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PUBLICATIONS (* graduate student author, ** undergraduate author, ***postdoc) ( PDFs available upon request to sarahcoh@sfsu.edu , or you may find PDF downloads of older papers at this website: http://biology.sfsu.edu/faculty/sarah-cohen , if you scroll to the bottom of the page). McGowen, M., et al. (including S. Ayyagari*, CS Cohen). 2024. Rangewide phylogeographic structure of the endangered Irrawaddy dolphin (Orcaella brevirostris) using expanded sampling from contemporary and historical specimens. Marine Mammal Science DOI: 10.1111/mms.13159 Nydam M, Lemmon A, Lemmon E, Ziegler K, Cohen CS, Palomino-Alvarez L, and C. Gissi. 2023. Phylogenomics and systematics of botryllid ascidians, and implications for the evolution of allorecognition. Front. Ecol. Evol. Sec. Evolutionary Developmental Biology. Vol 11 doi: 10.3389/fevo.2023.1214191 Hess RA, Erickson OA, Cole RB, Isaacs JM, Alvarez-Clare S, Arnold J, Augustus-Wallace A, Ayoob JC, Berkowitz A, Branchaw J, Burgio KR, Cannon CH, Ceballos RM, Cohen CS, Coller H, Disney J, Doze VA, Eggers MJ, Ferguson EL, Gray JJ, Greenberg JT, Hoffmann A, Jensen-Ryan D, Kao RM, Keene AC, Kowalko JE, Lopez SA, Mathis C, Minkara M, Murren CJ, Ondrechen MJ, Ordoñez P, Osano A, Padilla-Crespo E, Palchoudhury S, Qin H, Ramírez-Lugo J, Reithel J, Shaw CA, Smith A, Smith RJ, Tsien F, Dolan EL. Virtually the Same? Evaluating the Effectiveness of Remote Undergraduate Research Experiences. CBE Life Sci Educ. 2023 Jun;22(2):ar25. doi: 10.1187/cbe.22-01-0001. PMID: 37058442; PMCID: PMC10228262. Halpern B, Boettiger C, Dietze M, Gephart J, Gonzalez P, Grimm N, Groffman P, Gurevitch J, Hobbie S, Komatsu K, Kroeker K, Lahr H, Lodge D, Lortie C, Lowndes J, Micheli F, Possingham H, Ruckelshaus M, Scarborough C, Wood C, Wu G, Aoyama L, Arroyo E, Bahlai C, Beller E, Blake R, Bork K, Branch T, Brown N, Brun J, Bruna E, Buckley L, Burnett J, Castorani M, Cheng S, Cohen S, Couture J, Crowder L, Dee L, Dias A, Diaz‐Maroto I, Downs M, Dudney J, Ellis E, Emery K, Eurich J, Ferriss B, Fredston A, Furukawa H, Gagné S, Garlick S, Garroway C, Gaynor K, González A, Grames E, Guy‐Haim T, Hackett E, Hallett L, Harms T, Haulsee D, Haynes K, Hazen E, Jarvis R, Jones K, Kandlikar G, Kincaid D, Knope M, Koirala A, Kolasa J, Kominoski J, Koricheva J, Lancaster L, Lawlor J, Lowman H, Muller‐Karger F, Norman K, Nourn N, O'Hara C, Ou S, Padilla‐Gamino J, Pappalardo P, Peek R, Pelletier D, Plont S, Ponisio L, Portales‐Reyes C, Provete D, Raes E, Ramirez‐Reyes C, Ramos I, Record S, Richardson A, Salguero‐Gómez R, Satterthwaite E, Schmidt C, Schwartz A, See C, Shea B, Smith R, Sokol E, Solomon C, Spanbauer T, Stefanoudis P, Sterner B, Sudbrack V, Tonkin J, Townes A, Valle M, Walter J, Wheeler K, Wieder W, Williams D, Winter M, Winterova B, Woodall L, Wymore A, Youngflesh C. Priorities for synthesis research in ecology and environmental science. Ecosphere. 2023 January 11; 14(1):-. Available from: https://onlinelibrary.wiley.com/doi/10.1002/ecs2.4342 DOI: 10.1002/ecs2.4342 Reyes R, Pham O, Fergusson R, Ceberio N, Clark C, Cohen C, Fuse M, Pennings P. SCIP: a self-paced summer coding program creates community and increases coding confidence. [Preprint]. 2022 December 27 . DOI: 10.1101/2022.12.27.52195 Duncan M, Chow B, Myron K, Stone J, Hubbell M, Schriock E, Hunt C, Khtikian K, Cohen S. First report of genetic data from two invasive Watersipora (Bryozoa) species in the central California coast rocky intertidal. Aquatic Invasions. 2022; 17(2):136-152. Available from: https://www.reabic.net/aquaticinvasions/2022/issue2.aspx DOI: 10.3391/ai.2022.17.2.01 Erickson O, Cole R, Isaacs J, Alvarez-Clare S, Arnold J, Augustus-Wallace A, Ayoob J, Berkowitz A, Branchaw J, Burgio K, Cannon C, Ceballos R, Cohen CS, Coller H, Disney J, Doze V, Eggers M, Farina S, Ferguson E, Gray J, Greenberg J, Hoffman A, Jensen-Ryan D, Kao R, Keene A, Kowalko J, Lopez S, Mathis C, Minkara M, Murren C, Ondrechen MJ, Ordonez P, Osano A, Padilla-Crespo E, Palchoudhury S, Qin H, Lugo JR, Reithel J, Shaw C, Smith A, Smith R, Summers A, Tsien F, and E Dolan. 2022. How do we do this at a distance? A descriptive study of remote undergraduate research programs during COVID-19. CBE-Life Sciences Education 21(1). https://www.lifescied.org/doi/10.1187/cbe.21-05-0125 Nyda m M.L., Lemmon A.R, Cherry J.R., Kortyna ML, Clancy DL*, Hernandez C*, Cohen CS. 2021. Phylogenomic and morphological relationships among the botryllid ascidians (Subphylum Tunicata, Class Ascidiacea, Family Styelidae). Scientific Reports, 11(1):8351. doi: 10.1038/s41598-021-87255-2. Melroy, L.M.* and CS Cohen. 2021. Temporal and spatial variation in population structure among brooding sea stars in the genus Leptasterias . Ecology and Evolution. http://doi.org/10.1002/ece3.7283 . Hossfeld D*, Ling L, Cohen CS. 2020. Experimental investigation of tidal and freshwater influence on Symbiodiniaceae abundance in Anthopleura elegantissima . PLoS ONE, https://doi.org/10.1371/journal.pone.0238361 Jaffe N*, Eberl R***, Bucholz J**, Cohen CS. 2019. Sea star wasting disease demography and etiology in the brooding sea star Leptasterias spp. PLoS ONE 14(11): e0225248. https://doi.org/10.1371/journal.pone.0225248 Weinberg RB*, Clancy DL*, Cohen CS. 2019. Genotypic variability following fusion in the invasive colonial tunicate Didemnum vexillum . Invertebr Biol. 2019;00:e12263. https://doi.org/10.1111/ivb.12263 Caballero S., Dove V., Jackson-Ricketts J., Junchompoo C., Cohen S, Hines E. 2018. Mitochondrial DNA diversity and population structure in the Irrawaddy dolphin (Orcaella brevirostris ) from the Gulf of Thailand and the Mekong River. Marine Mammal Science, DOI: 10.1111/mms.12518. Cohen CS. 2018. "Marine extinctions" guest essay in Chapter 3, Perspectives section of book, Endangered Species: A Reference Handbook, authored by Jan Randall. ABC-CLIO Contemporary World Issues series , pp. 177-180. Melroy L.*, Smith R**., and CS Cohen. 2017. Phylogeography of direct-developing sea stars in the genus Leptasterias in relation to San Francisco Bay outflow in central California. Marine Biology 64: 152- .DOI: 10.1007/s00227-017-3184-z (Note: shared first authorship between Melroy and Smith) Sheets, E*., Cohen CS, Ruiz GM, Rocha RM. 2016. Investigating the widespread introduction of a tropical marine fouling species . Ecology and Evolution 6 (8): 2453–2471. DOI: 10.1002/ece3.2065 Cohen, CS. 2016. Revision of the Urochordata section in Brusca, RC and Shuster, SM, Chapter 27, Phylum Chordata: Cephalochordata and Urochordata. Invertebrates, 3rd edition, Sinauer Press. Moczek AP, Sears, KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu C, Cohen CS, De Tomaso AW, Gilbert SF, Hall B, Love A, Lyons DC, Sanger T, Smith J, Specht C, Vallejo-Marin M, Extavour CG. 2015. The significance and scope of evolutionary developmental biology: a vision for the 21st century . Evolution and Development 17(3): 198-219. DOI: 10.1111/ede.12125 Ort BS***, Cohen CS, Boyer KE, Reynolds LK, Tam SM***, Wyllie-Echeverria S. 2014. Conservation of Eelgrass (Zostera marina ) Genetic Diversity in a Mesocosm-Based Restoration Experiment. PLoS ONE 9(2): e89316. doi:10.1371/journal.pone.0089316 Goulding T. C*., Cohen, CS. 2014. Phylogeography of a marine acanthocephalan: lack of cryptic diversity in a cosmopolitan parasite of mole crabs. Journal of Biogeography, 41: 965–976. doi: 10.1111/jbi.12260 Craig, C*., W. Kimmerer, C.S. Cohen. 2014. A DNA-based method for investigating feeding by copepod nauplii. J. Plankton Research, 36 (1): 271-275. published 10.14.2013, https://doi.org/10.1093/plankt/fbt104 Ort, B***, Cohen, CS, Boyer, KE, Wyllie-Echeverria, S. 2012. Genetic diversity within and among eelgrass (Zostera marina ) beds in the San Francisco Bay. Journal of Heredity, doi: 10.1093/jhered/ess022 . Cohen, C.S., McCann, L, Davis, T., Shaw, L., Ruiz, G. 2011. Discovery and significance of the colonial tunicate Didemnum vexillum in Alaska. Aquatic Invasions : 6 (3): 263-271. doi: 10.3391/ai.2011.1 Robinson, G. and 19 authors including C. Sarah Cohen. 2010. Empowering 21st Century Biology. BioScience 60:11, 923-930 Nacci, D.,M. Huber, D. Champlin, S. Jayaraman, S. Cohen, E. Gauger**, A. Fong*, M. Gomez-Chiarri. 2009. Trade-offs of contemporary evolution: pathogen susceptibility in a chemically-tolerant estuarine fish population. Environmental Pollution, 157: 857- 864. Eberl, R.*, S. Cohen, F. Cipriano, and E. Carpenter. 2007. Genetic diversity and population structure of the pelagic harpacticoid copepod Macrosetella gracilis on rafts of the bloom-forming cyanobacterium Trichodesmium spp. Aquatic Biology, 1: 33-43. Burnett, K., and 25 authors including S. Cohen. 2007. Fundulus as the premier teleost model in environmental biology: opportunities for new insights using genomics. Comparative Biochemistry and Physiology, Part D 2, 257-286. Cohen, S., J. Tirindelli*, M. Gomez-Chiarri, D. Nacci. 2006. Functional implications of Major Histocompatibility (MH) variation using estuarine fish populations.Integrative and Comparative Biology 46 (6): 1016-1029. Cohen, S. 2002. MHC variation in natural populations of an estuarine fish: high levels of variation and relationship to severe environmental stress. Molecular Biology and Evolution 19 (11): 1870-1880. https://academic.oup.com/mbe/article/19/11/1870/1012454 Cohen, S. and D. Nacci. 2002. Effects of dioxin-like compound (DLC) contamination on an estuarine fish species: adaptive changes at specific loci. Conference proceedings, US/Vietnam Scientific Conference on Agent Orange/Dioxins, March 3-6, 2002, Hanoi, Vietnam. Saito, Y., Shirae, M., Okuyama, M., and S. Cohen. 2001. Phylogeny of botryllid ascidians. In, "The Biology of Ascidians", ed H. Sawada, H. Yokosawa, CC Lambert, Springer, Tokyo, pp. 315-320. Cohen, S. 2000. Botryllid ascidian invasions: genetic and behavioral evidence for multi-species invasions and character divergence following introductions. In, Proceedings of the First National Conference on Marine Bioinvasions, MIT Sea Grant. Cohen, S., Saito, Y. and I. Weissman. 1998. Evolution of allorecognition in botryllid ascidians inferred from a molecular phylogeny. Evolution 52(3):746-756. Cohen, S. 1996. The effects of contrasting modes of fertilization on levels of inbreeding in the marine invertebrate genus Corella . Evolution 50(5): 1896-1907. Cohen, C. S. and R. Strathmann. 1996. Embryos at the edge of tolerance: effects of environment and structure of egg masses on supply of oxygen to embryos. Biol. Bull. 190: 8-15. https://www.journals.uchicago.edu/doi/epdf/10.2307/1542671 Dethier, M., Graham, E., Cohen, S., and L. Tear. 1993. Visual and random-point percent cover estimations: "Objective is not always better." Mar. Ecol. Prog. Ser. 96: 93-100. Petersen, C., Warner, R., Cohen, S., Hess, H. and A. Sewell. 1992. Variation in pelagic fertilization rates: Implications for production estimates, mate choice, and the spatial distribution of mating. Ecology 73: 391-401. Cohen, S. 1990. Outcrossing in field populations of two species of self-fertile ascidians. J. Exp. Mar. Biol. Ecol. 140: 147-158. Hess, H., Bingham, B., Cohen, S., Grosberg, R., Jefferson, W. and L. Walters. 1988. The scale of genetic differentiation in Leptosynapta clarki (Heding), an infaunal brooding holothuroid. J. Exp. Mar. Biol. Ecol. 122: 187-194. ____________

SFSU Marine Invertebrate Collections and Resources The San Francisco State University Marine Invertebrate teaching collection Housed on the second floor of Hensill Hall on the main SFSU campus on 19th Avenue in SF, the collection comprises over 742 marine invertebrate specimens focused on Pacific Ocean collection sites ranging from Washington state to Baha California in Mexico. The oldest specimen dates from 1897 and the collection contains invertebrates identified by many collectors, including students, researchers, and natural historians, including a few by Ed Ricketts of Cannery Row fame, in Pacific Grove, California. Containing 15 phyla, the collection includes a wide array of diverse marine invertebrate species. Many students have assisted in curating the collection for use in the Marine Invertebrate Zoology and Marine Ecology classes. Recent student curators include: Fall 2017--Margaret Johnson, Cecilia Hernandez, and Rachel Weinberg Previous years, an incomplete list--Benson Chow, Noah Jaffe, Anton Horwath, Joseph Spaulding, Ann Holmes, Katie Nuessly, and more. For information on specimens, please contact Dr. Sarah Cohen, sarahcoh@sfsu.edu. The collections at the Oceanography Institute in Nha Trang, Vietnam are on public display, allowing the public to see a view of the cataloging of natural history into a systematics collection. photo: CS Cohen Speci al Invertebrate Chordate papers at San Francisco St ate University Ascidian reprints, personal papers, and books collection of Dr. T odd Newberry , Emeritus Professor of Biology, University of California, Santa Cruz and Dr. Donald P. Abbott , Hopkins Marine Station, Stanford University. These materials were generously donated by Dr. Todd Newberry. With funding from an SFSU IRA award, graduate student Benson Chow is sorting, cataloging, archiving, and scanning selected materials, some of which will be available on the web in the future. This collection is housed at the EOS Center at the Romberg Tiburon Campus of San Francisco State. If you wish to use the materials, please contact Dr. Sarah Cohen, sarahcoh@sfsu.edu. Some materials are additionally on loan to Gretchen Lambert, Seattle, Washington. The wet collections associated with Dr Abbott's work at Stanford are housed in the California Academy of Sciences. Marine parasitology references donated by Dr. Michael Moser, UC Berkeley A variety of reference works and textbooks kindly donated by Dr Michael Moser are available at EOS/Romberg Tiburon Center. Please contact Sarah Cohen, sarahcoh@sfsu.edu , for further information. ___________________________________________________________________________________________ Collecting Information Califor nia Fish and Game permits NOAA National Marine Sanctuary permits Other local useful permit information Other collections Other invertebrate resources CAS Pillar Point Invertebrate Biodiversity survey pictures : https://www.inaturalist.org/projects/pillar-point-tidepools-bioblitz

Colleagues & Collaborators U.S. Roger Bland, Physics Department, SFSU Dr Lorriane Ling, Stanford University Exploratorium , San Francisco Smithsonian Environmental Research Center, Marine Invasions Research Lab Tammy Davis, Alaska Dept. of Fish and Game, Juneau Linda Shaw, NOAA, Juneau, Alaska Linda Walters, University of Central Florida Dianna Padilla, Stony Brook University Bruce Collette, Smithsonian National Museum of Natural History Marnie Chapman, University of Alaska, Southeast Mark Hahn, Woods Hole Oceanographic Institute Diane Nacci, US EPA, Atlantic Ecology Division Marta Gomez-Chiarri, University of Rhode Island Gretchen Lambert , Friday Harbor Laboratories, University of Washington Liz Alter, Moss Landing Marine Laboratories Jim Carlton, Williams College, Mystic Seaport Maritime Studies Program Megumi Strathmann, University of Washington Sitka Tribe of Alaska Sitka Sound Science Center Sitka Conservation Society California Academy of Sciences Paul Bourdeau lab, Humboldt State University Marie Nydam, Soka University, California Meg Daly, Ohio State University Drew Harvell, Cornell University Olivia Graham, Cornell University Ian Hewson, Cornell University Ellen Hines, Geography Department, SFSU International Rosana M. da Rocha , Universidade Federal do Parana, PR, Brasil Susana Caballero, Universidad de los Andes, Bogota, Colombia Yas Saito , Shimoda Marine Research Center, University of Tsukuba, Japan Noa Shenkar, Tel Aviv University, Israel C armela Gissi, Dip. Bioscienze, Università degli Studi di Milano, Milano, Italy Francesca Griggio, Dip. Bioscienze, Università degli Studi di Milano, Milano, Italy Riccardo Brunetti, Museo di Storia Naturale di Venezia, Venezia, Italy Francesco Mastrototaro, Dip. Biologia, Università di Bari, Bari, Italy Maria Ana Tovar-Hernandez, GEOMAR, Mexico A few local Citizens Science and outreach projec ts California Academy of Sciences Citizen Science Projects , led by Rebecca Johnson and Alison Young Bay Area King Tide Announcement CA Dept. of Public Health Toxic Phytoplankton Volunteer Monitoring Program

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