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Nathan Upham

Asst Research Professor
Faculty, TEMPE Campus, Mailcode 4501
Senior Global Futures Scientist
Faculty, TEMPE Campus, Mailcode 4501
Biography: 

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.

Nate received his Ph.D. 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 post-doc at McMaster University studying the largest mammalian genome (Tympanoctomys vizcacha rats in Argentina). In 2015, he moved to Yale University as a post-doc on the VertLife Terrestrial project where he led construction of a comprehensive new tree of life for ~6,000 species of mammals. In February 2020, he joined the Biodiversity Knowledge Integration Center in ASU's School of Life Sciences where he is an Assistant Research Professor and Associate Curator of Mammals in the ASU Natural History Collections. Since 2021, he is funded by the National Institutes of Health to study the evidence underlying mammal-to-virus interactions globally.

As a faculty member, Nate has promoted opportunities to underrepresented students through ASU's Justice, Equity, Diversity, and Inclusion (JEDI) Biocollections Scholar Program and the JEDI Inclusive Teaching Program. Prior to coming to ASU, his mentorship experiences in Chicago Public Schools, at the Field Museum, and in the communities surrounding McMaster and Yale Universities involved outreach and mentoring to K-12 students to provide supportive models for scientific careers.

Education: 

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

Images
Mammal tree of life

Mammal tree of life

See more info on the data and methods underlying this time-calibrated phylogeny here and read the full paper in PLOS Biology here.
Mammal Diversity Database

Mammal Diversity Database

See the real-time curation of mammal taxonomy here on this open-access database run in partnership with the American Society of Mammalogists.
Host-pathogen knowledge graphs

Host-pathogen knowledge graphs

Much written knowledge is undigitized, forming dark data. Efforts of our group have focused on digitally connecting dark data to form host-virus knowledge graphs.
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).

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)

 

 

Fall 2021
Course NumberCourse Title
BIO 495Undergraduate Research
Spring 2021
Course NumberCourse Title
BIO 345Evolution
BIO 495Undergraduate Research
Presentations: 

Previous: Instructor of record

 

Yale University, Postdoctoral Teaching Scholar, Foundations in Biology: Evolution & Ecology (Fall 2019).

 

Yale University, Scientific Teaching Fellow, Biological Sciences (Spring 2016).

McMaster University, Primary Lecturer, introductory-level class of ~700 students: Biodiversity, Evolution & Humanity, Department of Biology (Fall 2014)

 

Invited seminars

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.

2017-present. Taxonomy Advisor, IUCN Small Mammal Specialist Group.

 

Invited Working Groups

2020-present. Consortium of European Taxonomic Facilities-Distributed System of Scientific Collections (CETAF-DiSSCo) COVID-19 Taskforce, group of biodiversity collections-oriented scientists in the US, Europe, and South America working to liberate host-virus ecological data.

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)

Sociedade Brasileira de Mastozoologia, SBMz (2012-2013)

 

Graduate Faculties / Mentoring History: 

Primary Graduate Advisor

Ángel Luis Robles Fernández (2021-present; co-advised with Nico Franz), Evolutionary Biology PhD program at Arizona State University.

 

Mentoring Undergraduate Students

Arizona State University students (2 ♀), mammal host-virus interactions (2021-present).

Western Connecticut State University student (♂), systematics of rodents (2020-present).

iNaturalist intern & Ursinus College student (♂), taxonomy research on mammals (2019).

Yale University student (♀), biodiversity research for Mammal Diversity Database project (2018).

Yale University student (♀), summer biodiversity research for the Map of Life project (2016).

Loyola University student (♀; at FMNH); summer & honors research on bat phylogenetics (2012).

Cornell University student (♀; at FMNH); summer project on rodent morphometrics (2012).

University of Wisconsin-Madison student (♀; at FMNH); project on rodent life-history traits (2011).

Occidental College student (♀; at MLZ); honors research on kangaroo mice phylogenetics (2006-7).

 

Service: 

K-12 Outreach Experience

New Haven, CT

- Science Fair judge at Worthington Hooker Middle School (2017, 2018).

Hamilton, Canada

- Weekly tutor, Empowerment Squared program for Liberian immigrants (2014-15).

- Weekly tutor, Reading Buddies & Homework Help, Hamilton Public Library (2013-14).

   Chicago, IL

- Program Facilitator, Project Exploration’s “Brothers4Science” program for 6-8th grade boys at Ariel Community Academy (10 weeks, 2012).

- Host for “Talk to the Scientist Hour” programs, Field Museum’s Pritzker Laboratory (2012-13).

- My research on digital touch-screen, Field Museum’s DNA Discovery Center exhibit (2012-13).

- Lecturer on anatomy for Project Exploration’s Junior Paleontologists course (8-12th gr.; 2012).

- Discussed science careers with 7th grade class, Young Women’s Leadership School (2012).

- Lecturer on mammalogy for Project Exploration’s All Girls Expedition course (8-12th gr.; 2011).

- Presented specimens to 7-8th graders, Project Exploration’s Sisters4Science courses (2010-2012).

- Weekly tutoring in 8th grade geometry, Canter Middle School (2010).

- Public presentation of mammal specimens, Field Museum Member’s Nights (2009-12).