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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. ____________

Welcome to the Cohen Lab Welcome to Sarah Cohen's SFSU Evolutionary Ecology Lab in the Biology Department and at the Estuary and Ocean Science Center on the Romberg Tiburon Campus Welcome Fall 2023 Grad Students Berenice Baca-Ceballos Dorhkas Ramos Anti-racism and Inclusive Diversity resources from CSU COAST INTERESTS Research Interests of Sarah Cohen I am interested in how ecological, behavioral, and environmental features shape evolution and genetic systems in diverse organisms. Most of our work in marine and estuarine settings has asked questions about how life history, physiological, or behavioral attributes of species affect population structure. Often the results directly address questions about coastal and marine conservation related to our ability to detect, predict, and remediate anthropogenic effects on natural populations. In addition, I have a particular interest in the ecology and evolution of recognition systems and have been investigating this both in colonial invertebrates and estuarine fishes. Current projects include: immunogenetic (Major Histocompatibility Complex) variation in fish populations of varying size, the use of genetic markers to detect anthropogenic effects related to invasions, reproductive ecology of sea stars, distributions of parasites in estuarine and marine hosts, evolved tolerance for contaminants in estuarine populations, genetic tools for estimating population linkage in estuarine and marine species including urchins, lobsters, fish, seastars, copepods, seagrasses, and tunicates, and phylogenetic relationships between various marine taxa at the family level (e.g., fish and tunicates). Other projects have included oxygen diffusion in egg masses of snails and worms and implications for egg mass design, mating systems and inbreeding depression in tunicates, intertidal biodiversity surveys and methods, and behavioral variation in colonial marine invertebrates. We use research methods ranging from the high to very low tech, indoor to outdoor, and dry to wet. Subscribe Form Join Thanks for subscribing!

Research Interests We are interested in how ecological, behavioral, and environmental features shape evolution and genetic systems in diverse organisms. Most of our work in marine and estuarine settings has asked questions about how life history, physiological, or behavioral attributes of species affect population structure and how population structure may influence changes in life history traits. Often the results of our research directly address questions about coastal and marine conservation related to our ability to detect, predict, and remediate anthropogenic effects on natural populations. This approach combining basic questions in ecology and evolution with applied issues in biology is carried out in pressing environmental situations that frequently feature non model taxa where methods development is also required. Thus, a signature feature of work in our lab is developing or adapting new field and laboratory methods to address environmentally relevant issues, often related to climate change. Some organisms and systems where this work is carried out including host/pathogen/symbiont interactions, seagrass restoration, sea star populations and wasting disease, endangered and endemic populations, invasive species and range extensions, and the impact of contaminants on local populations in estuarine settings. In addition, we have a particular interest in the ecology and evolution of recognition systems. In vertebrates (fish, mice, and dolphins in our research), we use the immune recognition loci, the Major Histocompatibility Complex or MHC, to ask how high variability is maintained or lost under varying population conditions (both demographic and selective). In invertebrate chordates (aka tunicates or sea squirts), we make use of blood-mediated recognition loci that control colony fusion in the botryllid ascidians and gamete recognition loci in the solitary ascidian Ciona. We are additionally testing fusion genetics in the highly invasive didemnid ascidian Didemnum vexillum. We have additional interests in systematics of sea stars and sea squirts (aka ascidians) and we work with the California Academy of Sciences and other museums to carry out morphological and molecular analyses related to global biogeography and systematics. The biotic diversity of the Philippines is a particular focus with ascidians as part of the NSF-funded Cal Academy Biotic Survey of the center of the center of marine biodiversity in the Verde Island Passage. Leptasterias systematics is a focus on the northeast Pacific coast related to shifting clade distributions prior to and following the recent epidemic of wasting disease. For descriptions of a few projects, click below: EOS MOLECULAR LAB Find the seahorse and tunicate Photo by Adriana Perez Below you can find information on a few of the many subjects and projects we are interested in. Biodiversity May, RM, PLOS Biology, 2011, Why worry about how many species and their loss? Conservation: The preservation and careful management of natural, and not so natural, habitats EPA Cleanups: Communities around New Bedford Harbor Invasive species RESEARCH PROJECTS Research Organisms Inside a botryllid! Note the brooded embryos. Photo by Patrick Lee, SFSU undergrad. Measuring leptasterias in the intertidal.

Welcome to the updated Cohen Lab website!

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