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    Hydrologic regime alteration and influence factors in the Jialing River of the Yangtze River, China

    Ge, J., Peng, W., Wei, H. W., Qu, X. & Singh, S. Quantitative assessment of flow regime alteration using a revised range of variability methods. Water 10(5), 597 (2018).Article 

    Google Scholar 
    Latrubesse, E. M. et al. Damming the rivers of the Amazon basin. Nature 546(7658), 363–369 (2017).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Meade, R. H. & Moody, J. A. Causes for the decline of suspended-sediment discharge in the Mississippi River system, 1940–2007. Hydrol. Process 24(1), 35–49 (2010).
    Google Scholar 
    Fathi, M. M., Awadallah, A. G., Abdelbaki, A. M. & Haggag, M. A new Budyko framework extension using time series SARIMAX model. J. Hydrol. 570(2019), 827–838 (2019).ADS 
    Article 

    Google Scholar 
    Wang, H., Liu, J. & Guo, W. The variation and attribution analysis of the runoff and sediment in the lower reach of the Yellow River during the past 60 years. Water Supply 21(6), 3193–3209 (2021).Article 

    Google Scholar 
    Guo, S. L., Guo, J., Hou, Y., Xiong, L. & Hong, X. Prediction of future runoff change based on Budyko hypothesis in Yangtze River basin. Adv. Water Sci. 26(02), 151–160 (2015).
    Google Scholar 
    Zhang, X., Dong, Z., Gupta, H., Wu, G. & Li, D. Impact of the three gorges dam on the hydrology and ecology of the Yangtze River. Water 590(8), 1–18 (2016).ADS 
    CAS 

    Google Scholar 
    Zhang, J., Zhang, M., Song, Y. & Lai, Y. Hydrological simulation of the Jialing River Basin using the MIKE SHE model in changing climate. J. Water Clim. Change 12(6), 1–20 (2021).
    Google Scholar 
    Richter, B. D., Baumgartner, J. V., Powell, J. & Braun, P. D. A method for assessing hydrologic alteration within ecosystems. Conserv. Biol. 10(4), 1163–1174 (1996).Article 

    Google Scholar 
    Richter, B. D., Baumgartner, J. V., Wigington, B. & Braun, D. How much water does a river need?. Freshw. Biol. 37(1), 231–249 (1997).Article 

    Google Scholar 
    Richter, B. D., Baumgartner, J. V., Braun, D. P. & Powell, J. A spatial assessment of hydrologic alteration within a river network. Regul. River Res. Manag. 14(4), 329–340 (1998).Article 

    Google Scholar 
    Guo, W., Xu, G., Shao, J., Bing, J. & Chen, X. Research on the middle and lower reaches of the Yangtze River and lake’s hydrological alterations based on RVA. In IOP Conference Series: Earth and Environmental Science Vol 153, No 6, 062047.1–062047.8 (2018).Guo, W., Li, Y., Wang, H. & Zha, H. Assessment of eco-hydrological regime of lower reaches of Three Gorges Reservoir based on IHA-RVA. Resour. Environ. Yangtze Basin 27(09), 2014–2021 (2018).
    Google Scholar 
    Zuo, Q. & Liang, S. Effects of dams on river flow regime based on IHA/RVA. Proc. Int. Assoc. Hydrol. Sci. 368(368), 275–276 (2015).
    Google Scholar 
    Mwedzi, T., Katiyo, L., Mugabe, F. T., Bere, T. & Kuoika, O. L. A spatial assessment of stream-flow characteristics and hydrologic alterations, post dam construction in the Manyame catchment, Zimbabwe. Water Sa 42(2), 194–202 (2016).CAS 
    Article 

    Google Scholar 
    Liu, J., Chen, J., Xu, J., Lin, Y. & Zhou, M. Attribution of runoff variation in the headwaters of the Yangtze River based on the Budyko hypothesis. Int. J. Environ. Res. Public Health 16(14), 2506.1-2506.15 (2019).
    Google Scholar 
    Yan, D. Using budyko-type equations for separating the impacts of climate and vegetation change on runoff in the source area of the yellow river. Water 12(12), 3418.1-3418.15 (2020).ADS 

    Google Scholar 
    Gunkel, A. & Lange, J. Water scarcity, data scarcity and the Budyko curve—An application in the Lower Jordan River Basin. J. Hydrol. Reg. Stud. 12(C), 136–149 (2017).Article 

    Google Scholar 
    Fathi, M. M., Awadallah, A. G., Abdelbaki, A. M. & Haggag, M. A new Budyko framework extension using time series SARIMAX model. J. Hydrol. 570, 827–838 (2019).ADS 
    Article 

    Google Scholar 
    Li, Y., Fan, J. & Liao, Y. Variation characteristics of streamflow and sediment in the Jialing river basin in the past 60 years. Mt. Res. 38(03), 339–348 (2020).
    Google Scholar 
    Liu, Y., Li, F. & Xu, X. Impacts of hydropower development on hydrological regime in mainstream of mid-lower Jialing River. Yangtze River 45(05), 10–15 (2014).
    Google Scholar 
    Zhou, Y. et al. Distinguishing the multiple controls on the decreased sediment flux in the Jialing River basin of the Yangtze River, Southwestern China. CATENA 193(C), 104593.1-104593.11 (2020).
    Google Scholar 
    Zeng, X. et al. Changes and relationships of climatic and hydrological droughts in the Jialing River Basin, China. PLoS ONE 10(11), e0141648 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Yan, M., Fang, G. H., Dai, L. H., Tan, Q. F. & Huang, X. F. Optimizing reservoir operation considering downstream ecological demands of water quantity and fluctuation based on IHA parameters. J. Hydrol. 4(2021), 126647 (2021).Article 

    Google Scholar 
    Wei, R., Liu, J., Zhang, T., Zeng, Q. & Dong, X. Attribution analysis of runoff variation in the upper-middle reaches of Yalong river. Resour. Environ. Yangtze Basin 29(07), 1643–1652 (2020).
    Google Scholar 
    Xie, J. H., Yu, J. H., Chem, H. S. & Hsu, P. C. Sources of subseasonal prediction skill for heatwaves over the Yangtze river basin revealed from three S2S models. Adv. Atmos. Sci. 37(12), 1435–1450 (2020).Article 

    Google Scholar 
    Guo, W., Li, Y., Wang, H. & Cha, H. Temporal variations and influencing factors of river runoff and sediment regimes in the Yangtze River, China. Desalin. Water Treat. 174(2020), 258–270 (2020).Article 

    Google Scholar 
    Tian, X. et al. Hydrologic alteration and possible underlying causes in the Wuding River, China. Sci. Total Environ. 693, 133556.1-133556.9 (2019).Article 
    CAS 

    Google Scholar 
    Tang, B., Wang, W. C. & Fan, X. Study on the influence of reservoir dispatch of the upper Yangtze river on the runoff control. E3S Web Conf. 283(18), 01030 (2021).
    Google Scholar 
    Liu, Y. et al. Characteristics and resource status of main commercial fish in the middle reaches of Jialing River, China. J. Appl. Environ. Biol. 27(04), 837–847 (2021).
    Google Scholar 
    Sun, Z., Zhang, M. & Chen, Y. Protection of the rare and endemic fish in the conservation area located in the upstream of the Yangtze River. Freshw. Fish. 44(06), 3–8 (2014).
    Google Scholar 
    Chen, Q. H. et al. Impacts of climate change and LULC change on runoff in the Jinsha River Basin. J. Geogr. Sci. 30(01), 85–102 (2020).Article 

    Google Scholar 
    Cui, L., Wang, Z. & Deng, L. Vegetation dynamics based on NDVI in Yangtze River Basin (China) during 1982–2015. IOP Conf. Ser. Materials Sci. Eng. 780(2020), 062049 (2020).Article 

    Google Scholar 
    Wang, Y., Wang, S., Wu, M. & Wang, S. Impacts of the land use and climate changes on the hydrological characteristics of Jialing River Basin. Res. Soil Water Conserv. 26(01), 135–142 (2019).
    Google Scholar 
    Wu, Y. L. & Pu, H. W. Y. The influence of hydropower station on sand content detection in Jialing River. Technol. Dev. Enterp. 38(9), 55–58 (2019).
    Google Scholar 
    Zhuo, Z., Qian, Z., Jiang, H., Wang, H. & Guo, W. Evaluation of hydrological regime in Xiangjiang basin on IHA-RVA method. China Rural Water Hydropower 8(2020), 188–192 (2020).
    Google Scholar 
    Chen, L. et al. Temporal characteristics detection and attribution analysis of hydrological time-series variation in the seagoing river of southern China under environmental change. Acta Geophys. 66(5), 1151–1170 (2018).ADS 
    Article 

    Google Scholar 
    Zhang, R., Liu, J., Mao, G. & Wang, L. Flow regime alterations of upper Heihe River based on improved RVA. Arid Zone Res. 38(01), 29–38 (2021).
    Google Scholar 
    Sun, Y. & Wang, X. Changes in runoff and driving force analysis in the key section of the Yellow River diversion project. J. Hydroecol. 41(06), 19–26 (2020).
    Google Scholar 
    Zhang, L., Dawes, W. R. & Walker, G. R. Response of mean annual evapotranspiration to vegetation changes at catchment scale. Water Resour. Res. 37(3), 701–708 (2001).ADS 
    Article 

    Google Scholar 
    Fu, B. Calculation of soil evaporation. Acta Meteor. Sin. 02(1981), 226–236 (1981).
    Google Scholar 
    Liu, J., Zhang, Q., Singh, V. P. & Shi, P. Contribution of multiple climatic variables and human activities to streamflow changes across China. J. Hydrol. 545(2016), 145–162 (2016).
    Google Scholar 
    Yang, D., Zhang, S. & Xu, X. Attribution analysis for runoff decline in Yellow River Basin during past fifty years based on Budyko hypothesis. Sci. Sinica 45(10), 1024–1034 (2015).
    Google Scholar 
    Schreiber, P. Ber die Beziehungen zwischen dem Niederschlag und der Wasserführung der Flüsse in Mitteleuropa. Meteorol. Z. 21, 441–452 (1904).Budyko, M. Evaporation under Natural Conditions (Gidrometeorizdat, Leningrad, Russia, 1948).Pike, J. The estimation of annual run-off from meteorological data in a tropical climate. J. Hydrol. 2, 116–123 (1964).Ol’dekop, E. On evaporation from the surface of river basins. Trans. Meteorol. Obs. 4, 200 (1911). More

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    Houseflies harbor less diverse microbiota under laboratory conditions but maintain a consistent set of host-associated bacteria

    The copy numbers for 16S and ITS1 rRNA, and the sequencing depth for all samples are presented in Supplementary File 3 (qPCR data, Sequencing Rarefaction Curves). An average of 14,265.25 reads per housefly sample for the V4 16SrRNA and 16,149.4 reads per housefly sample for the ITS1 were retained after quality filtering. After quality filtering of the egg-laying substrate samples, an average of 10,371.75 reads were retained per sample for the V4 16SrRNA, and an average of 25,479.75 reads were retained per sample for the ITS1 region. The extracted DNA from newly emerged adult houseflies of the Spanish laboratory strain (12 samples in total, newly emerged adults, three replicates from four generations, strain SP100) returned a low copy number for the fungal ITS1 (qPCR data, Supplementary File 3) and a low number of acquired sequencing reads; they were therefore omitted from any further analysis of the fungal microbiota. In addition, the mitochondrial COI phylogeny showed that the Dutch wild-caught strain and the Dutch laboratory strain, which were sampled from the same locality at different times, are in close proximity and form a separate clade from the Spanish lab strain phylotypes (Supplementary File 2).The housefly microbiota alpha-diversity is determined by sampling environmentAbsolute richness (number of ASVs), Shannon index, and Phylogenetic diversity for all housefly strains and developmental stages are shown in Fig. 1. The highest bacterial alpha diversity was observed for the wild-caught housefly population GK0. Strain was an important factor for separating Shannon biodiversity levels both for newly emerged (F = 4.37, P  More

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    Albedo changes caused by future urbanization contribute to global warming

    Land coverUrban landscapes are characterized by small clusters of patches, forming land mosaics that are distinct from natural landscapes. An accurate estimation of climate forcing requires a land cover dataset at high resolutions that does not omit small urban patches. In this study, the RF estimates are based on 500-m and 1-km land cover datasets. This fine resolution is necessary to preserve spatial details of small urban patches while avoiding the large underestimation of urban land areas at coarse resolution (e.g., ~19% underestimation at 10 km compared to that at 1 km)3. We used 500-m resolution MODIS Land Cover product (MCD12Q1v006) for historical land cover changes. For future urban land cover distributions, we used the global urban land expansion products simulated under the SSPs for 2030–2100 (i.e., Chen-2020)4. The simulation performance was tested using historical urban expansion from 2000 to 2015 based on Global Human Settlement Layer51, where the agreement between simulated and observed urban land was evaluated using the Figure of Merit (FoM) indicator52 that has showed similar or better values than those reported in other existing land simulation applications4. The high-resolution Chen-2020 also shows very high spatial consistency with the prominent coarse resolution global urban land projection LUH2 that is recommended in CMIP64. Considering different scenarios is also necessary to account for the uncertainties of future socioeconomic and environmental conditions, so we included simulated urban lands under three scenarios (Supplementary Table 1): Sustainability -SSP1, Middle of the Road – SSP2, and Fossil-fueled Development – SSP553. Within each SSP scenario, the product provides a likelihood map of each grid becoming urban, based on 100 urbanization simulations. We used the likelihood map to account for spatial uncertainties of urban expansion by deriving 90% confidence intervals of projected urban land demand within a SSP scenario. We used the MODIS IGBP Land Cover classes (Supplementary Table 2) and resampled the original 500-m resolution MODIS products in 2018 to 1-km resolution to match the future simulations when it was used as a baseline year. To isolate the independent effect of urbanization (vs other types of land uses) in future estimates, land covers that are not converted to urban are assumed to have the same cover types as in 2018 (i.e., the baseline year). Though there are other global land cover products for current periods, we choose the MODIS IGBP land cover products because the albedo look-up maps (LUMs) were based on IGBP land cover types (see Albedo Look-Up Maps).To further evaluate the uncertainties caused by different projections of future urbanization, we also included the other two SSPs from Chen-2020, and another two 1-km resolution urban land cover products projected for the future for the purpose of comparison. The other two products include four projections of SRES scenarios (i.e., A1, B1, A1B, and B2) (i.e., Li-2017 mentioned above)3 and one without scenario description but assumed historical development would continue (i.e., Zhou-2019 mentioned above)2. These projections of future urban land expansion were calibrated with different historical urban land products and can be regarded as independent.Albedo look-up maps (LUMs)Albedo Look-Up Maps (LUMs)31 were derived from the intersection of MODIS land cover54 and surface albedo55 products, which are used to determine the albedo values for each IGBP land cover type by month and by location. Monthly means of white-sky (i.e., diffuse surface illumination condition) and black sky (i.e., direct surface illumination condition) during 2001–2011 were processed for snow-free and snow-covered periods for each of the 17 IGBP land cover classes at spatial resolutions of 0.05°−1°31. The LUMs have been verified by comparing the reconstructed albedo using the LUMs with the original MODIS albedo, which shows very similar values31. We used the LUMs at a resolution of 1° due to the significantly fewer missing values, to assure the spatial continuity of albedo changes at a global scale while keeping the matches with the 1° resolution of radiation data and RF kernels. The underlying assumption is that albedo of the same land cover type varies insignificantly within a 1° grid.Snow and radiation productSnow cover can significantly change the albedo of land regardless of cover types (Supplementary Fig. 4). In this study, we tally monthly albedo using snow-free and snow-covered categories in estimating RF. Past and present snow-free and snow-covered conditions were derived from level 3 MODIS/Terra Snow Cover (MOD10CM.006)56 at 0.05° spatial resolution and resampled to a 1° spatial resolution. Monthly means of 2001–2005 vs 2015–2019 were used for 2001 and 2018 respectively. For future periods, ensemble mean snow cover for each year and month, projected under the CMIP5 framework for three Representative Concentration Pathway (RCP) scenarios (i.e., RCP2.6, RCP4.5, and RCP8.5) were used (for more details see Supplementary Note 2B). By comparing the model outputs with MODIS observations for a recent decade (2006–2015), we found that the multi-model mean snow cover was systematically biased compared to MODIS observations. Consequently, we calibrated the ensemble mean projections by subtracting the biases for the grids. In each 10th year of the future (e.g., 2030, 2040, etc.), the decadal monthly mean snow cover (e.g., 2026–2035 for 2030, and 2036–2045 for 2040, etc.) was used for the year.We used the long-term monthly averages (1981–2010) of diffuse and direct incoming surface solar radiation reanalysis Gaussian grid product from National Centers for Environmental Prediction (NCEP)57. Visible and near infrared beam downward radiation and diffuse downward radiation from NCEP were used to compute the white-sky and black-sky fractions. As for snow cover, ensemble mean shortwave radiation at surface (SWSF) and at top-of-atmosphere (SWTOA) projected from CMIP5 models (Supplementary Note 3C) for RCP2.6, RCP4.5, and RCP8.5 were collected for empirically computing future albedo kernels (see section 3.4 below).Radiative kernelsRadiative kernels were used to compute top-of-atmosphere RF due to small perturbations of temperature, water vapor, and albedo. We used the latest state-of-the-art albedo kernels calculated with CESM v1.1.258 to compute RF in 2018 relative to 2001. In brief, the albedo kernel is the change in top-of-atmosphere radiative flux for a 0.01 change in surface albedo. The CESM1.1.2 kernels are separated into clear- and all-sky illumination conditions. We used the all-sky kernels because we include both black-sky and white-sky albedos. For future periods, because there are no available radiative kernels produced from general circulation models, we approximated the future kernels using an empirical parameterization following Bright et al.59:$${K}_{m}left(iright)={{SW}}^{{SF}}(i)times {sqrt}left(frac{{{SW}}^{{SF}}(i)}{{{SW}}^{{TOA}}(i)}right)/(-100)$$
    (1)
    where m is the month, i is the location, and SWSF and SWTOA are the surface and top-of-atmosphere shortwave radiation; dividing by −100 is for matching the CESM1.1.2 kernel definition of a 0.01 change in surface albedo.Estimation of albedo change and RFWe analyzed the RF in 2018 due to albedo changes caused by urbanization since 2001 (2018–2001), and in the future from 2030 to 2100 at decadal intervals (i.e., 2030, 2040, 2050, …, and 2100) since 2018 under three illustrative scenarios: SSP1-2.6, SSP2-4.5, and SSP5-8.5, which combine SSP-based urbanization projections and RCP-based climate projections. The three illustrative scenarios were selected following the scenario designation of the latest IPCC report50 and represent low greenhouse gas (GHG) emissions with CO2 emissions declining to net zero around or after 2050, intermediate GHG emissions with CO2 emissions remaining around current levels until the mid-century, and very high CO2 emissions that roughly double from current levels by 2050, respectively. We selected 2018 as the baseline year to divide the past from the future because 2018 was the latest year with available MODIS land cover products at the time of this study. We used ArcGIS 10.6 to produce spatial maps of all variables, including area of each land cover type within a 1° × 1°-grid, snow cover, albedo, radiation, and kernels, and R 3.6.1 to compute the RF.We focused only on albedo changes induced by urbanization, including the conversions from all other 16 IGBP land cover types to urban land. The changes of albedo for each grid (x, y) of a month (m) were obtained by computing the difference between albedo of that grid in the baseline year (t = t0) and in a later year (t = t1) with urban expansion:$${triangle alpha }_{m,t1-t0}(x,y)={alpha }_{m,t=t1}(x,y)-{alpha }_{m,t=t0}(x,y)$$
    (2)
    where αm, t = t1 (x, y) and αm, t = t0) (x, y) is the albedo for each grid (x,y) of a month (m) at the base year and later year respectively; the grid-scale albedo is computed as the weighted sum of albedo by land cover types with the weighing factor corresponding to areal percentage of a land cover within the grid. The albedo for each land cover type of a grid was then obtained by applying the albedo LUMs that provide spatially continuous black-sky, white-sky, snow-covered, and snow-free albedo maps for a given month for each land cover. Firstly, monthly mean albedo is computed as:$${alpha }_{m,t}(x,y)=mathop{sum }limits_{l=1}^{17}mathop{sum }limits_{s=0}^{1}mathop{sum }limits_{r=0}^{1}{{f}_{l,t}(x,y){f}_{s,m,t}(x,y)f}_{r,m,t}(x,y)left({alpha }_{l,s,r,m}(x,y)right)$$
    (3)
    where m is the month, t is the year, l is the land cover type, fl is the proportion of a cover type within the grid, fs,m,t is the fraction for snow-covered (s = 0) and snow-free (s = 1) conditions of the time (m, t), fr,m,t (x, y) is the fraction for white-sky (r = 0) or black-sky (r = 1) conditions of the time, and αl,s,r,m (x, y) is the albedo for land cover type l in month m that is extracted from the albedo LUMs corresponding to snow condition (s) and radiation condition (r). The annual mean albedo change is reported as the mean of monthly albedo change:$${triangle alpha }_{t1-t0}(x,y)=frac{1}{12}mathop{sum }limits_{m=1}^{m=12}({alpha }_{m,t=t1}(x,y)-{alpha }_{m,t=t0}(x,y))$$
    (4)
    The conversion of other land covers to urban land can contribute differently to the global RF, as the total area that is converted into urban land is different among non-urban land covers and the albedo differences between urban land and non-urban land cover types vary. To estimate the proportional contributions of different land conversions, we first decomposed the total albedo of each grid into the proportion of each land cover type:$${alpha }_{l,m,t}(x,y)={f}_{l,m,t}(x,y)mathop{sum }limits_{s=0}^{1}mathop{sum }limits_{r=0}^{1}{f}_{s,m,t}(x,y){f}_{r,m,t}(x,y)left({alpha }_{l,s,r,m}(x,y)right)$$
    (5)
    The global RF due to albedo change caused by conversion from each non-urban land cover type (l ≠ 13) to urban land (l = 13) (see Supplementary Table 2 land cover labels) was calculated as:$${{RF}}_{triangle alpha ,l(lne 13),{global}}=frac{1}{{A}_{{Earth}}}mathop{sum }limits_{i=1}^{n}mathop{sum }limits_{m=1}^{12}{({alpha }_{13,m,t=t1}left(iright)-{alpha }_{l,m,t=t0}left(iright))Delta p}_{lto 13}left(iright){Area}left(iright){K}_{m}(i)$$
    (6)
    where i refers to a grid, n is the total number of pixels on global lands, AEarth is the global surface area (5.1  ×  108 km2), α13,m,t = t1) (i) is the albedo of urban land in month m in the later year with urban expansion, αl,m,t = t0 (i) is the albedo of a targeted non-urban land cover type in the base year t0, Δpl→13 is the percentage of the non-urban land cover type that is converted to urban land in the year t1 compared to year t0, Area(i) is the area of the pixel, and Km (i) is the radiative kernel at the grid.The global RF due to urbanization-induced albedo changes was then calculated as:$${{RF}}_{triangle alpha ,{global}}=mathop{sum }limits_{l=1}^{17}{{RF}}_{triangle alpha ,l,{global}}(l,ne, 13)$$
    (7)
    GWP: CO2-equivalentWe followed GWP calculations by explicitly accounting for the lifetime and dynamic behavior of CO2 to convert RF to CO2 equivalent60,61:$${GWP}[{kg},{of},{{CO}}_{2}-{eq}]=frac{{int }_{t=0}^{{TH}}{{RF}}_{triangle alpha ,{global}}(t)}{{k}_{{CO}_2}{int }_{t=0}^{{TH}}{y}_{{{CO}}_{2}}(t)}$$
    (8)
    where kCO2 is radiative efficiency of CO2 in the atmosphere (W/m2/kg) at a constant background concentration of 389 ppmv, which is taken as 1.76  ×  1015 W/m2/kg62, and RF∆α,global is the global RF caused by albedo changes (W/m2). ({y}_{{{CO}}_{2}}) is the impulse-response function (IRF) for CO2 that ranges from 1 at the time of the emission pulse (t = 0) to 0.41 after 100 years, and here it is set to a mean value of 0.52 over 100 years60. The time horizon (TH) of our GWP calculations was fixed at 100 years following IPCC standards and previous studies60,63,64.Global mean surface air temperature changeWe estimated the 100-year global mean surface temperature change for the estimated RF by adopting an equilibrium climate sensitivity (ECS), defined as the global mean surface air temperature increase that follows a doubling of pre-industrial atmospheric carbon dioxide (RF = 3.7 W/m2). Given a value of RF induced by a forcing agent, the temperature change is estimated as RF/3.7 × ECS. To consider the uncertainties of ECS, we adopted a mean value of 3 °C and a very likely (90% confidence interval) range of 2–5 °C following IPCC AR650. Without knowing the exact distribution shape of ECS and future albedo-change-induced RF, we created a log-normal distribution (Supplementary Note 4) to approximate their asymmetric distribution through numerical simulation. We then conducted Monte Carlo simulations that draw 5000 random samples from each distribution to jointly estimate the uncertainties of global mean surface air temperature changes. We report the mean and 90% interval ranges of the change in temperature. More

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    Rapid Eocene diversification of spiny plants in subtropical woodlands of central Tibet

    Reich, P. B. et al. The evolution of plant functional variation: traits, spectra, and strategies. Int. J. Plant Sci. 164, S143–S164 (2003).
    Google Scholar 
    Cornelissen, J. H. C. et al. A handbook of protocols for standardised and easy measurement of plant functional traits worldwide. Aust. J. Bot. 51, 335–380 (2003).
    Google Scholar 
    Liu, X. J. & Ma, K. P. Plant functional traits concepts, applications and future directions. Sci. Sin. Vitae 45, 325–339 (2015).
    Google Scholar 
    Diaz, S., Cabido, M. & Casanoves, F. Plant functional traits and environmental filters at a regional scale. J. Veg. Sci. 9, 113–122 (1998).
    Google Scholar 
    Kraft, N. J. B., Godoy, O. & Levine, J. M. Plant functional traits and the multidimensional nature of species coexistence. Proc. Natl Acad. Sci. USA 112, 797–802 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Barton, K. E. Tougher and thornier: general patterns in the induction of physical defence traits. Func. Ecol. 30, 181–187 (2016).
    Google Scholar 
    Adler, P. B., Fajardo, A., Kleinhesselink, A. R. & Kraft, N. J. B. Trait-based tests of coexistence mechanisms. Ecol. Lett. 16, 1294–1306 (2013).PubMed 

    Google Scholar 
    Wright, S. J. et al. Functional traits and the growth–mortality trade-off in tropical trees. Ecology 91, 3664–3674 (2010).PubMed 

    Google Scholar 
    Wright, I. J. et al. The worldwide leaf economics spectrum. Nature 428, 821–827 (2004).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Ruiz-Jaen, M. C. & Potvin, C. Can we predict carbon stocks in tropical ecosystems from tree diversity? Comparing species and functional diversity in a plantation and a natural forest. New Phytol. 189, 978–987 (2011).PubMed 

    Google Scholar 
    Grubb, P. J. A positive distrust in simplicity-lessons from plant defences and from competition among plants and among animals. J. Ecol. 80, 585–610 (1992).
    Google Scholar 
    Hanley, M. E., Lamont, B. B., Fairbanks, M. M. & Rafferty, C. M. Plant structural traits and their role in anti-herbivore defence. Perspect. Plant Ecol. 8, 157–178 (2007).
    Google Scholar 
    Burns, K. C. Spinescence in the New Zealand flora: parallels with Australia. N. Z. J. Bot. 54, 273–289 (2016).
    Google Scholar 
    Goheen, J. R., Young, T. P., Keesing, F. & Palmer, T. M. Consequences of herbivory by native ungulates for the reproduction of a savanna tree. J. Ecol. 95, 129–138 (2007).
    Google Scholar 
    Goldel, B., Kissling, W. D. & Svenning, J.-C. Geographical variation and environmental correlates of functional trait distributions in palms (Arecaceae) across the New World. Bot. J. Linn. Soc. 179, 602–617 (2015).
    Google Scholar 
    Alves-Silva, E. & Del-Claro, K. Herbivory causes increases in leaf spinescence and fluctuating asymmetry as a mechanism of delayed induced resistance in a tropical savanna tree. Plant Ecol. Evol. 149, 73–80 (2016).
    Google Scholar 
    Cooper, S. M. & Ginnett, T. F. Spines protect plants against browsing by small climbing mammals. Oecologia 113, 219–221 (1998).ADS 
    PubMed 

    Google Scholar 
    Charles-Dominique, T. et al. Spiny plants, mammal browsers, and the origin of African savannas. Proc. Natl Acad. Sci. USA 113, E5572–E5579 (2016).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ratnam, J., Tomlinson, K. W., Rasquinha, D. N. & Sankaran, M. Savannahs of Asia: antiquity, biogeography, and an uncertain future. Philos. Trans. R. Soc. B. 371, 20150305 (2016).
    Google Scholar 
    Scholes, R. & Archer, S. Tree-grass interactions in savannas. Annu. Rev. Ecol. Syst. 28, 517–544 (1997).
    Google Scholar 
    Cerling, T. E. Development of grasslands and savannas in East Africa during the Neogene. Palaeogeogr. Palaeoclimatol. Palaeoecol. 97, 241–247 (1992).
    Google Scholar 
    Brown, R. W. Additions to the flora of the Green River formation. U. S. Geol. Surv. Prof. Paper, U. S. Gov. Print. Off. 154-J, 279–292 (1929).Manchester, S. Oligocene fossil plants of the John Day Formation, Oregon. Or. Geol. 49, 115d–127d (1987).
    Google Scholar 
    Meyer, H. W. & Manchester, S. R. Oligocene Bridge Creek flora of the John Day Formation, Oregon (Univ. California Press, 1997).Lancucka-Srodoniowa, M. Tortonian flora from the “Gdow Bay” in the south of Poland. Acta Palaeobot. 7, 1–134 (1966).
    Google Scholar 
    Yuan, J. et al. Rapid drift of the Tethyan Himalaya terrane before two-stage India-Asia collision. Natl Sci. Rev. 8, nwaa173 (2021).PubMed 

    Google Scholar 
    Spicer, R. A. et al. Why the ‘Uplift of the Tibetan Plateau’is a myth. Natl Sci. Rev. 8, nwaa091 (2021).PubMed 

    Google Scholar 
    Spicer, R. A. Tibet, the Himalaya, Asian monsoons and biodiversity–In what ways are they related? Plant Divers. 39, 233–244 (2017).PubMed 
    PubMed Central 

    Google Scholar 
    DeCelles, P. G., Kapp, P., Gehrels, G. E. & Ding, L. Paleocene-Eocene foreland basin evolution in the Himalaya of southern Tibet and Nepal: implications for the age of initial India-Asia collision. Tectonics 33, 824–849 (2014).ADS 

    Google Scholar 
    Royden, L. H., Burchfiel, B. C. & van der Hilst, R. D. The geological evolution of the Tibetan Plateau. Science 321, 1054–1058 (2008).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Deng, T., Wu, F. X., Zhou, Z. K. & Su, T. Tibetan Plateau: an evolutionary junction for the history of modern biodiversity. Sci. China Earth Sci. 63, 172–187 (2020).ADS 

    Google Scholar 
    Favre, A. et al. The role of the uplift of the Qinghai‐Tibetan Plateau for the evolution of Tibetan biotas. Biol. Rev. 90, 236–253 (2015).PubMed 

    Google Scholar 
    Su, T. et al. A Middle Eocene lowland humid subtropical “Shangri-La” ecosystem in central Tibet. Proc. Natl Acad. Sci. USA 117, 32989–32995 (2020).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Scientific Expedition Team to the Qinghai-Xizang Plateau. Vegetation of Xizang (Tibet) (Sci. Press, 1988).Liu. X. H. Paleoelevation History and Evolution of the Cenozoic Lunpola basin, Central Tibet. Doctoral thesis (Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 2018).Xiong, Z. Y. et al. The rise and demise of the Paleogene Central Tibetan Valley. Sci. Adv. 8, eabj0944 (2022).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Reichgelt, T., West, C. K. & Greenwood, D. R. The relation between global palm distribution and climate. Sci. Rep. 8, 4721 (2018).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Farnsworth, A. et al. Paleoclimate model-derived thermal lapse rates: towards increasing precision in paleoaltimetry studies. Earth Planet. Sci. Lett. 564, 116903 (2021).CAS 

    Google Scholar 
    Spicer, R. A. et al. Why do foliar physiognomic climate estimates sometimes differ from those observed? Insights from taphonomic information loss and a CLAMP case study from the Ganges Delta. Palaeogeogr. Palaeoclimatol. Palaeoecol. 302, 381–395 (2011).
    Google Scholar 
    Walter, H. Vegetation of the Earth and Ecological Systems of the Geo-biosphere (Springer Berlin Heidelb., 1973).Burley, J. Encyclopedia of Forest Sciences (Acad. Press, 2004).Deng, T. et al. A mammalian fossil from the Dingqing Formation in the Lunpola Basin, northern Tibet, and its relevance to age and paleo-altimetry. Sci. Bull. 57, 261–269 (2012).CAS 

    Google Scholar 
    Ma, P. F. et al. Late Oligocene-early Miocene evolution of the Lunpola Basin, central Tibetan Plateau, evidences from successive lacustrine records. Gondwana Res. 48, 224–236 (2017).ADS 

    Google Scholar 
    Hempson, G. P., Archibald, S. & Bond, W. J. A continent-wide assessment of the form and intensity of large mammal herbivory in Africa. Science 350, 1056–1061 (2015).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Spicer, R. A. The formation and interpretation of plant fossil assemblages. Adv. Bot. Res. 16, 95–191 (1989).
    Google Scholar 
    Gibson, D. J. Grasses and Grassland Ecology (Oxford Univ. Press, 2009).Eltringham, S. K. The Hippos: Natural History and Conservation (Princeton Univ. Press, 1999).Jiang, H. et al. Oligocene Koelreuteria (Sapindaceae) from the Lunpola Basin in central Tibet and its implication for early diversification of the genus. J. Asian Earth Sci. 175, 99–108 (2019).ADS 

    Google Scholar 
    Liu, J. et al. Biotic interchange through lowlands of Tibetan Plateau suture zones during Paleogene. Palaeogeogr. Palaeoclimatol. Palaeoecol. 524, 33–40 (2019).
    Google Scholar 
    Jia, L. B. et al. First fossil record of Cedrelospermum (Ulmaceae) from the Qinghai-Tibetan Plateau: implications for morphological evolution and biogeography. J. Syst. Evol. 57, 94–104 (2019).
    Google Scholar 
    Su, T. et al. No high Tibetan Plateau until the Neogene. Sci. Adv. 5, eaav2189 (2019).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Zhang, Y. L., Li, B. Y. & Zheng, D. A discussion on the boundary and area of the Tibetan Plateau in China. Geol. Res. 21, 1–8 (2002).
    Google Scholar 
    Yao, T. D. et al. From Tibetan Plateau to Third Pole and Pan-Third Pole. Bull. Chin. Acad. Sci. 32, 924–931 (2017).
    Google Scholar 
    Spicer, R. A., Farnsworth, A. & Su, T. Cenozoic topography, monsoons and biodiversity conservation within the Tibetan Region: an evolving story. Plant Divers. 42, 229–254 (2020).PubMed 
    PubMed Central 

    Google Scholar 
    Liu, X. H., Xu, Q. & Ding, L. Differential surface uplift: Cenozoic paleoelevation history of the Tibetan Plateau. Sci. China Earth Sci. 59, 2105–2120 (2016).ADS 
    CAS 

    Google Scholar 
    Ding, L., Li, Z. Y. & Song, P. P. Core fragments of Tibetan Plateau from Gondwanaland united in Northern Hemisphere. Bull. Chin. Acad. Sci. 32, 945–950 (2017).
    Google Scholar 
    Deng, T. & Ding, L. Paleoaltimetry reconstructions of the Tibetan Plateau: progress and contradictions. Natl Sci. Rev. 2, 417–437 (2015).CAS 

    Google Scholar 
    Li, S. F. et al. Orographic evolution of northern Tibet shaped vegetation and plant diversity in eastern Asia. Sci. Adv. 7, eabc7741 (2021).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ding, L. et al. The Andean-type Gangdese Mountains: Paleoelevation record from the Paleocene–Eocene Linzhou Basin. Earth Planet. Sci. Lett. 392, 250–264 (2014).ADS 
    CAS 

    Google Scholar 
    Deng, T. et al. Review: implications of vertebrate fossils for paleo-elevations of the Tibetan Plateau. Glob. Planet. Change 174, 58–69 (2019).ADS 

    Google Scholar 
    Westerhold, T. et al. An astronomically dated record of Earth’s climate and its predictability over the last 66 million years. Science 369, 1383–1387 (2020).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Nemani, R. R. et al. Climate-driven increases in global terrestrial net primary production from 1982 to 1999. Science 300, 1560–1563 (2003).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Hopkins, W. G. Introduction to Plant Physiology (John Wiley & Sons, 1999).Sun, J. M., Liu, W. G., Liu, Z. H. & Fu, B. H. Effects of the uplift of the Tibetan Plateau and retreat of Neotethys ocean on the stepwise aridification of mid-latitude Asian interior. Bull. Chin. Acad. Sci. 32, 951–958 (2017).
    Google Scholar 
    Zong, G. F. Cenezoic Mammals and Environment of Hengduan Mountains Region (China Ocean Press, 1996).Deng, T. et al. An Oligocene giant rhino provides insights into Paraceratherium evolution. Commun. Biol. 4, 639 (2021).PubMed 
    PubMed Central 

    Google Scholar 
    Young, T. P., Stanton, M. L. & Christian, C. E. Effects of natural and simulated herbivory on spine lengths of Acacia drepanolobium in Kenya. Oikos 101, 171–179 (2003).
    Google Scholar 
    Karban, R. & Myers, J. H. Induced plant responses to herbivory. Annu. Rev. Ecol. Syst. 20, 331–348 (1989).
    Google Scholar 
    Huntly, N. Herbivores and the dynamics of communities and ecosystems. Annu. Rev. Ecol. Syst. 22, 477–503 (1991).
    Google Scholar 
    Asner, G. P. et al. Large-scale impacts of herbivores on the structural diversity of African savannas. Proc. Natl Acad. Sci. USA 106, 4947–4952 (2009).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sankaran, M., Augustine, D. J. & Ratnam, J. Native ungulates of diverse body sizes collectively regulate long‐term woody plant demography and structure of a semi‐arid savanna. J. Ecol. 101, 1389–1399 (2013).
    Google Scholar 
    Staver, A. C. & Bond, W. J. Is there a ‘browse trap’? Dynamics of herbivore impacts on trees and grasses in an African savanna. J. Ecol. 102, 595–602 (2014).
    Google Scholar 
    Bakker, E. S. et al. Combining paleo-data and modern exclosure experiments to assess the impact of megafauna extinctions on woody vegetation. Proc. Natl Acad. Sci. USA 113, 847–855 (2016).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Spicer, R. A. et al. The topographic evolution of the Tibetan Region as revealed by palaeontology. Palaeobio. Palaeoenv. 101, 213–243 (2021).
    Google Scholar 
    Rowley, D. B. & Currie, B. S. Palaeo-altimetry of the late Eocene to Miocene Lunpola basin, central Tibet. Nature 439, 677–681 (2006).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Sun, J. M. et al. Palynological evidence for the latest Oligocene-early Miocene paleoelevation estimate in the Lunpola Basin, central Tibet. Palaeogeogr. Palaeoclimatol. Palaeoecol. 399, 21–30 (2014).
    Google Scholar 
    DeCelles, P. G., Kapp, P., Ding, L. & Gehrels, G. E. Late Cretaceous to middle Tertiary basin evolution in the central Tibetan Plateau: Changing environments in response to tectonic partitioning, aridification, and regional elevation gain. Geol. Soc. Am. Bull. 119, 654–680 (2007).ADS 

    Google Scholar 
    Tang, H. et al. Extinct genus Lagokarpos reveals a biogeographic connection between Tibet and other regions in the Northern Hemisphere during the Paleogene. J. Syst. Evol. 57, 670–677 (2019).
    Google Scholar 
    Wang, T. X. et al. Fossil fruits of Illigera (Hernandiaceae) from the Eocene of central Tibetan Plateau. J. Syst. Evol. 59, 1276–1286 (2021).
    Google Scholar 
    Del Rio, C. et al. Asclepiadospermum gen. nov., the earliest fossil record of Asclepiadoideae (Apocynaceae) from the early Eocene of central Qinghai-Tibetan Plateau, and its biogeographic implications. Am. J. Bot. 107, 126–138 (2020).PubMed 

    Google Scholar 
    Xu, Z. Y. The Tertiary and its petroleum potential in the Lunpola Basin, Tibet. Oil Gas. Geol. 1, 153–158 (1980).
    Google Scholar 
    Zhang, K. X. et al. Paleogene-Neogene stratigraphic realm and sedimentary sequence of the Qinghai-Tibet Plateau and their response to uplift of the plateau. Sci. China Earth Sci. 53, 1271–1294 (2010).ADS 

    Google Scholar 
    Wu, Y. F. & Chen, Y. Y. Fossil cyprinid fishes from the late Tertiary of north Xizang, China. Vertebrata Palasiat. 18, 15–20 (1980).
    Google Scholar 
    Wu, F. X., Miao, D. S., Chang, M. M., Shi, G. L. & Wang, N. Fossil climbing perch and associated plant megafossils indicate a warm and wet central Tibet during the late Oligocene. Sci. Rep. 7, 878 (2017).ADS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cai, C. Y., Huang, D. Y., Wu, F. X., Zhao, M. & Wang, N. Tertiary water striders (Hemiptera, Gerromorpha, Gerridae) from the central Tibetan Plateau and their palaeobiogeographic implications. J. Asian Earth Sci. 175, 121–127 (2017).ADS 

    Google Scholar 
    Low, S. L. et al. Oligocene Limnobiophyllum (Araceae) from the central Tibetan Plateau and its evolutionary and palaeoenvironmental implications. J. Syst. Palaeontol. 18, 415–431 (2020).
    Google Scholar 
    Bell, A. D. & Bryan, A. Plant Form: An Illustrated Guide to Flowering Plant Morphology (Timber Press, 2008).Zanne, A. E. et al. Three keys to the radiation of angiosperms into freezing environments. Nature 506, 89–92 (2014).ADS 
    CAS 
    PubMed 

    Google Scholar 
    Revell, L. J. phytools: an R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol. 3, 217–223 (2012).
    Google Scholar 
    Paradis, E. & Schliep, K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics. 35, 526–528 (2019).CAS 
    PubMed 

    Google Scholar 
    Harmon, L. J., Weir, J. T., Brock, C. D., Glor, R. E. & Challenger, W. GEIGER: investigating evolutionary radiations. Bioinformatics. 24, 129–131 (2008).CAS 
    PubMed 

    Google Scholar 
    Maddison, W. P. Confounding asymmetries in evolutionary diversification and character change. Evolution 60, 1743–1746 (2006).PubMed 

    Google Scholar 
    Forest, C. E., Molnar, P. & Emanuel, K. A. Palaeoaltimetry from energy conservation principles. Nature 374, 347–350 (1995).ADS 
    CAS 

    Google Scholar 
    Valdes, P. J. et al. The BRIDGE HadCM3 family of climate models: HadCM3@ Bristol v1.0. Geosci. Model Dev. 10, 3715–3743 (2017).ADS 
    CAS 

    Google Scholar 
    Gough, D. O. Solar interior structure and luminosity variations. Sol. Phys. 74, 21–34 (1981).ADS 
    CAS 

    Google Scholar 
    Foster, G. L., Royer, D. L. & Lunt, D. J. Future climate forcing potentially without precedent in the last 420 million years. Nat. Commun. 8, 14845 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Cox, P. M. Description of the “TRIFFID” Dynamic Global Vegetation Model. 1–16 (Met Office Hadley Centre, 2001).Cox, P., Huntingford, C. & Harding, R. A canopy conductance and photosynthesis model for use in a GCM land surface scheme. J. Hydrol. 212, 79–94 (1998).ADS 

    Google Scholar 
    McInerney, F. A., Strömberg, C. A. E. & White, J. W. C. The Neogene transition from C3 to C4 grasslands in North America stable carbon isotope ratios of fossil phytoliths. Paleobiology 37, 23–49 (2011).
    Google Scholar 
    Lu, H. Y. et al. Phytoliths as quantitative indicators for the reconstruction of past environmental conditions in China II: palaeoenvironmental reconstruction in the Loess Plateau. Quat. Sci. Rev. 25, 945–959 (2006).ADS 

    Google Scholar  More

  • in

    Sex differences in the winter activity of desert hedgehogs (Paraechinus aethiopicus) in a resource-rich habitat in Qatar

    Nagy, K. A. Field metabolic rate and food requirement scaling in mammals and birds. Ecol. Monogr. 57, 111–128 (1987).Article 

    Google Scholar 
    Anderson, K. J. & Jetz, W. The broad-scale ecology of energy expenditure of endotherms. Ecol. Lett. 8, 310–318 (2005).Article 

    Google Scholar 
    Terrien, J., Perret, M. & Aujard, F. Behavioral thermoregulation in mammals: A review. Front. Biosci. 16, 1428–1444 (2011).Article 

    Google Scholar 
    Mery, F. & Burns, J. G. Behavioural plasticity: An interaction between evolution and experience. Evol. Ecol. 24, 571–583 (2010).Article 

    Google Scholar 
    Brockmann, H. J. The evolution of alternative strategies and tactics. Adv. Study Behav. 30, 1–51 (2001).Article 

    Google Scholar 
    Milling, C. R., Rachlow, J. L., Johnson, T. R., Forbey, J. S. & Shipley, L. A. Seasonal variation in behavioral thermoregulation and predator avoidance in a small mammal. Behav. Ecol. 28, 1236–1247 (2017).Article 

    Google Scholar 
    Guiden, P. W. & Orrock, J. L. Seasonal shifts in activity timing reduce heat loss of small mammals during winter. Anim. Behav. 164, 181–192 (2020).Article 

    Google Scholar 
    Cotton, C. L. & Parker, K. L. Winter activity patterns of northern flying squirrels in sub-boreal forests. Can. J. Zool. 78, 1896–1901 (2000).Article 

    Google Scholar 
    Long, R. A., Martin, T. J. & Barnes, B. M. Body temperature and activity patterns in free-living arctic ground squirrels. J. Mammal. 86, 314–322 (2005).Article 

    Google Scholar 
    Zschille, J., Stier, N. & Roth, M. Gender differences in activity patterns of American mink Neovison vison in Germany. Eur. J. Wildl. Res. 56, 187–194 (2010).Article 

    Google Scholar 
    Geiser, F. Hibernation. Curr. Biol. 23, R188–R193 (2013).CAS 
    PubMed 
    Article 

    Google Scholar 
    Gür, M. K. & Gür, H. Age and sex differences in hibernation patterns in free-living Anatolian ground squirrels. Mamm. Biol. 80, 265–272 (2015).Article 

    Google Scholar 
    Kisser, B. & Goodwin, H. T. Hibernation and overwinter body temperatures in free-ranging thirteen-lined ground squirrels, Ictidomys tridecemlineatus. Am. Midl. Nat. 167, 396–409 (2012).Article 

    Google Scholar 
    Dmi’el, R. & Schwarz, M. Hibernation patterns and energy expenditure in hedgehogs from semi-arid and temperate habitats. J. Comp. Physiol. B 155, 117–123 (1984).Article 

    Google Scholar 
    Abu Baker, M. A. et al. Caught basking in the winter sun: Preliminary data on winter thermoregulation in the Ethiopian hedgehog, Paraechinus aethiopicus in Qatar. J. Arid Environ. 125, 52–55 (2016).ADS 
    Article 

    Google Scholar 
    McKechnie, A. E. & Mzilikazi, N. Heterothermy in Afrotropical mammals and birds: A review. Integr. Comp. Biol. 51, 349–363 (2011).PubMed 
    Article 

    Google Scholar 
    Wacker, C. B., McAllan, B. M., Körtner, G. & Geiser, F. The role of basking in the development of endothermy and torpor in a marsupial. J. Comp. Physiol. B 187, 1029–1038 (2017).PubMed 
    Article 

    Google Scholar 
    Brown, K. J. & Downs, C. T. Basking behaviour in the rock hyrax (Procavia capensis) during winter. Afr. Zool. 42, 70–79 (2007).Article 

    Google Scholar 
    Humphries, M. M., Thomas, D. W. & Kramer, D. L. The role of energy availability in mammalian hibernation: A cost-benefit approach. Physiol. Biochem. Zool. 76, 165–179 (2003).PubMed 
    Article 

    Google Scholar 
    Field, K. A. et al. Effect of torpor on host transcriptomic responses to a fungal pathogen in hibernating bats. Mol. Ecol. 27, 3727–3743 (2018).CAS 
    Article 

    Google Scholar 
    Bieber, C., Cornils, J. S., Hoelzl, F., Giroud, S. & Ruf, T. The costs of locomotor activity? Maximum body temperatures and the use of torpor during the active season in edible dormice. J. Comp. Physiol. B 187, 803–814 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Eto, T. et al. Individual variation of daily torpor and body mass change during winter in the large Japanese field mouse (Apodemus speciosus). J. Comp. Physiol. B 188, 1005–1014 (2018).PubMed 
    Article 

    Google Scholar 
    Zervanos, S. M., Maher, C. R. & Florant, G. L. Effect of body mass on hibernation strategies of woodchucks (Marmota monax). (2014).Ford, R. G. Home range in a patchy environment: Optimal foraging predictions. Am. Zool. 23, 315–326 (1983).Article 

    Google Scholar 
    Czenze, Z. J. & Willis, C. K. R. Warming up and shipping out: Arousal and emergence timing in hibernating little brown bats (Myotis lucifugus). J. Comp. Physiol. B 185, 575–586 (2015).PubMed 
    Article 

    Google Scholar 
    Batavia, M., Nguyen, G., Harman, K. & Zucker, I. Hibernation patterns of Turkish hamsters: Influence of sex and ambient temperature. J. Comp. Physiol. B 183, 269–277 (2013).PubMed 
    Article 

    Google Scholar 
    Kato, G. A. et al. Individual differences in torpor expression in adult mice are related to relative birth mass. J. Exp. Biol. 221, jeb171983 (2018).PubMed 
    Article 

    Google Scholar 
    Williams, C. T. et al. Sex-dependent phenological plasticity in an arctic hibernator. Am. Nat. 190, 854–859 (2017).PubMed 
    Article 

    Google Scholar 
    Healy, J. E., Burdett, K. A., Buck, C. L. & Florant, G. L. Sex differences in torpor patterns during natural hibernation in golden-mantled ground squirrels (Callospermophilus lateralis). J. Mammal. 93, 751–758 (2012).Article 

    Google Scholar 
    Wang, Y., Yuan, L.-L., Peng, X., Wang, Y. & Yang, M. Experimental study on hibernation patterns in different ages and sexes of daurian ground squirrel (Spermophilus Dauricus). Shenyang Shifan Daxue Xuebao (Ziran Kexue Ban) 27, 351–355 (2009).
    Google Scholar 
    Siutz, C., Franceschini, C. & Millesi, E. Sex and age differences in hibernation patterns of common hamsters: Adult females hibernate for shorter periods than males. J. Comp. Physiol. B 186, 801–811 (2016).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Michener, G. R. Sexual differences in over-winter torpor patterns of Richardson’s ground squirrels in natural hibernacula. Oecologia 89, 397–406 (1992).ADS 
    PubMed 
    Article 

    Google Scholar 
    Boyles, J. G., Bennett, N. C., Mohammed, O. B. & Alagaili, A. N. Torpor patterns in Desert Hedgehogs (Paraechinus aethiopicus) represent another new point along a thermoregulatory continuum. Physiol. Biochem. Zool. 90, 445–452 (2017).PubMed 
    Article 

    Google Scholar 
    Reeve, N. Hedgehogs (Poyser, 1994).
    Google Scholar 
    He, K. et al. An estimation of erinaceidae phylogeny: A combined analysis approach. PLoS One 7, e39304 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Schoenfeld, M. & Yom-Tov, Y. The biology of two species of hedgehogs, Erinaceus europaeus concolor and Hemiechinus auritus aegyptius, Israel. Mammalia 49, 339–356 (1985).Article 

    Google Scholar 
    Haigh, A., O’Riordan, R. M. & Butler, F. Nesting behaviour and seasonal body mass changes in a rural Irish population of the Western hedgehog (Erinaceus europaeus). Acta Theriol. (Warsz) 57, 321–331 (2012).Article 

    Google Scholar 
    Rasmussen, S. L., Berg, T. B., Dabelsteen, T. & Jones, O. R. The ecology of suburban juvenile European hedgehogs (Erinaceus europaeus) in Denmark. Ecol. Evol. 9, 13174–13187 (2019).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Jensen, A. B. Overwintering of European hedgehogs (Erinaceus europaeus) in a Danish rural area. Acta Theriol. (Warsz) 49, 145–155 (2004).Article 

    Google Scholar 
    Jackson, D. B. The breeding biology of introduced hedgehogs (Erinaceus europaeus) on a Scottish Island: Lessons for population control and bird conservation. J. Zool. 268, 303–314 (2006).Article 

    Google Scholar 
    Rautio, A., Valtonen, A., Auttila, M. & Kunnasranta, M. Nesting patterns of European hedgehogs (Erinaceus europaeus) under northern conditions. Acta Theriol. (Warsz) 59, 173–181 (2014).Article 

    Google Scholar 
    Hallam, S. L. & Mzilikazi, N. Heterothermy in the southern African hedgehog, Atelerix frontalis. J. Comp. Physiol. B 181, 437–445 (2011).PubMed 
    Article 

    Google Scholar 
    South, K. E., Haynes, K. & Jackson, A. C. Hibernation Patterns of the European Hedgehog, Erinaceus europaeus, at a Cornish Rescue Centre. Animals 10, 1418 (2020).PubMed Central 
    Article 

    Google Scholar 
    Gillies, A. C., Ellison, G. T. H. & Skinner, J. D. The effect of seasonal food restriction on activity, metabolism and torpor in the South African hedgehog (Atelerix frontalis). J. Zool. 223, 117–130 (1991).Article 

    Google Scholar 
    Gazzard, A. & Baker, P. J. Patterns of feeding by householders affect activity of hedgehogs (Erinaceus europaeus) during the hibernation period. Animals 10, 1344 (2020).PubMed Central 
    Article 

    Google Scholar 
    Dmiel, R. & Schwarz, M. Hibernation patterns and energy expenditure in hedgehogs from semi-arid and temperate habitats. J. Comp. Physiol. B 155, 117–123 (1984).Article 

    Google Scholar 
    Fowler, P. A. & Racey, P. A. Daily and seasonal cycles of body temperature and aspects of heterothermy in the hedgehog Erinaceus europaeus. J. Comp. Physiol. B 160, 299–307 (1990).CAS 
    PubMed 
    Article 

    Google Scholar 
    Rutovskaya, M. V. et al. The dynamics of body temperature of the Eastern European hedgehog (Erinaceus roumanicus) during winter hibernation. Biol. Bull. 46, 1136–1145 (2019).Article 

    Google Scholar 
    Harrison, D. L. & Bates, P. J. J. The Mammals of Arabia Vol 354 (Harrison Zoological Museum Sevenoaks, 1991).
    Google Scholar 
    Al-Musfir, H. M. & Yamaguchi, N. Timings of hibernation and breeding of Ethiopian Hedgehogs, Paraechinus aethiopicus in Qatar. Zool. Middle East 45, 3–10 (2008).Article 

    Google Scholar 
    Pettett, C. E., Al-Hajri, A., Al-Jabiry, H., Macdonald, D. W. & Yamaguchi, N. A comparison of the Ranging behaviour and habitat use of the Ethiopian hedgehog (Paraechinus aethiopicus) in Qatar with hedgehog taxa from temperate environments. Sci. Rep. 8, 1–10 (2018).Article 
    CAS 

    Google Scholar 
    Abu Baker, M. A., Reeve, N., Conkey, A. A. T., Macdonald, D. W. & Yamaguchi, N. Hedgehogs on the move: Testing the effects of land use change on home range size and movement patterns of free-ranging Ethiopian hedgehogs. PLoS One 12, e0180826 (2017).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Yamaguchi, N., Al-Hajri, A. & Al-Jabiri, H. Timing of breeding in free-ranging Ethiopian hedgehogs, Paraechinus aethiopicus, from Qatar. J. Arid Environ. 99, 1–4 (2013).ADS 
    Article 

    Google Scholar 
    Alagaili, A. N., Bennett, N. C., Mohammed, O. B. & Hart, D. W. The reproductive biology of the Ethiopian hedgehog, Paraechinus aethiopicus, from central Saudi Arabia: The role of rainfall and temperature. J. Arid Environ. 145, 1–9 (2017).ADS 
    Article 

    Google Scholar 
    Pettett, C. E. et al. Daily energy expenditure in the face of predation: Hedgehog energetics in rural landscapes. J. Exp. Biol. 220, 460–468 (2017).PubMed 
    Article 

    Google Scholar 
    Kraus, C., Eberle, M. & Kappeler, P. M. The costs of risky male behaviour: Sex differences in seasonal survival in a small sexually monomorphic primate. Proc. R. Soc. B Biol. Sci. 275, 1635–1644 (2008).Article 

    Google Scholar 
    Mzilikazi, N. & Lovegrove, B. G. Reproductive activity influences thermoregulation and torpor in pouched mice, Saccostomus campestris. J. Comp. Physiol. B 172, 7–16 (2002).PubMed 
    Article 

    Google Scholar 
    Richter, M. M., Barnes, B. M., O’reilly, K. M., Fenn, A. M. & Buck, C. L. The influence of androgens on hibernation phenology of free-living male arctic ground squirrels. Horm. Behav. 89, 92–97 (2017).CAS 
    PubMed 
    Article 

    Google Scholar 
    Haigh, A., Butler, F. & O’Riordan, R. M. Courtship behaviour of western hedgehogs (Erinaceus europaeus) in a rural landscape in Ireland and the first appearance of offspring. Lutra 55, 41–54 (2012).
    Google Scholar 
    Nicol, S. C., Morrow, G. E. & Harris, R. L. Energetics meets sexual conflict: The phenology of hibernation in Tasmanian echidnas. Funct. Ecol. 33, 2150–2160 (2019).Article 

    Google Scholar 
    Pettett, C. W., Macdonald, D., Al-Hajiri, A., Al-Jabiry, H. & Yamaguchi, N. Characteristics and demography of a free-ranging Ethiopian Hedgehog, Paraechinus aethiopicus, population in Qatar. Animals 10, 951 (2020).PubMed Central 
    Article 

    Google Scholar 
    Kenward, R. E. A Manual for Wildlife Radio Tagging (Academic Press, 2000).
    Google Scholar 
    R Core Team. R: A Language and Environment for Statistical Computing (R Core Team, 2021).
    Google Scholar 
    Fox, J. & Weisberg, S. An R Companion to Applied Regression (Sage, 2019).
    Google Scholar  More

  • in

    Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.)

    Hassani, M. A., Durán, P. & Hacquard, S. Microbial interactions within the plant holobiont. Microbiome 6(1), 58. https://doi.org/10.1186/s40168-018-0445-0 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sapp, M., Ploch, S., Fiore-Donno, A. M., Bonkowski, M. & Rose, L. E. Protists are an integral part of the Arabidopsis thaliana microbiome. Environ Microbiol 20(1), 30–43. https://doi.org/10.1111/1462-2920.13941 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Herrera Paredes, S. & Lebeis, S. L. Giving back to the community: Microbial mechanisms of plant–soil interactions. Funct. Ecol. 30(7), 1043–1052. https://doi.org/10.1111/1365-2435.12684 (2016).Article 

    Google Scholar 
    Nath, A. & Sundaram, S. Microbiome community interactions with social forestry and agroforestry. In Microbial services in restoration ecology (eds Singh, J. S. & Vimal, S. R.) 71–82 (Elsevier, 2020).Chapter 

    Google Scholar 
    Rodriguez, P. A. et al. Systems biology of plant–microbiome interactions. Mol. Plant 12(6), 804–821. https://doi.org/10.1016/j.molp.2019.05.006 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Guttman, D. S., McHardy, A. C. & Schulze-Lefert, P. Microbial genome-enabled insights into plant–microorganism interactions. Nat. Rev. Genet. 15(12), 797–813. https://doi.org/10.1038/nrg3748 (2014).CAS 
    Article 
    PubMed 

    Google Scholar 
    Lewin, S., Francioli, D., Ulrich, A. & Kolb, S. Crop host signatures reflected by co-association patterns of keystone bacteria in the rhizosphere microbiota. Environ. Microb. 16(1), 18. https://doi.org/10.1186/s40793-021-00387-w (2021).CAS 
    Article 

    Google Scholar 
    Trivedi, P., Leach, J. E., Tringe, S. G., Sa, T. & Singh, B. K. Plant–microbiome interactions: From community assembly to plant health. Nat. Rev. Microbiol. 18(11), 607–621. https://doi.org/10.1038/s41579-020-0412-1 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bardelli, T. et al. Effects of slope exposure on soil physico-chemical and microbiological properties along an altitudinal climosequence in the Italian Alps. Sci. Total Environ. 575, 1041–1055. https://doi.org/10.1016/j.scitotenv.2016.09.176 (2017).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Francioli, D., van Ruijven, J., Bakker, L. & Mommer, L. Drivers of total and pathogenic soil-borne fungal communities in grassland plant species. Fungal Ecol. 48, 100987. https://doi.org/10.1016/j.funeco.2020.100987 (2020).Article 

    Google Scholar 
    Hamonts, K. et al. Field study reveals core plant microbiota and relative importance of their drivers. Environ. Microbiol. 20(1), 124–140. https://doi.org/10.1111/1462-2920.14031 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Trivedi, P., Batista, B. D., Bazany, K. E. & Singh, B. K. Plant–microbiome interactions under a changing world: Responses, consequences and perspectives. New Phytol. 234(6), 1951–1959. https://doi.org/10.1111/nph.18016 (2022).Article 
    PubMed 

    Google Scholar 
    Hawkes, C. V. et al. Extension of plant phenotypes by the foliar microbiome. Annu. Rev. Plant Biol. 72(1), 823–846. https://doi.org/10.1146/annurev-arplant-080620-114342 (2021).CAS 
    Article 
    PubMed 

    Google Scholar 
    Hunter, P. The revival of the extended phenotype: After more than 30 years, Dawkins’ extended phenotype hypothesis is enriching evolutionary biology and inspiring potential applications. EMBO Rep. 19(7), e46477. https://doi.org/10.15252/embr.201846477 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Thapa, S. & Prasanna, R. Prospecting the characteristics and significance of the phyllosphere microbiome. Ann. Microbiol. 68(5), 229–245. https://doi.org/10.1007/s13213-018-1331-5 (2018).CAS 
    Article 

    Google Scholar 
    Vacher, C. et al. The phyllosphere: Microbial jungle at the plant-climate interface. Annu. Rev. Ecol. Evol. Syst. 47(1), 1–24. https://doi.org/10.1146/annurev-ecolsys-121415-032238 (2016).Article 

    Google Scholar 
    Copeland, J. K., Yuan, L., Layeghifard, M., Wang, P. W. & Guttman, D. S. Seasonal community succession of the phyllosphere microbiome. Mol. Plant Microbe Interact. 28(3), 274–285. https://doi.org/10.1094/mpmi-10-14-0331-fi (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    Pérez-Bueno, M. L., Pineda, M., Díaz-Casado, E. & Barón, M. Spatial and temporal dynamics of primary and secondary metabolism in Phaseolus vulgaris challenged by Pseudomonas syringae. Physiol. Plant. 153(1), 161–174. https://doi.org/10.1111/ppl.12237 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bodenhausen, N., Bortfeld-Miller, M., Ackermann, M. & Vorholt, J. A. A Synthetic community approach reveals plant genotypes affecting the phyllosphere microbiota. PLoS Genet. 10(4), e1004283. https://doi.org/10.1371/journal.pgen.1004283 (2014).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Giauque, H. & Hawkes, C. V. Climate affects symbiotic fungal endophyte diversity and performance. Am. J. Bot. 100(7), 1435–1444. https://doi.org/10.3732/ajb.1200568 (2013).Article 
    PubMed 

    Google Scholar 
    Rodriguez, R. J. et al. Stress tolerance in plants via habitat-adapted symbiosis. ISME J. 2(4), 404–416. https://doi.org/10.1038/ismej.2007.106 (2008).Article 
    PubMed 

    Google Scholar 
    Trivedi, P., Mattupalli, C., Eversole, K. & Leach, J. E. Enabling sustainable agriculture through understanding and enhancement of microbiomes. New Phytol. 230(6), 2129–2147. https://doi.org/10.1111/nph.17319 (2021).Article 
    PubMed 

    Google Scholar 
    Delmotte, N. et al. Community proteogenomics reveals insights into the physiology of phyllosphere bacteria. Proc. Natl. Acad. Sci. 106(38), 16428–16433. https://doi.org/10.1073/pnas.0905240106%JProceedingsoftheNationalAcademyofSciences (2009).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Vorholt, J. A. Microbial life in the phyllosphere. Nat. Rev. Microbiol. 10(12), 828–840. https://doi.org/10.1038/nrmicro2910 (2012).CAS 
    Article 
    PubMed 

    Google Scholar 
    Kembel, S. W. et al. Relationships between phyllosphere bacterial communities and plant functional traits in a neotropical forest. Proc. Natl. Acad. Sci. 111(38), 13715–13720. https://doi.org/10.1073/pnas.1216057111 (2014).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Whipps, J. M., Hand, P., Pink, D. & Bending, G. D. Phyllosphere microbiology with special reference to diversity and plant genotype. J. Appl. Microbiol. 105(6), 1744–1755. https://doi.org/10.1111/j.1365-2672.2008.03906.x (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    Bai, Y. et al. Functional overlap of the Arabidopsis leaf and root microbiota. Nature 528(7582), 364–369. https://doi.org/10.1038/nature16192 (2015).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Laforest-Lapointe, I., Messier, C. & Kembel, S. W. Host species identity, site and time drive temperate tree phyllosphere bacterial community structure. Microbiome 4(1), 27. https://doi.org/10.1186/s40168-016-0174-1 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Sapkota, R., Knorr, K., Jørgensen, L. N., O’Hanlon, K. A. & Nicolaisen, M. Host genotype is an important determinant of the cereal phyllosphere mycobiome. New Phytol. 207(4), 1134–1144. https://doi.org/10.1111/nph.13418 (2015).CAS 
    Article 
    PubMed 

    Google Scholar 
    Grady, K. L., Sorensen, J. W., Stopnisek, N., Guittar, J. & Shade, A. Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops. Nat. Commun. 10(1), 4135. https://doi.org/10.1038/s41467-019-11974-4 (2019).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Latz, M. A. C. et al. Succession of the fungal endophytic microbiome of wheat is dependent on tissue-specific interactions between host genotype and environment. Sci. Total Environ. 759, 143804. https://doi.org/10.1016/j.scitotenv.2020.143804 (2021).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Rastogi, G. et al. Leaf microbiota in an agroecosystem: Spatiotemporal variation in bacterial community composition on field-grown lettuce. ISME J. 6(10), 1812–1822. https://doi.org/10.1038/ismej.2012.32 (2012).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Bao, L. et al. Seasonal variation of epiphytic bacteria in the phyllosphere of Gingko biloba, Pinus bungeana and Sabina chinensis. FEMS Microbiol. Ecol. 96, 3. https://doi.org/10.1093/femsec/fiaa017 (2020).CAS 
    Article 

    Google Scholar 
    Ding, T. & Melcher, U. Influences of plant species, season and location on leaf endophytic bacterial communities of non-cultivated plants. PLoS ONE 11(3), e0150895. https://doi.org/10.1371/journal.pone.0150895 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Perreault, R. & Laforest-Lapointe, I. Plant-microbe interactions in the phyllosphere: Facing challenges of the anthropocene. ISME J. https://doi.org/10.1038/s41396-021-01109-3 (2021).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Redford, A. J. & Fierer, N. Bacterial succession on the leaf surface: A novel system for studying successional dynamics. Microb. Ecol. 58(1), 189–198. https://doi.org/10.1007/s00248-009-9495-y (2009).Article 
    PubMed 

    Google Scholar 
    Campisano, A. et al. Temperature drives the assembly of endophytic communities’ seasonal succession. Environ. Microbiol. 19(8), 3353–3364. https://doi.org/10.1111/1462-2920.13843 (2017).Article 
    PubMed 

    Google Scholar 
    Ren, G. et al. Response of soil, leaf endosphere and phyllosphere bacterial communities to elevated CO2 and soil temperature in a rice paddy. Plant Soil 392(1), 27–44. https://doi.org/10.1007/s11104-015-2503-8 (2015).CAS 
    Article 

    Google Scholar 
    Konapala, G., Mishra, A. K., Wada, Y. & Mann, M. E. Climate change will affect global water availability through compounding changes in seasonal precipitation and evaporation. Nat. Commun. 11(1), 3044. https://doi.org/10.1038/s41467-020-16757-w (2020).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Parmesan, C. & Yohe, G. A globally coherent fingerprint of climate change impacts across natural systems. Nature 421(6918), 37–42. https://doi.org/10.1038/nature01286 (2003).ADS 
    CAS 
    Article 
    PubMed 

    Google Scholar 
    Donn, S., Kirkegaard, J. A., Perera, G., Richardson, A. E. & Watt, M. Evolution of bacterial communities in the wheat crop rhizosphere. Environ. Microbiol. 17(3), 610–621. https://doi.org/10.1111/1462-2920.12452 (2015).Article 
    PubMed 

    Google Scholar 
    Francioli, D., Schulz, E., Buscot, F. & Reitz, T. Dynamics of soil bacterial communities over a vegetation season relate to both soil nutrient status and plant growth phenology. Microb. Ecol. 75(1), 216–227. https://doi.org/10.1007/s00248-017-1012-0 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Breitkreuz, C., Buscot, F., Tarkka, M. & Reitz, T. Shifts between and among populations of wheat rhizosphere Pseudomonas, Streptomyces and Phyllobacterium suggest consistent phosphate mobilization at different wheat growth stages under abiotic stress. Front. Microbiol. 10, 3109–3109. https://doi.org/10.3389/fmicb.2019.03109 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Na, X. et al. Plant stage, not drought stress, determines the effect of cultivars on bacterial community diversity in the rhizosphere of broomcorn millet (Panicum miliaceum L.). Front. Microbiol. 10, 828. https://doi.org/10.3389/fmicb.2019.00828 (2019).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ad-hoc-AG-Boden. Bodenkundliche Kartieranleitung 438 (Schweizerbart, 2005).
    Google Scholar 
    Zadoks, J. C., Chang, T. T. & Konzak, C. F. A decimal code for the growth stages of cereals. Weed Res. 14(6), 415–421. https://doi.org/10.1111/j.1365-3180.1974.tb01084.x (1974).Article 

    Google Scholar 
    Cannell, R. Q., Belford, R. K., Gales, K., Dennis, C. W. & Prew, R. D. Effects of waterlogging at different stages of development on the growth and yield of winter wheat. J. Sci. Food Agric. 31(2), 117–132. https://doi.org/10.1002/jsfa.2740310203 (1980).Article 

    Google Scholar 
    Drew, M. C. Soil aeration and plant root metabolism. Soil Sci. 154(4), 259–268 (1992).ADS 
    Article 

    Google Scholar 
    Meyer, W. et al. Effect of irrigation on soil oxygen status and root and shoot growth of wheat in a clay soil. Aust. J. Agric. Res. https://doi.org/10.1071/AR9850171 (1985).Article 

    Google Scholar 
    Riehm, H. Bestimmung der laktatlöslichen Phosphorsäure in karbonathaltigen Böden. Phosphorsäure 1, 167–178. https://doi.org/10.1002/jpln.19420260107 (1943).Article 

    Google Scholar 
    Murphy, J., & Riley, J. P. A modified single solution method for the determination of phosphate in natural waters. Anal. Chim. Acta 27, 31–36. https://doi.org/10.1016/S0003-2670(00)88444-5 (1962).CAS 
    Article 

    Google Scholar 
    Francioli, D., Lentendu, G., Lewin, S. & Kolb, S. DNA metabarcoding for the characterization of terrestrial microbiota—pitfalls and solutions. Microorganisms 9(2), 361 (2021).CAS 
    Article 

    Google Scholar 
    Chelius, M. K. & Triplett, E. W. The diversity of archaea and bacteria in association with the roots of Zea mays L. Microb. Ecol. 41(3), 252–263. https://doi.org/10.1007/s002480000087 (2001).CAS 
    Article 
    PubMed 

    Google Scholar 
    Redford, A. J., Bowers, R. M., Knight, R., Linhart, Y. & Fierer, N. The ecology of the phyllosphere: Geographic and phylogenetic variability in the distribution of bacteria on tree leaves. Environ. Microbiol. 12(11), 2885–2893. https://doi.org/10.1111/j.1462-2920.2010.02258.x (2010).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 1. https://doi.org/10.14806/ej.17.1.200 (2011).Article 

    Google Scholar 
    Callahan, B. J. et al. DADA2: High-resolution sample inference from Illumina amplicon data. Nat. Methods 13(7), 581. https://doi.org/10.1038/Nmeth.3869 (2016).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Francioli, D. et al. Flooding causes dramatic compositional shifts and depletion of putative beneficial bacteria on the spring wheat microbiota. Front. Microbiol. 12, 3371. https://doi.org/10.3389/fmicb.2021.773116 (2021).Article 

    Google Scholar 
    Anderson, M. J. Permutational multivariate analysis of variance (PERMANOVA). In Wiley StatsRef: Statistics Reference Online 1–15 (Wiley, 2017).
    Google Scholar 
    Dray, S., Legendre, P. & Blanchet, G. Packfor: Forward Selection with Permutation. R package version 0.0‐8/r100 ed. (2011).Oksanen, J. et al. vegan: Community Ecology Package. R package version 2.5-2. ed. (2018).Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12(6), R60. https://doi.org/10.1186/gb-2011-12-6-r60 (2011).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Lahti, L. & Sudarshan, S. Tools for Microbiome Analysis in R. Version 2.1.28. ed. (2020).R Core Team. R: A Language and Environment for Statistical Computing (R Foundation for Statistical Computing, 2020).
    Google Scholar 
    Chen, S. et al. Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization. Microbiome 7(1), 136. https://doi.org/10.1186/s40168-019-0750-2 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Wang, J. et al. Wheat and rice growth stages and fertilization regimes alter soil bacterial community structure, but not diversity. Front. Microbiol. 7, 1207. https://doi.org/10.3389/fmicb.2016.01207 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Comby, M., Lacoste, S., Baillieul, F., Profizi, C. & Dupont, J. Spatial and temporal variation of cultivable communities of co-occurring endophytes and pathogens in wheat. Front. Microbiol. 7, 403. https://doi.org/10.3389/fmicb.2016.00403 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Robinson, R. J. et al. Endophytic bacterial community composition in wheat (Triticum aestivum) is determined by plant tissue type, developmental stage and soil nutrient availability. Plant Soil 405(1), 381–396. https://doi.org/10.1007/s11104-015-2495-4 (2016).CAS 
    Article 

    Google Scholar 
    Sapkota, R., Jørgensen, L. N. & Nicolaisen, M. Spatiotemporal variation and networks in the mycobiome of the wheat canopy. Front. Plant Sci. https://doi.org/10.3389/fpls.2017.01357 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chaudhry, V. et al. Shaping the leaf microbiota: Plant–microbe–microbe interactions. J. Exp. Bot. 72(1), 36–56. https://doi.org/10.1093/jxb/eraa417 (2020).CAS 
    Article 
    PubMed Central 

    Google Scholar 
    Liu, Z., Cheng, R., Xiao, W., Guo, Q. & Wang, N. Effect of off-season flooding on growth, photosynthesis, carbohydrate partitioning, and nutrient uptake in Distylium chinense. PLoS ONE 9(9), e107636. https://doi.org/10.1371/journal.pone.0107636 (2014).ADS 
    CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Rosa, M. et al. Soluble sugars. Plant Signal. Behav. 4(5), 388–393. https://doi.org/10.4161/psb.4.5.8294 (2009).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Chen, H., Qualls, R. G. & Blank, R. R. Effect of soil flooding on photosynthesis, carbohydrate partitioning and nutrient uptake in the invasive exotic Lepidium latifolium. Aquat. Bot. 82(4), 250–268. https://doi.org/10.1016/j.aquabot.2005.02.013 (2005).CAS 
    Article 

    Google Scholar 
    Bacanamwo, M. & Purcell, L. C. Soybean dry matter and N accumulation responses to flooding stress, N sources and hypoxia. J. Exp. Bot. 50(334), 689–696. https://doi.org/10.1093/jxb/50.334.689 (1999).CAS 
    Article 

    Google Scholar 
    Boem, F. H. G., Lavado, R. S. & Porcelli, C. A. Note on the effects of winter and spring waterlogging on growth, chemical composition and yield of rapeseed. Field Crop. Res. 47(2), 175–179. https://doi.org/10.1016/0378-4290(96)00025-1 (1996).Article 

    Google Scholar 
    Kozlowski, T. T. Plant responses to flooding of soil. Bioscience 34(3), 162–167. https://doi.org/10.2307/1309751 (1984).Article 

    Google Scholar 
    Topa, M. A. & Cheeseman, J. M. 32P uptake and transport to shoots in Pinuus serotina seedlings under aerobic and hypoxic growth conditions. Physiol. Plant. 87(2), 125–133. https://doi.org/10.1111/j.1399-3054.1993.tb00134.x (1993).CAS 
    Article 

    Google Scholar 
    Colmer, T. D. & Flowers, T. J. Flooding tolerance in halophytes. New Phytol. 179(4), 964–974. https://doi.org/10.1111/j.1469-8137.2008.02483.x (2008).CAS 
    Article 
    PubMed 

    Google Scholar 
    Gibbs, J. & Greenway, H. Mechanisms of anoxia tolerance in plants. I. Growth, survival and anaerobic catabolism. Funct. Plant Biol. 30(1), 1–47. https://doi.org/10.1071/PP98095 (2003).CAS 
    Article 
    PubMed 

    Google Scholar 
    Board, J. E. Waterlogging effects on plant nutrient concentrations in soybean. J. Plant Nutr. 31(5), 828–838. https://doi.org/10.1080/01904160802043122 (2008).CAS 
    Article 

    Google Scholar 
    Smethurst, C. F., Garnett, T. & Shabala, S. Nutritional and chlorophyll fluorescence responses of lucerne (Medicago sativa) to waterlogging and subsequent recovery. Plant Soil 270(1), 31–45. https://doi.org/10.1007/s11104-004-1082-x (2005).CAS 
    Article 

    Google Scholar 
    Thomson, C. J., Atwell, B. J. & Greenway, H. Response of wheat seedlings to low O2 concentrations in nutrient solution: II. K+/Na+ selectivity of root tissues. J. Exp. Bot. 40(9), 993–999. https://doi.org/10.1093/jxb/40.9.993 (1989).Article 

    Google Scholar 
    Barrett-Lennard, E. G. The interaction between waterlogging and salinity in higher plants: Causes, consequences and implications. Plant Soil 253(1), 35–54. https://doi.org/10.1023/A:1024574622669 (2003).CAS 
    Article 

    Google Scholar 
    Granzow, S. et al. The effects of cropping regimes on fungal and bacterial communities of wheat and faba bean in a greenhouse pot experiment differ between plant species and compartment. Front. Microbiol. 8, 902. https://doi.org/10.3389/fmicb.2017.00902 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Gdanetz, K. & Trail, F. The wheat microbiome under four management strategies, and potential for endophytes in disease protection. Phytobiomes J. 1(3), 158–168. https://doi.org/10.1094/PBIOMES-05-17-0023-R (2017).Article 

    Google Scholar 
    Shade, A., McManus, P. S., Handelsman, J. & Zhou, J. Unexpected diversity during community succession in the apple flower microbiome. MBio 4(2), e00602-00612. https://doi.org/10.1128/mBio.00602-12 (2013).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Guo, J. et al. Seed-borne, endospheric and rhizospheric core microbiota as predictors of plant functional traits across rice cultivars are dominated by deterministic processes. New. Phytol. 230(5), 2047–2060. https://doi.org/10.1111/nph.17297 (2021).Article 
    PubMed 

    Google Scholar 
    Allwood, J. W. et al. Profiling of spatial metabolite distributions in wheat leaves under normal and nitrate limiting conditions. Phytochemistry 115, 99–111. https://doi.org/10.1016/j.phytochem.2015.01.007 (2015).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Li, Y. et al. Plant phenotypic traits eventually shape its microbiota: A common garden test. Front. Microbiol. 9, 2479. https://doi.org/10.3389/fmicb.2018.02479 (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Xiong, C. et al. Plant developmental stage drives the differentiation in ecological role of the maize microbiome. Microbiome 9(1), 171. https://doi.org/10.1186/s40168-021-01118-6 (2021).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Schlechter, R. O., Miebach, M. & Remus-Emsermann, M. N. P. Driving factors of epiphytic bacterial communities: A review. J. Adv. Res. 19, 57–65. https://doi.org/10.1016/j.jare.2019.03.003 (2019).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Mathur, P., Mehtani, P. & Sharma, C. (2021). Leaf Endophytes and Their Bioactive Compounds. In Symbiotic Soil Microorganisms: Biology and Applications, (eds Shrivastava, N. et al.) 147–159 (Cham, Springer International Publishing, 2021).Aquino, J., Junior, F. L. A., Figueiredo, M., De Alcântara Neto, F. & Araujo, A. Plant growth-promoting endophytic bacteria on maize and sorghum1. Pesq. Agrop. Trop. https://doi.org/10.1590/1983-40632019v4956241 (2019).Article 

    Google Scholar 
    Gamalero, E. et al. Screening of bacterial endophytes able to promote plant growth and increase salinity tolerance. Appl. Sci. 10(17), 5767 (2020).CAS 
    Article 

    Google Scholar 
    Borah, A. & Thakur, D. Phylogenetic and functional characterization of culturable endophytic actinobacteria associated with Camellia spp. for growth promotion in commercial tea cultivars. Front. Microbiol. 11, 318. https://doi.org/10.3389/fmicb.2020.00318 (2020).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Haidar, B. et al. Population diversity of bacterial endophytes from jute (Corchorus olitorius) and evaluation of their potential role as bioinoculants. Microbiol. Res. 208, 43–53. https://doi.org/10.1016/j.micres.2018.01.008 (2018).Article 
    PubMed 

    Google Scholar 
    Bind, M. & Nema, S. Isolation and molecular characterization of endophytic bacteria from pigeon pea along with antimicrobial evaluation against Fusarium udum. J. Appl. Microbiol. Open Access 5, 163 (2019).
    Google Scholar 
    de Almeida Lopes, K. B. et al. Screening of bacterial endophytes as potential biocontrol agents against soybean diseases. J. Appl. Microbiol. 125(5), 1466–1481. https://doi.org/10.1111/jam.14041 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Müller, T. & Behrendt, U. Exploiting the biocontrol potential of plant-associated pseudomonads: A step towards pesticide-free agriculture?. Biol. Control 155, 104538. https://doi.org/10.1016/j.biocontrol.2021.104538 (2021).CAS 
    Article 

    Google Scholar 
    Safin, R. I. et al. Features of seeds microbiome for spring wheat varieties from different regions of Eurasia. In: International Scientific and Practical Conference “AgroSMART: Smart Solutions for Agriculture”, 766–770 (Atlantis Press).Adler, P. B. & Drake, J. Environmental variation, stochastic extinction, and competitive coexistence. Am. Nat. 172(5), E186–E195. https://doi.org/10.1086/591678 (2008).Article 

    Google Scholar 
    Gilbert, B. & Levine, J. M. Ecological drift and the distribution of species diversity. Proc. R. Soc. B 284(1855), 20170507. https://doi.org/10.1098/rspb.2017.0507 (2017).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Fitzpatrick, C. R. et al. Assembly and ecological function of the root microbiome across angiosperm plant species. Proc. Natl. Acad. Sci. 115(6), E1157–E1165. https://doi.org/10.1073/pnas.1717617115 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Freschet, G. T. et al. Root traits as drivers of plant and ecosystem functioning: Current understanding, pitfalls and future research needs. New Phytol. 232(3), 1123–1158. https://doi.org/10.1111/nph.17072 (2021).Article 
    PubMed 

    Google Scholar 
    Kembel, S. W. & Mueller, R. C. Plant traits and taxonomy drive host associations in tropical phyllosphere fungal communities. Botany 92(4), 303–311. https://doi.org/10.1139/cjb-2013-0194 (2014).Article 

    Google Scholar 
    Leff, J. W. et al. Predicting the structure of soil communities from plant community taxonomy, phylogeny, and traits. ISME J. 12(7), 1794–1805. https://doi.org/10.1038/s41396-018-0089-x (2018).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Ulbrich, T. C., Friesen, M. L., Roley, S. S., Tiemann, L. K. & Evans, S. E. Intraspecific variability in root traits and edaphic conditions influence soil microbiomes across 12 switchgrass cultivars. Phytobiom. J. 5(1), 108–120. https://doi.org/10.1094/pbiomes-12-19-0069-fi (2021).Article 

    Google Scholar 
    Arduini, I., Orlandi, C., Pampana, S. & Masoni, A. Waterlogging at tillering affects spike and spikelet formation in wheat. Crop Pasture Sci. 67(7), 703–711. https://doi.org/10.1071/CP15417 (2016).CAS 
    Article 

    Google Scholar 
    Ding, J. et al. Effects of waterlogging on grain yield and associated traits of historic wheat cultivars in the middle and lower reaches of the Yangtze River, China. Field Crops Res. 246, 107695. https://doi.org/10.1016/j.fcr.2019.107695 (2020).Article 

    Google Scholar 
    Malik, I., Colmer, T., Lambers, H. & Schortemeyer, M. Changes in physiological and morphological traits of roots and shoots of wheat in response to different depths of waterlogging. Austral. J. Plant Physiol. 28, 1121–1131. https://doi.org/10.1071/PP01089 (2001).Article 

    Google Scholar 
    Pampana, S., Masoni, A. & Arduini, I. Grain yield of durum wheat as affected by waterlogging at tillering. Cereal Res. Commun. 44(4), 706–716. https://doi.org/10.1556/0806.44.2016.026 (2016).Article 

    Google Scholar 
    Xu, L. et al. Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria. Proc. Natl. Acad. Sci. 115(18), E4284–E4293. https://doi.org/10.1073/pnas.1717308115%JProceedingsoftheNationalAcademyofSciences (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Angel, R. et al. The root-associated microbial community of the world’s highest growing vascular plants. Microb. Ecol. 72(2), 394–406. https://doi.org/10.1007/s00248-016-0779-8 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Edwards, J. A. et al. Compositional shifts in root-associated bacterial and archaeal microbiota track the plant life cycle in field-grown rice. PLoS Biol. 16(2), e2003862. https://doi.org/10.1371/journal.pbio.2003862 (2018).CAS 
    Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kuźniar, A. et al. Culture-independent analysis of an endophytic core microbiome in two species of wheat: Triticum aestivum L. (cv. ‘Hondia’) and the first report of microbiota in Triticum spelta L. (cv. ‘Rokosz’). Syst. Appl. Microbiol. 43(1), 126025. https://doi.org/10.1016/j.syapm.2019.126025 (2020).CAS 
    Article 
    PubMed 

    Google Scholar 
    Soldan, R. et al. Bacterial endophytes of mangrove propagules elicit early establishment of the natural host and promote growth of cereal crops under salt stress. Microbiol. Res. 223–225, 33–43. https://doi.org/10.1016/j.micres.2019.03.008 (2019).CAS 
    Article 
    PubMed 

    Google Scholar 
    Truyens, S., Weyens, N., Cuypers, A. & Vangronsveld, J. Bacterial seed endophytes: Genera, vertical transmission and interaction with plants. Environ. Microbiol. Rep. 7(1), 40–50. https://doi.org/10.1111/1758-2229.12181 (2015).Article 

    Google Scholar 
    Chimwamurombe, P. M., Grönemeyer, J. L. & Reinhold-Hurek, B. Isolation and characterization of culturable seed-associated bacterial endophytes from gnotobiotically grown Marama bean seedlings. FEMS Microbiol. Ecol. 92, 6. https://doi.org/10.1093/femsec/fiw083 (2016).CAS 
    Article 

    Google Scholar 
    Eid, A. M. et al. Harnessing bacterial endophytes for promotion of plant growth and biotechnological applications: An overview. Plants 10(5), 935 (2021).CAS 
    Article 

    Google Scholar 
    Mareque, C. et al. The endophytic bacterial microbiota associated with sweet sorghum (Sorghum bicolor) is modulated by the application of chemical N fertilizer to the field. Int. J. Genom. 2018, 7403670. https://doi.org/10.1155/2018/7403670 (2018).CAS 
    Article 

    Google Scholar 
    Francioli, D. et al. Mineral vs organic amendments: Microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies. Front. Microbiol. 7, 1446. https://doi.org/10.3389/fmicb.2016.01446 (2016).Article 
    PubMed 
    PubMed Central 

    Google Scholar 
    Schrey, S. D. & Tarkka, M. T. Friends and foes: Streptomycetes as modulators of plant disease and symbiosis. Antonie Van Leeuwenhoek 94(1), 11–19. https://doi.org/10.1007/s10482-008-9241-3 (2008).Article 
    PubMed 

    Google Scholar 
    Patel, J. K., Madaan, S. & Archana, G. Antibiotic producing endophytic Streptomyces spp. colonize above-ground plant parts and promote shoot growth in multiple healthy and pathogen-challenged cereal crops. Microbiol. Res. 215, 36–45. https://doi.org/10.1016/j.micres.2018.06.003 (2018).CAS 
    Article 
    PubMed 

    Google Scholar 
    Yi, Y.-S. et al. Antifungal activity of Streptomyces sp. against Puccinia recondita causing wheat leaf rust. J. Microbiol. Biotechnol. 14(2), 422–425 (2004).CAS 

    Google Scholar 
    Sperdouli, I. & Moustakas, M. Leaf developmental stage modulates metabolite accumulation and photosynthesis contributing to acclimation of Arabidopsis thaliana to water deficit. J. Plant. Res. 127(4), 481–489. https://doi.org/10.1007/s10265-014-0635-1 (2014).CAS 
    Article 
    PubMed 

    Google Scholar  More

  • in

    eDNA metabarcoding as a promising conservation tool to monitor fish diversity in Beijing water systems compared with ground cages

    Zou, K. et al. eDNA metabarcoding as a promising conservation tool for monitoring fish diversity in a coastal wetland of the Pearl River Estuary compared to bottom trawling. Sci. Total Environ. 702, 134704 (2020).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Almond, R., Grooten, M. & Peterson, T. Living Planet Report 2020-Bending the Curve of Biodiversity Loss (World Wildlife Fund, 2020).
    Google Scholar 
    Beverton, R. Fish resources; threats and protection. Neth. J. Zool. 42, 139–175 (1991).Article 

    Google Scholar 
    Jackson, S. & Head, L. Australia’s mass fish kills as a crisis of modern water: Understanding hydrosocial change in the Murray-Darling Basin. Geoforum 109, 44–56 (2020).Article 

    Google Scholar 
    Rees, H. C. et al. REVIEW: The detection of aquatic animal species using environmental DNA—a review of eDNA as a survey tool in ecology. J. Appl. Ecol. 51, 1450–1459 (2014).CAS 
    Article 

    Google Scholar 
    Rees, H. C. et al. The application of eDNA for monitoring of the Great Crested Newt in the UK. Ecol. Evol. 4, 4023–4032 (2014).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wang, C. et al. Research on the biodiversity of Qinhuai River based on environmental DNA metabacroding. Acta Ecol. Sin. 42, 611–624 (2022).Article 

    Google Scholar 
    Deiner, K., Walser, J.-C., Mächler, E. & Altermatt, F. Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA. Biol. Cons. 183, 53–63 (2015).Article 

    Google Scholar 
    Thomsen, P. F. et al. Monitoring endangered freshwater biodiversity using environmental DNA. Mol. Ecol. 21, 2565–2573 (2012).CAS 
    PubMed 
    Article 

    Google Scholar 
    Miralles, L., Parrondo, M., Hernandez de Rojas, A., Garcia-Vazquez, E. & Borrell, Y. J. Development and validation of eDNA markers for the detection of Crepidula fornicata in environmental samples. Mar. Pollut. Bull. 146, 827–830 (2019).CAS 
    PubMed 
    Article 

    Google Scholar 
    Takahara, T., Minamoto, T., Yamanaka, H., Doi, H. & Kawabata, Z. Estimation of fish biomass using environmental DNA. PLoS ONE 7, e35868 (2012).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Aglieri, G. et al. Environmental DNA effectively captures functional diversity of coastal fish communities. Mol. Ecol. 30, 3127–3139 (2020).PubMed 
    Article 

    Google Scholar 
    Yang, H. et al. Effectiveness assessment of using riverine water eDNA to simultaneously monitor the riverine and riparian biodiversity information. Sci. Rep. 11, 24241 (2021).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Altermatt, F. et al. Uncovering the complete biodiversity structure in spatial networks: the example of riverine systems. Oikos 129, 607–618 (2020).Article 

    Google Scholar 
    Stat, M. et al. Combined use of eDNA metabarcoding and video surveillance for the assessment of fish biodiversity. Conserv. Biol. 33, 196–205 (2019).PubMed 
    Article 

    Google Scholar 
    Hallam, J., Clare, E. L., Jones, J. I. & Day, J. J. Biodiversity assessment across a dynamic riverine system: A comparison of eDNA metabarcoding versus traditional fish surveying methods. Environ. DNA 3, 1247–1266 (2021).Article 

    Google Scholar 
    Gao, W. Beijing Vertebrate Key (Beijing Publishing House, 1994).
    Google Scholar 
    Wang, H. Beijing Fish and Amphibians and Reptiles (Beijing Publishing House, 1994).
    Google Scholar 
    Chen, W., Hu, D. & Fu, B. Research on Biodiversity of Beijing Wetland (Science Press, 2007).
    Google Scholar 
    Zhang, C. et al. Fish species diversity and conservation in Beijing and adjacent areas. Biodivers. Sci. 19, 597–604 (2011).Article 

    Google Scholar 
    Yamamoto, S. et al. Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea. Sci. Rep. 7, 40368 (2017).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Shaw, J. L. A. et al. Comparison of environmental DNA metabarcoding and conventional fish survey methods in a river system. Biol. Cons. 197, 131–138 (2016).Article 

    Google Scholar 
    Fu, M., Xiao, N., Zhao, Z., Gao, X. & Li, J. Effects of Urbanization on Ecosystem Services in Beijing. Res. Soil Water Conserv. 23, 235–239 (2016).
    Google Scholar 
    Hao, L. & Sun, G. Impacts of urbanization on watershed ecohydrological processes: progresses and perspectives. Acta Ecol. Sin. 41, 13–26 (2021).
    Google Scholar 
    Su, G. et al. Human impacts on global freshwater fish biodiversity. Science 371, 835–838 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Yan, B. et al. Effects of urban development on soil microbial functional diversity in Beijing. Res. Environ. Sci. 29, 1325–1335 (2016).CAS 

    Google Scholar 
    Xiao, N., Gao, X., Li, J. & Bai, J. Evaluation and Conservation Measures of Beijing Biodiversity (China Forestry Publishing House, 2018).
    Google Scholar 
    Xu, S., Wang, Z., Liang, J. & Zhang, S. Use of different sampling tools for comparison of fish-aggregating effects along horizontal transect at two artificial reef sites in Shengsi. J. Fish. China 40, 820–831 (2016).
    Google Scholar 
    Miya, M. et al. MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. R. Soc. Open Sci. 2, 150088 (2015).ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Zhang, J., Kobert, K., Flouri, T. & Stamatakis, A. PEAR: a fast and accurate Illumina Paired-End reAd mergeR. Bioinformatics (Oxford, England) 30, 614–620 (2014).CAS 
    Article 

    Google Scholar 
    Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics (Oxford, England) 34, 884–890 (2018).Article 
    CAS 

    Google Scholar 
    Edgar, R. C. Search and clustering orders of magnitude faster than BLAST. Bioinformatics (Oxford, England) 26, 2460–2461 (2010).CAS 
    Article 

    Google Scholar 
    Callahan, B. J., McMurdie, P. J. & Holmes, S. P. Exact sequence variants should replace operational taxonomic units in marker-gene data analysis. ISME J. 11, 2639–2643 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Iwasaki, W. et al. MitoFish and MitoAnnotator: A mitochondrial genome database of fish with an accurate and automatic annotation pipeline. Mol. Biol. Evol. 30, 2531–2540 (2013).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Wang, H. Beijing Fish Records (Beijing Publishing House, 1984).
    Google Scholar 
    Du, L. et al. Fish community characteristics and spatial pattern in major rivers of Beijing City. Res. Environ. Sci. 32, 447–457 (2019).
    Google Scholar 
    Shen, W. & Ren, H. TaxonKit: A practical and efficient NCBI taxonomy toolkit. J. Genet. Genomics 48, 844–850 (2021).PubMed 
    Article 

    Google Scholar 
    Karr, J. R. Assessment of biotic integrity using fish communities. Fisheries 6, 21–27 (1981).Article 

    Google Scholar 
    Zhang, C. & Zhao, Y. Fishes in Beijing and Adjacent Areas (China. Science Press, 2013).
    Google Scholar 
    Wu, H. & Zhong, J. Fauna Sinica, Osteichthyes, Perciformess(Five),Gobioidei (Science Press, 2008).
    Google Scholar 
    Di, Y. et al. Distribution of fish communities and its influencing factors in the Nansha and Beijing sub-center reaches of the Beiyun River. Acta Sci. Circumst. 41, 156–163 (2020).
    Google Scholar 
    Walters, D. M., Freeman, M. C., Leigh, D. S., Freeman, B. J. & Pringle, C. M. in Effects of Urbanization on Stream Ecosystems Vol. 47 American Fisheries Society Symposium 69–85 (2005).Hu, X., Zuo, D., Liu, B., Huang, Z. & Xu, Z. Quantitative analysis of the correlation between macrobenthos community and water environmental factors and aquatic ecosystem health assessment in the North Canal River Basin of Beijing. Environ. Sci. 43, 247–255 (2022).
    Google Scholar 
    Kadye, W. T., Magadza, C. H. D., Moyo, N. A. G. & Kativu, S. Stream fish assemblages in relation to environmental factors on a montane plateau (Nyika Plateau, Malawi). Environ. Biol. Fishes 83, 417–428 (2008).Article 

    Google Scholar 
    Smith, T. A. & Kraft, C. E. Stream fish assemblages in relation to landscape position and local habitat variables. Trans. Am. Fish. Soc. 134, 430–440 (2005).Article 

    Google Scholar 
    Blabolil, P. et al. Environmental DNA metabarcoding uncovers environmental correlates of fish communities in spatially heterogeneous freshwater habitats. Ecol. Ind. 126, 107698 (2021).CAS 
    Article 

    Google Scholar 
    Xie, R. et al. eDNA metabarcoding revealed differential structures of aquatic communities in a dynamic freshwater ecosystem shaped by habitat heterogeneity. Environ. Res. 201, 111602 (2021).CAS 
    PubMed 
    Article 

    Google Scholar 
    Qu, C. et al. Comparing fish prey diversity for a critically endangered aquatic mammal in a reserve and the wild using eDNA metabarcoding. Sci. Rep. 10, 16715 (2020).CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Pont, D. et al. Environmental DNA reveals quantitative patterns of fish biodiversity in large rivers despite its downstream transportation. Sci. Rep. 8, 10361 (2018).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Doble, C. J. et al. Testing the performance of environmental DNA metabarcoding for surveying highly diverse tropical fish communities: A case study from Lake Tanganyika. Environ. DNA 2, 24–41 (2020).Article 

    Google Scholar 
    Xu, N. et al. Monitoring seasonal distribution of an endangered anadromous sturgeon in a large river using environmental DNA. Sci. Nat. 105, 62 (2018).Article 
    CAS 

    Google Scholar 
    Laramie, M. B., Pilliod, D. S. & Goldberg, C. S. Characterizing the distribution of an endangered salmonid using environmental DNA analysis. Biol. Cons. 183, 29–37 (2015).Article 

    Google Scholar 
    Harper, L. R. et al. Development and application of environmental DNA surveillance for the threatened crucian carp (Carassius carassius). Freshw. Biol. 64, 93–107 (2019).CAS 
    Article 

    Google Scholar 
    Ushio, M. et al. Quantitative monitoring of multispecies fish environmental DNA using high-throughput sequencing. Metabarcoding Metagenomics 2, e2329 (2018).
    Google Scholar 
    Evans, N. T. et al. Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding. Mol. Ecol. Resour. 16, 29–41 (2015).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Gloor, G. B., Macklaim, J. M., Pawlowsky-Glahn, V. & Egozcue, J. J. Microbiome datasets are compositional: and this is not optional. Front. Microbiol. 8, 2224 (2017).PubMed 
    PubMed Central 
    Article 

    Google Scholar 
    Harrison, J. B., Sunday, J. M. & Rogers, S. M. Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proc. Biol. Sci. 286, 20191409 (2019).CAS 
    PubMed 
    PubMed Central 

    Google Scholar 
    Kelly, R. P., Shelton, A. O. & Gallego, R. Understanding PCR processes to draw meaningful conclusions from environmental DNA studies. Sci. Rep. 9, 12133 (2019).ADS 
    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Civade, R. et al. Spatial representativeness of environmental DNA metabarcoding signal for fish biodiversity assessment in a natural freshwater system. PLoS ONE 11, e0157366 (2016).PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar 
    Barnes, M. A. et al. Environmental conditions influence eDNA persistence in aquatic systems. Environ. Sci. Technol. 48, 1819–1827 (2014).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Shogren, A. J. et al. Water flow and biofilm cover influence environmental DNA detection in recirculating streams. Environ. Sci. Technol. 52, 8530–8537 (2018).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar 
    Zhao, B., van Bodegom, P. M. & Trimbos, K. The particle size distribution of environmental DNA varies with species and degradation. Sci. Total Environ. 797, 149175 (2021).ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar  More

  • in

    Simulation-based evaluation of two insect trapping grids for delimitation surveys

    Key delimitation trapping survey performance factorsTrap attractivenessThe performance of the current Medfly design was unexpectedly inferior to that of the leek moth even with a more vagile target insect, 2.8 times greater trap density in the core, and a grid size over three times larger. Despite all those factors, p(capture) for the leek moth grid with 1/λ = 20 m was 15 percentage points greater than that for Medfly at 30 days duration. Thus, trap attractiveness was the key determinant for delimiting survey performance, as it was for detection13.One straightforward way to improve p(capture) and the accuracy of boundary setting, while also cutting costs, would be to develop more attractive traps. Poorly attractive traps include food-based attractants48 and traps based solely on visual stimuli36. But developing better traps is difficult. Pheromone-based attractants generally perform best49, but these are unavailable for many insects. For instance, scientists have searched for decades for effective pheromones for Anastrepha suspensa (Loew) and A. ludens (Loew) without success50. Common issues include the complexity of components, costs of synthesis, and chemical stability.Trap densitiesAll else being equal, increasing the trap density will generally improve p(capture) for any survey grid, and intuitively this can help compensate for using less attractive traps. However, the impact of increasing density is limited when attractiveness is low13,47, and large surveys or grids with many traps can become prohibitively expensive51. The Medfly grid designers likely understood that the available trap and lure was not highly attractive, and used higher densities in inner bands to try to reach some desired (non-quantitative) survey performance level. By contrast, the designers of the leek moth grid used a (constant) density three times smaller, likely because the trap and lure were known to be relatively strong. Here, for both species, marginal ROI decreased as densities increased (Tables 2, 3). Hence, increasing densities has limited benefit, but may be useful when better lures are unavailable13.In that context, the use of variable densities in the Medfly grid is understandable. At its standard size, the survey grid would require 8,100 traps if the core trap density were constant (Table 1). The designers likely intuited that lower densities could be used in outer bands because captures there were less likely. However, doing so reduces the likelihood of detection in outer bands and could increase the possibility of undetected egress, especially with longer survey durations. As far as we know, natural egress has not been raised as a concern following the numerous Medfly quarantines that have used this survey grid over the years, in Southern California in particular52.Generally, however, we think the variable Medfly grid densities run counter to delimitation goals. Greater core and Band 2 densities have proportionally more impact on p(capture), but only a few detections in the core are necessary to confirm the presence of the population (Goal 1), and inner area detections probably contribute little to boundary setting (see below). Therefore, lower or intermediate densities (at most) may be optimal for the core when considering ROI. For the outer bands, increasing densities might improve boundary setting (Goal 2) and help mitigate potential egress, but the sizes of those bands already limit cost efficiency (Table 2), making greater densities less advisable. Our simulation results can help elucidate how to balance these interests to achieve delimitation goals while minimizing costs47.Grid size considerationsThe simulation results indicated that the standard survey sizes for these two pests were excessive. We have verified that empirically for Medfly using trapping detections data53. A 14.5-km grid has been widely used for many other insects in the CDFA (2013) guidelines10, such as Mexfly and OFF, and the same analysis indicated that those are also oversized for use in short-term delimitation surveys53. From the same analysis, the predicted survey radius for leek moth, with D = 500 m2 per day, would be 2,382 m, or a diameter of nearly 4.8 km, which matches the results here. Similarly, Dominiak and Fanson45 analyzed trapping data for Qfly and found that the recommended quarantine area distance of 15 km could be reduced to 3 to 4 km.Grids with radii larger than 4.8-km only seem necessary for highly vagile insects, those with D ≥ 50,000 m2 per day47. This should not be surprising. Small insect populations are unlikely to move very far31,54, especially if hosts are available20,39,55. The (proposed) short duration of a delimitation survey would also limit dispersal potential (see below). Many delimiting survey plans may be oversized, because they were developed before much dispersal research had been done37, thus uncertainty was high. Our dispersal distance analysis included species with a wide range of dispersal abilities, so it can be used generally to choose smaller survey grid radii53.Reducing grid sizes down to about 4.8-km diameters may have little impact on p(capture), since detections in bands outside that distance contributed little to overall performance. The cores of both the leek moth and Medfly grids accounted for 86 percent or more of overall p(capture). While core area detections will confirm the presence of the population, they are less useful for defining spatial extent. The furthest detections from the presumed source are usually used to delimit the incursion46,56 (although in our experience formal boundary setting exercises seem rare). Delimiting surveys may often yield few captures anyway, because adventive populations can be very small and subject to high mortality31. Because size reductions eliminate traps in proportionally larger outer areas, the impact on survey costs is substantial. Removing just the outermost bands of each grid would directly reduce costs by $11,200 for leek moth (400 traps) and by $7,488 for Medfly (288 traps; Table 1).Another reason for the large size of the standard Medfly grid may be that it was designed for monitoring and management in addition to delimitation57. Medfly quarantines end after at least three generations without a detection, so the surveys may last for months. The grid size was reportedly originally determined by multiplying the estimated dispersal distance by three (PPQ, personal communication), to account for uncertainty. This implies that the estimated distance was about 2,400 m per 30 days. Thus, the design may not have been built for the 30-d duration used here, but our recommended design is valid if a shorter delimitation activity without further monitoring is appropriate.Although it seemed too large for leek moth, an 8-km grid for delimitation could be appropriate for some other moths. For example, the delimiting survey plans for Spodoptera littoralis (Boisduval) and S. exempta Walker use this size9. S. littoralis is described as dispersing “many miles”, and S. exempta can travel hundreds of miles9, which clearly exceeds the described dispersal ability of leek moth. On the other hand, the survey plan for summer fruit tortrix moth (Adoxophyes orana Fischer von Röeslerstamm) also specifies an 8-km grid for delimitation but contains little information on dispersal, suggesting only that most movement is local8. Like leek moth, a 4.8-km grid for that species seems likely to be more appropriate.Limiting egress potential is probably the main consideration when setting survey size, but uncertainty about the source population location may also be a factor. Survey grids placed over the earliest insect detection may sometimes be off center from the location of the source population54. However, so far as we know for our agency, most adventive populations have been localized, based on post-discovery detections (PPQ, personal communication). Likewise, we have found53 and other researchers have found that dispersal distances for different species in outbreaks and mark-recapture studies are often less than 1 km58,59,60. That may often be the case for detection networks of traps (e.g., for high risk fruit flies), which increase the likelihood of capture before the population has had much time to grow and disperse. Here, we focused explicitly on localized populations, but allowed for uncertainty in the simulations by varying outbreak locations over one mile in the central part of the grid. If the outbreak population is very large and has extensively spread out (e.g., spotted lanternfly, Lycorma delicatula (White) in 201461), delimitation will not be localized, but “area-wide”2. The results here do not apply to area-wide outbreaks, and we are currently studying how to effectively delimit them.Optimizing delimitation surveysMany trapping survey designs in use were based not on “hard” science but on local experience62. Scientists have recognized the need for more cost-effective surveillance strategies63,64. Quantitatively assessing p(capture) in different designs for the same target pest allows us to determine grid sizes and densities that lower costs while maintaining performance. Results here demonstrated that the sizes and densities of these two survey grids could be optimized to save up to $20,244 per survey for the leek moth and $38,168 per survey for the Medfly. In practical terms, that means more than five leek moth surveys could be run for the cost of one standard design survey. Additionally, over seven Medfly delimitation surveys could be funded by the budget of one standard plan. The magnitudes of reduction seen here may be typical, since about 90 percent of the costs in trapping surveys are for transportation and maintenance related to traps65.Quantifying survey performance was not possible until very recently, so it has been little discussed in the literature5,66, and no standard thresholds exist. We think 0.5 may be a reasonable minimum threshold for the choice of p(capture), to try to ensure that population detection is “more likely than not”. Designs that aim to maximize p(capture) could be realistic with high attractiveness traps, but those designs seem very likely to have lower ROIs (e.g., Table 2). Even for the most serious insect pests, we think targeting near-perfect population detection during delimitation is likely not justified. Designs achieving p(capture) from 0.6 to 0.75 could be highly effective in terms of both costs and performance.Another potential area of improvement is grid shape. Circular grids perform as well as square grids but use fewer traps and less service area to achieve equivalent p(capture)47. Moreover, detections in the corners of a square grid are evidence that insects could have traveled beyond the square along the axes, resulting in uncertain boundary setting. Most published survey grids are square10,46, but many field managers tend to use approximately circular trapping grids in the field (PPQ, personal communication). The conversion to a circular grid with a radius of half the square side length reduces the area and number of traps by around 21 percent47. Our findings were consistent with that value.This new quantification ability also indicates that some delimiting survey designs in the U.S.A. may not be performing as well as expected47. For instance, the delimiting survey design for Mexfly uses approximately 31 traps per km2 in the core of a 14.5 km square grid11, but the traps are only weakly attractive (1/λ ≈ 5 m). In this scenario, p(capture) was only around 0.23 with a 30-d survey duration47. A much greater density ( > 80 traps per km2) could be used in the core to achieve p(capture) ≥ 0.5, but this may not be feasible depending on the survey budget.Technical and modeling considerationsExamining diffusion-based movement for these two insects in TrapGrid can give insight into why simulations indicated that smaller grids may be adequate47. The value of σ for Medfly after 30 days is only about 1,550 m. In a normal distribution, σ = 1,550 m gives a 95th percentile distance of 2,550 m, which is similar to the estimated distance above of 2,400 m. Over 90 days, σ = 2,700 m for Medfly, which gives a 95th percentile distance of 4,441 m, still much shorter than the grid radius of 7,250 m. A 95th percentile of 7,250 m requires σ ≈ 4,408 m, which equals t = 253 days. In addition, the maximum total distance (up to 39 days after detection) we observed in trapping detections data for Medfly in Florida was about 4,800 m53.The same calculations for leek moth give σ ≈ 490 m for 30 days, with a 95th percentile distance of only 806 m. That is half the length of the recommended shortened radius above of 2.4 km, and nearly five times shorter than the radius of the standard 8-km grid. A 95th percentile of 4,000 m requires σ = 2,432 m, which implies t = 740 days, which is about two years. Therefore, the leek moth grid is arguably even more oversized than the Medfly grid.The default capture probability calculation in the current version (Ver. 2019-12-11) of TrapGrid is not sensitive to population size32 and does not consider the effects of ambient factors (e.g., wind speed and direction, rainfall, temperature). Many other factors can also impact trapping survey outcomes, such as topography of the environment, availability of host plants, seasonality of pest, and population dynamics. These factors are not considered in the current version of TrapGrid. More