W. James Cooper , PhD

Assistant professor · he/him/his


I am a native of the Florida Gulf-Coast. My family originally received a land grant from the Spanish crown in the late 1700's and many descendants still live in the same community. 

Undergraduate research with Dr. William (Doc) Herrnkind at FSU provided my first exposure to marine science. THANK YOU DOC! Masters studies with Dr. Scott Steppan (also at FSU) examined developmental factors that had profound effects on restricting marsupial evolution. My lab remains focused on studies of developmental constraint. During the years between my BS and MS degrees I performed science education outreach at FSU’s Turkey Point Marine Lab and my involvement in outreach has continued since that time. I did my doctoral work at the University of Chicago with Dr. Mark Westneat, who was also curator of the fish collection at the Field Museum. My focus on biomechanics, collection-based studies, phylogenetics, taxonomy and field expeditions are legacies of my time working with Mark. Post-doctoral research at Syracuse University with Dr. Craig Albertson heavily influenced my interest in evolvability and underscored the advantages of combining work with model and non-model species. Doc, Scott, Mark and Craig have my everlasting gratitude.


Research Interests

I am an evolutionary-developmental (Evo-Devo) biologist whose research program integrates evolutionary studies of fish feeding mechanics with investigations of skull development. My broad goal is to understand the factors that direct evolution down particular paths as organismal lineages diversify into different ecological niches. 

I am currently developing research programs focused on larval fishes in the Salish Sea and experimental studies of development using genetically modified zebrafish. My joint position in the Department of Biology and Western’s new Marine and Coastal Science program facilitates the combination of these efforts. 

Our lab integrates a number of different research techniques such as morphometric analyses of cranial form, high-speed video analyses of fish feeding mechanics, gene expression labeling, studying how cell-to-cell signaling coordinates skull development, evolutionary analyses of phenotypic and ecological diversification, molecular phylogenetics, ichthyology, taxonomy and others.

Because we approach our work from many directions the lab can accommodate people with a wide range of interests. All lab members become familiar with how investigations in our individual subject areas intersect and combine to provide a deeper understanding of the factors that shape evolutionary diversification.

An over-arching theme in our research is merging comparative investigations of non-model organisms with experimental studies of zebrafish. Our evolutionary work examines cranial form and function in multiple fishes from the same lineage in order to: 1) describe large-scale patterns in adaptive radiations; and 2) identify specific aspects of skull anatomy that play important roles in the biomechanics of fish feeding. We then conduct laboratory experiments to understand how the morphologies of mechanically significant cranial features are determined during fish development. This work utilizes an array of genetically modified zebrafish lines to study bone morphogenesis. The combination of these efforts allows us to identify aspects of developmental organization that have either promoted or constrained specific evolutionary changes in skull morphology, bite mechanics, and feeding ecology.

Educational & Professional Experience

Current position, Assistant Professor, Western Washington University (2020)

Joint appointment: Department of Biology & Marine and Coastal Science

Ph.D. – The University of Chicago (2006)

M.S. – The Florida State University (2000)

B.S. – The Florida State University (1991)

Post-Doc – Syracuse University (2007-2011)

Biology Faculty – Washington State University (2011-2020)

Recent Publications

Identification codes for particular co-authors:

      U        Undergraduate student

      G        Graduate student

      U/G    Began the work as an undergraduate, continued as a graduate student

      HST    High-school teacher

W. James Cooper, Rachel VanHall – U/G, Elly Sweet, Holly Milewski– U/G, Zoey DeLeon– U, Amy Verderber– HST, Adrian DeLeon– U, Demi Galindo– U/G, Orissa Lozano – HST. 2020 (cover article). Functional morphogenesis from embryos to adults: late development shapes trophic niche in coral reef damselfishes. Evolution & Development, 22(3): 221-240. https://onlinelibrary.wiley.com/toc/1525142x/2020/22/3

Demi Galindo– U/G, Elly Sweet, Zoey DeLeon– U, Mitchel Wagner– U, Adrian DeLeon– U, Casey Carter– U/G, Sarah McMenamin, and W. James Cooper. (2019). Thyroid hormone modulation during zebrafish development recapitulates evolved diversity in danionin jaw protrusion mechanics. Evolution & Development, 21(5), 231-246. doi:10.1111/ede.12299

Sarah McMenamin, Casey Carter– U/G, W. James Cooper. 2017. Thyroid Hormone Stimulates the Onset of Adult Feeding Kinematics in Zebrafish. Zebrafish. 14 (6):517-525.

W. James Cooper, Casey B. CarterU/G, Andrew ConithG, Aaron N. Rice and Mark W. Westneat. 2017. The evolution of jaw protrusion mechanics has been tightly coupled to bentho-pelagic divergence in damselfishes (Pomacentridae). Journal of Experimental Biology. 220 (4): 652-666. DOI: 10.1242/jeb.143115.

W. James Cooper and Francesco Santini. 2016. A Revised Damselfish Taxonomy with a Description of the Tribe Microspathodontini (Giant Damselfishes). Invited, peer-reviewed book chapter. The Biology of Damselfishes. Eric Parmentier and Bruno Frederich, ed. CRC Press, Boca Raton, FL

Bruno Frédérich, W. James Cooper, and Rosalía Aguilar– G. 2016. Form, ecomorphology and iterative ecological radiation. Invited, peer-reviewed book chapter. The Biology of Damselfishes. Eric Parmentier and Bruno Frederich, ed. CRC Press, Boca Raton, FL

Pierre Le Pabic, W. James Cooper and Thomas F. Schilling. 2016. Developmental basis of phenotypic integration in two Lake Malawi cichlids. EvoDevo. 7(3). DOI: 10.1186/s13227-016-0040-z

Andrew J. SmithG, Nathan Nelson-ManeyU, Kevin Parson, W. James Cooper, and R. Craig Albertson. 2015. Body Shape Evolution in Sunfishes: Divergent Paths to Accelerated Rates of Speciation in the Centrarchidae. Evolutionary Biology. 42(3): 283-295.

W. James Cooper, R. Craig Albertson, Richard E. Jacob and Mark W. Westneat. 2014. Re-description and reassignment of the damselfish Abudefduf luridus (Cuvier, 1830) using both traditional and geometric morphometric approaches. Copeia 14 (3): 473-480.

W. James Cooper, Rachel M. WirgauU/G, Elly M. Sweet, and R. Craig Albertson. 2013. Deficiency of zebrafish fgf20a results in aberrant skull remodeling that mimics both human cranial disease and evolutionarily important fish skull morphologies. Evolution & Development. 15(6): 426-441

R. Craig Albertson, W. James Cooper and Kenneth Mann. 2012. More than meets the eye: Functionally salient changes in internal bone architecture accompany divergence in cichlid feeding mode. International Journal of Evolutionary Biology. 2012: 538146 (9 pages). doi:10.1155/2012/538146

W. James Cooper, James Wernle, Kenneth Mann, and R. Craig Albertson. 2011. Functional and Genetic Integration in the Skulls of Lake Malawi Cichlids. Evolutionary Biology. 38(3): 316-334

Parsons, K., V. AndreevaG, W. J. Cooper, P. C. Yelick, and R. C. Albertson.  2011. Morphogenesis of the zebrafish jaw: Development beyond the embryo, in M. Westerfield, H. W. Detrich and L. I. Zon, eds. Methods in Cell Biology: The Zebrafish, 3rd Edition. Elsevier Academic Press Inc., San Diego.

W. James Cooper, & Scott J. Steppan. 2010. Developmental Constraint on the Evolution of Marsupial Forelimb Morphology. Australian Journal of Zoology. 58(1): 1-15

W. James Cooper, Kevin Parsons, Alyssa McIntyreU, Brittany KernU, Alana McGee-MooreU, and R. Craig Albertson. 2010. Bentho-pelagic divergence of cichlid feeding architecture was prodigious and consistent during multiple adaptive radiations within African rift-lakes. PLoS ONE.  5(3): e9551. doi:10.1371/journal.pone.0009551

Kevin Parsons, W. James Cooper, and R. Craig Albertson. 2009. Limits of Principal Components Analysis for Producing a Common Trait Space: Implications for Inferring Selection, Contingency, and Chance in Evolution. PLoS ONE. 4:11 e7957.  doi:10.1371/journal.pone.0007957

W. James Cooper, Lydia L Smith, & M. W. Westneat. 2009. Exploring the radiation of a diverse reef fish family: Phylogenetics of the damselfishes (Pomacentridae), with new classifications based on molecular analyses of all genera. Molecular Phylogenetics and Evolution. 52:1-16

W. James Cooper & M. W. Westneat. 2009. Form and Function of Damselfish Skulls: Rapid and Repeated Evolution into a limited Number of Trophic Niches. BMC Evolutionary Biology. 9:24.   doi:10.1186/1471-2148-9-24

W. James Cooper. 2009. The Biogeography Of Damselfish Skull Evolution: A Major Radiation Throughout The Indo-West Pacific Produces No Unique Skull Shapes. in The Proceedings of the 11th International Coral Reef Symposium

W. James Cooper, & R. C. Albertson. 2008. Quantification and variation in experimental studies of morphogenesis. Developmental Biology. 321: 295-302

Rice, A. N., W. James Cooper, & M. W. Westneat. 2008. Diversification of coordination patterns during feeding behaviour in Cheiline wrasses. Biological Journal of the Linnean Society. 93(2): 289-308

M. W. Westneat, O. Betz, R. Blob, K. Fezzaa, & W. James Cooper. & W. Lee. 2003 (cover article). Tracheal respiration in insects visualized with synchrotron X-ray imaging. Science. 299 (5606): 558-560