2025 Publications from the Department of Ecology and Evolution (updated Sept.2025)

• Xu, Liang, Emily Zakem, and J.L. Weissman. 2025. “Improved maximum growth rate prediction from microbial genomes by integrating phylogenetic information”. Nature Communications. https://doi-org.proxy.library.stonybrook.edu/10.1038/s41467-025-59558-9
• Buchanan, Pearse J., Xin Sun, J. L. Weissman, Daniel McCoy, Daniele Bianchi, and Emily Zakem. 2025. "Oxygen intrusions sustain aerobic nitrite-oxidizing bacteria in anoxic marine zones." Science. https://doi-org.proxy.library.stonybrook.edu/10.1126/science.ado0742
• Zakem, Emily J., Jesse McNichol*, J. L. Weissman*, Yubin Raut, Liang Xu, Elisa R. Halewood, Craig A. Carlson, Stephanie Dutkiewicz, Jed A. Fuhrman, and Naomi M. Levine. 2025. "Predictable functional biogeography of marine microbial heterotrophs." Science. https://doi-org.proxy.library.stonybrook.edu/10.1126/science.ado5323
• Samantha J. Gleich. Lisa Y. Mesrop, Jacob A. Cram, J.L. Weissman, Sarah K. Hu, Yi-Chun Yeh, Jed A. Fuhrman, and David A. Caron. 2025. “With a little help from my friends: Importance of protist-protist interactions in structuring marine protistan communities in the San Pedro Channel” mSystems. https://doi-org.proxy.library.stonybrook.edu/10.1128/msystems.01045-24 
• Nasa Sinnott-Armstrong, Desiree Forsythe, Jane M Benoit, Callie R. Chappell, Lisa S. Y. Coe, Bruno Francesco Rodrigues de Oliveira, Natalya Evans, Anna C. Fagre, Jonathan M. Gilligan, Maria Hamilton, Colin Moran Henneberry, Suzanne L. Ishaq, Juliet Johnston, Erin Krichilsky, Jamie Alcira Lopez, Kay McMonigal, Melanie Ortiz Alvarez de la Campa, Rahmeen Rahman, Nicole E. Schwartz, Lauren Talluto, Eric J. Taylor, José M. Vargas-Muñiz, and J. L. Weissman. 2025. "Protect Transgender Scientists". Science. https://doi-org.proxy.library.stonybrook.edu/10.1126/science.ady0962
• Green, DR, KT Uno, ER Miller, CS Feibel, EE Aoron, CC Beck, A Grossman, FM Kirera, MM Kirinya, LN Leakey, C Liutkus-Pierce, FK Manthi, EK Ndiema, IO Nengo, C Nyete, J Rowan, GA Russo, WJ Sanders, TM Smiley, P Princehouse, NS Vitek,  & TP Cleland. 2025. 29 million years of diverse mammalian proteomes recovered from the East African Rift System. Nature 643: 712-718.
• Jahn, AE, D de Angeli Dutra, JA Bell, JH Dispotot, A Fecchio, ED Ketterson, KMD Kuabara, TM Smiley, TB Verret, JD Weckstein, EJ Williams, & DJ Becker. 2025. Between- and within-population drivers of haemosporidian prevalence and diversity in American robins (Turdus migratorius). Journal of Avian Biology 3: e03430.
• Jahn, AE, K Koller, LB Martin, TM Smiley, TB Verret, ED Ketterson, EJ Williams, & DJ Becker. 2025. Temporal patterns, behavioral drivers, and physiological correlates of West Nile virus exposure in American robins (Turdus migratorius). Ecological and Evolutionary Physiology 98(3): 133-206.
• Muthukrishnan, R, TM Smiley, PO Title, A Fudickar, A Jahn, & J Lau. 2025. Chasing the niche: Escaping climate change threats in time, space, and place. Global Change Biology. Media coverage: https://eri.iu.edu/news-and-events/_news/archive/2025/20250529-study-highlights-complexities-of-species-response-to-climate-change.html
• Marder, E, TM Smiley, BJ Yanites, K Kravitz. 2025. Direct effects of mountain uplift and topography on biodiversity. Science, 387(6740): 1287-1291. All authors contributed equally to this work. Highlighted by Science: https://www.science.org/doi/epdf/10.1126/science.adx5174. Media coverage: https://news.iu.edu/college/live/news/44827-iu-geoscientists-co-author-study-that-finds; https://nautil.us/as-mountains-rise-biodiversity-blooms-1205605/; https://www.earth.com/news/how-rising-mountains-give-birth-to-new-species/
• Thomas M. Grothues, Dianna K. Padilla, A. Sulan Kolatan, Christina M. K. Kaunzinger, Philip Parker, Steven N. Handel. 2025. Life as a design element of hardened urban shorelines.  Estuaries and Coasts  48, 48 (2025). https://doi.org/10.1007/s12237-024-01475-z
• Samuel J. Gurr, Genevieve Bernatchez, Mark Dixon, Lisa Keith, Deborah Hart, Lisa Milke, Dylan H. Redman, Louis Plough, George Sennefelder, Sheila Stiles, David Veilleux, Gary H. Wikfors, Katherine McFarland, Shannon L. Meseck, Dianna K. Padilla. 2025. Within and cross-generational effects of elevated seawater pCO₂ on larval bay scallops Argopecten irradians (L). Journal of Shellfish Research 44:185-195.