Jonathan Pauli

Jon Pauli

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Associate Professor

221 Russell Labs
1630 Linden Drive
Madison, WI 53706
Phone:  (608) 890-0285

Lab Website


Wildlife ecology



Degree Institution Major Field Granted
B.S. University of Wisconsin – Stevens Point Wildlife & Biology 2002
M.S. University of Wyoming Zoology & Physiology 2005
Ph.D. University of Wyoming Ecology 2010


Courses Taught


I enjoy actively involving and educating developing scientists in wildlife ecology and biology. My teaching approach integrates hands on experiences in the field and laboratory with interactive lectures and readings from peer-reviewed literature. I currently instruct two courses on campus: 1) Wildlife Techniques (FWE 561) and 2) the ecology section of General Biology (BIO 152).

Wildlife Techniques is an advanced undergraduate course for wildlife majors that surveys of the techniques and methodologies that wildlife biologists use to conduct research, and make management decisions. The course is organized with a week-by-week approach, highlighting both traditional and “cutting-edge” techniques used to study free-ranging animal populations. An emphasis is placed on pairing hands-on activities in the field with data organization and summary in the laboratory. For me, it has been an honor helping to carry our department’s long tradition of instructing Wildlife Techniques, a course that was originally offered by Aldo Leopold in the 1940s. For more information on our course project at the UW Lakeshore Nature preserve, click here

General Biology (Ecology Section) is a large (300+ students per section) introductory course for biology majors. I instruct the Ecology section of the course. Although the vast majority of students enrolled in General Biology are not interested in an “ecology track”, I’m always delighted to see undergraduates sorting through the various biology discipline awakened to how fascinating ecological systems are — I’m particularly enthused when some of those students end up pursuing an ecology-related major on campus.

Photos: Left: Aldo Leopold instructing a wildlife class, 1943 Right: Agricultural Hall Lecture Hall, Bryce Richter, UW-Madison © Board of Regents of the University of Wisconsin System  


Selected Publications

Google Scholar Profile


Publications since 2015

Shipley, A.A, M.J. Sheriff, J.N. Pauli, and B. Zuckerberg. Weather and land cover create a predictable “stress-scape” for a winter-adapted bird. Landscape Ecology.

Sultaire, S.M., J.M. Humphreys, B. Zuckerberg, J.N. Pauli and G.J. Roloff. in press. Spatial variation in bioclimatic relationships for a snow-adapted species along a discontinuous southern range boundary. Journal of Biogeography.

Rodriguez Curras, M., E. Donadio, A.D. Middleton, and J.N. Pauli. in press. Perceived risk structures the space use of competing carnivores. Behavioral Ecology.

Smith, M.M., J.H. Gilbert, E.R. Olson, K.T. Scribner, T.R. Van Deelen, J.F. Van Stappen, B.W. Williams, J.E. Woodford, and J.N. Pauli. in press. A recovery network leads to the natural recolonization of an archipelago and a potential trailing edge refuge. Ecological Applications.

Smith, G.B., J.M. Tucker, and J.N. Pauli. in press. Habitat and drought influence the diet of an unexpected mycophagist: fishers in the Sierra Nevada, California. Journal of Mammalogy.

Scott, A.M., J.H. Gilbert, and J.N. Pauli. in press. Small mammal dynamics in snow-covered forests. Journal of Mammalogy.

Gudex-Cross, D., S.R. Keyser, B. Zuckerberg, D. Fink, L. Zhu, J.N. Pauli, and V.C. Radeloff. 2021. Winter Habitat Indices (WHIs) for the contiguous US and their relationship with winter bird diversity. Remote Sensing of Environment 255:112309.

Perrig, P.L., S.A. Lambertucci, P.A.E. Alarcón, A.D. Middleton, J. Padró, P.I. Plaza, G. Blanco, J.A. Sánchez-Zapata, J.A. Donázar and J.N. Pauli. in press. Limited sexual segregation in a dimorphic avian scavenger, the Andean condor. Oecologia.

Pauli, J.N. and M. Egerstedt. 2021. Robot ecology: An inspiration for future ecologists. BioScience.

Martin, M.E., K.M. Moriarty, and J.N. Pauliin press. Scale and season influence resource selection of a snow-adapted forest carnivore, the Pacific marten. Landscape Ecology.

Padro, J., P.L. Perrig, S.A. Lambertucci, J.N. Pauli. in press. Andean and California condors possess dissimilar genetic composition but exhibit similar demographic histories. Ecology and Evolution.

Manlick, P.J. and J.N. Pauli. 2020Human disturbance increases trophic niche overlap in terrestrial carnivore communities. Proceedings of the National Academy of Sciences 117(43): 26842-26848.

Bougie T.A., N.W. Byer, C.N. Lapin, M.Z. Peery, J.E. Woodford, J.N. Pauli. 2020. Wood turtle (Glyptemys insculpta) nest protection reduces depredation and increases success, but annual variation influences its effectiveness. Canadian Journal of Zoology 98(11).

Thompson, K.L., B. Zuckerberg, W.P. Porter and J.N. Pauli. in press. The decline of a hidden and expansive microhabitat: the subnivium. Frontiers in Ecology and the Environment.

Fitzpatrick, M.J., W.P. Porter, J.N. Pauli, M.R. Kearney, M. Notaro, B. Zuckerberg. 2020Future winters present a complex energetic landscape of decreased costs and reduced risk for a freeze-tolerant amphibian, the wood frog (Lithobates sylvaticus). Global Change Biology 26(11): 6350-6362.

Wilson, E.C., B. Zuckerberg, M.Z. Peery and J.N. Pauli. 2020. The past, present and future impacts of climate and land use change on snowshoe hares along their southern range boundary. Biological Conservation 249: 108731.

Smith, J.A., E. Donadio, O.R. Bidder, J.N. Pauli, M.J. Sheriff, P.L. Perrig, and A.D. Middleton. 2020. Where and when to hunt? Decomposing predation success of an ambush carnivore. Ecology: e03172.

Silverthorne, K.M., P.L. Perrig, S.A. Lambertucci, and J.N. Pauliin press. Isotopic niche partitioning in avian scavenger communities of South America. Journal of Raptor Research.

Manlick, P.J., S.K. Windels, J.E. Woodford, and J.N. Pauli. 2020. Can landscape heterogeneity promote carnivore coexistence in human-dominated landscapes? Landscape Ecology 35: 2013-2027.

Perrig, P.L., S.A. Lambertucci, J. Cruz, P.A.E. Alarcon, PI. Plaza, A.D. Middleton, G. Blanco, J.A. Sanchez-Zapata, J. A. Donazar, J.N. Pauli. 2020.  Identifying conservation priority areas for the Andean condor in southern South America. Biological Conservation 243: 108494.

Parsons, M.A., J.C. Lewis, J.N. Pauli, T. Chestnut, J.I. Ransom, D.O. Werntz, and L.R. Prugh. 2020. Prey of reintroduced fishers and their habitat relationships in the Cascades Range, Washington. Forest Ecology and Management 460: 117888.

Martin, M.E., K.M. Moriarty, and J.N. Pauli. 2020. Forest structure and snow depth alter the movement patterns and subsequent expenditures of a forest carnivore, the Pacific marten. Oikos 129: 356-366.

Pauli, J.N., P.J. Manlick, P.S. Dharampal, Y. Takizawa, Y. Chikaraishi, L.J. Niccolai, J.A. Grauer, K.L. Black, M. Garces Restrepo, P.L. Perrig, E.C. Wilson, M.E. Martin, M. Rodriguez Curras, T.A. Bougie, K.L. Thompson, M.M. Smith, and S.A. Steffan. 2019. Quantifying niche partitioning and multichannel feeding among tree squirrels. Food Webs 21: e00124.

Gigliotti, L.C., N.D. Berg, R. Boonstra, S.M. Cleveland, D.R. Diefenbach, E.M. Gese, J.S. Ivan, K. Kielland, C.J. Krebs, A.V. Kumar, L.S. Mills, J.N. Pauli, B. Underwood, E.C. Wilson, and M.J. Sheriff. 2019. Latitudinal variation in snowshoe hare (Lepus americanus) body mass: A test of Bergmann’s Rule. Canadian Journal of Zoology 98(2): 88-95.

Kelt, D.A., E.J. Heske, S.Sommer, Arpat Ozgul, J.L. Orrock, L. Prugh, J.N. Pauli, X. Lambin, M.K. Oli, and R. Sollmann. 2019. Advances in population ecology and species interactions in mammals. Journal of Mammalogy 100: 965-1007.

Perrig, P.L., E.D. Fountain, S.A. Lambertucci, and J.N. Pauli. 2019. Demography of avian scavengers after Pleistocene megafaunal extinction. Scientific Reports 9: 9680.

Padro, J., J.N. Pauli, P.L. Perrig, and S.A. Lambertucci. 2019. Genetic consequences of social dynamics in the Andean condor: the role of sex and age. Behavioral Ecology and Sociobiology 73:100.

Fitzpatrick, M.J., B. Zuckerberg, J.N. Pauli, M.R. Kearney, K.L. Thompson, L.C. Werner, W.P. Porter. 2019. Modeling the distribution of niche space and risk for a freeze-tolerant ectotherm, Lithobates sylvaticus. Ecosphere 10: e02788.

Demeny, K., M. McLoon, B. Winesett, J. Fastner, E. Hammerer, and J.N. Pauli. 2019. Food subsidies of Raccoons in anthropogenic landscapes. Canadian Journal of Zoology 97: 654-657. **Authors were undergraduates enrolled in Wildlife Capstone (FWE 599)**

Shipley, A.A., M.J. Sheriff, J.N.Pauli, and B. Zuckerberg. 2019. Snow roosting reduces temperature-associated stress in a wintering bird. Oecologia 190: 309–321.

Savage, A.R., P.J. Manlick, M.C. Romanski, and J.N. Pauli. 2019. A reclassification of red squirrels, Tamiasciurus hudsonicus (Rodentia: Sciuridae), on Isle Royale. Biological Journal of the Linnaean Society 127: 213-223.

Smith, J.A., E. Donadio, J.N. Pauli, M.J. Sheriff, and A.D. Middleton. 2019. Habitat complexity mediates the predator-prey space race. Ecology 100: e02724.

Smith, J.A., E. Donadio, J.N. Pauli, M.J. Sheriff, and A.D. Middleton. 2019. Integreating temporal refugia in landscapes of fear: Prey exploit predator downtimes to forage in risky places. Oecologia 189: 883–890.

Perrig, P.L., S.A. Lambertucci, E. Donadio, J. Padro, and J.N. Pauli. 2019. Monitoring vultures in the 21st century: the need for standardized protocols. Journal of Applied Ecology 4: 796-801.

Kirby, R., H.E. Johnson, M.W. Alldredge, J.N. Pauli2019. The cascading effects of human food on hibernation and cellular aging in free-ranging black bears. Scientific Reports 9: 2197.

Grauer, J.A., J.H. Gilbert, J.E. Woodford, D. Eklund, S. Anderson, and J.N. Pauli. 2019. Modest immigration can rescue a reintroduced carnivore population. Journal of Wildlife Management 83: 567-576.

Manlick, P.J., S. Petersen, K.M. Moriarty, and J.N. Pauli. 2018. Stable isotopes reveal limited Eltonian niche conservatism across carnivore populations. Functional Ecology 33: 335-345.

Wilson, E.C., A.A. Shipley, B. Zuckerberg, M.Z. Peery and J.N. Pauli. 2018. An experimental translocation identifies habitat features that buffer camouflage mismatch in snowshoe hares. Conservation Letters.

Garces-Restrepo, M., M.Z. Peery, and J.N. Pauli. 2018. The demography of a resource specialist in the tropics: Cecropia trees and the fitness of three-toed sloths. Proceedings of the Royal Society B 286: 1-9.

Egerstedt, M., J.N. Pauli, G. Notomista, and S. Hutchinson. 2018. Robot ecology: constraint-based control design for long duration autonomy. Annual Reviews in Control 46: 1-7.

Larson, R.C., R. Kirby, N. Kryshak, M. Alldredge, D.B. McDonald, and J.N. Pauli. 2018. The genetic structure of American black bears populations in the southern Rocky Mountains. Intermountain Journal of Sciences 24: 1-6.

Manlick, P.J., M. Romanski, and J.N. Pauli. 2018. Dynamic colonization history in a rediscovered Isle Royale carnivore. Scientific Reports 8: 12711.

Black, K.L., S.K. Petty, V. Radeloff, and J.N. Pauli. 2018. The Great Lakes Region is a melting pot for vicariant red fox (Vulpes vulpes) populations. Journal of Mammology 99: 1229-1236.

Thompson, K.L., B. Zuckerberg, W.P. Porter, and J.N. Pauli. 2018. The phenology of the subnivium. Environmental Research Letters 13: 064037.

Padro, J., S.A. Lambertucci, P.L. Perrig, and J.N. Pauli. 2018. Evidence of genetic structure in a wide-ranging and highly mobile soaring scavenger, the Andean condor. Diversity and Distributions 24: 1534-1544.

Pauli, J.N., E. Donadio, and S.A. Lambertucci. 2018. The corrupted carnivore: how humans are rearranging the return of the carnivore-scavenger relationship. Ecology 99: 2122-2124.

Zuckerberg, B. and J.N. Pauli. 2018. Conserving and managing the subnivium. Conservation Biology 32: 774-781.

Garces-Restrepo, M.J.N. Pauli, and M.Z. Peery. 2018. Natal dispersal of tree sloths in a human-dominated landscape: Implications for tropical biodiversity conservation. Journal of Applied Ecology 55: 2253-2262.

Kirby, R.C. Freeh, J.H. Gilbert, J.F. Olson, J.N. Pauli. 2018. Poor body condition and diet diversity in a harvested population of fishers. Wildlife Biology 2018, wlb-00334.

Fountain, E.D., J.N. Pauli, P.J. Palsboll, J. Kang, D.J. Tempel, M.Z. Peery. 2018. Genomics meets applied ecology: Characterizing habitat quality for sloths in a tropical agro-ecosystem. Molecular Ecology 27: 41-53.

Grauer, J., J.H. Gilbert, J.E. Woodford, D. Eklund, S. Anderson, J.N. Pauli. 2017. Unexpected genetic composition of a reintroduced carnivore population. Biological Conservation 215: 246-253.

Pauli, J.N. 2017. Island Hopping Leads to Unforeseen Connections: The Arising Researcher. The Bulletin of the Ecological Society of America 98: 195-196.

Garces-Restrepo, M.F., M.Z. Peery, B. Reid, J.N. Pauli. 2017. Individual reproductive strategies shape the mating system of tree sloths. Journal of Mammalogy 98:1417-1425.

Kirby, R., D.M. MacFarland, J.N. Pauli. 2017. Consumption of intentional food subsidies by a hunted carnivore. Journal of Wildlife Management 81: 1161-1169.

Manlick, P.J., J.E. Woodford, B. Zuckerberg, and J.N. Pauli. 2017. Niche compression intensifies competition between reintroduced American martens (Martes americana) and fishers (Pekania pennanti). Journal of Mammalogy 98: 690-702.

Kirby, R., M.W. Alldredge, J.N. Pauli. 2017. Environmental, not individual, factors drive markers of biological aging in black bears. Evolutionary Ecology.

Fountain, E.D., J.N. Pauli, J.E. Mendoza, J. Carlson and M.Z. Peery. 2017. Cophylogenetics and biogeography reveal a coevolved relationship between sloths and their symbiont algae. Molecular Phylogenetics and Evolution 110: 73-80.

Pauli, J.N., S.D. Newsome, J.A. Cook, C. Harrod, S.A. Steffan, C.J.O. Baker, M. Ben-David, D. Bloom, G.J. Bowen, T.E. Cerling, C. Cicero, C. Cook, M. Dohm, P.S. Dharampal, G. Graves, R. Gropp, K.A. Hobson, C. Jordan, B. MacFadden, S. Pilaar Birch, J. Poelen, S. Ratnasighnam, L. Russell, C.A. Stricker, M.D. Uhen, C.T. Yarnes, and B. Hayden. 2017. Why we need a centralized repository for isotopic data. Proceedings of the National Academy of Sciences 114: 2997-3001.

Steffan, S.S., Y. Chikaraishi, P. Dharampal, J.N. Pauli, C. Guédot, H. Ohkouchi. 2017. Unpacking brown food-webs: Animal trophic identity reflects rampant microbivory. Ecology and Evolution 7: 3535-3541.

Pauli, J.N., C.C. Carey, M.Z. Peery. 2017. Green sloths and brown cows: the role of dominant vertebrate herbivores in carbon emissions for tropical agro-ecosystems. Mammal Review 47:164-168.

Moss, W.M., M.W. Alldredge, K. Logan, and J.N. Pauli. 2016. Human expansion precipitates niche expansion for an opportunistic apex predator (Puma concolor). Scientific Reports 6: 39639.

Perrig, P.L., E. Donadio, A.D. Middleton, and J.N. Pauli. 2016. Puma predation subsidizes an obligate scavenger in the high Andes. Journal of Applied Ecology 54: 846-853.

Kirby, R., M.W. Alldredge, J.N. Pauli. 2016. The diet of black bears tracks the human footprint across a rapidly developing landscape. Biological Conservation 200: 51-59.

Manlick, P.J., J.E. Woodford, J.H. Gilbert, D. Eklund, J.N. Pauli. 2016. Augmentation provides nominal genetic and demographic rescue for an endangered carnivore. Conservation Letters 10: 178-185.

Sultaire, S.M., J.N. Pauli, K.J. Martin, M.W. Meyer, and B. Zuckerberg. 2016. Extensive forests and persistent snow cover promote snowshoe hare occupancy in Wisconsin. Journal of Wildlife Management 80: 894-905.

Pauli, J.N., M.Z. Peery, E.D. Fountain, W.H. Karasov. 2016. Arboreal folivores limit their energetic output, all the way to slothfulness. American Naturalist 188: 196-204.

Sultaire, S., J.N. Pauli, K. Martin, M. Meyer, M. Notaro, and B. Zuckerberg. 2016. Climate change surpasses land use change in the contracting range boundary of a winter-adapted mammal. Proceedings of the Royal Society B 283.

Fountain, E.D., J.N.Pauli, B.N. Reid, P.J. Palsbøll, and M.Z. Peery. 2016. Finding the right coverage: The impact of coverage and sequence quality on SNP genotyping error rates. Molecular Ecology Resources 16: 966-978.

Pokallus, J.W. and J.N. Pauli. 2016. Predation shapes the movement of a well-defended species even when nutritionally stressed. Behavioral Ecology 27:470-475.

Moss, W., M. Alldredge and J.N. Pauli. 2016. Quantifying risk and resource use for a large carnivore (Puma concolor) in an expanding urban-wildland interface. Journal of Applied Ecology 53: 371-378.

Dill-McFarland K.A., P.J. Weimer, M.Z. Peery, J.N. Pauli and G. Suen. 2016. Diet specialization selects for an unusual and simplified gut microbiota in two- and three-toed sloths. Environmental Microbiology 18: 1391-1402.

Steffan, S.A., Y. Chikaraishi, C.R. Currie, H. Horn, H.R. Gaines-Day, J.N. Pauli, J.E. Zalapa, and N. Ohkouchi. 2015. Microbes are trophic analogs of animals. Proceedings of the National Academy of Sciences 112:15119 -15124.

Garwood, T., R. Ziobro, K. Keene, A. Waller, and J.N. Pauli. 2015. Diet, habitat use and size of an urban population of coyotes obtained noninvasively. Urban Naturalist 5: 1-8.  **Authors were undergraduates enrolled in Wildlife Capstone (FWE 599)**

Petty, S.K., B. Zuckerberg and J.N. Pauli. 2015. Winter conditions and land cover structure the subnivium, a seasonal refuge beneath the snow. PLOS ONE 10: e0127613.

Pauli, J.N., W.E. Moss, P.J. Manlick, E.D. Fountain, R. Kirby, S.M. Sultaire, P.L. Perrig, J.E. Mendoza, J.W. Pokallus, T.H. Heaton. 2015. Examining the uncertain origin and management role of martens on Prince of Wales Island, Alaska. Conservation Biology 29:1257-1267.

Pauli, J.N., S.A. Steffan and S.D. Newsome. 2015. It is time for IsoBank. Bioscience 65: 229-230.

Pokallus, J.W. and J.N. Pauli. 2015. Population dynamics of a northern-adapted mammal: disentangling the influence of predation and climate change. Ecological Applications 25:1546–1556.

Mendoza, J.E., M.Z. Peery, G.A. Gutiérrez, G. Herrera, and J.N. Pauli. 2015. Resource use by the two-toed sloth (Choloepus hoffmanni) and the three-toed sloth (Bradypus variegatus) differs in a shade-grown agro-ecosystem. Journal of Tropical Ecology 31: 49-55.


See Dr. Jonathan Pauli’s CV for a complete list of publications.