Sonke Johnsen | Scholars@Duke

Sonke Johnsen
Professor in the Department of Biology

Current Appointments & Affiliations

Professor in the Department of Biology, Biology, Trinity College of Arts & Sciences 2012
Faculty Network Member of the Duke Institute for Brain Sciences, Duke Institute for Brain Sciences, University Institutes and Centers 2008
Associate of the Duke Initiative for Science & Society, Duke Science & Society, Initiatives 2017

Contact Information

301 Bio Sci Bldg, Durham, NC 27708
Duke Box 90338, Durham, NC 27708-0338
sjohnsen@duke.edu (919) 660-7321
lab website

Background
Education, Training, & Certifications
- Ph.D., University of North Carolina at Chapel Hill 1996
- B.A., Swarthmore College 1988
Duke Appointment History
- Associate Professor of Biology, Biology, Trinity College of Arts & Sciences 2007 - 2012
- Director of Graduate Studies for the Department of Biology, Biology, Trinity College of Arts & Sciences 2008 - 2011
- Assistant Professor of Biology, Biology, Trinity College of Arts & Sciences 2001 - 2007
Recognition
In the News
- APR 23, 2018 National Geographic
  
  How Deep-Sea Fish Are So Exceptionally Black
- MAR 12, 2018
  
  How the Color-Changing Hogfish Sees With Its Skin
- FEB 13, 2017
  
  Mismatched Eyes Help Squid Survive Oceans Twilight Zone
- NOV 3, 2016
  
  Midwater Ocean Creatures Use Nanotech Camouflage
- AUG 23, 2016
  
  In the Ocean, Clever Camouflage Beats Super Sight
- AUG 23, 2016 Cosmos Magazine
  
  Sonke Johnsen: In the ocean, invisibility trumps ultra-vision
- MAY 18, 2016 Science News
  
  Sönke Johnsen: Some animals ‘see’ the world through oddball eyes
- FEB 29, 2016
  
  Black Widows: Obvious to Predators, Stealthy to Prey
- JAN 8, 2016 Science Daily
  
  Post-exercise fog muddies a see-through shrimp’s cloak of invisibility
- DEC 2, 2015
  
  Camouflaged Cuttlefish Employ Electrical Stealth
- APR 1, 2015
  
  Johnsen's Book wins PROSE Award
- AUG 19, 2014 The New York Times
  
  Sönke Johnsen explores a world of creatures that hide in the open
Expertise
Global Scholarship
- Research
  - Australia (Country)
Research
Selected Grants
- The Sigsbee Deep Expedition- Exploration of light in the water column below 1000m awarded by National Oceanic and Atmospheric Administration 2017 - 2019
- Long-range Geomagnetic Navigation in Sea Turtles: An Interdisciplinary Approach to awarded by University of North Carolina - Chapel Hill 2014 - 2018
- Cleaner Shrimp and Client Fish: Combining Phylogenetics and Visual Ecology to Understand the Evolution of Mutualistic Interactions awarded by National Geographic Society 2015 - 2016
- Bioluminescence in the Deep-sea Benthos II awarded by Nova Southeastern University 2015
- Dynamic Camouflage in Benthic and Pelagic Cephalopods: awarded by Office of Naval Research 2009 - 2015
- Collaborative Research: Midwater animal models: Optical measurement of metabolic transitions awarded by National Science Foundation 2009 - 2013
- Operation Deep-Scope 2007: Characterization of cliff ecosystems using new technologies awarded by National Oceanic and Atmospheric Administration 2007 - 2009
- Collaborative Research: Transparency: Ultrastructural and biochemical specialization in muscular and ocular tissues awarded by National Science Foundation 2005 - 2009
- Selective Invisibility Based on the Differing Temporal Resolutions of Sea Turtles and Billfish Under Low Light Condition awarded by National Oceanic and Atmospheric Administration 2005 - 2006
- Mathematical Model of the Visual Abilities of Sea Turtles and Pelagic Fishes awarded by National Oceanic and Atmospheric Administration 2003
Publications & Artistic Works
Selected Publications
- Book Sections
  - Zylinski, S, and Johnsen, S. "Visual cognition in deep-sea cephalopods: What we don’t know and why we don’t know it." In Cephalopod Cognition, 223-241. January 1, 2014. Full Text
  - Marshall, J, and Johnsen, S. "Camouflage in marine fish." In Animal Camouflage: Mechanisms and Function, 186-211. January 1, 2011. Full Text
- Conference Papers
  - Bagge, LE, and Johnsen, S. "Anti-reflective invisibility cloak: monolayers of spheres reduce cuticle reflectance in hyperiid amphipods." March 2017. Link to Item
  - Caves, EM, Chen, CC, and Johnsen, S. "Coarse vision isn't useless vision: cleaner shrimp use monochromatic, low-resolution vision to detect client fish." March 2017. Link to Item
  - Johnsen, S, and Ruxton, GD. "Join Now! The increased visibility of large groups of aquatic and aerial organisms is far outweighed by the benefits of aggregation." March 2017. Link to Item
  - Thomas, KN, Vecchione, M, and Johnsen, S. "What big eyes you have: Eye allometry and visual range in deep-sea cephalopods." March 2017. Link to Item
  - Bagge, LE, Kinsey, ST, and Johnsen, S. "The limits of an invisibility cloak: transparent shrimp become opaque after multiple tail-flipping escapes." March 2016. Link to Item
  - Brandley, N, Caves, E, and Johnsen, S. "Do warning signals exploit an evolutionary constraint on insect visual acuity?." March 2016. Link to Item
  - Caves, EM, Brandley, NC, and Johnsen, S. "Visual acuity in fish: the effects of eye morphology, environment, and ecology." March 2016. Link to Item
  - Johnsen, S, Gagnon, YL, Marshall, NJ, and Cronin, TW. "Another beautiful hypothesis slain by an ugly fact: Polarization vision does not increase the sighting distance of silvery fish." March 2016. Link to Item
  - Johnsen, S. "What Next? Unanswered questions about extraocular photoreception and how we might answer them." March 2016. Link to Item
  - Thomas, KN, Robison, BH, and Johnsen, S. "The perks of being cock-eyed: Orientation and visual characteristics of histioteuthid squids." March 2016. Link to Item
  - Caves, EM, Frank, TM, and Johnsen, S. "Colorblind colorful animals: Spectral sensitivity, temporal resolution, and spatial resolution in three species of cleaner shrimp." April 2015. Link to Item
  - Palmer, G, and Johnsen, S. "By the light of the silvery moon: The effect of lunar phase on the color of twilight and its implications for animal behavior." April 2015. Link to Item
  - Akre, KL, and Johnsen, S. "Proportional psychophysics and the evolution of behavior: The broad influence of Weber's law." 2014. Link to Item
  - Bagge, LE, Kier, WM, and Johnsen, S. "Clearly camouflaged: muscle architecture in transparent shrimp." 2014. Link to Item
  - Bedore, CN, Kajiura, SM, and Johnsen, SJ. "Bioelectric crypsis in cephalopods reduces detection by shark predators." 2014. Link to Item
  - Johnsen, S, Sawicka, E, Reynolds, R, and Stramski, D. "Through the looking glass: The structure of the oceanic light field and its implications for mirror-based camouflage." 2014. Link to Item
  - Bagge, LE, and Johnsen, S. "Looking at invisibility: anti-reflective structures and strategies in hyperiid amphipods." April 2013. Link to Item
  - Brandley, NC, Johnson, MG, and Johnsen, S. "Reduction of an aposematic signal: the role of microhabitat in North American black widows (Latrodectus)." April 2013. Link to Item
  - Gagnon, YL, and Johnsen, S. "Visual acuity in deep-sea fish and mollusks." April 2013. Link to Item
  - Johnsen, S, Nilsson, D-E, and Warrant, EJ. "Why do giant squid have giant eyes?." April 2013. Link to Item
  - Sweeney, AM, Johnsen, S, Gagnon, Y, Morse, DE, and Stramski, D. "Jurassic marine photonics: Squid dynamic iridescence and predation by large extinct marine reptiles." April 2013. Link to Item
  - Brandley, NC, and Johnsen, S. "The black widow's hourglass: a covert aposematic signal?." April 2012. Link to Item
  - Johnsen, S, and Marshall, NJ. "Through the looking glass: Are silvery fish safe from viewers with polarization vision?." April 2012. Link to Item
  - Speiser, DI, Gagnon, YL, Chhetri, RK, Oldenburg, AL, and Johnsen, S. "Optical coherence tomography (OCT) reveals that scallop eyes may have bifocal optics." April 2012. Link to Item
  - Zylinski, S, and Johnsen, S. "CAMOUFLAGE WITHOUT COMPROMISE: CEPHALOPODS SWITCH BETWEEN TRANSPARENCY AND PIGMENTATION TO OPTIMIZE CRYPSIS IN THE DEEP." December 2011. Link to Item
  - Baldwin, FJL, and Johnsen, S. "When love is blind: Vision constrained by molting during mating in the female blue crab." March 2011. Link to Item
  - Johnsen, S, and Marshall, NJ. "Using sunglasses to find the best burger in town: Polarization vision as a camouflage breaker in pelagic predators." March 2011. Link to Item
  - Speiser, DI, and Johnsen, S. "Seeing through rocks: Chitons use calcium carbonate lenses to form images." March 2011. Link to Item
  - Baldwin, JL, and Johnsen, S. "Does this color make my claws look phat? Evaluating claw color preferences in male blue crabs, Callinectes sapidus." July 2010. Link to Item
  - Bhandiwad, AA, and Johnsen, S. "Now you see it, now you don't: the effects of salinity and temperature on the transparency of the ghost shrimp, Palaemonetes pugio." July 2010. Link to Item
  - Johnsen, S, and Haddock, SHD. "A glowing benthic animal is hard to find: A photographic and spectroscopic survey of bioluminescence on the deep-sea floor." July 2010. Link to Item
  - Speiser, DI, Loew, ER, and Johnsen, S. "Spectral sensitivity of the concave mirror eyes of scallops: The influence of habitat and longitudinal chromatic aberration." July 2010. Link to Item
  - Baldwin, JL, and Johnsen, S. "Pining for Pinups: the importance of color in mate choice of the blue crab Callinectes sapidus." February 2009. Link to Item
  - Johnsen, S, and Kier, WM. "You can hide, but you can't run: trade-offs between muscle activation and transparency in glass catfish." February 2009. Link to Item
  - Speiser, DI, and Johnsen, S. "The optics and evolution of scallop eyes." February 2009. Link to Item
  - Sweeney, AM, Matz, MV, Morse, DE, and Johnsen, S. "Patterns of S-crystallin evolution are correlated with optical acuity in cephalopods." February 2009. Link to Item
  - Johnsen, S. "Visual Ecology on the high seas." December 2006. Link to Item
  - Speiser, DI, Sweeney, AM, and Johnsen, S. "Scallops respond to simulated particles in flow." December 2006. Link to Item
  - Sweeney, A, and Johnsen, S. "Evolution of high-acuity vision in coleoid cephalopods." December 2006. Link to Item
  - Johnsen, S, Kelber, A, Warrant, EJ, Sweeney, AM, Widder, EA, Lee, RL, and Hernandez-Andres, J. "The color of night: Twilight and nocturnal illumination and its effects on color perception." December 2005. Link to Item
  - Mora, CV, Johnsen, S, and Lohmann, KJ. "Detection of polarized light by loggerhead sea turtles (Caretta caretta)." December 2005. Link to Item
  - Speiser, DI, and Johnsen, S. "Wavelength-dependent phototaxis as a depth regulating mechanism in a ctenophore." December 2005. Link to Item
  - Sweeney, A, Des Marais, DL, Ban, A, and Johnsen, S. "Evolving refractive index: How lens protein evolution contributed to high-resolution squid vision." December 2005. Link to Item
  - Tuthill, JC, and Johnsen, S. "Polarization vision in crayfish enhances motion detection." December 2005. Link to Item
  - Blevins, EL, and Johnsen, S. "Spatial vision in the echinoid genus Echinometra." December 2004. Link to Item
  - Johnsen, S. "The red and the black: Bioluminescence and the color of animals in the deep sea." December 2004. Link to Item
  - Sweeney, A, and Johnsen, S. "Evolution of complex optics in squid lenses." December 2004. Link to Item
  - Costello, MJ, Gilliland, KP, Freel, CD, Fowler, WC, and Johnsen, S. "Mie light scattering analysis of human age-related nuclear cataracts." April 2004. Link to Item
  - Johnsen, S. "Troubles in flashlight world: The effects of water turbidity and visual acuity on the success of counterillumination in deep-sea species." December 2003. Link to Item
  - Sweeney, AM, and Johnsen, S. "Biological optical instruments in the deep sea." December 2003. Link to Item
  - Johnsen, S. "Minors or colors? Successful fashions for crypsis in the pelagic realm." December 2002. Link to Item
  - Sweeney, A, Jiggins, C, and Johnsen, S. "Bio-optics and visual ecology of Heliconius color patterns." December 2002. Link to Item
- Journal Articles
  - Schweikert, LE, Fitak, RR, and Johnsen, S. "De novo transcriptomics reveal distinct phototransduction signaling components in the retina and skin of a color-changing vertebrate, the hogfish (Lachnolaimus maximus)." Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology (February 28, 2018). Full Text
  - Bagge, LE, Kinsey, ST, Gladman, J, and Johnsen, S. "Transparent anemone shrimp (Ancylomenes pedersoni) become opaque after exercise and physiological stress in correlation with increased hemolymph perfusion." The Journal of experimental biology 220, no. Pt 22 (November 2017): 4225-4233. Full Text
  - Fitak, RR, and Johnsen, S. "Bringing the analysis of animal orientation data full circle: model-based approaches with maximum likelihood." The Journal of experimental biology 220, no. Pt 21 (November 2017): 3878-3882. Full Text
  - Marshall, J, and Johnsen, S. "Fluorescence as a means of colour signal enhancement." Philosophical transactions of the Royal Society of London. Series B, Biological sciences 372, no. 1724 (July 2017). (Review) Full Text
  - Taylor, BK, Johnsen, S, and Lohmann, KJ. "Detection of magnetic field properties using distributed sensing: a computational neuroscience approach." Bioinspiration & biomimetics 12, no. 3 (May 19, 2017): 036013-. Full Text
  - Johnsen, S. "Open Questions: We don't really know anything, do we? Open questions in sensory biology." BMC biology 15, no. 1 (May 17, 2017): 43-. Full Text
  - Caves, EM, Sutton, TT, and Johnsen, S. "Visual acuity in ray-finned fishes correlates with eye size and habitat." The Journal of experimental biology 220, no. Pt 9 (May 2017): 1586-1596. Full Text Open Access Copy
  - Cronin, TW, Fasick, JI, Schweikert, LE, Johnsen, S, Kezmoh, LJ, and Baumgartner, MF. "Coping with copepods: do right whales (Eubalaena glacialis) forage visually in dark waters?." Philosophical transactions of the Royal Society of London. Series B, Biological sciences 372, no. 1717 (April 2017). Full Text
  - Fitak, RR, Wheeler, BR, Ernst, DA, Lohmann, KJ, and Johnsen, S. "Candidate genes mediating magnetoreception in rainbow trout (Oncorhynchus mykiss)." Biology letters 13, no. 4 (April 2017). Full Text
  - Thomas, KN, Robison, BH, and Johnsen, S. "Two eyes for two purposes: in situ evidence for asymmetric vision in the cockeyed squids Histioteuthis heteropsis and Stigmatoteuthis dofleini." Philosophical transactions of the Royal Society of London. Series B, Biological sciences 372, no. 1717 (April 2017). Full Text
  - Tedore, C, and Johnsen, S. "Using RGB displays to portray color realistic imagery to animal eyes." Current zoology 63, no. 1 (February 2017): 27-34. Full Text
  - Bagge, LE, Osborn, KJ, and Johnsen, S. "Nanostructures and Monolayers of Spheres Reduce Surface Reflections in Hyperiid Amphipods." Current biology : CB 26, no. 22 (November 2016): 3071-3076. Full Text
  - Cronin, TW, and Johnsen, S. "Extraocular, Non-Visual, and Simple Photoreceptors: An Introduction to the Symposium." Integrative and comparative biology 56, no. 5 (November 2016): 758-763. Full Text
  - Speiser, DI, Gagnon, YL, Chhetri, RK, Oldenburg, AL, and Johnsen, S. "Examining the Effects of Chromatic Aberration, Object Distance, and Eye Shape on Image-Formation in the Mirror-Based Eyes of the Bay Scallop Argopecten irradians." Integrative and comparative biology 56, no. 5 (November 2016): 796-808. Full Text
  - Ruxton, GD, and Johnsen, S. "The effect of aggregation on visibility in open water." Proceedings. Biological sciences 283, no. 1839 (September 2016). Full Text
  - Cronin, TW, Gagnon, YL, Johnsen, S, Marshall, NJ, and Roberts, NW. "Comment on "Open-ocean fish reveal an omnidirectional solution to camouflage in polarized environments"." Science (New York, N.Y.) 353, no. 6299 (August 2016): 552-. Full Text
  - Johnsen, S, Gagnon, YL, Marshall, NJ, Cronin, TW, Gruev, V, and Powell, S. "Polarization vision seldom increases the sighting distance of silvery fish." Current biology : CB 26, no. 16 (August 2016): R752-R754. (Letter) Full Text
  - Tedore, C, and Johnsen, S. "Disentangling the visual cues used by a jumping spider to locate its microhabitat." The Journal of experimental biology 219, no. Pt 15 (August 2016): 2396-2401. Full Text
  - Wilkins, L, Marshall, NJ, Johnsen, S, and Osorio, D. "Modelling colour constancy in fish: implications for vision and signalling in water." The Journal of experimental biology 219, no. Pt 12 (June 2016): 1884-1892. Full Text
  - Johnsen, S. "How to measure color using spectrometers and calibrated photographs." The Journal of experimental biology 219, no. Pt 6 (March 2016): 772-778. (Review) Full Text
  - Zylinski, S, Osorio, D, and Johnsen, S. "Cuttlefish see shape from shading, fine-tuning coloration in response to pictorial depth cues and directional illumination." Proceedings. Biological sciences 283, no. 1826 (March 2016): 20160062-. Full Text
  - Caves, EM, Frank, TM, and Johnsen, S. "Spectral sensitivity, spatial resolution and temporal resolution and their implications for conspecific signalling in cleaner shrimp." The Journal of experimental biology 219, no. Pt 4 (February 2016): 597-608. Full Text Open Access Copy
  - Brandley, N, Johnson, M, and Johnsen, S. "Aposematic signals in North American black widows are more conspicuous to predators than to prey." Behavioral Ecology 27, no. 4 (2016): 1104-1112. Full Text
  - Costello, MJ, Brennan, LA, Mohamed, A, Gilliland, KO, Johnsen, S, and Kantorow, M. "Identification and Ultrastructural Characterization of a Novel Nuclear Degradation Complex in Differentiating Lens Fiber Cells." PloS one 11, no. 8 (January 2016): e0160785-. Full Text
  - Bedore, CN, Kajiura, SM, and Johnsen, S. "Freezing behaviour facilitates bioelectric crypsis in cuttlefish faced with predation risk." Proceedings. Biological sciences 282, no. 1820 (December 2015): 20151886-. Full Text Open Access Copy
  - Gagnon, YL, Sutton, TT, and Johnsen, S. "Corrigendum to "Visual acuity in pelagic fishes and mollusks" [Vis. Res. 92 (2013) 1-9] doi:10.1016/j.visres.2013.08.007." Vision Research 115 (October 1, 2015): 155-156. Full Text
  - Tedore, C, and Johnsen, S. "Immunological dependence of plant-dwelling animals on the medicinal properties of their plant substrates: a preliminary test of a novel evolutionary hypothesis." Arthropod-Plant Interactions 9, no. 5 (October 2015): 437-446. Full Text
  - Baldwin Fergus, JL, Johnsen, S, and Osborn, KJ. "A unique apposition compound eye in the mesopelagic hyperiid amphipod Paraphronima gracilis." Current biology : CB 25, no. 4 (February 2015): 473-478. Full Text
  - Palmer, G, and Johnsen, S. "Downwelling spectral irradiance during evening twilight as a function of the lunar phase." Applied optics 54, no. 4 (February 2015): B85-B92. Full Text
  - Baldwin Fergus, JL, Johnsen, S, and Osborn, KJ. "A unique apposition compound eye in the mesopelagic hyperiid amphipod paraphronima gracilis." Current Biology 25, no. 4 (January 1, 2015): 473-478. Full Text
  - Taniguchi, DAA, Gagnon, Y, Wheeler, BR, Johnsen, S, and Jaffe, JS. "Cuttlefish Sepia officinalis Preferentially Respond to Bottom Rather than Side Stimuli When Not Allowed Adjacent to Tank Walls." PloS one 10, no. 10 (January 2015): e0138690-. Full Text
  - Tedore, C, and Johnsen, S. "Visual mutual assessment of size in male Lyssomanes viridis jumping spider contests." Behavioral Ecology 26, no. 2 (2015): 510-518. Full Text
  - Johnsen, S, Gassmann, E, Reynolds, RA, Stramski, D, and Mobley, C. "The asymmetry of the underwater horizontal light field and its implications for mirror-based camouflage in silvery pelagic fish." Limnology and Oceanography 59, no. 6 (November 2014): 1839-1852. Full Text
  - Dougherty, LF, Johnsen, S, Caldwell, RL, and Marshall, NJ. "A dynamic broadband reflector built from microscopic silica spheres in the 'disco' clam Ctenoides ales." Journal of the Royal Society, Interface 11, no. 98 (September 2014): 20140407-. Full Text
  - Muchhala, N, Johnsen, S, and Smith, SD. "Competition for hummingbird pollination shapes flower color variation in Andean solanaceae." Evolution; international journal of organic evolution 68, no. 8 (August 2014): 2275-2286. Full Text
  - Gagnon, YL, Speiser, DI, and Johnsen, S. "Simplifying numerical ray tracing for characterization of optical systems." Applied optics 53, no. 21 (July 2014): 4784-4790. Full Text
  - Akre, KL, and Johnsen, S. "Psychophysics and the evolution of behavior." Trends in ecology & evolution 29, no. 5 (May 2014): 291-300. Full Text
  - Nilsson, D-E, Warrant, E, and Johnsen, S. "Computational visual ecology in the pelagic realm." Philosophical transactions of the Royal Society of London. Series B, Biological sciences 369, no. 1636 (January 6, 2014): 20130038-. Full Text
  - Akre, KL, and Johnsen, S. "Psychophysics and the evolution of behavior." Trends in Ecology and Evolution 29, no. 5 (January 1, 2014): 291-300. (Review) Full Text
  - Gagnon, YL, Speiser, DI, and Johnsen, S. "Simplifying numerical ray tracing for characterization of optical systems." Applied Optics 53, no. 21 (January 1, 2014): 4784-4790. Full Text
  - Johnsen, S. "Hide and seek in the open sea: pelagic camouflage and visual countermeasures." Ann Rev Mar Sci 6 (2014): 369-392. (Review) Full Text Link to Item
  - Mohamed, A, Gilliland, KO, Metlapally, S, Johnsen, S, and Costello, MJ. "Simple fixation and storage protocol for preserving the internal structure of intact human donor lenses and extracted human nuclear cataract specimens." Molecular Vision 19 (November 21, 2013): 2352-2359.
  - Warrant, EJ, and Johnsen, S. "Vision and the light environment." Current Biology 23, no. 22 (November 18, 2013). Full Text
  - Brandley, NC, Speiser, DI, and Johnsen, S. "Eavesdropping on visual secrets." Evolutionary Ecology 27, no. 6 (November 1, 2013): 1045-1068. Full Text
  - Costello, MJ, Mohamed, A, Gilliland, KO, Fowler, WC, and Johnsen, S. "Ultrastructural analysis of the human lens fiber cell remodeling zone and the initiation of cellular compaction." Experimental Eye Research 116 (November 1, 2013): 411-418. Full Text
  - Gagnon, YL, Sutton, TT, and Johnsen, S. "Visual acuity in pelagic fishes and mollusks." Vision Res 92 (November 2013): 1-9. Full Text Link to Item
  - Nilsson, D-E, Warrant, EJ, Johnsen, S, Hanlon, RT, and Shashar, N. "The giant eyes of giant squid are indeed unexpectedly large, but not if used for spotting sperm whales." BMC EVOLUTIONARY BIOLOGY 13 (September 8, 2013). Full Text Link to Item
  - Tedore, C, and Johnsen, S. "Pheromones exert top-down effects on visual recognition in the jumping spider Lyssomanes viridis." J Exp Biol 216, no. Pt 9 (May 1, 2013): 1744-1756. Full Text Link to Item
  - Costello, MJ, Brennan, LA, Basu, S, Chauss, D, Mohamed, A, Gilliland, KO, Johnsen, S, Menko, AS, and Kantorow, M. "Autophagy and mitophagy participate in ocular lens organelle degradation." Experimental Eye Research 116 (2013): 141-150. Full Text
  - Johnsen, S, Frank, TM, Haddock, SHD, Widder, EA, and Messing, CG. "Light and vision in the deep-sea benthos: I. Bioluminescence at 500-1000 m depth in the Bahamian islands." J Exp Biol 215, no. Pt 19 (October 1, 2012): 3335-3343. Full Text Link to Item
  - Baldwin, J, and Johnsen, S. "The male blue crab, Callinectes sapidus, uses both chromatic and achromatic cues during mate choice." J Exp Biol 215, no. Pt 7 (April 1, 2012): 1184-1191. Full Text Link to Item
  - Tedore, C, and Johnsen, S. "Weaponry, color, and contest success in the jumping spider Lyssomanes viridis." Behav Processes 89, no. 3 (March 2012): 203-211. Full Text Link to Item
  - Johnsen, S. "The optics of life: A biologist's guide to light in nature." The Optics of Life: A Biologist's Guide to Light in Nature (January 19, 2012).
  - Johnsen, S. "Anything that involves a photon and an animal." Curr Biol 22, no. 1 (January 10, 2012): R6-R7. (Interview) Link to Item
  - Johnsen, S. "Sonke Johnsen." CURRENT BIOLOGY 22, no. 1 (January 10, 2012): R6-R7. Full Text Link to Item
  - Brandley, NC, and Johnsen, S. "Eavesdropping on visual secrets (Submitted)." Evolutionary Ecology (2012). (Academic Article)
  - Costello, MJ, Burette, A, Weber, M, Metlapally, S, Gilliland, KO, Fowler, WC, Mohamed, A, and Johnsen, S. "Electron tomography of fiber cell cytoplasm and dense cores of multilamellar bodies from human age-related nuclear cataracts." Experimental Eye Research 101 (2012): 72-81. Full Text
  - Costello, MJ, Chauss, D, Mohamed, A, Gilliland, KO, Johnsen, S, Bates, M, Brennan, LA, and Kantorow, M. "Autophagy and Mitophagy in the Ocular Lens (Submitted)." Journal of Cell Science (2012). (Academic Article)
  - Frank, TM, Johnsen, S, and Cronin, TW. "Light and vision in the deep-sea benthos: II. Vision in deep-sea crustaceans." Journal of Experimental Biology 215, no. 19 (2012): 3344-3353. Full Text
  - Frank, TM, and Johnsen, S. "Light and vision in the deep-sea benthos. II. Special visual adaptations in deep-sea benthic crustaceans." Journal of Experimental Biology 215 (2012): 3344-3353. (Academic Article)
  - Holt, AL, Sweeney, AM, Johnsen, S, and Morse, DE. "A highly distributed Bragg stack with unique geometry provides effective camouflage for Loliginid squid eyes (Journal of the Royal Society Interface (2011) 8, (1386-1399) DOI: 10.1098/rsif.2010.0702)." Journal of the Royal Society Interface 9, no. 68 (2012): 600--. Full Text
  - Moore, BA, Kamilar, JM, Collin, SP, Bininda Emonds, ORP, Dominy, NJ, Hall, MI, Heesy, CP, Iwaniuk, AN, Johnsen, S, Lisney, TJ, Loew, ER, Moritz, G, Nava, SS, Warrant, EJ, Yopak, KE, and Fernández Juricic, E. "A novel method for comparative analysis of retinal specialization traits from topographic maps." Journal of Vision 12, no. 1-24 (2012). (Academic Article)
  - Moore, BA, Kamilar, JM, Collin, SP, Bininda Emonds, ORP, Dominy, NJ, Hall, MI, Heesy, CP, Johnsen, S, Lisney, TJ, Loew, ER, Moritz, G, Nava, SS, Warrant, EJ, Yopak, KE, and Fernández Jurici, E. "Are all vertebrate retinas configured the same? Implications for the evolution of acute vision. (Submitted)" Proceedings of the Royal Society of London, Series B (2012). (Academic Article)
  - Moore, BA, Kamilar, JM, Collin, SP, Bininda-Emonds, ORP, Dominy, NJ, Hall, MI, Heesy, CP, Johnsen, S, Lisney, TJ, Loew, ER, Moritz, G, Nava, SS, Warrant, E, Yopak, KE, and Fernández-Juricic, E. "A novel method for comparative analysis of retinal specialization traits from topographic maps." Journal of Vision 12, no. 12 (2012). Full Text
  - Nilsson, D-E, Warrant, EJ, Johnsen, S, Hanlon, R, and Shashar, N. "A unique advantage for giant eyes in giant squid." Current Biology 22, no. 8 (2012): 683-688. Full Text
  - Zylinski, S, and Johnsen, S. "Mesopelagic cephalopods switch between transparency and pigmentation to optimize camouflage in the deep." Curr Biol 21, no. 22 (November 22, 2011): 1937-1941. Full Text Link to Item
  - Baldwin, J, and Johnsen, S. "Effects of molting on the visual acuity of the blue crab, Callinectes sapidus." J Exp Biol 214, no. Pt 18 (September 15, 2011): 3055-3061. Full Text Link to Item
  - Speiser, DI, Eernisse, DJ, and Johnsen, S. "A chiton uses aragonite lenses to form images." Curr Biol 21, no. 8 (April 26, 2011): 665-670. Full Text Link to Item
  - Johnsen, S, Marshall, NJ, and Widder, EA. "Polarization sensitivity as a contrast enhancer in pelagic predators: lessons from in situ polarization imaging of transparent zooplankton." Philos Trans R Soc Lond B Biol Sci 366, no. 1565 (March 12, 2011): 655-670. Full Text Link to Item
  - Bhandiwad, A, and Johnsen, S. "The effects of salinity and temperature on the transparency of the grass shrimp Palaemonetes pugio." J Exp Biol 214, no. Pt 5 (March 1, 2011): 709-716. Full Text Link to Item
  - Speiser, DI, Loew, ER, and Johnsen, S. "Spectral sensitivity of the concave mirror eyes of scallops: potential influences of habitat, self-screening and longitudinal chromatic aberration." J Exp Biol 214, no. Pt 3 (February 1, 2011): 422-431. Full Text Link to Item
  - Holt, AL, Sweeney, AM, Johnsen, S, and Morse, DE. "A highly distributed Bragg stack with unique geometry provides effective camouflage for Loliginid squid eyes." Journal of the Royal Society Interface 8, no. 63 (2011): 1386-1399. Full Text
  - Jackson, E, and Johnsen, S. "Orientation to objects in the sea urchin strongylocentrotus purpuratus depends on apparent and not actual object Size." Biological Bulletin 220, no. 2 (2011): 86-88.
  - Jaffe, JS, Simonet, F, Laxton, B, Roberts, PLD, Zylinski, S, Johnsen, S, and Sweeney, AM. "Omni-Cam and the Sub Sea Holodeck: Systems for recording in-situ radiance and simulating underwater optical environments in the lab (Submitted)." Marine Technology Society Journal (2011). (Academic Article)
  - Shashar, N, Johnsen, S, Lerner, A, Sabbah, S, Chiao, C-C, Mäthger, LM, and Hanlon, RT. "Underwater linear polarization: Physical limitations to biological functions." Philosophical Transactions of the Royal Society B: Biological Sciences 366, no. 1565 (2011): 649-654. Full Text
  - Speiser, DI, Eernisse, D, and Johnsen, S. "Chitons eye have calcitic lenses and provide spatial vision." Current Biology 21 (2011): 665-670. (Academic Article)
  - Speiser, DI, Loew, ER, and Johnsen, S. "Spectral sensitivity of the concave mirror eyes of scallops: The influence of habitat and longitudinal chromatic aberration." Journal of Experimental Biology 214 (2011): 422-431. (Academic Article)
  - Sweeney, AM, Boch, CA, Johnsen, S, and Morse, DE. "Twilight spectral dynamics and the coral reef invertebrate spawning response." Journal of Experimental Biology 214, no. 5 (2011): 770-777. Full Text
  - Tedore, CA, and Johnsen, S. "The function of male-male threat displays in the jumping spider Lyssomanes viridis." Behavioural Processes (online for now) (2011). (Academic Article)
  - Yerramilli, D, and Johnsen, S. "Spatial vision in the purple sea urchin Strongylocentrotus purpuratus (Echinoidea)." J Exp Biol 213, no. 2 (January 15, 2010): 249-255. Full Text Open Access Copy Link to Item
  - Costello, MJ, Johnsen, S, Metlapally, S, Gilliland, KO, Frame, L, and Balasubramanian, D. "Multilamellar spherical particles as potential sources of excessive light scattering in human age-related nuclear cataracts." Experimental Eye Research 91, no. 6 (2010): 881-889. Full Text
  - Baldwin, J, and Johnsen, S. "The importance of color in mate choice of the blue crab Callinectes sapidus." J Exp Biol 212, no. Pt 22 (November 2009): 3762-3768. Full Text Link to Item
  - Johnsen, S, and Lohmann, KJ. "An inner ear magnetoreceptor? Reply." PHYSICS TODAY 62, no. 2 (February 2009): 14-14. Full Text Link to Item
  - Marlow, H, Speiser, DI, Matus, D, Johnsen, S, Seaver, EC, and Martindale, MQ. "The evolution of a complex trait: Photoreception in the Metazoa (In preparation)." Nature (2009). (Academic Article)
  - Speiser, DI, and Johnsen, S. "Scallops visually respond to the size and speed of virtual particles." J Exp Biol 211, no. Pt 13 (July 2008): 2066-2070. Full Text Link to Item
  - Costello, MJ, Johnsen, S, Metlapally, S, Gilliland, KO, Ramamurthy, B, Krishna, PV, and Balasubramanian, D. "Ultrastructural analysis of damage to nuclear fiber cell membranes in advanced age-related cataracts from India." Experimental Eye Research 87, no. 2 (2008): 147-158. Full Text
  - Gilliland, KO, Johnsen, S, Metlapally, S, Costello, MJ, Ramamurthy, B, Krishna, PV, and Balasubramanian, D. "Mie Light Scattering Calculations for Multilamellar Bodies in Indian Age-Related Nuclear Cataracts." Molecular Vision 14 (2008): 572-582. (Academic Article)
  - Gilliland, KO, Johnsen, S, Metlapally, S, Costello, MJ, Ramamurthy, B, Krishna, PV, and Balasubramanian, D. "Mie light scattering calculations for an Indian age-related nuclear cataract with a high density of multilamellar bodies." Molecular Vision 14 (2008): 572-582.
  - Johnsen, S, and Lohmann, KJ. "Magnetoreception in animals." Physics Today 61, no. 3 (2008): 29-35. Full Text
  - Matz, MV, Frank, TM, Marshall, NJ, Widder, EA, and Johnsen, S. "Giant Deep-Sea Protist Produces Bilaterian-like Traces." Current Biology 18, no. 23 (2008): 1849-1854. Full Text
  - Metlapally, S, Costello, MJ, Gilliland, KO, Ramamurthy, B, Krishna, PV, Balasubramanian, D, and Johnsen, S. "Analysis of nuclear fiber cell cytoplasmic texture in advanced cataractous lenses from Indian subjects using Debye-Bueche theory." Experimental Eye Research 86, no. 2 (2008): 434-444. Full Text
  - Speiser, DI, and Johnsen, S. "Comparative morphology of the concave mirror eyes of scallops (Pectinoidea)." American Malacological Bulletin 26, no. 1-2 (2008): 27-33.
  - Sweeney, AM, Haddock, SHD, and Johnsen, S. "Comparative visual acuity of coleoid cephalopods (Integrative and Comparative Biology 47, 6, (808-814) DOI: 10.1093/icb/icm092)." Integrative and Comparative Biology 48, no. 1 (2008): 158--. Full Text
  - Johnsen, S. "Does new technology inspire new directions? Examples drawn from pelagic visual ecology." Integr Comp Biol 47, no. 6 (December 2007): 799-807. Full Text Link to Item
  - Sweeney, AM, Haddock, SHD, and Johnsen, S. "Comparative visual acuity of coleoid cephalopods." Integr Comp Biol 47, no. 6 (December 2007): 808-814. Full Text Link to Item
  - Johnsen, S, Mattern, E, and Ritz, T. "Light-dependent magnetoreception: quantum catches and opponency mechanisms of possible photosensitive molecules." J Exp Biol 210, no. Pt 18 (September 2007): 3171-3178. Full Text Link to Item
  - Sweeney, AM, Des Marais, DL, Ban, Y-EA, and Johnsen, S. "Evolution of graded refractive index in squid lenses." J R Soc Interface 4, no. 15 (August 22, 2007): 685-698. Full Text Link to Item
  - Costello, MJ, Johnsen, S, Gilliland, KO, Freel, CD, and Fowler, WC. "Predicted light scattering from particles observed in human age-related nuclear cataracts using mie scattering theory." Investigative Ophthalmology and Visual Science 48, no. 1 (2007): 303-312. Full Text
  - Gagnon, YL, Shashar, N, Warrant, EJ, and Johnsen, S. "Light scattering from pelagic zooplankton: measurements at different angles and modeling corresponding sighting distances." Journal of Experimental Biology 210 (2007): 3728-3735. (Academic Article)
  - Gagnon, YL, Shashar, N, Warrant, EJ, and Johnsen, SJ. "Light scattering by selected zooplankton from the Gulf of Aqaba." Journal of Experimental Biology 210, no. 21 (2007): 3728-3735. Full Text
  - Martin, CH, and Johnsen, S. "A field test of the Hamilton-Zuk hypothesis in the Trinidadian guppy (Poecilia reticulata)." Behavioral Ecology and Sociobiology 61, no. 12 (2007): 1897-1909. Full Text
  - Sweeney, A, Haddock, SHD, and Johnsen, S. "Comparative visual acuity of coleoid cephalopods." Integrative and Comparative Biology 47, no. 808-814 (2007). (Academic Article)
  - Johnsen, S, Kelber, A, Warrant, E, Sweeney, AM, Widder, EA, Lee, RL, and Hernández-Andrés, J. "Crepuscular and nocturnal illumination and its effects on color perception by the nocturnal hawkmoth Deilephila elpenor." J Exp Biol 209, no. Pt 5 (March 2006): 789-800. Full Text Link to Item
  - Leech, DM, and Johnsen, S. "UV vision and the Feeding Ecology of Juvenile Bluegill Sunfish, Lepomis machrochirus." Canadian Journal of Fisheries and Aquatic Sciences 63 (2006): 2183-2190. (Academic Article)
  - Leech, DM, and Johnsen, S. "Ultraviolet vision and foraging in juvenile bluegill (Lepomis macrochirus)." Canadian Journal of Fisheries and Aquatic Sciences 63, no. 10 (2006): 2183-2190. Full Text
  - Tuthill, JC, and Johnsen, S. "Polarization sensitivity in the red swamp crayfish Procambarus clarkii enhances the detection of moving transparent objects." Journal of Experimental Biology 209, no. 9 (2006): 1612-1616. Full Text
  - Johnsen, S, and Lohmann, KJ. "The physics and neurobiology of magnetoreception." Nat Rev Neurosci 6, no. 9 (September 2005): 703-712. (Review) Full Text Link to Item
  - Johnsen, S. "The red and the black: bioluminescence and the color of animals in the deep sea." Integr Comp Biol 45, no. 2 (April 2005): 234-246. Full Text Link to Item
  - Johnsen, S. "Visual ecology on the high seas." MARINE ECOLOGY PROGRESS SERIES 287 (2005): 281-285. Link to Item
  - Weissburg, MJ, Browman, HI, Fields, DM, Hemmi, JM, Zeil, J, Higgs, DM, Johnsen, S, Mead, KS, Mogdans, J, Nevitt, GA, Bonadonna, F, Walker, MM, and Dennis, TE. "Sensory biology: Linking the internal and external ecologies of marine organisms." Marine Ecology Progress Series 287 (2005): 263-307.
  - Blevins, E, and Johnsen, S. "Spatial vision in the echinoid genus Echinometra." J Exp Biol 207, no. Pt 24 (November 2004): 4249-4253. Full Text Link to Item
  - Johnsen, S, Widder, EA, and Mobley, CD. "Propagation and perception of bioluminescence: factors affecting counterillumination as a cryptic strategy." Biol Bull 207, no. 1 (August 2004): 1-16. Full Text Link to Item
  - Gilliland, KO, Freel, CD, Johnsen, S, Fowler, C, and Costello, MJ. "Random distribution of multilamellar bodies in human age-related nuclear cataracts." Experimental Eye Research 79 (2004): 563-576. (Academic Article)
  - Gilliland, KO, Freel, CD, Johnsen, S, Fowler, WC, and Costello, MJ. "Distribution, spherical structure and predicted Mie scattering of multilamellar bodies in human age-related nuclear cataracts." Experimental Eye Research 79, no. 4 (2004): 563-576. Full Text
  - Johnsen, S, and Sosik, HM. "Shedding light on light in the ocean." Oceanus 43 (2004): 24-28. (Academic Article)
  - Marsili, S, Salganik, RI, Albright, CD, Freel, CD, Johnsen, S, Peiffer, RL, and Costello, MJ. "Cataract formation in a strain of rats selected for high oxidative stress." Experimental Eye Research 79, no. 5 (2004): 595-612. Full Text
  - Johnsen, S. "Lifting the cloak of invisibility: the effects of changing optical conditions on pelagic crypsis." Integr Comp Biol 43, no. 4 (August 2003): 580-590. Full Text Link to Item
  - Sweeney, A, Jiggins, C, and Johnsen, S. "Insect communication: Polarized light as a butterfly mating signal." Nature 423, no. 6935 (May 1, 2003): 31-32. Full Text Link to Item
  - Avens, L, Wang, JH, Johnsen, S, Dukes, P, and Lohmann, KJ. "Responses of hatchling sea turtles to rotational displacements." Journal of Experimental Marine Biology and Ecology 288, no. 1 (2003): 111-124. Full Text
  - Johnsen, S, and Sosik, HM. "Cryptic coloration and mirrored sides as camouflage strategies in near-surface pelagic habitats: Implications for foraging and predator avoidance." Limnology and Oceanography 48, no. 3 (2003): 1277-1288.
  - Johnsen, S. "Cryptic and conspicuous coloration in the pelagic environment." Proc Biol Sci 269, no. 1488 (February 7, 2002): 243-256. Full Text Link to Item
  - Johnsen, S. "Hidden in plain sight: the ecology and physiology of organismal transparency." Biol Bull 201, no. 3 (December 2001): 301-318. (Review) Full Text Link to Item
  - Johnsen, S, and Widder, EA. "Ultraviolet absorption in transparent zooplankton and its implications for depth distribution and visual predation." Marine Biology 138, no. 4 (2001): 717-730. Full Text
  - Johnsen, S. "Transparent animals." Scientific American 282, no. 2 (2000): 80-89.
  - Lohmann, KJ, and Johnsen, S. "The neurobiology of magnetoreception in vertebrate animals." Trends in Neurosciences 23, no. 4 (2000): 153-159. Full Text
  - Widder, EA, and Johnsen, S. "3D spatial point patterns of bioluminescent plankton: A map of the 'mine field'." Journal of Plankton Research 22, no. 3 (2000): 409-420.
  - Johnsen, S, Balser, EJ, Fisher, EC, and Widder, EA. "Bioluminescence in the deep-sea cirrate octopod Stauroteuthis syrtensis verrill (Mollusca: Cephalopoda)." Biological Bulletin 197, no. 1 (1999): 26-39.
  - Johnsen, S, Balser, EJ, and Widder, EA. "Light-emitting suckers in an octopus [3]." Nature 398, no. 6723 (1999): 113-114. Full Text
  - Johnsen, S, and Kier, WM. "Shade-seeking behaviour under polarized light by the brittlestar Ophioderma brevispinum (Echinodermata: Ophiuroidea)." Journal of the Marine Biological Association of the United Kingdom 79, no. 4 (1999): 761-763. Full Text
  - Johnsen, S, and Widder, EA. "The physical basis of transparency in biological tissue: Ultrastructure and the minimization of light scattering." Journal of Theoretical Biology 199, no. 2 (1999): 181-198. Full Text
  - Widder, EA, Johnsen, S, Bernstein, SA, Case, JF, and Neilson, DJ. "Thin layers of bioluminescent copepods found at density discontinuities in the water column." Marine Biology 134, no. 3 (1999): 429-437. Full Text
  - Johnsen, S, and Kier, WM. "Damage due to solar ultraviolet radiation in the brittlestar Ophioderma brevispinum (Echinodermata: Ophiuroidea)." Journal of the Marine Biological Association of the United Kingdom 78, no. 2 (1998): 681-684.
  - Johnsen, S, and Widder, EA. "Transparency and visibility of gelatinous zooplankton from the Northwestern Atlantic and Gulf of Mexico." Biological Bulletin 195, no. 3 (1998): 337-348.
  - Johnsen, S. "Identification and localization of a possible rhodopsin in the echinoderms Asterias forbesi (asteroidea) and Ophioderma brevispinum (Ophiuroidea)." Biological Bulletin 193, no. 1 (1997): 97-105.
  - Johnsen, S. "Extraocular sensitivity to polarized light in an echinoderm." Journal of Experimental Biology 195 (1994): 281-291.
  - Kauffman, SA, and Johnsen, S. "Coevolution to the edge of chaos: Coupled fitness landscapes, poised states, and coevolutionary avalanches." Journal of Theoretical Biology 149, no. 4 (1991): 467-505.
  - Arniella, MB, Fitak, RR, and Johnsen, S. "Unmapped sequencing reads identify additional candidate genes linked to magnetoreception in rainbow trout (Published online)." Environmental Biology of Fishes . Full Text
  - Caves, EM, and Johnsen, S. "AcuityView : An r package for portraying the effects of visual acuity on scenes observed by an animal (Published online)." Edited by F Parrini. Methods in Ecology and Evolution . Full Text
Teaching & Mentoring
Recent Courses
- BIOLOGY 293: Research Independent Study 2018
- BIOLOGY 427S: Current Topics in Sensory Biology 2018
- BIOLOGY 493: Research Independent Study 2018
- BIOLOGY 792: Research 2018
- NEUROSCI 427S: Current Topics in Sensory Biology 2018
- BIOLOGY 791T: Tutorial 2016
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