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    Microbacterium kunmingensis sp. nov., an attached bacterium of Microcystis aeruginosa

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    Save the world’s forest giants from infernos

    Gigantic trees occur in only a few regions on Earth. Some of the world’s largest eucalypts, for example, are on the island of Tasmania, off southeastern Australia. As wildfires increase in severity and frequency as a result of climate change, we urge the authorities to protect these trees by adopting measures similar to those applied to safeguard California’s redwood forests.
    Competing Interests
    The authors declare no competing interests. More

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    Signals of local bioclimate-driven ecomorphological changes in wild birds

    Study areaWe conducted field studies in both regions from August to March, each year from 2012 to 2016. In north India, we selected the two traditional breeding colonies of the Painted Storks, viz., the Delhi Zoo (28° 36′ N 77° 14′ E) and Keoladeo National Park (KNP) (27° 17′ N 77° 52′ E), Bharatpur, Rajasthan (Fig. 1). In the Delhi Zoo, close to the river Yamuna, the Painted Storks nest in the traditional heronries with other colonial nesters, Little Cormorant, Indian Cormorant, Black-headed Ibis, and Night Heron38. The KNP, a Ramsar site spread over 29 km2, situated at the confluence of the rivers Gambhir and Banganga on the western edge of the Gangetic basin, supports diverse fauna, flora, and a mosaic of habitats, wetlands, woodlands, scrub forests, grasslands, and heronries39. In 2013, we recorded 680 adults and 310 nests in the Delhi Zoo and 1584 adults and 430 nests of Painted Storks in the KNP.We selected the Vedanthangal Bird Sanctuary (VBS), the nesting colonies at Melmaruvathur Lake, and Koonthankulam Bird Sanctuary (KBS). The KBS & VBS are the newly declared Ramsar sites in Tamil Nadu, south India. The VBS (12° 32′ 02″ N and 79° 52′ 29″ E) is a 40.3-hectare community reserve effectively protected by the state Forest Department, Tamil Nadu, and Vedanthangal villagers40. It is the oldest breeding waterbird reserve in south India, located 85 km southwest of Chennai. More than 40 species of waterbirds, both residents and migrants, live here. Along with the other 17 heronry species, the Painted Storks build nests every year from November to April during its breeding season. The Painted Stork nesting colonies at Melmaruvathur Lake (12° 25′ 53″ N and 79° 49′ 36″ E) are about 20 km away from the VBS. Here, the Painted Storks build nests at 1.8–5 m above the water level, on trees of Acacia nilotica and Barringtonia acutangula on mounds surrounded by water41. In 2012, we recorded a total of 3185 nests in the VBS, with a maximum number of nests belonging to Spot-billed Pelican (1050 nests) followed by Painted Stork (550 nests), Asian Open-bill (770 nests), and others.Birds have been breeding in Melmaruvathur Lake since 2013, and we counted 80 nests of Spot-billed pelican, 45 nests of Oriental White Ibis, and 56 nests of Painted Stork during the winter of the year 2014. The Lake is spread over 0.19 km2 with islets (mounds) with four clusters of Acacia nilotica and Barringtonia acutangula trees. Rainwater and domestic sewage from the neighboring residential complex are the primary water source, and recreational boating attracts a large crowd visiting the Melmaruvathur temple41. KBS (8° 29′ 44″ N and 77° 45′ 30″ E) is about a 1.3 km2 protected area, declared a bird sanctuary in 1994 and an Important Bird Area40. It comprises Koonthankulam and Kadankulam irrigation tanks actively protected and managed by the local community. We noticed the frequent failures of breeding events due to water shortages related to monsoon failures in VBS and KBS. In 2015, we also observed Painted Storks’ breeding failure across northern India for unknown reasons; therefore, data could not be collected for those periods.Bioclimatic variablesWe obtained the bioclimatic variable, particularly temperature at 2 m height for all the four study sites, from the National Aeronautics and Space Administration (NASA) Langley Research Center (LaRC) Prediction of Worldwide Energy Resource (POWER) Project funded through the NASA Earth Science/Applied Science Program. The monthly average data from 2010 to 2020 was downloaded from the POWER Project’s Hourly 2.0.0 version on 2022/01/04.Digital images of Painted Storks collected under field conditionsUsing Binoculars (Olympus 10X50), Digital Cameras (Canon 5D Mark III and Sony handy-cam), we monitored and recorded all active nests with juveniles and adult Painted Storks twice a week. The nests were on trees, 3–7 m in height, and chicks and adults were visible, which aided the photography. Nests were numbered for our records by taking note of tree branching patterns, the nest’s position on the tree, and other local identification marks. Numbering the nests helped us identify the individuals associated with a given nest and avoided re-recording the same individual (pseudoreplication). Storks show site fidelity42,43, and hence we assumed the same breeding pairs occupied the same nesting site.During the initial months of the breeding seasons, pairing and copulations of the breeding pairs could be readily noticeable. We took consecutive photographs when they were copulating at the nest. After disengagement following the copulation, the birds (male and female) standing side by side at the nest were also photographed. The first author noted all the relevant spatial orientations of males and females during each copulation event in the field notes. Thus nearly 100 copulations involving different individuals of the Painted Storks pair were photographed. To minimize measurement errors, we selected for further analysis only the images of males and females standing parallel and close to each other, perpendicular to the camera. Since we used the digital images of the free-living Storks, we did not have the freedom to choose all morphological features resulting in some missing values. Therefore, we selected a hundred and forty-eight individuals for the analysis from nearly 1500 localized adults. The technique has an efficiency of less than 10% of the population, more efficient than the traditional capture, measure, and release of individuals. Though many individuals were recorded, only a few were subjected to the analyses. Moreover from the digital images, not all the morphological characters of the individuals were measured. The birds’ orientation towards the camera assumes importance because the correct direction ensures maximum exposure of body parts in the picture. In many pictures, correct orientation was missing as the birds were behind other individuals or branches of the trees or leaves. Therefore, selecting the right digital image becomes crucial. Keeping all the above criteria, we filtered images that were later included in the analysis.Calibrations of subject-distance using Exif MetadataWe extracted the EXIF metadata from each JPEG image of Painted Stork. EXIF metadata includes the filename, type, date, and time of the image captured, image width and height in pixels, camera model, lens information, field of view, focal length, and subject-distance. The subject-distance (Painted Stork distance from the camera) being a critical variable and its Exif metadata were standardized with the following equation.$${text{Subject{-}distance}} = 0.7864 times {text{(EXIF subject{-}distance)}}^{{1.0301}}$$
    (1)
    Using the Eq. (1) derived from an earlier study5, we regressed actual subject-distance with the Exif subject-distance from the images. Then multiplying with the field of view, available as Exif metadata (angle of view) with standardized subject-distance (Eq. 1), the total image size (length and width) in metric units was estimated. We excluded the cropped or manipulated images because Image (size) estimation is possible only for the images coming straight from the camera with EXIF tags. The methodological details for calibration and estimation of in-situ measurements of the morphological variables are given in Mahendiran et al.5.Measurements of the morphological variablesWe created a TPS file for JPEG images of Painted Storks with the TPSUtility Program44. Using the TPS file in the TPSDig (v. 2.17) program44, we measured the selected characters (morphological variables) in pixels. Later, it was used along with the total image size to estimate the size of the specific morphological features in metric units, following Mahendiran et al.5. Ten different morphological variables were measured: Bill length (upper and lower mandible), tibia & tarsus length of both legs, distances among the ear, nostril and corners of the mouth, and body length. We estimated the dimensions of the rigid body parts, viz., bill length, tibia, and tarsus using the given methodology13,15,21. Bill length is the distance from the tip of the upper mandible to the beginning of skin corners near nostrils, the proximal end of the beak (marked as ‘a’ in Fig. 3); Tibia length is the distance from the joint of the tibia-tarsus to the feathers (marked as ‘b’ in Fig. 3); Tarsus length is the distance between the tibia-tarsus joint and foot (marked as ‘c’ in Fig. 3). We took measurements of each individual’s right and left legs and other characters, viz., inter-distances among the nostril, corner of the eye, corner of the mouth on each side (marked as ‘d’, ‘e’, ‘f’ in Fig. 3). Body depth is the distance from the base of the neck near the breast to the tip of the tail (marked as ‘g’ in Fig. 3).Data analysisWe performed the statistical analysis in R45, primarily through the nlme, ggbiplot, nnet, tidyverse, devtools packages. We did not have the freedom to measure a few morphological variables due to the problems mentioned above, which led to missing values in the datasets. We filled the missing values with the impute function using the R Core team45 through mice & VIM packages. When the missing values are high in numbers, we discard the data rather than use the impute function. Since almost about 70% of the lower mandible values were missing, we discarded them and ended up having only nine morphological variables in the final analysis. Moreover, the lower mandible is movable, with the mouth being open and closed, producing a considerable variation in measurements.We designed the matrix (Individuals × Region × Sex) representing the intraspecific variations concerning the region and sexes of Painted Storks46. The individuals are in rows (R), their region in column (C1), and sex in column (C2). We considered the regional variations as a sequence of the latitudinal gradient of the study sites. The values of the individuals (R) were the selected morphological variables. This matrix helped us investigate the critical questions relating to eco-geographic variations and sexual dimorphism.To determine whether temperature varied between study sites, we conducted a two-way ANOVA to analyse the effect of study sites (between North India (DZ & KNP) and South India (VBS & KBS)) and months of the year on the temperature at 2 m. For each character, Dimorphism Index (DI) was calculated as a mean value of female divided by the mean male, multiplied by 100, following the method of Urfi and Kalam15. We estimated the general body size of Painted Storks from the selected morphological variables through Principal Component Analysis (PCA) and tested hypotheses on Eco-geographic variations (Bergmann’s or Allen’s rules)2,47 and the sexual dimorphism15,48. The dimension reduction through PCA was carried out after the imputation as there were a few missing values. Body depth was omitted only for the principal component analysis due to many missing values. However, the values of all the characters are presented in the summary statistics in Table 1. The first principal component is characterized as a measure of size, and subsequent components describe various aspects of shape; therefore, it is considered a measure of general body size15,48,49. The PC1 indicated the body size variation, and PC2 revealed leg length variation (tibia and tarsus). We used nested ANOVA to test their body size variation between regions and sexes. The sexes nested within the region explained the eco-geographic rules and sexual selection patterns.Using a multinomial logistic regression model, we compared the Painted Storks’ northern male (NM), southern male (SM), and female (SF) with the reference category, northern female (NF). Then, we classified the data through multinomial log-linear and feed-forward neural network models. We predicted the Painted Stork’s region and sex using the Machine Learning (ML) algorithms through open-source software Waikato Environment for Knowledge Analysis (WEKA.3.9.5) implemented in Java50. WEKA has standard Machine learning/data-mining algorithms with pre-processing tools generating insightful knowledge from the Painted Storks’ morphological data.Using the R and Python interfaces, we used different ML software frameworks, libraries, and computer programs, viz., TensorFlow and Keras, and extensively explored the WEKA workbench environment to predict the sex and region of the Painted Stork. We used the k-fold cross-validation (k = 10) to avoid overlapping test sets, including splitting the data into k subsets of equal size, using each subset for testing and the remainder for training. We analyzed using the WEKA on a Lenovo ThinkPad P53s Mobile Workstation with the 8th Gen Intel® Core i7 @ 1.80 GHz processor, 48 GB DDR4 Memory, NVIDIA® Quadro® P520 with 2 GB GDDR5 Graphics. The performance criteria for all the eight models were assessed by using the Precision (TP/(TP + FP)), Recall (TP/(TP + FN)), Area under Curve (AUC) = (Sensitivity + Specificity)/2, Accuracy = (TP + TN)/(TP + TN + FP + FN), where TP, TN, FN and FP are the acronyms of true positive, true negative, false negative and false positive, respectively. We used the WEKA experimenter environment to test the statistical significance of the selected Machine Learning algorithms. We performed the Paired T-tester based on the number of correctly classified instances and areas under the curve. More

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    Calibrating the zenith of dinosaur diversity in the Campanian of the Western Interior Basin by CA-ID-TIMS U–Pb geochronology

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    Tracking 21st century anthropogenic and natural carbon fluxes through model-data integration

    External datasetsWoody biomass carbon dataThe dataset by ref. 16 maps annual global woody biomass carbon densities for 2000–2019 at a spatial resolution of ~10 km. The annual estimates represent averages for the tropical regions and growing-season (April–October) averages for the extra-tropical regions. Ref. 16 analyse global trends of gains and losses in woody biomass carbon for 2000–2019. Overall, they find that grid cells with (significant) net gains of vegetation carbon are by a factor of 1.4 more abundant than grid cells with net losses of vegetation carbon, indicating that there is a global greening trend when only considering the areal extent of biomass gains and not the magnitude of carbon gains. Their regionally distinct analysis of trends shows that almost all regions, except for the tropical moist forests in South America and parts of Southeast Asia, experienced net gains in biomass carbon. On the country scale, the largest net increase in biomass carbon is shown in China, which is mainly attributed to the large-scale afforestation programs in the southern part of the country and increased carbon uptake of established forests. On the other hand, the largest vegetation carbon losses are shown for Brazil and Indonesia, which is partly attributed to deforestation, degradation, and drought events. All of the mentioned trends have been found to be significant16. The decreasing carbon sink in Brazil is in line with ref. 44, who, considering both natural and anthropogenic fluxes, show that the southeastern Amazon has even turned from a carbon sink to a carbon source, mainly owing to fire emissions from forest clearing. Isolating carbon fluxes in intact, old-growth Amazonian rainforests (i.e., SLAND,B), ref. 45 also find evidence for a significantly decreasing carbon sink due to the negative effects of increasing temperatures and droughts on carbon uptake since the 1990s.The dataset was remapped to the BLUE resolution of 0.25∘ through conservative remapping (i.e., area-weighted averaging).ERA-5 dataThe ERA-5 variables were downloaded from the Copernicus Climate Data Store (https://cds.climate.copernicus.eu/cdsapp#!/home). Monthly air temperature (Ta) at 2 m height was averaged over each year, and annual precipitation was calculated by taking the sum of the monthly total precipitation (P). Both variables were regridded from the original resolution of ~0.1° to 0.25° resp. to the TRENDY resolution of 0.5° through conservative remapping.TRENDY dataWe used the TRENDY model ensemble version 8 (conducted for the 2019 GCB; ref. 8). We used net biome production (NBP) and annual vegetation carbon stocks (cVeg) for 2000–2018 from four different model setups (S2, S3, S5, and S6) and eight resp. 13 DGVMs (depending on the data available). The selection of DGVMs is done as in ref. 19 (Supplementary Tab. 3), but we included one additional model (ISAM) for the S2 simulations. The terrestrial biomass carbon sink (SLAND,B) was calculated for 13 DGVMs following the GCB 2020 approach, i.e., from the S2 simulation, which is the simulation without LULCC (i.e., fixed pre-industrial land cover) under transient environmental conditions (climate, nitrogen deposition, CO2 evolution). SLAND,B is the annual difference of cVeg and makes no statements about the further fate of biomass if cVeg decreases. SLAND,B, therefore, should not be interpreted as equivalent to the flux to/from the atmosphere, since parts of cVeg may be transferred to litter, dead wood, or soil. The same applies to our BLUE estimates of SLAND,B, ensuring comparability between our BLUE estimates and the TRENDY estimates. Increases (decreases) of cVeg between two years are a net uptake (release) of carbon from the terrestrial biosphere. The global sums of biomass carbon stocks under transient climate and CO2 were calculated from the S3 setup (LULCC under historical environmental conditions), whereas the S5 setup provides biomass carbon under constant present-day environmental forcing (closest to the classical bookkeeping approach). In line with the GCB, ELUC was calculated under historical environmental conditions as the difference in NBP between the S2 and S3 simulations (ELUC = NBP_S2 – NBP_S3). ELUC under constant present-day environmental forcing was calculated as the difference in NBP between the S6 (fixed pre-industrial land cover under present-day environmental forcing) and S5 simulations (ELUC = NBP_S6 – NBP_S5)19. All datasets were remapped to a common resolution of 0.5∘ through conservative remapping (area-weighted average) for the data analysis.Assimilation of observed woody biomass carbon in BLUEThe observed woody biomass carbon densities by ref. 16 are assimilated in BLUE in several steps.Carbon transfer in the default setup of BLUEThe BLUE simulation is started in AD 850. Biomass and soil vegetation carbon densities are based on ref. 17, which are converted to exponential time constants. A detailed explanation of the exponential model can be found in ref. 5.While in the default setup, changes are only due to LULCC, our assimilation approach now introduces environmental effects on woody vegetation carbon by assimilating the observed woody biomass carbon densities in BLUE from 2000 onward according to the methodological considerations explained below.Calculation of woody biomass carbon densities for different land cover types and PFTsWithin each 0.25° cell of the global grid, the (remapped) woody biomass carbon density from ref. 16 must be the sum of woody biomass carbon stored in all woody PFTs of all woody land cover types. The distribution of the woody biomass carbon across PFTs and land cover types is achieved by distributing the observed (i.e., actual) woody biomass carbon densities (ρBa) from ref. 16 across the two land cover types (j) and the eight PFTs (l) that can be woody vegetation (primary land, called virgin, “v” in BLUE and secondary, “s”, land) according to the fraction of total woody biomass carbon (fB) contained in each land cover type and each PFT (fB,j,l) as estimated by BLUE. fB,j,l varies for different PFTs and land cover types, depending on their history of LULCC and their potential for carbon uptake (i.e., the potential carbon densities).fB,j,l is extracted from the default simulations for the first year of the time series (i.e., 2000) and calculated for subsequent years from the BLUE simulations using the assimilated woody vegetation carbon densities for that year:$${f}_{B,j,l}(t)=frac{{C}_{B,j,l}(t)}{{C}_{B}(t)}$$
    (1)
    where CB is the woody biomass carbon stock.Consequently, the assimilated woody biomass carbon stock per cover type and PFT (CB_as,j,l) at each time step can be calculated as:$${C}_{B_as,j,l}(t)={rho }_{Ba}(t);*;A;*;{f}_{B,j,l}(t)$$
    (2)
    with j{v, s}; l{1. . 8}; t{2000. . 2019}. A is the area per grid cell.Thresholds for excluding inconsistent woody biomass carbon densitiesWe eliminate unrealistically large values for woody biomass carbon densities that our assimilation framework produces. Woody biomass carbon densities in BLUE that exceed the highest value (~374 t ha−1) of the original dataset indicate inconsistencies between the observed woody biomass carbon estimates and the fractional grid cell areas per PFT and land cover types that BLUE simulates. To account for uncertainties related to the criteria for exclusion of grid cells, multiple threshold approaches are applied and the results are compared. To maintain a temporally and spatially consistent time series of woody biomass carbon, grid cells that are excluded according to the chosen threshold approach are interpolated through linear barycentric interpolation. A first approach relies on a uniform upper threshold of More

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