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NEWS AND VIEWS
19 October 2021

Rhinoceros genomes uncover family secrets

Genomes from living and extinct rhinos reveal that different species evolved as a result of geographic isolation. A comparison of DNA from different species also shows that rhinos have long displayed low genetic variability.

Desire Lee Dalton

0
&

Stefan Prost

1

Desire Lee Dalton

Desire Lee Dalton is at the South African National Biodiversity Institute, Pretoria 0001, South Africa.

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Stefan Prost

Stefan Prost is at the South African National Biodiversity Institute, Pretoria 0001, South Africa, and in the Department of Behavioural and Cognitive Biology, University of Vienna, the Konrad Lorenz Institute of Ethology at the Vetmeduni Vienna, and the Natural History Museum, Vienna, Austria.

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Historically, rhinos were once abundant throughout Europe, Asia and Africa1. Today, five species of rhinoceros survive as small populations in Asia and Africa, and are all threatened with extinction2. Although well studied, there is debate in the literature about evolutionary relationships between modern and extinct rhinos, with three hypotheses being proposed (Fig. 1a–c). Writing in Cell, Liu et al.3 analyse contemporary and ancient rhinoceros DNA to piece together the puzzle of the rhino’s evolutionary history.

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Study areaThe study area (78 000 km2) is located between 68–71°N and 20–26°E, with strong climatic gradients, ranging from wet maritime to relatively dry continental, over tens of kilometers. The landscape of this climatically sensitive high-latitude region has been affected by multiple glaciations in the past. It includes the Scandes Mountains near the Arctic Ocean and low-relief areas to the south and east. The majority of the region (52%) is underlain by sporadic permafrost. Continuous and discontinuous permafrost are limited to the highest mountains of the study area (2% and 7%, respectively)17,26. This large proportion of sporadic, typically warm and shallow permafrost in the study area indicates that ground thermal response to climate warming can be rapid27. Our data do not cover low-relief plateaus of continuous permafrost (similar to northern Siberia and Alaska), where the generally high ice content of soil may lead to different and enhanced LSP responses under climate warming (e.g., ice wedge degradation and surface ponding) with altered AGB feedbacks43,44.LSP observationsThe data consist of 2917 study sites (each 25 m × 25 m) and includes previously combined observations (both in-situ [n = 581] and remote-sensing [n = 2336]) of the active surface features of three cryogenic LSP common in the area: cryoturbation, solifluction, and nivation. These LSP are mainly associated with seasonal freeze–thaw processes. Cryoturbation (i.e., frost churning) is a general term for soil movement caused by differential heave, and it creates typical surface features such as patterned ground, frost boils and hummocky terrain5. Solifluction is the slow mass wasting of surficial deposits through frost creep and permafrost flow, where gravitation causes frost-heaved soil to settle downwards during the summer thaw, creating features of lobes and terraces50. In addition, solifluction also includes gelifluction which is a mass wasting process caused by high porewater pressure in unconsolidated surface debris creating similar lobes and terraces5,50. We use the term nivation to collectively designate various weathering and fluvial processes which are intensified and depicted by the presence of snowbeds (which in general are melting in mid-July – late-August) and nivation hollows28,51. We expect the presence of such a snowbed to be an indication of active nivation processes, since in these environments the year-to-year spatial snow patters are fairly consistent31.The rationale behind LSP sampling is described in previous geomorphic studies which served as a basis for the used protocol52,53. Due to the large study domain, study objectives (focus on distribution of active surface features, not on activity itself) and modeling resolution (50 m × 50 m), we used a visual method to estimate the presence/absence of the mapped LSP. We used high-resolution aerial photography (spatial resolution of 0.25 m−2) and targeted field surveys (GPS accuracy ~5 m; Garmin eTrex personal navigator) to construct the LSP dataset. A binary variable (1 = presence, 0 = absence) was assigned to each LSP to indicate their evident activity (or absence). The activity/absence of the LSP was visually estimated based on the evidence in ground surface, indicated by e.g., frost-heaving, cracking, microtopography (e.g., erosional and depositional forms), soil displacement indicative to a process form (e.g., solifluction lobes, patterned ground), changes in vegetation cover and late-lying snow. Such indicators average the LSP activity over several years. Even small areas with slight indication of activity were considered active processes. However, such a protocol based on a visual assessment is susceptible for incorrect activity classification; solifluction may be active despite having a complete vegetation cover19 and the presence of late-lying snowbed, although being a good indication28, does not necessarily mean that active nivation processes are present.Remotely sensed vegetation indexFor obtaining remotely sensed vegetation index for the study area, we employed a maximum-value compositing approach. We downloaded all available clear sky (less than 80% land cloud cover) Landsat OLI 8 images overlapping the study area from June to September between 2013 and 2017 (total of 1086 scenes) from the United States Geological Survey (USGS) database (http:\earthexplorer.usgs.gov). Images were USGS surface reflectance products, which were preprocessed (georeferencing, projection, and atmospheric corrections) by USGS54. Landsat-8 satellite is the latest addition to the Landsat mission that has provided repeated land surface information globally since the 1970’s and is the most commonly used fine-scale satellite system for vegetation mapping. The native resolution of the Landsat OLI sensor is 30 m for the spectral bands used in the image processing steps of this study.Normalized difference vegetation index (NDVI), a widely used spectral index to estimate the amount of green vegetation, was calculated as55:$$({{{{{rm{rho }}}}}}{{{{{rm{NIR}}}}}}-{{{{{rm{rho }}}}}}{{{{{rm{red}}}}}})/({{{{{rm{rho }}}}}}{{{{{rm{NIR}}}}}}+{{{{{rm{rho }}}}}}{{{{{rm{red}}}}}})$$
(1)
where ρNIR and ρred are the surface reflectance for their respective Landsat bands, 0.851–0.879 (mu)m and 0.636–0.673 (mu)m.USGS provides pixel-based quality assessment bands for all surface reflectance products. These bands were used to mask clouds, snow, water, and other low-quality pixels from the individual NDVI scenes. Additionally, if the NDVI images still had unphysical values over 1 or under -1, these pixels and their surroundings of 100 m radius were excluded. We determined maximum values for each 30 m resolution pixel of the study area individually. After masking cloud, snow, and water from the scenes, obvious scattered erroneous NDVI values remained in some scenes. Therefore, we excluded the values outside the pixel-based 95% percentile prior to maximum composite.The CFmask cloud detection algorithm that is used to generate the quality assessment band has clear difficulties in distinguishing small snow patches from clouds. As such, a large portion of late-lying snow beds were repeatedly and incorrectly classified as clouds. Moreover, the CFmask algorithm creates buffers around the cloud pixels54, hence much information was lost around the snow patches that were incorrectly identified as clouds. After these processing steps, some pixels around the extreme late-lying snow beds had still too low number of NDVI records to provide reliable NDVI values for the maximum composite. To fill these small and scattered gaps in the initial maximum NDVI composite, we selected 74 mostly cloud-free scenes between August and September. For these 74 scenes, we manually digitized cloud masks to exclude cloud-contaminated pixels with high certainty. Moreover, every pixel must have passed the following quality checks to be included in the gap-filling composite: not classified as water in the USGS quality assessment band; normalized difference snow index (NDSI) value less than 0.4, and blue band reflectance less than 0.1 (to exclude snow); reflectance of red band between 0.03 and 0.4 (second check for water and snow, and deepest shadows); NDVI between 0 and 0.4 (lower threshold to exclude snow and water contamination; higher threshold to exclude erroneous values, as very late snowbed habitats always have very limited vegetation cover). Additionally, if the NDVI images had unphysical values over 1 or under -1, these pixels and their surroundings (200 m radius) were excluded. Pixels in the 74 selected images which passed these checks, were then used to create a secondary maximum NDVI composite that was used to fill the gaps in the initial maximum NDVI composite. The secondary composite comprised 0.4% of the pixels in the final composite. Among all 2917 LSP observation sites, 2.9% were located within the gaps in the initial maximum NDVI composite, and thus received their maximum NDVI values from the secondary NDVI composite.In the used Landsat data, the nivation sites were not covered by snow, but instead were associated with generally lower AGB values as nival processes affect the vegetation’s structure and composition (Supplementary Table 1).Above-ground biomass dataAbove-ground biomass (AGB) reference data were collected from two regions, with a total of 433 sites that represent an area of > 4000 km2 (Supplementary Fig. 9). The first dataset (hereafter BM region 1; centering to ca. 69°N, 21°E) was collected between 2008 and 2011, and the second dataset (BM region 2; centering to ca. 70°N, 26.2°E) between 2015 and 2017. Both study regions are representative of an arctic and alpine treeline ecotone and include data from mountain birch forest to barren oroarctic tundra56,57.The BM region 1 dataset consists of 309 field sites (each 10 m × 10 m), which are located around eight different massifs covering a wide range of environmental conditions (Supplementary Figs. 9–10). Sampling was performed in transects to cover various aspects of the slope (i.e., topoclimatic conditions), starting from the foothill of the mountain, and ending at the summit. A plot was systematically established at every 20 m increase in elevation and recorded with a GPS device. Four clip-harvest biomass samples (20 cm × 20 cm) were taken 5 m from the plot center in every cardinal direction. Two samples were used in bare mountaintops (north, south). The clip-harvest samples were dried for 48 h at +65 °C, and dry weight was recorded. The sample biomass values were converted to g m-2 and the average sample value was calculated for each site (Supplementary Fig. 9). The original BM region 1 dataset contains forest and treeline plots, but these were excluded from the final analyses due to an incomparable tree sampling strategy with BM region 2, which could introduce uncertainty into biomass estimates.The BM region 2 data were collected from three different massifs having an elevation range from 120 m to 1064 m (Supplementary Fig. 9). The biomasses were sampled from 102 sites (each 24 m × 24 m in size) that were chosen using a stratified sampling to cover gradients of thermal radiation (potential incoming solar radiation), soil moisture (topographic wetness index, TWI) and vegetation zone (forest, treeline, and alpine zones). Radiation and TWI were calculated from a 10 m digital elevation model (DEM, provided by the National Land Surveys of Finland and Kartverket, the Norwegian mapping authority), and assigned to one of three classes based on observation percentiles (breaks at 20% and 80%) leading to total of 27 strata. Vegetation zones were digitized based on aerial imagery. After the first field survey, 22 sites were added to account for vegetation types that were not sufficiently represented by the GIS-based stratification. Thus, the total sample size of the BM region 2 dataset is 124 AGB sites.The same clip-harvest sample protocol was used as in BM region 1; additional samples were also taken from 12 m in every cardinal direction, thus each site had eight AGB samples (Supplementary Fig. 9). Trees with diameter at breast height (DBH) greater than 20 mm were measured from a 900 m2 circular plot, which corresponds to the size of the NDVI product resolution. Large stems (DBH  > 80 mm in the forest and 40 mm at the treeline) were measured from the whole plot, whereas smaller stems were measured from five subplots. Specifically, the center subplot was 100 m2, and the four subplots located at 8 m to every cardinal direction were each 12.5 m2. For the subplot observations, we used a plot expansion factor (900/150 = 6) to generalize the observations for the whole plot assuming a homogeneous forest structure i.e., each subplot stem represents six trees within the 900 m2 plot. A total of 98% of the measured stems were mountain birch (Betula pubescens ssp. czerepanovii), making it the most abundant species in the area. For predicting stem biomass, we used the average of three allometric equations58,59,60, in order to reduce the uncertainty related to the transferability of an individual allometric model. In addition, Populus tremula (1% of the observations) were found on low-altitude south-facing slopes, and Salix caprea (1%) in moist, nutrient-rich sites. Species-specific models61,62 were used to estimate their respective stem biomasses. Individual pines (Pinus sylvestris) were scattered in the area but were not present in any of the sampled plots.The plots of above-ground tree biomass were converted to g m−2 and added to the mean clip-harvest AGB to obtain the total vascular plant AGB for each site. The BM region 1 and BM region 2 datasets were combined, and the NDVI value was extracted from the site center coordinates.Spatial autocorrelation (SAC) is a common property of any spatial dataset and means that observations are related to one another by the geographical distance63. SAC in the model residuals violates the independence assumption commonly required by statistical models and can lead to inflated hypothesis testing and biased model estimates64. To investigate whether the plot-scale AGB data are spatially autocorrelated, we calculated semivariogram which describes the spatial dependency between the observations as a function of distance between the point pairs65. Semivariogram were calculated as:$${{{{{rm{gamma }}}}}}(h)=frac{1}{2N(h)}mathop{sum }limits_{i=1}^{{N}_{h}}{left(Zleft({s}_{i}right)-Zleft({s}_{i}+hright)right)}^{2}$$
(2)
where N(h) denotes the number of data pairs within distance h, and (Zleft({s}_{i}right)) is an observation (or model residual) in location i. For the calculation, we used R package gstat66 (version 2.0-0). A visual inspection of the semivariogram indicated spatial autocorrelation at short distances (“AGB” in Supplementary Fig. 11). Therefore, for the NDVI-AGB conversion, we used a generalized least squares modeling (GLS, as implemented in R package nlme67 [version 3.1-137]) that can explicitly account for SAC in the data. For the modeling, the AGB values were log(x+0.1) transformed. The GLS, where AGB was modeled as a function of NDVI, were fitted assuming an exponential spatial correlation structure:$$gamma left(hright)={c}_{0}+cleft(1-{e}^{-h/a}right)$$
(3)
where ({c}_{0}) is the difference between the intercept and origin (i.e., the “nugget” parameter in geostatistics), (c) is the amount of variance (i.e., the “sill”) and a represents the distance of spatial dependency (i.e., the “range”). The fitted GLS was as follows:$${{log }}left({AGB}right)=-1.038629+9.725572times {NDVI}$$
(4)
The estimated spatial correlation parameters were c0 = 0.516, c = 0.484 and a = 260.605, indicating that the distance of spatial autocorrelation extends to ca. 261 m. The semivariogram for the model residuals indicated a notable reduction in the amount of spatial autocorrelation compared to the AGB data (Supplementary Fig. 11). The fitted model explained 70.6% of the deviance in the data. When the predicted values were converted back to the response scale, the model explained 60.5% of the deviance. Therefore, for the subsequent analyses we use the above-ground biomass estimated by the model.Environmental predictorsIn addition to LSP, we used climate, topography, and soil predictors to model AGB. Gridded monthly average temperatures and precipitation data (1981–2010; spatial resolution 50 m × 50 m) based on a large collection ( > 950) of Fennoscandian meteorological stations were used in a spatial interpolation scheme17. Three climate predictors—growing degree days (GDD, °C, base temperature 5 °C), mean February air temperature (Tfeb, °C) and water balance (WAB, mm)—were calculated from the gridded climate data. WAB is the difference between total annual precipitation and potential evapotranspiration (PET), which was estimated from the monthly air temperature and precipitation data68:$${PET}=58.93times {T}_{{above}0^circ C}/12$$
(5)
These climatic predictors were selected to represent different aspects of climate that are critical for tundra vegetation: heat requirements, cold tolerance and moisture availability. In addition, two local scale topographic predictors were calculated from a DEM (spatial resolution of 50 m × 50 m, provided by the National Land Survey Institutes of Finland, Norway, and Sweden): topographic wetness index69 (TWI, a proxy for soil moisture) and potential annual direct solar radiation70 (MJ cm-2 a-1). Slope angle was initially considered as a potential predictor for AGB but was later omitted due to the strong correlation with TWI (-0.93, P ≤ 0.001). We also calculated peat cover (%) from a digital land cover classification71. Here, the native resolution of 100 m was resampled at 50 m to match the resolution of the climatic and topographic predictors, using nearest-neighbor interpolation. The binary peat cover variable was transformed to a continuous scale using a spatial mean filter of 3 × 3 pixels52. Finally, the topmost soil layer of a global gridded soil database72 was used to obtain pH data. Again, the original resolution of 250 m was also resampled to 50 m resolution using bilinear interpolation.Our fine-scale data revealed strong environmental gradients over the 78,000 km2 study area (Supplementary Table 1), most of which were only moderately inter-correlated (Spearman’s correlation coefficient  More

Airborne hyperspectral and thermal image acquisitionWe scanned over one million olive and almond trees between 2011 and 2019 with an airborne imaging spectroscopy and thermal imaging facility targeting infected and healthy trees in seven different regions located in Apulia (Italy), Majorca (Balearic Islands, Spain), Alicante, Cordoba and Seville (mainland Spain). In olive groves, over 200,000 and 372,000 trees were imaged from Xf and Vd outbreaks, respectively. In almond groves, we scanned over 132,000 trees from Xf outbreaks in Alicante and Majorca. To evaluate the effects induced by abiotic stress on spectral plant traits, we surveyed over 370,000 healthy trees (outside the outbreak areas) comprising olive and almond species subjected to a wide range of water stress conditions.We surveyed these areas with airborne hyperspectral and thermal cameras on board a manned aircraft flying at 500 m altitude above ground, yielding 40 cm and 60 cm spatial resolution, respectively. We used a hyperspectral camera (VNIR model, Headwall Photonics, Fitchburg, MA, USA) collecting 260 bands in the 400–885 nm region at 1.85 nm/pixel and 12-bit radiometric resolution with a frame rate of 50 Hz. With this spectral configuration, we captured imagery at 6.4 nm full-width at half-maximum (FWHM) bandwidth and obtained an instantaneous field of view (IFOV) of 0.93 mrad and an angular field of view (FOV) of 49.82 deg with an 8 mm focal length lens. The hyperspectral sensor was radiometrically calibrated in the laboratory using an integrating sphere (CSTM-USS-2000C Uniform Source System, LabSphere, North Sutton, NH, USA). At the time of flight, we measured aerosol optical thickness at 550 nm using a Sunphotometer (Microtops II S model 540, Solar LIGHT Co., Philadelphia, PA, USA). We then applied the resulting atmospheric correction of the calibrated radiance imagery with the SMARTS model51 to derive surface reflectance spectra. We carried out ortho-rectification of the hyperspectral imagery (PARGE, ReSe Applications Schläpfer, Wil, Switzerland) with readings acquired by the inertial measuring unit on board the airborne platform (IG500 model, SBG Systems, France). We applied spatial binning through object-based image analysis, thus increasing the signal-to-noise ratio (SNR) of the instrument. Additionally, we conducted spectral binning to reduce the number of spectral bands (260 bands at 1.85 nm resolution). SNR reached >300:1 after binning. We acquired high-resolution tree-crown temperature images with a thermal camera (FLIR SC655, FLIR Systems, USA) at 640 × 480 pixels resolution using a 24.6 mm f/1.0 lens, sensitive to the 7.5–14 μm spectral range and sensitivity below 50 mK.We identified individual trees in the high-resolution hyperspectral and thermal images using object-based crown detection and segmentation methods52. We then calculated the mean hyperspectral radiance, reflectance and temperature for each pure tree crown within every orchard under evaluation. We based our image segmentation methods on Niblack53 and Sauvola and Pietikäinen54, which allowed the isolation of tree crowns from the soil and shadow components. The segmentation of each tree crown was assessed visually to ensure a minimum number of pure vegetation pixels were selected within each tree crown and also spectrally to evaluate the purity of the reflectance extracted from the crown to avoid spectral mixture with soil, shadows and background components24,35.Collection of Xf and Vd biotic stress field dataField assessments of Xf- and Vd-infected trees were carried out from outbreaks affecting olive and almond species in the indicated regions of Italy and Spain between 2011 and 201924,35,52. During these campaigns, we performed quantitative PCR (qPCR)55 for Xf in olive and almond (Alicante), recombinase-polymerase-amplification (RPA) using the AmplifyRP XRT + test (Agdia®, Inc., Elkhart, IN)56 for Xf in almond (Majorca) or conventional PCR57 assays for Vd, as well as visual assessments in individual trees of disease incidence (DI) and disease severity (DS). A sample was considered positive if Ct values were ≤36 and amplification curves were exponential. PCR/qPCR data for model analysis were transformed to 0 and 1, for negative and positive results, respectively, and Ct values were not used in the analysis (see Supplementary Table 2 for the PCR/qPCR primer sequences for Vd and Xf). DS was scored using a 0–4 rating scale according to the percentage of the tree crown showing disease symptoms.In Apulia, the Xf-olive database comprised a total of 15 olive groves surveyed during the June 2016 and July 2017 campaigns. Visual assessments for infection were conducted on 7296 trees (3324 in 2016 and 3972 in 2017). In 2016, 1886 symptomatic (and 1438 asymptomatic) trees were surveyed (762 trees labelled as DS = 1; 802 DS = 2; 250 DS = 3 and 72 DS = 4). In 2017, 1365 were reported as symptomatic (and 2607 asymptomatic) (686 DS = 1; 542 DS = 2; 122 DS = 3 and 15 DS = 4). qPCR assays were carried out to diagnose Xf infection in 77 olive trees, whereby 39 trees tested negative (qPCR = 0) and 38 tested positive (qPCR = 1).On the island of Majorca and at the Alicante province, the field-based Xf-almond database comprised a total of 19 almond groves surveyed in 2018 and 2019, respectively. In Alicante, the field surveys covered 83 ha with 9 almond groves consisting of 943 almond trees. During the field campaigns, almond trees were visually assessed to evaluate Xf-induced DI and DS indices. From this analysis, we identified 593 symptomatic trees and 350 asymptomatic trees. Out of all symptomatic trees, 163 were rated as DS = 1, 214 DS = 2, 157 DS = 3, and 59 DS = 4. Furthermore, qPCR analysis was carried out on 226 almond trees to diagnose Xf infection, resulting in 48 non-infected (qPCR = 0) almond trees and 178 infected trees (qPCR = 1). In Majorca, field surveys in July 2019 covered a total of 2803 ha and comprised 10 almond groves. During the field campaigns, visual observations were carried out on over 4048 almond trees to assess DI and DS, yielding 1387 symptomatic and 2661 asymptomatic trees. From symptomatic trees, 537 were rated as DS = 1449 DS = 2, 359 DS = 3 and 42 DS = 4. We conducted AmplifyRP XRT + assays on 265 almond trees for diagnosing Xf infection the same day they were sampled and identified 141 negative trees (qPCR = 0) and 124 positive trees (qPCR = 1).We carried out physiological measurements of leaf chlorophyll, anthocyanins, flavonoids and nitrogen contents with a Dualex Scientific + (Force-A, Orsay, France) instrument as well as leaf reflectance (400–1000 nm spectral range) and steady-state chlorophyll fluorescence (Ft) using the PolyPen RP400 and FluorPen FP100 instruments (Photon Systems Instruments, Drasov, Czech Republic) during the field evaluations of almond and olive groves conducted in Majorca, Alicante and Apulia regions. In the Xf-olive study site in Apulia, we generated 1023 leaf measurements with Dualex, 1543 single leaf reflectance spectra, as well as 1402 Ft readings over 67 olive trees. In the Xf-almond study sites in Majorca, we measured 1242 leaves with Dualex, 1094 leaves with the PolyPen and 1218 with the Fluorpen instruments from 87 almond trees across a wide range of disease severity levels. For the Xf-almond study sites located at Alicante, we conducted 1649 leaf measurements with Dualex, 632 leaf measurements with PolyPen and 563 leaf measurements with FluorPen FP100 over 43 almond trees.We assessed Vd-infected olive trees from 11 olive groves by surveying an area of over 3000 ha in Castro del Rio and Ecija, southern Spain, in 2011 and 2013, respectively. In Castro del Rio, we conducted visual assessments in an infected area of 96 ha comprising 1878 olive trees, thus identifying 1569 asymptomatic and 283 symptomatic olive trees. Out of the 283 symptomatic trees, 218 were rated as DS = 1; 45 DS = 2; 12 DS = 3 and 8 DS = 4. We measured leaf Fs and Fm’ fluorescence parameters from 25 leaves per tree using a PAM-2100 Pulse-Amplitude Modulated Fluorometer (Heinz Walz GMBH, Effeltrich, Germany). In addition, leaf PRI570 was measured from 25 leaves per tree using a custom-made PlantPen device (Photon System Instrument, Drasov, Czech Republic). Finally, we measured leaf conductance (Gs) on five leaves per tree using a leaf porometer (model SC-1, Decagon Devices, Washington, DC, USA). In the Écija region, the surveyed area covered 3424 ha, and 5223 olive trees were evaluated. We performed visual assessment to determine DI and DS indices of Vd-infected trees, identifying 5040 asymptomatic olive trees. Of the remaining 183 olive trees that were symptomatic, 112 were trees rated as DS = 1; 41 DS = 2; 22 DS = 3 and 8 DS = 4.Trees were evaluated for disease severity and incidence by visual assessment in each outbreak region. PCR assays were carried out on a subset of these trees within each orchard to (i) validate that the pathogen (Xf or Vd) was actually present and the biotic source of symptoms; and (ii) validate that asymptomatic (DS = 0) but infected (PCR = 1) trees were detected using the hyperspectral plant traits estimated through the methodology described in this paper. In general, PCR assays are (i) time consuming and costly, and (ii) difficult to make in large infected trees due to the non-uniform distribution of the infection within each tree crown. These PCR data for each tree along with the field evaluations of DS, DI and non-destructive physiological measurements derived for each tree within every orchard were matched with the high-resolution hyperspectral images to build the biotic databases used in this study. We carried out the field work at each orchard guiding the evaluations and measurements using a high-resolution image to map the location of each tree within the orchard. Due to the planting grids typical of almond and olive species, which were not contiguous or in row-structured patterns, the identification of each individual tree in the images was straightforward.Collection of abiotic stress field dataWe monitored over 3600 ha of olive and almond groves located outside any infected area in Cordoba and Seville, Southern Spain. We performed a multitemporal analysis to study the spectral plant-trait alterations induced by abiotic stress relative to healthy olive and almond trees with data we collected over a 468 ha area comprising two olive and one almond groves throughout July 2016 and August 2017 growing seasons. We analysed 2975 olive and 1964 almond trees in 2016, and 2865 olive and 2063 and almond trees in 2017. At both study sites, we monitored the midday stem water potential (SWP) using a pressure chamber (Soil Moisture Equipment Corp. model 3000, Santa Barbara, CA, USA) on 16 trees per grove. SWP values showed differences between two existing irrigation levels (well-watered and mild water stress), averaging –1.7 and –1.9 MPa across the season in the case of almonds. In olive, SWP in one of the groves reached –3.8 and –3.5 MPa. In 2017, water potential levels averaged –2.9 and –2.0 MPa. In the second grove, irrigation levels were higher, reaching an average SWP of –1.5 MPa. We used an additional study site located in Casariche (Seville province), southern Spain, to validate the results obtained from the multitemporal analysis. This study site covered 3371 ha containing 55 olive groves grown under irrigated and rainfed conditions, with 21,071 olive trees used for statistical analysis.The multitemporal dataset was used to evaluate the water-induced abiotic stress by quantifying the evolution of the importance of the most sensitive spectral traits by clustering non-stressed trees (C0) against groups of trees exposed to increasing levels of water stress (C1 to C4). The multitemporal component of this assessment enabled the evaluation of every single tree across time, therefore selecting the trees for each cluster based on a sustained water stress level, avoiding the selection of trees under short-term stress dynamics. Thus, the clusters were determined based on their CWSI levels, and only the trees with stable water stress levels across two consecutive years (2016 and 2017) were selected for the analysis. For this purpose, we did not include trees that deviated beyond 95% of the CWSI differences calculated between the first and second year in the analysis. After this trimming step, we retained 5484 olive trees (from 5566 trees) and 3652 almond trees (from 3882 almond trees). Trees were then grouped through CWSI clustering analysis using a modified three-sigma rule58. This rule describes the density of a distribution within standard deviation bands on both sides of the mean point into the 68th, 95th and 99.7th percentiles58, representing µ ± σ, µ ± 2σ and µ ± 3σ, respectively. The first interval defined by the classic three-sigma rule (µ ± σ) represented most trees, while the third interval (µ ± 3σ) consisted of very few trees, raising issues for the determination of statistical significance analysis. Based on this observation, we adjusted the breakpoints between groups as follows: we classified those trees that were in the lowest 10th percentile as C0. Trees between the 10th and 68th percentiles (µ + σ) were classified as C1, trees between the 68th and 85th percentile were classified as C2, trees between the 85th and 95th percentile were classified as C3 and finally the trees over the 95th (µ + 2σ) percentile were classified as C4. We thus selected 488 C0, 3066 C1, 1090 C2, 618 C3 and 222 C4 olives trees. Likewise, we grouped almond trees into 390 C0, 1776 C1, 1248 C2, 214 C3 and 24 C4 clusters. Moreover, the analysis of the contribution of a given trait was performed using ML modelling strategies to classify unstressed trees against the clusters defined above that were exposed to increasing levels of water stress. Furthermore, we assessed the consistency of the obtained indicators by performing the classification between stressed and non-stressed trees at an independent olive study site. For this purpose, we evaluated our predictors and compared their contribution over an additional site (Casariche).Model inversion methods for plant-trait estimationWe quantified chlorophyll content (Ca+b), carotenoid content (Cx+c), anthocyanin content (Anth.), mesophyll structure (N), leaf area index (LAI) and average leaf angle (leaf inclination distribution function or LIDF) by radiative transfer model inversion of PROSPECT-D59 and 4SAIL60, as in Zarco-Tejada et al.24. We inverted PROSPECT-D + 4SAIL using a look-up-table (LUT) generated with randomised input parameters. The LUT was generated with 100,000 simulations within fixed ranges (Supplementary Table 3). We implemented a wavelet analysis61 into six wavelets by a Gaussian kernel, estimating the parameters in the top 1% entries ranking the lowest root mean square error (RMSE) values. We then retrieved each plant trait independently by training supported vector machine (SVM) algorithms using the simulated reflectance data as input. We built SVMs in Matlab (MATLAB; Statistics and Machine Learning toolbox and Deep Learning toolbox; Mathworks Inc., Matick, MA, USA) using a Gaussian kernel (radial basis function) with hyperparameters optimised for each model. The training processes were carried out in parallel using the Matlab parallel computing toolbox. With these trained models, we then used the spectral reflectance extracted from the delineated crowns (as show in Fig. 1) to predict plant traits for each individual tree at each study site. The model inversions were carried out for each tree using the crown reflectance. The latter was calculated as an average across all the pixels belonging to the tree crown, delineated using segmentation. This method52 avoids the problem of pixels from within-crown shadows, from tree edges or from sunlit or shaded soil background affecting the spectra, as it retrieves the plant traits from pure sunlit vegetation components of the trees. We also calculated narrow-band spectral indices from reflectance spectra (Supplementary Table 1), which are sensitive to leaf traits and potentially related to disease-induced symptoms. Tree-crown radiance and temperature were used to calculate sun-induced chlorophyll fluorescence at 760 nm (SIF@760) and the crop water stress index (CWSI)37. SIF@760 was quantified using the O2-A in-filling Fraunhofer Line Depth (FLD) method63 and CWSI was calculated by incorporating the tree temperature and the weather data obtained at each study site37.Statistical analysisWe implemented random forest (RF)64 algorithms to classify healthy vs. infected (biotically stressed) trees, and non-stressed vs. water (i.e. abiotically) stressed trees for both tree species. RF algorithms have been widely used in remote sensing studies since they have shown excellent classification accuracies and high processing speeds with high-dimensional data62 and have shown to be accurate in detection of several diseases29,65,66,67. The spectral plant traits estimated by radiative transfer model inversion (Ca+b, Cx+c, Anth., LAI and LIDF), CWSI and SIF@760 were used as inputs for the models. In addition, using a recursive feature elimination approach68 the narrow-band indices that improved the classification in terms of overall accuracy (OA) and kappa coefficient (κ) were added to the models. The pool of narrow-band indices was reduced based on a variance inflation factor (VIF) analysis69 to avoid collinearity among the input features.The RF algorithms were built in Matlab and the hyperparameters were optimised using Bayesian optimisation. The importance of a feature using the RF algorithm was assessed based on the permutation of out-of-bag (OOB) predictor methodology70. To compare the relative differences of the spectral traits in classification of the biotic and abiotic stress, the importance was normalised by dividing the importance of each trait by the highest contribution obtained for each pathogen/species. For the RF models, 500 iterations were run by randomly partitioning each dataset into training (80% of samples) and testing sets (20% of samples). For the training subset, a balanced number of samples from each class was randomly selected at each iteration. The importance obtained by the OOB permutation algorithms was used to build a feature-weighted random forest algorithm (based on Liu and Zhao45), accounting for the importance of each variable on the classification process, evaluating the model against PCR data and visual observations for each biotic stress dataset in terms of OA and κ levels.Probabilities of the predictions were obtained for each sample71 and the uncertain trees were assessed. To extract the uncertainty for each individual tree on the classification, we evaluated the probability distribution for each class from each dataset independently. Then, those trees with a classification probability below the 68th percentile (µ [mean] + σ [standard deviation]) were considered as uncertain and incorporated into a second-stage classification process. The second stage consisted of an unsupervised graph theory–based spectral clustering algorithm72 and included traits selected by focusing on the divergent biotic–abiotic stress obtained from the biotic and the abiotic stress databases. Spectral clustering was performed in R using the kernlab package73.To determine the spectral traits that differed between Xf- and Vd-infected plants and those from the abiotic pathway, we first normalised the importance of the specific traits independently. Then, we compared the common traits between abiotic and biotic stress sets, selecting only biotic stress-related traits that differed in ratio by >0.5 over their homologous abiotic stress trait values. Traits that were only expressed under biotic stress conditions and that showed a normalised importance over 0.5 were included for the second-stage classification process only including those divergent-specific biotic and abiotic stress-related spectral traits as inputs. Specifically, NPQI, Anth. and SIF@760 were considered for the classification of Xf-infected olive trees. Ca+b, SIF@760 and PRIn were used for classifying Xf-infected almond trees. Furthermore, NPQI, Anth. and B spectral traits were selected for classifying uncertain Vd-infected olive trees. Finally, we validated our feature-weighted methodology coupled with the second-stage spectral clustering method against qPCR assays and visual assessment of symptom severity.Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article. More