Nathan Upham

Assistant Professor,

School of Life Sciences

Other ASU affiliations

Evolutionary Biology (PhD) program

Senior Global Futures Scientist, Global Futures Scientists and Scholars

Walton Center for Planetary Health 777 E University Dr Tempe, AZ 85281
Mail code: 4501

Campus: Tempe
‌

Long Bio

Nate Upham is an ecologist and evolutionary biologist with core interests in how species-species, species-environment, and species-pathogen interactions have evolved through time and across the tree of life. He studies wild mammals, especially desert rodents, to ask how new species are formed (speciation), how they die out (extinction), and how they interact to share pathogens (disease ecology) and generate biodiversity (ecological diversification). He integrates approaches in field mammalogy, paleontology, phylogenomics, network theory, and bioinformatics to query the ecological origins of evolutionary dynamics in the mammal tree of life.

Upham received his doctorate from The University of Chicago’s Committee on Evolutionary Biology in 2014, studying the molecular and fossil relationships of Neotropical caviomorph rodents. He then did a short postdoc at McMaster University studying the largest mammalian genome (Tympanoctomys vizcacha rats in Argentina). In 2015, he moved to Yale University as a postdoc on the VertLife Terrestrial project where he led construction of a comprehensive new tree of life for ~6,000 species of mammals. In 2020, he joined the Biodiversity Knowledge Integration Center (BioKIC) in ASU's School of Life Sciences as an assistant research professor. In 2022, he was hired to a tenure-track position as an assistant professor in SOLS, with lab space in the newly constructed Walton Center for Planetary Health. He has been funded by the National Institutes of Health to study the evidence underlying mammal-to-virus interactions globally, and has initiated work on rodent and viral population genomics in Arizona's Madrean sky island region.

As a faculty member, Upham has promoted opportunities to underrepresented students in his own lab, and by assisting with ASU's Biocollections Scholar Program (2021-2022) and the March Mammal Madness competition (Genetics Team, 2022-present). Prior to coming to ASU, he was a mentor in Chicago Public Schools and performed outreach to K-12 students at the Field Museum and in the communities surrounding McMaster and Yale Universities, aiming to open more doors to organismal biology careers.

Education

Ph.D. Evolutionary Biology, University of Chicago, Chicago, IL. 2014
M.S. Evolutionary Biology, University of Chicago, 2010
M.A. Biology, Occidental College, Los Angeles, CA., 2008
B.A. Biology , Occidental College, 2006

Curriculum Vitae

Images

Mammal tree of life

Mammal Diversity Database

Host-pathogen knowledge graphs

Research Website URL

https://n8u.org/

Google Scholar URL

https://scholar.google.com/citations?hl=en&user=zIn4NoUAAAAJ&view_op=list_works…

Research Interests

I study evolution, ecology, and biodiversity from a spatial and temporal perspective, integrating data from molecules (DNA), fossils, and species traits to investigate when and where groups of species originated, at what evolutionary rates, and in relation to which paleo-environmental factors. My research is centered on mammalian evolution and has focused on unique lineages of rats and mice in the tropical Americas (spiny rats, hutias, and relatives), deserts of North and South America (kangaroo mice and vizcacha rats), and most recently across global Mammalia.

Through fieldwork and genomic and phylogenetic approaches, I ask questions that aim to uncover core dynamics of the eco-evolutionary process at biogeographic and population genetic scales. I also seek to translate our findings to wide audiences through diversity & inclusion efforts and by teaching courses, always with the aim to encourage biodiversity conservation in the tropical and arid ecosystems where I work.

Publications

* = co-first authors; ^ = corresponding

preprint. *Stewart, T. A., Yoo, I., and *Upham, N. S. The coevolution of mammae number and litter size. bioRxiv: https://doi.org/10.1101/2020.10.08.331983 (in review at eLife).

preprint. Upham, N. S., Esselstyn, J. A., and Jetz, W. Ecological causes of speciation and species richness in mammals. BioRxiv: https://doi.org/10.1101/504803 (now split, for Ecol Letters and Current Biology).

Accepted. 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 characterization of global tetrapod traits addresses data gaps and biases. PLOS Biology, https://doi.org/10.1101/2023.03.04.531098v3. 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. https://doi.org/10.1093/jmammal/gyae019

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. https://doi.org/10.1016/j.virol.2023.05.006

2023. ^Upham, N.S., & ^Landis, M.J. Genomics expands the mammalverse. Science, 380, 358–359. https://doi.org/10.1126/science.add2209. Code: Github | Zenodo. Press: ASU | ScienceNews | Nature

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. https://doi.org/10.1016/j.virol.2023.02.004

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. https://doi.org/10.1038/s41467-022-35215-3. Press: Over 200 news stories, including The Guardian, IFLscience.

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. https://doi.org/10.1007/s00705-022-05574-9

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. https://doi.org/10.1016/j.isci.2022.105101

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. https://doi.org/10.3897/biss.6.94252

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. https://doi.org/10.3897/biss.6.93670

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. https://doi.org/10.3897/biss.6.90864

2022. Abraham, J., Upham, N.S., Serrano, A.D., Jesmer, B. Evolutionary causes and consequences of ungulate migration. Nature Ecology & Evolution. https://doi.org/10.1038/s41559-022-01749-4. 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. https://doi.org/10.1111/jbi.14330

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. https://doi.org/10.1111/cobi.13852

2021. Upham N.S., Poelen J.H., Paul D., Groom Q.J., Simmons N.B., Vanhove M.P.M., Bertolino S., Reeder D.M., Bastos-Silveira C., Sen A., Sterner B., Franz N.M., Guidoti M., Penev L., Agosti D. Liberating host–virus knowledge from biological dark data. The Lancet Planetary Health. https://doi.org/10.1016/S2542-5196(21)00196-0

2021. Upham N.S., Esselstyn J.A., Jetz W. Molecules and fossils tell distinct yet complementary stories of mammal diversification. Current Biology. https://doi.org/10.1016/j.cub.2021.07.012

2021. Greenberg D.A., Pyron R.A., Johnson L.G.W., Upham N.S., Jetz W., Mooers A.Ø. Evolutionary legacies in contemporary tetrapod imperilment. Ecology Letters. https://doi.org/10.1111/ele.13868

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. https://doi.org/10.3897/biss.5.75587

2021. Groom Q., Adriaens T., Bertolino S., Phelps K., Poelen J., Reeder D., Richardson D., Simmons N., and Upham N.S. 2021. Holistic understanding of contemporary ecosystems requires integration of data on domesticated, captive and cultivated organisms. Biodiversity Data Journal. 9:e65371. https://doi.org/10.3897/BDJ.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. https://ojs.aaai.org/index.php/AAAI/article/view/17750

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: Biological Sciences. 288: 20202905. https://doi.org/10.1098/rspb.2020.2905

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. Genomic insights into the host specific adaptation of the Pneumocystis genus and emergence of the human pathogen Pneumocystis jirovecii. Communications Biology 4: 1-14. https://doi.org/10.1038/s42003-021-01799-7

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 https://doi.org/10.1007/s40656-021-00366-x

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. https://doi.org/10.5281/zenodo.4270050

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. https://doi.org/10.1111/geb.13198

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. https://doi.org/10.3897/biss.4.59199

2020. Sen A., Franz N., Sterner B., Upham N. S. The Automated Taxonomic Concept Reasoner. Biodiversity Information Science and Standards. 4:e59074. https://doi.org/10.3897/biss.4.59074

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. https://doi.org/10.3897/biss.4.59006

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. https://doi.org/10.3897/biss.4.59234

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 (DOI: 10.1093/biosci/biaa064). Press: The Conversation.

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, Phys.org, 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, Phys.org, 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, Phys.org.

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. Special Feature, including cover image by NSU.

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, Yale Scientific.

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.

(full publications listed here)

Teaching Website URL

https://n8u.org/teaching/

Courses

2024 Fall

Course Number	Course Title
BIO 495	Undergraduate Research

2024 Spring

Course Number	Course Title
BIO 345	Evolution
BIO 495	Undergraduate Research
BIO 345	Evolution
BIO 345	Evolution
BIO 345	Evolution
BIO 345	Evolution
BIO 499	Individualized Instruction

2023 Fall

Course Number	Course Title
BIO 495	Undergraduate Research
BIO 498	Pro-Seminar
BIO 598	Special Topics

2023 Spring

Course Number	Course Title
BIO 345	Evolution
BIO 495	Undergraduate Research

2022 Fall

Course Number	Course Title
BIO 495	Undergraduate Research

2022 Spring

Course Number	Course Title
BIO 495	Undergraduate Research

2021 Fall

Course Number	Course Title
BIO 495	Undergraduate Research

2021 Spring

Course Number	Course Title
BIO 495	Undergraduate Research
BIO 345	Evolution
BIO 345	Evolution
BIO 345	Evolution

Presentations

Invited seminars

2024. University of California, Riverside, Department of Biology Seminar Series: Querying the mammalverse of genomes, ecologies, and species

2023. Proxima Symposium, Iniciativa Proxima Brazilian Foundation, Porto Alegre, Brazil [declined]

2023. University of South Florida, Integrative Biology Seminar Series: Mammal-centric spillover risk modeling: species meaning and ecological context are key

2022. EcoHealth Alliance, EHA Seminar Series: Mammal-centric spillover risk modeling: species meaning and ecological context are key

2022. Swiss Institute for Bioinformatics, SIB Literature Serves group (SIBiLS): Developing a system to predict emerging infectious diseases

2022. Arizona State University, Molecular and Cellular Biology Seminar Series: Evolution of the Largest Mammalian Genome — and other tails/tales.

2022. Museums and Pathogens in the Americas (MEPA): Pathogen spillover from wild mammals to humans: taxonomic and ecological data curation are the key to accurate risk modeling.

2022. University of Oslo, Natural History Museum: Mammal species, evolution, and ecology.

2022. Angelo State University, Department of Biology: Ecology, pathogens, and the mammal tree of life.

2021. Argentine Mammal Society (Jornadas Argentinas de Mastozoología), main talk for the e-JAM.21 event: Mammal species, ecology, and turnover.

2021. McMaster University, Department of Biology: Mammal species, ecology, and turnover.

2021. Brazilian Mammal Society (Sociedade Brasileira de Mastozoologia), keynote for the MOCÓ event: Mammal species, ecology, and turnover.

2021. University of Colorado at Denver, Department of Integrative Biology: Mammal evolutionary past as a key to the ecology of present-day species.

2021. University of Memphis, Department of Biological Sciences, Annual Graduate Student Invited Seminar (BioGSA): Mammal evolutionary past as a key to connecting the ecological present.

2021. Arizona State University, School of Life Sciences, New Faculty Seminar series: Mammal evolutionary past as a key to the ecological present.

2020. TDWG 2020 Virtual Conference. Symposium on “Using Collections to Mitigate and Prevent Zoonotic Disease”: Liberating host-virus data from COVID-19 lockdown.

2020. CETAF-DiSCCo Covid-19 Taskforce public event. Biodiversity knowledge hub for Covid-19 and preventing future pandemics. Link to YouTube-streamed talk (10 minutes).

2020. Yale University, Lab of Ruslan Medzhitov. Mammalian tree of life as an essential tool for comparative biology.

2020. Yale University, Yale Institute for Biospheric Studies (YIBS) seminar series. Ecological causes of uneven mammalian diversity.

2019. Universidade de São Paulo, Departamento de Ecologia. Ecological causes of birth and death in the mammal tree of life.

2019. Yale-CAPES Seminars in Biomedical Sciences, Porto Alegre, Brazil. Mammalian tree of life as an essential tool for comparative biology.

2019. University of Rutgers Newark, Biological Sciences. Ecological causes of speciation and species richness in the mammal tree of life.

2019. Western Connecticut State University, Department of Biological and Environmental Sciences. Why are there so many rodents? And other (r)evolutionary questions.

2019. Smithsonian Institution, National Museum of Natural History. Uniting micro- and macro-evolution in the Mammalia tree of life.

2019. Field Museum of Natural History, A. Watson Armour seminar series. Ecology unites micro- and macro-evolution in the mammal tree of life.

2019. Portland State University, Department of Biology seminar series. Mammalian tree of life and the inverse latitudinal gradient of speciation rates.

2019. Natural History Museum of Los Angeles County, Research & Collections seminar series. Mammalian tree of life from ancient lineages to modern backyards.

2019. Columbia University, E3B Department seminar series. The ecology of species diversification in the mammal tree of life.

Professional Associations

Current Positions

2016-present. Chair, Biodiversity Committee, American Society of Mammalogists.

2023-present. Chair, Ad hoc Digital Publications Committee, American Society of Mammalogists.

2024-present. Deputy Chair for Systematics and Taxonomy, IUCN SSC Small Mammal Specialist Group.

2017-2024. Taxonomy Advisor, IUCN SSC Small Mammal Specialist Group.

2021-present. Member, Global Bat Taxonomy Working Group of the IUCN SSC Bat Specialist Group.

2024-present. Co-Chair, Bat Eco-Interactions Working Group (within the Global Union of Bat Diversity Networks)

Invited Working Groups

2020-present. Bat Eco-Interactions Working Group (part of the Global Union of Bat Diversity Networks, GBatNet), consisting of weekly meetings of biodiversity collections-oriented scientists in the US, Europe, and South America working to liberate bat-related ecological data. Developed from the Consortium of European Taxonomic Facilities-Distributed System of Scientific Collections (CETAF-DiSSCo) COVID-19 Taskforce.

2020-present. Museums and Emerging Pathogens in the Americas (MEPA), group of researchers, policy makers, and advanced students from 9 countries in Central, North, and South America.

2018-present. North American Rodents Landscapes Ecology & Evolution (NARLEE) Working Group, adding rodent evolution expertise to 30-person RCN of geologists, modelers, biologists.

2020. ViralMuse Taskforce, group for multi-disciplinary conversation about linking natural history collections with public health efforts, especially regarding host-pathogen relationships.

2017. State of the Tree of Life (SoToL) Working Group, invited to represent Mammalia in 40-person group spanning microbes, sponges, fungi, plants, and animals.

Society Memberships and Service

American Society of Mammalogists, ASM (2005-present)

Board of Directors (2014-2017)

Conservation Committee (2012-present)

Biodiversity Committee (2016-present)

Systematic Collections Committee (2011-present)

American Society of Naturalists (2013-present)

American Association for the Advancement of Science, AAAS (2006-2010, 2017-present)

Society of Systematic Biologists, SSB (2009-2011, 2013, 2017-present)

Canadian Society for Ecology and Evolution (2014-2015)

European Society for Evolutionary Biology (2013)

Sociedad Argentina para el Estudio de los Mamíferos, SAREM (2012-2014)