Selected Publications of UW Botany faculty, staff and student

(Jan 2015 - )

Please visit the department's website for the complete list:


☼ Lopez, B.E., Burgio, K.R., Carlucci, M.B., Palmquist, K.A., Parada, A., Weinberger, V.P., Hurlbert, A.H., 2016. A new framework for inferring community assembly process using phylogenetic information, relevant traits and environmental gradients. One Ecosystem 1:1-24.
DOI: 10.3897/oneeco.1.e9501
  • Functional and phylogenetic diversity are increasingly used to infer the important community assembly processes that have structured local communities, which is one of the most fundamental issues in ecology. However, there are critical assumptions and pitfalls associated with these analyses, which can create ambiguity in interpreting results.
  • We present a conceptual framework which integrates three approaches to reduce the likelihood of drawing incorrect conclusions from analyses of functional and phylogenetic diversity (FD and PD, respectively): testing hypotheses for how diversity measures and ecological processes vary along an environmental gradient, analysis of both FD and PD in concert, and careful selection of traits related to processes of interest for inclusion in FD analyses.
  • This framework has the potential to enhance comparability between studies, allow for testing of alternative hypotheses regarding changes in community assembly processes along gradients, and improve interpretations of FD and PD analyses.
☼ Mitchell, S.M., Palmquist, K.A., Cohen. S., Christensen, N.L., 2015. Patterns of vegetation composition and diversity in pine-dominated ecosystems of the lower Coastal Plain of North Carolina: implications for ecosystem restoration. Forest Ecology and Management 356:64-73.
DOI: doi:10.1016/j.foreco.2015.07.035
  • Longleaf pine ecosystems of the Atlantic Coastal Plain have experienced considerable change over the past two centuries, largely due to agricultural activities and fire suppression.
  • Previous efforts to restore longleaf pine stands have focused on the potential of fire-suppressed longleaf pine woodlands. However, it is unclear what the potential is for loblolly pine stands to act as a ’surrogate’ environment for the restoration of the often species-rich herbaceous layer of longleaf pine woodlands.
  • To assess the effectiveness of longleaf pine restoration treatments in existing loblolly pine stands, we analyzed the drivers of plant community composition in loblolly pine stands with mechanical mid-story removal treatments, untreated loblolly pine stands, and longleaf pine stands.
  • While stand types were largely distinct from each other in their vegetation composition, there was compositional overlap among some longleaf and loblolly pine stands due to similarity in soil properties, most importantly, low soil organic matter.
  • Thus, an assessment of the soil properties of loblolly pine stands may allow for an identification of candidate sites for which longleaf pine restoration treatments may be most effective.
Palmquist, K.A., Peet, R.K., Mitchell S.R., 2015. Scale-dependent responses of longleaf pine vegetation to fire frequency and environmental context across two decades. Journal of Ecology 103:998-1008.
DOI: 10.1111/1365-2745.12412
  • We resampled a unique, nested permanent vegetation plot data set in the longleaf pine ecosystem of the southeastern USA after 20 years to determine how environmental context and fire frequency jointly influence vegetation change across multiple spatial scales (0.01–1000 m²)
  • We detected a scale-dependent response in the vegetation over time; most notably, species richness increased significantly at 1 to 1000 m², remained constant at 0.1 m², and decreased at 0.01 m². In general, the magnitude of vegetation change increased as fire frequency and silt percentage increased
  • We believe this study lays the groundwork for understanding how fire and environmental filtering jointly influence vegetation dynamics across space and time in fire-dependent grasslands and woodlands.


Baker, R.L., Leong, W.F., Brock, M.T., Markelz R.J.C, Convington, M.F., Devisetty, U.P., Edwards, C.E., Mallof, J., Welch, S., Weinig, C., 2015. Modeling development and quantitative trait mapping reveal independent genetic modules for leaf size and shape. New Phytologist. 208:257-268.
DOI: 10.1111/nph.13509
  • The value of many traits (e.g., height, leaf length) increases over time as organisms grow and develop, and growth trajectories reflect the integrated effects of genetic and environmental factors; yet, measurements of most traits are commonly taken only once or a few times within the organism's lifespan.
  • We measured leaf lengths and widths in Brassica rapa recombinant inbred lines (RILs) throughout ontogeny. We modeled leaf growth and allometry (leaf shape) as function valued traits (FVT), and examined genetic correlations between these traits and aspects of phenology, physiology, and ?tness. We used RNA-seq to construct a SNP linkage map and mapped trait quantitative trait loci (QTL).
  • We found genetic trade-offs between leaf size and growth rate FVT and uncovered differences in genotypic and QTL correlations involving FVT vs single-timepoint measurements. We identi?ed leaf shape as a genetic module independent of length and width and identi?ed selection on FVT parameters of development.
  • The results are relevant to understanding basic aspects of leaf development, and to optimizing crop development (e.g. altering leaf shape without affecting other leaf traits).
☼ de Montaigu, A., Giakountis, A., Rubin, M., Tóth, R., Cremer, F., Sokolova, V., Porri, A., Reymond, M., Weinig, C., Coupland, C. 2015. Natural diversity in daily rhythms of gene expression contributes to phenotypic variation. PNAS 112(3):905-910.
DOI: 10.1073/pnas.1422242112
  • Daily rhythms of gene expression are thought to benefit most organisms by ensuring that biological processes are activated at the optimal time of day.
  • Our study shows empirically that natural genetic variation at circadian clock genes regulates plant traits of agricultural importance, such as size.
☼ Kerwin, R., Feusier, J., Corwin J., Rubin, M., Lin, C., Muok, A., Larson, B., Li, B., Joseph, B., Francisco, M., Copeland, D., Weinig, C., Kliebenstein, D.J. 2015. Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulates field fitness. eLife 2015;4:e05604.
DOI: 10.7554/eLife.05604
  • Natural selection is commonly thought to erode genetic variation in wild populations; yet, standing variation for many quantitative traits is higher than predicted from the balance between erosion of variation by natural selection and the addition of new variation by mutation. This observation suggests that other mechanisms must act to maintain segregating genetic variation.
  • Glucosinolate compounds (GSL) confer defense against herbivore damage. Through inter-crossing of lines with different alleles at glucosinolate loci, we developed a panel of experimental plants that differed in their defensive phenotypes, and we raised these genotypes in the field in Wyoming to determine associated fitness effects.
  • We find that variation in these naturally polymorphic GSL genes affected fitness in each of our environments, but the pattern fluctuated such that highly fit genotypes in one trial displayed lower fitness in another. These results indicate that environmental heterogeneity may contribute to the maintenance of GSL variation.
☼ Qinguang, X., Lou, P., Hermand, V., Aman, R., Park, H.J., Yun, D, Kim, W.Y., Salmela, M.J., Ewers, B.E., Weinig, C., Khan, S.L., Schaible D.L., McClung C.R. 2015. Allelic polymorphism of GIGANTEA is responsible for naturally occurring variation in circadian period in Brassica rapa. PNAS 112:3829-3834.
DOI: 10.1073/pnas.1421803112
  • The circadian clock is thought to adaptively coordinate diverse biological processes with changes in the environment over the course of the day.
  • In the current study, we show that GIGANTEA, a gene originally described in the model system, Arabidopsis, affects circadian rhythms, flowering time, and stress tolerance in the near-relative crop, Brassica rapa.
  • The results demonstrate translation of research from model systems to important crop species.
Salmela, M.J., Greenham, K., Lou, P., McClung, R., Ewers, B.E., Weinig, C. 2015. Variation in circadian rhythms is maintained among and within populations in Boechera stricta. Plant, Cell & Environment.
DOI: 10.1111/pce.12670
  • A circadian clock that cycles near 24 hrs is hypothesized to improve fitness, because its function enables a match between biological functions within an individual and daily (as well as seasonal) environmental changes. Yet, many organisms have clocks that deviate significantly from 24 hrs, raising the question as to how genetic variation in the clock is maintained.
  • Using the native species, Boechera stricta, which occurs widely throughout WY, including in the nearby Snowy and Laramie ranges, we find a) that the range of genotypic variation in the clock expressed within a single WY population reflects over half the range of variation expressed among a global sample of Arabidopsis populations, b) that the circadian clock correlates both positively with growth and negatively with allocation patterns, and c) seasonal environmental heterogeneity on its own seems unlikely to maintain genetic variation in growth.
  • The observed fitness tradeoffs may be one factor that maintains genetic variation in the clock.
Yarkhunova, U., Edwards, C.E., Ewers, B.E., Baker, R.L., Aston, T.L., Robertson McClung, C., Lou, P., Weinig, C. 2015. Selection during crop diversification involves correlated evolution of the circadian clock and ecophysiological traits in Brassica rapa. New Phytologist.
DOI: 10.1111/nph.13758
  • Crop selection leads to dramatic morphological changes, in which allocation to the harvestable component increases. Shifts in allocation are predicted to impact (as well as rely on) physiological traits; yet, little is known about these patterns.
  • Mustard crops (oilseed, turnip, and cabbage) differed in gas exchange; oilseed varieties had higher net carbon assimilation and stomatal conductance relative to vegetable types. Over evolutionary time, changes in the circadian clock are correlated with gas exchange and size. Crop differences in gas exchange are also associated with leaf traits that affect photosynthesis (stomatal density, epidermal thickness, and numbers of palisade layers).
  • Brassica crop diversification involves correlated evolution of circadian and physiological traits, which is potentially relevant to understanding targets for crop improvement

Environmental Change

☼ Korfanta, N.M., Mobley, M.L., Burke I.C., 2015. Fertilizing western rangelands for ungulate conservation: an assessment of benefits and risks. Wildlife Society Bulletin. 39(1): 1-8.
DOI: 10.1002/wsb.519
  • Wildlife managers in Wyoming have recognized that energy development is resulting in reductions of mule deer, likely because of deteriorating habitat extent and contiguity.
  • In recent years, a mitigation strategy was developed that involved fertilizing sagebrush habitat with nitrogen, with the goal of increasing forage protein content to improve the density of food resources.
  • Fertilization over a very large extent was initiated, in the absence of data supporting the efficacy of this strategy
  • In this paper, we review the available literature to assess the likely consequences of nitrogen fertilization on sagebrush ecosystems.
Martyn, T.E., Beltz, C. W., Palmquist, K. A., Pennington, V. E., Rottler, C. R., Lauenroth, W. K., 2015. Daubenmire versus line-point intercept: A response to Thacker et al. (2015). Rangelands 37(4):158-160.
DOI: 10.1016/j.rala.2015.05.004
  • Thacker et al. compared two common techniques for assessing greater sage-grouse habitat: Daubenmire quadrats and line-point intercept sampling.
  • Sampling only 16 Daubenmire quadrats may not have been adequate to support Thacker et al.’s assertion that line-point sampling yields higher cover values and that the two methods are not comparable.
  • Using data from sagebrush ecosystems in Montana, we show that mean percent cover changes depending on the number of Daubenmire quadrats sampled and that 16 Daubenmire quadrats may not be sufficient to accurately characterize sagebrush vegetation.
Palmquist, K.A., Schlaepfer, D.R., Bradford, J.B., Lauenroth, W. K., 2016. Mid-latitude shrub steppe plant communities: Climate change consequences for soil water resources. Ecology. 97(9):2342-2354
DOI: 10.1002/ecy.1457
  • In the coming century, climate change is projected to impact precipitation and temperature regimes worldwide, with especially large effects in drylands.
  • We use big sagebrush ecosystems as a model dryland ecosystem to explore the impacts of altered climate on ecohydrology and the implications of those changes for big sagebrush plant communities using a process-based soil water model, SOILWAT to model all components of daily water balance using site-specific vegetation parameters and site-specific soil properties for multiple soil layers across 898 sites in the western US.
  • Our modeling results suggest wetter winter and early spring soil conditions in the future, while soils are expected to dry out earlier in the year, resulting in potentially longer drier summer conditions. If winter precipitation cannot offset drier summer conditions in the future, we expect big sagebrush regeneration and survival will be negatively impacted, potentially resulting in shifts in the relative abundance of big sagebrush plant functional groups.
☼ Otgonsuren, A., Lauenroth, W.K., Burke, I.C., Mobley, M.L., 2015. Sagebrush steppe recovery on 30-90 year old abandoned oil and gas wells. Ecosphere 6(7):115.
DOI: 10.1890/ES14-00175.1
  • We measured the natural recovery of the sagebrush plant community across a chronosequence of 29 oil and gas well sites, and estimated that it takes at least 87 years for Wyoming big sagebrush cover and fewer than 70 years for big sagebrush to recover.
  • While grasses and non-sagebrush shrubs recovered rapidly, forbs, which account for the largest portion of species richness in sagebrush plant communities, had not recovered at all after 87 years. None of the invasive plants that are common in disturbed big sagebrush communities were found on any of the well pads.
  • Reclamation efforts in disturbed big sagebrush plant communities in southwestern Wyoming should target big sagebrush and forbs.
☼ Schlaepfer, D.R., Taylor, K.A., Pennington, V.E., Nelson, K.N., Martyn, T.E., Rottler, C.M., Lauenroth, W.K., Bradford, J.B. 2015. Simulated big sagebrush regeneration supports predicted changes at the trailing and leading edges of distribution shifts. Ecosphere 6.
DOI: 10.1890/ES14-00208.1
  • Big sagebrush is the dominant species over the majority of drylands of the western US and is at the center of concerns about habitat destruction and population viability of the greater sage grouse.
  • Species distribution modeling, which has been criticized for its lack of demographic information, has suggested locations for contracting and expanding portions of the big sagebrush distribution under future climate change.
  • Using a processed based model of germination and establishment we found decreased regeneration potential at the trailing edge and increases at the leading edge of the big sagebrush distribution under future climate change.
  • These results support the findings of species distribution modeling and have important implications for long-term management of big sagebrush and associated species such as greater sage grouse.


Borkhuu, B., Peckham, S.D., Ewers, B.E., Norton U., Pendall, E., 2015. Does soil respiration decline following bark beetle induced forest mortality? Evidence from a lodgepole pine forest. Agricultural and Forest Meteorology 214-215:201-207.
DOI: 10.1016/j.agrformet.2015.08.258
  • We studied bark beetle infestation effects on a forest ecosystem for five years.
  • Live tree basal area declined, caused by up to 80% stand mortality.
  • Soil respiration was strongly correlated with live basal area and root biomass.
  • Within stands, soil respiration was not altered by increasing mortality

Remote Sensing

Sivanpillai, R., Congalton R.G., 2016. Future Landsat Data Needs at the Local and State Levels: An AmericaView Perspective. Photogrammetric Engineering & Remote Sensing 82(8):617-623.
DOI: 10.14358/PERS.82.8.617
  • Feedback from Landsat user community has played a key role for making improvements to future missions
  • This paper describing the outcome from inputs recevied from experts with AmericaView (AV), a non-proft organization aimed at promoting remote sensing applications in the US
  • These recommendations provide valuable insights to USGS and NASA to further their discussions about the design and operation of future Landsat missions

Systematics & Floristics

☼ Aguirre-Santoro, J.B., Brown, G.K., Evans, T.M., Salguerio F., Alves-Ferreria, M., Wendt, T., 2015. Is Ronnbergia (Bromeliaceae, Bromelioideae ) a geographically disjunct genus? Evidence from morphology and chloroplast DNA sequence data. Phytotaxa 219:261-275.
DOI: 10.11646/phytotaxa.219.3.6
  • Molecular and morphological data show the genus Ronnbergia to be polyphyletic with the lineages. One clade is restricted to Atlantic Forest of eastern Brazil, the other two occur from northwestern South America into Central America.
  • Species currently placed in Ronnbergia are most closely related to species currently placed in the polyphyletic genus Aechmea.
☼ Evans, T.M., Jabaily, R.S, de Faria, A.P.G., de Sousa, L.O.F., Wendt, T., Brown, G.K., 2015. Phylogenetic Relationships in Bromeliaceae subfamily Bromelioideae based on Chloroplast DNA Sequence Data. Systematic Botany 41(1):116-128.
DOI: 10.1600/036364415X686413
  • This is the largest molecular phylogenetic study of Bromeliaceae subfamily Bromelioideae, to date.
  • The large complex genus Aechmea (ca. 260 sp.) is highly polymorphic.
  • Early divergent lineages in the subfamily include Bromelia, Deinacanthon, Fascicularia, Ochagavia, and Fernseea.

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