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*Co-first authors. @Corresponding author(s).

In review / pre-prints

preprint. *Stewart, T. A., Yoo, I., and Upham, N. S.* The coevolution of mammae number and litter size. bioRxiv. In review at eLife.

preprint. @Upham, N. S., Esselstyn, J. A., Jetz, W. Ecological causes of speciation and species richness in the mammal tree of life. bioRxiv. In review / split. Attention on Twitter.


2021. @Upham, N. S., Poelen, J. H., Paul, D. L., Groom, Q. J., Simmons, N. B., Vanhove, M. P. M., Bertolino, S., Reeder, D. M., Bastos-Silveira, C., Sen, A., Sterner, B., Franz, N., Guidoti, M., Penev, L., and Agosti, D. Liberating host–virus knowledge from biological dark data. The Lancet Planetary Health

2021. @Upham, N. S., Esselstyn, J. A., and Jetz, W. Molecules and fossils tell distinct yet complementary stories of mammal diversification. Current Biology.

2021. Greenberg D.A., Pyron R.A., Johnson L.G.W., Upham N.S., Jetz W., Mooers A.Ø. 2021. Evolutionary legacies in contemporary tetrapod imperilment. Ecology Letters.

2021. Sterner B., Upham N.S., Gupta P., Powell C., Franz N. Wanted: Standards for FAIR taxonomic concept representations and relationships. Biodiversity Information Science and Standards. 5:e75587.

2021. Groom Q., Adriaens T., Bertolino S., Phelps K., Poelen J., Reeder D., Richardson D., Simmons N., and Upham N.S.. Holistic understanding of contemporary ecosystems requires integration of data on domesticated, captive and cultivated organisms. Biodiversity Data Journal. 9:e65371.

2021. Sen, A., Sterner, B., Franz, N., Powel, C., and Upham N.S.. Combining Machine Learning & Reasoning for Biodiversity Data Intelligence. Proceedings of the AAAI Conference on Artificial Intelligence, 35: 14911-14919.

2021. Dávalos, L. M., Duncan, C., Upham, N. S., Harrison, X., Turvey, S. T. Where the wild things were: biological and environmental extinction predictors in the world’s most depleted mammal fauna. Proceedings of the Royal Society: B. 288: 20202905.

2021. Cisse O.H., Ma L., Dekker J.P., Khil P.P., Youn J.-H., Brenchley J.M., Blair R.V., Pahar B., Chabe M., Rompay K.K.A.V., Keesler R., Sukura A., Hirsch V., Kutty G., Liu Y., Li P., Chen J., Song J., Weissenbacher-Lang C., Xu J., Upham N.S., Stajich J.E., Cuomo C.A., Cushion M.T., Kovacs J.A. 2020. Genomic insights into the host specific adaptation of the Pneumocystis genus and emergence of the human pathogen Pneumocystis jirovecii. Communications Biology 4: 1-14.

2021. Sterner B., Elliott S., Upham N.S., Franz N.M. Bats, objectivity, and viral spillover risk. History & Philosophy of the Life Sciences 43:7


2020. Alhajeri, B. H., Fourcade, Y., Upham, N. S., and Alhaddad, H. A global test of Allen’s rule in rodents. Global Ecology and Biogeography.

2020. Upham N.S., Agosti D., Poelen J., Penev L., Paul D., Reeder D., Simmons N.B., Csorba G., Groom Q., Dimitrova M., Miller J. Liberating Biodiversity Data From COVID-19 Lockdown: Toward a knowledge hub for mammal host-virus information. Biodiversity Information Science and Standards 4: e59199.

2020. Sen A., Franz N., Sterner B., Upham N. S. The Automated Taxonomic Concept Reasoner. Biodiversity Information Science and Standards. 4:e59074.

2020. Sterner B., Upham N.S., Sen A., Franz N. Avenues into Integration: Communicating taxonomic intelligence from sender to recipient. Biodiversity Information Science and Standards 4: e59006.

2020. Franz N., Sterner B., Upham N.S., and Hernández K.C. Redesigning the Trading Zone between Systematics and Conservation: Insights from Malagasy mouse lemur classifications, 1982 to present. Biodiversity Information Science and Standards 4: e59234.

2020. Cook, J. A., Satoru, A., Armién, B., Bates, J., Carrion Bonilla, C. A., de Souza Cortez, M. B., Dunnum, J. L., Ferguson, A. W., Anwarali Khan, F. A., Paul, D. L., Reeder, D. M., Simmons, N. B., Thiers, B. M., Thompson, C. W., Upham, N. S., Vanhove, M. P. M., Webala, P. W., Weksler, M., Yanagihara, R., Soltis, P. S. Integrating biodiversity infrastructure into pathogen discovery and mitigation of epidemic infectious diseases. BioScience. Press: The Conversation.


Our Mammalia-wide phylogeny made the cover of the Dec 2019 issue of PLOS Biology.
2019. @Upham, N. S., Esselstyn, J. A., Jetz, W. Inferring the mammal tree: species-level sets of phylogenies for questions in ecology, evolution, and conservation. PLOS Biology. 17(12): e3000494. Cover art. Data:, Github, Dryad. Press: Cosmos, ScienceDaily, Attention on Twitter.

2019. McDonough, M. M., Upham, N. S., and Ferguson, A. W. Nurturing the generations: the role of the American Society of Mammalogists in supporting students and early career scientists. Journal of Mammalogy 100: 690-700.

2019. Maestri, R., Upham, N. S., and Patterson B.D. Tracing the diversification history of a Neogene rodent invasion into South America. Ecography 42: 683-695.


2018. *Burgin, C. J., *Colella, J. P., and @Upham, N. S. How many species of mammals are there? Journal of Mammalogy. 99: 1-14. Press: IFLscience, International Business Times,, EurekAlert!, Teinteresa (Madrid).


2017. (alphabetical) *Cooke, S. B. *Dávalos, L. M., *Mychajliw, A. M., *Turvey, S. T., and *Upham, N. S. Anthropogenic extinction dominates Holocene declines of West Indian mammals. Annual Review of Ecology, Evolution, and Systematics. 48: 301-327. Press: Newsweek, Nature E&E Blog, New Scientist, LiveScience, Lab Manager,

This photo of Solenodon paradoxus I took near Punta Cana, DR in 2015 made the cover of our Aug 2017 Special Feature on Caribbean mammals.
2017. @Upham, N. S. and Borroto-Páez, R. Molecular phylogeography of endangered Cuban hutias within the Caribbean radiation of capromyid rodents. Journal of Mammalogy 98: 950-963.

2017. @Upham, N. S. Past and present of insular Caribbean mammals: understanding Holocene extinctions to inform modern biodiversity conservation. Journal of Mammalogy 98: 913-917.

2017. @Lim, B. K., Loureiro, L. O., Upham, N. S., and Brocca, J. L. Phylogeography of Dominican Republic bats and systematic relationships in Neotropics. Journal of Mammalogy 98: 986-993.

2017. @Evans, B. J., @Upham, N. S., Golding, G. B., Ojeda, R. A., and Ojeda, A. A. Evolution of the largest mammalian genome. Genome Biology and Evolution 9: 1711-1724. Press: ScienceDaily, CBC Radio, The Molecular Ecologist.

2017. @Maestri, R., Monteiro, L. R., Fornel, R., Upham, N. S., Patterson B.D., and Freitas, T.R.O. The ecology of a continental evolutionary radiation: Is the radiation of sigmodontine rodents adaptive? Evolution 71: 610-632. Press: Evolution Digest.

2017. @Fabre, P.-H., Upham, N. S., Emmons, L. H., Justy, F., Leite, Y. L. R., Loss, A. C., Orlando, L., Tilak, M.-K., Patterson, B. D., and Douzery, E. J. P. Mitogenomic phylogeny, diversification, and biogeography of South American spiny rats. Molecular Biology and Evolution 34: 613–633.


2016. Lacher, T. E., Murphy, W. J., Rogan, J., Smith, A. T., and Upham, N. S. Evolution, phylogeny, ecology, and conservation of the clade Glires: Lagomorpha and Rodentia. Pp. 15-26 In: Handbook of the Mammals of the World: Volume 6. Lagomorphs and Rodents I. (D. E. Wilson, T.E. Lacher, Jr., and R. A. Mittermeier, eds.). Lynx Ediciones, Barcelona.


2015. @Upham, N. S. and @Patterson, B.D. Evolution of caviomorph rodents: a complete phylogeny and timetree for living genera. Pp. 63-120 In: Biology of caviomorph rodents: diversity and evolution (A.I. Vassallo and D. Antenucci, eds.). SAREM Series A, Buenos Aires, Argentina.

2015. @D’Elía, G., Teta, P., Upham, N. S., Patterson, B. D., and Pardiñas, U. F. J. Description of a new soft-haired mouse, genus Abrothrix (Sigmodontinae), from the temperate Valdivian rainforest. Journal of Mammalogy 96: 839-853. Press: Diario Austral.


2014. @Patterson, B. D. and Upham, N. S. A newly recognized family of mammals from the Horn of Africa, the Heterocephalidae (Rodentia: Ctenohystrica). Zoological Journal of the Linnean Society 172: 942-963.

2014. @Patterson, B. D. and Upham, N. S. A study in contrasts: two extensive Neotropical radiations. Frontiers in Ecology and Evolution 2: 44.


2013. Upham, N. S., Ojala-Barbour, R., Brito, J., Velazco, P. M., and @Patterson, B. D. Transitions between Andean and Amazonian centers of endemism in the radiation of some arboreal rodents. BMC Evolutionary Biology 13:191. Highly accessed article (6000+ views). Featured on my graduate program website.

2013. @Upham, N. S., and J. C. Hafner. Do nocturnal rodents in the Great Basin Desert avoid moonlight?. Journal of Mammalogy. 94: 59-72. Press: ScienceLife blog.


2012. @Upham, N. S. and B. D. Patterson. Diversification and biogeography of the Neotropical caviomorph lineage Octodontoidea (Rodentia: Hystricognathi). Molecular Phylogenetics and Evolution 63: 417-429.

2012. @Light, J. E., Hafner, J. C., Upham, N. S., and Reddington, E. Conservation genetics of kangaroo mice, genus Microdipodops. Journal of Mammalian Evolution 20: 129-146.


2011. @Hafner, J. C., and Upham, N. S.. Phylogeography of the dark kangaroo mouse, Microdipodops megacephalus: cryptic lineages and dispersal routes in North America’s Great Basin. Journal of Biogeography 38: 1077-1097.


2008. @Hafner, J. C., Upham, N. S., Reddington, E. and Torres, C. W. Phylogeography of the pallid kangaroo mouse, Microdipodops pallidus: a sand-obligate endemic of the Great Basin, western North America. Journal of Biogeography 35: 2102-2118.


2020. Burgin, C. J., Widness, J., and Upham, N. S. Introduction. Pp. 23-40 In: Illustrated Checklist of the Mammals of the World (C. J. Burgin, D. E. Wilson, R. A. Mittermeier, A. B. Rylands, T. E. Lacher, and W. Sechrest, eds.). Lynx Ediciones, Barcelona.

2020. Dávalos, L. M., and Upham, N. S. Coronavirus was low risk until it wasn’t. Climate change is the same. Medium, 27 Mar 2020.

2017. Ceríaco, L. M. et al. and 490 signatories (incl Upham, N. S.) Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences. Zootaxa 4196: 435-445.

2016. @Pérez, M. E., and @Upham, N. S. [Review] Mammals of South America, Volume 2: Rodents. Ameghiniana 53: 523-525.

2014. Upham, N. S. At the edge of what we know. The Human Geographic, issue 1 (online multi-media magazine, popular article on vizcacha rat fieldwork in Argentina).


2020. Poelen J, Upham N. S., Agosti D, Ruschel T, Guidoti M, Reeder D, et al. CETAF-DiSCCo/COVID19-TAF biodiversity-related knowledge hub working group: indexed biotic interactions and review summary. Zenodo.

2020. Mast A.R., Paul D.L., Rios N., Krimmel E.R., Bruhn R., Shorthouse D.P., Simmons N.B., Upham N.S., Soltis P. 2020. Rapid Creation of a Data Product for the World’s Specimens of Horseshoe Bats and Relatives, a Known Reservoir for Coronaviruses. Zenodo.

2020. Upham, N. S. Natural history specimens collected and/or identified and deposited. [Data set]. Zenodo.


2014. Upham, N. S. Ecological diversification and biogeography in the Neogene: Evolution of a major lineage of American and Caribbean rodents (Caviomorpha, Octodontoidea). Unpubl. Ph.D. dissertation, University of Chicago, xvi + 272 pp. Abstract published in Mastozoología Neotropical 21: 193-194.

2008. Upham, N. S. Rodent activity in relation to moonlight in sandy and open habitats of the Great Basin Desert. Unpubl. M.A. thesis, Occidental College, viii + 65 pp.

2006. Upham, N. S. Phylogeography of the dark kangaroo mouse, Microdipodops megacephalus. B.A. thesis, Occidental College, 35 pp.


Stewart, T. A., Yoo, I., and Upham, N. S. The coevolution of mammae number and litter size: testing the one-half rule.

Upham, N. S. and Patterson, B. D. Testing for adaptively radiating clades in a major lineage of rodents.