monterey Bay, California. Limnology and Oceanography 23: 626-635.

Silver, M.W., A.L. Shanks, and J.D. Trent. 1978. Marine snow: Microplankton habitat and source of small-scale patchiness in pelagic populations. Science 201: 371-373.

Mattison, J.E., J.D. Trent, A.L. Shanks, T.B. Akin, and J.S. Pearse. 1977. Movement and feeding activity of Red Sea urchins (Strongylocentrotus franciscanus) adjacent to a kelp forest. Marine Biology 39: 25-30.


I have broad research interests (biological oceanography, animal behavior, intertidal ecology, larval biology). If I had to point to a general theme to my research I think that it is my fascination with the interaction of the physical realm and the biological. Much of my work seems to be at the interface between physical and biology oceanography. For example, much of my present research effort is directed at understanding how the dispersal of larval invertebrates and fish is affected by currents and the behavioral of larvae. There is probably a second theme that runs through my work; I am strongly driven by my curiosity. Early in my career, I discovered that if I was observant and followed my curiosity, I could make novel discoveries. Through out my career, I have tried to pay attention to my observations and serendipity and to actively follow these leads. A number of papers have come from this effort. When training students (undergraduate or graduate), one of my primary goals is to persuade them to follow their curiosity as this leads to novel and creative discovers (and besides it is fun).