@article{eastburn_campbell_dennison_anderegg_barrett_fekety_flake_huffman_kannenberg_kerr_et al._2024, title={Ecological and climatic transferability of airborne lidar-driven aboveground biomass models in Piñon-Juniper woodlands}, volume={61}, ISSN={["1943-7226"]}, DOI={10.1080/15481603.2024.2363577}, abstractNote={Piñon-juniper (PJ) woodlands are an expansive and dynamic dryland ecosystem in the US that encompass a wide range of spatial, temporal, and ecological diversity. The dynamism of PJ woodland extent and abundance over space and time is attributable to variability in species compositions, stand structures, climatic conditions, and disturbance patterns. PJ aboveground biomass (AGB) quantification is important for understanding its role in the global carbon cycle, for tracking climate change impacts, and for informing forest management practices. Quantifying AGB in PJ woodlands is challenging due to complex vegetation structure. Although airborne laser scanning (ALS) has proven effective in estimating PJ AGB in local scale studies, these efforts only capture a fraction of the overall PJ range leaving open an important question as to whether a broad-scale, ecosystem-wide effort to map PJ woodland AGB could be successful. This research seeks to determine whether AGB predictive models built in ecologically distinct portions of PJ's range can be accurately applied to prediction of AGB in other portions of the range. Using a large database of 497 field plots compiled from eight sources and a random forest modeling framework, transferability between predictive models was evaluated by grouping field reference plots into two clustering categories based on PJ characteristics: one category generated with environmental variables (climate and topography) and the other using species compositions. For both clustering categories, models trained on one cluster were used to predict AGB in every other cluster within that category. Relatively distinct clusters, such as those characterized by notably higher temperatures and precipitation totals or dominated by a unique species, had high transferability when models were trained on the distinct cluster and applied to other clusters, but low transferability when other clusters were tested on the distinct cluster. High training transferability for distinct clusters is likely due to the inability of random forests to extrapolate beyond the range of training data, while the high testing transferability is likely due to ecological reasons. Therefore, it is important to capture the distinct environments and species compositions within the range of PJ woodlands when training a range-wide model to map PJ AGB. With the eventual goal of a range-wide PJ AGB map, we developed a preliminary range-wide model of PJ woodland AGB using our entire field reference dataset. The bootstrapped accuracy assessment of the range wide model (median R2 = 0.52; median rRMSE = 0.49) suggests promise for future comprehensive PJ AGB maps. However, high AGB values in the range-wide model were under-predicted, suggesting that gathering additional field plots in high AGB PJ woodlands has the potential to enhance the accuracy of the predictive model across the range of PJ AGB.}, number={1}, journal={GISCIENCE & REMOTE SENSING}, author={Eastburn, Jessie F. and Campbell, Michael J. and Dennison, Philip E. and Anderegg, William R. L. and Barrett, Kevin J. and Fekety, Patrick A. and Flake, Samuel W. and Huffman, David W. and Kannenberg, Steven A. and Kerr, Kelly L. and et al.}, year={2024}, month={Dec} }
 @article{hoffmann_flake_rossatto_de antonio_durigan_abreu_2024, title={Stem wound healing is dependent upon bark and trunk growth rates in Brazilian savanna}, ISSN={["1432-2285"]}, DOI={10.1007/s00468-023-02477-3}, journal={TREES-STRUCTURE AND FUNCTION}, author={Hoffmann, William A. and Flake, Samuel W. and Rossatto, Davi R. and De Antonio, Ariadne C. and Durigan, Giselda and Abreu, Rodolfo C. R.}, year={2024}, month={Jan} }
 @article{zeller_povak_manley_flake_hefty_2023, title={Managing for biodiversity: The effects of climate, management and natural disturbance on wildlife species richness}, ISSN={["1472-4642"]}, DOI={10.1111/ddi.13782}, abstractNote={AbstractAimManagers are increasingly facing an uncertain future given changing climates and ecological trajectories. The interacting effects of climate, natural disturbance, and management actions complicate future projections, and there is a need for approaches that integrate these factors—especially for predicting future vegetation and species richness.LocationCentral Sierra Nevada Mountains, USA.MethodsWe used outputs from a spatially explicit landscape disturbance succession model that incorporated forest management actions, disturbance, and climate to estimate habitat and potential species richness for 202 vertebrate species and five functional groups from 2020 to 2100. We examined species richness outcomes of three forest management scenarios under three climate trajectories. We modelled broadscale drivers of landscape‐level species richness, and proximate effects of management and disturbance at each pixel.ResultsClimate and forest management scenario had significant effects on potential species richness across the landscape, particularly at lower elevations; however, only management had significant effects at higher elevations. We found no effect of the interaction between climate and management scenario. The historical climate and the minimal management scenario generally resulted in higher species richness compared with other scenarios. Positive proximate effects generally included mechanical thinning and prescribed fire, as well as low and medium severity fire and beetle outbreaks. High severity fire had a consistently negative effect on species richness. We also quantified the contribution of protected areas and found that protected areas had higher species richness compared with ecologically similar unprotected lands, especially in climate futures that deviated from the historical climate.Main ConclusionsOur findings highlight that managing for biodiversity is complex, and effects of climate, disturbance, and management differ among species, functional groups, topography and scales. However, landscape disturbance succession models provide a science‐based tool for untangling broadscale drivers and proximate effects of biodiversity and managing for ecological integrity in a changing climate.}, journal={DIVERSITY AND DISTRIBUTIONS}, author={Zeller, Katherine A. and Povak, Nicholas A. and Manley, Patricia and Flake, Samuel W. and Hefty, Kira L.}, year={2023}, month={Oct} }
 @article{flake_honda_pilon_hoffmann_durigan_2022, title={Not all trees can make a forest: Tree species composition and competition control forest encroachment in a tropical savanna}, ISSN={["1365-2745"]}, DOI={10.1111/1365-2745.13820}, abstractNote={Abstract


Forest encroachment into savannas is a widespread phenomenon, the rate of which may depend on soil conditions, species composition or changes in stand structure. As savanna specialist trees are replaced by generalist species, rates of stand development may increase. Because generalists can persist in forests, they are likely to grow more quickly and survive longer in dense stands, compared to savanna specialists. Furthermore, the faster growth rates of generalists may allow them to overtop and outcompete savanna specialists, causing rapid species turnover.

We measured growth and survival of 6,147 individuals of 112 species of savanna and generalist tree species over a period of 10 years in an ecological reserve in Assis, São Paulo State, Brazil. We modelled growth and mortality as a function of soil texture and nutrients, tree size, competitive neighbourhood, and membership in savanna or generalist (species which can persist in forests and savannas) functional groups.

Tree growth and survival was strongly influenced by competition, as estimated by the basal area of trees taller than a focal tree. At the stand level, savanna species are unable to contribute basal area growth in closed stands, while generalist species continue to increase in basal area even at high stand basal area. This phenomenon is driven by differences in growth and mortality. Generalists grew faster than savanna species, both in height and diameter. This difference in growth rates led to savanna species becoming suppressed more rapidly than generalists. When suppressed, savanna species were more than twice as likely to die than were generalists. Soils had inconsistent and mostly weak effects which were difficult to separate from gradients of stand structure.

Synthesis. We demonstrate that the presence of generalist trees accelerates the rates of basal area accumulation due to their greater growth rates and tolerance of shading. Generalists outcompete savanna trees by growing faster in the open and overtopping savanna specialists. Due to the slow growth and high mortality of savanna species in the shade, they are unable to form closed‐canopy stands. Accounting for differences among functional types and development of vegetation structure is critical for modelling forest encroachment.

}, journal={JOURNAL OF ECOLOGY}, author={Flake, Samuel W. and Honda, Eliane A. and Pilon, Natashi A. L. and Hoffmann, William A. and Durigan, Giselda}, year={2022}, month={Jan} }
 @article{flake_abreu_durigan_hoffmann_2021, title={Savannas are not old fields: Functional trajectories of forest expansion in a fire-suppressed Brazilian savanna are driven by habitat generalists}, ISSN={["1365-2435"]}, DOI={10.1111/1365-2435.13818}, abstractNote={Abstract


Under fire suppression, many tropical savannas transform into forests. Forest expansion entails changes in environmental variables and plant community structure. We hypothesized that forest expansion into savanna results in a shift in community‐weighted mean functional traits from stress tolerance to competitiveness, with generalist species having trait values intermediate between those of specialists of savanna and forest habitats.

We studied 30 plots distributed over three savanna–forest boundaries undergoing forest expansion in the Brazilian Cerrado, capturing a gradient from open savanna to recently formed forest. We measured functional traits of 116 woody species of savanna specialist, generalist and forest specialist functional groups and quantified changes in species composition and mean traits across the basal area gradient.

We identified two main axes of species traits. The first separated forest and generalist species from savanna specialists, with the latter possessing traits associated with resistance to disturbance and stress— such as thick leaves, thick bark, slower height growth and lower shade tolerance. Our second trait axis separated shrubs and understorey trees from pioneer species. Generalist species’ traits did not differ substantially from forest species, nor did they tend to have a typical pioneer strategy.

Community‐weighted trait means changed linearly with forest development. There was a steady increase in traits associated with competitive dominance rather than stress tolerance and fire resistance, indicating a wholesale shift in the selective environment. Several of these patterns—for example, increasing height and decreasing light requirements—are common in old‐field succession. In contrast to old‐field succession, we found that SLA increased, leaf thickness decreased and wood density stayed constant.

The assembly of forests appears to be shaped by environmental filters that contribute to a functional trajectory distinct from most other studied ecosystems. Our results highlight the importance of the functional composition of the early community and of the early colonizers of the open environment. Differences between savanna and forest specialists reflect the selective effects of the contrasting environments, while the traits of generalists—and their interaction with environmental filters—drive the dynamics of forest expansion.

A free Plain Language Summary can be found within the Supporting Information of this article.}, journal={FUNCTIONAL ECOLOGY}, author={Flake, Samuel W. and Abreu, Rodolfo C. R. and Durigan, Giselda and Hoffmann, William A.}, year={2021}, month={May} }
 @article{urza_weisberg_chambers_board_flake_2019, title={Seeding native species increases resistance to annual grass invasion following prescribed burning of semiarid woodlands}, volume={21}, ISSN={["1573-1464"]}, DOI={10.1007/s10530-019-01951-9}, number={6}, journal={BIOLOGICAL INVASIONS}, author={Urza, Alexandra K. and Weisberg, Peter J. and Chambers, Jeanne C. and Board, David and Flake, Samuel W.}, year={2019}, month={Jun}, pages={1993–2007} }
 @article{flake_weisberg_2019, title={Fine-scale stand structure mediates drought-induced tree mortality in pinyon-juniper woodlands}, volume={29}, ISSN={["1939-5582"]}, DOI={10.1002/eap.1831}, abstractNote={AbstractSevere drought has resulted in widespread tree die‐off events in forests and woodlands globally and is forecast to become more frequent in coming decades. Tree mortality is a complex process influenced by climate, soils, characteristics of individual trees, interactions between trees, and the dynamics of pests and pathogens. The role of stand structure and stand density in mediating the resistance of trees to drought remains poorly understood, especially in semiarid woodlands, which are expected to be highly susceptible to future severe drought. We sampled permanent plots in central Nevada woodlands dominated by single‐leaf pinyon pine and Utah juniper before and after a severe multi‐year drought (2013–2015) to investigate the importance of climate, tree attributes, and local‐neighborhood stand structure on tree mortality and canopy dieback at the level of individual trees and 0.1‐ha plots. We observed widespread tree mortality of pinyon at approximately eight times the reported background mortality rate, and substantial canopy dieback in both pinyon and juniper. Both species were more prone to mortality and dieback in hotter, drier sites. Canopy dieback was associated with both long‐term average climate and the severity of recent drought, with elevated mortality on sites with higher water deficits, average summer temperatures, and vapor pressure deficits. Soils also played a role in tree dieback, with greater mortality on deeper soils. While mortality was driven largely by climate at coarse scales, fine‐scale stand structure interacted with climate to mediate mortality and dieback. Neighborhood statistics showed that trees were susceptible to competitive influence, and pinyon trees were especially sensitive to neighborhood density on drier sites. Mortality and dieback were associated with diverse, co‐occurring insect and parasitic plant mortality agents. Canopy dieback prior to the drought was strongly associated with tree mortality during the drought, implying that current widespread defoliation caused by these agents may foreshadow future elevated woodland decline. Fine‐scale influences such as stand structure and soil characteristics play a key role in the long‐term dynamics of semiarid woodlands, and these factors should be considered in predictive models of forest and woodland susceptibility to drought.}, number={2}, journal={ECOLOGICAL APPLICATIONS}, author={Flake, Samuel W. and Weisberg, Peter J.}, year={2019}, month={Mar} }
 @article{hoffmann_flake_abreu_pilon_rossatto_durigan_2019, title={Rare frost events reinforce tropical savanna-forest boundaries}, volume={107}, ISSN={["1365-2745"]}, DOI={10.1111/1365-2745.13047}, abstractNote={Abstract


The ability of vegetation to ameliorate or exacerbate environmental extremes can generate feedbacks that mediate the distribution of biomes. It has been suggested that feedbacks between vegetation and frost damage may be important for maintaining savanna, particularly at the edge of the tropics.

We quantified frost damage and air temperature across a network of 30 permanent plots distributed across tropical savanna–forest boundaries in Brazil during an uncommonly hard frost.

Tree cover strongly buffered temperatures during frost events, such that forest sites were up to 5°C warmer than nearby sites occupied by open shrub savanna. Consequently, in forest, woody plants were not damaged, but in savanna, there was extensive dieback of trees and shrubs. Within savanna, frost had disproportionately large effects on small individuals, likely due to colder temperatures near the ground and the lower thermal mass of thin stems. Across species, frost tolerance was strongly correlated with latitudinal range limit, revealing the importance of minimum temperature as a species filter at the regional scale. Counterintuitively, savanna species, which are adapted to open habitats where frost is more likely, were more vulnerable to cold than were forest species and experienced more than twice the amount of leaf damage as co‐occurring forest species.

Synthesis. Frost reinforces the effects of fire on vegetation structure by preferentially damaging trees in open environments and generating high loads of dead, flammable fuels. However, frost does not currently occur with sufficient frequency in the region to maintain open savanna by itself. Nevertheless, it occurs with sufficient frequency and severity that it likely acts as an environmental filter and evolutionary selective factor for some of the most frost‐sensitive species.

}, number={1}, journal={JOURNAL OF ECOLOGY}, author={Hoffmann, William A. and Flake, Samuel W. and Abreu, Rodolfo C. R. and Pilon, Natashi A. L. and Rossatto, Davi R. and Durigan, Giselda}, year={2019}, month={Jan}, pages={468–477} }