Philippa Kaur

UPRLIMET is our response to a need for a consistent method for predicting the upper extent of trout in all streams across land ownerships within our region. By developing and implementing the model using LiDAR-derived flowline hydrography, we offer a standardized, spatially explicit, spatially contiguous (where LiDAR hydrography is available), and high-quality fish-distribution layer based on the probability of fish presence. UPRLIMET maps both the probability of trout and the upper limit of trout across landscapes, ownerships, and jurisdictions, and better captures the upper extent of fish in headwater reaches relative to previous approaches allowing for a cross-boundary distribution map on which decision-makers and managers can base policies and regulations.This work provides a transferable prediction modeling framework for systematically and comprehensively estimating the upper distribution limit of fish, which could be calibrated and implemented in watersheds and for fish species around the globe. Although the dependency on LiDAR-derived data here may be seen as a limitation to broader implementation of this method, the method is scalable to any resolution, and LiDAR is becoming increasingly ubiquitous in the United States through the U.S. Geological Survey 3D Elevation Program, which is funding LiDAR acquisitions across the United States. Furthermore, LiDAR data is available globally via data from GEDI and ICESAT-2 satellites that offer coarser resolution (~ 25-m) data that are still superior to either ASTER or SRTM derived-DEMs26, 27.Minimizing prediction errors for the upper limit of trout is important to decision support and management planning because it ensures that forest-harvest regulations and management prescriptions are aligned. It is important to note that the prediction error estimates from this study are derived from the NSpCV process, except for models using 20% slope thresholds or unaltered parameterization of Fransen’s model13, because it is likely that the NSpCV estimates are conservative. They tended to overestimate error, as evidenced by the fact that the Refit model (i.e. Fransen’s optimal model13 refit to our data) exhibited a larger MAE than the unchanged optimal Fransen model13. This unexpected result was likely due to applying the NSpCV routine on the Refit model, resulting in the use of many intermediate models to characterize predictive performance using randomized subsets of independent training and test data. In contrast, the optimal Fransen model13 was developed independently using the data in this study and thus error could be evaluated directly without subsampling imposed by NSpCV.The relatively low error for the two-stage model that becomes UPRLIMET suggests that it more accurately characterizes the upper limit of fish than all other models considered in this study, including the Fransen model13, which has been used for estimating upper limit of fish regionally. Although some of the models exhibited relatively small differences in error relative to the model that became UPRLIMET, small differences in predicted upper limit locations when considered in aggregate across multiple watersheds can potentially alter management decisions and expected outcomes. Differences in predictive performance and error between UPRLIMET and the optimal Fransen model13 are likely attributed to high-accuracy hydrography and hydro-topographic data (as LiDAR-derived DEMs were not available in western Washington in 2006), which allowed a finer-scale of analysis (i.e., 5-m vs 10-m reaches). Additionally, the fact that UPRLIMET was fit to data solely from western Oregon likely offers predictive performance gains when applied to western Oregon when compared to the Fransen model13 that was fit to data from western Washington.Quantifying the predicted accuracy associated with applying UPRLIMET to western Washington will require new data and is outside the intended scope of this study. However, we think it is reasonable to infer findings from UPRLIMET across regions with similar climatic and hydro-topographic conditions including northwestern California, western Oregon, western Washington, and southwestern British Columbia, especially given the broad availability of LiDAR-derived DEMs. This conclusion is supported the fact that both the Fransen13 and Refit models produced similar logistic regression coefficients (Data S5) and similar Matthews Correlation Coefficients (Data S6), suggesting that feature space of the two models is similar. This evidence is further corroborated by the high degree of overlap observed among the distributions of each of the four predictor variables for both western Oregon and Washington. We acknowledge that UPRLIMET does not contain identical predictor variables to Fransen’s model13 but maintain that they are similar enough in purpose that it is reasonable to assume that the feature space similarities are retained.When we undertook this study, we hypothesized that a prediction model based on RF would offer superior predictive performance over those based on LR, given the availability of 67 predictor variables and RF’s demonstrated superior predictive performance in ecological applications23,24,25. However, our results suggests no improvement is offered by including more than four of the 67 environmental predictors examined, and that no clear advantage is offered by employing the more complex RF model, as evidenced by the top three of the top five prediction models being four-variable LR model algorithms (Fig. 3; Data S3.) The general importance of these variables to so many models is likely due to the strong linear relationships in the response of fish or no fish in logit space given the slopes of the curves in the partial dependence profiles (Fig. 4). This finding is congruent with the fundamental premise of LR, which is to explain and predict a response with a functional relationship, whereas RF deliberately focuses only on maximizing prediction accuracy with many decision trees28. Additional advantages to prediction models based on LR include the following: relatively better extrapolation performance over RF29, the simplicity of transferring a LR model to another processing platform using the model coefficients (versus the black box of RF decisions), and the immensely reduced computational processing times associated with LR model fitting and prediction. These advantages are especially key to this work, where there may be a desire to implement the model on other landscapes without the requisite expertise in doing so using the R software30. However, there are tradeoffs, as LR is more sensitive to the influence of outliers and multi-collinearity among variables, and overfitting is an increasing concern as the number of predictor variables increase, whereas RF tends to be robust to these concerns, but is more likely to produce a high-variance, low-bias prediction model31.Although there is no single, general explanation for distribution limits of species32, the intersection of stream size, slope, and elevation together locate the upper limit of fish. Stream size corresponds to major ecosystem changes along a stream continuum including for energy sources, ecosystem metabolism, habitat characteristics, and biodiversity33, as well as the upper distribution limit of fish, as shown here. As expected, stream size accounts for the top two variables in the model suggesting that it is the major driver of the upper distribution limit of fish with the probability of trout increasing with increasing upstream stream length and upstream drainage area. Our finding proposes that downstream stream reaches are more likely to have fish. Although the underlying mechanisms have multiple influences, factors related to increasing stream size, such as increasing habitat size, habitat complexity, stability, or temperature variability34 have been shown to be important. Similarly, stream size is the most sensitive factor in intrinsic potential models for Chinook Salmon (O. tshawytscha35). Slope, the next variable of importance influencing the upper extent of fish, exerts control on physical habitats in streams, including channel morphology, hydraulics, sediment transport, substrate, and habitat36. Steep slopes drastically prevent trout from reaching areas above waterfalls or impassable chutes of over 25% slope, but trout can be found in streams channels without barriers at slopes as high as 28%7, 14, 37. Other fishes, such as Coho Salmon (O. kisutch) and steelhead (O. mykiss) are generally not found above 12% slope38. Interestingly, survival of fishes that make it upstream or are introduced above barriers may be facilitated by a geomorphic setting that is less prone to debris flows and other episodic sediment fluxes and has a greater resilience to flooding resulting from wider valley and greater floodplain connectivity39. Elevation or vertical topographic position may indirectly integrate broad influences of other landscape-scale or climate factors or also indirectly capture stream size, influencing the likelihood of fish presence. Frequently, species richness increases at lower elevations40, and we suggest that elevation also contributes to species distribution limits, as is the case for the Endangered Species Act listed Bull Trout (Salvelinus confluentus)41. The multiple factors associated with elevation correspond to the relationship found for stream size that smaller streams are less likely to have fish. Ultimately, the intersection of stream size, slope, and elevation guide us to finding the upper extent of fish in streams.Physical influences have been proposed to be more limiting to fish distributions upstream, such as near the upper extent of fish, whereas biological factors are probably more important downstream33. Although 67 environmental predictor variables representing geologic, soil, climatic, and hydro-topographic conditions at local and patch scales are evaluated (Data S1), only the hydro-topographic variables of stream size, slope, and elevation are important to predicting the upper limit of fish in UPRLIMET. In fact, the top 9 models (Fig. 3; Data S3) relied on just four to five hydro-topographic variables, most of which were patch-scale variables or elevation at 1000 m, all of which incorporate a broader extent of influence. This suggests that local scale variables that contribute to fish limits, including slope or riparian influences may need to be further explored. In addition, some of the remaining 63 variables present in UPRLIMET, such as precipitation and air temperature, are important drivers of within-network trout distributions and contribute to their connectivity. Some of these predictor variables appear in the 10th ranked 26-variable RF-O-SR1 model (Data S2; Data S4; Data S8), but the influence appears to be dubious for isolating the upper limit and explaining variation in fish occurrence because MAE of upper limit was substantially higher than the 9 models with lower MAEs (Fig. 3; Data S3), and the lower MCC of the associated RF-O sub-model (Data S6). It is likely that other combinations of the 67 predictor variables, including precipitation, may be more important when this model development and evaluation framework is applied elsewhere, especially if those areas contain fishes or are places that are vulnerable to changing water temperatures and streamflow regimes. In addition, biological factors may be a concern in other watersheds, including invasive species and fish stocking which can limit the longitudinal distribution and the upstream extent of fishes.Given the large geographic extent of this study, we expected other variables such as precipitation to be more important drivers, however due to a combination of a wet water year, a lack of precipitation gradient in the study area, coarse grain data, and location of fish in streams this was not the case. For example, 2017 was a wetter than normal water year53, and it may be that the gradient of precipitation variation in western Oregon was not strong enough to explain the variation in the spatial distribution of trout occurrence. All climate data, including the precipitation data were sourced from relatively coarse-scale (800 m) PRISM data. The inability to adequately downscale precipitation to characterize how precipitation truly varies within and between patches, especially along elevational gradients, likely confounded how the model interprets the influence of precipitation. Trout occurrence was on perennial streams, which is likely far enough downstream of locations where variation in precipitation was the dominant influence on streamflow permanence and consequently would not have been a factor.Stream network structure plays a key role in the upper limits of fish. Upper limits for fish can occur at either lateral or terminal points13 and when mapping these points, differences were seen for UPRLIMET relative to other datasets. Lateral limits end in the tributary stream just above where it connects with a mainstem stream. Terminal limits include both mid-stream terminal limits where fish drop out in the middle of a stream channel owing to a soft (i.e., transient barrier or puttering out) or hard (i.e., waterfall) edge, and confluence terminal limits where the upper limit of fish ends at the confluence. For example, when closely examining the 14 watersheds where we have overlapping information across various datasets and models, UPRLIMET and the Fransen optimal model13 exhibit substantial agreement in their lateral limits. However, the largest differences are in their terminal ends, especially terminal mid-stream limits, probably owing to hydro-topographic changes that contribute to fish occurrence at confluences, which are more pronounced than mid-stream. Accordingly, the logic in the stopping rule is likely important in identifying specific upper extent of fish distributions in reaches that end mid-stream.Differences among databases for the upper distribution limits of fish come from both the upper limit points and depiction of fish-bearing reaches, underscoring the importance of having a shared map with common coverage of the fish extent across landscapes and ownerships. Differences among mapped distributions can result from source information, relating to whether it is modeled or occurrence data. Models, such as UPRLIMET, can be applied across a broad extent based on model parameters and training data, thereby offering broad coverage for distributions (and quantifiable error) across the landscape, ownerships, and jurisdictions. However, models are limited by accuracy and fit. As such, they can incorrectly predict distributions in some areas, especially if there are prediction features not yet trained with the model data where prediction would require extrapolation of the model. This makes both the training dataset and modeled extent important considerations, as models are only as good as the data used to develop them. Updating UPRLIMET with new data as it becomes available will help to expand the prediction domain, improve accuracy, and allow the model to do more interpolation than extrapolation.Distributions based on occurrence information depend heavily on data availability, data quality, and access. Differences in data availability can lead to inconsistent coverage across landscapes and ownerships, with high coverage in some watersheds and low to no coverage in others. Inconsistent coverage can lead to errors that are difficult to quantify across landscapes, ownerships, and survey crews. Occurrence information also depends on the ability to survey watersheds and gain access across ownership types, including on private lands that do not have the same assurances of access as public lands, resulting in information asymmetry42, 43. Data quality also depends on the spatial accuracy of the points of uppermost fish, which are a function of GPS quality and error, and can drastically change the modeled results, as these points are used in the training dataset. Differences among mapped distribution limits also result from differences in field protocols on designating last fish. For example, some crews note fish distribution limits where they visually see the last fish, whereas others note it upstream of where they saw last fish, based on habitat features that would limit fish. With the advent of LiDAR-derived DEMs and associated LiDAR-derived stream hydrography, like those available in much of western Oregon, have revealed additional flowlines in watersheds compared to previous topographic maps, which adds more potential tributaries to survey for fish-distribution assessments. When these new previously unmapped tributaries are paired with a model, such as UPRLIMET, a common information set is available across landowners, managers, and agencies for the upper extent of fish. This helps policymakers determine where to apply regulations that support fisheries and forest management, based on the upper fish limit.Next steps for applying and expanding the model include addressing current data gaps. More information and observations about the upper distribution limits of fish beyond western Oregon would be needed to properly expand the spatial scope of the model. The upper extent of fish is at the detection limit of many current technologies, including global nativation satellite system (GNSS), geographic information systems (GIS), and LiDAR, especially in forested landscapes. Better precision of GNSS coordinates from observations would help greatly. From an ecological perspective, we could focus on fish distribution limits that vary seasonally or interannually to better understand which stream features and hydrologic parameters influence those endpoints. We also need information related to locations of barriers, including culverts, waterfalls, and knickpoints to understand their influence on contemporary distributions. Incorporating variables representing riparian conditions as well as leveraging higher-resolution DEMs ( More

Overview of modeling frameworkWe have used a range of econometric, economic, and agricultural land surface models to analyze the factors driving land-use change in order to assess their ecological, agricultural, climatic and economic impacts. These multi-scale models differ in their methodologies, scale of interest, and resolution, but they are very complementary and could provide a unique opportunity to analyze public policy scenario effects on land-use and resulting changes in ecosystem carbon and biodiversity.Among these models, the economic land use model Nexus Land Use (NLU)29,30 and the agricultural supply-side model Agriculture, Recomposition de l’Offre et Politique Agricole (AROPAj)31 coupled with a spatial econometric model32 have allowed us to estimate the impact on EU land-use of a scenario involving a 50% reduction in N synthetic fertilizers compared to a baseline scenario. In the present study, we use these land-use scenarios to force ORCHIDEE-crop (Organising Carbon and Hydrology in Dynamic Ecosystems), an agricultural land surface model16,33 and Projecting Responses of Ecological Diversity in Changing Terrestrial Systems (PREDICTS)34, a biodiversity model to simulate, respectively, ecosystem C and biodiversity changes across the EU covering the domain 35.25°N and 69.25°N in latitude and 9.25°W and 34.25°W in longitude. The schematic (Fig. 1) provides a brief overview of the modelling framework applied in this study.Figure 1Schematic diagram illustrating the coupling of multi-scale land-use models. The multi-scale models coupled in this study are econometric, and economic models (NLU and AROPAj), an agricultural land surface model (ORCHIDEE-crop), and a biodiversity model (PREDICTS). Coupling means, we use the output of one model as an input to other models. In addition, we have performed one-way coupling and there is no two-way interaction between models. Each economic model generates two land-use maps corresponding to Baseline and Halving-N scenario which are inputs (2 from NLU and 2 from AROPAj) to ORCHIDEE-crop and PREDICTS. The ecosystem carbon (C) sequestration is simulated by ORCHIDEE-crop and biodiversity indicators are simulated by PREDICTS model. The abbreviations ‘BaseNLU’ and ‘HaNNLU’ means Baseline and Halving-N land-use map generated by NLU model. The abbreviations ‘BaseAR’ and ‘HaNAR’ means Baseline and Halving-N land-use map generated by AROPAj model.Full size imageIn order to link the land use output data from the AROPAj and NLU models with the ORCHIDEE-crop and PREDICTS models, the first step is to match land uses and crops between the models (see Table 1). AROPAj and NLU crops are classified into ORCHIDEE-crop plant functional types (PFTs): C3 winter and summer crops, C4 summer crop and C3/C4 natural grass (see “Model descriptions” section for a detailed description of ORCHIDEE-crop PFTs). The AROPAj and NLU crops are also classified into the PREDICTS crop types: annual, perennial, N-fixing. The AROPAj and NLU “rangeland” and “pasture” categories are found in PREDICTS but in ORCHIDEE-crop they are considered to fall within the C3 natural grassland PFT. Finally, NLU and AROPAJ forest and other natural areas are classified as “primary” natural areas (with low anthropogenic use) or “secondary” (intermediate to high anthropogenic environmental use) according to the land use map of these areas35. For ORCHIDEE-crop, they are classified as natural forest PFTs. Note that the fallow areas described in AROPAj that are part of crops are classified as “grass” PFT in ORCHIDEE-crop and as “minimum” intensity annual crops in PREDICTS.Table 1 Table of correspondences between the land uses and crops represented in the AROPAJ/NLU and ORCHIDEE models and PREDICTS.Full size tableThe land-use and land cover changes described in the following sub-section are used as inputs to ORCHIDEE-crop and PREDICTS from both the NLU and AROPAj models’ output.Land-use change scenariosLand-use changes in the EU are simulated for the present day using two scenarios: (1) a business as usual scenario (Baseline) and (2) a scenario involving a policy to reduce mineral nitrogen use by 50% from the Baseline (Halving-N). The land-use changes in Halving-N and Baseline are computed by both NLU and AROPAj models. In the latter model, the computed land-use changes result from coupling between AROPAj and a spatial econometric model. Since there are differences in the nature of the models (supply-side model versus partial equilibrium model) and their underlying data, the Baseline scenarios in the NLU and AROPAj frameworks are different. A detailed description of the differences and a discussion of their implications on the production and area of different land-uses is provided in Lungarska et al.36. EU plant production is 370 and 383 MtDM (Million tons of Dry Matter) respectively based on the application of 12 TgN (Tera grams) of N fertilizer in AROPAj and NLU. Crops, grasslands, and forests cover respectively, 116, 57 and 234 Mha in NLU and respectively 94 (including fallow land), 38 and 142 Mha in AROPAj. In AROPAj and NLU, the 50% N reduction is achieved indirectly by increasing the N input price from present-day figures36.The land-use changes output from AROPAj and NLU are supplied as inputs to the ORCHIDEE-crop and PREDICTS models. The land-use changes are matched with corresponding plant functional types (PFTs) in ORCHIDEE-crop and land-uses in PREDICTS (see Table 1). “Model descriptions” section provides a detailed description of the ORCHIDEE-crop and PREDICTS models.Model descriptionsHere, we describe the ORCHIDEE-crop and PREDICTS models that quantify the impacts of halving N fertilizer consumption in the EU. Table 2 presents a brief overview of the two models.Table 2 Overview of the ORCHIDEE-crop and PREDICTS models input and output.Full size tableA detailed description of ORCHIDEE-crop: This model is a process-based agricultural land surface model that integrates crop-specific phenology based on Simulateur mulTidisciplinaire pour les Cultures Standard (STICS)37,38. Carbon allocation is based on the plant-based hybrid model from the original ORCHIDEE allocation scheme39 and a crop specific formulation of STICS providing leaf, root, and shoot biomass, grain maturity time, litter production, and litter and soil carbon decomposition. The harvest date is calculated after grains reach maturity40. The ORCHIDEE-crop model has no explicit nitrogen cycle but accounts empirically for the effect of N fertilization by increasing the maximum Rubisco- and light-limited leaf photosynthetic rates as a function of the amount of N applied, using a Michaelis–Menten function40. Also, ORCHIDEE-crop is calibrated against observations, which showed a good match between modeled observed aboveground biomass, crop yield, and daily carbon40. This version of the model currently uses three crop PFTs: C3 winter, C3 summer and C4 summer. Forests are classified as Broadleaf, Needle leaf, Deciduous, Temperate and Boreal. Up to 11 non-cropland vegetation types can co-exist with crops on a grid point of the model, according to prescribed land cover information. A gridded simulation of ORCHIDEE-crop requires 30-min time step meteorological forcing (air temperature, specific humidity, incoming shortwave and longwave radiation, rainfall), which can be interpolated in time from gridded climate analysis data or atmospheric models. In this study, this model is used to quantify the ecosystem C variables.A detailed description of PREDICTS: The PREDICTS database was collated by searching the published literature for studies where terrestrial biodiversity (including plants, fungi, vertebrates, and invertebrates) was sampled using consistent methods across multiple sites, which vary in the pressures faced. The land use and intensity of each site have been assessed and categorized in a consistent way41,42,43. Authors of studies were contacted to ask for the raw biodiversity data where this was not already available41,42. Most records in the PREDICTS database refer to the number of individuals of a species at a site; this makes it possible to compute a range of biodiversity indices. To estimate biodiversity responses to human impacts across such a global and heterogeneous dataset, linear mixed-effects models are used; random intercepts account for differences in biogeographic factors, sampling methodology and taxonomic focus, and the spatial layout of sites within studies. Using the PREDICTS database to assess the impact of human pressures on biodiversity assumes that space-for-time substitution is valid44; it assumes that the sites have reached equilibrium and so the impact of pressures on biodiversity over time can be observed across space and that the relationship between biodiversity and drivers do not vary over time.SR is calculated as the number of species at each site; it is a widely used measure of biodiversity and is both simple and intuitive. Responses of SR to land use and intensity were modelled using generalized linear mixed effects models and with a Poisson error structure; an observation-level random effect was included to account for overdispersion45. This model is then used to project SR in each grid of a 0.5° map and expressed as a percentage of the SR level in primary vegetation from land use harmonization map35.To estimate BII change with land use and intensity, two models are required. Total abundance was first calculated as the sum of all individuals at each site; it was then rescaled within the study (so that the maximum within a study is 1) and was square-root transformed before modelling as a function of land use and intensity, to account for non-normality of the model residuals (a Poisson error structure could not be used as abundance data can include non-integer data e.g. densities). Inclusion of a random slope for land use within the study was supported (based on Akaike’s Information Criterion). Compositional similarity was then calculated as the asymmetric Jaccard index, comparing each baseline site (primary vegetation) with all other sites, and logit transformed with an adjustment of 0.01 (to account for non-normality of the model residuals). Compositional similarity was then modelled as a function of land use and intensity (coarsened so that only perennial crops were allowed to differ across intensities), including the environmental and geographic distance between sites as control variables, whose effects were permitted to differ among land use and intensity levels (these variables were cube-root and log-transformed respectively to improve residual distribution). To calculate BII, total abundance (expressed as a percentage of their level in primary vegetation) and compositional similarity (expressed as a percentage of their level in primary vegetation)46 are projected for each grid of a 0.5° map; these two maps are then multiplied to give abundance-based BII19. The PREDICTS models include different levels of management (intensive, light or minimal) and different types of land cover (forest, pasture, rangeland, annual cropland, perennial cropland, and urban zones). The coefficients of these mixed-effect models and a detailed description of the link between the PREDICTS models and NLU are available in Prudhomme et al.46. The spatial predictions of biodiversity were computed using a python pipeline, which was developed specifically for the PREDICTS project (https://github.com/ricardog/raster-project).In our modeling framework, the impact of halving N fertilizer goes through two steps: (i) we calculate the effect of this reduction of N fertilizer on agricultural yield, and (ii) calculate the effect of the yield reduction on biodiversity. By keeping yield as a proxy of agricultural land use intensification as proposed in Prudhomme et al.46, we include not only the direct effect of the reduction of N fertilizer on biodiversity but also the effects correlated to this reduction of N fertilizer such as the reduction of other chemical inputs (P and K fertilizers and pesticides). While the effect of the change in N fertilization on yield is calculated by the classical concave production function in agronomy29, the effect of the change in yield is calculated by coupling the NLU land use model and the PREDICTS biodiversity model46. For each category of crops (annual, perennial, leguminous), the coupling consists of estimating (using a Generalized Additive Model [GAM]) the share of each intensity class (minimum, light, intense) as a function of the average calorie yield based on the average crop yield maps from a plant growth model. The maps describing the share of land use intensities are from Newbold et al.19 Similarly for pasture, the share of each intensity class (light, intense) is estimated with the help of a GAM as a function of ruminant density.SimulationsOur experimental design focuses on assessing the effects of a 50% reduction in present-day N fertilizer use levels across the EU. The choice of halving N fertilizer in EU agriculture is related to the “Farm to Fork” strategy, which puts forward the ambition for 2030 to reduce nutrient losses to the environment from both organic and mineral fertilizers by at least 50%. The results from NLU (and its nitrogen balance module) show that this level of reduction corresponds to a 50% reduction in nutrient losses (nitrogen and phosphorus) aimed by the Farm to Fork strategy as a part of the European Green Deal. AROPAj models exclusively the EU countries (in 2012, there were 28 member states) while NLU simulations cover the EU and the rest of the world (EU being a part of the European region as represented by the model). However, the N reduction policy implemented in the EU alone and the comparison of the results conducted only for the EU. All EU member states are considered but for some of them we present results. A total of four simulations corresponding to four land-use maps (two from AROPAj and two from NLU, see Fig. 1) are performed in the ORCHIDEE-crop model and also in the PREDICTS model. In addition to changes in the area of different land-uses, changes in mineral N input are accounted for in both models. However, changes in organic N input and crop rotations are not accounted for. In ORCHIDEE-crop 55% of the carbon harvested from croplands is exported but the remaining residues are returned to the soils.ORCHIDEE-crop simulation details: the model simulations are performed over a domain covering the EU. Four idealized simulations are carried out using the ORCHIDEE-crop model by forcing present-day meteorological data (2006–2010), levels of N fertilizer (150 KgN/ha) and atmospheric CO2 concentration (385 ppm). The four simulations include Halving-N and Baseline corresponding to AROPAj and NLU land-use scenarios (two ORCHIDEE-crop simulations per economic model). All four simulations start from the year 2010 climate and carbon cycle conditions with a recycled climate (2006–2010) for 150 years. For the year 2010, climate and carbon cycle conditions are obtained from the output of historical simulations. Historical simulations from the year 1901 to the year 2010 are performed for both AROPAj and NLU Baseline scenario land-use land cover maps. In addition, these historical simulations started from an equilibrium state of soil carbon, energy and water cycle variables corresponding to the year 1901. The 1901 equilibrium state is determined by running a 350-year spin-up simulation corresponding to a recycled climate (1901–1910). The observation-based climate forcing data from the Global Soil Wetness Project was only available starting from the year 1901. The drift in soil carbon over the last 100 years of the 350-year simulations is less than 1%. The equilibrium state simulations corresponding to the year 1901 were necessary to have stabilized biophysical and ecosystem C variables across the EU. Other forcing variables, e.g. atmospheric CO2 concentration (296.57 ppm), N-fertilization rate (32 KgN/ha), harvest index (0.25), and also the phenology parameters for short-cycle variety winter and summer crops16 corresponding to the year 1901 were prescribed.PREDICTS simulation details: the PREDICTS model represents changes in broad-sense biodiversity in different land-uses and intensities of land-use relative to a reference land-use (as the biodiversity metrics assessed include all terrestrial biodiversity for which data are present in the PREDICTS database including plants, fungi, vertebrates and invertebrates). Here the reference ecosystem is a primary natural ecosystem. Biodiversity changes are then reported as a percentage by dividing the obtained biodiversity levels by the level of biodiversity present in the primary natural ecosystem. This simulation is performed for each grid point on a map of the EU for land-use scenarios corresponding to Baseline and Halving-N for both economic models, AROPAj and NLU (Fig. 1).Breakdown method for biodiversity and carbon changesThe Halving-N and Baseline scenarios provide contrasted land-use maps according to the assumptions of economic and land-use models36. This results in different plant and animal production, and different land-uses at the European scale in each model. A price shock on inputs, as represented in the Halving-N scenario compared to the Baseline scenario, can induce (1) a spatial reallocation of production or (2) production changes47. Here, we separate out the effects of these two mechanisms on biodiversity (species richness) and carbon indicators (NPP and soil carbon) by decomposing the overall environmental differences between the Halving-N and the Baseline scenarios. The breakdown is not possible for the BII indicator because this indicator is the product of two indicators: abundance and a similarity indicator of ecological communities.First, we breakdown the carbon and biodiversity differences by land-use type. The breakdown for carbon is straightforward because the carbon changes are computed for each land-use. The biodiversity changes associated with each land-use are computed by setting no changes in the other PREDICTS model land-uses. The sum of the biodiversity changes for each land-use is thus equal to the overall change in biodiversity.For each land-use i (forest, grassland and cropland), we separate out the carbon and biodiversity differences between the Halving-N and the Baseline scenarios into two effects in accordance with Eq. (1): (i) the carbon and biodiversity difference associated with the area difference—called “Area effect”, and (ii) the carbon and biodiversity difference associated with the difference in biodiversity and carbon sequestration per unit area—called “Intensity effect”. The “Area effect” corresponds to the change in carbon sequestration and biodiversity associated with a change in the land-use area. For example, a reduction in grassland area leads to reduction in the C sequestration and biodiversity associated with this area. The “Intensity effect” corresponds to a change in the C sequestration and biodiversity per unit area. For example, a reallocation of production toward places with high soil C content leads to an increase in the carbon stock per hectare or an increase in crop yield leads to a reduction in the biodiversity per unit of cropland. Thus, the “Intensity effect” corresponds to the effect of a production reallocation on C sequestration, and the effect of land-use intensity on biodiversity.We use the Logarithmic Mean Division Index (LMDI) method, which breaks down the target values into several main influencing factors based on mathematical identity transformation48 as follows.$$Delta {E}_{i}=Delta {E}_{i}^{A}+Delta {E}_{i}^{I}$$
(1)
(Delta {E}_{i}) is the difference in the environmental indicator between the Halving-N and the Baseline scenarios. Superscript ‘A’ denotes area effect and ‘I’ denotes intensity effect. Subscript ‘i’ denotes different land-use (e.g. forests, grassland, cropland etc.). (Delta {E}_{i}^{A}) is the difference in the environmental indicator between the Halving-N and the Baseline scenarios associated with the difference in area. (Delta {E}_{i}^{I}) is the difference between the Halving-N and the Baseline scenarios associated with the different intensity per unit of area of the environmental indicator.$$Delta {E}_{i}^{A}=frac{{E}_{i}^{hN}-{E}_{i}^{b}}{ln({E}_{i}^{hN})-{ln(E}_{i}^{b})}times lnleft(frac{{A}_{i}^{hN}}{{A}_{i}^{b}}right)$$
(2)
({E}_{i}^{hN}) is the level of the environmental indicator in the Halving-N (superscript hN) scenario. ({E}_{i}^{b}) is the level of the environmental indicator in the Baseline (superscript b). ({A}_{i}^{hN}) is the area of land-use i in the Halving-N scenario. ({A}_{i}^{b}) is the area of land-use i in the Baseline$$Delta {E}_{i}^{I}=frac{{E}_{i}^{hN}-{E}_{i}^{b}}{ln({E}_{i}^{hN})-ln({E}_{i}^{b})}times lnleft(frac{{e}_{i}^{hN}}{{e}_{i}^{b}}right)$$
(3)
Equation (3) is same as Eq. (2) but for the intensity of the environmental indicator ({e}_{i}).The breakdown of the differences in the environmental indicators is performed between the Halving-N scenario and the Baseline. A positive variation ((Delta {E}_{i} >0)) indicates a higher environmental indicator in the Halving-N scenario compared to the Baseline without implying any temporal variation since the scenarios compare the environmental indicator status in 2012 in the AROPAj and in the NLU land-uses. Conversely, a negative variation ((Delta {E}_{i} More

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Efforts to keep oil-palm plantations from crowding out tropical rainforests could threaten biodiversity in other habitats1.

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doi: https://doi.org/10.1038/d41586-022-04179-1

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Environmental and competitive filtering is most important for future tree survivalWe find that individual functional traits of each tree were most important for individual tree survival (40–87%) for all study sites, followed by forest dynamics (16–28%) and functional diversity (10–26%) (Fig. 2). Nevertheless, importance proportions substantially varied in each study site. While individual functional traits were least important in the mixed mountainous forest under reference climate (no climate warming), individual functional traits showed highest influence in the mixed temperate forest under future climate change (Fig. 2).Figure 2Relative importance of functional diversity, forest dynamics and individual traits for individual tree survival under reference climate and future climate conditions (RCP 4.5). Panels correspond to alpine needle-leaved (A), mixed mountainous (B), mixed temperate (C) and temperate broad-leaved (D) forests. Left bars in each panel illustrate reference climate (no warming) and right bars future climate (RCP4.5). Colours indicate forest dynamics (grey), functional diversity (yellow) and individual functional traits (blue). Forest dynamics include the number of locally competing trees ( > 5 m in height) and local biomass as a proxy for the successional status.Full size imageTree survival depends on a mixture of environmental (e.g. climate) and natural competitive filtering, which excludes trees with trait combinations that underperform under local conditions16. Therefore, the high importance of individual functional traits across all study sites suggests a strong environmental and competitive filtering. Under future climate, the importance of individual functional traits generally increases or remains at high levels (Fig. 2). This shows that environmental and competitive filtering through functional traits are important processes to select best performing trees for the future, although being different for each forest type.Changing forest composition and trait shifts require large functional portfolio to secure forest resistanceUnder future climate, we observe trait shifts within plant functional types and strong changes of the forest composition (Figs. 3, 4). Especially in the alpine and mixed forests, the proportion of broad-leaved trees increases to at least ~ 70% towards the end of the twenty-first century (Fig. 3). The changing climate alters environmental and competitive filtering simultaneously, whereby broad-leaved trees become more productive, survive better and increasingly outcompete needle-leaved trees. For instance, in the two mixed forests survival probabilities of broad-leaved trees (high SLA) increase by about ~ 10%, whereas the survival of needle-leaved (low SLA) trees is reduced by 10% to 30% in a warmer climate (see Supplementary Figs. S7, S8, Panel A). Locally better adapted and competitive broad-leaved trees can replace needle-leaved trees if they die and secure the forest’s overall biomass in the future. Nevertheless, our simulated forests still contain significant amounts of needle-leaved trees in the year 2099 in the two coldest study areas (Fig. 3, red and blue lines). Therefore, mixed tree communities with high functional diversity, where broad- and needle-leaved trees coexist, contain a broad range of functional niches out of which the best suitable plant strategies emerge and result in better resistance to climate change.Figure 3Forest compositions and changes in the proportion of broad-leaved trees (summergreen and evergreen plant functional type combined) under climate change (RCP 4.5) from 2000 to 2099 for each study site. The fraction of broad-leaved trees, as simulated by LPJmL-FIT for each site, increases gradually in almost every forest type reaching at least about 70% by the end of the century. Pictures depict snapshots from visualization of model output in the years 2000 and 2099, respectively. For a full animation of all sites from 2000 to 2099 please see Supplementary Video 1.Full size imageFigure 4Trait distributions of specific leaf area in year 2000 and 2099, respectively, under future climate change (RCP 4.5). Arrows indicate trait shifts within plant functional types: BL-S Broad-leaved summergreen, BL-E Broad-leaved evergreen, T-NL Temperate needle-leaved, B-NL Boreal needle-leaved. For more detailed distributions see Supplementary Figs. S3 and S4.Full size imageSimultaneously, we observe strong trait shifts in SLA within plant functional types across all study sites under climate change (Fig. 4). In general, the community of broad-leaved trees shift to lower SLA, while boreal needle-leaved trees are strongly reduced or slowly replaced by their temperate equivalent with higher SLA (Supplementary Fig. S3A, dark blue colours). In contrast, wood density distributions remain relatively broad and do not shift strongly under climate change (Supplementary Fig. S4). Throughout the century, the increasingly warmer climate filters new trait combinations leading to changes in the community composition within and across PFTs (see Supplementary Discussion B). Those trait shifts emerge from changes in the composition within PFTs and newly establishing PFTs, and could be less drastic if trait adaptation of tree individuals was considered (see “Limitations and outlook” section). The points raised above show, that trait ranges within and between PFTs should be wide to cover potential future trait shifts that secure future forest resistance.All this suggests that functionally diverse forests are more resistant to future climate changes, due to their rich portfolio of traits. Broad trait distributions both within and between PFTs form the fundament for environmental and competitive filtering to select the most productive trees, securing the forest’s overall biomass under changing conditions. But can functional diversity further strengthen forest resistance beyond portfolio effects?Functional complementarity helps young trees to surviveWe find that, in addition to port-folio effects, functional diversity increases forest resistance by supporting the survival of young trees to changing climate conditions via trait complementarity. Our results indicate, that trees benefit from functional diversity if they grow in tree communities with high FR, high FDv and low FE (Supplementary Figs. S6–S9, Panel D–F in each figure). Here, functional traits lay highly separated (FDv and FE) and span a broad range in the functional trait space (FR), enabling functional complementarity. Under these conditions the survival of trees increases up to + 16.8% (± 1.6%) depending on the study site and climate (Table 1). This effect is highest in the alpine and mountainous forests (14–17%), whereas it is less prominent or has an opposite effect in the two temperate forests (− 7% to 6%). That suggests, that complementarity effects are stronger in cold-limited and mixed forests where a marked cold winter season fosters a co-existence between broadleaved and needle-leaved trees. Both PFTs are specialized in fixing carbon during different times of the annual cycle: Due to their leaf phenology, needle-leaved trees can already be productive when broad-leaved trees are still in progress of unfolding or shedding their leaves. On the other hand, broad-leaved trees are more productive than needle-leaved trees during warmer months. If coexistence is given, these phenological differences enable complementarity and reduce competition among PFTs. That overall increases tree survival, because trees can invest more carbon in their stems and defensive structures if competition is lower. Therefore, we argue that phenological complementary can enhance tree survival and thus forest resistance. An in-depth discussion of those mechanisms is further found in Supplementary Discussion A.Table 1 Additional survival probabilities for trees in each forest site under reference climate (central column) and future climate (RCP4.5, right column) in case FR and FDv are high, while FE is low.Full size tableSurprisingly, our results show that those complementary effects are much more important for small trees ( 10 m) in right panel, respectively. Functional diversity and forest dynamics are more important for small trees compared to large trees, whereas individual functional traits matter most for large trees. This pattern was found to be consistent across all sites (see Supplementary Table S6).Full size imageFunctionally diverse understoreys unlock the synergy of filtering and complementary effectsOur findings underline the role of functionally diverse trees in the understoreys for forest resistance. On the one hand, functional diversity supports the survival of understorey trees via functional trait complementarity. On the other hand, they form the fundament for competitive and environmental filtering. Only diverse tree communities have trait pools large enough to ensure that their tree portfolio holds trait combinations best suited for changing climate conditions. Therefore, we argue that functional diversity does not only support tree survival through complementarity, but is a prerequisite for filtering resistant trees in the first place.To profit constantly from functional diversity of the understory and ensure constant adaptation, a diverse age structure is a prerequisite. Depending on the forest type, trees are distributed in a broad range of different height and age classes in our study (Supplementary Fig. S5, Supplementary Video 1). This multi-aged structure is preserved under climate change (Supplementary Fig. S5) and allows gradual changes through constant environmental and competitive filtering in the future.In this study, we simulate forests without any human interference or management. Our results are therefore to be interpreted in the context of environmental and competitive filtering as observed in natural forests. Most managed forests lack this natural filtering effect as they are less dense and diverse in their age-structure. Functionally diverse trees in the understorey could provide the fundament for climate adapted multi-aged forests, as they constantly form new better adapted tree generations with natural competition and succession allowed. Therefore, we fully underline the importance of functionally diverse understorey trees and natural competition as the fundament for future forest resistance.Management implicationsThe results of this study highlight the importance of functionally diverse understorey trees. However, browsing by game might damage new tree saplings and limit tree diversity in the understorey. In addition, invasive species like Prunus serotina or herbaceous competition might hinder forest succession and the establishment of woody native species in European forests20,21. Therefore, regulating game, limiting the spread of invasive species and controlling herbaceous vegetation should be considered in future management practices where tree diversity in the understorey seeks to be increased or maintained. Moreover, insufficient dispersal of functionally different tree species might limit the establishment of functionally diverse trees in the understorey. Future forest management may consider to artificially plant functionally different tree species if dispersal from surrounding forests cannot be guaranteed. On the other hand, forests that already contain functionally diverse trees in the understorey should be preserved.In this study, a clear trend from needle-leaved to broad-leaved trees is captured at all sites, whereas within broad-leaved PFTs a shift to lower specific leaf area and higher leaf longevities indicates that future forests might especially benefit from longer vegetation periods (earlier leaf onset, later senescence). Therefore, forests containing broad-leaved tree individuals with high phenological plasticity could be more resistant. The broad simulated wood density ranges, which persist under climate change, imply beneficial effects for forest communities entailing a range of different growing strategies, i.e. early to late successional species. Therefore, we argue that forest fragmentation should be reduced or reversed to foster some natural dispersal of early and late successional species.This study intended to explore the potentials of functionally diverse forests as a possibility to stabilize forests under climate change over a large climatic gradient. The model used in this study operates on the more general level of functional traits and their diversity rather than on species level (see “Methods” section and Supplementary Methods A). Consequently, management implications regarding suitable specific tree species are beyond the scope of this study. However, we think that our results will stimulate the discussion on the importance of functional tree traits and their diversity for species selection.Limitations and outlookThis study focussed on identifying the importance of functional diversity for future tree survival to advance our understanding on the role of biodiversity for future forest resistance using the flexible-trait Dynamic Global Vegetation Model LPJmL-FIT. The general approach of LPJmL-FIT is to simulate biogeographic dynamics purely based on environmental and competitive filtering (see “Methods” section, Supplementary Methods A). Due to missing processes in the model and the ambiguity of former human influence, drawing site-specific implications on future forest dynamics must be taken with caution (see Supplementary Discussion D).Moreover, processes not yet captured in the LPJmL-FIT model, might play a role and could lower forest resistance in the future, which is why we recommend relying on a trait space as broad as possible.Including more climate scenarios would widen the envelope of possible future pathways by considering climate model uncertainties. Insect outbreaks and pathogens might put pressure to the already drought- and temperature-stressed trees and heavily accelerate mortality especially of needle-leaved trees, although functionally diverse forests are less vulnerable to bark beetle outbreaks22,23. Multi-layered forests showed higher growth resilience to structural disturbances such as wind-throw24, likely enhancing the importance of individual tree height and reduce the survival probability of large trees25. Belowground competition and trait plasticity could favour complementarity effects further. Variable rooting strategies could further reduce competition for soil water and thereby increase individual drought resistance of trees26. Trait plasticity can contribute to tree survival by widening niche, further increasing complementarity effects. However, trait plasticity remains one of the most challenging objectives in vegetation modelling as observational data and modelling approaches are scarce27, leaving it open how far trait relationships would hold under climate change. Considering more functional traits in our analysis might increase the overall predictive power of the random forest models. Even though the explained variance increased with the number of analysed traits explaining ecosystem properties in long-term grassland experiments, such improvement is limited as abiotic factors and their interactions with plant traits might be more important for prediction28. We conclude that simulating future forest dynamics dominated by environmental and natural competitive filtering requires to integrate both, abiotic and biotic drivers on forest dynamics. Machine learning techniques are increasingly used in forest ecological research—but mainly applied in the processing of field and forest inventory data29,30. Machine learning can help to understand the complexity of interactions and provide deeper insights into the underlying ecological process in a modelling study as we have shown here using LPJmL-FIT simulation results. Random forest analyses are suitable for a variety of data and applications because they are relatively robust to different data structures. Importance analysis can help to identify the role of underlying processes in complex models and to visualize their changes in a simple way. In doing so, model development is advanced by making use of large data sets, opening the door to further theory building and deeper understanding of plant trait ecology. More