Sonke Johnsen | Scholars@Duke

Sonke Johnsen
Professor of Biology

Current Appointments & Affiliations

Professor of Biology, Biology, Trinity College of Arts & Sciences 2012
Professor in the Division of Marine Science and Conservation, Marine Science and Conservation, Nicholas School of the Environment 2022
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 - Chapel Hill 1996
- B.A., Swarthmore College 1988
Previous Appointments & Affiliations
- 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
- JAN 3, 2023 Pratt School of Engineering
  
  Glassfrogs Hide Red Blood Cells in Their Liver to Become Transparent
- DEC 9, 2022 Duke Research Blog
  
  Traveling With Friends Helps Even Mixed-Up Migrators Find Their Way
- NOV 5, 2020
  
  Check This Out! Watch Whales Catch Their Favorite Food By Blowing Bubbles
- JUL 16, 2020
  
  Ultra-Black Skin Allows Some Fish to Lurk Unseen
- JUL 13, 2020
  
  Green is More Than Skin-Deep for Hundreds of Frog Species
- MAR 10, 2020
  
  To Make Ultra-Black Materials That Won’t Weigh Things Down, Consider the Butterfly
- FEB 24, 2020
  
  Solar Storms Could Scramble Whales' Navigational Sense
- JUN 24, 2019 CNN
  
  Monsters from the Deep: Duke-Led Research Team Captures Rare Video of Giant Squid
- SEP 18, 2018 Duke Arts
  
  Portrait of a Scientist as a Photographer
- JUN 8, 2018 Interdisciplinary Studies
  
  Project on Color Vision of Shrimp Helps Biology Students See Data Science in New Light
- MAY 30, 2018
  
  Details That Look Sharp to People May be Blurry to Their Pets
- 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
Awards & Honors
- Best Publication in 2020. Deep-Sea Biological Society. 2021
- top 50 Publication in chemistry or materials science. Nature Communications journal . 2021
Expertise
Global Scholarship
- Research
  - Australia (Country)
Research
Selected Grants
- Collaborative Research: Visual adaptations in hydrothermal vent shrimp and the role in feeding modalities and habitat selection awarded by National Science Foundation 2022 - 2025
- Magnetoreception in Marine Animals and Bio-Inspired Algorithms for Long-range, GPS-free Navigation awarded by University of North Carolina - Chapel Hill 2020 - 2023
- Persistent Aquatic Living Sensors Analysis and Support Services awarded by Northrop Grumman Corporation 2018 - 2023
- The International Human Frontier Science Program Organization awarded by International Human Frontier Science Program Organization 2018 - 2022
- Long-range Geomagnetic Navigation in Sea Turtles: An Interdisciplinary Approach to Localizing Magnetite-based Biological Magnetoreceptors awarded by University of North Carolina - Chapel Hill 2014 - 2020
- The Sigsbee Deep Expedition- Exploration of light in the water column below 1000m awarded by National Oceanic and Atmospheric Administration 2017 - 2020
- 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: An interdisciplinary approach to crypsis based on color, reflection, and bioluminescence awarded by Office of Naval Research 2009 - 2015
- Collaborative Research: Midwater animal models: Optical measurement of metabolic transitions in transparent pelagic biota 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 Conditions 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
External Relationships
- Dahlio Philanthropies
- Florida International University
- Netflix Inc
- zoological lighting institute
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Taboada, Carlos, Jesse Delia, Maomao Chen, Chenshuo Ma, Xiaorui Peng, Xiaoyi Zhu, Laiming Jiang, et al. “Glassfrogs conceal blood in their liver to maintain transparency.” Science (New York, N.Y.) 378, no. 6626 (December 2022): 1315–20. https://doi.org/10.1126/science.abl6620.
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  - Granger, Jesse, and Sönke Johnsen. “Collective movement as a solution to noisy navigation and its vulnerability to population loss.” Proceedings. Biological Sciences 289, no. 1987 (November 2022): 20221910. https://doi.org/10.1098/rspb.2022.1910.
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  - Cooke, Steven J., Jordanna N. Bergman, William M. Twardek, Morgan L. Piczak, Grace A. Casselberry, Keegan Lutek, Lotte S. Dahlmo, et al. “The movement ecology of fishes.” Journal of Fish Biology 101, no. 4 (October 2022): 756–79. https://doi.org/10.1111/jfb.15153.
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  - Notar, Julia C., Bernice Meja, and Sönke Johnsen. “Testing Mechanisms of Vision: Sea Urchin Spine Density Does Not Correlate With Vision-Related Environmental Characteristics.” Integrative and Comparative Biology, July 2022, icac119. https://doi.org/10.1093/icb/icac119.
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  - Davis, Alexander, Matthew N. Zipple, Danae Diaz, Susan Peters, Stephen Nowicki, and Sönke Johnsen. “Influence of visual background on discrimination of signal-relevant colours in zebra finches (Taeniopygia guttata).” Proceedings. Biological Sciences 289, no. 1976 (June 2022): 20220756. https://doi.org/10.1098/rspb.2022.0756.
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  - Johnsen, Sönke, and Steven H. D. Haddock. “Macropinna.” Current Biology : Cb 32, no. 6 (March 2022): R256–57. https://doi.org/10.1016/j.cub.2022.02.020.
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  - Green, P. A., E. M. George, K. A. Rosvall, S. Johnsen, and S. Nowicki. “Testosterone, signal coloration, and signal color perception in male zebra finch contests.” Ethology : Formerly Zeitschrift Fur Tierpsychologie 128, no. 2 (February 2022): 131–42. https://doi.org/10.1111/eth.13247.
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  - Granger, Jesse, Steven A. Cummer, Kenneth J. Lohmann, and Sönke Johnsen. “Environmental sources of radio frequency noise: potential impacts on magnetoreception.” Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology 208, no. 1 (January 2022): 83–95. https://doi.org/10.1007/s00359-021-01516-z.
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  - Johnsen, Sonke, and Steven H. D. Haddock. “Macropinna.” Current Biology 32, no. 6 (2022): R256–57.
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  - Wale, N., R. C. Fuller, S. Johnsen, M. L. Turrill, and M. A. Duffy. “The visual ecology of selective predation: Are unhealthy hosts less stealthy hosts?” Ecology and Evolution 11, no. 24 (December 1, 2021): 18591–603. https://doi.org/10.1002/ece3.8464.
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  - Robinson, N. J., S. Johnsen, A. Brooks, L. Frey, H. Judkins, M. Vecchione, and E. Widder. “Studying the swift, smart, and shy: Unobtrusive camera-platforms for observing large deep-sea squid.” Deep Sea Research Part I: Oceanographic Research Papers 172 (June 1, 2021). https://doi.org/10.1016/j.dsr.2021.103538.
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  - Caves, Eleanor M., and Sönke Johnsen. “The sensory impacts of climate change: bathymetric shifts and visually mediated interactions in aquatic species.” Proceedings. Biological Sciences 288, no. 1949 (April 2021): 20210396. https://doi.org/10.1098/rspb.2021.0396.
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  - Kingston, Alexandra C. N., Daniel R. Chappell, Loann Koch, Sönke Johnsen, and Daniel I. Speiser. “The orbital hoods of snapping shrimp have surface features that may represent tradeoffs between vision and protection.” Arthropod Structure & Development 61 (March 2021): 101025. https://doi.org/10.1016/j.asd.2020.101025.
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  - Caves, Eleanor M., Patrick A. Green, Matthew N. Zipple, Dhanya Bharath, Susan Peters, Sönke Johnsen, and Stephen Nowicki. “Comparison of Categorical Color Perception in Two Estrildid Finches.” The American Naturalist 197, no. 2 (February 2021): 190–202. https://doi.org/10.1086/712379.
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  - Davis, Alexander L., Kate N. Thomas, Freya E. Goetz, Bruce H. Robison, Sönke Johnsen, and Karen J. Osborn. “Ultra-black Camouflage in Deep-Sea Fishes.” Current Biology : Cb 30, no. 17 (September 2020): 3470-3476.e3. https://doi.org/10.1016/j.cub.2020.06.044.
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  - Schweikert, Lorian E., Alexander L. Davis, Sönke Johnsen, and Heather D. Bracken-Grissom. “Visual perception of light organ patterns in deep-sea shrimps and implications for conspecific recognition.” Ecology and Evolution 10, no. 17 (September 2020): 9503–13. https://doi.org/10.1002/ece3.6643.
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  - Ernst, David A., Robert R. Fitak, Manfred Schmidt, Charles D. Derby, Sönke Johnsen, and Kenneth J. Lohmann. “Pulse magnetization elicits differential gene expression in the central nervous system of the Caribbean spiny lobster, Panulirus argus.” Journal of Comparative Physiology. A, Neuroethology, Sensory, Neural, and Behavioral Physiology 206, no. 5 (September 2020): 725–42. https://doi.org/10.1007/s00359-020-01433-7.
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  - Johnsen, Sönke, Kenneth J. Lohmann, and Eric J. Warrant. “Animal navigation: a noisy magnetic sense?” The Journal of Experimental Biology 223, no. Pt 18 (September 2020): jeb164921. https://doi.org/10.1242/jeb.164921.
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  - Taboada, Carlos, Andrés E. Brunetti, Mariana L. Lyra, Robert R. Fitak, Ana Faigón Soverna, Santiago R. Ron, María G. Lagorio, et al. “Multiple origins of green coloration in frogs mediated by a novel biliverdin-binding serpin.” Proceedings of the National Academy of Sciences of the United States of America 117, no. 31 (August 2020): 18574–81. https://doi.org/10.1073/pnas.2006771117.
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  - Caves, E. M., L. E. Schweikert, P. A. Green, M. N. Zipple, C. Taboada, S. Peters, S. Nowicki, and S. Johnsen. “Variation in carotenoid-containing retinal oil droplets correlates with variation in perception of carotenoid coloration.” Behavioral Ecology and Sociobiology 74, no. 7 (July 1, 2020). https://doi.org/10.1007/s00265-020-02874-5.
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  - Davis, Alexander L., Tracey T. Sutton, William M. Kier, and Sönke Johnsen. “Evidence that eye-facing photophores serve as a reference for counterillumination in an order of deep-sea fishes.” Proceedings. Biological Sciences 287, no. 1928 (June 2020): 20192918. https://doi.org/10.1098/rspb.2019.2918.
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  - Fitak, Robert R., Benjamin R. Wheeler, and Sönke Johnsen. “Effect of a magnetic pulse on orientation behavior in rainbow trout (Oncorhynchus mykiss).” Behavioural Processes 172 (March 2020): 104058. https://doi.org/10.1016/j.beproc.2020.104058.
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  - Davis, Alexander L., H Frederik Nijhout, and Sönke Johnsen. “Diverse nanostructures underlie thin ultra-black scales in butterflies.” Nature Communications 11, no. 1 (March 2020): 1294. https://doi.org/10.1038/s41467-020-15033-1.
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  - Granger, Jesse, Lucianne Walkowicz, Robert Fitak, and Sönke Johnsen. “Gray whales strand more often on days with increased levels of atmospheric radio-frequency noise.” Current Biology : Cb 30, no. 4 (February 2020): R155–56. https://doi.org/10.1016/j.cub.2020.01.028.
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  - Costello, M Joseph, Kurt O. Gilliland, Ashik Mohamed, Kevin L. Schey, Sönke Johnsen, Lisa A. Brennan, and Marc Kantorow. “Novel mitochondrial derived Nuclear Excisosome degrades nuclei during differentiation of prosimian Galago (bush baby) monkey lenses.” Plos One 15, no. 11 (January 2020): e0241631. https://doi.org/10.1371/journal.pone.0241631.
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  - Johnsen, Sonke. “Development of Innovative Techniques for Exploring Novel Submarine Springs on the Gulf of Mexico Outer Continental Shelf.” Oceanography 33, no. 1 (2020): 96–96.
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  - Johnsen, Sonke. “Journey into Midnight.” Oceanography 33, no. 1 (2020): 96–96.
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  - Caves, Eleanor M., Stephen Nowicki, and Sönke Johnsen. “Von Uexküll Revisited: Addressing Human Biases in the Study of Animal Perception.” Integrative and Comparative Biology 59, no. 6 (December 2019): 1451–62. https://doi.org/10.1093/icb/icz073.
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  - Harris, Olivia K., Alexandra C. N. Kingston, Caitlin S. Wolfe, Soumitra Ghoshroy, Sönke Johnsen, and Daniel I. Speiser. “Core-shell nanospheres behind the blue eyes of the bay scallop Argopecten irradians.” Journal of the Royal Society, Interface 16, no. 159 (October 2019): 20190383. https://doi.org/10.1098/rsif.2019.0383.
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  - Caves, Eleanor M., Catherine Chen, and Sönke Johnsen. “The cleaner shrimp Lysmata amboinensis adjusts its behaviour towards predatory versus non-predatory clients.” Biology Letters 15, no. 9 (September 2019): 20190534. https://doi.org/10.1098/rsbl.2019.0534.
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  - Schweikert, Lorian E., Eleanor M. Caves, Sarah E. Solie, Tracey T. Sutton, and Sönke Johnsen. “Variation in rod spectral sensitivity of fishes is best predicted by habitat and depth.” Journal of Fish Biology 95, no. 1 (July 2019): 179–85. https://doi.org/10.1111/jfb.13859.
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  - Zipple, Matthew N., Eleanor M. Caves, Patrick A. Green, Susan Peters, Sönke Johnsen, and Stephen Nowicki. “Categorical colour perception occurs in both signalling and non-signalling colour ranges in a songbird.” Proceedings. Biological Sciences 286, no. 1903 (May 2019): 20190524. https://doi.org/10.1098/rspb.2019.0524.
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  - Ritschard, Elena A., Robert R. Fitak, Oleg Simakov, and Sönke Johnsen. “Genomic signatures of G-protein-coupled receptor expansions reveal functional transitions in the evolution of cephalopod signal transduction.” Proceedings. Biological Sciences 286, no. 1897 (February 2019): 20182929. https://doi.org/10.1098/rspb.2018.2929.
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  - Marshall, N Justin, Samuel B. Powell, Thomas W. Cronin, Roy L. Caldwell, Sonke Johnsen, Viktor Gruev, T-H Short Chiou, Nicholas W. Roberts, and Martin J. How. “Polarisation signals: a new currency for communication.” The Journal of Experimental Biology 222, no. Pt 3 (February 2019): jeb134213. https://doi.org/10.1242/jeb.134213.
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  - Foster, James J., John D. Kirwan, Basil El Jundi, Jochen Smolka, Lana Khaldy, Emily Baird, Marcus J. Byrne, Dan-Eric Nilsson, Sönke Johnsen, and Marie Dacke. “Orienting to polarized light at night - matching lunar skylight to performance in a nocturnal beetle.” The Journal of Experimental Biology 222, no. Pt 2 (January 2019): jeb188532. https://doi.org/10.1242/jeb.188532.
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  - Schweikert, Lorian E., Robert R. Fitak, Eleanor M. Caves, Tracey T. Sutton, and Sönke Johnsen. “Spectral sensitivity in ray-finned fishes: diversity, ecology and shared descent.” The Journal of Experimental Biology 221, no. Pt 23 (November 2018): jeb189761. https://doi.org/10.1242/jeb.189761.
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  - Eisthen, Heather L., Kenneth M. Halanych, Darcy B. Kelley, Stephanie A. White, Steven M. Phelps, and Steven M. 66 additional authors. “New NSF policy will stifle innovation.” Science (New York, N.Y.) 362, no. 6412 (October 2018): 297–98. https://doi.org/10.1126/science.aav4793.
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  - Fitak, R. R., E. M. Caves, and S. Johnsen. “Orientation in Pill Bugs: An Interdisciplinary Activity to Engage Students in Concepts of Biology, Physics & Circular Statistics.” American Biology Teacher 80, no. 8 (October 1, 2018): 608–18. https://doi.org/10.1525/abt.2018.80.8.608.
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  - Caves, Eleanor M., Patrick A. Green, Matthew N. Zipple, Susan Peters, Sönke Johnsen, and Stephen Nowicki. “Categorical perception of colour signals in a songbird.” Nature 560, no. 7718 (August 2018): 365–67. https://doi.org/10.1038/s41586-018-0377-7.
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  - Dreyer, David, Barrie Frost, Henrik Mouritsen, Anja Günther, Ken Green, Mary Whitehouse, Sönke Johnsen, Stanley Heinze, and Eric Warrant. “The Earth's Magnetic Field and Visual Landmarks Steer Migratory Flight Behavior in the Nocturnal Australian Bogong Moth.” Current Biology : Cb 28, no. 13 (July 2018): 2160-2166.e5. https://doi.org/10.1016/j.cub.2018.05.030.
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  - Fitak, R. R., and S. Johnsen. “Green sea turtle (Chelonia mydas) population history indicates important demographic changes near the mid-Pleistocene transition.” Marine Biology 165, no. 7 (July 1, 2018). https://doi.org/10.1007/s00227-018-3366-3.
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  - Caves, Eleanor M., Patrick A. Green, and Sönke Johnsen. “Mutual visual signalling between the cleaner shrimp Ancylomenes pedersoni and its client fish.” Proceedings. Biological Sciences 285, no. 1881 (June 2018): 20180800. https://doi.org/10.1098/rspb.2018.0800.
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  - Fitak, Robert R., Lorian E. Schweikert, Benjamin R. Wheeler, David A. Ernst, Kenneth J. Lohmann, and Sönke Johnsen. “Near absence of differential gene expression in the retina of rainbow trout after exposure to a magnetic pulse: implications for magnetoreception.” Biology Letters 14, no. 6 (June 2018): 20180209. https://doi.org/10.1098/rsbl.2018.0209.
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  - Arniella, M. B., R. R. Fitak, and S. Johnsen. “Unmapped sequencing reads identify additional candidate genes linked to magnetoreception in rainbow trout.” Environmental Biology of Fishes 101, no. 5 (May 1, 2018): 711–21. https://doi.org/10.1007/s10641-018-0731-5.
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  - Caves, Eleanor M., Nicholas C. Brandley, and Sönke Johnsen. “Visual Acuity and the Evolution of Signals.” Trends in Ecology & Evolution 33, no. 5 (May 2018): 358–72. https://doi.org/10.1016/j.tree.2018.03.001.
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  - Schweikert, Lorian E., Robert R. Fitak, and Sönke Johnsen. “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 204, no. 5 (May 2018): 475–85. https://doi.org/10.1007/s00359-018-1254-4.
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  - Caves, E. M., and S. Johnsen. “AcuityView: An r package for portraying the effects of visual acuity on scenes observed by an animal.” Methods in Ecology and Evolution 9, no. 3 (March 1, 2018): 793–97. https://doi.org/10.1111/2041-210X.12911.
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  - Bracken-Grissom, H., E. Widder, S. Johnsen, C. Messing, and T. Frank. “Decapod diversity associated with deep-sea octocorals in the Gulf of Mexico.” Crustaceana 91, no. 10 (January 1, 2018): 1267–75. https://doi.org/10.1163/15685403-00003829.
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  - Haddock, S. H. D., L. M. Christianson, W. R. Francis, S. Martini, C. W. Dunn, P. R. Pugh, C. E. Mills, et al. “Insights into the biodiversity, behavior, and bioluminescence of deep-sea organisms using molecular and maritime technology.” Oceanography 30, no. 4 (December 1, 2017): 38–47. https://doi.org/10.5670/OCEANOG.2017.422.
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  - Bagge, Laura E., Stephen T. Kinsey, Justin Gladman, and Sönke Johnsen. “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): 4225–33. https://doi.org/10.1242/jeb.162362.
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  - Fitak, Robert R., and Sönke Johnsen. “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): 3878–82. https://doi.org/10.1242/jeb.167056.
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  - Marshall, Justin, and Sonke Johnsen. “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): 20160335. https://doi.org/10.1098/rstb.2016.0335.
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  - Caves, Eleanor M., Tracey T. Sutton, and Sönke Johnsen. “Visual acuity in ray-finned fishes correlates with eye size and habitat.” The Journal of Experimental Biology 220, no. Pt 9 (May 2017): 1586–96. https://doi.org/10.1242/jeb.151183.
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  - Johnsen, Sönke. “Open Questions: We don't really know anything, do we? Open questions in sensory biology.” Bmc Biology 15, no. 1 (May 2017): 43. https://doi.org/10.1186/s12915-017-0385-3.
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  - Taylor, Brian K., Sönke Johnsen, and Kenneth J. Lohmann. “Detection of magnetic field properties using distributed sensing: a computational neuroscience approach.” Bioinspiration & Biomimetics 12, no. 3 (May 2017): 036013. https://doi.org/10.1088/1748-3190/aa6ccd.
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  - Cronin, Thomas W., Jeffry I. Fasick, Lorian E. Schweikert, Sönke Johnsen, Lorren J. Kezmoh, and Mark F. Baumgartner. “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): 20160067. https://doi.org/10.1098/rstb.2016.0067.
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  - Fitak, Robert R., Benjamin R. Wheeler, David A. Ernst, Kenneth J. Lohmann, and Sönke Johnsen. “Candidate genes mediating magnetoreception in rainbow trout (Oncorhynchus mykiss).” Biology Letters 13, no. 4 (April 2017): 20170142. https://doi.org/10.1098/rsbl.2017.0142.
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  - Thomas, Kate N., Bruce H. Robison, and Sönke Johnsen. “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): 20160069. https://doi.org/10.1098/rstb.2016.0069.
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  - Tedore, Cynthia, and Sönke Johnsen. “Using RGB displays to portray color realistic imagery to animal eyes.” Current Zoology 63, no. 1 (February 2017): 27–34. https://doi.org/10.1093/cz/zow076.
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  - Bagge, Laura E., Karen J. Osborn, and Sönke Johnsen. “Nanostructures and Monolayers of Spheres Reduce Surface Reflections in Hyperiid Amphipods.” Current Biology : Cb 26, no. 22 (November 2016): 3071–76. https://doi.org/10.1016/j.cub.2016.09.033.
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  - Cronin, Thomas W., and Sönke Johnsen. “Extraocular, Non-Visual, and Simple Photoreceptors: An Introduction to the Symposium.” Integrative and Comparative Biology 56, no. 5 (November 2016): 758–63. https://doi.org/10.1093/icb/icw106.
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  - Speiser, Daniel I., Yakir Luc Gagnon, Raghav K. Chhetri, Amy L. Oldenburg, and Sönke Johnsen. “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. https://doi.org/10.1093/icb/icw099.
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  - Ruxton, Graeme D., and Sönke Johnsen. “The effect of aggregation on visibility in open water.” Proceedings. Biological Sciences 283, no. 1839 (September 2016): 20161463. https://doi.org/10.1098/rspb.2016.1463.
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  - Cronin, Thomas W., Yakir Luc Gagnon, Sönke Johnsen, N Justin Marshall, and Nicholas W. Roberts. “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. https://doi.org/10.1126/science.aaf4481.
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  - Johnsen, Sönke, Yakir L. Gagnon, N Justin Marshall, Thomas W. Cronin, Viktor Gruev, and Samuel Powell. “Polarization vision seldom increases the sighting distance of silvery fish.” Current Biology : Cb 26, no. 16 (August 2016): R752–54. https://doi.org/10.1016/j.cub.2016.07.030.
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  - Tedore, Cynthia, and Sönke Johnsen. “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. https://doi.org/10.1242/jeb.129122.
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  - Wilkins, Lucas, N Justin Marshall, Sönke Johnsen, and D. Osorio. “Modelling colour constancy in fish: implications for vision and signalling in water.” The Journal of Experimental Biology 219, no. Pt 12 (June 2016): 1884–92. https://doi.org/10.1242/jeb.139147.
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  - Johnsen, Sönke. “How to measure color using spectrometers and calibrated photographs.” The Journal of Experimental Biology 219, no. Pt 6 (March 2016): 772–78. https://doi.org/10.1242/jeb.124008.
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  - Zylinski, Sarah, D. Osorio, and Sonke Johnsen. “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. https://doi.org/10.1098/rspb.2016.0062.
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  - Caves, Eleanor M., Tamara M. Frank, and Sönke Johnsen. “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. https://doi.org/10.1242/jeb.122275.
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  - Brandley, N., M. Johnson, and S. Johnsen. “Aposematic signals in North American black widows are more conspicuous to predators than to prey.” Behavioral Ecology 27, no. 4 (January 1, 2016): 1104–12. https://doi.org/10.1093/beheco/arw014.
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  - Costello, M Joseph, Lisa A. Brennan, Ashik Mohamed, Kurt O. Gilliland, Sönke Johnsen, and Marc Kantorow. “Identification and Ultrastructural Characterization of a Novel Nuclear Degradation Complex in Differentiating Lens Fiber Cells.” Plos One 11, no. 8 (2016): e0160785. https://doi.org/10.1371/journal.pone.0160785.
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  - Bedore, Christine N., Stephen M. Kajiura, and Sönke Johnsen. “Freezing behaviour facilitates bioelectric crypsis in cuttlefish faced with predation risk.” Proceedings. Biological Sciences 282, no. 1820 (December 2015): 20151886. https://doi.org/10.1098/rspb.2015.1886.
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  - Tedore, C., and S. Johnsen. “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 14, 2015): 437–46. https://doi.org/10.1007/s11829-015-9386-8.
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  - Gagnon, Y. L., T. T. Sutton, and S. Johnsen. “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): 155–56. https://doi.org/10.1016/j.visres.2015.07.001.
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  - Tedore, C., and S. Johnsen. “Visual mutual assessment of size in male Lyssomanes viridis jumping spider contests.” Behavioral Ecology 26, no. 2 (February 11, 2015): 510–18. https://doi.org/10.1093/beheco/aru222.
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  - Baldwin Fergus, Jamie L., Sönke Johnsen, and Karen J. Osborn. “A unique apposition compound eye in the mesopelagic hyperiid amphipod Paraphronima gracilis.” Current Biology : Cb 25, no. 4 (February 2015): 473–78. https://doi.org/10.1016/j.cub.2014.12.010.
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  - Palmer, Glenn, and Sönke Johnsen. “Downwelling spectral irradiance during evening twilight as a function of the lunar phase.” Applied Optics 54, no. 4 (February 2015): B85–92. https://doi.org/10.1364/ao.54.000b85.
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  - Taniguchi, Darcy A. A., Yakir Gagnon, Benjamin R. Wheeler, Sönke Johnsen, and Jules S. Jaffe. “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. https://doi.org/10.1371/journal.pone.0138690.
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  - Dougherty, Lindsey F., Sönke Johnsen, Roy L. Caldwell, and N Justin Marshall. “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. https://doi.org/10.1098/rsif.2014.0407.
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  - Muchhala, Nathan, Sönke Johnsen, and Stacey Dewitt Smith. “Competition for hummingbird pollination shapes flower color variation in Andean solanaceae.” Evolution; International Journal of Organic Evolution 68, no. 8 (August 2014): 2275–86. https://doi.org/10.1111/evo.12441.
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  - Gagnon, Yakir Luc, Daniel I. Speiser, and Sönke Johnsen. “Simplifying numerical ray tracing for characterization of optical systems.” Applied Optics 53, no. 21 (July 2014): 4784–90. https://doi.org/10.1364/ao.53.004784.
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  - Akre, Karin L., and Sönke Johnsen. “Psychophysics and the evolution of behavior.” Trends in Ecology & Evolution 29, no. 5 (May 2014): 291–300. https://doi.org/10.1016/j.tree.2014.03.007.
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  - Johnsen, S., E. Gassmann, R. A. Reynolds, D. Stramski, and C. Mobley. “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 (January 1, 2014): 1839–52. https://doi.org/10.4319/lo.2014.59.6.1839.
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  - Johnsen, Sönke. “Hide and seek in the open sea: pelagic camouflage and visual countermeasures.” Annual Review of Marine Science 6 (January 2014): 369–92. https://doi.org/10.1146/annurev-marine-010213-135018.
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  - Nilsson, Dan-E, Eric Warrant, and Sönke Johnsen. “Computational visual ecology in the pelagic realm.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 369, no. 1636 (January 2014): 20130038. https://doi.org/10.1098/rstb.2013.0038.
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  - Brandley, N. C., D. I. Speiser, and S. Johnsen. “Eavesdropping on visual secrets.” Evolutionary Ecology 27, no. 6 (November 1, 2013): 1045–68. https://doi.org/10.1007/s10682-013-9656-9.
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  - Costello, M Joseph, Lisa A. Brennan, Subharsee Basu, Daniel Chauss, Ashik Mohamed, Kurt O. Gilliland, Sönke Johnsen, Sue Menko, and Marc Kantorow. “Autophagy and mitophagy participate in ocular lens organelle degradation.” Exp Eye Res 116 (November 2013): 141–50. https://doi.org/10.1016/j.exer.2013.08.017.
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  - Gagnon, Yakir L., Tracey T. Sutton, and Sönke Johnsen. “Visual acuity in pelagic fishes and mollusks.” Vision Research 92 (November 2013): 1–9. https://doi.org/10.1016/j.visres.2013.08.007.
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  - Warrant, Eric J., and Sönke Johnsen. “Vision and the light environment.” Current Biology : Cb 23, no. 22 (November 2013): R990–94. https://doi.org/10.1016/j.cub.2013.10.019.
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  - Costello, M Joseph, Ashik Mohamed, Kurt O. Gilliland, W Craig Fowler, and Sönke Johnsen. “Ultrastructural analysis of the human lens fiber cell remodeling zone and the initiation of cellular compaction.” Exp Eye Res 116 (November 2013): 411–18. https://doi.org/10.1016/j.exer.2013.10.015.
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  - Nilsson, Dan-E, Eric J. Warrant, Sönke Johnsen, Roger T. Hanlon, and Nadav Shashar. “The giant eyes of giant squid are indeed unexpectedly large, but not if used for spotting sperm whales.” Bmc Evolutionary Biology 13 (September 2013): 187. https://doi.org/10.1186/1471-2148-13-187.
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  - Tedore, Cynthia, and Sönke Johnsen. “Pheromones exert top-down effects on visual recognition in the jumping spider Lyssomanes viridis.” The Journal of Experimental Biology 216, no. Pt 9 (May 2013): 1744–56. https://doi.org/10.1242/jeb.071118.
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  - Mohamed, Ashik, Kurt O. Gilliland, Sangeetha Metlapally, Sönke Johnsen, and M Joseph Costello. “Simple fixation and storage protocol for preserving the internal structure of intact human donor lenses and extracted human nuclear cataract specimens.” Mol Vis 19 (2013): 2352–59.
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  - Frank, Tamara M., Sönke Johnsen, and Thomas W. Cronin. “Light and vision in the deep-sea benthos: II. Vision in deep-sea crustaceans.” The Journal of Experimental Biology 215, no. Pt 19 (October 2012): 3344–53. https://doi.org/10.1242/jeb.072033.
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  - Johnsen, Sönke, Tamara M. Frank, Steven H. D. Haddock, Edith A. Widder, and Charles G. Messing. “Light and vision in the deep-sea benthos: I. Bioluminescence at 500-1000 m depth in the Bahamian islands.” The Journal of Experimental Biology 215, no. Pt 19 (October 2012): 3335–43. https://doi.org/10.1242/jeb.072009.
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  - Costello, M Joseph, Alain Burette, Mariko Weber, Sangeetha Metlapally, Kurt O. Gilliland, W Craig Fowler, Ashik Mohamed, and Sönke Johnsen. “Electron tomography of fiber cell cytoplasm and dense cores of multilamellar bodies from human age-related nuclear cataracts.” Exp Eye Res 101 (August 2012): 72–81. https://doi.org/10.1016/j.exer.2012.06.005.
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  - Baldwin, Jamie, and Sönke Johnsen. “The male blue crab, Callinectes sapidus, uses both chromatic and achromatic cues during mate choice.” The Journal of Experimental Biology 215, no. Pt 7 (April 2012): 1184–91. https://doi.org/10.1242/jeb.067512.
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  - Nilsson, Dan-Eric, Eric J. Warrant, Sönke Johnsen, Roger Hanlon, and Nadav Shashar. “A unique advantage for giant eyes in giant squid.” Current Biology : Cb 22, no. 8 (April 2012): 683–88. https://doi.org/10.1016/j.cub.2012.02.031.
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  - Holt, A. L., A. M. Sweeney, S. Johnsen, and D. E. Morse. “Erratum: 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 (March 7, 2012): 600. https://doi.org/10.1098/rsif.2011.0811.
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  - Tedore, Cynthia, and Sönke Johnsen. “Weaponry, color, and contest success in the jumping spider Lyssomanes viridis.” Behavioural Processes 89, no. 3 (March 2012): 203–11. https://doi.org/10.1016/j.beproc.2011.10.017.
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  - 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.
  - Brandley, N. C., and S. Johnsen. “Eavesdropping on visual secrets (Submitted).” Evolutionary Ecology, 2012.
  - Costello, M. J., D. Chauss, A. Mohamed, K. O. Gilliland, S. Johnsen, M. Bates, L. A. Brennan, and M. Kantorow. “Autophagy and Mitophagy in the Ocular Lens (Submitted).” Journal of Cell Science, 2012.
  - Johnsen, Sönke. “Anything that involves a photon and an animal.” Current Biology : Cb 22, no. 1 (January 2012): R6–7. https://doi.org/10.1016/j.cub.2011.11.035.
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  - Moore, B. A., J. M. Kamilar, S. P. Collin, O. R. P. Bininda Emonds, N. J. Dominy, M. I. Hall, C. P. Heesy, et al. “A novel method for comparative analysis of retinal specialization traits from topographic maps.” Journal of Vision 12, no. 1–24 (2012).
  - Moore, B. A., J. M. Kamilar, S. P. Collin, O. R. P. Bininda Emonds, N. J. Dominy, M. I. Hall, C. P. Heesy, et al. “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.
  - Moore, Bret A., Jason M. Kamilar, Shaun P. Collin, Olaf R. P. Bininda-Emonds, Nathaniel J. Dominy, Margaret I. Hall, Christopher P. Heesy, et al. “A novel method for comparative analysis of retinal specialization traits from topographic maps.” Journal of Vision 12, no. 12 (January 2012): 13. https://doi.org/10.1167/12.12.13.
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  - Frank, T. M., and S. Johnsen. “Light and vision in the deep-sea benthos. II. Special visual adaptations in deep-sea benthic crustaceans.” Journal of Experimental Biology 215 (2012): 3344–53.
  - Zylinski, Sarah, and Sönke Johnsen. “Mesopelagic cephalopods switch between transparency and pigmentation to optimize camouflage in the deep.” Current Biology : Cb 21, no. 22 (November 2011): 1937–41. https://doi.org/10.1016/j.cub.2011.10.014.
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  - Holt, Amanda L., Alison M. Sweeney, Sönke Johnsen, and Daniel E. Morse. “A highly distributed Bragg stack with unique geometry provides effective camouflage for Loliginid squid eyes.” Journal of the Royal Society, Interface 8, no. 63 (October 2011): 1386–99. https://doi.org/10.1098/rsif.2010.0702.
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  - Baldwin, Jamie, and Sönke Johnsen. “Effects of molting on the visual acuity of the blue crab, Callinectes sapidus.” The Journal of Experimental Biology 214, no. Pt 18 (September 2011): 3055–61. https://doi.org/10.1242/jeb.056861.
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  - Jackson, Emily, and Sönke Johnsen. “Orientation to Objects in the Sea Urchin Strongylocentrotus purpuratus depends on apparent and not actual object size.” The Biological Bulletin 220, no. 2 (April 2011): 86–88. https://doi.org/10.1086/bblv220n2p86.
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  - Speiser, Daniel I., Douglas J. Eernisse, and Sönke Johnsen. “A chiton uses aragonite lenses to form images.” Current Biology : Cb 21, no. 8 (April 2011): 665–70. https://doi.org/10.1016/j.cub.2011.03.033.
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  - Bhandiwad, Ashwin, and Sönke Johnsen. “The effects of salinity and temperature on the transparency of the grass shrimp Palaemonetes pugio.” The Journal of Experimental Biology 214, no. Pt 5 (March 2011): 709–16. https://doi.org/10.1242/jeb.049296.
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  - Johnsen, Sönke, N Justin Marshall, and Edith A. Widder. “Polarization sensitivity as a contrast enhancer in pelagic predators: lessons from in situ polarization imaging of transparent zooplankton.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 366, no. 1565 (March 2011): 655–70. https://doi.org/10.1098/rstb.2010.0193.
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  - Shashar, Nadav, Sönke Johnsen, Amit Lerner, Shai Sabbah, Chuan-Chin Chiao, Lydia M. Mäthger, and Roger T. Hanlon. “Underwater linear polarization: physical limitations to biological functions.” Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences 366, no. 1565 (March 2011): 649–54. https://doi.org/10.1098/rstb.2010.0190.
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  - Sweeney, Alison M., Charles A. Boch, Sonke Johnsen, and Daniel E. Morse. “Twilight spectral dynamics and the coral reef invertebrate spawning response.” The Journal of Experimental Biology 214, no. Pt 5 (March 2011): 770–77. https://doi.org/10.1242/jeb.043406.
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  - Speiser, Daniel I., Ellis R. Loew, and Sönke Johnsen. “Spectral sensitivity of the concave mirror eyes of scallops: potential influences of habitat, self-screening and longitudinal chromatic aberration.” The Journal of Experimental Biology 214, no. Pt 3 (February 2011): 422–31. https://doi.org/10.1242/jeb.048108.
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  - Speiser, D. I., D. Eernisse, and S. Johnsen. “Chitons eye have calcitic lenses and provide spatial vision.” Current Biology 21 (2011): 665–70.
  - Tedore, C. A., and S. Johnsen. “The function of male-male threat displays in the jumping spider Lyssomanes viridis.” Behavioural Processes (Online for Now), 2011.
  - Jaffe, J. S., F. Simonet, B. Laxton, P. L. D. Roberts, S. Zylinski, S. Johnsen, and A. M. Sweeney. “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.
  - Speiser, D. I., E. R. Loew, and S. Johnsen. “Spectral sensitivity of the concave mirror eyes of scallops: The influence of habitat and longitudinal chromatic aberration.” Journal of Experimental Biology 214 (2011): 422–31.
  - Costello, M Joseph, Sönke Johnsen, Sangeetha Metlapally, Kurt O. Gilliland, Lesley Frame, and Dorairajan Balasubramanian. “Multilamellar spherical particles as potential sources of excessive light scattering in human age-related nuclear cataracts.” Exp Eye Res 91, no. 6 (December 2010): 881–89. https://doi.org/10.1016/j.exer.2010.09.013.
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  - Yerramilli, D., and S. Johnsen. “Spatial vision in the purple sea urchin Strongylocentrotus purpuratus (Echinoidea).” The Journal of Experimental Biology 213, no. 2 (January 2010): 249–55. https://doi.org/10.1242/jeb.033159.
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  - Baldwin, Jamie, and Sönke Johnsen. “The importance of color in mate choice of the blue crab Callinectes sapidus.” The Journal of Experimental Biology 212, no. Pt 22 (November 2009): 3762–68. https://doi.org/10.1242/jeb.028027.
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  - Johnsen, Sönke, and Kenneth J. Lohmann. “An inner ear magneto-receptor?” Physics Today 62, no. 2 (February 2009): 14–14. https://doi.org/10.1063/1.4797051.
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  - Marlow, H., D. I. Speiser, D. Matus, S. Johnsen, E. C. Seaver, and M. Q. Martindale. “The evolution of a complex trait: Photoreception in the Metazoa (In preparation).” Nature, 2009.
  - Speiser, D. I., and S. Johnsen. “Comparative morphology of the concave mirror eyes of scallops (Pectinoidea).” American Malacological Bulletin 26, no. 1–2 (December 29, 2008): 27–33. https://doi.org/10.4003/006.026.0204.
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  - Matz, Mikhail V., Tamara M. Frank, N Justin Marshall, Edith A. Widder, and Sönke Johnsen. “Giant deep-sea protist produces bilaterian-like traces.” Current Biology : Cb 18, no. 23 (December 2008): 1849–54. https://doi.org/10.1016/j.cub.2008.10.028.
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  - Costello, M. J., Sönke Johnsen, Sangeetha Metlapally, Kurt O. Gilliland, Balasubramanya Ramamurthy, Pravin V. Krishna, and Dorairajan Balasubramanian. “Ultrastructural analysis of damage to nuclear fiber cell membranes in advanced age-related cataracts from India.” Exp Eye Res 87, no. 2 (August 2008): 147–58. https://doi.org/10.1016/j.exer.2008.05.009.
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  - Speiser, Daniel I., and Sönke Johnsen. “Scallops visually respond to the size and speed of virtual particles.” The Journal of Experimental Biology 211, no. Pt 13 (July 2008): 2066–70. https://doi.org/10.1242/jeb.017038.
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  - Sweeney, A. M., S. H. D. Haddock, and S. Johnsen. “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 (July 1, 2008): 158. https://doi.org/10.1093/icb/icn002.
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  - Gilliland, Kurt O., Sonke Johnsen, Sangeetha Metlapally, M Joseph Costello, Balasubramanya Ramamurthy, Pravin V. Krishna, and Dorairajan Balasubramanian. “Mie light scattering calculations for an Indian age-related nuclear cataract with a high density of multilamellar bodies.” Mol Vis 14 (March 24, 2008): 572–82.
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  - Johnsen, S., and K. J. Lohmann. “Magnetoreception in animals.” Physics Today 61, no. 3 (March 11, 2008): 29–35. https://doi.org/10.1063/1.2897947.
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  - Metlapally, S., M. J. Costello, K. O. Gilliland, B. Ramamurthy, P. V. Krishna, D. Balasubramanian, and S. Johnsen. “Analysis of nuclear fiber cell cytoplasmic texture in advanced cataractous lenses from Indian subjects using Debye-Bueche theory.” Exp Eye Res 86, no. 2 (February 2008): 434–44. https://doi.org/10.1016/j.exer.2007.11.018.
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  - Gilliland, K. O., S. Johnsen, S. Metlapally, M. J. Costello, B. Ramamurthy, P. V. Krishna, and D. Balasubramanian. “Mie Light Scattering Calculations for Multilamellar Bodies in Indian Age-Related Nuclear Cataracts.” Molecular Vision 14 (2008): 572–82.
  - Johnsen, Sönke. “Does new technology inspire new directions? Examples drawn from pelagic visual ecology.” Integrative and Comparative Biology 47, no. 6 (December 2007): 799–807. https://doi.org/10.1093/icb/icm017.
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  - Sweeney, Alison M., Steven H. D. Haddock, and Sönke Johnsen. “Comparative visual acuity of coleoid cephalopods.” Integrative and Comparative Biology 47, no. 6 (December 2007): 808–14. https://doi.org/10.1093/icb/icm092.
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  - Gagnon, Y. L., N. Shashar, E. J. Warrant, and S. J. Johnsen. “Light scattering by selected zooplankton from the Gulf of Aqaba.” The Journal of Experimental Biology 210, no. Pt 21 (November 2007): 3728–35. https://doi.org/10.1242/jeb.003251.
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  - Martin, C. H., and S. Johnsen. “A field test of the Hamilton-Zuk hypothesis in the Trinidadian guppy (Poecilia reticulata).” Behavioral Ecology and Sociobiology 61, no. 12 (October 1, 2007): 1897–1909. https://doi.org/10.1007/s00265-007-0430-2.
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  - Johnsen, Sönke, Erin Mattern, and Thorsten Ritz. “Light-dependent magnetoreception: quantum catches and opponency mechanisms of possible photosensitive molecules.” The Journal of Experimental Biology 210, no. Pt 18 (September 2007): 3171–78. https://doi.org/10.1242/jeb.007567.
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  - Sweeney, Alison M., David L. Des Marais, Yih-En Andrew Ban, and Sönke Johnsen. “Evolution of graded refractive index in squid lenses.” Journal of the Royal Society, Interface 4, no. 15 (August 2007): 685–98. https://doi.org/10.1098/rsif.2006.0210.
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  - Costello, M Joseph, Sönke Johnsen, Kurt O. Gilliland, Christopher D. Freel, and W Craig Fowler. “Predicted light scattering from particles observed in human age-related nuclear cataracts using mie scattering theory.” Invest Ophthalmol Vis Sci 48, no. 1 (January 2007): 303–12. https://doi.org/10.1167/iovs.06-0480.
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  - Sweeney, A., S. H. D. Haddock, and S. Johnsen. “Comparative visual acuity of coleoid cephalopods.” Integrative and Comparative Biology 47, no. 808–814 (2007).
  - Gagnon, Y. L., N. Shashar, E. J. Warrant, and S. Johnsen. “Light scattering from pelagic zooplankton: measurements at different angles and modeling corresponding sighting distances.” Journal of Experimental Biology 210 (2007): 3728–35.
  - Leech, D. M., and S. Johnsen. “Ultraviolet vision and foraging in juvenile bluegill (Lepomis macrochirus).” Canadian Journal of Fisheries and Aquatic Sciences 63, no. 10 (October 1, 2006): 2183–90. https://doi.org/10.1139/F06-107.
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  - Tuthill, John C., and Sönke Johnsen. “Polarization sensitivity in the red swamp crayfish Procambarus clarkii enhances the detection of moving transparent objects.” The Journal of Experimental Biology 209, no. Pt 9 (May 2006): 1612–16. https://doi.org/10.1242/jeb.02196.
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  - Johnsen, Sönke, Almut Kelber, Eric Warrant, Alison M. Sweeney, Edith A. Widder, Raymond L. Lee, and Javier Hernández-Andrés. “Crepuscular and nocturnal illumination and its effects on color perception by the nocturnal hawkmoth Deilephila elpenor.” The Journal of Experimental Biology 209, no. Pt 5 (March 2006): 789–800. https://doi.org/10.1242/jeb.02053.
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  - Leech, D. M., and S. Johnsen. “UV vision and the Feeding Ecology of Juvenile Bluegill Sunfish, Lepomis machrochirus.” Canadian Journal of Fisheries and Aquatic Sciences 63 (2006): 2183–90.
  - Johnsen, Sönke, and Kenneth J. Lohmann. “The physics and neurobiology of magnetoreception.” Nature Reviews. Neuroscience 6, no. 9 (September 2005): 703–12. https://doi.org/10.1038/nrn1745.
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  - Johnsen, Sönke. “The red and the black: bioluminescence and the color of animals in the deep sea.” Integrative and Comparative Biology 45, no. 2 (April 2005): 234–46. https://doi.org/10.1093/icb/45.2.234.
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  - Weissburg, M. J., H. I. Browman, D. M. Fields, J. M. Hemmi, J. Zeil, D. M. Higgs, S. Johnsen, et al. “Sensory biology: Linking the internal and external ecologies of marine organisms.” Marine Ecology Progress Series 287 (February 18, 2005): 263–307. https://doi.org/10.3354/meps287263.
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  - Johnsen, S. “Visual ecology on the high seas.” Marine Ecology Progress Series 287 (January 1, 2005): 281–85.
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  - Blevins, Erin, and Sönke Johnsen. “Spatial vision in the echinoid genus Echinometra.” The Journal of Experimental Biology 207, no. Pt 24 (November 2004): 4249–53. https://doi.org/10.1242/jeb.01286.
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  - Marsili, Stefania, Rudolf I. Salganik, Craig D. Albright, Christopher D. Freel, Sonke Johnsen, Robert L. Peiffer, and M Joseph Costello. “Cataract formation in a strain of rats selected for high oxidative stress.” Exp Eye Res 79, no. 5 (November 2004): 595–612. https://doi.org/10.1016/j.exer.2004.06.008.
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  - Gilliland, Kurt O., Christopher D. Freel, Sonke Johnsen, W. Craig Fowler, and M Joseph Costello. “Distribution, spherical structure and predicted Mie scattering of multilamellar bodies in human age-related nuclear cataracts.” Exp Eye Res 79, no. 4 (October 2004): 563–76. https://doi.org/10.1016/j.exer.2004.05.017.
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  - Johnsen, Sönke, Edith A. Widder, and Curtis D. Mobley. “Propagation and perception of bioluminescence: factors affecting counterillumination as a cryptic strategy.” The Biological Bulletin 207, no. 1 (August 2004): 1–16. https://doi.org/10.2307/1543624.
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  - Gilliland, K. O., C. D. Freel, S. Johnsen, C. Fowler, and M. J. Costello. “Random distribution of multilamellar bodies in human age-related nuclear cataracts.” Experimental Eye Research 79 (2004): 563–76.
  - Johnsen, S., and H. M. Sosik. “Shedding light on light in the ocean.” Oceanus 43 (2004): 24–28.
  - Johnsen, Sönke. “Lifting the cloak of invisibility: the effects of changing optical conditions on pelagic crypsis.” Integrative and Comparative Biology 43, no. 4 (August 2003): 580–90. https://doi.org/10.1093/icb/43.4.580.
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  - Sweeney, Alison, Christopher Jiggins, and Sönke Johnsen. “Insect communication: Polarized light as a butterfly mating signal.” Nature 423, no. 6935 (May 2003): 31–32. https://doi.org/10.1038/423031a.
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  - Avens, L., J. H. Wang, S. Johnsen, P. Dukes, and K. J. Lohmann. “Responses of hatchling sea turtles to rotational displacements.” Journal of Experimental Marine Biology and Ecology 288, no. 1 (March 25, 2003): 111–24. https://doi.org/10.1016/S0022-0981(03)00002-9.
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  - Johnsen, S., and H. M. Sosik. “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 (January 1, 2003): 1277–88. https://doi.org/10.4319/lo.2003.48.3.1277.
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  - Johnsen, Sönke. “Cryptic and conspicuous coloration in the pelagic environment.” Proceedings. Biological Sciences 269, no. 1488 (February 2002): 243–56. https://doi.org/10.1098/rspb.2001.1855.
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  - Johnsen, S. “Hidden in plain sight: the ecology and physiology of organismal transparency.” The Biological Bulletin 201, no. 3 (December 2001): 301–18. https://doi.org/10.2307/1543609.
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  - Johnsen, S., and E. A. Widder. “Ultraviolet absorption in transparent zooplankton and its implications for depth distribution and visual predation.” Marine Biology 138, no. 4 (January 1, 2001): 717–30. https://doi.org/10.1007/s002270000499.
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  - Lohmann, K. J., and S. Johnsen. “The neurobiology of magnetoreception in vertebrate animals.” Trends in Neurosciences 23, no. 4 (April 2000): 153–59. https://doi.org/10.1016/s0166-2236(99)01542-8.
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  - Johnsen, S. “Transparent animals.” Scientific American 282, no. 2 (February 2000): 80–89. https://doi.org/10.1038/scientificamerican0200-80.
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  - Widder, E. A., and S. Johnsen. “3D spatial point patterns of bioluminescent plankton: A map of the 'mine field'.” Journal of Plankton Research 22, no. 3 (January 1, 2000): 409–20. https://doi.org/10.1093/plankt/22.3.409.
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  - Johnsen, S., and W. M. Kier. “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 (August 1, 1999): 761–63. https://doi.org/10.1017/S0025315498000940.
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  - Widder, E. A., S. Johnsen, S. A. Bernstein, J. F. Case, and D. J. Neilson. “Thin layers of bioluminescent copepods found at density discontinuities in the water column.” Marine Biology 134, no. 3 (August 1, 1999): 429–37. https://doi.org/10.1007/s002270050559.
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  - Johnsen, S., and E. A. Widder. “The physical basis of transparency in biological tissue: Ultrastructure and the minimization of light scattering.” Journal of Theoretical Biology 199, no. 2 (July 21, 1999): 181–98. https://doi.org/10.1006/jtbi.1999.0948.
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  - Johnsen, S., E. J. Balser, and E. A. Widder. “Light-emitting suckers in an octopus.” Nature 398, no. 6723 (March 11, 1999): 113–14. https://doi.org/10.1038/18131.
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  - Johnsen, S., E. J. Balser, E. C. Fisher, and E. A. Widder. “Bioluminescence in the deep-sea cirrate octopod Stauroteuthis syrtensis verrill (Mollusca: Cephalopoda).” Biological Bulletin 197, no. 1 (January 1, 1999): 26–39. https://doi.org/10.2307/1542994.
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  - Johnsen, S., and E. A. Widder. “Transparency and visibility of gelatinous zooplankton from the Northwestern Atlantic and Gulf of Mexico.” Biological Bulletin 195, no. 3 (January 1, 1998): 337–48. https://doi.org/10.2307/1543145.
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  - Johnsen, S., and W. M. Kier. “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 (January 1, 1998): 681–84. https://doi.org/10.1017/S0025315400041758.
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  - Johnsen, S. “Identification and localization of a possible rhodopsin in the echinoderms Asterias forbesi (Asteroidea) and Ophioderma brevispinum (Ophiuroidea).” The Biological Bulletin 193, no. 1 (August 1997): 97–105. https://doi.org/10.2307/1542739.
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  - Johnsen, S. “Extraocular sensitivity to polarized light in an echinoderm.” The Journal of Experimental Biology 195 (October 1994): 281–91. https://doi.org/10.1242/jeb.195.1.281.
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  - Johnsen, S., and W. M. Kier. “Intramuscular crossed connective tissue fibres: skeletal support in the lateral fins of squid and cuttlefish (Mollusca: Cephalopoda).” Journal of Zoology 231, no. 2 (January 1, 1993): 311–38. https://doi.org/10.1111/j.1469-7998.1993.tb01921.x.
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  - Kauffman, S. A., and S. Johnsen. “Coevolution to the edge of chaos: coupled fitness landscapes, poised states, and coevolutionary avalanches.” Journal of Theoretical Biology 149, no. 4 (April 1991): 467–505. https://doi.org/10.1016/s0022-5193(05)80094-3.
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- Book Sections
  - Zylinski, S., and S. Johnsen. “Visual cognition in deep-sea cephalopods: What we don’t know and why we don’t know it.” In Cephalopod Cognition, 223–41, 2014. https://doi.org/10.1017/CBO9781139058964.014.
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  - Marshall, J., and S. Johnsen. “Camouflage in marine fish.” In Animal Camouflage: Mechanisms and Function, 186–211, 2011. https://doi.org/10.1017/CBO9780511852053.011.
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  - Leech, D. M., and S. Johnsen. “Light, Biological Receptors.” In Encyclopedia of Inland Waters, 671–81, 2009. https://doi.org/10.1016/B978-012370626-3.00073-9.
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- Conference Papers
  - Caves, E. M., and S. Johnsen. “The sensory impacts of climate change: Bathymetric shifts and visually-mediated interactions in aquatic species.” In Integrative and Comparative Biology, 61:E122–23, 2021.
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  - Davis, A. L., K. N. Thomas, F. E. Goetz, B. H. Robison, S. Johnsen, and K. J. Osborn. “Hiding in the deep: ultra-black camouflage in fishes.” In Integrative and Comparative Biology, 61:E184–E184, 2021.
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  - Granger, J., and S. Johnsen. “Magnetoreception and the radio sun.” In Integrative and Comparative Biology, 61:E328–E328, 2021.
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  - Johnsen, S., K. L. Lohmann, and E. J. Warrant. “The wobbly compass needle: are the peculiarities of magnetic orientation behavior partially explained by low signal relative to noise?” In Integrative and Comparative Biology, 61:E421–22, 2021.
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  - Meja, B., J. C. Notar, and S. Johnsen. “Insects go with flow: A mathematical model of induced flow and cooling during flight.” In Integrative and Comparative Biology, 61:E1199–E1199, 2021.
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  - Notar, J. C., B. Meja, and S. Johnsen. “A living shag rug: Sea urchin spine density differs by habitat and has consequences for vision.” In Integrative and Comparative Biology, 61:E657–58, 2021.
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  - Nowicki, S., E. M. Caves, P. A. Green, M. N. Zipple, D. Bharath, S. Peters, and S. Johnsen. “Differences in categorical color perception between two estrildid finches.” In Integrative and Comparative Biology, 61:E658–59, 2021.
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  - Davis, A. L., H. F. Nijhout, and S. Johnsen. “Convergent evolution of ultra-black butterfly scales.” In Integrative and Comparative Biology, 60:E53–E53, 2020.
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  - Fitak, R. R., B. R. Wheeler, L. C. Naisbett-Jones, M. M. Scanlan, D. L. G. Noakes, and S. Johnsen. “Time-dependent Characterization of Candidate Magnetoreception Genes in the Brain of Chinook Salmon.” In Integrative and Comparative Biology, 60:E71–E71, 2020.
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  - Go, M., J. C. Notar, and S. Johnsen. “Associative learning in the brittle star Ophioderma brevispinum.” In Integrative and Comparative Biology, 60:E329–E329, 2020.
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  - Granger, J., L. Walkowicz, R. Fitak, and S. Johnsen. “Gray Whales Strand More Often on Days With Increased Levels of Atmospheric Radio Frequency Noise.” In Integrative and Comparative Biology, 60:E89–E89, 2020.
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  - Harris, O. K., A. C. N. Kingston, N. R. Steichmann, S. Johnsen, and D. I. Speiser. “How and why are the blue eyes of scallops blue?” In Integrative and Comparative Biology, 60:E96–E96, 2020.
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  - Johnsen, S., and E. M. Caves. “How our perceptual and cognitive biases may influence our study of animal vision.” In Integrative and Comparative Biology, 60:E113–E113, 2020.
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  - Notar, J. C., and S. Johnsen. “Trends in Spatial Acuity Across the Sea Urchins.” In Integrative and Comparative Biology, 60:E388–E388, 2020.
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  - Nowicki, S., E. M. Caves, L. E. Schweikert, P. A. Green, C. Taboada, M. N. Zipple, S. Peters, and S. Johnsen. “Carotenoid Concentration in Avian Retinal Oil Droplets Correlates with Color Discrimination Across a Perceptual Category Boundary.” In Integrative and Comparative Biology, 60:E175–E175, 2020.
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  - Schweikert, L. E., A. L. Davis, S. Johnsen, and H. D. Bracken-Grissom. “Vision and Bioluminescence in Deep-sea Shrimps: Implications for Conspecific Recognition.” In Integrative and Comparative Biology, 60:E209–E209, 2020.
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  - Solie, S. E., and S. Johnsen. “Contrast Sensitivity and Spatial Resolution in the Trinidadian Guppy (Poecilia reticulata).” In Integrative and Comparative Biology, 60:E421–E421, 2020.
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  - Johnsen, S., and H. F. Nijhout. “Super-black butterfly uses stealth technology: honeycomb absorbing structures in the scales of the wings of Trogonoptera brookiana.” In Integrative and Comparative Biology, 59:E112–E112. OXFORD UNIV PRESS INC, 2019.
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  - Notar, J. C., and S. Johnsen. “Sea Urchin Vision in Featureless vs. Spatially Complex Environments.” In Integrative and Comparative Biology, 59:E170–E170. OXFORD UNIV PRESS INC, 2019.
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  - Schweikert, L. E., E. M. Caves, R. R. Fitak, S. E. Solie, T. T. Sutton, and S. Johnsen. “Patterns and Predictors of Spectral Sensitivity Variation in Fishes.” In Integrative and Comparative Biology, 59:E209–E209. OXFORD UNIV PRESS INC, 2019.
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  - Caves, E. M., M. N. Zipple, P. A. Green, S. Peters, S. Johnsen, and S. Nowicki. “Categorical Perception of Color Along a Blue-Green Continuum in Female Zebra Finches.” In Integrative and Comparative Biology, 59:E33–E33. OXFORD UNIV PRESS INC, 2019.
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  - Green, P. A., E. M. Caves, M. N. Zipple, S. Peters, S. Johnsen, and S. Nowicki. “Categorical Perception of a Carotenoid-based Assessment Signal.” In Integrative and Comparative Biology, 59:E87–E87. OXFORD UNIV PRESS INC, 2019.
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  - Bagge, L. E., W. M. Kier, and S. Johnsen. “The ultrastructure of transparent shrimp.” In Integrative and Comparative Biology, 58:E9–E9. OXFORD UNIV PRESS INC, 2018.
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  - Bedore, C. N., R. E. Hueter, and S. Johnsen. “Visual Ecology of the White Shark and Shortfin Mako.” In Integrative and Comparative Biology, 58:E15–E15. OXFORD UNIV PRESS INC, 2018.
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  - Caves, E. M., P. A. Green, and S. Johnsen. “Signaling in the Cleaner Shrimp-Client Fish Mutualism: Combining Behavior, Network Analysis, and Sensory Physiology.” In Integrative and Comparative Biology, 58:E32–E32. OXFORD UNIV PRESS INC, 2018.
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  - Ernst, D. A., R. R. Fitak, M. Schmidt, C. D. Derby, S. Johnsen, and K. J. Lohmann. “A Magnetic Pulse Induces Differential Gene Expression in the Spiny Lobster Central Nervous System.” In Integrative and Comparative Biology, 58:E59–E59. OXFORD UNIV PRESS INC, 2018.
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  - Fitak, R. R., B. R. Wheeler, L. E. Schweikert, D. A. Ernst, K. J. Lohmann, and S. Johnsen. “Candidate magnetoreception genes in the brain and retina of trout.” In Integrative and Comparative Biology, 58:E65–E65. OXFORD UNIV PRESS INC, 2018.
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  - Johnsen, S., K. J. Osborn, K. N. Thomas, and B. H. Robison. “From the Moon in the Sky to the Deep Blue Sea: Using Lunar Optics to Understand the Blackness of Mesopelagic Fish.” In Integrative and Comparative Biology, 58:E107–E107. OXFORD UNIV PRESS INC, 2018.
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  - Notar, J. C., and S. Johnsen. “Do (Eyeless) Sea Urchins Have Color Vision?” In Integrative and Comparative Biology, 58:E165–E165. OXFORD UNIV PRESS INC, 2018.
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  - Ritschard, E. A., R. R. Fitak, and S. Johnsen. “Sensory insights from the molecular evolution of GPCRs in the Octopus bimaculoides genome.” In Integrative and Comparative Biology, 58:E406–E406. OXFORD UNIV PRESS INC, 2018.
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  - Schweikert, L. E., R. R. Fitak, M. S. Grace, and S. Johnsen. “Dermal Photoreception May Provide Sensory Feedback for Dynamic Coloration.” In Integrative and Comparative Biology, 58:E205–E205. OXFORD UNIV PRESS INC, 2018.
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  - Thomas, K. N., M. Vecchione, and S. Johnsen. “Now you see me, now you don't: Cephalopod visual ranges and implications for deep-sea visual ecology.” In Integrative and Comparative Biology, 58:E232–E232. OXFORD UNIV PRESS INC, 2018.
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  - Costello, M Joseph, Ashik Mohamed, Kurt Gilliland, Sonke Johnsen, and Kevin Schey. “High resolution confocal microscopy of potential newly described nuclear excisosomes in primate lenses.” In Investigative Ophthalmology & Visual Science, Vol. 58. ASSOC RESEARCH VISION OPHTHALMOLOGY INC, 2017.
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  - Bagge, L. E., and S. Johnsen. “Anti-reflective invisibility cloak: monolayers of spheres reduce cuticle reflectance in hyperiid amphipods.” In Integrative and Comparative Biology, 57:E197–E197. OXFORD UNIV PRESS INC, 2017.
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  - Caves, E. M., C. C. Chen, and S. Johnsen. “Coarse vision isn't useless vision: cleaner shrimp use monochromatic, low-resolution vision to detect client fish.” In Integrative and Comparative Biology, 57:E221–E221. OXFORD UNIV PRESS INC, 2017.
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  - Johnsen, S., and G. D. Ruxton. “Join Now! The increased visibility of large groups of aquatic and aerial organisms is far outweighed by the benefits of aggregation.” In Integrative and Comparative Biology, 57:E305–E305. OXFORD UNIV PRESS INC, 2017.
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  - Thomas, K. N., M. Vecchione, and S. Johnsen. “What big eyes you have: Eye allometry and visual range in deep-sea cephalopods.” In Integrative and Comparative Biology, 57:E429–E429. OXFORD UNIV PRESS INC, 2017.
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  - Bagge, L. E., S. T. Kinsey, and S. Johnsen. “The limits of an invisibility cloak: transparent shrimp become opaque after multiple tail-flipping escapes.” In Integrative and Comparative Biology, 56:E9–E9. OXFORD UNIV PRESS INC, 2016.
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  - Brandley, N., E. Caves, and S. Johnsen. “Do warning signals exploit an evolutionary constraint on insect visual acuity?” In Integrative and Comparative Biology, 56:E23–E23. OXFORD UNIV PRESS INC, 2016.
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  - Caves, E. M., N. C. Brandley, and S. Johnsen. “Visual acuity in fish: the effects of eye morphology, environment, and ecology.” In Integrative and Comparative Biology, 56:E32–E32. OXFORD UNIV PRESS INC, 2016.
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  - Johnsen, S. “What Next? Unanswered questions about extraocular photoreception and how we might answer them.” In Integrative and Comparative Biology, 56:E103–E103. OXFORD UNIV PRESS INC, 2016.
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  - Johnsen, S., Y. L. Gagnon, N. J. Marshall, and T. W. Cronin. “Another beautiful hypothesis slain by an ugly fact: Polarization vision does not increase the sighting distance of silvery fish.” In Integrative and Comparative Biology, 56:E103–E103. OXFORD UNIV PRESS INC, 2016.
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  - Thomas, K. N., B. H. Robison, and S. Johnsen. “The perks of being cock-eyed: Orientation and visual characteristics of histioteuthid squids.” In Integrative and Comparative Biology, 56:E221–E221. OXFORD UNIV PRESS INC, 2016.
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  - Caves, E. M., T. M. Frank, and S. Johnsen. “Colorblind colorful animals: Spectral sensitivity, temporal resolution, and spatial resolution in three species of cleaner shrimp.” In Integrative and Comparative Biology, 55:E27–E27. OXFORD UNIV PRESS INC, 2015.
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  - Palmer, G., and S. Johnsen. “By the light of the silvery moon: The effect of lunar phase on the color of twilight and its implications for animal behavior.” In Integrative and Comparative Biology, 55:E138–E138. OXFORD UNIV PRESS INC, 2015.
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  - Akre, K. L., and S. Johnsen. “Proportional psychophysics and the evolution of behavior: The broad influence of Weber's law.” In Integrative and Comparative Biology, 54:E4–E4. OXFORD UNIV PRESS INC, 2014.
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  - Bagge, L. E., W. M. Kier, and S. Johnsen. “Clearly camouflaged: muscle architecture in transparent shrimp.” In Integrative and Comparative Biology, 54:E9–E9. OXFORD UNIV PRESS INC, 2014.
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  - Bedore, C. N., S. M. Kajiura, and S. J. Johnsen. “Bioelectric crypsis in cephalopods reduces detection by shark predators.” In Integrative and Comparative Biology, 54:E15–E15. OXFORD UNIV PRESS INC, 2014.
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  - Johnsen, S., E. Sawicka, R. Reynolds, and D. Stramski. “Through the looking glass: The structure of the oceanic light field and its implications for mirror-based camouflage.” In Integrative and Comparative Biology, 54:E102–E102. OXFORD UNIV PRESS INC, 2014.
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  - Costello, M., Ashik Mohamed, Kurt Gilliland, William Fowler, and Sonke Johnsen. “Fiber Cell Compaction in Adult Human Lenses Begins Near the Remodeling Zone in the Outer Cortex.” In Investigative Ophthalmology & Visual Science, Vol. 54. ASSOC RESEARCH VISION OPHTHALMOLOGY INC, 2013.
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  - Bagge, L. E., and S. Johnsen. “Looking at invisibility: anti-reflective structures and strategies in hyperiid amphipods.” In Integrative and Comparative Biology, 53:E242–E242. OXFORD UNIV PRESS INC, 2013.
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  - Brandley, N. C., M. G. Johnson, and S. Johnsen. “Reduction of an aposematic signal: the role of microhabitat in North American black widows (Latrodectus).” In Integrative and Comparative Biology, 53:E22–E22. OXFORD UNIV PRESS INC, 2013.
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  - Gagnon, Y. L., and S. Johnsen. “Visual acuity in deep-sea fish and mollusks.” In Integrative and Comparative Biology, 53:E73–E73. OXFORD UNIV PRESS INC, 2013.
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  - Johnsen, S., D. -. E. Nilsson, and E. J. Warrant. “Why do giant squid have giant eyes?” In Integrative and Comparative Biology, 53:E104–E104. OXFORD UNIV PRESS INC, 2013.
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  - Sweeney, A. M., S. Johnsen, Y. Gagnon, D. E. Morse, and D. Stramski. “Jurassic marine photonics: Squid dynamic iridescence and predation by large extinct marine reptiles.” In Integrative and Comparative Biology, 53:E210–E210. OXFORD UNIV PRESS INC, 2013.
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  - Brandley, N. C., and S. Johnsen. “The black widow's hourglass: a covert aposematic signal?” In Integrative and Comparative Biology, 52:E19–E19. OXFORD UNIV PRESS INC, 2012.
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  - Johnsen, S., and N. J. Marshall. “Through the looking glass: Are silvery fish safe from viewers with polarization vision?” In Integrative and Comparative Biology, 52:E87–E87. OXFORD UNIV PRESS INC, 2012.
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  - Speiser, D., Y. L. Gagnon, R. K. Chhetri, A. L. Oldenburg, and S. Johnsen. “Optical coherence tomography (OCT) reveals that scallop eyes may have bifocal optics.” In Integrative and Comparative Biology, 52:E165–E165. OXFORD UNIV PRESS INC, 2012.
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  - Zylinski, S., and S. Johnsen. “CAMOUFLAGE WITHOUT COMPROMISE: CEPHALOPODS SWITCH BETWEEN TRANSPARENCY AND PIGMENTATION TO OPTIMIZE CRYPSIS IN THE DEEP.” In Journal of Shellfish Research, 30:1023–1023. NATL SHELLFISHERIES ASSOC, 2011.
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  - Baldwin, Fergus J. L., and S. Johnsen. “When love is blind: Vision constrained by molting during mating in the female blue crab.” In Integrative and Comparative Biology, 51:E6–E6. OXFORD UNIV PRESS INC, 2011.
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  - Johnsen, S., and N. J. Marshall. “Using sunglasses to find the best burger in town: Polarization vision as a camouflage breaker in pelagic predators.” In Integrative and Comparative Biology, 51:E64–E64. OXFORD UNIV PRESS INC, 2011.
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  - Speiser, D., and S. Johnsen. “Seeing through rocks: Chitons use calcium carbonate lenses to form images.” In Integrative and Comparative Biology, 51:E130–E130. OXFORD UNIV PRESS INC, 2011.
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  - Baldwin, J. L., and S. Johnsen. “Does this color make my claws look phat? Evaluating claw color preferences in male blue crabs, Callinectes sapidus.” In Integrative and Comparative Biology, 50:E7–E7. OXFORD UNIV PRESS INC, 2010.
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  - Bhandiwad, A. A., and S. Johnsen. “Now you see it, now you don't: the effects of salinity and temperature on the transparency of the ghost shrimp, Palaemonetes pugio.” In Integrative and Comparative Biology, 50:E205–E205. OXFORD UNIV PRESS INC, 2010.
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  - Johnsen, S., and S. H. D. Haddock. “A glowing benthic animal is hard to find: A photographic and spectroscopic survey of bioluminescence on the deep-sea floor.” In Integrative and Comparative Biology, 50:E83–E83. OXFORD UNIV PRESS INC, 2010.
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  - Speiser, D., E. R. Loew, and S. Johnsen. “Spectral sensitivity of the concave mirror eyes of scallops: The influence of habitat and longitudinal chromatic aberration.” In Integrative and Comparative Biology, 50:E166–E166. OXFORD UNIV PRESS INC, 2010.
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  - Costello, M. J., S. Johnsen, K. O. Gilliland, S. Metlapally, and D. Balasubramanian. “Direct Evidence for Spherical Multilamellar Bodies as Sources of Excess Light Scattering in Human Age-Related Nuclear Cataracts.” In Investigative Ophthalmology & Visual Science, Vol. 51. ASSOC RESEARCH VISION OPHTHALMOLOGY INC, 2010.
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  - Baldwin, J. L., and S. Johnsen. “Pining for Pinups: the importance of color in mate choice of the blue crab Callinectes sapidus.” In Integrative and Comparative Biology, 49:E9–E9. OXFORD UNIV PRESS INC, 2009.
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  - Johnsen, S., and W. M. Kier. “You can hide, but you can't run: trade-offs between muscle activation and transparency in glass catfish.” In Integrative and Comparative Biology, 49:E86–E86. OXFORD UNIV PRESS INC, 2009.
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  - Speiser, D., and S. Johnsen. “The optics and evolution of scallop eyes.” In Integrative and Comparative Biology, 49:E160–E160. OXFORD UNIV PRESS INC, 2009.
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  - Sweeney, A. M., M. Matz, D. E. Morse, and S. Johnsen. “Patterns of S-crystallin evolution are correlated with optical acuity in cephalopods.” In Integrative and Comparative Biology, 49:E166–E166. OXFORD UNIV PRESS INC, 2009.
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  - Johnsen, S. “Visual Ecology on the high seas.” In Integrative and Comparative Biology, 46:E69–E69. OXFORD UNIV PRESS INC, 2006.
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  - Speiser, D. I., A. M. Sweeney, and S. Johnsen. “Scallops respond to simulated particles in flow.” In Integrative and Comparative Biology, 46:E134–E134. OXFORD UNIV PRESS INC, 2006.
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  - Sweeney, A., and S. Johnsen. “Evolution of high-acuity vision in coleoid cephalopods.” In Integrative and Comparative Biology, 46:E139–E139. OXFORD UNIV PRESS INC, 2006.
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  - Johnsen, S., A. Kelber, E. J. Warrant, A. M. Sweeney, E. A. Widder, R. L. Lee, and J. Hernandez-Andres. “The color of night: Twilight and nocturnal illumination and its effects on color perception.” In Integrative and Comparative Biology, 45:1021–1021. OXFORD UNIV PRESS INC, 2005.
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  - Mora, C. V., S. Johnsen, and K. J. Lohmann. “Detection of polarized light by loggerhead sea turtles (Caretta caretta).” In Integrative and Comparative Biology, 45:1047–1047. OXFORD UNIV PRESS INC, 2005.
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  - Speiser, D. I., and S. Johnsen. “Wavelength-dependent phototaxis as a depth regulating mechanism in a ctenophore.” In Integrative and Comparative Biology, 45:1197–1197. OXFORD UNIV PRESS INC, 2005.
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  - Sweeney, A., D. L. Des Marais, A. Ban, and S. Johnsen. “Evolving refractive index: How lens protein evolution contributed to high-resolution squid vision.” In Integrative and Comparative Biology, 45:1080–1080. OXFORD UNIV PRESS INC, 2005.
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  - Tuthill, J. C., and S. Johnsen. “Polarization vision in crayfish enhances motion detection.” In Integrative and Comparative Biology, 45:1204–1204. OXFORD UNIV PRESS INC, 2005.
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  - Blevins, E. L., and S. Johnsen. “Spatial vision in the echinoid genus Echinometra.” In Integrative and Comparative Biology, 44:526–526. OXFORD UNIV PRESS INC, 2004.
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  - Johnsen, S. “The red and the black: Bioluminescence and the color of animals in the deep sea.” In Integrative and Comparative Biology, 44:578–578. OXFORD UNIV PRESS INC, 2004.
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  - Sweeney, A., and S. Johnsen. “Evolution of complex optics in squid lenses.” In Integrative and Comparative Biology, 44:649–649. OXFORD UNIV PRESS INC, 2004.
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  - Costello, M. J., K. P. Gilliland, C. D. Freel, W. C. Fowler, and S. Johnsen. “Mie light scattering analysis of human age-related nuclear cataracts.” In Investigative Ophthalmology & Visual Science, 45:U170–U170. ASSOC RESEARCH VISION OPHTHALMOLOGY INC, 2004.
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  - Johnsen, S. “Troubles in flashlight world: The effects of water turbidity and visual acuity on the success of counterillumination in deep-sea species.” In Integrative and Comparative Biology, 43:808–808. SOC INTEGRATIVE COMPARATIVE BIOLOGY, 2003.
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  - Sweeney, A. M., and S. Johnsen. “Biological optical instruments in the deep sea.” In Integrative and Comparative Biology, 43:1016–1016. SOC INTEGRATIVE COMPARATIVE BIOLOGY, 2003.
    Link to Item
  - Johnsen, S. “Minors or colors? Successful fashions for crypsis in the pelagic realm.” In Integrative and Comparative Biology, 42:1251–1251. SOC INTEGRATIVE COMPARATIVE BIOLOGY, 2002.
    Link to Item
  - Sweeney, A., C. Jiggins, and S. Johnsen. “Bio-optics and visual ecology of Heliconius color patterns.” In Integrative and Comparative Biology, 42:1321–1321. SOC INTEGRATIVE COMPARATIVE BIOLOGY, 2002.
    Link to Item
- Datasets
  - Green, Patrick, Sonke Johnsen, Matthew N. Zipple, stephen Nowicki, Eleanor M. Caves, and Susan Peters. “Data and scripts from: Categorical perception of colour signals in a songbird,” June 12, 2018. https://doi.org/10.7924/r4rx96r99.
    Data Access
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