PEER-REVIEWED ARTICLES

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*Co-first authors. ^last/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.

2024

In Press. ^*Hernández Hernández, N.A., ^*Robles Fernández, A.L., and ^Upham, N.S. Environmental suitability throughout the late Quaternary explains population genetic diversity. Ecography.

2024. Bjornson, S., Verbruggen, H., ^Upham, N.S., and ^Steenwyk, J. Reticulate Evolution: Detection and Utility in the Phylogenomics Era. Molecular Phylogenetics and Evolution.

2024. Moura, M.R., Ceron, K., Guedes, J.J.M., Chen-Zhao, R., Sica, Y.V., Hart, J., Dorman, W., Gonzalez-del-Pliego, P., Ranipeta, A., Catenazzi, A.., Werneck, F.P., Toledo, L.F., Upham, N.S., Tonini, J.F.R., Colston, T.J., Guralnick, R., Bowie, R.C.K., Pyron, R.A., Jetz, W. A phylogeny-informed characterisation of global tetrapod traits addresses data gaps and biases. PLOS Biology, 22(7), e3002658. Data and code: Zenodo

2024. Marsh, C.J., Sica, Y.V., ^Upham, N.S., & ^Jetz, W. Response to Arbogast and Kerhoulas [re Marsh et al. 2022]. Journal of Mammalogy, gyae019.

2023

2023. Lund, M.C., Larsen, B.B., Rowsey, D.M., Otto, H.W., Gryseels, S., Kraberger, S., Custer, J.M., Steger, L., Yule, K.M., Harris, R.E., Worobey, M., Doorslaer, K.V., Upham, N.S., & Varsani, A. Using archived and biocollection samples towards deciphering the DNA virus diversity associated with rodent species in the families Cricetidae and Heteromyidae. Virology. 585, 42–60.

2023. Upham, N. S., & Landis, M. J. Genomics expands the mammalverse (free-access link). Science, 380, 358–359. Code: Github | Zenodo

2023. Harding, C., Larsen, B. B., Otto, H. W., Potticary, A. L., Kraberger, S., Custer, J. M., Suazo, C., Upham, N. S., Worobey, M., Van Doorslaer, K., & Varsani, A. Diverse DNA virus genomes identified in fecal samples of Mexican free-tailed bats (Tadarida brasiliensis) captured in Chiricahua Mountains of southeast Arizona (USA). Virology, 580, 98–111.

2023. Michielsen, N. M., Goodman, S. M., Soarimalala, V., Geer, A. A. E. van der, Dávalos, L. M., Saville, G. I., Upham, N.S., & Valente, L. The macroevolutionary impact of recent and imminent mammal extinctions on Madagascar. Nature Communications. Press: Over 200 news stores, including The Guardian and IFLscience.

2022

2022. Harding, C., Larsen, B.B., Gryseels, S., Otto, H.W., Suazo, C., Kraberger, S., Upham, N.S., Worobey, M., Van Doorslaer, K., Varsani, A. Discovery of three cycloviruses in fecal samples of silver-haired bats samples from Arizona (USA). Archives of Virology.

2022. Balk M.A., Deck J., Emery K.F., Walls R.L., Reuter D., LaFrance R., Arroyo-Cabrales J., Barrett P., Blois J., Boileau A., Brenskelle L., Cannarozzi N.R., Cruz J.A., Dávalos L.M., de la Sancha N.U., Gyawali P., Hantak M.M., Hopkins S., Kohli B., King J.N., Koo M.S., Lawing A.M., Machado H., McCrane S.M., McLean B., Morgan M.E., Pilaar Birch S., Reed D., Reitz E.J., Sewnath N., Upham N.S., Villaseñor A., Yohe L., Davis E.B., Guralnick R.P. 2022. A solution to the challenges of interdisciplinary aggregation and use of specimen-level trait data. iScience, 105101.

2022. Prado, L. R., Upham, N.S., Franz, N., & Sterner, B. Extending Recognition for Taxonomic Curation Beyond the Traditional Authorities. Biodiversity Information Science and Standards, 6, e94252.

2022. Upham, N.S., Powell, C., Prado, L., Franz, N., and Sterner, B. Extended Taxonomic Curation: Moving beyond species lists to linking species data. Biodiversity Information Science and Standards, 6, e93670.

2022. Groom, Q., Adriaens, T., Bertolino, S., Phelps, K., Poelen, J., Reeder, D., Richardson, D., Simmons, N., Trekels, M., and Upham, N.S. The Importance of Collecting and Archiving Data on Domestic and Cultivated Organisms. Biodiversity Information Science and Standards, 6, e90864.

2022. Abraham, J., Upham, N.S., Serrano, A.D., Jesmer, B. Evolutionary causes and consequences of ungulate migration. Nature Ecology & Evolution. Data: Dryad. Press: News & Views, NPR Phoenix (KJZZ).

2022. Marsh, C.J., Sica, Y.V., Burgin, C.J., Dorman, W.A.…[142 other authors]…, @Upham, N.S., @Jetz, W. Expert range maps of global mammal distributions harmonised to three taxonomic authorities. Journal of Biogeography.

2022. Munstermann M.J., Heim N.A., McCauley D.J., Payne J.L., Upham N.S., Wang S.C., Knope M.L. A global ecological signal of extinction risk in terrestrial vertebrates. Conservation Biology. 36:3 e13852.

2021

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

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.

2019

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: Vertlife.org, Github, Dryad. Press: Cosmos, ScienceDaily, Phys.org. 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

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, Phys.org, EurekAlert!, Teinteresa (Madrid).

2017

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, Phys.org.

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

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

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

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

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

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

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

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.

NON-REFEREED PUBLICATIONS

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).

DATA PAPERS

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. http://doi.org/10.5281/zenodo.3839098

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. https://doi.org/10.5281/zenodo.4047200

2020. Upham, N. S. Natural history specimens collected and/or identified and deposited. [Data set]. Zenodo. https://doi.org/10.5281/zenodo.3858103

THESES

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.

MANUSCRIPTS IN PREP

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.