Ecology

Data sourcesThis study builds on two datasets; 666 livestock anthrax outbreaks collected over 60 years (1957–2017) by the Kenya Directorate of Veterinary Services (KDVS), and 13 reported anthrax outbreaks we investigated between 2017 and 201811,13. These datasets were combined with data from targeted active anthrax surveillance we conducted in 2019–2020 (see below) to define anthrax suitable areas in Kenya, including hotspots, and subsequently assessed effectiveness of livestock vaccination as a control strategy.Targeted active surveillance-collected anthrax data, 2019–2020Active anthrax surveillance was conducted for 12 months between 2019 and 2020 in randomly selected areas to ensure representation of all AEZs of the country. AEZs are land units defined based on the patterns of soil, landforms and climatic characteristics. Kenya has seven AEZs that include agro-alpine, high potential, medium potential, semi-arid, arid, very-arid and desert. In 2013, Kenya devolved governance into 47 semi-autonomous counties that are subdivided into 290 subcounties which are in turn divided into 1450 administrative wards, the smallest administrative units in the country. Using a geographic map that condensed Kenya into five AEZs; agro-alpine, high potential, medium potential, semi-arid, and arid/very arid zones, we randomly selected 4 administrative sub-counties from each AEZ (N = 20). To increase geographic spread of the study and enhance detection of anthrax outbreaks, we surveilled the larger administrative county (consisting of 20 to 45 administrative wards) where the randomly selected sub-counties were located. As shown in Fig. S1, we ultimately carried out the active anthrax surveillance in 18 counties, containing 523 administrative wards, the latter being used for measuring spatial association (see below).We conducted the surveillance between April 2019 and June 2020, through 523 animal health practitioners (AHPs), one in each ward, after intensive training to identify anthrax using a standard case definition, and to collect and electronically transmit the data weekly using telephone-based short messaging system (SMS) to a central server hosted by KDVS. Regarding case definition, any livestock death classified as anthrax through clinical or laboratory diagnosis was considered an anthrax event. Using standard guidelines issued by the KDVS, a clinical diagnosis was made by the AHPs across the country as an acute cattle, sheep or goat disease characterized by sudden death with or without bleeding from natural orifices, accompanied by absence of rigor mortis. Further, if the carcass was accidentally opened, failure of blood to clot and/or the presence of splenomegaly were included. In pigs, symptoms included swelling of the face and neck with oedema. A laboratory confirmed anthrax was diagnosed using Gram and methylene blue stains followed by identification of the capsule and typical rod-shaped B. anthracis in clinical specimens that the AHPs submitted to the central or regional veterinary investigation laboratories in Kenya. One case of anthrax in either species was considered an outbreak.During the surveillance, the programmed server sent prompting texts directly to the AHPs’ cell phones every Friday of each week for the 52 weeks. The AHPs interacted with the platform by responding to prompting questions sent via SMS to their telephones. Data were securely stored in an online encrypted platform which was subsequently downloaded into Ms Excel for analysis. This surveillance detected 119 anthrax outbreaks, whose partial data were used to model effects of climate change on future anthrax distribution in Kenya14. Here, we integrated these active surveillance data with other datasets to conduct detailed ENM and kernel-smoothed density mapping with a goal of refining suitable anthrax areas including crystalizing hotspots in the country.Anthrax outbreak incidence per livestock population by countyWe knew the total number of livestock per county and wards by species for the active surveillance period. The counties represented the level of disease management including vaccine distribution while the wards within counties represented the modeling unit for targeting control. Therefore, we estimated the outbreak incidence as the total number of outbreaks per livestock species per 100,000 head of that species.Ecological niche modeling and validationWe used boosted regression tree (BRT) algorithm as previously published13. In those studies, we estimated the geographic distribution of anthrax in southern Kenya using 69 spatially unique outbreak points (thinned from the 86 outbreaks in the records) and 18 environmental variables resampled to 250 m resolution. In this study, the final experiments were run with a learning rate (lr) = 0.001, bagging fraction (br) = 5, and maximum tree = 2500. We then mapped anthrax suitability as the mean output of the 100 experiments and the lower 2.5% and upper 97.5% mapped as confidence intervals. We determined variable contribution and derived partial dependence as previously described13. As BRTs are a random walk and each experiment randomly resamples training and test data, it was necessary to repeat those outputs along with the map predictions.Here, our goal was to evaluate the BRT models built with records data from 2011 to 2017 data and use the predict function to calculate model accuracy metrics using the 2017–2020 outbreaks as presence points and the sub-counties reporting zero outbreaks during the 2019–2020 active surveillance period as absence points. The model of southern Kenya was projected onto all of Kenya using climate variables clipped to the whole of Kenya. We tested the BRT models in two ways; first, evaluating 2011–2017 data models with holdout data using a random resampling and multi-modeling approach. Here, we report the area under curve (AUC) for each of the original training/testing split into the 69 historical points and the 2017–2020 data serving as independent data, the latter representing true model validation. Second, to determine the total percentage of surveillance data predicted and map areas of anthrax suitability to compare with kernel density estimates (see below), we produced a dichotomized map using the Youden index cutoff17 following Otieno et al.14.Outbreak concentrations from kernel density estimation (KDE)To describe the spatial concentration of reported outbreaks, we calculated descriptive spatial statistics, including the spatial mean, standard distance, and standard deviational ellipse of outbreak locations from the prospective surveillance dataset following Blackburn et al.18 These spatial statistics help to differentiate the geographic focus (spatial mean) and dispersion of outbreak reports from year to year and across the sampling period. We then conducted kernel density estimation (KDE) to visualize the concentration of anthrax outbreaks per square kilometer per year and across the study period18. We used the spatstat package for all KDE analyses using the quadratic kernel function19:$$fleft( x right) = frac{1}{{nh^{2} }} mathop sum limits_{i = 1}^{n} Kleft( {frac{{x – X_{i} }}{h}} right)$$where h is the bandwidth, x-Xi is the distance to each anthrax outbreak i. Finally, K is the quadratic kernel function, defined as:$$Kleft( x right) = frac{3}{4}left( {1 – x^{2} } right), left| x right| le 1$$$$Kleft( x right) = 0,x > 1$$This function was employed to estimate anthrax outbreak concentration across space using each outbreak weighted as one. We calculated the bandwidth (kernel) using hopt that uses the sample size (number of outbreaks) and the standard distance to estimate bandwidth. Finally, we estimated bandwidth for each year and then averaged them to apply the same fixed bandwidth for each year under study in Q-GIS version 3.1.8. The resulting outputs were map surfaces representing the spatial concentrations of outbreaks across the country per 1 km2 for each study year and all study years combined. For this study, we used the cutoff criteria of Nelson and Boots19 to identify outbreak hotspots as areas with density values in the upper 25%, 10%, and 5% of outbreak concentrations. The analyses identified these areas by year (2017–2020) and for all surveillance years combined.Local spatial clustering at the ward levelAnthrax outbreak incidence per livestock speciesThe ENM and KDE-derived maps provide a first estimate of potential risk and outbreak concentration, respectively. We were also interested in estimating anthrax outbreak intensity relative to livestock populations at a local level. For the active surveillance period, we knew the total number of outbreaks per ward (the smallest administrative spatial unit) by livestock species. For this two-year period, we estimated the ward-level outbreak incidence as the total number of outbreaks per livestock species per 10,000 head of that species. To estimate livestock population per ward, we extracted the values in the raster file of the areal weighted gridded livestock of the world data using the zonal statistic routine in Q-GIS version 3.1.8, into the polygon consisting of all pixels per ward as the total population19,20. We calculated outbreak incidence as the number of outbreaks per ward cattle population per 10,000 cattle for each administrative ward. We limited this analysis to those 18 counties participating in the active surveillance study (Fig. S1), as we could appropriately assume any ward with no reports was a ‘true zero’ for the estimation. Given that most reported outbreaks were in domestic cattle (see results below), we here report those results involving cattle alone. Given the overall high number of wards and the high number of wards without outbreaks, we performed the empirical Bayes smoothing and spatial Bayes smoothing routines in GeoDa version 1.12.1.161 to reduce the variance in anthrax incidence estimates20,21. To evaluate smoothing routine performance, we box plotted rates per ward and selected the method with the greatest reduction in outliers21. Smoothed rates were mapped as choropleth map in Q-GIS version 3.1.8 using the four equal area bins.Spatial cluster analysisWe used Local Moran’s I16 to test for spatial cluster of livestock anthrax in cattle using the smoothed outbreak incidence estimates. The Local Moran’s I statistic tests whether individual wards are part of spatial cluster, like incidence estimates surrounded by similar estimate (high-high or low-low) or spatial outliers where wards with significantly high or low estimates are surrounded by dissimilar values (high-low or low–high). The local Moran’s I is written as16:$$I_{i} = Z_{i} sum W_{ij} Z_{j}$$where Ii is the statistic for a ward i, Zi is the difference between the incidence at i and the mean anthrax incidence rate for all of wards in the study, Zj is the difference between anthrax risk at ward j and the mean for all wards. Wij is the weights matrix. In this study, the 1st order queen contiguity was employed. Here, Wij equals 1/n if a ward shared a boundary or vertex and 0 if not. For this study, Local Moran’s I was performed on the wards using 999 permutations and p = 0.05 using GeoDa version 1.12.1.161.Assessing effectiveness of cattle vaccination in burden hotspotsAs a first estimate of how we might scale up livestock anthrax vaccination efforts in Kenya, we slightly adjusted a simple published anthrax outbreak simulation model in a cattle population. For this study we applied an early mathematical approach of Funiss and Hahn22 to simulate anthrax at the ward level. While other recent models are available23,24, these are difficult to parameterize or require time series data we could not derive with the surveillance approach in this study. Like the more recent models, Funiss and Hahn22 assumed anthrax transmission was driven by cattle accessing spore-contaminated environments. Here the proportion of infected cattle each day depended on the population of susceptible animals in the population and probability of getting infected. This probability depends on environmental contamination (“a”), and a fraction of anthrax carcasses in the environment on a day (“f,”). Each day, the newly infected cattle are transferred to an incubation period vector, “d,” waiting to die following a probability “p”. In this model, all infected animals, “n,” die following the incubation periods given by the vector, “p”, in which pi is the probability of a cow dying i days after the infection. Following death, the cattle are transferred to a carcass state, providing a direct infection source to the susceptible cattle via environmental contamination. Environmental contamination “a,” is therefore defined as the number of spores ingested by an animal in a day. This environmental contamination depends on spores from carcasses and an assumed spore decay rate γ22.The complete set of difference equations with a daily time step is given by:$${text{S}}_{(t + 1)} = {text{S}}_{(t)} – {text{ S}}_{(t)} *left( {{1} – {text{e}}^{{ – left( {{text{a}}_{t} + gamma {text{f}}_{{{text{t}} + 1}} } right)}} } right)$$$${text{I}}_{(t + 1)} = {text{I}}_{(t)} + {text{ S}}_{(t)} *left( {{1} – {text{e}}^{{ – left( {{text{a}}_{{text{t}}} + gamma {text{f}}_{{{text{t}} + {1}}} } right)}} } right)$$where the expression (left( {{1} – {text{e}}^{{ – left( {{text{a}}_{t} + gamma {text{f}}_{{{text{t}} + 1}} } right)}} } right)) denotes the probability of an animal becoming infected and at + γft+1 is the mean number of spores ingested by a cow in a day. The equation for environmental contamination, a, is given by:$${text{a}}_{t + 1} {-}{text{a}}_{{text{t}}} = alpha {text{a}}_{{text{t}}} + beta {text{c}}_{{{text{t}} + {1}}}$$The newly infected animals die after a certain number of days. The distribution of incubation periods is given by the vector, p. On each day, the new cases are placed in a due-to-die vector, d, and when they die, they are subsequently moved down one step to fresh carcasses, ft. The fresh carcasses provide a direct source of infection to the susceptible cattle via the ‘fresh carcass term’, γ. These carcasses decay or are scavenged or disposed by man. The equation expressing the disseminating carcasses, c, is:$${text{C}}_{t + 1} – {text{c}}_{t} = {text{f}}_{t + 1} – delta {text{c}}_{t}$$The model parameters variables are provided in Table 1 and are similar to those used by Funiss and Hahn22 to generate a standard run. We ran the model for one year and extrapolated to cattle population in the identified hotspot wards.Table 1 Model parameters and variables.Full size table More

Site selection and sampling strategyField sites (Table 1) were selected to represent typical natural vegetation types showing little or no signs of disturbance. Although much of the natural vegetation of China has been altered by human activities, there are still extensive areas of natural vegetation. Access to these areas is facilitated by the existence of a number of ecological transects39,40, the ChinaFlux network (http://www.chinaflux.org) and the Chinese Ecosystem Research Network (http://www.cern.ac.cn/0index/index.asp).About half the sites in CPTDv1 used a stratified sampling approach and this approach was used at all of the new sites added in the CPTDv2. This sampling strategy involves sampling the dominant species within each vegetation stratum so as to be able to characterise trait values at community level18. Specifically, a total of 25 trees, 5 shrubs, 5 lianas or vines, and 5 understorey species (grasses, forbs) were sampled at each site. When there were less than 25 trees at a site, all of the tree species were sampled and additional examples from the other categories were included up to the maximum of 40 species. If there are more than the maximum sampling number in any one category, then the dominant (i.e. most common) representatives of each category were sampled. Sampled individuals of each species were mature, healthy plants. In principle, sun leaves (i.e. leaves in the canopy and fully exposed to sunlight) were sampled. For true shade-tolerant and understory species, the sampled individuals were those in well-lit environments and isolated to minimize interactions with other individuals.Nineteen sites from Xinjiang included in CPTDv1 used a simplified sampling strategy, where only canopy species were sampled. Sixteen sites from Xinjiang were particularly depauperate and thus only a limited number of species were sampled without consideration of abundance. These sites are retained in the database because they sample extremely arid location with α typically less than 0.25Species identification and taxonomic standardisationSampled plants were identified in the field by a taxonomist familiar with the local vegetation, most usually using a regional flora. Species names were subsequently standardised using the online version of the Flora of China (http://www.efloras.org/flora_page.aspx?flora_id=2). Where field-identified species were not accepted or included in the Flora of China, and thus could not be assigned unambiguously to an accepted taxonomic name, we cross-checked whether the species were listed in the Plant List (http://www.theplantlist.org/) (or alternative sources such as the Virtual Herbarium of China, Plants of the World Online or TROPICOS) in order to identify synonyms for these accepted names that were recognised by the Flora of China. In cases where we were unable to identify an accepted name consistent with the Flora of China, we retained the field-assigned name by default (Fig. 3). The decisions about taxonomy are described in the CPTDv2 table “Taxonomic Standardisation” (Table 2). The names assigned originally in the field and the accepted standardized names used in the database are given in the CPTDv2 table “Species Translations” (Table 3). When species were recognised in the Flora of China, we provide the Chinese translation of the species name. The written Chinese nomenclature system does not follow the Linnaean system, so this table of “Species Chinese Name” is designed to facilitate the use of the database by botanists in China (Table 4). There are no translations of names that are not recognized by the Flora of China and are used in the database by default.Fig. 3Flowchart showing the decision tree used to determine the names used in the China Plant Database (accepted names) and encapsulated in the Taxonomic Standardization table. ‘=1’ and ‘ >1’ indicate the number of Synonyms is equal or more than one.Full size imageDataset collection methodsPhotosynthetic pathwayInformation on photosynthetic pathway (Table 5) was obtained for each species from the literature. There are a large number of literature compilations on the photosynthetic pathway of Chinese plants (e.g.41,42,43,44,45,46. Where this information was not available from Chinese studies we used similar compilations from other regions of the world (e.g.47,48,49,50,51,52. Since C4 plants have much less carbon discrimination than C3 plants, the measurements on δ13C were also used as an indicator of the photosynthetic pathway53,54,55,56. δ13C value of –20‰ was applied as a threshold of C3 photosynthetic pathway distinction54. Information about photosynthetic pathway was not included for a species unless confirmed from the literature or δ13C measurements.Leaf physical and chemical traitsPhysical and chemical properties (Table 6) were measured on samples collected in the field following standard methods37. At least 10 g of leaves were collected for each species. Sunlit leaves of tree species were obtained with long-handled twig shears. The samples were subdivided for the measurement of specific leaf area, leaf dry matter content and the contents of carbon, nitrogen, phosphorus and potassium. Recorded values were the average of three replicates. Leaf area was determined by scanning five leaves (or more in the case of small leaves, to make up a total area ≥20 cm2 per species) with a laser scanner. Areas (Average LA) were measured using Photoshop on the scanned images. Leaf fresh weight was measured in the field. Dry weight was obtained after air drying for several days and then oven drying at 75 °C for 48 hours. Leaf dry matter content (LDMC) was expressed as leaf oven-dry weight divided by fresh weight. Specific leaf area (SLA) was then expressed as the ratio between leaf area and leaf dry mass. LMA is the inverse of SLA. Leaf carbon content (Cmass) was measured by the potassium dichromate volumetric method and leaf nitrogen content (Nmass) by the Micro-Kjeldahl method. Leaf phosphorus (Pmass) was analysed colorimetrically (Shimadzu UV-2550). Leaf potassium (Kmass) was measured by Flame Atomic Emission Spectrophotometry (PE 5100 PC). The area-based leaf chemical contents (Carea, Narea, Parea, Karea) were derived as a product of mass-based content and LMA. δ13C (d13C:12C) and δ15N (d15N:14N) were measured using the Isotope Ratio Mass Spectrometer (Thermo Fisher Scientific Inc., USA; Finnigan Corporation, San Jose, CA).Photosynthetic traitsSeveral different methods were used to characterise photosynthetic traits (Supplementary Table 1). Chlorophyll fluorescence measurements were made at the sites along Northeast China Transect. These measurements were recorded as the potential (Fv/Fm) and actual (QY) rates of photosynthetic electron transport. QY is correlated with photosynthetic rate, although it also includes the diversion of electrons to non-photosynthetic activities such as the elimination of reactive oxygen species57. Measurements of photosynthetic traits at most of the sites (about 68% of samples with photosynthetic measurements) were derived from leaf gas-exchange measurements in light-saturated conditions under either ambient or high CO2 levels, made with a portable infrared gas analyser (IRGA) system (LI-6400; Li-Cor Inc., Lincoln, NB, USA). Sunlit terminal branches from the upper canopy were collected and re-cut under water immediately prior to measurement. Measurements were made in the field with relative humidity and chamber block temperature close to that of the ambient air at the time of measurement, and a constant airflow rate (500 μmol s−1). The maximum capacity of carboxylation (Vcmax) and electron-transport (Jmax) were calculated from the light-saturated rate of net CO2 fixation at ambient and high CO2 level respectively using the one-point method for Vcmax58 and two-point method for Jmax59. Although it was indicated that applying one-point method could result in around 20% error in measuring photosynthetic capacity60, this time-saving method indeed allows much more samples to be measured in the field. For sites in CPTDv1, the Vcmax and Jmax values were made on a single specimen of each species at each site, due to the time-consuming nature of the measurement. For the newly collected sites in CPTDv2, for each species the Vcmax and Jmax were measured on three samples collected from three individual tress. The average values were recorded in the database. For Vcmax measurements, the CO2 level was set as the ambient atmospheric CO2 level, ranging from 380 ppm to 400 ppm. The leaves were exposed to a typical photosynthetic photon flux density (PPFD) of 1800 μmol m−2 s−1 with the light source. Pre-processing method was applied to determine the saturating PPFD for alpine plants, which goes up to 2000 μmol m−2 s−1 in the high elevation sites from Mountain Gonga. For Jmax measurements, the CO2 level was set as 1500 ppm or 2000 ppm to avoid any limitation on photosynthesis via carboxylation.There are a few cases (1 site from Cai, et al.61, and 8 sites from Zheng and Shangguan62, Zheng and Shangguan63), where field-measured ratio of leaf internal- to ambient-CO2 concentration (ci:ca) were not provided. In these cases, estimates of the ci:ca ratio were made from δ13C measurements using the method of64 to calculate isotopic discrimination (Δ) from δ13C (correcting for atmospheric δ13C, approximated as a function of time of collection and latitude), and the Ubierna and Farquhar65 method to calculate isotopic discrimination (Δ) from δ13C considering discrimination during stomatal diffusion and carboxylation. The R code for calculating Vcmax and Jcmax from original data was provided (seeing Code availability).Hydraulic traitsCPTDv2 contains information on four important hydraulic traits: specific sapwood conductivity, the sapwood to leaf area ratio (Huber value, vH), turgor loss point and wood density (Table 7). Hydraulic traits were measured on branches with a diameter wider than 7 mm, cut as close to the bifurcation point as possible to minimize any effect of measurement location on measured area. A section was taken from the part of the branch nearest to the bifurcation point, and the cross-sectional area of the xylem was measured at both ends of this section using digital calipers. Sapwood area was calculated as the average of these two measurements. All leaves attached to the branch were removed and dried at 70 °C for 72 hours before weighing. The total leaf area was obtained from dry mass and LMA. vH was calculated as the ratio of sapwood area and leaf area. The vH value recorded for each species at each site was the average of three measurements made on branches from different individuals.Five branches from at least three mature individuals of each species at each site were collected, wrapped in moist towels and sealed in black plastic bags, and then immediately transported to the laboratory. All the samples were re-cut under water, put into water and sealed in black plastic bags to rehydrate overnight. Sapwood-specific hydraulic conductivity, (KS) was measured using the method of Sperry, et al.66. Segments (10–15 cm length) were cut from the rehydrated branches and flushed using 20 mmol L−1 KCl solution for at least 30 minutes (to remove air from the vessels) until constant fluid dripped from the section. The segments were then placed under 0.005 MPa pressure to record the time (t) they took to transport a known water volume (W, m3). Length (L, m), sapwood area of both ends (S1 and S2, m2) and temperature (Tm, °C) were recorded. Sapwood-specific hydraulic conductivity at measurement temperature (KS,m, mol m−1 s−1 MPa−1) was calculated using Eq. (1). This was transformed to KS at mean maximum temperature during the growing season (KS,gt) and standard temperature (KS25) following Eqs. (2–3):$${K}_{S,m}={W,L{rho }_{w}/[0.005,t({S}_{1}+{S}_{2})/2]}(1000/,18)$$
(1)
$${K}_{S,t}={K}_{S,m}{eta }_{m}/{eta }_{t}$$
(2)
$$eta =1{0}^{-3}exp[A+B/,(C+T)]$$
(3)
where ηm and ηt (Pa s) are the water viscosity at measurement temperature and transformed temperature (i.e. mean maximum daytime temperature during the growing season and at a standard temperature of 25 °C), respectively, and ρw (kg m−3) is the density of water. The parameter values used in Eq. (3) were A = −3.719, B = 580 and C = −13867.A small part of each sapwood segment was used to measure wood density, the ratio of dry weight to volume of sapwood. After removal of bark and heartwood, the volume of sapwood was measured by displacement and the sapwood dry weight was obtained after drying at 70 °C for 72 hours to constant weight.The method described by Bartlett, et al.68 was used for the rapid determination of turgor loss point (Ψtlp). After rehydration overnight, discs were sampled using a 6-mm-diameter punch from mature, healthy leaves collected on each branch, avoiding major and minor veins. Leaf discs wrapped in foil were frozen in liquid nitrogen for at least 2 minutes and then punctured 20 times quickly with sharp-tipped tweezers. Five repeat experiments using leaves from multiple individuals were carried out for every species at each site. The osmotic potential (Ψosm) was measured with a VAPRO 5600 vapor pressure osmometer (Wescor, Logan, UT, USA) and Ψtlp (in MPa) was calculated as:$${Psi }_{tlp}=0.83{2Psi }_{osm}-0.631$$
(4)
Morphometric traitsThe morphometric trait data (Supplementary Table 2) were measured systematically by the same people (SPH and ICP) at all the sites. A standardized template for the field measurement of morphometric traits was used (Supplementary Table 5). This template provides a checklist of the traits and the categories used to describe them. The leaf traits assessed were texture, colour, size, thickness, orientation, display, shape, margin form, the presence of hairs, pubescence, pruinosity or rugosity, the presence of surface wax, hypostomatism, marginal curling (involute, revolute), smell (aromatic or fetid), the presence of a terminal notch or drip-tip, surface patterning, succulence, the presence and positioning of spines or thorns on the leaves. Illustrations of the various categories used in the classification of leaf margin and leaf shape are provided in supplementary materials, together with the template for leaf size categories (Supplementary Figs. 1–3). Although the distinction between spines and thorns is sometimes based on the source material (where thorns are derived from shoots and buds, and spines from any part of the leaf containing vascular material), here the differentiation is based on the shape of the protrusion (where thorns are triangular in shape and can be branched, and spines are unbranched and linear features). The checklist template also includes a limited amount of information on stem traits, such as form, colour, whether the stem is photosynthetic, the presence of stem hairs, pubescence, or pruinosity, and the presence of spines or thorns. For woody plants (trees, shrubs, climbers), the checklist also includes information on bark type (deciduous or not, with an indication of whether the bark is strip or chunk deciduous), the presence of furrowing, and also the presence of spines or thorns.Plant Functional TypesThe database includes information on life form, plant phenology, leaf form and leaf phenology (Table 8). Although these four pieces of information are used by many modellers in the definition of plant functional types (PFTs)69,70, they are not strictly species-specific traits. Thus, some species can occur as a tree, a small tree or a shrub (e.g. Cyclobalanopsis obovatifolia), or as a shrub or liana (e.g. Smilax discotis), depending on environmental conditions. Similarly, some species can behave as an evergreen or deciduous plant, depending on moisture availability (e.g. Ulmus parvifolia). Thus, this information is recorded for individual species at each site and no attempt was made to ensure that a given species was classified identically at all sites. In total 20 distinct life forms were recognized, including tree, small tree, low to high shrub, erect dwarf shrub, prostrate dwarf shrub, trailing shrub, liana, climber, forb, cushion forb, rosette forb, graminoid, bamboo, cycad, geophyte, stem succulent, succulent, pteridophyte, epiphyte, parasite. Plant phenology is recorded as perennial, biennial or annual. The primary distinction in leaf phenology is between deciduous and evergreen, but the classification used in the database also recognizes facultative deciduousness (semi-deciduous) and leaf-exchangers (i.e. plants that retain their leaves for nearly the whole year but drop and replace all of the leaves in a single short period, rather than replacing some leaves continuously through the year as evergreens do). The concept of leaf phenology is only relevant for woody plants (trees, shrubs, lianas) and so is not recorded for e.g. forbs or climbers.VegetationThe local vegetation was not recorded in the field at each site, and in any case such descriptions are hard to standardize. The CPTDv2 database contains information on vegetation type extracted from the digital vegetation map of China at the scale of 1:1 million71, which uses 55 plant communities (48 natural plant communities and seven cropping systems). CPTDv2 further provides information on vegetation clusters aggregated from those fundamental plant communities from the Vegetation Atlas of China based on their bioclimatic context72. CPTDv2 also contains information on potential natural vegetation (PNV), derived from an updated version of the73 global mapping of PNV. This PNV map was produced using pollen-based vegetation reconstructions as a target, a set of 160 spatially explicit co-variate data sets representing the climatic, topographic, geologic, and hydrological controls on plant growth and survival, and an ensemble machine-learning approach to account for the relationships between vegetation types and these covariates (Table 9). The original version of the map had a spatial resolution of 1 km; the updated version used here (https://github.com/Envirometrix/PNVmaps) has a resolution of 250 m.ClimateClimatological estimates of monthly temperature, precipitation and fraction of sunshine hours were derived from records from 1814 meteorological stations (740 stations have observations from 1971 to 2000, the rest from 1981 to 1990: China Meteorological Administration, unpublished data), interpolated to a 0.01 grid using a three-dimensional thin-plate spline (ANUSPLIN version 4.36;74. These monthly climatological data were used directly to calculate the mean temperature of the coldest month (MTCO), mean annual temperature (MAT), mean monthly precipitation (MMP) and mean annual precipitation (MAP). Bioclimatic variables at each site were calculated from the interpolated monthly temperature, precipitation and fraction of sunshine hours using the Simple Process-Led Algorithms for Simulating Habitats (SPLASH) model75. The bioclimatic variables include total annual photosynthetically active radiation during the growing season when mean daily temperatures are >0 °C (PAR0), the daily mean photosynthetically active radiation during the growing season (mPAR0), growing degree days above a baseline of 0 °C (GDD0), the daily mean temperature during the growing season (mGDD0), the ratio of actual to equilibrium evapotranspiration (α), and a moisture index (MI) defined as the ratio of mean annual precipitation to potential evapotranspiration. We also calculated the timing of peak rainfall and rainfall seasonality, using metrics described in Kelley, et al.76 (Supplementary Table 3).The topography in the Gongga region is complex, and the standard climate data set is inadequate to capture the elevation impacts of local climate at the sites there13. We therefore also provide alternative estimates of climatic variables for the Gongga elevation transects using 17 weather stations from the region with records from January 2017 to December 2019 (Supplementary Table 4). These 17 stations range in elevation from 422 m to 3951 m, in latitude from 28° to 31° N, and in longitude from 99.1° to 103.8° E. The climatological records for each station were downloaded from China Meteorological Data Service Centre, National Meteorological Information Centre (http://data.cma.cn/data/detail/dataCode/A.0012.0001.html). The monthly maximum and minimum temperature, precipitation, percentage of possible sunshine hours were extracted. The monthly mean temperature was calculated as the average of maximum and minimum temperature. The elevationally-sensitive ANUSPLIN interpolation scheme74 was used to provide estimates of meteorological variables at each site as described above. The bioclimatic variables were calculated following the same methodology as the 0.01 grid data described above.SoilSoil was not sampled in the field, but to facilitate analyses we provide soil information extracted from the Harmonized World Soil Database (HWSD) v1.277 (Table 10). The HWSD v1.2 is a high-resolution (0.05°) soil database with soil characteristics determined from real soil profiles. The soil properties were estimated in a harmonized way, where the actual soil profile data and the development of pedotransfer rules were undertaken in cooperation with ISRIC and ESBN drawing on the WISE soil profile database and some earlier works78,79. The HWSD v1.2 provides information for the uppermost soil layer (0–30 cm) and the deeper soil layer (30–100 cm). Although HWSD v1.2 contains information on a large number of soil properties, we only extracted information on soil texture (sand fraction, silt fraction and clay fraction), the content of organic carbon, soil pH in water, and cation exchange capacity. More

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Russia invades UkraineThe global science community was quick to condemn Russian’s invasion of Ukraine in February. Research organizations moved fast to cut ties with Russia, stopping funding and collaborations, and journals came under pressure to boycott Russian authors.The situation escalated when Russian forces attacked Europe’s largest nuclear power plant, Zaporizhzhia, in March, prompting fears of a nuclear accident. Russian troops continue to occupy the power plant. Since the invasion began, thousands of civilians have been killed and millions displaced; many others, including scientists, have fled the country.The war has affected research in space and climate science, disrupted fieldwork and played a significant part in the global energy crisis. The invasion could also precipitate a new era for European defence research.JWST delights astronomers

Stephans Quintet, a grouping of five galaxies, taken by NASA’s James Webb Space Telescope.Credit: NASA, ESA, CSA, and STScI via Getty

NASA’s James Webb Space Telescope (JWST) — the most complex telescope ever built — reached its destination in space in January after decades of planning. In July, astronomers were awed by the telescope’s first image — of thousands of distant galaxies in the constellation Volans. Since then, the US$10-billion observatory has captured a steady stream of spectacular images, and astronomers have been working feverishly on early data. Insights include detailed observations of an exoplanet, and leading contenders for the most distant galaxy ever seen.NASA also decided not to rename the telescope, despite calls from some astronomers to do so because the telescope’s namesake, a former NASA administrator, held high-ranking government positions in the 1950s and 1960s, when the United States systematically fired gay and lesbian government employees. A NASA investigation “found no evidence that Webb was either a leader or proponent of firing government employees for their sexual orientation”, the agency said in a statement in November.AI predicts protein structuresResearchers announced in July that they had used the revolutionary artificial-intelligence (AI) network AlphaFold to predict the structures of more than 200 million proteins from roughly one million species, covering almost every known protein from all organisms whose genomes are held in databases. The development of AlphaFold netted its creators at the London-based AI company DeepMind, owned by Alphabet, one of this year’s US$3-million Breakthrough prizes — the most lucrative awards in science.AlphaFold isn’t the only player on the scene. Meta (formerly Facebook), in California, has developed its own AI network, called ESMFold, and used it to predict the shapes of roughly 600 million possible proteins from bacteria, viruses and other microorganisms that have not been isolated or cultured. Scientists are using these tools to dream up proteins that could form the basis of new drugs and vaccines.Monkeypox goes global

The monkeypox virus (shown here as a coloured transmission electron micrograph) is related to the smallpox virus.Credit: CDC/Science Photo Library

The rapid global spread of monkeypox (recently renamed ‘mpox’ by the World Health Organization) this year caught many scientists off guard. Previously, the virus had mainly been confined to Central and West Africa, but from May this year, infections started appearing in Europe, the United States, Canada and many other countries, mostly in young and middle-aged men who have sex with men. The virus is related to smallpox, and the circulating strain only rarely causes severe disease or death. But its fast spread led the World Health Organization to declare the global outbreak a ‘public-health emergency of international concern’, the agency’s highest alert level, in July.As cases soared, researchers got to work trying to understand the dynamics of the disease. Studies confirmed that it is transmitted primarily through repeated skin-to-skin contact, and trials of possible treatments got under way. Existing smallpox vaccines were also used to suppress the virus in some countries. Six months after mpox infections first started increasing, vaccination efforts and behavioural changes seemed to have curbed its spread in Europe and the United States. Researchers predict a range of scenarios from here — the most hopeful being that the virus fizzles out in non-endemic countries over the next few months or years.The Moon has a revivalThe Moon has become a popular destination for space missions this year. First off the launch pad, in August, was South Korea’s Danuri probe, which is expected to arrive at its destination in January and orbit the Moon for a year. The mission is the country’s first foray beyond Earth’s orbit and is carrying a host of experiments.Last month, NASA’s hotly anticipated Artemis programme — which aims to send astronauts to the Moon in the next few years — finally kicked off with the launch of an uncrewed capsule called Orion, a joint venture with the European Space Agency. As part of a test flight to see whether the system can transport people safely to the Moon, the capsule flew out past the Moon and made its way back to Earth safely this month.A lunar spacecraft made by a Japanese company launched this month. ispace’s M1 lander is aiming to be the first of several private ventures to land on the surface of the Moon next year. The lander will carry two rovers, one for the United Arab Emirates and another for the Japan Aerospace Exploration Agency, JAXA. The rovers will be a first for both countries.Climate-change funding

People cross a flooded highway in Sindh province, Pakistan in August.Credit: Waqar Hussein/EPA-EFE/Shutterstock

There were many reasons to feel despondent about the United Nations Climate Change Conference of the Parties (COP27) in Egypt last month, but an agreement on a new ‘loss and damage’ fund was one bright spot. The fund will help low- and middle-income countries to cover the cost of climate-change impacts, such as the catastrophic floods in Pakistan this year, which caused more than US$30 billion worth of damage and economic losses.But calls at COP27 to phase out fossil fuels were blocked by oil-producing states, and many blamed the lack of progress on the energy crisis sparked by Russia’s invasion of Ukraine. High natural-gas prices have led some European nations to rely temporarily on coal. Global carbon emissions from fossil fuels are expected to hit 37.5 billion tonnes this year, a new record. The window to limit warming to 1.5–2 ºC above pre-industrial temperatures is disappearing fast — and might even have passed.Omicron’s offspring drive the pandemicOmicron and its descendants dominated all other coronavirus variants this year. The fast-spreading strain was first detected in southern Africa in November 2021, and quickly spread around the globe. From early on, it was clear that Omicron could evade immune-system defences more successfully than previous variants, which has meant that vaccines are less effective. Throughout the year, a diverse group of immune-dodging offshoots of Omicron has emerged, making it challenging for scientists to predict coming waves of infection.Vaccines based on Omicron variants have been rolled out in some countries in the hope they will offer greater protection than previous jabs, but early data suggest the extra benefit is modest. Nasal sprays against COVID-19 have also become a tool in the vaccine arsenal. The idea is that these stop the virus at the site where it first takes hold. In September, China and India approved needle-free COVID-19 vaccines that are delivered through the nose or mouth, and many similar vaccines are in various stages of development.Pig organs transplanted into people

Surgeons in Baltimore, Maryland transplanted the first pig heart into a person in January.Credit: EyePress News/Shutterstock

In January, US handyman David Bennett became the first person to receive a transplanted heart from a genetically modified pig — a crucial first step in determining whether animals could provide a source of organs for people who need them. Bennett survived for another eight weeks after the transplant, but researchers were impressed that he lived for that long, given that the human immune system attacks non-genetically modified pig organs in minutes. A few months later, two US research groups independently reported transplanting pig kidneys into three people who had been declared legally dead because they did not have brain function. The organs weren’t rejected and started producing urine. Researchers say the next step is clinical trials to test such procedures thoroughly in living people.Elections and science

Luís Inácio Lula da Silva was elected president of Brazil in October.Credit: Fabio Vieira/FotoRua/NurPhoto via Getty

National elections in Brazil, Australia and France brought relief for many researchers. After three years of science-damaging policies under right-wing president Jair Bolsonaro, Brazil narrowly elected leftist labour leader and former president Luiz Inácio Lula da Silva to lead the country in October. Scientists are hopeful that Lula’s return will result in a desperately needed boost to research funding and greater protection for the Amazon rainforest.French researchers were buoyed by President Emmanuel Macron’s victory over far-right candidate Marine Le Pen in April, and the election of Anthony Albanese as prime minister in Australia in May was seen as a good thing for science and climate-change action, too. In China, Xi Jinping cemented his legacy with an historic third term as head of the Chinese Communist Party. Xi has placed science and innovation at the heart of his country’s growth strategy.In other nations, it was unclear how research would fare under new leaders, such as Giorgia Meloni, the far-right candidate elected as Italy’s first female prime minister in October. Science was not a priority for the United Kingdom’s three prime ministers this year, although they have retained previous commitments to raise research funding. After Boris Johnson reisgned, Liz Truss was in the position for just seven weeks before she too resigned and the current Prime Minister Rishi Sunak took over.Environmental push beginsThis week, conservation and political leaders are attempting to finalize a global deal to protect the environment. The UN’s Convention on Biological Diversity Conference of the Parties (COP15) is under way in Montreal, Canada. A new biodiversity treaty, known as the post-2020 Global Diversity Framework, has been delayed by more than two years because of the COVID-19 pandemic. Progress towards an agreement has been slow, and the deal looked under threat when negotiations stalled over financing during international talks in Nairobi in June. Financial pledges from some nations to support biodiversity helped discussions to move forward, but estimates suggest that US$700 billion more is needed annually to protect the natural world. At the meeting, delegates will hopefully agree on targets to stabilize species’ declines by 2030 and reverse them by mid-century. More

Mild shading facilitates sesquiterpenoid accumulation and growth in Atractylodes lancea rhizomeTo determine a concrete shading value for the production of high-quality and high-yielding AR, we examined the major compounds, including the sesquiterpenoids hinesol (Hin), β-eudesmol (Edu), and atractylone (Atl), and the polyacetylene atractylodin (Atd), as well as the biomass of AR at different growth stages (Fig. 1A–C) under various light intensities. The sum of these four volatile oils as the total volatile oil content was subsequently analyzed. The results revealed that the accumulation of volatile oils was significantly different (p  More

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