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The framework of Swin MSIWe established the first Swin Transformer-based mosquito species identification (Swin MSI) model, with the help of self-constructed image dataset and multi-adjustment-test. Gradient-weighted class activation mapping was used to visualize the identification process (Fig. 1a). The key Swin Transformer block was described on Fig. 1b. Based on practical needs, Swin MSI was additional designed to identify Culex pipiens Complex on the subspecies level (Fig. 1c) and novel mosquito (which was defined as ones beyond 17 species in our dataset) classification attribution (Fig. 1d). Detailed results are shown in the following sections.Figure 1The Framework of Swin MSI. (a)The basic architecture for mosquito features extraction and identification. Attention visualization generated by filters at each layer are shown. (b) Details for Swin Transformer block. (c) For mosquito within our dataset 17 species, output is the top 5 confidence species. (d) For mosquito beyond 17 species (defined as novel species), whether the output is a species or a genus is decided after comparing with confidence threshold.Full size imageMosquito datasetsWe established the highest-definition and most-balanced mosquito image dataset to date. The mosquito image dataset covers 7 genera and 17 species (including 3 morphologically similar subspecies in the Cx. pipiens Complex), which covers the most common and important disease-transmitting mosquitoes at the global scale, with a total of 9,900 mosquito images. The image resolution was 4464 × 2976 pixels. The specific taxonomic status and corresponding images are shown in Fig. 2. Due to the limitation of field collection, Ae. vexans, Coquillettidia ochracea, Mansonia uniformis, An. vagus and Toxorhynchites splendens only have females or only have males. In addition, each mosquito species included 300 images of both sexes, which was large enough and same number for each species, in order to balance the capacity and variety of training sets.Figure 2Taxonomic status and index of mosquito species included in this study Both male and female mosquitoes were photographed from different angles such as dorsal, left side, right side, ventral side, etc. Except for 5 species, each mosquito includes 300 images of both sexes, and the resolution of mosquito photos were 4464 × 2976. Cx. pipiens quinquefasciatus, Cx. pipiens pallens, and Cx. pipiens molestus (subspecies level, in dark gray background) were 3 subspecies in Cx. pipiens Complex (species level).Full size imageWorkflow for mosquito species identificationA three-stage flowchart of building best deep learning model for identification of mosquito species model was adopted (Fig. 3). The first learning stage was conducted by three CNNs (the Mask R-CNN, DenseNet, and YOLOv5) and three transformer models (the Detection Transformer, Vision Transformer, and Swin Transformer). Based on the performance of the first-stage model and the real mosquito labels, the second learning stage involved adjusting the model parameters of the three Swin Transformer variants (T, B, and L) to compare their performances. The third learning stage involved testing the effects of inputting differently sized images (384 × 384 and 224 × 224) to the Swin Transformer-L model; finally, we proposed a deep learning model for mosquito species identification (Swin MSI) to test the recognition effects of different mosquito species. The model was validated on different mosquito species, with a focus on the identification accuracy of three subspecies within the Cx. pipiens Complex and the detection effect of novel mosquito species.Figure 3Flowchart of testing deep learning model for intelligent identification of mosquito species.Full size imageComparison between the CNN model and Transformer model results (1st round of learning)Figure 4a shows the accuracies obtained for the six different computer vision network models tested on the mosquito picture test set. The test results show that the transformer network model had a higher mosquito species discrimination ability than the CNN.Figure 4Comparison of mosquito recognition effects of computer vision network models and variants. (a) Comparison of mosquito identification accuracy between 3 CNNs and 3 Transformer; (b) The best effect CNN (YOLOv5) training set loss curve(blue), validation set loss curve(green) and validation set accuracy curve(orange); (c) The best effect Transformer (Swin Transformer) training set loss curve, validation set loss curve and validation set accuracy curve. (d) Swin-MSI-T test result confusion matrix; (e) Swin-MSI -B test result confusion matrix; (f) Swin-MSI -L test result confusion matrix. Confusion matrix of mosquito labels in which odd numbers represent females and even numbers represent males. The small squares in the confusion matrix represent the recognition readiness rate, from red to green, the recognition readiness rate is getting higher and higher An. sinensis: 1, 2; Cx. pipiens quinquefasciatus: 3, 4; Cx. pipiens pallens: 5, 6; Cx. pipiens molestus: 7,8 Cx. modestus: 9,10; Ae. albopictus: 11, 12 Ae. aegypti: 13, 14; Cx. pallidothorax: 15, 16 Ae. galloisi: 17,18 Ae. vexans: 19, 20; Ae. koreicus: 21, 22 Armigeres subalbatus: 23, 24; Coquillettidia ochracea: 25, 26 Cx. gelidus: 27, 28 Cx. triraeniorhynchus: 29, 30 Mansonia uniformis: 31, 32 An. vagus: 33, 34 Ae. elsaie: 35,36 Toxorhynchites splendens: 37, 38.Full size imageIn the CNN training process (applied to YOLOv5), the validation accuracy requires more than 110 epochs to grow to 0.9, and the validation loss requires 110 epochs to drop to a flat interval; in contrast, during the training step, these losses represent a continuously decreasing process. These results indicate that the deep learning model derived based on the Swin Transformer algorithm was able to achieve a higher recognition accuracy in less time than the rapid convergence ability of the CNN during the iterative process (Fig. 4b).The Swin Transformer model exhibited the highest test accuracy of 96.3%. During the training process, the loss of this model could stabilize after 30 epochs, and its validation accuracy could grow to 0.9 after 20 epochs; during the validation step, the loss can drop to 0.36 after 20 epochs, after which the loss curve fluctuated but did not produce adverse effects (Fig. 4c). Based on the excellent performance of the Swin Transformer model, this model was used as the baseline to carry out the subsequent analyses.Swin Transformer model variant adjustment (2nd round of learning)Following testing performed to clarify the superior performance of the Swin Transformer algorithm, we chose different Drop_path_rate, Embed_dim and Depths parameter settings and labeled the parameter sets as the Swin Transformer-T, Swin Transformer-B, and Swin Transformer-L variants. Drop_path is an efficient regularization method, and an asymmetric Drop_path_rate is beneficial for supervised representation learning when using image classification tasks and Transformer architectures. The Embed_dim parameter represents the image dimensions obtained after the input red–green–blue (RGB) image is calculated by the Swin Transformer block in stage 1. The Depths parameter is the number of Swin Transformer blocks used in the four stages. The parameter information and test results are shown in Table 1. Due to the increase in the Swin Transformer block and Embed_dim parameters in stage 3, the recognition accuracies of the three variants were found to be 95.8%, 96.3%, and 98.2%, Correspondingly, the f1 score were 96.2%, 96.7% and 98.3%; thus, these variants could effectively improve the mosquito species identification ability in a manner similar to the CNN by increasing the number of convolutional channels to extract more features and improve the overall classification ability. In this study, the Swin Transformer-L variant, which exhibited the highest accuracy, was selected as the baseline for the next work.Table 1 Parameters and test accuracy of three variants of Swin Transformer.Full size tableBy plotting a confusion matrix of the test set results derived using the three Swin Transformer variants, we clearly obtained the proportion of correct and incorrect identifications in each category to visually reflect the mosquito species discrimination ability (Fig. 4d–f). In the matrix, the darker diagonal colors indicate higher identification rate accuracies of the corresponding mosquito categories. Among them, five mosquito species were missing because the Ae. vexans, Coquillettidia ochracea, Mansonia uniformis, An. vagus and Toxorhynchites splendens species were represented in the dataset by only females or only males. The confusion matrix shown in Panel C lists the lowest number of mosquito species identification error points and the lowest accuracy level obtained in each category, suggesting that the Swin Transformer-L model has a better classification performance than the Swin Transformer-T and Swin Transformer-B models.Effect of the input image size on the discrimination ability (3rd round of learning)To investigate the relationship between the input image size and mosquito species identification performance, in this study, we conducted a comparison test between input images with sizes of 224 × 224 and 384 × 384, based on the Swin Transformer-L model, and identified 8 categories of mosquito identification accuracy differences. These test results are shown in Table 2. When using an image size of 224 × 224 pixels, the batch_size parameter was set to 16, and when using an image size of 384 × 384 pixels, the batch_size parameter was set to 4; under these conditions, the proportion of utilized video memory accounted for 67%, as shown in Eq. 4, and this was consistent with the description of the relationship between the size of self-attentive operations during the operation of the Swin Transformer model when 384 × 384 pixels images were used. The time required for the Transformer-L model to complete all the training sessions was excessive, reaching 126 h and even exceeding the 124 h required by the YOLOv5 model, which was found to require the highest computation time during the training process in this work. Long-term training process could more fully reflect the performance differences between models. Fortunately and actually, the response speed of the model will not be affected by the training time. Compared to the accuracy of 98.2% obtained for 224 × 224 inputs, the 384 × 384 input image size derived based on the Swin Transformer-L model provided a higher mosquito species identification accuracy of 99.04%, representing an improvement of 0.84%.$$Omega ({text{W}} – {text{MSA}}) = 4{text{HWC}}^{2} + 2{text{M}}^{2} {text{HWC}}$$
(1)
Table 2 Comparison of recognition accuracy for different input image sizes.Full size tableVisualizing and understanding the Swin MSI modelsTo investigate the differences in the attentional features utilized by the Swin MSI and taxonomists for mosquito species identification, we applied the Grad-CAM method to visualize the Swin MSI attentional areas on mosquitoes at different stages. Because the Swin Transformer has different attentional ranges among its multi-head self-attention steps in different stages, different attentional weights can be found on different mosquito positions. In stage 1, the feature dimension of each patch was 4 × 4 × C, thus enabling the Swin Transformer’s multi-head self-attention mechanism to give more attention to the detailed parts of the mosquitoes, such as their legs, wings, antennae, and pronota. In stage 2, the feature dimension of each patch was 8 × 8 × 2C, enabling the Swin Transformer’s multi-head self-attention mechanism to focus on the bodies of the mosquitoes, such as their heads, thoraces, and abdomens. In stage 3, when the feature dimension of each patch was 16 × 16 × 4C, the Swin Transformer’s multi-head self-attention mechanism could focus on most regions of the mosquito, thus forming a global overall attention mechanism for each mosquito (Fig. 5). This attentional focus process is essentially the same as the process used by taxonomists when classifying mosquito morphology, changing from details to localities to the whole mosquito.Figure 5Attention visualization of representative mosquitoes of the genera Ae., Cx., An., Armigeres, Coquillettidia and Mansonia. This is a visualization for identifying the regions in the image that can explain the classification progress. Images of Toxorhynchites contain only males, with obvious differences in morphological characteristics, are not shown.Full size imageAe. aegypti is widely distributed in tropical and subtropical regions around the world and transmits Zika, dengue and yellow fever. A pair of long-stalked sickle-shaped white spots on both shoulder sides of the mesoscutum, with a pair of longitudinal stripes running through the whole mesotergum, is the most important morphological identification feature of this species. This feature was the deepest section in the attention visualization, indicating that the Swin MSI model also recognized it as the principal distinguishing feature. In addition, the abdominal tergum of A. aegypti is black and segments II-VII have lateral silvery white spots and basal white bands; the model also focused on these areas.Cx. triraeniorhynchus is the main vector of Japanese encephalitis; this mosquito has a small body size, a distinctive white ring on the proboscis (its most distinctive morphological feature), and a peppery color on its whole body. Similarly, the model constructed herein focused on both the head and abdominal regions of this species.An. sinensis is the top vector of malaria in China and has no more than three white spots on its anterior wing margin and a distinct white spot on its marginal V5.2 fringe; this feature was observed in Stage 2, at which time the modelstrongly focused on the corresponding area.The most obvious feature of Armigeres subalbatus is the lateral flattening and slightly downward curving of its proboscis; the observation of the attention visualization revealed that the constructed model focused on these regions from Stage 1 to Stage 3. The mesoscutum and abdominal tergum were not critical and were less important for identification than the proboscis, and the attention visualization results correspondingly show that the neural network focused less on these features.Coquillettidia ochracea belongs to the Coquillettidia genus and is golden yellow all over its body, with the most pronounced abdomen among the analyzed species. The model showed a consistent morphological taxonomic focus on the abdomen of this species.Mansonia uniformis is a vector of Malayan filariasis. The abdominal tergum of this species is dark brown, and its abdominal segments II-VII have yellow terminal bands and lateral white spots, which are more obvious than the dark brown feature on proboscis. Through the attention visualization, we determined that the Swin MSI model was more concerned with the abdominal region features than with the proboscis features.Subspecies-level identification tests of mosquitos in the Culex pipiens ComplexFine-grained image classification has been the focus of extensive research in the field of computer vision25,26. Based on the test set (containing 270 images) constructed herein for three subspecies of the Cx. pipiens Complex, the subspecies and sex identification accuracies were 100% when the Swin MSI model was used.The morphological characteristics of Cx. pipiens quinquefasciatus, Cx. pipiens pallens, and Cx. pipiens molestus within the Cx. pipiens Complex are almost indistinguishable, but their host preferences, self-fertility properties, breeding environments, and stagnation overwintering strategies are very different27. Among the existing features available for morphological classification, the stripes on the abdominal tergum of Cx. pipiens quinquefasciatus are usually inverted triangles and are not connected with the pleurosternums, while those of Cx. pipiens pallens are rectangular and are connected with the pleurosternums. Cx. pipiens molestus is morphologically more similar to Cx. pipiens pallens as an ecological subspecies of the Cx. pipiens Complex. However, taxonomists do not recommend using the unstable feature mentioned above as the main taxonomic feature for differentiation. By analyzing the attention visualization results of these three subspecies (last three rows on Fig. 5), we found that the neural networks of Cx. pipiens quinquefasciatus, Cx. pipiens pallens, and Cx. pipiens molestus still focused on the abdominal regions, as shown in dark red. The area of focus of these neural networks differ from that of the human eye, and the results of this study suggest that the Swin MSI model can detect finely granular features among these three mosquito subspecies that are indistinguishable to the naked human eye.Novel mosquito classification attributionAfter we performed a confidence check on the successfully identified mosquito images in the dataset, the lowest confidence value was found to be 85%. A higher confidence threshold mean stricter evaluation criteria, which can better reflect the powerful performance of the model. Therefore, 0.85 was set as the confidence threshold when judging novel mosquitoes. When identifying 10 unknown mosquito species, the highest derived species confidence level was below 85%; when the results were output to the genus level (Fig. 1d), the average probability of obtaining a correct judgment was 96.26%accuracy and 98.09% F1-score (Table 3). The images tested as novel Ae., Cx. and An. mosquito were from Minakshi and Couret et al.28,29.Table 3 Probability of correct attribution of novel species.Full size table More

Seed sampling and germinationSeed from ten trees from each of 21 native Scottish Scots pine populations (Table 1) were collected in March 2007 and germinated at the James Hutton Institute, Aberdeen (latitude 57.133214, longitude −2.158764) in June 2007. Populations were chosen to represent the species’ native range in Scotland and to include three populations from each of the seven seed zones (Fig. 2). There was no selection of seed-trees on the basis of any traits except for the possession of cones on the date of sampling. Ten seed trees were sampled from each population according to a spatial protocol designed to cover a circle of approximately 1 km in diameter located around a central tree. The sampling strategy identified nine points each in a pre-determined random direction from the central point, whilst stratifying the number sampled with increasing distance from the central point in the ratio 1: 3: 5. This strategy avoids over-sampling the areas close to the centre point. For smaller fragments of woodland, or where only a few trees with cones were present, then the directions of the sampled trees from the central tree were maintained to give a wide coverage of the woodland area, but the distances between trees varied but were never closer than 50 m. To break dormancy, seeds were soaked for 24 hours on the benchtop at room temperature, after which they were stored in wet paper towels and refrigerated in darkness at 3–5 °C for approximately 4 weeks. Seeds were kept moist and transferred to room temperature until germination began (approx. 5–7 days), then transplanted to 8 cm × 8 cm × 9 cm, 0.4 L pots filled with Levington’s C2a compost and 1.5 g of Osmocote Exact 16–18 months slow release fertiliser and kept in an unheated glasshouse. The compost was covered with a layer of grit to reduce moss and liverwort growth. Seedlings from the same mother tree are described as a family and are assumed to be half-siblings.Table 1 Locations and basic environmental data for the populations sampled for seed to establish the trial. See the maternal traits dataset15 for precise data for each mother tree sampled.Full size tableExperimental design: nurseriesThe full collection consisted of 210 families (10 families from each of 21 populations) each consisting of 24 half sibling progeny (total 5,040 individuals); needle tissue was sampled from each seedling and preserved for long term storage, one needle on silica gel, 2–5 needles at −20 °C. After transfer into pots, 8 seedlings per family were moved to one of three nurseries (total 1,680 seedlings per nursery): outdoors at Inverewe Gardens in western Scotland (nursery in the west of Scotland: coded NW, latitude 57.775714, longitude −5.597181, Fig. 2); outdoors in a fruit cage (to minimise browsing) at the James Hutton Institute in Aberdeen (nursery in the east of Scotland: NE); in an unheated glasshouse at the James Hutton Institute in Aberdeen (nursery in a glasshouse: NG). Trees were arranged in 40 randomised trays (blocks) in each nursery. Each block contained two trees per population (total 42 trees). Watering was automatic in NG, and manually as required for NE and NW. No artificial light was used in any of the nurseries. In May 2010 the seedlings from NG were moved outdoors to Glensaugh in Aberdeenshire (latitude 56.893567, longitude −2.535736). In 2010 all plants were repotted into 19 cm (3 L) pots containing Levingtons CNSE Ericaceous compost with added Osmocote STD 16–18 month slow release fertilizer.Experimental design: field sitesIn 2012 the trees were transplanted to one of three field sites: Yair in the Scottish Borders (field site in the south of Scotland: FS, latitude 55.603625, longitude −2.893025); Glensaugh (field site in the east of Scotland: FE); and Inverewe (field site in the west of Scotland: FW). All trees transplanted to FS were raised in the NG and all but four of the trees transplanted to FE were raised locally in the NE (the remainder were grown in NG). In contrast, following mortality and ‘beating up’ (filling gaps where saplings had died), the FW experiment ultimately contained cohorts of trees raised in each of the three nurseries as follows: 290 grown locally in the NW; 132 were grown in the NG; and 82 were grown in the NE.Site historiesThe Yair site (FS) had previously been used for growing Noble fir (Abies procera) for Christmas trees and Lodgepole pine (Pinus contorta), a section of the former were felled and chipped to create a clear area prior to planting. The planting site is also adjacent to a large block of commercial Sitka spruce (Picea sitchensis) forestry, and the Glenkinnon Burn Site of Special Scientific Interest (SSSI NatureScot site code 736; EU site code 135445), an area of mixed broadleaf woodland. Prior to planting, major areas of tall weeds were strimmed. The site was protected by a deer fence. The experiment was planted 8–11 October 2012. The Glensaugh site (FE) is in Forestry Compartment 3 of the Glensaugh Research Station, adjacent to Cleek Loch. It is thought to have been cleared of Scots pine and Larch (Larix decidua) around 1917, after which it reverted to rough grazing. An attempt to reseed part of the site in the 1980s was unsuccessful and it quickly reverted to rough grazing for a second time. The whole site (within which the experimental area is embedded) was deer fenced and re-planted under the Scottish Rural Development Programme (SRDP) in 2012. The experimental plot was planted up 7–9 March 2012. The Inverewe site (FW) had previously been a Sitka spruce and Lodgepole pine plantation (50:50 mix) that had been clear-felled in 2010 following substantial windthrow. The experimental site was deer fenced in early 2012, and the experiment was planted 12–16 March 2012, followed by beating up on 27–28 March 2013 and 22–24 October 2013. There had been minimal preparation of the site in line with current practice for restocking sites. The experimental site is included in the Inverewe Forest Plan, which included deer fencing of a larger area (2014) around the experimental site. Planting of this area was completed in early 2015, funded by NTS (National Trust for Scotland), although natural regeneration is also taking place.At each site, trees were planted in randomised blocks at 3 m × 3 m spacing. There are four randomised blocks in both FS and FE and three in FW. A guard row of Scots pine trees was planted around the periphery of the blocks and between blocks B and C at FS. Each block comprised one individual from each of eight (of the 10 sampled) families per 21 populations (168 trees). Although most families (N = 159) were represented at each of the three sites, families with insufficient trees (N = 9) were replaced in one site (FS) with a different family from the same population. Each experimental site was designed with redundancy such that, if thinning becomes necessary as the trees mature, then the systematic removal of trees (i.e. trees 1,3,5,7, etc of row 1, and 2,4,6,8, etc of row 2, 1,3,5,7,etc of row 3) will maintain a balanced design of the experiment, with sufficient family and population representation to provide an ongoing experiment with full geographic coverage.The field sites generally experience different climates, with FW typically warmer and wetter and with more growing degree days per year and a much longer growing season than both FE and FS (Table 2). The coldest site with the shortest growing season is generally FE.Table 2 Average climatic variables at field sites Glensaugh (FE), Inverewe (FW) and Yair (FS) from planting in 2012 until 2020. Climatic variables are derived from data provided by the Met Office (daily mean, minimum and maximum temperatures and monthly rainfall).Full size tablePhenotype assessmentsMaternal traitsFollowing seed collection, a range of traits were measured in the mother trees in order to control for maternal effects in subsequent measurements of their progeny (Table 3). For each mother tree, measurements of height and diameter at breast height (DBH) were taken, and ten cones were collected and assessed in detail. Cone width and length were measured prior to drying the cones (when they were still closed). Cone weight was measured post-drying. Seed removed from each cone was assessed for total weight (after wings had been removed) and for the count and percentage of seeds which were classed as viable (viable seed were those which had both a wing and an obvious seed). No further seed sorting was applied.Table 3 Traits assessed in mother trees, cones, seeds (dataset: Maternal), nursery seedlings (dataset: Nursery) and field trials (dataset: Field). Within the datasets, traits are recorded in a single column for each year using the format Code-Year (e.g. absolute height in 2008 = HA08) except for the maternal traits datasets which were all measured in 2007.Full size tableNursery traitsSeedling phenotype assessments were performed annually from 2007–2010 for three different trait types: phenology (budburst and growth cessation); form (total number of buds, needle length); cumulative growth (stem diameter and height, canopy width). Measurements of tree form and cumulative growth traits were taken after the end of each growing season. Phenology was assessed weekly during the spring and autumn of 2008 for budburst and growth cessation, respectively. Budburst was defined as the number of days from 31 March 2008 to the time when newly emerged green needles were observed (budburst stage 6: Fig. 3). In some seedlings in 2008, a secondary flush of growth occurred from terminal buds that had formed during the summer of that year. Therefore, growth cessation was defined retrospectively as the number of days from 10 September 2008 to the date when a terminal bud had formed on the leading shoot of the seedling, providing no further growth was observed either on the stem below that bud, nor from the bud itself. Canopy width (widest point) was measured at two perpendicular points in the horizontal plane. Needle length was measured for three needles per tree. Mortality was recorded each year from 2007 to 2010.Fig. 3Phenological stages of bud burst in Pinus sylvestris assessed in field trials. Inset numbers correspond to budburst stage. Budburst stage 1: bud dormant; 2: bud swelling and showing signs of linear expansion; 3: scales open at base revealing green tissue. Remaining bud remains encased by smooth bud scales; 4: scales open along length of shoot revealing green tissue and partially visible needles; 5: white tipped needles visible along length of the shoot; 6: green needles emerging away from the shoot (bottle brush appearance) along its entire length; 7: Needles have separated and next year’s terminal bud is usually formed and clearly visible.Full size imageField traitsTree height was measured in the field in the winter after each growing season from 2013 at FE and FW, and from 2014 to 2020 at all sites. Height was taken as the vertical measurement in cm from top bud straight to the ground. Basal stem diameter was measured at the end of the growing season for trees growing at FE and FW from 2014 to 2020 and for FS in 2020.Phenology assessments were performed in spring at each site from 2015 to 2019. Seven distinct stages of budburst (assessed on the terminal bud) were defined (Fig. 3) although only stages 4 to 6 are included in the dataset and considered for analysis due to high proportions of missing data for the early and late stages. Each tree was assessed for budburst stage at weekly intervals from early spring until budburst was complete. In order to allow comparisons within and among sites and years, the date at which each stage of budburst occurred was considered relative to 31 March of that year. For example, 25 May 2019 is recorded as 55 days since 31 March 2019. The duration of budburst (time taken to reach stage 6 from stage 4) was also estimated.When trees progressed through budburst stages rapidly, skipping a stage between assessments, a mean value was taken from the two assessment dates. For example, if a tree was at stage 4 on day 55 and was recorded as stage 6 at the next assessment on day 62, it is assumed to have reached stage 5 at day 58.5. More

Each of the 23 key variables can be used for analysis. To validate the dataset, we used five plant-related variables (diversity of order, family, genus, species and species endemic to China) to demonstrate the process of using the dataset for analysis as follows:(1) For the four variables of plant taxa “order”, “family”, “genus” and “species”, the similarity and difference in spatial distribution pattern of diversity of different taxa in the Qinling-Daba Mountains climate transition zone were analyzed. The spatial distribution pattern of the diversity of the four taxa is shown in Fig. 3, which is increasingly lower from south (low latitude) to north (high latitude). This result is consistent with the classical latitudinal gradient model of plant diversity. The boundary between higher diversity in the south and lower diversity in the north is roughly located in the area of Funiu Mountains in the eastern Qinling-Daba Mountains, Taibai Mountains in the central Qinling-Daba Mountains and Baishui River in the western Qinling-Daba Mountains. However, with the reduction in taxon scale, the spatial distribution pattern of diversity tends to be complex. Orders (Fig. 3a) and families (Fig. 3b) can be divided by lines, while genera (Fig. 3c) need thicker lines, and species (Fig. 3d) can only be divided by polygons. Figure 3 shows that the taxonomic groups of families are more clearly divided, while species can only be divided by staggered bands. Therefore, when dividing the north–south boundary, the family taxon scale is appropriate, whereas the species scale is more appropriate when studying the north–south transition zone.Fig. 3Spatial distribution of diversity of orders, families, genera and species. (a) The blue dotted line is basically the dividing line of the order diversity of 50 species. The order diversity to the north of the blue dotted line is lower than 50 species, and the order diversity to the south of the blue dotted line is higher than 50 species. (b) The blue dotted line is basically the dividing line of the family diversity of 150 species. The family diversity to the north of the blue dotted line is lower than 150 species, and the family diversity to the south of the blue dotted line is higher than 150 species. (c) The thicker blue dotted line is basically the dividing line of genus diversity of 578–681 species. The genus diversity to the north of the blue dotted line is lower than 578 species, and the genus diversity to the south of the blue dotted line is higher than 681 species. (d) The blue area is basically the dividing line of species diversity of 1385–1618 species. The species diversity to the north of the blue dotted line is lower than 1385 species, and the species diversity to the south of the blue dotted line is higher than 1618 species.Full size imageThe dataset can also count the orders, families and genera that appear in 58 nature reserves, indicating that these orders, families and genera are widely distributed in this area, while the orders, families and genera that only appear in a single nature reserve indicate that these taxa are unique to this nature reserve in this area, reflecting their locality and uniqueness, which is helpful to understanding the specific distribution of plants in detail. The relevant statistics are as follows:
There are 28 orders present in every nature reserve:
Liliales, Dipsacales, Lamiales, Fabales, Ericales, Poales, Saxifragales, Malpighiales, Malvales, Asterales, Fagales, Gentianales, Geraniales, Ranunculales, Rosales, Solanales, Apiales, Cornales, Brassicales, Caryophyllales, Dioscoreales, Santalales, Myrtales, Asparagales, Celastrales, Sapindales, Alismatales, and Boraginales.The order that only appears in one nature reserve is Petrosaviales, which appears in the Dabashan Nature Reserve in Chongqing.
There are 51 families present in every nature reserve:
Liliaceae, Primulaceae, Plantaginaceae, Lamiaceae, Euphorbiaceae, Cannabaceae, Juncaceae, Fabaceae, Poaceae, Elaeagnaceae, Betulaceae, Apocynaceae, Violaceae, Malvaceae, Crassulaceae, Campanulaceae, Asteraceae, Orchidaceae, Polygonaceae, Orobanchaceae, Onagraceae, Gentianaceae, Geraniaceae, Ranunculaceae, Rubiaceae, Rosaceae, Caprifoliaceae, Thymelaeaceae, Apiaceae, Cyperaceae, Cornaceae, Paeoniaceae, Brassicaceae, Amaryllidaceae, Caryophyllaceae, Rhamnaceae, Santalaceae, Asparagaceae, Celastraceae, Sapindaceae, Adoxaceae, Araliaceae, Berberidaceae, Hydrangeaceae, Scrophulariaceae, Convolvulaceae, Urticaceae, Salicaceae, Papaveraceae, Iridaceae, and Boraginaceae.There are 15 families that only appear in one nature reserve, as shown in Table 2.Table 2 Endemic families of the nature reserves in the Qinling-Daba Mountains and surrounding areas.Full size table
There are 54 genera present in every nature reserve:
Patrinia, Polygonum, Sanicula, Plantago, Allium, Delphinium, Euphorbia, Juncus, Cynanchum, Trigonotis, Artemisia, Sorbus, Polygonatum, Scutellaria, Cirsium, Viburnum, Ajuga, Viola, Galium, Geranium, Salix, Epilobium, Gentiana, Ranunculus, Malus, Acer, Rubia, Rosa, Torilis, Lonicera, Adenophora, Philadelphus, Cornus, Paeonia, Rhamnus, Rumex, Carex, Thalictrum, Asparagus, Carpesium, Clematis, Potentilla, Euonymus, Eleutherococcus, Berberis, Spiraea, Rubus, Populus, Vicia, Silene, Iris, Poa, Aster, and Buddleja.There were 225 genera that only appeared in one nature reserve, as shown in Figshare file 269.(2) For the “species endemic to China” variable of plants, we can see from the diversity distribution pattern of species endemic to China in this region (Fig. 4) that the number of endemic species in the Qinling-Daba Mountains is higher than that of species outside of the region, which reflects the strong transition zone in the Qinling-Daba Mountains. The variables of species endemic to China obtained from the Qinling-Daba Mountains and their surroundings were clustered by the Bray–Curtis dissimilarity measure70 and Ward’s minimum variance (the clustering method recommended for plant cluster analysis). The clustering results are shown in Fig. 5a. At the same time, the clustering results are displayed in space. Figure 5b shows that category 3 extends from the east outside the Qinling-Daba Mountains to the Baishuijiang Nature Reserve inside the western Qinling-Daba Mountains, which is consistent with the fact that the Qinling-Daba Mountains are an important ecogeographical “corridor” connecting the east and the west.Fig. 4Spatial distribution of diversity of species endemic to China in the Qinling-Daba Mountains and adjacent areas.Full size imageFig. 5(a) Clustering results of Ward’s connection aggregation of species endemic to China in 58 nature reserves. (b) Spatial distribution of clustering results of species endemic to China; the larger the dot and the darker the color, the earlier it is merged into this category, and the smaller the dot and the lighter the color, the later it is merged into this category.Full size image More

SamplesThe intestine and muscle samples from 22 wild boars were collected between September 4 and March 2, 2020, in Namie town in Fukushima prefecture. Furthermore, control intestine samples were collected from three wild boars in Hyogo prefecture. Each location is depicted in Fig. 1. In each case, after the licensed hunters slaughtered the wild boar to be exterminated, only the tissue was transferred to the study.Measurement of radioactivityRadioactivity in the muscle samples was determined by gamma-ray spectrometry using high-purity germanium (HPGe) detectors (Ortec Co., Oak Ridge, TN, USA), as described in our previous report3. Gamma rays from 137Cs were observed.Exposure dose estimationIn order to estimate internal and external dose rates of the wild boars according to the ICRP publication 10826, we supposed the shapes of wild boars as prolate spheroids whose long axis was to be their body lengths. The short axis was given from their weight assuming their specific gravities were the same
as water. The dose rates were calculated from the contribution of 137Cs, not including
natural radionuclides. The energy deposition to the spheroids by beta and gamma rays from radionuclides were calculated by the numerical simulation with the use of the Particle and Heavy Ion Transport code System (PHITS)27. For the sake of simplicity, we supposed the spheroids consisted of only muscle, which would give overestimated values because muscle contains more radio cesium than other organs. The external exposure dose was calculated from the air dose rates which were observed from the monitoring post near the boars captured place. The average values of the air dose rates were obtained from fitting observed data of two years with decay curve. The background due to the natural radionuclides was estimated to be 0.05 µGy/h which was observed before the Fukushima Daiichi accident, and was removed before the fittings. The half-lives of the air dose rates were 2000–3000 days depending on the environment. Assuming the external exposure dose was ascribed to the 137Cs included in the surface of the ground. The amount of the 137Cs was calculated so as to reproduce the observed air does rates. Since the maximum range of the beta ray from 137Cs is a few millimeters, almost all of the beta ray from inside the body should be absorbed in the boar’s body, but the beta ray from outside the body would stop in its fur. The beta rays contribute 100% to internal exposure dose but 0% to external one. Since the linear attenuation coefficient for gamma rays from 137Cs is 0.084 cm−1 = (12 cm)−1, some of the gamma rays cannot stop in the body depending on the size of the body. The numerical simulation suggested that 65–90 percent of the gamma rays from 137Cs inside the body would go out, and 40–65 percent of the gamma rays from 137Cs outside would go through the body.Pathological analysisA piece of the small intestine was fixed in 10% neutral formalin at 4 °C for 24–48 h. Then, paraffin blocks were prepared for pathomorphological examination using hematoxylin and eosin (HE) staining.Gene expression analysisTotal RNA was extracted from the whole tissue of the intestine using TRIzol Reagent (Life Technologies, Inc., Frederic, MD, USA) according to the manufacturer’s instructions. RNA concentration was measured using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA), and cDNA was synthesized using random primers and SuperScript II (Life Technologies, Inc.). Real-time PCR for IFN-γ, TLR3, and CyclinG1 was performed using Brilliant SYBR Green QPCR Master Mix III (Stratagene, La Jolla, CA, USA) with an AriaMx system (Agilent Technologies, Santa Clara, CA, USA). Primer sequences were designed using Primer-BLAST with sequences obtained from GenBank as described in the previous report4. Amplification conditions were 95 °C for 3 min, 40 cycles at 95 °C for 5 s, and 60 °C for 20 s. Fluorescence signals measured during the amplification were analyzed. Ribosomal RNA primers were used as an internal control, and all data were normalized to constitutive rRNA values. Quantitative differences between the groups were analyzed using the AriaMx software (Agilent Technologies).Statistical analysisAll data are presented as mean ± standard error (SE) for each treatment group. Differences in mRNA expression among the groups were determined using the unpaired t-test with Welch’s correction. (Prism: GraphPad Software Inc., La Jolla, CA, USA). Differences were considered to be statistically significant at a P value of  More