Emily Fountain

Research Scientist and Genetics Lab Manager

Office Location

University of Wisconsin-Madison

Department of Forest and Wildlife Ecology

1630 Linden Drive

Madison, WI 53706-1598


I am interested in how genetics shape population demographics and adaptability. I currently run the genetics laboratory where our research focuses on how the evolutionary history of a species, as well as more recent environmental changes, influence population structure, dispersal, adaptation and diversity. My research uses genomics to understand historical and recent changes in populations of all three Spotted Owl subspecies (Strix occidentalis subsp.) to assist with conservation efforts. I also use genomics to study the Barred Owl (Strix varia) to understand its success as an invader in the Pacific Northwest leveraging samples from across the Barred Owl’s native range to understand the changes in behavior in the invasive range.

My past research projects have used similar techniques for studying diet in Marbled Murrelets, dispersal in sloths, and climate adaptation in turtles. I am actively working on new methods to understand how species will adapt (or not adapt) to changes in climate, habitat, and novel invaders using epigenetics and gene expression. My work in conservation genomics has led to valuable collaborations regarding the conservation of multiple iconic species. Our genomics laboratory is continually striving to use genomics as a tool helping conserve owls and other species.


Postdoctoral Research Associate | Orang-utan Conservation Genetics Project, 2017-2019

Postdoctoral Research Associate | University of Wisconsin – Madison, 2013-2016

PhD, Evolutionary Biology | Lincoln University, New Zealand, 2013

BS, Biology | University of Missouri- Columbia, 2007

Fountain, E.D., Kulzer, P.J., Golightly, R.T., Rivers, J.W., Pearson, S.F., Raphael, M.G., Betts, M.G., Nelson, S.K., Roby, D.D., Kryshak, N.F., Schneider, S. and Peery, M.Z. (2023). Characterizing the diet of a threatened seabird, the Marbled Murrelet, using high-throughput sequencing. Marine Ornithology.

Banes, G. L., Fountain, E. D., Karklus, A., Fulton, R. S., Antonacci-Fulton, L., and Nelson, J. O. (2022). Nine out of ten samples were mistakenly switched by The Orang-utan Genome Consortium. Scientific data9, 485.

Kryshak, N. F. and Fountain, E. D., Hofstadter, D. F., Dotters, B. P., Roberts, K. N., Wood, C. M., Kelly, K.G., Papraniku, I.F., Kulzer, P.J., Wray, A.K., Kramer, H.A. and Peery, M. Z. (2022). DNA metabarcoding reveals the threat of rapidly expanding barred owl populations to native wildlife in western North America. Biological Conservation, 273, 109678.

Byer, N.W., Fountain, E.D., Reid, B.N., Miller, K., Kulzer, P.J. and Peery, M.Z. (2021). Land use and life history constrain adaptive genetic variation and reduce the capacity for climate change adaptation in turtles. BMC Genomics, 22, 1-16.

Hofstadter, D., Kryshak, N., Gabriel, M., Wood, C., Wengert, G., Dotters, B., Roberts, K., Fountain, E. D., Kelly, K., Keane, J. Whitmore, S., Berrigan, W. and Peery, M. Z. (2021). High rates of anticoagulant rodenticide exposure in California Barred Owls are associated with the wildland–urban interface. Ornithological Applications, 24, duab036.

Smith, V. R., Vink, C. J., Fountain, E. D., Cruickshank, R. H., & Paterson, A. M. (2021). Niche modelling identifies low rainfall, but not soil type, as an important habitat requirement of the fossorial Australasian trapdoor spider genus Cantuaria (Hogg, 1902). Austral Ecology, 46, 1070-1083.

Fountain, E. D., Zhou, L., Liu, Q., Karklus, A., Meyers, J., Fontanilla, I. K. C., Rafael, N., Pei, E., Yu, J., Zhang, Q., Zhu, X., Yuan, Y. and Banes, G. L. (2021) Cross-species application of Illumina iScan microarrays for cost-effective, high-throughput SNP discovery. Frontiers in Ecology and Evolution, 9, 306.

Banes, G. L., Fountain, E. D., Karklus, A., Huang, H-M., Jang-Liaw, N-H., Burgess, D. L., Wendt, J., Moehlenkamp, C. and Mayhew, G. F. (2020). Genomic targets for high-resolution inference of kinship, ancestry and disease-causative genes in orang-utans (Genus: Pongo). BMC Genomics, 21, 1-9.

Perrig, P., Fountain, E. D., Lambertucci, S., and Pauli, J. N. (2019). Scavengers and megafauna extinctions: Demographic expansion of Andean condors despite community reassembly. Scientific Reports, 9, 1-9.

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

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

Wiseman, B. H., Fountain, E. D., Bowie, M. H., He, S., and Cruickshank, R. H. 2016. Vivid molecular divergence over volcanic remnants: The phylogeography of Megadromus guerinii on Banks Peninsula, New Zealand. New Zealand Journal of Zoology 1-12.

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

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

Fountain, E. D., Pugh, A. R., Wiseman, B. H., Smith, V. R., Cruickshank, R. H. and Paterson, A. M. 2015. On the captive rearing of Hadramphus tuberculatus (Pascoe 1877) (Coleoptera: Curculionidae: Molytinae): Is ex-situ conservation the lesser of two weevils? New Zealand Entomologist 1-10.

Pauli, J. N., Moss, W. E., Manlick, P. J., Fountain, E. D., Kirby, R., Sultaire, S. M., Perrig, P. L., Mendoza, J. E., Pokallus, J. W. and Heaton, T. H. 2015. Promoting exotics or protecting endemics? Uncertain histories, differing benchmarks and the case of martens in the Tongass National Forest. Conservation Biology 29:1257-1267.