Nathan Upham

ASU Natural History Collections
734 W Alameda Dr
Tempe
Asst Research Professor
Faculty
TEMPE Campus
Mailcode
4501

Biography

Nate Upham is an evolutionary biologist with core interests in how species ecologies have diversified 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 with their environment and each other to generate biodiversity (ecological diversification). He integrates approaches in field mammalogy, paleontology, phylogenomics, and bioinformatics to query the ecological origins of evolutionary lineages 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-NEON Biocollections.

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.

Google Scholar

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 outreach 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).

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

Courses

Spring 2021
Course Number Course Title
BIO 345 Evolution
BIO 495 Undergraduate Research

Presentations

Arizona State University

Spring 2021          BIO 345           Evolution

       

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

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 S�o 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.

 

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 Mam�feros, SAREM (2012-2014)

Sociedade Brasileira de Mastozoologia, SBMz (2012-2013)