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    Ecological and evolutionary dynamics of multi-strain RNA viruses

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    Ultrasonic antifouling devices negatively impact Cuvier’s beaked whales near Guadalupe Island, México

    Long-term acoustic data collectionPassive acoustic monitoring was conducted from November 19, 2018 to October 3, 2020, with 683 days of recording effort overall (Supplementary Table 2), using a High-frequency Acoustic Recording Package (HARP)37. The HARP was deployed in Bahía Norte, Guadalupe Island, located approximately 150 miles offshore of México’s Baja California Peninsula (Fig. 1). The HARP was bottom-mounted and deployed to a depth of approximately 1100 m, with a calibrated hydrophone suspended ~30 m above the seafloor. The same hydrophone was used for both deployments to facilitate data comparison. The omnidirectional hydrophone sensor (ITC-1042, International Transducer Corporation, Santa Barbara, CA) had an approximately flat (±3 dB) hydrophone sensitivity from 10 Hz to 100 kHz of −200 dB re V/μPa. The sensor was connected to a custom-built preamplifier board and bandpass filter. The calibrated system response was corrected for during analysis. Data were sampled continuously at a 200 kHz sampling rate with 16-bit quantization, effectively monitoring a frequency range of 10 Hz–100 kHz.Automatic detection and manual classification of beaked whale echolocation clicksBeaked whales can be acoustically identified by their echolocation clicks38. These signals are frequency-modulated (FM) upswept pulses, which appear to be species-specific and are distinguishable by their spectral and temporal features. Cuvier’s beaked whale echolocation signals are well differentiated from the acoustic signals of other beaked whale species. They are polycyclic with a characteristic FM pulse upsweep, peak frequency around 40 kHz, and uniform inter-pulse interval of about 0.4–0.5 s39,40. Additionally, Cuvier’s beaked whale FM pulses have characteristic spectral peaks at approximately 17 and 23 kHz.Beaked whale FM pulses were detected in the HARP data with an automated method using the MATLAB-based (Mathworks, Natick, MA) custom software program Triton (https://github.com/MarineBioAcousticsRC/Triton) and other MATLAB custom routines. After all potential echolocation signals were identified with a Teager–Kaiser energy detector41,42, an expert system discriminated between delphinid clicks and beaked whale FM pulses. A decision about presence or absence of beaked whale signals was based on detections within a 75 s segment. Only segments with more than seven detections were used in further analysis. All echolocation signals with a peak and center frequency below 32 and 25 kHz, respectively, a duration less than 355 μs, and a sweep rate of More

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    Bacterial diversity in surface sediments of collapsed lakes in Huaibei, China

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    First report of the blood-feeding pattern in Aedes koreicus, a new invasive species in Europe

    Study areaThe study area was located in Northeastern Italy (Fig. 2). Specifically, it encompassed 13 municipalities in the Valbelluna (located in Belluno Province), Valsugana, and Cembra valleys (located in Trento Province). The study area has a sub-continental, temperate climate, with cold, often snowy winters and warm, mild summers. Human settlements consist mainly of small villages composed of country houses with private gardens and public parks, all surrounded by forested areas; among the sampled municipalities, only Belluno and Feltre had more than 10,000 inhabitants.Figure 2Study area. Points represent the sampling sites marked with the ID number as in Tables 2 and 3. Background satellite image from Sentinel-2 cloudless (https://s2maps.eu), and urban places from OpenStreetMap contributors (https://openstreetmap.org). Map created using QGIS 3.22.Full size imageHost surveyThe presence and abundance of domestic animal hosts in each site were estimated through a door-to-door census. As the flight range of Ae. koreicus is unknown, a field inspection was performed within a 200-m radius of the sampling site, corresponding to the average flight distance of Ae. albopictus recorded in a study conducted in Italy46. The survey was carried out once in 2020. Residents were asked if they owned animals (dogs, cats, farm animals) and how many they had or, where possible, they were counted directly by the study team (visual inspection). The presence of wild ungulates was estimated according to data provided by the Forestry and Fauna Service—Wildlife Office of the Autonomous Province of Trento. The wild ungulate census was carried out in spring by visual inspection along transects, and repeated three times by hunters and personnel of the wildlife management provincial office.47. The average number of roe deer, red deer, and chamois in 2020 was considered for the analyses. Collected information was used to qualitatively estimate potential host availability in the sampling areas. Human population density in the areas surrounding the sampling point was estimated using the Global Human Settlement Database (GHS Data)48.Collection of Aedes koreicus and blood meal analysisSampling was carried out from 2013 to 2020 (from May to October) with different frequencies in the various years; most collections were made in 2020 (20 collections) and just one in 2019. In total, 23 different sites were sampled where Ae. koreicus were known to be present: 14 in Trento and 9 in Belluno Province, respectively (Table 1 and Supplementary Table S1 online), with altitudes ranging from 234 to 775 m a.s.l.6,16. Engorged mosquitoes were collected in public and private houses, garden centers, cemeteries, and from periurban dry-stone walls using a home-built handheld aspirator (a modified handheld vacuum) (Fig. 3). Mosquitoes were aspirated from shady areas under vegetation, walls, and catch basins. In addition, all engorged females collected during routine invasive mosquito surveillance were used for the analyses. In this surveillance, BG-sentinel traps (Biogents AG, Regensburg, Germany) baited with a BG-Lure cartridge (Biogents) were activated for 24 h fortnightly. Immediately after collection, each sample was placed in a cooler, transported to the laboratory, and stored at − 80 °C until molecular analysis.Figure 3Home-built handheld aspirator (a modified handheld vacuum).Full size imageSampled mosquitoes were identified at species level according to Montarsi et al.21 and ECDC guidelines for invasive mosquito surveillance in Europe49. Blood-fed females were isolated from collected mosquitoes to identify the blood meal host.DNA of single blood-fed mosquito samples, collected from 2013 to 2016, was extracted using Microlab Starlet automated liquid-handling workstations (Hamilton), using a MagMAX Pathogen RNA/DNA kit (Applied Biosystems, USA), according to the manufacturer’s instructions. DNA of a single abdomen of blood-fed mosquitoes, collected from 2017 to 2020, was extracted using QIAamp DNA Investigator kit tissues (Qiagen, Germany), following the manufacturer’s protocol. All samples were analyzed using a nested PCR with a specific set of primers targeting the vertebrate mitochondrial cytochrome c oxidase subunit I (COI) gene, as previously described50. The first PCR reaction was carried out in a total volume of 50 μl, containing 2 units of AmpliTaq Gold DNA Polymerase (Applied Biosystem, USA), 5 μl of 10X Buffer, 2.5 mM of MgCl2, 0.2 mM of each dNTP, 2.5 μl of DMSO, 0.2 mM of primers M13BCV-FW (5’-TGT AAA ACG ACG GCC AGT HAA YCA YAA RGA YAT YGG-3’) and BCV-RV1 (5’-GCY CAN ACY ATN CCY ATR TA-3’), and 5 μl of extracted DNA. The second PCR reaction was carried out in a total volume of 50 μl containing 2 units of AmpliTaq Gold DNA Polymerase (Applied Biosystem, USA), 5 μl of 10X Buffer, 2.0 mM of MgCl2, 0.2 mM of each dNTP, 2.5 μl of DMSO, 0.4.mM of primers M13 (5’-GTA AAA CGA CGG CCA GTG-3’) and BCV-RV2 (5’-ACY ATN CCY ATR TAN CCR AAN GG-3’), and 1 μl of the PCR products obtained during the first amplification step. The thermal profile of the first PCR consisted of activation at 95 °C for 10 min, followed by 40 cycles at 94 °C for 40 s, 45 °C for 40 s, and 72 °C for 1 min, with a final extension step of 7 min at 72 °C. The thermal profile of the second PCR consisted of activation for 10 min at 95 °C followed by 16 cycles of a touchdown protocol at 94 °C for 40 s, decreasing the annealing temperature from 60 °C to 45 °C for 40 s (1 °C/cycle), followed by 72 °C for 1 min. Then, 30 cycles at 94 °C for 40 s, 45 °C for 40 s, and 72 °C for 1 min, with a final extension step of 7 min at 72 °C. Negative controls were included during the extraction and amplification stages to confirm avoidance of contamination.The amplicons were sequenced in both directions using a 16-capillary ABI PRISM 3130xl Genetic Analyzer (Applied Biosystems, USA). To identify the blood meal host species, nucleotide sequences were compared with representative sequences available in the GenBank database using the Basic Local Alignment Search Tool (BLAST). Positive identification was made when  > 97% identity was attained between the query and subject sequence.Statistical analysisAs most of the identified hosts were either humans or wild ungulates (see Results), we investigated how the probability of feeding on these two host groups was affected by different abiotic factors. Specifically, we considered two binary response variables indicating whether or not the blood meal was acquired from a human/wild ungulate host. We developed univariate (i.e., with only one explanatory variable) generalized linear models (GLMs) with a binomial-distributed error structure, considering in turn, for each response variable, the following four explanatory covariates: (i) the altitude of the sampling point; (ii) the human population density in the area surrounding the sampling point, defined as 250 m square units, as per the Global Human Settlement Database48; (iii) the percentage of non-artificial land cover within different buffers (100, 250 and 500 m radius from the sampling point), as per the Corine Land Cover dataset (defined as the sum of the fractions of agricultural and forested areas)51; the distance associated with the model with the lowest AIC value was then selected; (iv) the minimum distance of the sampling point from the nearest pixel labeled as forest, according to the Corine category. All analyses, including plot creation, was performed using R v4.0.252 and “tidyverse”, “ggplot2”, and “gridExtra” libraries.Map in Fig. 1 was generated by QGIS 3.22 using Sentinel-2 cloudless as background satellite image and urban places from OpenStreetMap database53,54,55. More

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    Huge dataset shows 80% of US professors come from just 20% of institutions

    Hear the latest from the world of science, with Nick Petrić Howe and Benjamin Thompson.

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    In this episode:00:46 Inequalities in US faculty hiringIn the US, where a person gained their PhD can have an outsized influence on their future career. Now, using a decade worth of data, researchers have shown there are stark inequalities in the hiring process, with 80% of US faculty trained at just 20% of institutions.Research article: Wapman et al.09:01 Research HighlightsHow wildlife can influence chocolate production, and the large planets captured by huge stars.Research Highlight: A chocoholic’s best friends are the birds and the batsResearch Highlight: Giant stars turn to theft to snag jumbo planets11:42 Briefing ChatWe discuss some highlights from the Nature Briefing. This time, what science says about grieving for a public figure, and why suburban Australians are sharing increasingly sophisticated measures to prevent cockatoos from opening wheelie bins.Nature News: Millions are mourning the Queen — what’s the science behind public grief?The Guardian: ‘Interspecies innovation arms race’: cockatoos and humans at war over wheelie bin raidsSubscribe to Nature Briefing, an unmissable daily round-up of science news, opinion and analysis free in your inbox every weekday.Never miss an episode: Subscribe to the Nature Podcast on Apple Podcasts, Google Podcasts, Spotify or your favourite podcast app. Head here for the Nature Podcast RSS feed. More

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    Leaf water content contributes to global leaf trait relationships

    The theoretical modelThe model presented here builds on a recently developed metabolic theory based on biochemical kinetics. It describes a non-linear relationship between plant metabolic rate per unit of dry mass (Bs, nmol g−1 s−1), such as light-saturated photosynthetic rates and dark respiration rates, plant water content (S, g g−1), and temperature (in degrees K)19,20, i.e.$${B}_{{{{{{rm{s}}}}}}}={g}_{1}{e}^{{k}_{1}S/left({K}_{1}+Sright)}{e}^{-E/{kT}}$$
    (1)
    where g1 is a normalisation constant, k1 represents the maximum increase in specific metabolic rates due to changes in water content (i.e. from dehydrated to fully hydrated), K1 represents the water content when the mean reaction rate of cellular metabolism reaches one-half of its maximum, E is the activation energy, and k is Boltzmann’s constant. In this model S is defined on a dry mass basis (i.e. the ratio of plant water mass to plant dry mass) to broaden its range and better reflect the proportional changes in the amount of water in plant tissues20. Full details of the model’s assumptions can be found in the Methods and Huang et al.19,20. The model was tested and shown to hold true for a broad range of species and for whole plants and above- and belowground organs20. Here, we first applied the model to describe the quantitative effects of dry mass-based LWC (the ratio of leaf water mass to leaf dry mass) and temperature on the light-saturated leaf photosynthetic rate per unit of dry mass or leaf photosynthetic capacity (Ps, nmol CO2 g−1 s−1), which can be expressed as$${{{{{rm{ln}}}}}}left({P}_{{{mbox{s}}}}right)={{{{{rm{ln}}}}}}left(frac{{P}_{{{{{{rm{L}}}}}}}}{{M}_{{{{{{rm{L}}}}}}}}right)={{{{{rm{ln}}}}}}left({g}_{1}right)+frac{{k}_{1}cdot {{{{{rm{LWC}}}}}}}{{K}_{1}+{{{{{rm{LWC}}}}}}}-frac{E}{{kT}},$$
    (2)
    where PL is the light-saturated whole-leaf photosynthetic rate (nmol s−1). Equation 2 indicates that the log-transformed temperature-corrected Ps (i.e. Pscor) should increase with LWC, following Michaelis-Menten type hyperbolic response, i.e.$${{{{{rm{ln}}}}}}left({P}_{{{mbox{scor}}}}right)={{{{{rm{ln}}}}}}left({P}_{{{{{{rm{s}}}}}}}{e}^{E/{kT}}right)={{{{{rm{ln}}}}}}left({g}_{1}right)+frac{{k}_{1}cdot {{{{{rm{LWC}}}}}}}{{K}_{1}+{{{{{rm{LWC}}}}}}}.$$
    (3)
    Rearranging Eq. (2) shows that the temperature- and LWC-corrected whole-leaf photosynthetic rate (i.e. PLcor) should scale isometrically with ML, i.e.$${P}_{{{mbox{Lcor}}}}={P}_{{{{{{rm{L}}}}}}}{e}^{-{k}_{1}cdot {{{{{rm{LWC}}}}}}/left({K}_{1}+{{{{{rm{LWC}}}}}}right)}{e}^{E/{kT}}={g}_{1}{M}_{{{{{{rm{L}}}}}}}.$$
    (4)
    In this study, we refer to the temperature or water content correction as moving the temperature term ((frac{E}{{kT}})) or water content term ((frac{{k}_{1}cdot {{{{{rm{LWC}}}}}}}{{K}_{1}+{{{{{rm{LWC}}}}}}})) to the left-hand side of the model, an approach that has been commonly used in previous studies28.Following previous studies29,30,31, we assume that PL is proportional to AL, i.e. ({P}_{L}propto {A}_{L})because leaf area directly determines the light interception capacity1. Therefore, the quantitative relationship between SLA and LWC and temperature can be described as$${{{{{{mathrm{ln}}}}}}}left({{mbox{SLA}}}right)={{{{{{mathrm{ln}}}}}}}left(frac{{A}_{{{{{{rm{L}}}}}}}}{{M}_{{{{{{rm{L}}}}}}}}right)={{{{{{mathrm{ln}}}}}}}left({g}_{2}right)+frac{{k}_{1}cdot {{{{{rm{LWC}}}}}}}{{K}_{1}+{{{{{rm{LWC}}}}}}}-frac{E}{{kT}},$$
    (5)
    where g2 is another normalisation constant. Given that leaf area is a direct indicator of leaf photosynthetic capacity and that both traits reflect the long-term adaptation of plants to environmental change3,13, k1 in Eqs. (2) and (5) represent the maximum increase in mass-specific leaf photosynthetic capacity due to changes in water content. Since the temperature has a direct effect on the metabolic rates32 and productivity of ecosystems33, it is reasonable to assume that temperature can affect SLA globally34,35. Therefore, in this context T denotes the mean growing-season temperature (in degrees K), as SLA might be more responsive to long-term changes in temperature. Equation (5) predicts that SLA should increase with both LWC and the growing-season temperature. Rearranging Eq. (5) yields$${{{{{{mathrm{ln}}}}}}}left({{mbox{SL}}}{{{mbox{A}}}}_{{{mbox{cor}}}}right)={{{{{{mathrm{ln}}}}}}}left({{mbox{SLA}}}{e}^{E/{kT}}right)={{{{{{mathrm{ln}}}}}}}left({g}_{2}right)+frac{{k}_{1}cdot {{{{{rm{LWC}}}}}}}{{K}_{1}+{{{{{rm{LWC}}}}}}},$$
    (6)
    which predicts that the log-transformed temperature-corrected SLA (i.e. SLAcor) should increase with LWC following Michaelis-Menten dynamics. Likewise, by moving (frac{{k}_{1}cdot {{{{{rm{LWC}}}}}}}{{K}_{1}+{{{{{rm{LWC}}}}}}}) and (frac{E}{{kT}}) to the left-hand side and ML to the right-hand side of Eq. (5), we observe that the temperature- and LWC-corrected leaf area (i.e. ALcor) should scale isometrically with leaf mass, i.e.$${A}_{{{mbox{Lcor}}}}={A}_{{{{{{rm{L}}}}}}}{e}^{-{k}_{1}cdot {{{{{rm{LWC}}}}}}/left({K}_{1}+{{{{{rm{LWC}}}}}}right)}{e}^{E/{kT}}={g}_{2}{M}_{{{{{{rm{L}}}}}}}.$$
    (7)
    We note that the scaling of PLcor and ALcor with respect to ML will reveal how LWC mediates the scaling exponent of leaf trait relationships.Effects of LWC and temperature on leaf trait scalingThe numerical value of the exponent for the PL versus AL scaling relationship calculated from the empirical data was 0.99 (Supplementary Fig. 1; 95% CI = 0.95 and 1.02, r2 = 0.87), strongly supporting the model assumption that PL scales isometrically with AL. We then examined the effect of LWC on leaf trait scaling. The numerical value of the scaling exponent for the PL versus ML relationship was 0.95 (Fig. 2a; 95% CI = 0.92 and 0.99, r2 = 0.83). The non-linear relationship between Pscor and LWC described by Eq. (3) was supported by the empirical data (Fig. 2b; Supplementary Table 1). The non-linear model (Eq. 3) also had a lower Akaike’s Information Criterion score than the simple linear model between log-transformed Pscor and LWC (i.e. 793.5 versus 1988.8). After LWC and temperature were corrected (see Eq. 4), the numerical value of the scaling exponent became 0.97 (Fig. 2c; 95% CI = 0.94 and 1.01, r2 = 0.85), which was statistically indistinguishable from 1.0 (P  > 0.05), as predicted by the model. Likewise, the numerical value of the exponent (i.e. α) for the AL versus ML scaling relationship was 1.02 (Fig. 2d; 95% CI = 1.02 and 1.03, r2 = 0.92). Additional analyses using the pooled dataset showed that log-transformed SLA increased with LWC following Michaelis-Menten dynamics, as predicted by Eq. (6) (Fig. 2e; Supplementary Table 1). After the effects of LWC and temperature were accounted for (using Eq. 7), the numerical value of α became 1.01 (Fig. 2f; 95% CI = 1.00 and 1.01, r2 = 0.95). Thus, both of the scaling exponents numerically converged onto 1.0 once LWC and temperature were corrected. In addition, an inspection of the locally weighted smoothing (LOWESS) curves showed that the curvature in both scaling relationships was reduced after the effects of LWC and temperature were corrected, as predicted by the model (Fig. 2).Fig. 2: The quantitative effects of dry mass-based leaf water content (LWC) on leaf photosynthesis and SLA.a Scaling of leaf photosynthetic rate (PL, nmol s−1) with leaf dry mass (ML, g). b Non-linear fit to the relationship between temperature-corrected mass-specific leaf photosynthetic rate (Pscor, nmol g−1 s−1) and LWC (g g−1) based on Eq. (3). c Scaling of temperature- and LWC-corrected leaf photosynthetic rate (PLcor, nmol s−1) with ML (g). d Scaling of leaf area (AL, cm2) with leaf dry mass (ML, g). e Non-linear fit to the relationship between temperature-corrected specific leaf area (SLAcor, cm2 g−1) and LWC based on Eq. (6). f Scaling of temperature- and LWC-corrected leaf area (ALcor, cm2) with leaf dry mass (ML, g). Data with LWC greater than 25 were not shown in panel e for a better visualisation. LOWESS curves (blue lines) and 95% confidence intervals are shown.Full size imageThe results presented here show that temperature and LWC quantitatively correlate with other leaf traits, such as Ps and SLA (or LMA), as predicted by the model. The increases in Ps and SLA attenuate with increasing LWC (Fig. 2b, e), indicating that leaf water availability sets a constraint on the maximum Ps and SLA that leaves can reach. It has long been recognised that SLA is closely correlated with leaf growth rate and metabolic activity14,36,37. Therefore, it is reasonable to also expect that SLA, as well as Ps, will be quantitatively affected by LWC, which can change as a function of developmental status (such as leaf maturation and the accumulation of lignified tissues) and transiently as a function of evapotranspiration. LWC is also a reflection of species-specific adaptation to environmental conditions in different biomes. Nevertheless, our model, as well as the empirical data used to test it, reveal a broad and statistically robust correlation between critical leaf functional traits and leaf tissue water content. However, the observed variations in Pscor (Fig. 2b) suggest that in addition to temperature and LWC, other factors (e.g. plant phylogeny and soil fertility) may also affect leaf photosynthetic capacity, which is not accounted for in our model and should be critically examined in future research.Leaf area-mass scaling among different groupsThe numerical value of α varied across different plant growth forms, ecosystems, and latitudinal zones (Fig. 3 and Supplementary Table 2). In particular, the leaf area versus mass scaling relationship showed a clear pattern along a latitudinal gradient (Fig. 3c and Supplementary Table 2). The numerical value of α decreased from 1.10 in boreal regions (95% CI = 1.08 and 1.12, r2 = 0.91) to 1.00 in temperate regions (95% CI = 0.99 and 1.01, r2 = 0.91), and to 0.94 in tropical regions (95% CI = 0.92 and 0.95, r2 = 0.91). However, after correcting for the effects of LWC and temperature, as predicted, α converged onto 1.0 across all different groupings, and the r2 values of the scaling relationships also increased (Fig. 3 and Supplementary Table 2).Fig. 3: The exponents of leaf area-mass scaling with and without temperature and LWC corrections among different groups.a Comparison of scaling exponents among plant growth forms (n = 1688, 491, 1097, and 832 for forbs, graminoids, shrubs, and trees, respectively). b Comparison of scaling exponents among ecosystem types (n = 97, 1367, 1285, 1271, and 114 for deserts, forests, grasslands, tundra, and wetlands, respectively). c Comparison of scaling exponents among different latitudinal zones (n = 1111, 2113, and 910 for tropical, temperate, and boreal zones, respectively). Error bars indicate 95% confidence intervals.Full size imageOur analyses show that LWC also affects the numerical values of the exponents of leaf trait scaling relationships, which helps to explain why different works sometimes report significant differences in the exponents governing these relationships8,10. In particular, the numerical values of the scaling exponent governing the leaf area versus mass scaling relationship differ among different plant growth forms, ecosystems, and latitudinal zones (Fig. 3 and Supplementary Table 2), indicating that no invariant “scaling exponent” (i.e. α) holds true for the leaf area-mass scaling relationship. For example, in our dataset, α is significantly smaller than 1.0 in tropical regions (i.e. in keeping with a “diminishing returns” relationship in leaf area with respect to increasing leaf mass), close to 1.0 in temperate regions (i.e. a break-even relationship), and significantly larger than 1.0 in boreal regions (i.e. an “increasing returns” relationship). This shift in α along a latitudinal gradient may be associated with the different strategies to cope with variations in water availability, e.g. the high evapotranspiration rates in tropical regions may constrain increases in leaf area with increasing leaf mass, therefore resulting in diminishing returns, whereas, in boreal regions, the reduced water stress may enable plants to maximise leaf area to achieve relatively high photosynthetic capacities. Despite the variability in the numerical values of scaling exponents across different groups, the degree of curvature in these scaling relationships is reduced, and exponents converge onto unity after the effects of LWC and temperature are accounted for (Fig. 3), as predicted by the model (Eq. 7). This finding indicates that the variations in the exponent can, at least partially, be ascribed to the effects of LWC on SLA and the relative rate of increase in leaf area versus leaf mass. It is noteworthy that the numerical value of the scaling exponent for the PL versus ML relationship is also very close to 1.0, indicating the relatively weak effects of temperature and LWC on leaf photosynthesis-mass scaling. This may be partially attributed to the relatively limited number of data with concurrent LWC measurements and the adaptation of leaf traits to long-term temperature changes (see below for detailed discussion). Nevertheless, more measurements on LWC and leaf photosynthetic rates are needed to further test how LWC mediates leaf photosynthesis-mass scaling.Given that LWC was weakly correlated with ML (Supplementary Fig. 2, log-log slope = −0.01, 95% CI = −0.02 and 0, r2  More