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    Comprehensive climatic suitability evaluation of peanut in Huang-Huai-Hai region under the background of climate change

    Overview of the study areaBased on the actual cultivation of peanuts, the Huang-Huai-Hai region is selected as the study area (Fig. 1). The main body of the study area is the Huang-Huai-Hai Plain (North China Plain), which is a typical alluvial plain resulting from extensive sediment deposition carried by the Yellow River, the Huaihe River and the Haihe River and their tributaries, and the hills in central and southern Shandong Peninsula adjacent to it. Administrative zones include 5 provinces, 2 cities, 53 cities and 376 counties (districts). In China, The Huang-Huai-Hai region is an important production and processing centre for agricultural products, with a total land area of 4.10 × 105 square kilometers and cultivated fields of 2.15 × 107 hm2, accounting for 4.3% and 16.3% of the total amount of the country, respectively. It belongs to temperate continental monsoon climate with distinct seasons, accumulated temperature of 3600–4800 degrees above 10 °C, frost-free period of 170–200 days and annual precipitation of 500–950 mm27. The Huang-huai-hai region is the largest peanut growing area, accounting for more than 50% of the country’s peanut production and area28.Figure 1Location of the study areas. The figure was made in the ArcGIS 10.2 platform (https://www.esri.com/en-us/home).Full size imageData sourcesThe data used in the study mainly include meteorological data, geographic information data and crop data. The meteorological data comes from China Meteorological Information Center (http://data.cma.cn), including the daily maximum temperature (℃), daily minimum temperature (℃), daily average temperature (℃), daily precipitation (mm) and daily average wind speed (M/s) observed by 186 ground observation meteorological stations in the Huang-Huai-Hai region from 1960 to 2019 (Fig. 1). Geographic information data include elevation DEM data (resolution of 1 km × 1 km) and land use data in the study area, which are from the resource and environmental science and data center of Chinese Academy of Sciences (http://www.resdc.cn). Crop data, including peanut sowing area and yield data, are derived from the statistical yearbooks of provinces and cities in the study area and China Agricultural Technology Network (http://www.cast.net.cn).Data processingMeteorological data processingAnusplin software is a tool to interpolate multivariate data based on ordinary thin disks and local thin disk spline functions, enabling the introduction of covariates for simultaneous spatial interpolation of multiple surfaces, suitable for meteorological data time series29. First, the Anusplin software is used to spatially interpolate the meteorological data and suitability data of the peanut growing season (April to September) from 1960 to 2019 based on the elevation data with a resolution of 1 km × 1 km. The Inverse Distance Weight (IDW) interpolation can make the meteorological data after Anusplin interpolation maintain consistency with the original data, and is able to improve the interpolation accuracy. Finally, the meteorological and suitability data set with a resolution of 1 km × 1 km is obtained. ArcGIS and MATLAB software were used to count the median of regional meteorological factors in agricultural fields of different cities (counties), and the meteorological factors and suitability of different periods of peanut growth season in each city (county) were obtained.Yield data processingMany factors affect crop yield formation, which can be generally divided into three main categories: meteorological conditions, agronomic and technological measures, and stochastic factors. Agricultural technical measures reflect the development level of social production in a certain historical period and become time technology trend output, which is referred to as trend output for short, and meteorological production reflects short period yield components that are affected by meteorological elements. Stochastic factors account for a small proportion and are often ignored in actual calculations30. The specific calculation is as follows:$$Y={Y}_{t}+{Y}_{w}$$
    (1)

    where Y is the actual yield (single production) of the crop, Yt is the trend yield, and Yw is the meteorological yield.In this paper, a straight-line sliding average method is used to simulate the trend yield. The straight-line sliding average method is a very commonly used method to model yield, and it considers the change in the time series of yield within a certain stage as a linear function, showing a straight line, as the stage continuously slides, the straight line continuously changes the position, and the backward slip reflects the continuous change in the evolution trend of the yield history31. The regression models in each stage are obtained in turn, and the mean value of each linear sliding regression simulation value at each time point is taken as its trend yield value. The linear trend equation at some stage is:$${Y}_{i}left(tright)={a}_{i}+{b}_{i}t$$
    (2)
    where i = n-k + 1, is the number of equations; k is the sliding step; n is the number of sample sequences; t is the time serial number. Yi(t) is the function value of each equation at point t. there are q function values at point t. the number of q is related to n and k. Calculate the average value of each function value at each point:$$overline{{Y }_{i}(t)}=frac{1}{q}sum_{j=1}^{q}{Y}_{i}left(tright)$$
    (3)
    Connecting the (overline{{Y }_{i}(t)}) value of each point can represent the historical evolution trend of production. Its characteristics depend on the value of k. Only when k is large enough, the trend yield can eliminate the influence of short cycle fluctuation. After comparison and considering the length of yield series, k is taken as 5 in this paper.After the trend yield is obtained, the meteorological yield is calculated using Eq. (1), then the relative meteorological production is$${Y}_{r}=frac{{Y}_{w}}{{Y}_{t}}$$
    (4)
    The relative meteorological yield shows that the relative variability of yield fluctuation deviating from the trend, that is, the amplitude of yield fluctuation, is not affected by time and space, and is comparable. However, when the value is negative, it indicates that the meteorological conditions are unfavorable to the overall crop production, and the crop yield reduction, that is, the yield reduction rate32.Characteristics of spatial and temporal distribution of climatic resources in the Huang-Huai-Hai regionCollect meteorological resource data from 1960 to 2019. Taking 1960–1989 as the first three decades of the study and 1990–2019 as the last three decades, the climatic resource changes of peanut growth in the Huang-Huai-Hai region are analyzed by interpolation of heat resources (average temperature), water resources (precipitation) and light resources (sunshine hours) in the study area in two periods combined with topographic factors.Establishment of suitability modelAccording to the definition of phenological time and growth period of peanut planting practice in the Huang-Huai-Hai region, the growth season of peanut is divided into three growth periods and five growth stages (Table 1). Temperature, precipitation and sunshine hours are the necessary meteorological factors to determine the normal development of peanut. Therefore, combined with climatic resources in the study area, temperature, precipitation and sunshine suitability model was introduced to quantitatively analyze the suitability of peanut planting.Table 1 Division of peanut growth periods.Full size tableTemperature suitability modelTemperature is a very important factor in the growth period of peanut, and the change of temperature in different growth periods will have a great influence on the yield and quality of peanut. As a warm-loving crop, accumulated temperature plays a decisive role in the budding condition and nutrient growth stage of peanut. Temperature determines the quality of fruit and the final yield of peanut. Beta function33 is used to calculate temperature suitability, which is universal for crop-temperature relationship. The specific calculation is as follows:$${F}_{i}left(tright)=frac{(t-{t}_{1}){({t}_{h}-t)}^{B}}{({t}_{0}-{t}_{1}){({t}_{h}-{t}_{0})}^{B}}$$
    (5)
    where the value of B is shown in$$B=frac{{t}_{h}-{t}_{0}}{{t}_{0}-{t}_{1}}$$
    (6)
    where Fi(t) is the temperature suitability of a certain growth period; t is the daily average temperature of peanut at a certain development stage; t1, th and t0 are the lower limit temperature, upper limit temperature and appropriate temperature required for each growth period of peanut. Refer to the corresponding index system and combined with the peanut production practice in Huang-Huai-Hai region34,35,36, determine the three base point temperature of peanut in each growth period, as shown in the Table 2.Table 2 Three fundamental points temperature and crop coefficient of peanut at each growth stage in the study area.Full size tablePrecipitation suitability modelPeanut has a long growth period, which is nearly half a year. Insufficient or excessive water during the growth period has a great impact on the growth and development, pod yield and quality of peanut. Combined with the actual situation of Huang-Huai-Hai region and peanut precipitation / water demand index, the water suitability function is determined and calculated as follows:$${text{F}}_{{text{i}}} left( {text{r}} right) = left{ {begin{array}{*{20}l} {frac{{text{r}}}{{0.9{text{ET}}_{{text{c}}} }}} hfill & {r < 0.9E{text{T}}_{{text{c}}} } hfill \ 1 hfill & {0.9E{text{T}}_{{text{c}}} le r le 1.2E{text{T}}_{{text{c}}} } hfill \ {frac{{1.2{text{ET}}_{{text{c}}} }}{{text{r}}}} hfill & {r > 1.2E{text{T}}_{{text{c}}} } hfill \ end{array} } right.$$
    (7)
    where Fi(r) is the water suitability of a certain growth period; r is the accumulated precipitation of peanut in a certain development period; ETc is the water demand of peanut in each growth period.$${mathrm{ET}}_{mathrm{c}}={mathrm{K}}_{mathrm{c}}cdot {mathrm{ET}}_{0}$$
    (8)
    where Kc is the peanut crop coefficient (Table 2) and ET0 is the crop reference evapotranspiration, which is calculated by the Penman Monteith method recommended by the international food and Agriculture Organization (FAO).Sunshine suitability modelSunshine hours are an important condition for photosynthesis. The “light compensation point” and “light saturation point” of peanut are relatively high, and more sunshine hours are required for photosynthesis. Under certain conditions of water, temperature and carbon dioxide, photosynthesis increases or decreases with the increase or decrease of light. Relevant studies show that when the sunshine hours reach more than 55% of the available sunshine hours, the crops reach the appropriate state to reflect the light37. The following formula is used to calculate the sunshine suitability of peanut in each growth period.$${mathrm{F}}_{mathrm{i}}left(mathrm{s}right)=left{begin{array}{l}frac{mathrm{S}}{{mathrm{S}}_{0}} quad S{mathrm{S}}_{0}end{array}right.$$
    (9)
    where Fi(s) is the sunshine suitability of peanut in a certain development period, S is the actual sunshine hours in a certain growth period, S0 is 55% of the sunshine hours (L0), and the calculation method of L0 refers to the following formula.$${mathrm{L}}_{0}=frac{2mathrm{t}}{15}$$
    (10)
    $$mathrm{sin}frac{mathrm{t}}{2}=sqrt{frac{mathrm{sin}(45^circ -frac{mathrm{varnothing }-updelta -upgamma }{2})times mathrm{sin}(45^circ +frac{mathrm{varnothing }-updelta -upgamma }{2})}{mathrm{cosvarnothing }times mathrm{cosdelta }}}$$
    (11)
    where Φ is the geographic latitude, δ is the declination, γ is the astronomical refraction, t is the angle.Comprehensive suitability modelPeanut has different needs for meteorological elements such as temperature, sunshine and precipitation in different growth periods. In order to analyze the impact of meteorological factors in different growth periods on yield, correlation analysis was conducted between the suitability of temperature, precipitation and sunshine in each growth period and the relative meteorological yield of peanut, and the correlation coefficient of each growth period divided by the sum of the correlation coefficients of the whole growth period was used as the weight coefficient of the suitability of temperature, precipitation and sunshine in each growth period (Table 3). The climatic suitability of each single element in peanut growing season is calculated by using formulas (12) and (13):Table 3 The weight coefficients of climatic suitability at each growth stage.Full size table$$left{begin{array}{c}{mathrm{b}}_{mathrm{ti}}=frac{{mathrm{a}}_{mathrm{ti}}}{sum_{mathrm{i}=1}^{mathrm{n}}{mathrm{a}}_{mathrm{ti}}}\ {mathrm{b}}_{mathrm{ri}}=frac{{mathrm{a}}_{mathrm{ri}}}{{sum }_{mathrm{i}=1}^{mathrm{n}}{mathrm{a}}_{mathrm{ri}}}\ {mathrm{b}}_{mathrm{si}}=frac{{mathrm{a}}_{mathrm{si}}}{{sum }_{mathrm{i}=1}^{mathrm{n}}{mathrm{a}}_{mathrm{si}}}end{array}right.$$
    (12)
    $$left{begin{array}{c}F(t)={sum }_{mathrm{i}=1}^{mathrm{n}}left[{mathrm{b}}_{mathrm{ti}}{mathrm{F}}_{mathrm{i}}(mathrm{t})right]\ F(r)={sum }_{mathrm{i}=1}^{mathrm{n}}left[{mathrm{b}}_{mathrm{ri}}{mathrm{F}}_{mathrm{i}}(mathrm{r})right]\ F(s)={sum }_{mathrm{i}=1}^{mathrm{n}}left[{mathrm{b}}_{mathrm{si}}{mathrm{F}}_{mathrm{i}}(mathrm{s})right]end{array}right.$$
    (13)
    where bti, bri and bsi are the weight coefficients of temperature, precipitation and sunshine suitability in the i growth period respectively, ati, ari and asi are the correlation coefficients between temperature, precipitation and sunshine suitability and meteorological impact index of peanut yield in the i growth period respectively, and F(t), F(r) and F(s) are the temperature, precipitation and sunshine suitability in peanut growth season respectively.Then, the geometric average method is used to obtain the comprehensive suitability of peanut growth season, as shown in formula (14).$$F(S)=sqrt[3]{F(t)times F(r)times F(s)}$$
    (14)
    Verification of climatic zoning resultsDrought and flood disaster indexOn the basis of previous studies, in view of the different water demand of peanut in different development stages, this paper adds the water demand of peanut in different development stages as an important index to calculate, and constructs a standardized precipitation crop water demand index (SPRI) that can comprehensively characterize the drought and flood situation of peanut, so as to judge and analyze the occurrence of drought and flood disasters of peanut.Step 1: calculate the difference D between precipitation and crop water demand at each development stage$${D}_{i}={P}_{i}-{ET}_{ci}$$
    (15)
    where Pi is the precipitation in the i development period (mm), and ETci is the crop water demand in the i development period (mm).Step 2: normalize the data sequence.Since there are negative values in the original sequence, it is necessary to normalize the data when calculating the standardized precipitation crop water demand index. The normalized value is the SPRI value. The normalization method and drought and flood classification are consistent with SPEI index38,39,40.Chilling injury indexBased on the results of previous studies41, the abnormal percentage of caloric index was selected as the index of low-temperature chilling injury of peanut to judge and analyze the occurrence of chilling injury in different growth stages. The specific calculation process and formula are as follows:Step 1: calculate the caloric index of different development stages.Combined with the growth and development characteristics of peanut and considering the appropriate temperature, lower limit temperature and upper limit temperature at different growth stages of peanut, the caloric index can reflect the response of crops to environmental heat conditions. The average value of daily heat index is taken as the heat index of growth stage to reflect the influence of heat conditions in different growth stages on crop growth and development. Refer to formulas (5) and (6) to calculate the heat index Fi(t) at different development stages.Step 2: calculate the percentage of heat index anomaly$${I}_{ci}=frac{{F}_{i}(t)-overline{{F }_{i}(t)}}{overline{{F }_{i}(t)}}times 100%$$
    (16)
    where Ici is the Chilling injury index of stage i, Fi(t) is the heat index of stage i, and (overline{{F }_{i}(t)}) is the average value of the heat index of stage i over the years.Heat injury indexBased on the results of previous studies42, taking the average temperature of 26 °C, 30 °C and 28 °C and the daily maximum temperature of 35 °C, 35 °C and 37 °C as the critical temperature index to identify the heat damage of peanut in three growth stages, if this condition is met and lasts for more than 3 days, it will be recorded as a high temperature event.Disaster frequencyDisaster frequency (Pi) is defined as the ratio of the number of years of disaster at a certain station to the total number of years in the study period43, which is calculated by formula (17).$${P}_{i}=frac{n}{N}times 100%$$
    (17)
    where n is the number of years of disaster events to some extent at a certain growth period at a certain station, and N is the total number of years. More

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    Co-occurrence networks reveal more complexity than community composition in resistance and resilience of microbial communities

    Testing H1 and H2 at community composition levelAs noted above, the simple fact that fungi grow more slowly than bacteria is the basis of the hypotheses that (H1) fungal communities should be more resistant than bacterial communities to drought stress, and (H2) that fungal communities should be less resilient than bacterial communities when the stress is relieved by rewetting18. In addition to growth rate, these two hypotheses may be related to differences in the form of growth between fungi and bacteria. For example, multicellular hyphal growth versus unicellular division or the greater thickness of fungal cell walls as compared to those of bacteria47,48. We tested H1 and H2 at the community composition level by blending the fungal and bacterial datasets generated from the same leaf, root, rhizosphere and soil samples collected from field-grown sorghum that had been either irrigated as a control, or subjected to preflowering drought followed by regular wetting beginning at flowering10,11.We followed the approach of Shade et al.17 to detect resistance and resilience, which had been developed for univariate variables, e.g., richness. For multivariate data, e.g., community composition, we modified it by calculating pairwise community dissimilarity for two groups: within-group (control-control pairs, drought-drought pairs, or rewetting-rewetting pairs), and between-group (control-drought pairs, or control-rewetting pairs). Ecological resistance to drought stress is detected by comparing compositional dissimilarity of between-group pairs (control-drought pairs) against within-group pairs (control-control pairs and drought-drought pairs) for each of the droughted weeks (weeks 3–8). Ecological resilience to rewetting is detected by assessing, from before to after rewetting, the change in the difference of compositional dissimilarity between within-group pairs and between-group pairs. Here, the point just before rewetting was week 8 and the points after rewetting were weeks 9–17. A t-test was used to assess the statistical significance of the differences in resistance or resilience between bacterial and fungal communities at each time point for each compartment.To account for the different resolutions of ITS and 16 S, we compared bacterial 16 S OTUs against both fungal ITS, species-level OTUs as well the fungal family level (Supplementary Fig. 1). The results of analyses using either fungal families or OTUs are consistent. Out of 36 comparisons (15 roots, 15 rhizospheres and 6 soils), different family and OTUs results were detected in four instances. In two of these, significances detected by OTUs were not detected by family (root, weeks 4 and 17) and, in the other two cases, significances detected by family were not detected by OTUs (rhizosphere, weeks 7 and 8). (Fig. 1). We report only results that are consistent at both the species and family levels (Fig. 1).In line with our first hypothesis, H1, we found that the resistance to drought stress for fungal mycobiomes was consistently stronger than that for bacterial microbiomes for weeks 5 in root, weeks 4–6 in rhizosphere, and weeks 4 and 6–8 in soil (Fig. 1, Supplementary Fig. 1 and Supplementary Table 2). In support of our second hypothesis, H2, when the stress of pre-flowering drought was relieved by rewetting, we found that the resilience of the bacterial communities was consistently higher than that for the fungi in weeks 9–16 in root, and weeks 11–17 in rhizosphere (Fig. 1, Supplementary Fig. 1 and Supplementary Table 2).Surprisingly, we found that resilience was stronger for fungal than bacterial communities in the first week (week 9) of rewetting in the rhizosphere (Fig. 1, Supplementary Fig. 1 and Supplementary Table 2). This high resilience of fungi may be associated with the quick growth of sorghum roots when rewetted. The rhizosphere zone around these newly formed roots may be quickly colonized by soil fungi, a community that was weakly affected by drought. This result suggests that re-assembly of the rhizosphere microbial community is more complex than previously expected.The finding that fungal community composition in the soil is not shaped by drought prevented us from further detecting resilience (Fig. 1). Note fungal community in early leaves was excluded from analysis due to the high proportion of non-fungal reads in sequencing11.Testing H1 and H2 at all-correlation levelNext, we moved from the comparison of whole communities to correlation among individual bacterial and fungal taxa to test the hypotheses about resistance, H1, and resilience, H2. As noted above, previous research provided the foundation for the stress gradient hypothesis, which predicts an increase in positive associations in stress32,33,34,35,36,37. Further, ecological modeling predicts that negative associations promote stability40. Concerning specific associations, studies of Arabidopsis and associated microbes reported that positive associations are favored within kingdoms, i.e., within bacteria or within fungi, while negative associations predominate between kingdoms38,39. Given these foundations, concerning H1, we expected an increase in the proportion of positive correlation by drought stress that would be strongest for B-B, followed by F-F, and lastly by B-F; for H2 we expected rewetting to cause a decrease in the proportion of positive correlation, again most strongly for B-B, followed by F-F, and lastly by B-F.Overall, at the all-correlation level, we found no consistent support for the differences postulated for bacterial and fungal responses in H1. For example, strong increases in the proportion of positive correlations under drought could be found in all microbial pairings for some compartments (B-B in leaf and root, F-F in rhizosphere and soil, and B-F in root and rhizosphere) (Fig. 2a, Supplementary Figs. 2, 3). Neither did we find consistent support for the differences ascribed to bacteria and fungi in H2 as the strongest decreases in the proportion of positive correlations during rewetting occurred at F-F in rhizosphere and soil, and B-B in leaf and root (Fig. 2b, Supplementary Figs. 2, 3).Fig. 2: Correlations of microbes in drought stress and drought relief.Estimates of combined correlations (row a) show an increase in positive correlations under drought stress across the four compartments (root, black; rhizosphere, blue; soil, red; leaf, green). Data points underlying the lines in the figure are provided in the alternative version in Supplementary Fig. 2. This result is in line with the stress gradient hypothesis which posits that stressful environments favor positive associations because competition will be less intense than in benign environments32,33,36,37. Note that positive trends in combined correlations can arise in two ways. First, from an increase of positive correlations (row b) that exceeds the rise in negative correlations (row c), e.g., Leaf bacterial-bacterial (Bac-Bac) correlations or rhizosphere fungal-fungal (Fun-Fun) correlations in the drought period (Negative correlations in row C values are multiplied by −1 to facilitate comparison). Second, from a decrease in negative correlations that exceeds a decrease in positive correlations, e.g., root bacterial-bacterial correlations or root bacterial-fungal (Bac-Fun) correlations in drought. Combined (a), positive (b) and negative (c) estimates of correlation (Spearman’s rho, ρ) are given for four compartments (root, rhizosphere, soil and leaf), and three types of correlations (Bacterium-Bacterium, Fungus-Fungus, Bacterium-Fungus). T-tests (two sided) were carried out for linear mixed effect modelling that incorporates link type and compartments as random factors. Detailed distribution densities of correlations are presented in Supplementary Fig. 3. Source data are provided as a Source Data file.Full size imageWe found support for the stress gradient hypothesis because drought increased the relative frequency of positive correlations among microbial taxa (Fig. 2a, Supplementary Figs. 2, 3). The increases were due, largely, to B-B correlations in leaf and F-F correlations in the rhizosphere during drought, when the relative frequency of positive correlations was increased (Fig. 2b, Supplementary Figs. 2, 3) and the frequencies of negative correlations were decreased or weakly increased (Fig. 2c, Supplementary Figs. 2, 3). Less obvious increases in the relative frequency of positive correlations (such as B-B in root, F-F in soil, and B-F in root and rhizosphere) occurred where drought reduced both positive and negative correlations, but the losses of negative correlations exceeded those of positive correlations (Fig. 2, Supplementary Figs. 2, 3).In support of the expectation that correlations would be more negative between taxonomic groups than within taxonomic groups, we found that the relative frequency of positive correlations was generally lower for B-F than B-B and F-F correlations (Fig. 2, Supplementary Figs. 2, 3). Moreover, as ecological modeling has indicated that negative associations should promote stability of communities40, we hypothesize that B-F correlations would be more stable than B-B and F-F networks in response to drought stress. However, we found no support for this hypothesis, as B-F correlations (for example in root) did not always show the least response to drought stress (Fig. 2, Supplementary Figs. 2, 3).Testing H1 and H2 at species co-occurrence levelFor our final test of H1 (resistance) and H2 (resilience) we focused on co-occurrence networks based on significant, positive correlations. These networks have been reported to be destabilized for bacteria but not for fungi in mesocosms subject to drought stress19, and shown to be disrupted for bacteria in natural vegetation studied over gradients of increasing aridity41,42. Using these results as guides, for H1 we expected that drought stress should disrupt co-occurrence networks most strongly for B-B, followed by F-F, and lastly by B-F. For H2 we expected that relief of stress by rewetting should strengthen microbial co-occurrence networks most strongly for B-B, followed by F-F, and lastly by B-F.For this test we constructed microbial co-occurrence networks using significant positive pairwise correlations between microbial taxa, B-B, F-F and B-F, and compared the network complexity between fully irrigated control and drought, and between control and rewetting following drought. In general, we found no consistent support for the difference between bacteria and fungi inherent in H1. Rhizosphere was the one compartment where B-B vertices dropped and F-F vertices rose in response to drought, as expected, but this result was offset in root and soil, where vertices dropped in all networks, B-B, F-F and B-F (Figs. 3, 4; Supplementary Figs. 4, 5). Analysis by co-occurrence networks highlighted the differences between plant compartments. In root drought strongly disrupted networks of B-B, B-F and F-F, but in the other three compartments, network disruption was weaker, and networks were even enhanced by drought for F-F in rhizosphere and B-B in leaf (Figs. 3, 4).Fig. 3: Networks of significant positive cross-taxonomic group correlations (bacteria and fungi).a Fungal operational taxonomic units (OTUs) (blue) and bacterial OTUs (black) are graphed as nodes. Significant positive Spearman correlations are graphed as edges (ρ  > 0.6, false discovery rate adjusted P  More

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    CaliPopGen: A genetic and life history database for the fauna and flora of California

    Population genetic data collection from primary data sourcesFigure 4 describes the overall data collection workflow for the four datasets that comprise CaliPopGen. We first identified literature potentially containing population genetic data for California by querying the Web of Science Core Collection (https://webofknowledge.com/) for relevant literature from 1900 to 2020 with the terms: topic = (California*) AND topic = (genetic* OR genomic*) AND topic = (species OR taxa* OR population*). We included only empirical peer-reviewed literature and excluded unreviewed preprints. In using these search terms, our goal was to broadly identify genetic papers focused on California with population or species-level analyses, while avoiding purely phylogenetic studies or those focused on agricultural or model species. This resulted in 4,942 unique records.Fig. 4Flow chart of the data collection process that generated the CaliPopGen databases.Full size imageWe next screened titles and abstracts to retain articles that: (1) provided data on populations of species which are self-sustaining without anthropogenic involvement; (2) included at least some eukaryote species; (3) included population(s) sampled within California; (4) mentioned measures of genetic diversity or differentiation; and (5) were not reviews (thus restricting our search to only primary literature). We retained 1869 studies after this first pass of literature screening (see Technical Validation for estimate of inter- and intra-screener bias).Our second, more in-depth screening pass involved reading the full text of these 1869 studies. We had two goals. First, we confirmed that retained papers fully met all five of our inclusion criteria (the first screen was very liberal with respect to these criteria, and many papers failed to meet at least one criterion after close reading). Second, we eliminated papers where the data were not presented in a way that allowed us to extract population-level information. For example, many of the more systematics-focused studies pooled samples from large, somewhat ill-defined regions (“Sierra Nevada” or “Southern California”); if such regions were larger than 50 km in a linear dimension, we deemed them unusable for making geographically-informative inferences. Other studies presented summaries of population data, often in the form of phylogenetic networks or trees, but did not include information on actual population genetic parameters and therefore were not relevant to our database. We retained 528 publications after this second pass.From this set of papers, we extracted species, locality, and genetic data for each California population or sampling locality described in each study (Fig. 3A). This included Latin binomial/trinomial, English common name, population identifiers, and geographic coordinates of sampling sites. We also noted population/sampling localities that were interpreted as comprised of interspecific hybrids, and listed both parental species. We collected population genetic diversity and differentiation statistics for each unique genetic marker for each population/sampling locality; as a result, a sampling locality may have multiple entry rows, one for each locus or marker type. Parameters extracted for each population/marker combination include sample size, genetic marker type, gene targets, number of loci, years of sampling, and reported values for effective population size (Ne), expected (HE) and observed (HO,) heterozygosity, nucleotide diversity (π, pi), alleles-per-locus (APL), allelic richness (AR), percent polymorphic loci (PPL), haplotype diversity (HDIV), inbreeding coefficient (e.g. FIS, FIT, GIS), and pairwise population genetic comparison parameters (FST, GST, DST, Nei’s D, Jost’s D, or phi). We note that while there are technical differences between allelic richness and alleles-per-locus, source literature often used the terms interchangeably, and we include the parameters and their values as named in the source. We define marker type as the general category of genetic marker used (e.g., “microsatellite” or “nuclear”), while gene targets are the specific locus/loci (e.g., “COI”). We present these data in two separate datasets, one containing all population-level genetic summary statistics (Dataset 121, see Fig. 3C and detailed description in Table 1) and a second for estimates of pairwise genetic differentiation (Dataset 221, see Fig. 3D and detailed description in Table 2).Table 1 Description of the population genetic data in Dataset 121.Full size tableTable 2 Description of the pairwise genetic distance data in Dataset 221.Full size tableAll genetic data were extracted directly from the source literature. However, we also updated or added to the metadata for these population genetic values in several ways. We included kingdom, phylum, and a lower-level taxonomic grouping for each species (usually class), and updated scientific and common names based on the currently accepted taxonomy of the Global Biodiversity Information Facility22. When geographic coordinates were not provided for a sampling locality, as was frequently the case in the older literature, we used Google Maps (https://www.google.com/maps) to georeference localities based on either in-text descriptions or embedded figure maps guided by permanent landmarks like a bend in a river or administrative boundaries. Because this can only yield approximate coordinates, we recorded estimated accuracy as the radius of our best estimate of possible error in kilometers. If coordinates were provided in degree/minute/seconds, we used Google Maps to translate them to decimal degrees. In cases where coordinates were not provided and locality descriptions were too vague to determine coordinates with less than 50 km estimated coordinate error, we did not attempt to extract coordinates but still provide the genetic data. All coordinates are provided in the web Mercator projection (EPSG:3857). We excluded studies that reported genetic parameter values only for samples aggregated regionally (“Southern California” or “Sierra Nevada”). If marker type was not explicitly included, we classified marker type based on the gene targets reported, if provided.Life history trait data collectionTo increase the utility of CaliPopGen, we also assembled data on life history traits for all animal (Dataset 321) and plant (Dataset 421) species contained in Datasets 121 and 221. We assembled trait data that have previously been shown to correlate with genetic diversity, including those related to reproduction, life cycle, and body size, as well as conservation status (e.g.23,24,25,26,). Life history data were compiled by first referencing large online repositories, often specific to taxonomic groups, like the TRY plant trait database27, and the Royal Botanic Gardens Kew Seed Information Database28. If trait data for species of interest were unavailable from these compilations, we conducted keyword literature searches for each combination of species and life history trait, and extracted data from the primary literature. When data were not available for the subspecies or species for which we had genetic data, we report values for the next closest taxonomic level, up to and including family, as available in the literature.For both animals and plants, we defined habitat types as marine, freshwater, diadromous, amphibious, or terrestrial. Marine species include those that are found in brackish or wetland-marine habitats, as well as bird species that primarily reside in marine habitats. Freshwater species include those that are found in wetland-freshwater habitats, as well as species that primarily reside in freshwater. The diadromous category includes fish species that are catadromous or anadromous. We considered species to be amphibious if they have an obligatory aquatic stage in their life cycle, but also spend a significant portion of their life cycle on land. Terrestrial species were defined as those that spend most of their life cycle on land and are not aquatic for any portion of their life cycle. In a few cases (e.g., waterbirds that are both freshwater and marine, semi-aquatic reptiles), a species could reasonably be placed in more than one category, and we did our best to identify the primary life history category for such taxa. If the taxonomic identity of an entry was hybrid between species or subspecies, this was noted in the speciesID column and no life history data were reported.The CaliPopGen Animal Life History Traits Dataset 321 (description of dataset in Table 3) includes habitat type, lifespan, fecundity, lifetime reproductive success, age at sexual maturity, number of breeding events per year, mode of reproduction, adult length and mass, California native status, listing status under the US Endangered Species Act (ESA), listing status under the California Endangered Species Act (CESA), and status as a California Species of Special Concern (SSC). For some traits, value ranges were recorded–for example, minimum to maximum lifespan. In other cases, we recorded single values and, when available, a definition of this single value, (for example, minimum, average, or maximum lifespan). We report either the range of the age of sexual maturity (minimum to maximum), or a single value, depending on the available literature. For sexually dimorphic species, we report female adult length and weight when available, because female body size often correlates with fecundity. Across animal taxonomic groups, different measures of body size and length measurements are often used, reflecting community consensus on how to measure size. Given this variation, we report the type of length measurement, if available, as Standard Length (SL), Fork Length (FL), Total Length (TL), Snout-to-Vent Length (SVL), Straight-Line Carapace (SLC), or Wingspan (WS).Table 3 Description of the animal life-history data in Dataset 321.Full size tableThe CaliPopGen Plant Life History Traits Dataset 421 (description of dataset in Table 4) includes habitat type, lifespan, life cycle, adult height, self-compatibility, monoecious or dioecious, mode of reproduction, pollination and seed dispersal modes, mass per seed, California native status, NatureServe29 element ranks (global and state ranks, see Table 5 for definitions), listing status under the Federal Endangered Species Act (ESA), and listing status under the California Endangered Species Act (CESA). In contrast to most animal species, plant lifespan was typically reported as a single value. We define life cycles as the following: Annual: completes full life cycle in one year; Biennial: completes full life cycle in two years; Perennial: completes full life cycle in more than two years; Perennial-Evergreen: perennial and retains functional leaves throughout the year; Perennial-Deciduous: perennial and loses all leaves synchronously for part of the year. Some species are variable (for example, have annual and biennial individuals), and in those cases we attempted to characterize the most common modality.Table 4 Description of the plant life-history data in Dataset 421.Full size tableTable 5 Description of the Conservation status (Heritage Rank) from California Natural Diversity Database29.Full size tableBecause of the paucity of data available for chromists and fungi, we did not extract life history trait data for the relatively few species in these taxonomic groups.Data visualization and summaryWe used the R-package raster (v3.1–5) to visualize the spatial extent of the data in CaliPopGen in Fig. 3. Panel (A) shows a summary plot of all unique populations of both the Population Genetic Diversity in Dataset 121 and the Pairwise Population Differentiation in Dataset 221. Panel (B) shows the total number of unique populations in each California terrestrial ecoregion. Panel (C) depicts all data entries of Population Genetic Diversity Dataset 121, summed for each 20×20 km grid cell. Panel (D) shows the density of pairwise straight lines drawn between pairs of localities in the Pairwise Population Differentiation Dataset 221, depicted as the total number of lines per 20×20 km grid cell. The number of populations and species of both Datasets 121 & 221 are summarized for each marine and terrestrial ecoregion in Table 6.Table 6 Summary of total numbers of populations and species per California ecoregion, separately for population genetic and pairwise datasets.Full size table More

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    An 8-year record of phytoplankton productivity and nutrient distributions from surface waters of Saanich Inlet

    Sample collection and hydrographySampling was conducted aboard the University of Victoria’s MSV John Strickland either weekly, biweekly or monthly between 11 March 2010 and 15 November 2017 in Saanich Inlet at 48.59°N, 123.50°W (Fig. 1). To standardize measurements and due to biological significance, seawater was collected from the euphotic zone. Sampling depths corresponded to approximately 100, 50, 15, and 1% of the photosynthetically active radiation (PAR) at the surface (Io). These “light” depths were either determined using a CTD-mounted PAR sensor or a Secchi disk. CTD profiles were performed prior to each seawater cast to measure depth, temperature and conductivity of the water column, and PAR, fluorescence, and dissolved oxygen (when available).Seawater from each light depth was collected using Niskin or GO-FLO bottles on either a rosette sampler or an oceanographic wire. When possible, individual samples were collected directly from the Niskin or GO-FLO bottles. When time was not sufficient to allow direct sampling, bulk samples of seawater from each depth were collected into acid-washed polyethylene carboys, kept cold in the dark, and homogenized before sub-sampling for the individual measurements.Dissolved nutrientsFor the measurements of nitrite (NO2−), nitrate and nitrite (NO3− + NO2−), phosphate (PO43−) and Si(OH)4, seawater samples from each light depth were syringe-filtered through a combusted 0.7 µm (nominal porosity) glass fibre filter into acid-washed 30-mL polypropylene bottles and immediately frozen. All nutrient samples were stored at −20 °C until analysis. Concentrations of NO2−, NO3− + NO2−, PO43−, and Si(OH)4 were determined using an Astoria Nutrient Autoanalyzer (Astoria-Pacific, OR, USA) following the methodology of Barwell-Clarke and Whitney22. During 2014 and 2015, samples for the measurement of Si(OH)4 were collected separately from those for the other nutrients, filtered with a 0.6 µm polycarbonate membrane filter and stored at 4 °C. During this period, Si(OH)4 concentrations were determined manually using the molybdate blue colorimetric methodology23. Replicate (2 or 3) nutrient samples were taken at each depth; average data are presented in the published dataset and the figures (Fig. 2).Fig. 2Dissolved macronutrient concentrations in the euphotic zone of Saanich Inlet from March 11, 2010 to November 15, 2017. Left panels show depth-integrated concentrations (black bars on top) and time-series profiles (filled contour/scatter plots on bottom) for (A) nitrate plus nitrite (NO3− + NO2−), (B) phosphate (PO43−) and (C) silicic acid (Si(OH)4). In the time-series profiles, 2012–2013 data are not interpolated due to single-depth sampling. Grey shaded regions in top panels indicate the phytoplankton growing seasons considered for this study (March 1st – October 30th). Right panels show monthly-averaged depth profiles for the entire 8-year period, illustrating euphotic zone seasonality for each nutrient. The color scale bars on the far right apply to both the time-series vertical profiles and the 8-year seasonal plots. Sampling depths are indicated by round symbols. The year labels are positioned under the tick marks corresponding to January.Full size imageSuspended particulate matterTotal chlorophyll-aChlorophyll-a (Chl-a) was used as a proxy for phytoplankton biomass (Fig. 3A). For total Chl-a analysis, seawater samples (0.25–1 L) were gently vacuum filtered onto 0.7 µm (nominal porosity) glass fiber filters, which were then stored at −20 °C until analysis. Chl-a concentrations were determined using the acetone extraction and acidification method24,25. Acidification of samples decreased the likelihood of overestimation of Chl-a concentrations due to the presence of chlorophyll degradation products26. Filters were submerged in 10 mL of 90% acetone, sonicated for 10 minutes in an ice bath, and left to extract at −20 °C for 22 h. Following the extraction period, samples were allowed to equilibrate to room temperature (~2 h). Fluorescence of the acetone solution containing the extracted Chl-a was measured before and after acidification with 1.2 N hydrochloric acid using a Turner 10-AU fluorometer. The final concentrations of total Chl-a were calculated from measurements made before (Fo) and after (Fa) acidification using Eq. (1)25. The coefficient (τ) of Eq. (1), adapted from Strickland and Parsons25, was derived from a calibration of the Turner 10-AU fluorometer with known pure chlorophyll standards (Table 2).$${rm{C}}{rm{h}}{rm{l}} mbox{-} {rm{a}}(mu g,{L}^{-1})=frac{tau }{tau -1}ast ({rm{F}}{rm{o}}-{rm{F}}{rm{a}})ast 0.814ast left(frac{{rm{V}}{rm{o}}{rm{l}}.{rm{A}}{rm{c}}{rm{e}}{rm{t}}{rm{o}}{rm{n}}{rm{e}},{rm{e}}{rm{x}}{rm{t}}{rm{r}}{rm{a}}{rm{c}}{rm{t}}{rm{e}}{rm{d}}}{{rm{V}}{rm{o}}{rm{l}}.{rm{S}}{rm{e}}{rm{a}}{rm{w}}{rm{a}}{rm{t}}{rm{e}}{rm{r}},{rm{f}}{rm{i}}{rm{l}}{rm{t}}{rm{e}}{rm{r}}{rm{e}}{rm{d}}}right)$$
    (1)
    Fig. 3Biological particulate concentrations in the euphotic zone of Saanich Inlet from March 11, 2010 – November 15, 2017. Left panels show time-series profiles (filled contour/scatter plots) of (A) total chlorophyll-a (Total Chl-a), (B) particulate carbon (PC), (C) particulate nitrogen (PN), and (D) particulate biogenic silica (bSiO2). The 2012–2013 data are not interpolated due to single-depth sampling. In A, the bar plot in the top panel shows percent contribution of different size fractions to total Chl-a. In (B–D), black bars in top panels show depth-integrated concentrations. Grey shaded regions in bar plots indicate phytoplankton growing seasons considered for this study (March 1st – October 30th). Right panels show monthly-averaged depth profiles for the entire 8-year period, illustrating euphotic zone seasonality for each particulate. The color scale bars on the far right apply to both the time-series vertical profiles and the 8-year seasonal plots. Sampling depths are indicated by round symbols. The year labels are positioned under the tick marks corresponding to January.Full size imageSize fractionated chlorophyll-aTo determine the percent contributions of “pico” (0.7–2 µm), “small nano” (2–5 µm), “large nano” (5–20 µm) and “micro” ( >20 µm) phytoplankton to total Chl-a, seawater samples (0.25–1 L) separate from those used for total Chl-a) were consecutively filtered through 20, 5 and 2 µm polycarbonate membrane filters and 0.7 µm (nominal porosity) glass fiber filters. Between 2013 and 2017, the “pico” and “small nano” size classes were collected as one fraction (0.7–5 µm). Analysis of Chl-a concentrations for each size fraction followed the same procedure outlined for total Chl-a.Particulate carbon and nitrogenParticulate C and N measurements were obtained from seawater samples incubated for carbon (ρC) and nitrate uptake (ρNO3) rates (see section on “Uptake rates of carbon and nitrate” for methodology) (Fig. 3B,C). PC and PN measurements presented in this dataset were taken at the end of ρC and ρNO3 incubations; however, original (‘ambient’) values can be back calculated by subtracting the amount of C and N taken up during the incubation period from the final PC and PN values. The differences between after-incubation PC and PN data and back-calculated ambient values were not significantly different than the measurement error.Particulate biogenic silicaParticulate biogenic silica was used as a proxy for siliceous phytoplankton biomass (Fig. 3D). Seawater samples (0.5–1 L) from each depth were gently vacuum filtered through 0.6 µm polycarbonate membrane filters. Filters were folded and placed in polypropylene centrifuge tubes, dried for 48 h at 60 °C, and then stored in a desiccator at room temperature until analysis. Filters were digested with 4 mL of 0.2 M NaOH for 30–45 min in a water bath at 95 °C27. After digestion, samples were neutralized with 0.1 N HCl and cooled rapidly in an ice bath. Samples were centrifuged to separate out the undissolved lithogenic silica, and colorimetric analysis was performed on the supernatant. The transmittance of the samples, standards, and reverse-order reagent blanks were read at 820 nm using a Beckman DU 530 ultraviolet-visible (UV/Vis) spectrophotometer27,28.Uptake rates of carbon and nitrateSeawater samples (~0.5–1 L) were gently collected into clear polycarbonate bottles. One additional sample was collected from the 100% light depth, into a dark polycarbonate bottle, which did not allow light penetration. After the addition of the isotopic tracers (see below), bottles were placed into an acrylic incubator with constant seawater flow to maintain surface seawater temperature. Three acrylic tubes wrapped in colored and neutral density photo-film (to obtain 50, 15, and 1% of surface PAR) were used to incubate sample bottles under the same in-situ light conditions from which samples were collected. Samples from the 100% light level were placed inside the same acrylic incubator, but outside of the film-covered tubes. A LI-COR® LI-190 Quantum sensor was installed next to the incubator and continuously recorded incoming PAR for the entire incubation period. During sampling in 2010 and 2011, all experiments were performed using a shipboard incubator. For sampling from 2012 onwards, all experiments were done using an incubator on land (University of Victoria Aquatic Facility), which was connected to a seawater system maintained at local surface seawater temperature (approximately 9–12 °C depending on the time of year).Rates of C (ρC) and NO3 (ρNO3) uptake were determined using a stable isotope tracer-technique29,30 (Fig. 4). A single seawater sample from each light depth received a dual spike, with NaH13CO3 (99% 13C purity, Cambridge Isotope Laboratories) for the determination of ρC and Na15NO3 (98 + % 15N purity, Cambridge Isotopes Laboratories) for the determination of ρNO3. Isotope additions were made at approximately 10% of ambient dissolved inorganic carbon (DIC) and NO3− concentrations.Fig. 4Carbon and nitrate uptake rates in the euphotic zone of Saanich Inlet from March 11, 2010 – November 15, 2017. Left panels show depth-integrated rates (black-bars on top) and time-series profiles (filled contour/scatter plots below) of (A) carbon (ρC) and (B) nitrate (ρNO3) uptake rates. In the time-series profiles, 2012–2013 data are not interpolated due to single-depth sampling. Grey shaded regions in depth-integrated plots indicate phytoplankton growing seasons for this study (March 1st – October 30th). Right panels show monthly-averaged depth profiles for the entire 8-year period, illustrating euphotic zone seasonality for carbon and nitrate uptake. The color scale bars on the far right apply to both the total time-series vertical profiles and the 8-year seasonal plots. Sampling depths are indicated by round symbols. The year labels are positioned under the tick marks corresponding to January.Full size imageSpiked seawater samples were incubated for 24 h, except from 2010 to 2013 when the incubation period was 4 to 6 hr. After incubation, the entire sample was gently vacuum filtered onto a combusted 0.7 µm (nominal porosity) glass fibre filter. Filters were dried for 48 h at 60 °C and kept in a desiccator at room temperature until analysis. Filters were packed into pellets and sent to the Stable Isotope Facility at the University of California (UC) Davis for analysis of 13C and 15N enrichment, and total C and N content by continuous flow isotope ratio mass spectrometry and elemental analysis, respectively. For these measurements, UC Davis uses either an Elementar Vario EL Cube or Micro Cube elemental analyzer (Elementar Analysensysteme GmbH, Hanau, Germany) interfaced to either a PDZ Europa 20–20 isotope ratio mass spectrometer (Sercon Ltd., Cheshire, UK) or an Isoprime VisION IRMS (Elementar UK Ltd, Cheadle, UK).Carbon and NO3− uptake rates were calculated using Eq. 3 of Hama et al.29, and Eq. 3 and 6 of Dugdale and Wilkerson30, respectively.For samples incubated for less than 24 h, the daily C or NO3− uptake rates (ρX) were calculated using a PAR extrapolation method shown in Eq. (2):$$rho X(mu mol,{L}^{-1}da{y}^{-1})=left(rho X(mu mol,{L}^{-1}h{r}^{-1})divleft(frac{PAR,during,incubation}{Total,Daily,PAR}right)right)ast 24$$
    (2)
    Additionally, to account for NO3− uptake occurring under no light, ρNO3− was measured in dark bottles and this rate was added to the ρNO3− of each sample incubated for less than 24 h. The ρNO3− DARK was calculated following Eq. (3):$$rho N{O}_{3}DARK(mu mol,{L}^{-1}da{y}^{-1})=left(rho N{O}_{3}DARK(mu mol,{L}^{-1}h{r}^{-1})divleft(frac{Total,Daily,PAR-PAR,during,incubation}{Total,Daily,PAR}right)right)ast 24$$
    (3)
    PAR data used in Eqs. (2) and (3) came from the LI-COR® LI-190 Quantum sensor that was mounted beside the incubator. The seawater DIC value for each sample was calculated using a regression equation relating water density to DIC for Saanich Inlet31. Ambient NO3− concentrations were measured as described above. More