I am an ecologist with research interests at the confluence of community ecology, landscape ecology, and ecological restoration. Much of my current work focuses on understanding the effects of global change on ecological communities and informing conservation management decisions, and I am particularly interested in the effects of altered fire regimes on biodiversity.jesse-miller

I am currently a lecturer at Stanford University, where I am teaching inquiry-based ecology courses in collaboration with Tad Fukami. Previously, I spent two years as a postdoctoral researcher at the University of California-Davis, where I studied effects of fire severity and altered fire regimes on plant and lichen communities in Hugh Safford’s lab. I completed my Ph.D. in Ellen Damschen’s lab at the University of Wisconsin-Madison in 2016, where I studied the influence of habitat connectivity, fire history, and soil resource availability on plant community composition and vegetation structure in glades (shallow soil grasslands) in the Ozarks of Arkansas and Missouri.

Before graduate school I worked for several years as a field botanist, surveying for rare plants on federal land and conducting ecological studies for academic research labs. My research today is grounded in the natural history knowledge and skills I began developing earlier in my career.

I have taught ecology, botany, lichenology, and biology classes in several settings over the years. I love teaching, and I particularly enjoy leading field classes and helping people discover plants and lichens and the stories they tell.

I really enjoy communicating and collaborating with other researchers, land managers, field botanists and community members–I encourage you to contact me if we have similar interests!

You can find me on researchgate, google scholar, and twitter.

Contact: jedmiller {a} ucdavis . edu

My 2017-2018 undergrad research assistants at UC Davis, Kyle, Edward and Maaike (from left)









Panel 1


How can we maintain and restore biodiversity in a changing world? My research explores drivers of plant and lichen diversity at multiple scales in both natural and restored  systems.

I use field studies across large geographic areas, often in combination with remote sensing techniques, to examine the relative influences of disturbance, management practices, landscape context, and the local environment on communities. My research is grounded in the natural history knowledge and experience I have gained over many years working as a field botanist and ecologist in several regions of North America.

Currently, I am working in collaboration with the USDA Forest Service’s Regional Ecology Program to analyze interactive effects of fire severity, historical disturbance regimes, and spatial disturbance heterogeneity on post-fire plant and lichen communities in the Sierra Nevada.

I envision my research program as part of a larger movement to broaden conservation management and restoration ecology into a predictive science, where tools are available to help managers use landscape context, site environment, and plant functional traits to guide practices.

Examples of questions that guide my research :


What is the relative importance of landscape and local factors for plant and lichen diversity?

Plant and lichen communities can be influenced by both the local environment and the surrounding landscape, but how does their relative importance vary? I have found that habitat specialist plant species may be more sensitive to habitat spatial structure than generalists. I am currently testing how the size and connectivity of oak savannas influences lichen diversity relative to local environment and biogeographic factors in southern Oregon.

timepoint comparison
This comparison of an Ozark glade landscape in 1939 and 2014 shows that tree cover has increased dramatically.

How do plant and lichen functional traits respond to landscape context and disturbance history? Can functional differences between early successional species and late-successional species be used to inform management and restoration practices?

Functional traits can provide key information about how organisms respond to the environment. For example, dispersal traits may help explain species distributions in fragmented landscapes. Species dispersal traits along with persistence traits may also correspond to   differences between early and late successional plant species, with potentially important implications for ecological restoration. Using functional traits to inform conservation and management practices can potentially strengthen connections between basic and applied ecology. I am developing experimental manipulations of lichen community functional traits to test community assembly processes.

An old-growth soil crust lichen community in central Oregon


Epiphytic lichen community near the area that burned in the Long Fire in El Dorado County, California

When do altered disturbance regimes cause structural shifts in ecosystems, such as woody encroachment in grasslands, or forest conversion to shrublands? How do altered disturbance regimes affect biodiversity?

Wildfire frequency and severity has shifted away from the historical range of variation in many ecosystems. Previously, I have used aerial photo analyses to identify nonlinear patterns of woody encroachment in fire suppressed grasslands. My current work in the Sierra Nevada tests how plant and lichen communities respond to the increasing size of high-severity burn patches in montane forests.

Echinacea paradoxa, an Ozark glade endemic species, blooms in a dolomite glade

What factors shape the abundance, diversity and distributions of biological soil crust lichens?

Soil-dwelling lichens are an important component of biological soil crusts (the living, breathing skin of the earth), and contribute significantly to biodiversity in arid and semi-arid regions. These organisms play important ecological roles, such as preventing wind erosion and the invasion of exotic grasses. They have been little studied, in part because of their cryptic nature, and their distributions and environmental niches are often poorly understood. I have worked on collaborative studies of soil crust lichen communities in sagebrush country of central Oregon as well as the Ozarks.

Panel 2


(Popular / non-technical publications listed below)

Peer-reviewed publications:

Miller, J. E. D., J. Villella, D. Stone, A. Hardman. 2020. Using lichens as indicators of forest age and conservation value. Forest Ecology and Management 475: 118436.  Download PDFSupplemental materials (word doc)lichen conservation index rankings (spreadsheet)

Miller, J. E. D. and H. Safford. 2020. Are plant community responses to wildfire contingent upon historical disturbance regimes? In press, Global Ecology and Biogeography. Download PDF

Safford, H. & J. E. D. Miller. Updated California plant affinities for serpentine soil. 2020. In press, Madroño. Download preprint of accepted ms (PDF)  –  Download species serpentine affinity rankings (spreadsheet)

Kattke, G., G. Bönisch, S. Díaz, S. Lavorel, I. C. Prentice, P. Leadley, S. Tautenhahn, G. D. A. Werner…J. E. D. Miller…et al. (729 authors). 2020. TRY plant trait database – enhanced coverage and open access. Global Change Biology 26(1): 119-188.

Villella, J., J. E. D. Miller, A. Young, G. Carrey, A. Emanuels, and W. Miller. Tardigrades in the canopy: Associations with tree voles nests in southwest Oregon. Northwest Science 94(1): 24-30. Download PDF

Li, D., J. E. D. Miller, and S. Harrison. 2019. Climate drives loss of phylogenetic diversity in a grassland community. Proceedings of the National Academy of Sciences 116(40): 19989-19994. Download PDF

Miller, J. E. D., D. Li, M. Laforgia, and S. Harrison. 2019. Functional diversity is a passenger but not driver of drought-related plant diversity loss. Journal of Ecology, 107(5): 2033-2039. Download PDF – Supplement

Root, H., J. E. D. Miller, and R. Rosentreter. 2019. Grazing disturbance promotes exotic annual grasses by degrading biotic soil crust communities. Ecological Applications 30(1): e02016. Download PDF

Stevens, J., P. Fornwalt, and J. E. D. Miller. 2019. Fire severity and changing composition of understory plants. In press, Journal of Vegetation Science. Download PDF

Richter, C., M. Rejmánek, J.E.D. Miller, J. Weeks, K. Welch, H. Wiggins, and H. Safford. 2019. The local species diversity x fire severity relationship is hump-shaped in semiarid yellow pine and mixed conifer forests. Ecosphere 10(10). Download PDF

Miller, J. E. D., A. Ives, and E. Damschen. 2019. Functional traits and community composition: a comparison among community-weighted means, weighted correlations, and multilevel models. Methods in Ecology and Evolution 10(3): 415-425. Download PDF – Supplement and code

Miller, J. E. D., H. Root, and H. Safford. 2018. Altered fire regimes cause long-term lichen diversity losses. Global Change Biology, 24(10): 4909-4918Download PDF – Supplement

Miller, J. E. D., A. Ives, S. Harrison, and E. Damschen. 2018. Early- and late-flowering guilds respond differently to landscape spatial structure. Journal of Ecology 106(3): 1033-1045. Download PDF

Villella, J., T. Carlberg, D. Stone, J. E. D. Miller, N. Nelson, and L. Calabria. 2018. Diversity and floristic patterns of epiphytic macrolichens on white oak in the Cascade-Siskiyou region of Oregon. Opuscula Philolichenum 17: 299-318. Download PDF

Young, A., J. E. D. Miller, J. Villella, G. Carey, and W. Miller. 2018. Epiphyte type and sampling height impact mesofauna communities in Douglas-fir trees. Peer J 6:e5699.  Download PDF

Miller, J. E. D. and E. Damschen. 2017. Holding the line: Three decades of prescribed fires halt but do not reverse woody encroachment in naturally fragmented grasslands. Landscape Ecology 32(12): 2297-2310Download PDF

Miller, J. E. D.*, P. Hahn*, E. Damschen and J. Brennan**. 2017. Functional dependence underlies a positive plant-grasshopper richness relationship. Basic and Applied Ecology 21: 94-100. (*First two authors contributed equally;  **Mentored undergraduate) Download PDF – Supplemental materials

Miller, J. E. D., J. Villella, G. Carey, T. Carlberg and H. Root. 2017. Canopy distribution and survey detectability of a rare old-growth forest lichen. Forest Ecology and Management 392: 195–201. Download PDF

Miller, J. E. D. and E. Damschen. 2017. Biological soil crust cover is negatively related to vascular plant richness in Ozark sandstone glades. Journal of the Torrey Botanical Society 144(2):170-178. Download PDF

Grover, Shannon**, J. E. D. Miller, and E. Damschen. Indirect effects of landscape spatial structure and plant species richness on pollinator diversity in Ozark glades. Castanea, in press. (**Mentored undergraduate) Download PDF

Petersen, K., L. M. Calabria, J. E. D. Miller, J. Brown-Clay, L. Hynson, T. Steen, K. Johnston, A. Ulbrich, M. Miller and John Villella. 2017. Substrate age influences species richness and succession patterns of calicioid lichens and fungi. The Bryologist 120(1):19-24. Download PDF

Miller, Jesse E. D., Ellen I. Damschen, Susan P. Harrison, and James B. Grace. 2015. Landscape structure affects specialists but not generalists in naturally fragmented grasslands. Ecology 96:3323–3331. Download PDFOnline appendices

Miller, J.E.D., A. Rossman, R. Rosentreter, and J. Ponzetti. 2011. Lichen ecology and diversity of an Oregon sagebrush steppe: 1977 to the present. North American Fungi (6)2:1-15. Download PDF

Root, H.T., J.E.D. Miller, and B. McCune. 2011. Rarity and habitat associations of soil crust lichens. The Bryologist 114(4). Download PDF

Miller, J.E.D., B. McCune, D. Kofranek, J. Villella, R. Demmer, and K. Mergenthaller. 2011. Lichens from the South Slough and Horsfall Dunes on the Southern Oregon coast. Evansia 28(4). Download PDF

Miller, J.E.D. 2011. The Usnea rigida group in California and the Pacific Northwest. Bulletin of the California Lichen Society 18(1&2):3-5. Download PDF

Villella, J., S. Benson, T. Carlberg, J. Miller, R. Patton, and E. Peterson. 2010. The Lichens of the Horseshoe Ranch Wildlife Area. Bulletin of the California Lichen Society 17(1&2):9-12. Download PDF

Please see my CV for publications in preparation and review.

Popular / non-technical publications

Grasshoppers, glades, and ecological gradients. Missouri Prairie Journal, Spring issue 2018.

Fire may help Ozark grasslands (post on the UWMadScience Blog). 2017.

Panel 3

Teaching and outreach


Students in my field botany class investigate a wild peony population in southern Oregon (2010)

I enjoy teaching a range of topics related to ecology, lichenology, botany, science communication, and data analysis and visualization. As an educator, I strive to help all my students think critically, solve problems, and communicate effectively with diverse groups.

I help students develop as independent scientists by emphasizing skills for scientific inference, particularly study design and analysis methods. I also encourage students of ecology to gain inspiration and ideas by spending time observing the natural world.

jespon buildlings
Exploring urban lichen communities on the edge of campus — lichenology workshop for the UC Berkeley Jepson Herbarium (2018)

Taking students in the field is one of my favorite parts of teaching, and I love the unique opportunities for learning that occur hiking along a trail, where examples of connections between plant communities and landscape context are in panoramic abundance.

At Stanford, I designed an inquiry-based course where students learn by conducting ecological research, which I have now taught twice. As a group, we collect data on lichen microbiomes, lichen functional traits, environmental variables, and air pollution patterns in the vicinity of the Stanford campus. Students then develop independent projects using whatever parts of this dataset they find most interesting. Students learn to analyze their data using R, write final papers following the format of the journal Ecology, and make short videos for a general audience to communicate their findings. The course has received excellent student evaluations.

During my time as a postdoc at UC Davis, I designed and taught a three-credit lichenology course with lecture, lab and field components in UCD’s Environmental Science and Policy Department. Designing a course on one of my favorite topics was both a lot of fun and a great learning experience, and the course was attended by a group of motivated and enthusiastic students. California has a remarkably low ratio of lichenologists to lichen species, so I am pleased to note that almost a third of the students from my class engaged in independent research involving lichens after the course ended.

For more information on my teaching experience, please see my CV.

Students from my UC Davis Lichenology course try on Ramalina menziesii  (California’s state lichen) wigs on one of our field trips at the UCD Quail Ridge Reserve – a veritable lichen diversity hot-spot! See some of the creative outreach materials the students created.


I believe that connecting and communicating with diverse groups outside of academia is a key part of being a scientist. To this end, I build relationships with land managers, members of the conservation community, and the general public through collaborative projects, outreach events, and citizen science projects.

I particularly enjoy leading plant and lichen identification workshops for people of all experience levels, and usually do a few of these every year–see my twitter page for upcoming events. Please contact me if you’re interested in having me speak or lead a workshop at an event.

Presenting my research results to land managers at the Missouri Department of Conservation



Panel 4


I regularly collaborate with students on research projects related to plant and lichen community ecology, landscape ecology, and plant and lichen life history characteristics. I greatly enjoy mentoring, and usually work with one or two students each term.

If you’re interested in working with me on a mentored research project please contact me! I’m especially interested in working with motivated, creative students who are considering careers related to ecology, botany, conservation, etc.

Please see my CV for a list of projects previous students have worked on.


My 2017-2018 undergrad research assistants at UC Davis, Kyle, Edward and Maaike (from left)
IMG_1459 - Version 2
Damschen lab undergrads and grad students, Spring 2015
Sara (with her wizened mentor) presenting her glade community research at the end-of-semester poster session!
Brandon databases Ozark plants for donation to the Wisconsin Herbarium
Anisa hard at work on cutting-edge GIS analyses
John sorts grasshopper collections.
Shannon checks out Penstemon flowers on a fieldwork trip in the Ozarks
Damschen-Orrock undergrads Savannah, Mitul and John with Jesse and Phil, fall 2013