Full Publications Archive (2008

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y2025

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.
Sinnot-Amstrong et al., 2025: which highlights the elimination of federal funding of research on and health care for trans and gender non-conforming individuals and the elimination of DEI efforts to support such scientists.
Zakem et al. 2025: A study on the functional biogeography of marine heterotrophs, which play central roles in present and future ocean carbon sequestration.
Buchanan et al. 2025: Research on nitrite-oxidizing bacteria in open-ocean oxygen minimum zones, key regions for denitrification and nitrous oxide production.
Xu et al. 2025: Introduction of Phydon, a new package that estimates maximum bacterial growth rates by integrating codon statistics with phylogenetic information.

y2024

2024 Publications from the Department of Ecology and Evolution (updated Apr.2024)

Roesch E, Rosencrans JH, Hatch KA, Thacker RW. 2024. Inventory of shallow-water fouling invertebrates of Long Island, New York. Oceans 5(4): 825-839. doi: 10.3390/oceans5040047
Turner TL, Rouse GW, Weigel BL, Janusson C, Lemay MA, Thacker RW. 2024. Taxonomy and phylogeny of the family Suberitidae (Porifera: Demospongiae) in California. Zootaxa. 5447(1): 1-28. doi: 10.11646/zootaxa.5447.1.1
Gallagher, K., R. Herman, K. Walton, M.S. Dinniman, and H.J. Lynch. 2025. Pygoscelis penguins prefer different oceanographic and terrestrial habitats during the austral summer. In press at Ecosphere.
Pertierra, L.R., P. Convey, A. Barbosa, E. M. Biersma, D. Cowan, J. A. F. Diniz-Filho, A. de los Ríos, P. Escribano-Álvarez, C. I. Fraser, D. Fontaneto, M. Greve, H. J. Griffiths, M. Harris, K. A. Hughes, H. J. Lynch, R. J. Ladle, X. P. Liu, P. C. le Roux, R. Majewska, M. A. Molina-Montenegro, L. S. Peck, A. Quesada, C. Ronquillo, Y. Ropert-Coudert, L. G. Sancho, A. Terauds, G. Varliero, J. A. Vianna, A. Wilmotte, S. L. Chown, M. Á. Olalla-Tárraga, and J. Hortal. 2025. Frozen but lively: ecological research advances and key knowledge gaps in terrestrial and freshwater Antarctic biodiversity science. Science 387: 609-615.
VanCompernolle, M., ..., H.J. Lynch, ... et al. 2025. Vulnerability of highly-mobile and wide-ranging marine megafauna to global anthropogenic threats. In press at Conservation Biology.
Wethington, M.J., B. Sen, and H.J. Lynch. 2024. Predicting pack-ice seal occupancy of ice floes along the Western Antarctic Peninsula. PLoS ONE 19(12): e0311747.
Wu, H., C. Flynn, C. Hall, C. Che-Castaldo, D. Samaras, M. Schwaller, and H.J. Lynch. 2024. Penguin colony georegistration using camera pose estimation and phototourism. PLoS ONE 19(10): e0311038.
Sen, B., C. Che-Castaldo, H.J. Lynch, F. Ventura, M.A. LaRue, and S. Jenouvrier. 2024. Detecting stochasticity in population time series using a non-parametric test of intrinsic predictability. Methods in Ecology and Evolution doi: 10.1111/2041-210X.14423.
Kaczvinsky, C., H. Levy, S. Preston, C. Youngflesh, G. Clucas, H.J. Lynch, A.L. Smith, and T. Hart. The influence of biotic and abiotic factors on the bacterial microbiome of gentoo penguins (Pygoscelis papua) in their natural environment. 2024. Scientific Reports 14:17933.
Hallet, M., and H.J. Lynch. 2024. Update on the abundance and distribution of Macaroni Penguins (Eudyptes chrysolophus) in the Antarctic Peninsula region. Polar Biology 47: 607-615.
Gallagher, K., M. Cimino, M.S. Dinniman, and H.J. Lynch. 2024. Quantifying potential marine debris sources and potential threats to penguins on the West Antarctic Peninsula. Environmental Pollution 347: 123714.
Pertierra, L.R., G. Varliero, A. Barbosa, E.M. Biersma, P. Convey, S.L. Chown, D. Cowan, A. De los Rios, P. Escribano-Alvarez, D. Fontaneto, C.I. Fraser, M. Harris, K.A. Hughes, H.J. Griffiths, P.C. le Roux, X.P. Liu, H.J. Lynch, P.A. Martinez, M.A. Molina-Montenegro, M.A. Olalla-Tarraga, L. Peck, A. Quesada, Y. Ropert-Coudert, L. Sancho, A. Terauds, J.A. Vianna, A. Wilmotte, J. Hortal, and M. Greve. 2024. ANTALIFE 1.0 Biodiversity data checklist of all Antarctic terrestrial and freshwater life forms in the continent. Biodiversity Data Journal 12: e106199.
Herman, R.W., G. Clucas, J. Younger, J. Bates, B. Robinson, S. Reddy, J. Stepanuk, K. O’Brien, K. Veeramah, and H.J. Lynch. 2024. Whole genome sequencing reveals stepping stone dispersal buffered against founder effects in a range expanding seabird. Molecular Ecology 00:e17282.
Gleich, S. J., Mesrop, L. Y., Cram, J. A., Weissman, J. L., Hu, S. K., Yeh, Y. C., ... & Caron, D. A. (2025). With a little help from my friends: importance of protist-protist interactions in structuring marine protistan communities in the San Pedro Channel. mSystems, e01045-24.
Weissman, J. L., Chappell, C. R., Francesco Rodrigues de Oliveira, B., Evans, N., Fagre, A. C., Forsythe, D., ... & Advancing Queer and Trans Equity in Science (AQTES) Consortium. (2024). Queer-and trans-inclusive faculty hiring—A call for change. PLoS biology, 22(11), e3002919.
Xiao, W., Weissman, J. L., & Johnson, P. L. (2024). Ecological drivers of CRISPR immune systems. mSystems, 9(12), e00568-24.
Merchant, S., Weissman, J. L., & MacLa, E. (2024). Creating a Broader Impacts Culture. Journal of Community Engagement & Scholarship, 17(2).
Connors, E., Dutta, A., Trinh, R., Erazo, N., Dasarathy, S., Ducklow, H., ... & Bowman, J. S. (2024). Microbial community composition predicts bacterial production across ocean ecosystems. The ISME Journal, 18(1), wrae158.
Thonis, A. and H.R. Akçakaya. (2025). Perils of using range maps in macroecological models of species richness. Journal of Biogeography. https://doi.org/10.1111/jbi.15072
Butchart, S.H.M., H.R. Akçakaya, A.J. Berryman, T.M. Brooks, I.J. Burfield, J. Chanson, M.P. Dias, J.S. Donaldson, C. Hermes, C. Hilton-Taylor, M. Hoffmann, J.A. Luedtke, R. Martin, A. McDougall, K. Neam, B. Polidoro, D. Raimondo, A.S.L. Rodrigues, C. Rondinini, C. Rutherford, T. Scott, A.T. Simkins, S.N. Stuart, J. Vine. (2025). Measuring trends in extinction risk: a review of two decades of development and application of the Red List Index. Philosophical Transactions B, 380:20230206. https://doi.org/10.1098/rstb.2023.0206
H.R. Akçakaya. (2024). Extinction risk categorization in the IUCN Red List: comment on the US Endangered Species Act and acceptable risk. Biological Conservation, 299:110804. https://doi.org/10.1016/j.biocon.2024.110804
Thonis, A. and H.R. Akçakaya. (2024). Experimental evidence that competition strength scales with ecological similarity: A case study using Anolis lizards. Oecologia, 204: 451–465. https://doi.org/10.1007/s00442-023-05507-6
Şen, B., C. Che-Castaldo, and H.R. Akçakaya. (2024). The potential for species distribution models to distinguish source populations from sinks. Journal of Animal Ecology, 93: 1924–1934. https://doi.org/10.1111/1365-2656.14201
Cazalis, V., M. Di Marco, A. Zizka, S.H.M. Butchart, M. González-Suárez, M. Böhm, S.P. Bachman, M. Hoffmann, I. Rosati, F. De Leo, M. Jung, A. Benítez-López, V. Clausnitzer, P. Cardoso, T.M. Brooks, G. Mancini, P.M. Lucas, B.E. Young, H.R. Akçakaya, A.M. Schipper, C. Hilton-Taylor, M. Pacifici, C. Meyer, and L. Santini. (2024). Accelerating and standardising IUCN Red List assessments with sRedList. Biological Conservation, 298:110761. https://doi.org/10.1016/j.biocon.2024.110761
Loope, K.J., H.R. Akçakaya, and K.T. Shoemaker. (2024). Inflated predictions from a flawed model influenced the decision to deny federal protection for the gopher tortoise. Global Ecology and Conservation, e03089. https://doi.org/10.1016/j.gecco.2024.e03089
Thonis, A., A. Stansfield, and H.R. Akçakaya. (2024). Unravelling the role of tropical cyclones in shaping present species distributions. Global Change Biology, 30:e17232. https://doi.org/10.1111/gcb.17232
Henry, E. G., L. Santini, S. H. M. Butchart, M. González-Suárez, P. M. Lucas, A. Benítez-López, G. Mancini, M. Jung, P. Cardoso, A. Zizka, C. Meyer, H.R. Akçakaya, A. J. Berryman, V. Cazalis, and M. Di Marco. (2024). Modelling the probability of meeting IUCN Red List criteria to support reassessments. Global Change Biology, 30:e17119. https://doi.org/10.1111/gcb.17119
Layman, H., H.R. Akçakaya, A. Irwin, S. zu Ermgassen, P. Addison, M. Burgman. (2024). Short term solutions to biodiversity conservation in portfolio construction: Forward-looking disclosure and classification-based metrics. Business Strategy and the Environment, 33:1778-1793. https://doi.org/10.1002/bse.3570
Mancini, G., L. Santini, V. Cazalis, H.R. Akçakaya, P. M. Lucas, T. M. Brooks, W. Foden, and M. Di Marco. (2024). A standard approach for including climate change responses in IUCN Red List assessments. Conservation Biology. https://doi.org/10.1111/cobi.14227
Dr. Frederic Vencl (2025). Symbiosis and horizontal gene transfer promote herbivory in the megadiverse leaf beetles. Current Biology 35(1): 1-15. https://www.sciencedirect.com/science/article/pii/S0960982224016968
Dr. Ross Nehm, selected to serve on the National Science Foundation funded committee "Advancing AI in Science Education: A Comprehensive Approach to Equity, Inclusion, and Three-Dimensional Learning." Read More
Congrats to Dianna who makes an appearance in SBU’s new brand anthem video. View here.
Dr. Tara Smiley's New Article, linkages between Cenozoic mountain building and faunal change in the U.S. Read More .
Dr. Natasha Vitek - published article about the Oldest record of a crown anomaluroid rodent: Read More.
Yukilevich, Roman & Aoki, Fumio & Egan, Scott & Zhang, Linyi. (2024). Coevolutionary Interactions between Sexual and Habitat Isolation during Reinforcement. Cold Spring Harbor Perspectives in Biology. 16. a041431. 10.1101/cshperspect.a041431.
Joon-Hyun Song, Liliana M. Dávalos, Thomas MacCarthy, Mehdi Damaghi (2024). Evolvability of cancer-associated genes under APOBEC3A/B selection. iScience 109433, https://www.sciencedirect.com/science/article/pii/S2589004224006540
Neal Anthwal, Ronald P. Hall, Frederik Aneudy de la Rosa Hernandez, Michael Koger, Laurel R. Yohe, Brandon P. Hedrick, Kalina T.J. Davies, Gregory L. Mutumi, Charles C. Roseman, Elizabeth R. Dumont, Liliana M. Dávalos, Stephen J. Rossiter, Alexa Sadier, Karen E. Sears (2023). Cochlea development shapes bat sensory system evolution. The Anatomical Record 2023, 1-12. https://doi.org/10.1002/ar.25353
Natalie Weber, Martina Nagy, Wanda Markotter, Juliane Schaer -Sébastien J. Puechmaille, Jack Sutton, Liliana M. Dávalos, Marie-Claire Dusabe, Imran Ejotre, M. Brock Fenton, Mirjam Knörnschild, Adrià López-Baucells, Rodrigo A. Medellin, Markus Metz, Samira Mubareka, Olivier Nsengimana, M. Teague O’Mara, Paul A. Racey, Merlin Tuttle, Innocent Twizeyimana, Amanda Vicente-Santos, Marco Tschapka, Christian C. Voigt, Martin Wikelski, Dina K.N. Dechmann, DeeAnn M. Reeder (2023). Robust evidence for bats as reservoir hosts is lacking in most African virus studies: a review and call to optimize sampling and conserve bats. Biology Letters 19, 20230358. https://doi.org/10.1098/rsbl.2023.0358
Francisco X. Castellanos, Diana D. Moreno-Santillán, Graham M. Hughes, Nicole S. Paulat, Nicolette Sipperly, Alexis M. Brown, Katie Martin, Gregory M. Poterewicz, Marisa C.W. Lim, Amy L. Russell, Marianne S. Moore, Matthew G. Johnson, Angelique P. Corthals, David A. Ray, Liliana M. Dávalos (2023). The evolution of antimicrobial peptides in Chiroptera. Frontiers in Immunology 14. https://doi.org/10.3389/fimmu.2023.1250229
Levinton, Jeffrey S. (2024) Extinction in the Fossil Record. In: Scheiner Samuel M. (eds.) Encyclopedia of Biodiversity 3rd edition, vol. 7, pp. 319–335. Oxford: Elsevier. http://dx.doi.org/10.1016/B978-0-12-822562-2.00148-1
Gallagher, K., M. Cimino, M.S. Dinniman, and H.J. Lynch. 2024. Quantifying potential marine debris sources and potential threats to penguins on the West Antarctic Peninsula. Environmental Pollution 347: 123714.
Pertierra, L.R., G. Varliero, A. Barbosa, E.M. Biersma, P. Convey, S.L. Chown, D. Cowan, A. De los Rios, P. Escribano-Alvarez, D. Fontaneto, C.I. Fraser, M. Harris, K.A. Hughes, H.J. Griffiths, P.C. le Roux, X.P. Liu, H.J. Lynch, P.A. Martinez, M.A. Molina-Montenegro, M.A. Olalla-Tarraga, L. Peck, A. Quesada, Y. Ropert-Coudert, L. Sancho, A. Terauds, J.A. Vianna, A. Wilmotte, J. Hortal, and M. Greve. 2024. ANTALIFE 1.0 Biodiversity data checklist of all Antarctic terrestrial and freshwater life forms in the continent. Biodiversity Data Journal 12: e106199.
Herman, R.W., G. Clucas, J. Younger, J. Bates, B. Robinson, S. Reddy, J. Stepanuk, K. O’Brien, K. Veeramah, and H.J. Lynch. 2024. Whole genome sequencing reveals stepping stone dispersal buffered against founder effects in a range expanding seabird. Molecular Ecology 00:e17282.
Nehm, R.H. (2024). When less is more in living systems: subtractive cognitive biases and life science learning. Journal of Biological Education. DOI: 10.1080/00219266.2024.2320106
Sbeglia, G. Nehm, R.H. (2024). Building conceptual and methodological bridges between SSE’s Diversity, Equity, and Inclusion statement and educational actions in evolutionary biology. Evolution. DOI: https://doi.org/10.1093/evolut/qpae026
RG Duncan, R Krishnamoorthy, U Harms, M Haskel-Ittah, K Kampourakis, N Gericke, M Hammann, M Jimenez-Aleixandre, RH Nehm, MJ Reiss, A Yarden (2024). The sociopolitical in human genetics education. Science. Vol 383, Issue 6685 pp. 826-828
Nehm, R.H. (2024). Considering Explanatory Diversity and Holistic Understanding of Biological Phenomena. The American Biology Teacher. February. DOI: https://doi.org/10.1525/abt.2024.86.2.55
Nehm, R.H. (2024). AI in Biology Education Assessment: How Automation Can Drive Educational Transformation. In: Zhai, X. et al. (Eds.) Uses of Artificial Intelligence in STEM Education. Oxford University Press.
Dianna K Padilla and Daniel Grünbaum 2024 Preparing the Next Generation of Integrative Organismal Biologists. Integrative and Comparative Biology 64(3):1007-1018 DOI: 10.1093/icb/icae098
Samuel J. Gurr, Katherine McFarland, Genevieve Bernatchez, Mark S. Dixon, Lisa Guy, Lisa M. Milke, Matthew E. Poach, Deborah Hart, Louis V. Plough, Dylan H. Redman, George Sennefelder, Sheila Stiles, Gary H. Wikfors, Dianna K. Padilla, Shannon L. Meseck. 2024 Effects of food supply on northern bay scallops Argopecten irradians (L.) reared under two pCO2 conditions. Marine Ecology Progress Series 740:61-78
Dianna K Padilla, Lisa Milke, Morodoluwa Akin-Fajiye, Maria Rosa, Dylan Redman, Alyssa Liguori, Allison Rugila, David Veilleux, Mark Dixon, David Charifson, Shannon L. Meseck. 2024. Local differences in robustness to ocean acidification. Biology Open 13 (8)
Kendra J. Greenlee and Dianna K. Padilla. 2024. Modeling Organismal Responses to Changing Environments. Integrative And Comparative Biology 64(3):900-904 DOI: 10.1093/icb/icae131
Nicolas S. Anderson and Dianna K Padilla. 2024 Settlement and metamorphosis of the ribbed mussel, Geukensia demissa, in response to environmental cues. In Revision. Biological Bulletin In Press
Thomas M. Grothues, Dianna K. Padilla, A. Sulan Kolatan, Christina M. K. Kaunzinger, Philip Parker, Steven N. Handel. 2024. Life as a design element of hardened urban shorelines. Estuaries and Coasts Special Issue on Living Shorelines In Press
Poddar, U., Gurevitch, J., Meiners, S. J., & D’Andrea, R. (2024). Similar trait-based successional assembly in native and introduced plants despite species pool differences. Journal of Ecology, 00, 1–17. https://doi.org/10.1111/1365-2745.14304
Liliana M. Dávalos, Editor-in-Chief, The Quarterly Review of Biology, https://www.journals.uchicago.edu/toc/qrb/current
Gil-Gomez, A., J.S. Rest. 2024. Wiring between close nodes in molecular networks evolves more quickly than between distant nodes. Molecular Biology and Evolution, msae098, https://doi.org/10.1093/molbev/msae098.
Collier, J.L., J.S. Rest, L. Gallot-Lavallée, E. Lavington, A. Kuo, J. Jenkins, C. Plott, J. Pangilinan, C. Daum, I.V. Grigoriev, G.V. Filloramo, A. Vanclova, J.M. Archibald. 2023. The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses. Current Biology, 33(23), pp.5199-5207. https://www.sciencedirect.com/science/article/pii/S0960982223013684
Tara M. Smiley, Alireza Bahadori, E. Troy Rasbury, William E. Holt, and Catherine Badgley, 2024, Tectonic extension and paleoelevation influence mammalian diversity dynamics in the Basin and Range Province of western North America. Sci. Adv. 10, eadn6842(2024). DOI:10.1126/sciadv.adn6842
Title P.O., Singhal S., Grundler M.C., Costa G.C., Pyron R.A., Colston T.J., Grundler M.R., Prates I., Stepanova N., Jones M.E.H., Cavalcanti L.B.Q., Colli G.R., Di-Poï N., Donnellan S.C., Moritz C., Mesquita D.O., Pianka E.R., Smith S.A., Vitt L.J., Rabosky D.L. 2024. The macroevolutionary singularity of snakes. Science 383, 918-923.
True, J.R. and Abreu, E. 2024 Comparing learning outcomes of two collaborative activities on random genetic drift in an upper-division genetics course. Evolution: Education & Outreach 17(2) 17, 2 https://doi.org/10.1186/s12052-024-00195-z
Li, T., Zhang, R.S., and True, J.R. 2024 Genetic variation for sexual dimorphism in developmental traits in Drosophilamelanogaster. G3 jkae010, https://doi.org/10.1093/g3journal/jkae010
Lavrov DV, Diaz MC, Maldonado M, Morrow CC, Perez T, Pomponi SA, Thacker RW. (2023) Phylomitogenomics bolsters the high-level classification of Demospongiae (phylum Porifera). PLoS ONE 18(12): e0287281, https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0287281
Turner TL, Rouse GW, Weigel BL, Janusson C, Lemay MA, Thacker RW. 2024. Taxonomy and phylogeny of the family Suberitidae (Porifera: Demospongiae) in California. Zootaxa. 5447(1): 1-28. doi: 10.11646/zootaxa.5447.1.1
Vencl, F. V., et al., (2024). Effects of elevated CO2 and temperature on the performance of a diet specialized Neotropical herbivore and it's host plant. Biotropica, in press.
Vencl, F. V., Bartram, S., Winter, K., Boland, W., Srygley, R. B. (2024). Effects of elevated CO 2 and temperature on the performance of a diet specialized neotropical herbivore and it's host plant. Biotropica 56(6): e13371.
Kirsch, R., Okamura, Y., García-Lozano, M., Weiss, B., Keller, J., Vogel, H., Fukumori, K., Fukatsu, T., Konstantinov, A. S., Montagna, M., Moseyko, A. G., Riley, E. G., Slipinski, A., Vencl, F. V., Windsor, D. M., Salem, H., Kaltenpoth, M., Pauchet, Y. (2024).  Symbiosis and horizontal gene transfer promote herbivory in the megadiverse leaf beetles. Current Biology, in press.
Blackburn, D.C., Boyer, D.M., Gray, J.A., Winchester, J., Bates, J.M., Baumgart, S.L., Braker, E. Coldren, D., Conway, K.W., Rabosky, A.D., de la Sancha, N., Dillman, C.B., Dunnum, J.L., Early, C.M., Frable, B.W., Gage, M.W., Hanken, J., Maisano, J.A., Marks, B.D., Maslenikov, K.P., McCormack, J.E., Nagesan, R.S., Pandelis, G.G., Prestridge, H.L., Rabosky, D.L., Randall, Z.S., Robbins, M.B., Scheinberg, L.A., Spencer, C.L., Summers, A.P., Tapanila, L. Thompson, C.W., Tornabene, L., Watkins-Colwell, G.J., Welton, L.J., the oVert Project Team, and Stanley, E.L. 2024. Increasing the impact of vertebrate scientific collections through 3D-imaging: the openVertebrate (oVert) Thematic Collections Network. BioScience. 0:1-18. [Vitek Member of oVert project team, full list of team authors in supplementary data].https://doi.org/10.1093/biosci/biad120
Wilburn, B. P., Raper, K., Raposa, K. B., Gray, A. B., Mozdzer, T. J., & Watson, E. B. (2024). Promoting success in thin layer sediment placement: effects of sediment grain size and amendments on salt marsh plant growth and greenhouse gas exchange. Restoration Ecology. https://doi.org/10.1111/rec.14141
Cherneskie, K., Njie, D., Champlin, L., Perger, D. S., & Watson, E. (2024). Drainage Influences Coastal Salt Marsh Productivity and Soil Biogeochemistry. Aquatic Botany, 103772.
Champlin, L.K., Moore, T.N., Jeppesen, R., Haskins, J., Sayre, B. and Watson, E.B., 2024. Biological and physical controls on multidecadal acidification in a eutrophic estuary. Journal of Geophysical Research: Oceans, 129(3), e2023JC020405.
Shikuzawa J, Watson EB, Tanner K, Wilburn B, Fork SK, Larson S, Fountain MC, Thomsen A, Wasson K. 2024. Ecosystem functions of plant diversity: Comparisons from a large‐scale marsh restoration experiment in California, USA. Ecosphere 15(1):e4742.
Courtney, S., Montalto, F., & Watson, E. B. (2024). Climate and Vegetation Change in a Coastal Marsh: Two Snapshots of Groundwater Dynamics and Tidal Flooding at Piermont Marsh, NY Spanning 20 Years. Wetlands, 44(1), 8.

y2023

2023 Publications from the Department of Ecology and Evolution (updated Sep.2023)

H. Reşit Akçakaya, Kelsey Neam, Louise Hobin, Stefan Lötters, An Martel, Frank Pasmans, 2023. Assessing the extinction risks of amphibians impacted by infectious diseases. Biological Conservation, Volume 284, 110205, ISSN 0006-3207, https://doi.org/10.1016/j.biocon.2023.110205.
Cazalis, V., Santini, L., Lucas, P. M., González-Suárez, M., Hoffmann, M., Benítez-López, A., Pacifici, M., Schipper, A. M., Böhm, M., Zizka, A., Clausnitzer, V., Meyer, C., Jung, M., Butchart, S. H. M., Cardoso, P., Mancini, G., Reşit Akçakaya, H., Young, B. E., Patoine, G., & Di Marco, M., 2023. Prioritizing the reassessment of data deficient species on the IUCN Red List. Conservation Biology, 00, 00–00. https://doi.org/10.1111/cobi.14139.
Friederike C Bolam, Jorge Ahumada, H Reşit Akçakaya, Thomas M Brooks, Wendy Elliott, Sean Hoban, Louise Mair, David Mallon, Philip JK McGowan, Domitilla Raimondo, Jon Paul Rodríguez, Dilys Roe, Mary B Seddon, Xiaoli Shen, Simon N Stuart, James EM Watson, Stuart HM Butchart, 2023. Over half of threatened species require targeted recovery actions to avert human-induced extinction. Front Ecol Environ 2023; 21(2): 64–70, doi:10.1002/fee.2537
Etienne Georges Henry, Luca Santini, Stuart Butchart, Manuela Gonzalez-Suarez, Pablo Miguel Lucas, Ana Benitez-Lopez, Giordano Mancini, Martin Jung, Pedro Cardoso, Alexander Zizka, Carsten Meyer, H. Resit Akcakaya, Alex Berryman, Victor Cazalis, Moreno Di Marco, 2023. Modelling the probability of meeting IUCN Red List criteria to support reassessments. bioRxiv 2023.06.08.544254; doi: https://doi.org/10.1101/2023.06.08.544254.
Lloyd, N. A, Keating, L. M., Friesen, A. J., Cole, D. M., McPherson, J. M., Akçakaya, H. R., & Moehrenschlager, A., 2023. Prioritizing species conservation programs based on IUCN Green Status and estimates of cost-sharing potential. Conservation Biology, 37, e14051. https://doi.org/10.1111/cobi.14051.
Molly K Grace, Michael Hoffmann, Ellie Alexander, Michelle Kotulski, Bobby Deibler, H Reşit Akçakaya, Elizabeth L Bennett, Rebecca Young, Barney Long, 2022. New online training course launched for IUCN Green Status of Species, Oryx, 56-6, pp.809-810
Hannah Layman, H Resit Akcakaya, Amanda Irwin, Sophus zu Ermgassen, Prue Addison, Mark Burgman, 2023. Short term solutions to biodiversity conservation in portfolio construction: forward looking disclosure and taxonomy-based metrics, SocArXiv
Breitenbach, R., Ambros, S., Risko, G., Arcusa, I., Durland Donahou, A., & Wolovich, C. K., 2023. The importance of auditory, olfactory, and visual cues for insect foraging in owl monkeys (Aotus nancymaae). American Journal of Primatology, e23539. https://doi.org/10.1002/ajp.23539.
Yiming Wan, Joseph Cohen, Mariola Szenk, Kevin S Farquhar, Damiano Coraci, Rafał Krzysztoń, Joshua Azukas, Nicholas Van Nest, Alex Smashnov, Yi-Jye Chern, Daniela De Martino, Long Chi Nguyen, Harold Bien, Jose Javier Bravo-Cordero, Chia-Hsin Chan, Marsha Rich Rosner, Gábor Balázsi, 2023. Nonmonotone invasion landscape by noise-aware control of metastasis activator levels. Nat Chem Biol 19, 887–899 (2023). https://doi.org/10.1038/s41589-023-01344-z.
Andrew Torres, Spencer Cockerell, Michael Phillips, Gábor Balázsi, Kingshuk Ghosh, 2023. MaxCal can infer models from coupled stochastic trajectories of gene expression and cell division. Biophysical Journal, May 21, 2023,DOI: https://doi.org/10.1016/j.bpj.2023.05.01.
Lara F Tshering, Fu Luo, Savanah Russ, Mariola Szenk, Diana Rubel, Karis Tutuska, James G Rail, Gábor Balázsi, Michael M Shen, Flaminia Talos, 2023. Immune mechanisms shape the clonal landscape during early progression of prostate cancer. Developmental Cell, May 05, 2023,DOI: https://doi.org/10.1016/j.devcel.2023.04.010.
Senthilnathan, Athmanathan, and D'Andrea, Rafael, 2023, Niche Theory for Positive Plant–Soil Feedbacks, Ecology e3993, https://doi.org/10.1002/ecy.3993.
Delamonica, B., L. Davalos, M. Larijani, S. Anthony, T. MacCarthy, 2023. Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes. Virus Evolution 9(2): XX–XX. DOI: 10.1093/ve/vead047
Baldoni, C., W. Thomas, D. Von Elverfeldt, M. Reisert, J. Làzaro, M. Muturi, L.M. Dávalos, J.D. Nieland, D.K.N. Dechmann, 2023. Histological and MRI brain atlas of the common shrew, Sorex araneus, with brain region specific gene expression profiles. Frontiers in Neuroanatomy 17. DOI: 10.3389/fnana.2023.1168523
Osmanski, A.B., N.S. Paulat, J. Korstian, J.R. Grimshaw, M. Halsey, K.A.M. Sullivan, D.D. Moreno-Santillán°, C. Crookshanks, J. Roberts, C. Garcia, L.M. Dávalos, M.G. Johnson, L.D. Densmore, R. D. Stevens, Zoonomia Consortium, J. Rosen, J. M. Storer, R. Hubley, A.F.A. Smit, D.A. Ray, 2023. Insights into mammalian TE diversity via the curation of 200+ mammalian genome assemblies. Science 380(6643): eabn1430. DOI: 10.1126/science.abn1430
Paulat, N.S., J.M Storer, D.D. Moreno-Santillán, A.B. Osmanski, K. Sullivan, J.R Grimshaw, J. Korstian, M. Halsey, C.J Garcia, C. Crookshanks, J. Roberts, A.F.A. Smit, R. Hubley, J. Rosen, E.C. Teeling, S.C. Vernes, E. Myers, Zoonomia Consortium, D. Rojas, L.M. Dávalos, D.A. Ray, 2023. Chiropterans are a hotspot for horizontal transfer of DNA transposons in Mammalia. Molecular Biology and Evolution 40(5): msad092. DOI: 10.1093/molbev/msad092
Barreto, E., M. Lim, D. Rojas, L.M. Dávalos, A. Machac, C. Graham, 2023. Not all traits influence hummingbird diversification, but their evolutionary rates do. Proceedings of the Royal Society B: Biological Sciences 290(1997): 20221793. DOI: 10.1098/rspb.2022.1793
Mutumi, G.L., R.P. Hall, B.P. Hedrick, L.R. Yohe, A. Sadier, K.T.J. Davies, S.J. Rossiter, K.E. Sears, L.M. Dávalos, E.R. Dumont, 2023. Disentangling mechanical and sensory modules in the radiation of Noctilionoid bats. American Naturalist 202(8): 216-230. DOI: 10.1086/725368
Michielsen, N.M., S.M. Goodman, V. Soarimalala, A.A.E. van der Geer, L.M. Dávalos, G.I. Saville, N. Upham, L. Valente. 2023, The macroevolutionary impact of recent and imminent extinctions of mammals in Madagascar. Nature Communications 14, 14 (2023). DOI: 10.1038/s41467-022-35215-3.
Leadley, P., D. Obura, E. Archer, M.J. Costello, L.M. Dávalos, F. Essl, A. Hansen, S. Hashimoto, D. Leclère, A.S. Mori, E. Nicholson, A. Purvis, C. Rondinini, L. Shannon, X. Shen, E. Turak, P.H. Verburg, P. Visconti. 2022, Actions needed to achieve ambitious objectives of net gains in natural ecosystem areas by 2030 and beyond. PLOS Sustainability and Transformation 1(12): e0000040. DOI: 10.1371/journal.pstr.0000040.
Leadley, P., E. Archer, B. Bendandi, J. Cavender-Bares, L.M. Dávalos, F. DeClerck, G, Gann, E. Gonzales, S. Hashimoto, C. Krug, J.P. Metzger, E. Nicholson, Ü. Niinemets, D. Obura, B. Strassburg, B. Tansey, P. Verburg, A. Vidal, J. Watson, S. Woodley, M. Yasuhara. 2022, Setting ambitious international restoration objectives for terrestrial ecosystems for 2030 and beyond. PLOS Sustainability and Transformation 1(12): e0000039. DOI: 10.1371/journal. pstr.0000039.
Futuyma, D. J. 2023. The evolving evolutionary synthesis. In T. E. Dickins and B. J. A. Dickins (eds.), Evolutionary Biology: Contemporary and Historical Reflections Upon Core Theory, pp. 517-541. Springer Nature, Switzerland, https://doi.org/10.1007/978-3-031-22028-9.
Futuyma, D. J. 2023. Inclusive fitness theory prefigured: a reply to Rodrigues and Gardner. In T. E. Dickins and B. J. A. Dickins (eds.), Evolutionary Biology: Contemporary and Historical Reflections Upon Core Theory, pp.549-551. Springer Nature, Switzerland, https://doi.org/10.1007/978-3-031-22028-9.
[Book review] Futuyma, D. J. Applications of evolutionary science. Review of N. A. Johnson, Darwin’s Reach: 21st Century Applications of Evolutionary Biology (2021, CRC Press). Evolution 77:1167-1169 (2023).
George, A. M., 2022. Tale of two species of Stylissa (Porifera: Demospongiae: Scopalinida) from the west and east coasts of India, Zootaxa 5178 (1): 072–080. https://doi.org/10.11646/zootaxa.5178.1.4
George, A. M., Abdo, D., Wahab, M. A. A., Ekins, M., Hooper, J. N. A., & Whalan, S. (2023). Cryptic biodiversity inhabiting coral reef sponges. Marine Ecology, 00, e012747. https://doi.org/10.1111/maec.12747
Dirk Nikolaus Karger, Michael P. Nobis, Signe Normand, Catherine H. Graham, and Niklaus E. Zimmermann, 2023, CHELSA-TraCE21k – high-resolution (1 km) downscaled transient temperature and precipitation data since the Last Glacial Maximum, Climate of the Past 19 (2), 439-456, https://doi.org/10.5194/cp-19-439-2023.
Esteban A Guevara, Carolina Bello, Cristian Poveda, Ian R McFadden, Matthias Schleuning, Loïc Pellissier, Catherine H Graham, 2023, Hummingbird community structure and nectar resources modulate the response of interspecific competition to forest conversion, Oecologia, 1-10, https://doi.org/10.1007/s00442-023-05330-z.
Ian R McFadden, Agnieszka Sendek, Morgane Brosse, Peter M Bach, Marco Baity‐Jesi, Janine Bolliger, Kurt Bollmann, Eckehard G Brockerhoff, Giulia Donati, Friederike Gebert, Shyamolina Ghosh, Hsi‐Cheng Ho, Imran Khaliq, J Jelle Lever, Ivana Logar, Helen Moor, Daniel Odermatt, Loïc Pellissier, Luiz Jardim De Queiroz, Christian Rixen, Nele Schuwirth, J Ryan Shipley, Cornelia W Twining, Yann Vitasse, Christoph Vorburger, Mark KL Wong, Niklaus E Zimmermann, Ole Seehausen, Martin M Gossner, Blake Matthews, Catherine H Graham, Florian Altermatt, Anita Narwani, 2023, Linking human impacts to community processes in terrestrial and freshwater ecosystems, Ecology letters 26 (2), 203-218, https://doi.org/10.1111/ele.14153.
Esteban A Guevara, D Matthias Dehling, Carolina Bello, Matthias Schleuning, Loïc Pellissier, Tatiana Santander, Francisco Tobar, Catherine H Graham, 2023, Asymmetric effect of deforestation on the functional roles of interacting plants and hummingbirds, Research Square, DOI: https://doi.org/10.21203/rs.3.rs-2527763/v1.
Fernanda AS Cassemiro, James S Albert, Alexandre Antonelli, André Menegotto, Rafael O Wüest, Felipe Cerezer, Marco Túlio P Coelho, Roberto E Reis, Milton Tan, Victor Tagliacollo, Dayani Bailly, Valéria FB da Silva, Augusto Frota, Weferson J da Graça, Reginaldo Ré, Telton Ramos, Anielly G Oliveira, Murilo S Dias, Robert K Colwell, Thiago F Rangel, Catherine H Graham, 2023, Landscape dynamics and diversification of the megadiverse South American freshwater fish fauna, Proceedings of the National Academy of Sciences, 120 (2) e2211974120, https://doi.org/10.1073/pnas.2211974120.
Carolina Bello, Matthias Schleuning, Catherine H Graham, 2023, Analyzing trophic ecosystem functions with the interaction functional space, Trends in Ecology & Evolution, https://doi.org/10.1016/j.tree.2022.12.001.
Hsi-Cheng Ho, Jakob Brodersen, Martin M Gossner, Catherine H Graham, Silvana Kaeser, Merin Reji Chacko, Ole Seehausen, Niklaus E Zimmermann, Loïc Pellissier, Florian Altermatt, 2022, Blue and green food webs respond differently to elevation and land use, Nat Commun 13, 6415 (2022). https://doi.org/10.1038/s41467-022-34132-9.
François Duchenne, Rafael O Wüest, Catherine H Graham, 2022, Seasonal structure of interactions enhances multidimensional stability of mutualistic networks, Proceedings of the Royal Society B 289 (1982), 20220064, https://doi.org/10.1098/rspb.2022.0064.
Mathewson, P.D., Darnell, M.Z., Lane, Z.M., Yeghissian, T.G., Levinton, J.S., Porter, W.P. 2023. Incorporating species-specific morphology improves model predictions of thermal and hydric stress in the sand fiddler crab, Leptuca pugilator. Journal of Thermal Biology, 115 (2023) 103613, https://doi.org/10.1016/j.jtherbio.2023.103613.
Levinton, J.S., Arena, B., Pena, R., Darnell, M.Z. 2023. Superior performance of a trailing edge low-latitude population of an intertidal marine invertebrate. Journal of Experimental Marine Biology and Ecology, 563, 151896, ISSN 0022-0981, https://doi.org/10.1016/j.jembe.2023.151896.
Levinton, J.S. 2023, Estuarine benthos and climate change. Pp. 431-449, In: Kennish, M., Paerl, H., eds. Climate Change and Estuaries. Taylor and Francis, CRC Press, Boca Raton FL.
Levinton, J.S. 2023. Extinction in the fossil record. IN: Encyclopedia of Biodiversity, 3rd Edition, S.A. Levin, editor, Elsevier Publishing Co.
Levinton, Jeffrey S. 2023. The Bigger You Are, the Weaker You Are: Multispecies Evidence for the Weakening Combatant Hypothesis. Journal of Crustacean Biology. Volume 43, Issue 4, December 2023, ruad075, https://doi.org/10.1093/jcbiol/ruad075.
Wethington, M., C. Flynn, A. Borowicz, and H.J. Lynch. 2023, Adélie penguins north and east of the ‘Adélie gap’ continue to thrive in the face of dramatic declines elsewhere in the Antarctic Peninsula region. In press at Scientific Reports.
Talis, Emma, C. Che-Castaldo, and H.J. Lynch. 2023. Difficulties in summing distributions for abundance and potential solutions. PLoS ONE 18(1): e0280351.
Hughes, K.A., M. Santos, J. A. Caccavo, S. Chignell, N. Gardiner, N. Gilbert, A. Howkins, B. J. van Vuuren, J. R. Lee, D. Liggett, A. Lowther, H. Lynch, A. Quesada, H. Chul Shin, A. Soutullo, and A. Terauds. 2022, Ant-ICON ‘Integrated Science to Inform Antarctic and Southern Ocean Conservation’: a new SCAR research programme. Antarctic Science 34(6): 446-455.
Goncalves, B.C., M. Wethington, and H.J. Lynch. 2022, SealNet 2.0: Human-level fully-automated pack-ice seal detection in very-high resolution satellite imagery with CNN model ensembles. Remote Sensing 14(22): 5655.
Lee, J. R., A. Terauds, J. Carwardine, J. D. Shaw, R. A. Fuller, H. P. Possingham, S. L. Chown, P. Convey, N. Gilbert, K. A. Hughes, E. McIvor, S. Robinson, Y. Ropert-Coudert, D. Bergstrom, E. M. Biersma, C. Christian, D. Cowan, Y. Frenot, S. Jenouvrier, L. Kelley, M. J. Lee, H.J. Lynch, B. Njastad, A. Quesada, R. Roura, E.A. Shaw, D. Stanwell-Smith, M. Tsujimoto, D. H. Wall, A. Wilmotte, and I. Chadès. 2022, Threat management priorities for conserving Antarctic biodiversity. PLoS Biology 20(12): e3001921.
Michael Wethington, Clare Flynn, Alex Borowicz & Heather J. Lynch. 2023. Adélie penguins north and east of the ‘Adélie gap’ continue to thrive in the face of dramatic declines elsewhere in the Antarctic Peninsula region. Sci Rep 13, 2525 (2023). https://doi.org/10.1038/s41598-023-29465-4.
Boyle, J.H., Espeland, M., Sáfián, S., Ducarme, R., Gardiner, A.J., Coleman, J.W., Heath, A., Fisher, S., Collins, S.C., Martins, D.J. and Aduse‐Poku, K., 2023. Phylogeny of the Poritiinae (Lepidoptera: Lycaenidae), butterflies with ant associations and unusual lichenivorous diets. Systematic Entomology.
Gachogo, R., Karegi, I., Maina, B., Musyoki, V., Martins, D., Onyambu, F. and Kamau, J., 2022. Draft genome sequences of three emerging beta-lactamase-producing Escherichia coli in the camel production system in Northern Kenya. F1000Research, 11(1413), p.1413.
Rhodes, A.C., Plowes, R.M., Martins, D.J., Ng’Iru, I. and Gilbert, L.E., 2022. The invasiveness of Guinea grass (Megathyrsus maximus) is characterized by habitat and differing herbivore assemblages in its native and invaded range. NeoBiota, 78, pp.25-44.
Kim, K.W., De-Kayne, R., Gordon, I.J., Omufwoko, K.S., Martins, D.J., Ffrench-Constant, R. and Martin, S.H., 2022. Stepwise evolution of a butterfly supergene via duplication and inversion. Philosophical Transactions of the Royal Society B, 377(1856), p.20210207.
Liu, W., Smith, D.A., Raina, G., Stanforth, R., Ng'Iru, I., Ireri, P., Martins, D.J., Gordon, I.J. and Martin, S.H., 2022. Global biogeography of warning coloration in the butterfly Danaus chrysippus. Biology letters, 18(6), p.20210639.
Worsley-Tonks, K.E., Bender, J.B., Deem, S.L., Ferguson, A.W., Fèvre, E.M., Martins, D.J., Muloi, D.M., Murray, S., Mutinda, M., Ogada, D. and Omondi, G.P., 2022. Strengthening global health security by improving disease surveillance in remote rural areas of low-income and middle-income countries. The Lancet Global Health, 10(4), pp.e579-e584.
Collins, M., Ngetich, C., Owido, M., Getange, D., Harris, R., Bargul, J.L., Bodha, B., Njoroge, D., Muloi, D., Martins, D.J. and Villinger, J., 2022. Detection of antibodies to Ehrlichia spp. in dromedary camels and co-grazing sheep in northern Kenya using an Ehrlichia ruminantium polyclonal competitive ELISA. Microorganisms, 10(5), p.916.
Singh, K.S., De-Kayne, R., Omufwoko, K.S., Martins, D.J., Bass, C., Ffrench-Constant, R. and Martin, S.H., 2022. Genome assembly of Danaus chrysippus and comparison with the Monarch Danaus plexippus. G3, 12(3), p.jkab449.
Rabideau‐Childers, R., Angier, K.I., Dean, B.Z., Blumstein, M., Darling, W.S., Kennedy‐Yoon, A., Ziemke, C.H., Perez‐Martinez, C.A., Wu, D., Ye, W., Yekwayo, I. Kimuyu, D., Martins D. J., and N. E. Pierce, 2022. Evidence of nutrient translocation in response to smoke exposure by the East African ant acacia, Vachellia drepanolobium. Ecology and Evolution, 12(1), p.e8244.
Martins, D. J. (2022) Grasses of East Africa. Penguin Random House.
Nehm, R.H., 2023. AI in Biology Education Assessment: How Automation Can Drive Educational Transformation. In: Zhai, X. et al. (Eds.) Uses of Artificial Intelligence in STEM Education. Oxford University Press.
Ha, M. Nehm, R.H., 2023. Measuring Scientific Understanding Across International Samples: The Promise of Machine Translation and NLP-based Machine Learning Technologies. In: Yaneva & VonDavier (Eds.). Advancing National Language Processing in Educational Assessment. NCME (National Council on Measurement in Education). Routledge.
Bertolini R, Finch SJ and Nehm RH, 2023. An application of Bayesian inference to examine student retention and attrition in the STEM classroom. Front. Educ. 8:1073829. doi: 10.3389/feduc.2023.1073829
Nehm, R.H., 2023, Anchoring AI-based assessment research within broader educational contexts: Examples from biology education. in press.
Ha, M. Nehm, R.H., 2023, Measuring Scientific Understanding Across International Samples: The Promise of Machine Translation and NLP-based Machine Learning Technologies. NCME (National Council on Measurement in Education).
Bertolini R, Finch SJ and Nehm RH, 2023, An application of Bayesian inference to examine student retention and attrition in the STEM classroom. Front. Educ. 8:1073829. doi: 10.3389/feduc.2023.1073829.
ROSS H. NEHM, STEPHEN J. FINCH, AND GENA C. SBEGLIA, 2022, Is Active Learning Enough? The Contributions of MisconceptionFocused Instruction and ActiveLearning Dosage on Student Learning of Evolution, BioScience pp.1105-1117, https://doi.org/10.1093/biosci/biac073.
Sbeglia, G.C., Nehm, R.H., 2022, Measuring evolution learning: impacts of student participation incentives and test timing. Evo Edu Outreach 15, 9, https://doi.org/10.1186/s12052-022-00166-2.
Roberto Bertolini, Stephen J. Finch, Ross H. Nehm, 2022, Quantifying variability in predictions of student performance: Examining the impact of bootstrap resampling in data pipelines, Computers and Education: Artificial Intelligence, https://doi.org/10.1016/j.caeai.2022.100067.
Biological Bulletin 238:54-63 DM Charifson, PE Bourdeau, DK Padilla. 2022, Shell remodeling in response to increased risk of predation in a marine snail. Marine Ecology Progress Series 688, 57-67.
Maria Rosa and Dianna K Padilla. 2022, Determinants of food selection by bivalve larvae. Invertebrate Biology, e12366.
Alexandra M. Pamfilie, Austin M. Garner, Anthony P. Russell, Ali Dhinojwala, Peter H. Niewiarowski. Get to the point: Claw morphology impacts frictional interactions on rough substrates. Zoology, Volume 157, 2023, 126078, ISSN 0944-2006, https://doi.org/10.1016/j.zool.2023.126078.
Mariana Rius, Joshua S Rest, Gina V Filloramo, Anna M G Novák Vanclová, John M Archibald, Jackie L Collier. 2023, Horizontal gene transfer and fusion spread carotenogenesis among diverse heterotrophic protists, Genome Biology and Evolution, evad029, https://doi.org/10.1093/gbe/evad029.
Davidson KJ, Lamour J, Rogers A, Ely KS, Li Q, McDowell NG, Pivovaroff AL, Wolfe BT, Wright SJ, Zambrano A, Serbin SP (2023). Short term variation in leaf level water use efficiency in a tropical forest. New Phytologist. 237, 2069-2087. https://doi.org/10.1111/nph.18684
Yang D, Morrison BD, Hanston W, McMahon A, Baskaran L, Hayes DJ, Miller CE, Serbin SP (2023). Integrating very-high-resolution UAS data and airborne imaging spectroscopy to map the fractional composition of Arctic plant functional types in Western Alaska. Remote Sensing of Environment 286, 113430. https://doi.org/10.1016/j.rse.2022.113430
Dickman LT, Jonko AK, Linn RR, Altintas I, Atchley AL, Bär A, Collins AD, Dupuy J-L, Gallagher MR, Hiers JK, Hoffman CM, Hood SM, Hurteau MD, Jolly WM, Josephson A,Loudermilk EL, Ma W, Michaletz ST, Nolan RH, O’Brien JJ, Parsons RA, Partelli-Feltrin R, Pimont F, Resco de Dios V, Restaino J, Robbins ZJ, Sartor KA, Schultz-Fellenz E, Serbin SP, Sevanto SA, Shuman J, Sieg CH, Skowronski NS, Weise DR, Wright M, Xu C, Yebra M, Younes N (2023). Integrating plant physiology into simulation of fire behavior and effects. New Phytologist. In Press. https://doi.org/10.1111/nph.18770
Wolfe BT, Detto M, Zhang Y, Anderson-Teixera K, Brodribb T, Collins AD, Crawford C, Dickman LT, Ely KS, Francisco J, Gurry PD, Hancock H, King CT, Majekobaje AR, Mallett CJ, McDowell NG, Mendheim Z, Michaletz S, Myers DB, Price TJ, Rogers A, Sack L, Serbin SP, Siddiq Z, Willis D, Wu J, Zailaa J, Wright SJ (2023). Leaves as bottlenecks: The contribution of tree leaves to hydraulic resistance within the soil-plant-atmosphere continuum. Plant, Cell & Environment. 46, 736-746. https://doi.org/10.1111/pce.14524
Cicero C., Mason N.A., Oong Z., Title P.O., Morales M.E., Feldheim K.A., Koo M.S., Bowie R.C.K. 2022, Deep ecomorphological and genetic divergence in Steller’s Jays (Cyanocitta stelleri, Aves: Corvidae). Ecol Evol. 12:e9517, https://onlinelibrary.wiley.com/doi/10.1002/ece3.9517.
Vencl FV and Srygley RB, 2023. El Niño oscillations impact anti-predator defences to alter survival of an herbivorous beetle in a neotropical wet forest. Journal of Tropical Ecology, Volume XX, eX. https://doi.org/10.1017/S0266467423000226.
Deven N. Vyas, Istva´ n Koncz, Alessandra Modi, Bala´ zs Guszta´ v Mende, Yijie Tian,1 Paolo Francalacci, Martina Lari, Stefania Vai, Peter Straub, Zsolt Gallina, Tama´ s Szeniczey, Tama´ s Hajdu, Luisella Pejrani Baricco, Caterina Giostra, Rita Radzeviciute, Zuzana Hofmanova´ , Sa´ ndor E´ vinger, Zsolt Bernert, Walter Pohl, David Caramelli, Tivadar Vida, Patrick J. Geary, and Krishna R. Veeramah, 2023. Fine-scale sampling uncovers the complexity of migrations in 5th–6th century Pannonia. Current Biology, https://doi.org/10.1016/j.cub.2023.07.063
Lena K. Champlin, Andrea Woolfolk, Autumn J. Oczkowski, Audrey Rittenhouse, Andrew B. Gray, Kerstin Wasson, Farzana I. Rahman, Paula Zelanko, Nadine B. Quintana Krupinski, Rikke Jeppesen, John Haskins, Elizabeth B. Watson, 2023. Use of historical isoscapes to develop an estuarine nutrient baseline. Front. Mar. Sci., 06 September 2023, Sec. Marine Biogeochemistry, Volume 10 - 2023, https://doi.org/10.3389/fmars.2023.1257015.
Raposa KB, Woolfolk A, Endris CA, Fountain MC, Moore G, Tyrrell M, Swerida R, Lerberg S, Puckett BJ, Ferner MC, Hollister J. Burdick, D., Champlin, L,Krause JR, Haines, D.,Gray A.B., Watson E.B., Wasson, K. 2023, Evaluating Thin-Layer Sediment Placement as a Tool for Enhancing Tidal Marsh Resilience: a Coordinated Experiment Across Eight US National Estuarine Research Reserves. Estuaries and Coasts. 2023 Jan 16:1-21.
Carlton H, Champlin L, Jeppesen R, Haskins JC, Rahman FI, Watson EB. 2023, Tidal restrictions in a central Californian estuarine system are associated with higher mean pH, but increased low-pH exposure. Marine Ecology Progress Series. 2023 Jan 12;703:177-82.
Krause JR, Gannon ME, Oczkowski AJ, Schwartz MJ, Champlin LK, Steinmann D, Maxwell-Doyle M, Pirl E, Allen V, Watson E.B. 2022, Tidal Flushing Rather Than Non-Point Source Nitrogen Pollution Drives Nutrient Dynamics in A Putatively Eutrophic Estuary. Water. 2022 Dec 21;15(1):15.
Krause JR, Oczkowski AJ, Watson EB. 2023, Improved mapping of coastal salt marsh habitat change at Barnegat Bay (NJ, USA) using object-based image analysis of high-resolution aerial imagery. Remote Sensing Applications: Society and Environment. 2023 Jan 1;29:100910.
Wang J, Song G, Liddell M, Morellato P, Lee C, Yang D, Alberton B, Detto M, Ma X, Zhao Y, Yeung H, Zhang H, Ng M, Nelson B, Heute A (2023) An ecologically-constrained deep learning model for tropical leaf phenology monitoring using PlanetScope satellites. Remote Sensing of Environment. 286, 113429. https://doi.org/10.1016/j.rse.2022.113429

2022

2022 Publications from the Department of Ecology and Evolution

Grace, M.K., H.R. Akçakaya, E.L. Bennett, M. Boyle, C. Hilton-Taylor, M. Hoffmann, D. Money, A. Prohaska, R. Young, R. Young, B. Long. 2022. The impact of spatial delineation on the assessment of species recovery outcomes. Diversity 14, 742. https://doi.org/10.3390/d14090742
Bolam, F.C., J. Ahumada, H.R. Akçakaya, T. M. Brooks, W. Elliott, S. Hoban, L. Mair, D. Mallon, P.J.K. McGowan, D. Raimondo, J.P. Rodríguez, D. Roe, M.B. Seddon, X. Shen, S.N. Stuart, J.E.M. Watson, S.H.M. Butchart. 2022. Over half of threatened species require targeted recovery actions to avert human-induced extinction. Frontiers in Ecology and the Environment. https://doi.org/10.1002/fee.2537
Şen, B. and H.R. Akçakaya. 2022. Inter-specific variability in demographic processes affects abundance-occupancy relationships. Oecologia https://doi.org/10.1007/s00442-021-05085-5
Cazalis, V., M. Di Marco, S.H.M. Butchart, H.R. Akçakaya, M. González-Suárez, C. Meyer, V. Clausnitzer, M. Böhm, A. Zizka, P. Cardoso, A.M. Schipper, S.P. Bachman, B.E. Young, M. Hoffmann, A. Benítez-López, P.M. Lucas, N. Pettorelli, G. Patoine, M. Pacifici, T. Jörger-Hickfang, T.M. Brooks, C. Rondinini, S.L.L. Hill, P. Visconti, and L. Santini. 2022. Bridging the research-implementation gap in IUCN Red List assessments. Trends in Ecology & Evolution. https://doi.org/10.1016/j.tree.2021.12.002
Şen, B. and H.R. Akçakaya. 2022. Fecundity and density dependence can be estimated from mark-recapture data for making population projections. Ornithological Applications 124:1-14 https://doi.org/10.1093/ornithapp/duab064
Groner, V., O. Nicholas, T. Mabhaudhi, R. Slotow, H.R. Akçakaya, G. Mace, R. Pearson. 2022. Climate change, land cover change, and overharvesting threaten a widely used medicinal plant in South Africa. Ecological Applications 32(4):e2545 https://doi.org/10.1002/eap.2545
Fordham, D.A., S.C. Brown, H.R. Akçakaya, B.W. Brook, S. Haythorne, A. Manica, K.T. Shoemaker, J.J. Austin, B. Blonder, J. Pilowsky, C. Rahbek, and D. Nogues-Bravo. 2022. Process-explicit models reveal pathway to extinction for woolly mammoth using pattern-oriented validation. Ecology Letters 25:125–137. https://doi.org/10.1111/ele.13911
Roman Yukilevich, Fumio Aoki, 2022, Evolution of choosiness dictates whether search costs of mate choice enhance speciation by sexual selection, Journal of Evolutionary Biology, Vol. 35, Issue 8, pp. 1045-1059, https://doi.org/10.1111/jeb.14036
Balk, M., J. Deck, K.F. Emery, R.L Walls, D. Reuter, R. LaFrance, J. Arroyo-Cabrales, P. Barret, J. Blois, A. Boileau, L. Brenskelle, N.R. Cannarozzi, J.A. Cruz, L.M. Dávalos, M. Hantak, S. Hopkins, B. Kohli, J.N. King, M. Koo, M. Lawing, H. Machado, S.S. McCrane, B. McLean, M. Morgan, S. Pilaar-Birch, D. Reed, E.J. Reitz, N. de la Sancha, N. Sewnath, N.S. Upham, A. Villaseñor, L. Yohe, R.P Guralnick, E.B. Davis. Best practices for aggregating and reporting individual traits. iScience. DOI: 10.1016/j.isci.2022.105101
Yohe, L.R., M. Fabbri, D. Lee, K. Davies, T.P. Yohe, M. K. R. Sanchez, E. Rengifo, R. Hall, G. Mutumi, B.P. Hedrick, A. Sadier, N.B. Simmons, K.E. Sears, E. Dumont, S. Rossiter, B.-A. Bhullar, and L.M. Dávalos. Ecological Constraints on Highly Evolvable Olfactory Receptor Genes and Morphology. Evolution. DOI: 10.1111/evo.14591 *Join senior authors.
Leadley, P., D. Obura, L. Shannon, M. Cecilia, K. Millette, A. Rankovic, E. Archer, F. Ato, N. Bax, A. Kutchhi, J.M. Costello, L.M. Dávalos, F. de Oliveira Roque, F. DeClerck, L. Dee, F. Essl, S. Ferrier, S. Hashimoto, C. Ifejika, F. Isbell, M. Kok, S. Lavery, D. Leclère, R. Loyola, S. Lwasa, M. McGeoch, A.S. Mori, E. Nicholson, J. Manuel, K. Öllerer, S. Polasky, C. Rondinini, O. Selomane, B. Strassburg, R. Sumaila, D.P. Tittensor, E. Turak, L. Urbina, M. Vallejos, E. Vázquez-Domínguez, P. Verburg, P. Visconti, S. Woodley, J. Xu, S. Jellesmark. Achieving global biodiversity goals by 2050 requires urgent and integrated actions. One Earth 5(6): P597-603. DOI: 10.1016/j.oneear.2022.05.009
Doronina, L, G.M. Hughes, D. Moreno-Santillan, C. Lawless, T. Lonergan, L. Ryan, D. Jebb, B.M. Kirilenko, J.M. Korstian, L.M. Dávalos, S. C. Vernes, E.W. Myers, E.C. Teeling, M. Hiller, L.S. Jermin, J. Schmitz, M.S. Springer, D.A. Ray. Contradictory phylogenetic signals in the Laurasiatheria anomaly zone. Genes 13. DOI: 10.3390/genes13050766 *Equal contribution.
Mohammed, R.S., G. Turner, K. Fowler, M. Pateman, M.A. Nieves-Colón, L. Fanovich, S.B. Cooke, L.M. Dávalos, S.M. Fitzpatrick, C.M. Giovas, M. Stokowski, A.A. Wrean, M. Kemp, M.J. LeFebvre, A.M. Mychajliw. Colonial legacies influence biodiversity lessons: how past trade routes and power dynamics shape present day scientific research and professional opportunities for Caribbean scientists. American Naturalist. DOI: 10.1086/720154
The Quarterly Review of Biology, (general information) https://www.journals.uchicago.edu/journals/qrb/about (current issue) https://www.journals.uchicago.edu/toc/qrb/current
Kenneth J Davidson, Julien Lamour, Alistair Rogers, Shawn P Serbin, Late-day measurement of excised branches results in uncertainty in the estimation of two stomatal parameters derived from response curves in Populus deltoides Bartr. × Populus nigra L., Tree Physiology, Volume 42, Issue 7, July 2022, Pages 1377–1395, https://doi.org/10.1093/treephys/tpac006
Kenneth J. Davidson Julien Lamour, Alistair Rogers, Kim S. Ely, Qianyu Li, Nate G. McDowell, Alexandria L. Pivovaroff, Brett T. Wolfe, S. Joseph Wright, Alfonso Zambrano, and Shawn P. Serbin, Short term variation in leaf level water use efficiency in a tropical forest, New Phytologist, https://doi.org/10.1111/nph.18684
Gotsch SG, Williams CB, Bicaba R, Cruz-de Hoyos R, Darby A, Davidson KJ, Dix M, Duarte V, Glunk A, Green L, Ferguson B, Muñoz-Elizondo K, Murray JG, Picado-Fallas I, Nӕsborg R, Dawson TE, and Nadkarni N. (2022) Trade-offs between succulent and non-succulent epiphytes underlie variation in drought tolerance and avoidance. Oecologia. 198, 645-661. https://doi.org/10.1007/s00442-022-05140-9
Futuyma, D. J., and M. Kirkpatrick. 2022. Evolution, fifth edition. Oxford University Press.
Futuyma, D. J., editor (with H. B. Shaffer and D. Simberloff), Annual Review of Ecology, Evolution, and Systematics, vol 50-53 (2019 -2022).
Talis, Emma, C. Che-Castaldo, B. Sen, K. Krumhardt, and H.J. Lynch. 2022. Variability, skipped breeding, and heavy-tailed dynamics in an Antarctic seabird. In press at Journal of Animal Ecology 91: 2437-2450.
Lee, J.R., M. Waterman, J.D. Shaw, D.M. Bergstrom, H.J. Lynch, D.H. Wall, and S.A. Robinson. 2022. Islands in the ice: Perspectives on the potential impacts of Antarctic habitat transformation. Global Change Biology 28(20): 5865-5880.
El-Laham, Y., M. Bugallo, and H.J. Lynch. 2022. Switching state-space models for modeling penguin population dynamics. Environmental and Ecological Statistics 29: 607-624.
Herman, R., and H.J. Lynch. 2022. Age-structured model reveals prolonged immigration is key for colony establishment in Gentoo Penguins. Ornithological Applications 124(3): duac014, https://doi.org/10.1093/ornithapp/duac014.
Levinton, J.S. 2022. Marine Biology: Function, Biodiversity, Ecology. 6th Edition. Oxford University Press, New York, 548 pp.
Levinton, J.S. 2022. Mass Extinctions, IN: Encyclopedia of Biodiversity, 3rd Edition. S.A. Levin, editor, Elsevier Publishing Co.
Frost GV, Macander MJ, Bhatt US, Berner LT, Bjerke JW, Epstein HE, Forbes BC, Goetz SJ, Lara MJ, Phoenix GK, Serbin SP, Tømmervik H, Walker DA, Yang D (2022) Tundra Greenness. In Arctic Report Card 2022, M. L. Druckenmiller, R. L. Thoman, and T. A. Moon, Eds. https://doi.org/10.25923/g8w3-6v31
Crystal-Ornelas R, Varadharajan C, O'Ryan D, Beilsmith K, Bond-Lamberty B, Boye K, Burrus M, Cholia S, Christianson D, Crow M, Damerow J, Ely K, Goldman A, Heinz S, Hendrix V, Kakalia Z, Mathes K, O'Brien F, Pennington S, Robles E, Rogers A, Simmonds M, Velliquette T, Weisenhorn P, Welch J, Whitenack K, Agarwal D (2022). Enabling FAIR data in Earth and environmental science with community-centric (meta)data reporting formats. Scientific Data. 9, 700. https://doi.org/10.1038/s41597-022-01606-w
Thoman RL, Druckenmiller ML, Moon TA, Andreassen LM, Baker E, Ballinger TJ, Berner LT, Bernhard GH, Bhatt US, Bjerke JW, Boisvert LN, Box JE, Brettschneider B, Burgess D, Butler AH, Cappelen J, Christiansen HH, Decharme B, Derksen C, Divine D, Drozdov DS, Elias CA, Epstein HE, Farrell SL, Fausto RS, Fettweis X, Fioletov VE, Forbes BC, Frost GV, Gerland S, Goetz SJ, Grooß JU, Haas C, Hanna E, Hanssen BI, Heijmans MMPD, Hendricks S, Ialongo I,Isaksen K, Jensen CD, Johnsen B, Kaleschke L, Kholodov AL, Kim S-J, Kohler J, Korsgaard NJ, Labe Z, Lakkala K, Lara MJ, Lee SH, Loomis B, Luks B. Luojus K, Macander MJ, Magnússon RI, Malkova GV, Mankoff KD, Manney GL, Meier WN, Mote T, Mudryk L, Müller R, Nyland KE, Overland JE, Pálsson F, Park T, Parker CL, Perovich D, Petty A, Phoenix GK, Pinzon JE, Ricker R, Romanovsky VE, Serbin SP, Sheffield G, Shiklomanov NI, Smith SL, Stafford KM, Steer A, Streletskiy DA, Svendby T, Tedesco M, Thomson L, Thorsteinsson T, Tian-Kunze X, Timmermans ML, Tømmervik H,Tschudi M, Tucker CJ, Walker DA, Walsh JE, Wang M, Webster M, Wehrlé A, Winton Ø, Wolken G, Wood K, Wouters B, Yang D (2022) The Arctic. In: Blunden J and Boyer T, Eds. “State of the Climate in 2021”. Bulletin of the American Meteorological Society, 103, S1–S465. https://doi.org/10.1175/2022BAMSStateoftheClimate.1
Yang D, Morrison BD, Davidson KJ, Lamour J, Li Q, Nelson PR, Hantson W, Hayes DJ, Swetnam TL, McMahon A, Anderson J, Ely KS, Rogers A, Serbin SP (2022). Remote Sensing from Unoccupied Aerial Systems: Opportunities to Enhance Arctic Plant Ecology in a Changing Climate. Journal of Ecology. 110, 2812-2835. https://doi.org/10.1111/1365-2745.13976
Kamoske AG, Dahlin KM, Read QD, Record S,Stark SC, Serbin SP, Zarnetske PL (2022). Towards mapping biodiversity from above: Can fusing lidar and hyperspectral remote sensing predict taxonomic, functional, and phylogenetic tree diversity in temperate forests? Global Ecology and Biogeography, 31, 1440–1460. https://doi.org/10.1111/geb.13516
Dokoohaki H, Morrison BD, Raiho A, Serbin SP, Zarada K, Dramko L, Dietze M (2022). Development of an open-source regional data assimilation system in PEcAn v. 1.7.2: application to carbon cycle reanalysis across the contiguous US using SIPNET. Geoscientific Model Development. 15, 3233–3252. https://doi.org/10.5194/gmd-15-3233-2022
Hurtt GC, Andrews A, Bowman K, Brown ME, Chatterjee A, Escobar V, Fatoyinbo L, Griffith P, Guy M, Healey SP, Jacob DJ, Kennedy R, Lohrenz S, McGroddy ME, Morales V, Nehrkorn T, Ott L, Saatchi S, Carlo ES, Serbin SP, Tian H (2022) The NASA Carbon Monitoring System Phase 2 synthesis: scope, findings, gaps and recommended next steps. Environmental Research Letters. 17, 063010. https://iopscience.iop.org/article/10.1088/1748-9326/ac7407
Montes CM, Fox C, Sanz-Sáez A, Serbin SP, Kumagai E, Krause MD, Xavier A, Specht JE, Beavis WD, Bernacchi CJ, Diers BW, Ainsworth EA (2022) High-throughput characterization, correlation, and mapping of leaf photosynthetic and functional traits in the soybean (Glycine max) nested association mapping population. Genetics. 221, iyac065. https://doi.org/10.1093/genetics/iyac065
Nelson PR, Maguire AJ, Pierrat Z, Orcutt EL, Yang D, Serbin SP, Frost GV, Macander MJ, Magney TS, Thompson DR, Wang JA, Oberbauer SF, Zesati SV, Davidson SJ, Epstein HE, Unger S, Campbell PKE, Carmon N, Velez-Reyes M, Huemmrich KF (2022). Remote Sensing of Tundra Ecosystems Using High Spectral Resolution Reflectance: Opportunities and Challenges. Journal of Geophysical Research: Biogeosciences. 127, e2021JG006697. https://doi.org/10.1029/2021JG006697
Stavros EN, Chrone J, Cawse-Nicholson K, Freeman A, Glenn NF, Guild L, Kokaly R, Lee C, Luvall J, Pavlick R, Poulter , Schollaert-Uz S, Serbin SP, Thompson DR, Townsend PA, Turpie K, Yuen K, Thome K, Wang W, Zareh S-K, Nastal J, Bearden D, Miller CE, Schimel D (2022). Designing an Observing System to Study the Surface Biology and Geology (SBG) of the Earth in the 2020s. Journal of Geophysical Research: Biogeosciences, 127, e2021JG006471. https://doi.org/10.1029/2021JG006471
Li Q, Serbin SP, Lamour J, Davidson KJ, Ely KS, Rogers A (2022) Implementation and evaluation of the unified stomatal optimization approach in the Functionally Assembled Terrestrial Ecosystem Simulator (FATES). Geoscientific Model Development. 15, 4313-4329. https://doi.org/10.5194/gmd-2021-414
Davidson KJ, Lamour J, Rogers A, Serbin SP (2022) Late day measurement of excised branches results in uncertainty in the estimation of two stomatal parameters derived from response curves in Populus deltoides Bartr. x Populus nigra L. Tree Physiology. 42, 1377-1395. https://doi.org/10.1093/treephys/tpac006
Lamour J, Davidson KJ, Ely KS, Le Moguedec G, Leakey ADB, Li Q, Serbin SP, Rogers A (2022) An improved representation of the relationship between photosynthesis and stomatal conductance leads to more stable estimation of conductance parameters and improves the goodness-of-fit across diverse datasets. Global Change Biology. 28, 3537-3556. https://doi.org/10.1111/gcb.16103
Euskirchen ES, Serbin SP, Carman TB, Fraterrigo JM, Genet H, Iversen CM, Salmon V, McGuire AD (2022) Assessing dynamic vegetation model parameter uncertainty across Alaskan Arctic tundra plant communities. Ecological Applications. 32, e2499. https://doi.org/10.1002/eap.2499
Sabot MEB, De Kauwe MG, Pitman AJ, Medlyn BE, Ellsworth D, Martin-StPaul N, Wu J, Choat B, Limousin J-M, Mitchell PJ, Rogers A, Serbin SP (2022) One stomatal model to rule them all? Towards improved representation of carbon and water exchange in global models. Journal of Advances in Modelling Earth Systems. 14, e2021MS002761. https://doi.org/10.1029/2021MS002761
Rogers A, Serbin SP, Way DA (2022) Reducing model uncertainty of climate change impacts on high latitude carbon assimilation. Global Change Biology. 28, 1222-1247. https://doi.org/10.1111/gcb.15958
Song G, Wu S, Lee CKF, Serbin SP, Wolfe BT, Ng MK, Ely KS, Bogonovich M, Wang J, Lin Z, Saleska S, Nelson BW, Rogers A, Wu J (2022) Monitoring leaf phenology in moist tropical forests by applying a spuerpixel-based deep learning method to time-series images of tree canopies. Journal of Photogrammetry and Remote Sensing. 183, 18-33. https://doi.org/10.1016/j.isprsjprs.2021.10.023
Julia EF Stepanuk,Hyemi Kim,Janet A Nye,Jason J Roberts,Pat N Halpin,Debra L Palka,D Ann Pabst,William A McLellan,Susan G Barco,Lesley H Thorne, Subseasonal forecasts provide a powerful tool for dynamic marine mammal management, Front Ecol Environ 2022; doi:10.1002/fee.2506
Kelly JB, Carlson DE, Low JS, Thacker RW. 2022. Novel trends of genome evolution in highly complex tropical sponge microbiomes. Microbiome 10:164. https://doi.org/10.1186/s40168-022-01359-z
Title P.O., Swiderski D.L., Zelditch M.L. 2022. EcoPhyloMapper: an R package for integrating geographic ranges, phylogeny, and morphology. Methods in Ecology & Evolution. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13914
Pamfilie, A.M., Espinal, M.D., Vitek, N.S. 2022. Quantifying shell patterning helps identify species of Trionychidae. The Anatomical Record. Early View. https://onlinelibrary.wiley.com/doi/10.1002/ar.25064
Vitek, N.S., McDaniel, S.F., Bloch, J.I. 2022. Microevolutionary variation in molar morphology of Onychomys leucogaster decoupled from genetic structure. Evolution 76:2032-2048. https://onlinelibrary.wiley.com/doi/10.1111/evo.14576
Sousa, F.J., Cox, S.E., Hemming, S., Rasbury, E.T., Steponaitis, E., Hatton, K., Saslaw, M., Henkes, G., Princehouse, P., Vitek, N., Nengo, I. 2022. New Discovery of Oligocene Strata in the Topernawi Formation, Turkana County, Kenya. Frontiers in Earth Science 10:799097. https://www.frontiersin.org/articles/10.3389/feart.2022.799097/full
Vitek, N.S., Chen, H.** 2022. The impact of tooth wear on occlusal shape and the identification of fossils of New World porcupines (Rodentia: Erethizontidae). Journal of Mammalian Evolution 29:677-692. https://link.springer.com/10.1007/s10914-022-09601-z

Liu X, Gui L, Cui X,Butnor JR, Boyer EW, Yang D, Chen J, Fan B (2022) An automatic processing framework for in situ determination of ecohydrological root water content by ground-penetrating radar. IEEE Transactions on geoscience and remote sensing. 60, 4501715. https://ieeexplore.ieee.org/document/9386224

2021

2021 Publications from the Department of Ecology and Evolution

Molly K Grace, Elizabeth L Bennett, H Reşit Akçakaya, Craig Hilton-Taylor, Michael Hoffmann, Richard Jenkins, EJ Milner-Gulland, Ana Nieto, Richard P Young, Barney Long, 2021, IUCN launches Green Status of Species: a new standard for species recovery, Oryx, Volume 55, Issue 5, pp.651-652, DOI: https://doi.org/10.1017/S0030605321000880.
Molly K Grace, H Resit Akçakaya, Elizabeth L Bennett, Thomas M Brooks, Anna Heath, Simon Hedges, Craig Hilton‐Taylor, Michael Hoffmann, Axel Hochkirch, Richard Jenkins, David A Keith, Barney Long, David P Mallon, Erik Meijaard, EJ Milner‐Gulland, Jon Paul Rodriguez, PJ Stephenson, Simon N Stuart, Richard P Young, Pablo Acebes, Joanna Alfaro‐Shigueto, Silvia Alvarez‐Clare, Raphali Rodlis Andriantsimanarilafy, Marina Arbetman, Claudio Azat, Gianluigi Bacchetta, Ruchi Badola, Luís MD Barcelos, Joao Pedro Barreiros, Sayanti Basak, Danielle J Berger, Sabuj Bhattacharyya, Gilad Bino, Paulo AV Borges, Raoul K Boughton, H Jane Brockmann, Hannah L Buckley, Ian J Burfield, James Burton, Teresa Camacho‐Badani, Luis Santiago Cano‐Alonso, Ruth H Carmichael, Christina Carrero, John P Carroll, Giorgos Catsadorakis, David G Chapple, Guillaume Chapron, Gawsia Wahidunnessa Chowdhury, Louw Claassens, Donatella Cogoni, Rochelle Constantine, Christie Anne Craig, Andrew A Cunningham, Nishma Dahal, Jennifer C Daltry, Goura Chandra Das, Niladri Dasgupta, Alexandra Davey, Katharine Davies, Pedro Develey, Vanitha Elangovan, David Fairclough, Mirko Di Febbraro, Giuseppe Fenu, Fernando Moreira Fernandes, Eduardo Pinheiro Fernandez, Brittany Finucci, Rita Földesi, Catherine M Foley, Matthew Ford, Michael RJ Forstner, Néstor García, Ricardo Garcia‐Sandoval, Penny C Gardner, Roberto Garibay‐Orijel, Marites Gatan‐Balbas, Irene Gauto, Mirza Ghazanfar Ullah Ghazi, Stephanie S Godfrey, Matthew Gollock, Benito A González, Tandora D Grant, Thomas Gray, Andrew J Gregory, Roy HA van Grunsven, Marieka Gryzenhout, Noelle C Guernsey, Garima Gupta, Christina Hagen, Christian A Hagen, Madison B Hall, Eric Hallerman, Kelly Hare, Tom Hart, Ruston Hartdegen, Yvette Harvey‐Brown, Richard Hatfield, Tahneal Hawke, Claudia Hermes, Rod Hitchmough, Pablo Melo Hoffmann, Charlie Howarth, Michael A Hudson, Syed Ainul Hussain, Charlie Huveneers, Hélène Jacques, Dennis Jorgensen, Suyash Katdare, Lydia KD Katsis, Rahul Kaul, Boaz Kaunda‐Arara, Lucy Keith‐Diagne, Daniel T Kraus, Thales Moreira de Lima, Ken Lindeman, Jean Linsky, Edward Louis Jr, Anna Loy, Eimear Nic Lughadha, Jeffrey C Mangel, Paul E Marinari, Gabriel M Martin, Gustavo Martinelli, Philip JK McGowan, Alistair McInnes, Eduardo Teles Barbosa Mendes, Michael J Millard, Claire Mirande, Daniel Money, Joanne M Monks, Carolina Laura Morales, Nazia Naoreen Mumu, Raquel Negrao, Anh Ha Nguyen, Md Nazmul Hasan Niloy, Grant Leslie Norbury, Cale Nordmeyer, Darren Norris, Mark O'Brien, Gabriela Akemi Oda, Simone Orsenigo, Mark Evan Outerbridge, Stesha Pasachnik, Juan Carlos Pérez‐Jiménez, Charlotte Pike, Fred Pilkington, Glenn Plumb, Rita de Cassia Quitete Portela, Ana Prohaska, Manuel G Quintana, 2021, Testing a global standard for quantifying species recovery and assessing conservation impact, Conservation Biology, https://doi.org/10.1111/cobi.13756.
H Reşit Akçakaya, Axel Hochkirch, Jason T Bried, Roy HA van Grunsven, John P Simaika, Geert De Knijf, Sérgio Henriques, 2021, Calculating population reductions of invertebrate species for IUCN Red List assessments, Journal of Insect Conservation, volume 25, pp.377–382.
Bilgecan Şen, H Reşit Akçakaya, 2021, Inter-specific Variability in Demographic Processes Affects Abundance-Occupancy Relationships, bioRxiv, doi: https://doi.org/10.1101/2020.09.03.282004.
Damien A Fordham, Stuart C Brown, H Resit Akcakaya, Barry W Brook, Sean Haythorne, Andrea Manica, Kevin T Shoemaker, Jeremy J Austin, Benjamin Blonder, Julia Pilowsky, Carsten Rahbek, David Nogues-Bravo, 2021, Humans hastened the range collapse and extinction of woolly mammoth, bioRxiv, doi: https://doi.org/10.1101/2021.02.17.431706.
Molly K.Grace, H. Resit Akçakaya, Joseph W.Bull, Christina Carrero, Katharine Davies, Simon Hedges, Michael Hoffmann, Barney Long, Eimear M. Nic Lughadha, Gabriel M.Martin, Fred Pilkington, Malin C.Rivers, Richard P.Young, E.J.Milner-Gulland, 2021, Building robust, practicable counterfactuals and scenarios to evaluate the impact of species conservation interventions using inferential approaches, Biological Conservation, Volume 261, https://doi.org/10.1016/j.biocon.2021.109259.
Emily M Herstoff, Cédric L Meunier, Maarten Boersma, Stephen B Baines, 2021, Leveraging differences in multiple prey traits allows selective copepods to meet their threshold elemental ratios, Limnology and Oceanography, https://doi.org/10.1002/lno.11800.
Rafael D’Andrea, James P O’Dwyer, 2021, Competition for space in a structured landscape: The effect of seed limitation on coexistence under a tolerance‐fecundity trade‐off, Journal of Ecology, https://doi.org/10.1111/1365-2745.13613.
Armenteras-Pascual, D., L.M. Dávalos, J.S. Barreto, A. Miranda, A. Hernández-Moreno, C. Zamorano-Elgueta, T. M. González-Delgado, M. C. Meza, Javier Retana-Alumbreros. Fire-induced loss of the world’s most biodiverse forests in Latin America. Science Advances 7(33), eabd3357 DOI: 10.1126/sciadv.abd3357.
Santana, S.E.*, Z.A. Kaliszewska*, L.B. Leiser-Miller, M.E. Lauterbur, J.H. Arbour, L.M. Dávalos, J.A. Riffell. Fruit odorants mediate co-specialization in a multispecies plant-animal mutualism. Proceedings of the Royal Society B: Biological Sciences 288: 28820210312 DOI: 10.1098/rspb.2021.0312. *Equal contribution.
Lertxundi, U., S. Domingo-Echaburu, L.M. Dávalos, G. Orive. Drug pollution & Sustainable Developing Goals. Science of the Total Environment.
Yohe, L.R., L.B. Leiser-Miller, Z.A. Kaliszewska, P. Donat, S.E. Santana, L.M. Dávalos. Diversity in olfactory receptor repertoires is associated with dietary specialization in a genus of frugivorous bat. G3: Genes|Genomes|Genetics. DOI: 10.1093/g3journal/jkab260.
Moreno Santillan, D., T. Lama, Y.G. Guerrero, A. Brown, P. Donat, H. Zhao, S. Rossiter, L.R. Yohe, J. Potter, E.C. Teeling, S. Vernes, K.T.J. Davies, E. Myers, G. Hughes, Z. Huang, F. G. Hoffmann, A.P. Corthals, D. Ray*, L.M. Dávalos*. Large-Scale Genome Sampling Reveals Unique Immunity and Metabolic Adaptations in Bats. Molecular Ecology. DOI: 10.1111/MEC.16027. *Corresponding authors.
Hall, R.P., G. Mutumi, B.P. Hedrick, L.R. Yohe, A. Sadier, K.T.J. Davies, S.J. Rossiter, K. Sears, L.M. Dávalos, E.R. Dumont. Find the Food First: An Omnivorous Sensory Morphotype Predates Biomechanical Specialization for Plant Based Diets in Phyllostomid Bats. Evolution. DOI: 10.1111/evo.14270.
Murillo-Sandoval, P., E. Gjerdseth, C. Correa-Ayram, D. Wrathall, J. Van Den Hoek, L. M. Dávalos, R. Kennedy. No peace for the forest: Rapid, widespread land changes in the Andes-Amazon region following the Colombian civil war. Global Environmental Change 69: 102283. DOI: 10.1016/j.gloenvcha.2021.102283.
Turvey, S.T.*, C. Duncan, N.S. Upham, X. Harrison, L.M. Dávalos*. Where the wild things were: intrinsic and extrinsic extinction predictors in the world’s most depleted mammal fauna. Proceedings of the Royal Society B: Biological Sciences 288: 20202905. DOI: 10.1098/rspb.2020.2905. *Corresponding authors.
Lim, M., K. Bi, C. Witt, C. Graham, L. Dávalos. Pervasive genomic signatures of local adaptation to altitude across highland specialist Andean hummingbird populations. Journal of Heredity. DOI: 10.1093/jhered/esab008.
Potter, J.H.T., K.T J. Davies, L.R. Yohe, K. Warren, G. Tsagkogeorga, B.K. Lim, M. dos Reis, L.M. Dávalos, S.J. Rossite*. Dietary diversification and specialisation in neotropical bats facilitated by early molecular evolution. Molecular Biology and Evolution. DOI: 10.1093/molbev/msab028.
Potter, J.H.T.*, R. Drinkwater, K.T J. Davies, M.C.W. Lim, L.R. Yohe, X. Zhang, H. Chi, I. Levantis, B.K. Lim, C.C. Witt, G. Tsagkogeorga, M. dos Reis, Y. Liu, W. Furey, M.J. Whitley, D. Aksentijevic, L.M. Dávalos, S.J. Rossiter*, 2021, Nectar-feeding bats and birds show parallel molecular adaptations in sugar metabolism enzymes, Current Biology, DOI: 10.1016/j.cub.2021.08.018, *Corresponding authors.
Daniel E Dykhuizen, 2021, Public Health and Paul De Kruif, The Quarterly Review of Biology, 96, pp.127-132.
Futuyma, D. 2021. How Birds Evolve:What Science Reveals About Their Origin, Lives & Diversity. Princeton University Press.
Futuyma, D. J. 2021. How does phenotypic plasticity fit into evolutionary theory? In D. W. Pfennig (ed.), Phenotypic Plasticity and Evolution, pp. 349-366. CRC Press, Boca Raton.
O’Dea, R.E., Lagisz, M., Jennions, M.D., Koricheva, J., Noble, D.W.A., Parker, T.H., Gurevitch, J., Page, M.J., Stewart, G., Moher, D., Nakagawa, S., n.d. Preferred reporting items for systematic reviews and meta-analyses in ecology and evolutionary biology: a PRISMA extension. Biol. Rev. 2021. https://doi.org/10.1111/brv.12721.
Phoebe L. Zarnetske*, Jessica Gurevitch* [lead authors], Janet Franklin, Peter Groffman, Cheryl Harrison, Jessica Hellmann, Forrest M. Hoffman, Shan Kothari, Alan Robock, Simone Tilmes, Daniele Visioni, Jin Wu, Lili Xia, Cheng‐En Yang. 2021. Potential ecological impacts of climate intervention by reflecting sunlight to cool Earth. Proceedings of the National Academy of Sciences 2021 Vol. 118 No. 15 e1921854118; https://doi.org/10.1073/pnas.1921854118.
Gurevitch, J., Jadotte, Y. and A. Moyer. 2021. Meta-analysis in the Social Sciences. (Chapter) The Cambridge Handbook of Research Methods and Statistics for the Social and Behavioral Sciences, Volume 1 edited by Austin Lee Nichols; John Edlund. In press.
Tonjes, David and Jessica Gurevitch. 21 May 2021. Trash Talk: Garbage and the Infrastructure Bill (retitled, Better ways to manage LI’s trash). Newsday Opinion article.
Riley C Pena, Jeffrey Levinton, 2021, Two species of fiddler crab show no cost of bearing a sexually selected giant claw in predator escape behaviors, Journal of Experimental Marine Biology and Ecology, Volume 541, August 2021, 151570, https://doi.org/10.1016/j.jembe.2021.151570.
Thomas S Bianchi, Robert C Aller, Trisha B Atwood, Craig J Brown, Luis A Buatois, Lisa A Levin, Jeffrey S Levinton, Jack J Middelburg, Elise S Morrison, Pierre Regnier, Michael R Shields, Paul VR Snelgrove, Erik E Sotka, Ryan RE Stanley, 2021, What global biogeochemical consequences will marine animal–sediment interactions have during climate change? Elementa: Science of the Anthropocene (2021) 9 (1): 00180, https://doi.org/10.1525/elementa.2020.00180.
Jeffrey S Levinton, Brooke Arena, 2021, Direct and biometrical estimates of the closing force of major claws of the sand fiddler crab Leptuca pugilator (Bosc, 1801) (Decapoda: Brachyura: Ocypodidae): Support for the weakening combatant hypothesis, Journal of Crustacean Biology, Volume 41, Issue 2, June 2021, ruab007, https://doi.org/10.1093/jcbiol/ruab007
Tom Hart, Fiona Jones, Caitlin Black, Chris Lintott, Casey Youngflesh, Heather Lynch, Alasdair Davies, Eamonn Maguire, Andrew Zisserman, Carlos Arteta, Peter Barham, Colin Southwell, Louise Emmerson, Mark Jessopp, 2021, Time-lapse imagery is cheap and timely in the fight against colonial species' decline, Authorea Preprints, DOI: 10.22541/au.162686380.02020424/v1.
LR Pertierra, F Santos-Martin, KA Hughes, C Avila, JO Caceres, D De Filippo, S Gonzalez, SM Grant, H Lynch, C Marina-Montes, A Quesada, P Tejedo, T Tin, J Benayas, 2021, Ecosystem services in Antarctica: Global assessment of the current state, future challenges and managing opportunities, Ecosystem Services, Vol.49, pp.101299, https://doi.org/10.1016/j.ecoser.2021.101299.
Alex Borowicz, Heather J Lynch, Tyler Estro, Catherine Foley, Bento Gonçalves, Katelyn B Herman, Stephanie K Adamczak, Ian Stirling, Lesley Thorne, 2021, Social sensors for wildlife: Ecological opportunities in the era of camera ubiquity, Frontiers in Marine Science, Vol.8, pp.385, https://doi.org/10.3389/fmars.2021.645288.
Aymen Al-Saadi, Ioannis Paraskevakos, Bento Collares Gonçalves, Heather J Lynch, Shantenu Jha, Matteo Turilli, 2021, Comparing workflow application designs for high resolution satellite image analysis, Future Generation Computer Systems, https://doi.org/10.1016/j.future.2021.04.023.
Michael Schrimpf, Heather Lynch, 2021, The role of wind fetch in structuring Antarctic seabird breeding occupancy, Ibis, Vol.163, No.2, pp.695-705, https://doi.org/10.1111/ibi.12910.
Casey Youngflesh, Fiona M Jones, Heather J Lynch, Joan Arthur, Zuzana Ročkaiová, Holly R Torsey, Tom Hart, 2021, Large‐scale assessment of intra‐and inter‐annual breeding success using a remote camera network, Remote Sensing in Ecology and Conservation, Vol.7, No.1, pp.97-108, https://doi.org/10.1002/rse2.171.
Jonathon Handley, Marie-Morgane Rouyer, Elizabeth J Pearmain, Victoria Warwick-Evans, Katharina Teschke, Jefferson Hinke, Heather Lynch, Louise Emmerson, Colin Southwell, Gary Griffith, Cesar A Cardenas, Aldina Franco, Philip N Trathan, Maria P Dias, 2021, Marine important bird and biodiversity areas for penguins in Antarctica: Targets for conservation action, Frontiers in Marine Science, Vol.7, pp.1190, https://doi.org/10.3389/fmars.2020.602972.
Bento C Gonçalves, Heather J Lynch, 2021, Fine-Scale Sea Ice Segmentation for High-Resolution Satellite Imagery with Weakly-Supervised CNNs, Remote Sensing, 2021, 13(18), 3562; https://doi.org/10.3390/rs13183562.
Noah Strycker, Alex Borowicz, Michael Wethington, Steven Forrest, Vikrant Shah, Yang Liu, Hanumant Singh, Heather J Lynch, 2021, Fifty-year change in penguin abundance on Elephant Island, South Shetland Islands, Antarctica: results of the 2019–20 census, Polar Biology, 44, pages45–56 (2021).
Roberto Bertolini, Stephen J Finch, Ross H Nehm, 2021, Enhancing data pipelines for forecasting student performance: integrating feature selection with cross-validation, International Journal of Educational Technology in Higher Education, volume 18, pp.1-23, Article number: 44 (2021).
Karen Nicole Pelletreau, Tessa Andrews, Norris Armstrong, Mary A Bedell, Farahad Dastoor, Neta Dean, Susan Erster, Cori Fata-Hartley, Nancy Guild, Hamish Greig, David Hall, Jennifer K Knight, Donna Koslowsky, Paula Lemons, Jennifer Martin, Jill McCourt, John Merrill, Rosa Moscarella, Ross Nehm, Robert Northington, Brian Olsen, Luanna Prevost, Jon Stolzfus, Mark Urban-Lurain, Michelle K Smith, 2021, A clicker-based case study that untangles student thinking about the processes in the central dogma, CourseSource.
Xiaoming Zhai, Lehong Shi, Ross H Nehm, 2021, A meta-analysis of machine learning-based science assessments: factors impacting machine-human score agreements, Journal of Science Education and Technology, volume 30, pages361–379 (2021).
Roberto Bertolini, Stephen J Finch, Ross H Nehm, 2021, Testing the impact of novel assessment sources and machine learning methods on predictive outcome modeling in undergraduate biology, Journal of Science Education and Technology, volume 30, pages193–209 (2021).
Gena C Sbeglia, Justin A Goodridge, Lucy H Gordon, Ross H Nehm, 2021, Are Faculty Changing? How Reform Frameworks, Sampling Intensities, and Instrument Measures Impact Inferences about Student-Centered Teaching Practices, CBE—Life Sciences Education, Vol.20, No.3 pp.ar39, https://doi.org/10.1187/cbe.20-11-0259.
Alexandra P Hooks, Dianna K Padilla, 2021, Introduced predator elicits population-specific responses from prey, Biological Invasions, 23, pp.477–490.
Niamh B O’Hara, Steven J Franks, Nolan C Kane, Silas Tittes, Joshua S Rest, 2021, Evolution of pathogen response genes associated with increased disease susceptibility during adaptation to an extreme drought in a Brassica rapa plant population, BMC Ecology and Evolution, 21, pp.1-11.
Joanne Figueiredo, Joshua Rest, Sarah Adamo, Rebecca Grella, James Dilger, 2021, Nicotine Stimulates Peristalsis in N. Vectensis: From Behavior to Nicotinic Receptor Genes, Research Square, DOI:https://doi.org/10.21203/rs.3.rs-195699/v1.
Elena Hamann, Christopher S Pauli, Zoé Joly‐Lopez, Simon C Groen, Joshua S Rest, Nolan C Kane, Michael D Purugganan, Steven J Franks, 2021, Rapid evolutionary changes in gene expression in response to climate fluctuations, Molecular ecology, 30, pp.193.206, https://doi.org/10.1111/mec.15583.
Jeroen B Smaers, Ryan S Rothman, Daphne R Hudson, Amy M Balanoff, Brian Beatty, Dina KN Dechmann, Dorien de Vries, Jacob C Dunn, John G Fleagle, Christopher C Gilbert, Anjali Goswami, Andrew N Iwaniuk, William L Jungers, Max Kerney, Daniel T Ksepka, Paul R Manger, CS Mongle, F James Rohlf, N Adam Smith, Christophe Soligo, Vera Weisbecker, Kamran Safi, 2021, The evolution of mammalian brain size, SCIENCE ADVANCES, 28 Apr 2021, Vol 7, Issue 18, DOI: 10.1126/sciadv.abe2101.
F James Rohlf, 2021, Sampling Theory: For the Ecological and Natural Resource Sciences, QUARTERLY REVIEW OF BIOLOGY, Vo.96, No.1, pp.45-45.
F James Rohlf, 2021, Why Clusters and Other Patterns Can Seem to be Found in Analyses of High-Dimensional Data, Evolutionary Biology, volume 48, pages1–16 (2021).
Myers BJE, Weiskopf SR, Shiklomanov AN, Ferrier S, Weng E, Casey KA,Harfoot M, Jackson ST, Leidner AK, Lenton TM, Luikart G, Hiroyuki M, Pettoelli N, Rosa IMD, Ruane AC, Senay GB, Serbin SP, Tittensor DP, Beard DT (2021) A new approach to evaluate and reduce uncertainty of model-based biodiversity projections for conservation policy formulation. BioScience. 71, 1261-1273. https://doi.org/10.1093/biosci/biab094
Lamour J, Davidson KJ, Ely KS, Li Q, Serbin SP, Rogers A (2021) New calculations for photosynthesis measurement systems: what's the impact for physiologists and modelers? New Phytologist. 253, 592-598. https://doi.org/10.1111/nph.17762
Yang D, Morrison BD, Hantson W, Breen AL, McMahon A, Li Q, Salmon VG, Hayes DJ, Serbin SP (2021) Landscape-scale characterization of arctic tundra vegetation composition, structure, and function with a multi-sensor unoccupied aerial system. Environmental Research Letters. 16, 085005. https://doi.org/10.1088/1748-9326/ac1291
Lamour J, Davidson KJ, Ely KS, Anderson JA, Rogers A, Wu J, Serbin SP (2021) Rapid estimation of photosynthetic leaf traits of tropical plants in diverse environmental conditions using reflectance spectroscopy. PLoS One. 16, e0258791.
Souza DC, Jardine KJ, Rodrigues JVFC, Gimenez BO, Rogers A, McDowell N, Walker A, Higuchi N, Sampaio-Filho IJ, Chambers J (2021) Canopy position influences the degree of light suppression of leaf respiration in abundant tree genera in the Amazon Forest. Frontiers in Forest and Global Change. 4,723539.
Burnett AC, Anderson J, Davidson KJ, Ely KS, Lamour J, Li Q, Morrison BD, Yang D, Rogers A, Serbin SP (2021) A best-practice guide to predicting plant traits from leaf-level hyperspectral data using partial least square regression. Journal of Experimental Botany. 72, 6175-6189.
Burnett AC, Serbin SP, Davidson KJ, Ely KS, Rogers A (2021) Detection of the metabolic response to drought stress using hyperspectral reflectance. Journal of Experimental Botany. 72, 6474-6489.
Burnett AC, Serbin SP, Rogers A (2021) Source:sink imbalance detected with leaf and canopy-level spectroscopy in a field-grown crop. Plant, Cell & Environment. 44, 2466-2479.
Burnett AC, Serbin SP, Lamour J, Anderson J, Davidson KJ, Yang D, Rogers A (2021) Seasonal trends in photosynthesis and leaf traits in scarlet oak. Tree Physiology. 41, 1413-1424.
Thompson DR, Brodrick PG, Cawse-Nicholson K, Chadwick KD, Green RO, Poulter B, Serbin S, Shiklomanov A, Townsend P, Turpie K (2021) Spectral fidelity of Earth's terrestrial and aquatic ecosystems. JGR Biogeosciences. 2021JG006273.
Yan Z, Guo Z, Serbin SP, Song G, Zhao Y, Chen Y, Wu S, Wang J, Wang X, Li J, Wang B, Wu Y; Su Y, Wang H, Rogers A, Liu L, Wu J (2021) Spectroscopy outperforms leaf trait relationships for predicting photosynthetic capacity across different forest types. New Phytologist. 232, 134-147.
Crystal-Ornelas R, Varadharajan C, Bond-Lamberty B, Boye K, Burrus M, Cholia S, Crow M, Damerow J, Dearakonda R, Ely KS, Goldman A, Heinze S, Hendrix V, Kakalia Z, Pennington S, Robles E, Rogers A, Simmonds M, Velliquette T, Weierbach H, Weisenhorn P, Welch JN, Agarwal DA (2021). A guide to usig GitHub for developing and versioning data standards and reporting formats. Earth and Space Science. 8, e2021EA001797.
Rogers A, Dietz K-J, Gifford M, Lunn JE (2021) The importance of independent replication of treatments in plant science. Journal of Experimental Botany. 72, 5270-5274.
Pivovaroff AL, McDowell N, Wolfe BT, Christoffersen B, Davies S, Dickman LT, Grossiord C, Leff RT, Rogers A, Serbin SP, Wright SJ, Wu J, Xu C, Chambers JQ (2021) Hydraulic architecture explains species moisture dependency but not mortality rates across a tropical rainfall gradient. Biotropica. 53, 1213-1225.
Shiklomanov AN, Dietze MC, Fer I, Viskari T, Serbin SP (2021). Cutting out the middleman: calibrating and validating a dynamic vegetation model (ED2-PROSPECT5) using remotely sensed surface reflectance. Geoscientific Model Development. 14, 2603-2633
Ely KS, Rogers A, Agarwal DA, Ainsworth EA, Albert L, Ali A, Anderson J, Aspinwall MJ, Bellasio C, Bernacchi C, Bonnage S, Buckley TN, Bunce J, Burnett AC, Busch FA, Cavanagh A, Cernusak LN, Crystal-Ornelas R, Damerow J, Davidson KJ, De Kauwe MG, Dietze MC, Domingues TF, Dusenge ME, Ellsworth DS, Evans JR, Gauthier PPG, Gimenez BO, Gordon EP, Gough CM, AHalbritter AH, Hanson DT, Heskel M, Hogan JA, Hupp JR, Jardine K, Kattge J, Keenan T, Kromdijk J, Kumarathunge DP, Lamour J, Leakey ADB, LeBauer DS, Li Q, Lundgren MR, McDowell N, Meacham-Hensold K, Medlyn BE, Moore DJP, Negrón-Juárez R, Niinemets U, Osborne CP, Pivovaroff AL, Poorter H, Reed SC, Ryu Y, Sanz-Saez A, Schmiege SC, Serbin SP, Sharkey TD, Slot M, Smith NG, Sonawane BV, South PF, Souza DC, Stinziano JR, Stuart-Haëntjens E, Taylor SH, Tejera MD, Uddling J, Vandvik V,Varadharajan C, Walker AP, Walker BJ, Warren JM, Way DA, Wolfe BT, Wu J, Wullschleger SD, Xu C, Yan Z, Yang D (2021) A reporting format for leaf-level gas exchange data and metadata. Ecological Informatics. 61, 101232.
Way DA, Cook A, Rogers A (2021) The effect of rising CO2 concentration on terrestrial systems: scaling it up. New Phytologist. 229, 2383-2385.
Rogers A, Kumarathunge DP, Lombardozzi DL, Medlyn BE, Serbin SP, Walker AP (2021) Triose phosphate utilization limitation: an unnecessary complexity in terrestrial biosphere model representation of photosynthesis. New Phytologist. 230, 17-22.
Kamoske AG, Dahlin KM, Serbin SP, Stark SC (2021) Leaf traits and canopy structure together explain canopy functional diversity: an airborne remote sensing approach. Ecological Applications. In Press. 31, e02230.
Walker AP, Johnson AM, Rogers A, Anderson J, Bridges RA, Fisher RA, Lu D, Ricciutto DM, Serbin SP, Ye M (2021). Multi-hypothesis analysis of Farquhar and Collatz photosynthesis models reveals unexpected influence of empirical assumptions. Global Change Biology. 27, 804-822.
Fer I, Gardella AK, Shiklomanov AN, Serbin SP, De Kauwe MG, Raiho A, Johnston MR, Desai A, Viskari T, Quaife T, LeBauer DS, Cowdert EM, Koope R, Fisher JB, Poulter B, Duveneck MJ, Hoffman FM, Parton W, Mantooth J, Campbell EE, Haynes KD, Schaefer K, Wilcox KR, Dietze M (2021) Beyond Modeling: A Roadmap to Community Cyberinfrastructure for Ecological Data-Model Integration. Global Change Biology. 27, 13-26.
Matthew Houser, Abigail Sullivan, Tara Smiley, Ranjan Muthukrishnan, Elizabeth Grennan Browning, Adam Fudickar, Pascal Title, Jason Bertram, Maria Whiteman, 2021, What fosters the success of a transdisciplinary environmental research institute? Reflections from an interdisciplinary research cohort, Elementa: Science of the Anthropocene (2021) 9 (1): 00132. https://doi.org/10.1525/elementa.2020.00132.
T Akther, CG Easson, R Collin, RW Thacker, 2021, Comparing adult and larval microbiomes in the tropical sponges Neopetrosia sigmafera and Xestospongia bocatorensis, INTEGRATIVE AND COMPARATIVE BIOLOGY, Vol.61, pp.E1037-E1037.
Christopher J Freeman, Cole G Easson, Cara L Fiore, Robert W Thacker, 2021, Sponge–Microbe Interactions on Coral Reefs: Multiple Evolutionary Solutions to a Complex Environment, Frontiers in Marine Science, 20 July 2021, pp.917, https://doi.org/10.3389/fmars.2021.705053.
Joseph B Kelly, David E Carlson, Jun Siong Low, Tyler Rice, Robert W Thacker, 2021, The relationship between microbiomes and selective regimes in the sponge genus Ircinia, Frontiers in microbiology, Vol.12: 607289. doi: 10.3389/fmicb.2021.607289.
Kelly JB, Thacker RW. 2021. New shallow water species of Caribbean Ircinia Nardo, 1883 (Porifera: Irciniidae). Zootaxa 5072(4): 301-323. doi: 10.11646/zootaxa.5072.4.1
Freeman CJ, Easson CG, Fiore CL, Thacker RW. 2021. Sponge-microbe interactions on coral reefs: multiple evolutionary solutions to a complex environment. Frontiers in Marine Science 8:705053. doi: 10.3389/fmars.2021.705053
Kelly JB, Carlson DE, Low JS, Rice T, Thacker RW. 2021. The relationship between microbiomes and selective regimes in the sponge genus Ircinia. Frontiers in Microbiology 12:489. doi: 10.3389/fmicb.2021.607289
Eric S Haag, John R True, 2021, Developmental System Drift, Evolutionary developmental biology: a reference guide, pp.99-110.
Garrett A Roberts Kingman, Deven N Vyas, Felicity C Jones, Shannon D Brady, Heidi I Chen, Kerry Reid, Mark Milhaven, Thomas S Bertino, Windsor E Aguirre, David C Heins, Frank A von Hippel, Peter J Park, Melanie Kirch, Devin M Absher, Richard M Myers, Federica Di Palma, Michael A Bell, David M Kingsley, Krishna R Veeramah, 2021, Predicting future from past: The genomic basis of recurrent and rapid stickleback evolution, SCIENCE ADVANCES, 18 Jun 2021, Vol 7, Issue 25, DOI: 10.1126/sciadv.abg5285.
A Žegarac, L Winkelbach, J Blöcher, Y Diekmann, M Krečković Gavrilović, M Porčić, B Stojković, L Milašinović, M Schreiber, D Wegmann, KR Veeramah, S Stefanović, J Burger, 2021, Ancient genomes provide insights into family structure and the heredity of social status in the early Bronze Age of southeastern Europe, Scientific Reports, volume 11, Article number: 10072 (2021).
Kerry Reid, Michael A Bell, Krishna R Veeramah, 2021, Threespine Stickleback: A Model System For Evolutionary Genomics, Annual Review of Genomics and Human Genetics, Vol. 22:357-383, https://doi.org/10.1146/annurev-genom-111720-081402.
Kyunghun Min, Thomas F Jannace, Haoyu Si, Krishna R Veeramah, John D Haley, James B Konopka, 2021, Integrative multi-omics profiling reveals cAMP-independent mechanisms regulating hyphal morphogenesis in Candida albicans, doi: https://doi.org/10.1101/2021.03.08.433668.
Walter G Joyce, Jérémy Anquetin, Edwin-Alberto Cadena, Julien Claude, Igor G Danilov, Serjoscha W Evers, Gabriel S Ferreira, Andrew D Gentry, Georgios L Georgalis, Tyler R Lyson, Adán Pérez-García, Márton Rabi, Juliana Sterli, Natasha S Vitek, James F Parham, 2021, A nomenclature for fossil and living turtles using phylogenetically defined clade names, Swiss Journal of Palaeontology, volume 140, Article number: 5 (2021).
Natasha S Vitek, Paul E Morse, Doug M Boyer, Suzanne G Strait, Jonathan I Bloch, 2021, Evaluating the responses of three closely related small mammal lineages to climate change across the Paleocene–Eocene thermal maximum, Paleobiology, Volume 47, Issue 3, August 2021, pp.464-486, DOI: https://doi.org/10.1017/pab.2021.12.
Wang J, Yang D, Chen S, Zhu X, Wu S, Bogonovich M, Guo Z, Zhu Z, Wu J (2021) Automatic cloud and cloud shadow detection in tropical areas for PlanetScope satellite images. Remote Sensing of Environment. 264, 112604. https://doi.org/10.1016/j.rse.2021.112604

2020

2020 Publications from the Department of Ecology and Evolution

Akçakaya HR, Rodrigues ASL, Keith DA, Milner-Gulland EJ, Sanderson EW, Hedges S, Mallon DP, Grace MK, Long B, Meijaard E, Stephenson PJ. 2020. Assessing ecological function in the context of species recovery. Conservation biology 34:561–571. DOI: 10.1111/cobi.13425.
Bird JP, Martin R, Akçakaya HR, Gilroy J, Burfield IJ, Garnett S, Symes A, Taylor J, Şekercioğlu ÇH, Butchart SHM. 2020. Generation lengths of the world’s birds and their implications for extinction risk. Conservation Biology. DOI: 10.1111/cobi.13486.
Driessen F, Cushing T, Baines SJ. 2020. Retroperitoneal lymphatic malformation in a dog. Acta veterinaria Scandinavica 62:8. DOI: 10.1186/s13028-020-0506-9.
D’Andrea R, Gibbs T, P O'Dwy J. 2020. Emergent neutrality in consumer-resource dynamics. PLoS computational biology 16.
Barabás G, D’Andrea R. 2020. Chesson’s coexistence theory: reply. Ecology 101.
Wang K, Tian S, Galindo-González J, Dávalos LM, Zhang Y, Zhao H. 2020. Molecular adaptation and convergent evolution of frugivory in Old World and neotropical fruit bats. Molecular ecology. DOI: 10.1111/mec.15542.
Yohe LR, Davies KTJ, Simmons NB, Sears KE, Dumont ER, Rossiter SJ, Dávalos LM. 2020. Evaluating the performance of targeted sequence capture, RNA-Seq, and degenerate-primer PCR cloning for sequencing the largest mammalian multigene family. Molecular Ecology Resources 20:140–153. DOI: 10.1111/1755-0998.13093.
Dávalos LM, Austin RM, Balisi MA, Begay RL, Hofman CA, Kemp ME, Lund JR, Monroe C, Mychajliw AM, Nelson EA, Nieves-Colón MA, Redondo SA, Sabin S, Tsosie KS, Yracheta JM. 2020. Pandemics’ historical role in creating inequality. Science 368:1322–1323. DOI: 10.1126/science.abc8953.
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