Philippa Kaur

DataSpatial gridWe created a grid whose units measure 250 m by 250 m based on the census tract layer for the city of Rio de Janeiro from the Instituto Brasileiro de Geografia e Estatística [Brazilian Institute of Geography and Statistics] (IBGE) website https://www.ibge.gov.br/geociencias/organizacao-do-territorio/malhas-territoriais. Uninhabited locations were excluded.Dengue cases on the gridDengue is a disease of compulsory notification in Brazil, and cases are notified at the Sistema de Informação de Agravos de Notificação [Information System on Diseases of Compulsory Declaration] (SINAN). Dengue cases notified in Rio de Janeiro between January 2010 and March 2015 were geocoded according to address of residency, and then counted for each grid unit by the Secretariat of Health of the city. We obtained the monthly dengue cases data aggregated at the grid level.Population on the gridThe population data is obtained from the Census 2010 (IBGE) (https://www.ibge.gov.br/estatisticas/downloads-estatisticas.html) and it is available at the census tract level. The census tract areas vary in size and can be bigger than the unit of the grid, primarily in the least densely populated zones of the city. To overcome this issue, we cropped from the census tract layer the areas classified as non-urbanized (such as water bodies, swamps, agricultural areas, green areas, beaches, rocky outcrops) in 2010 by the City Hall of Rio de Janeiro (layer available at http://www.data.rio/datasets/uso-do-solo-2010). The population of each census tract is distributed randomly (uniformly) in the areas obtained after deleting the non-urban areas. The population within the units is computed by adding the grid layer. To create the grid and edit the census tract layer we used QGIS (version 3.6.3)45, and to obtain the population in the grid we used the R software46 with the packages tidyverse47 and sf48. We verify the accuracy of our estimated population by comparison with the WordPop dataset49 (see detailed description and Supplementary Fig. 12 and Supplementary Note 2). We chose the WorldPop dataset because: (i) the estimates are also calculated based on census data and are available for 2010, (ii) the pixel size is 100 m, smaller than the size of our grid unit, and (iii) it is open access.Since the units are in fact small and most of them conserve their area of 250 m by 250 m (Supplementary Fig. 1A), we consider population density as the population of each unit. For consistency, we do not consider units with small effective areas and/or populations sizes less than, or equal to, 10 in our analysis. In total, 8954/20212 units were so excluded. This choice circumvents the problem of high sensitivity to random population distribution, and urban vs. non-urban classification, in very small and/or sparsely populated areas. It also facilitates model simulation and does not affect the peak ratio pattern (Supplementary Fig. 1B).Peak ratio and spatial aggregationSince units are small, we binned them into G groups and aggregated their times series of reported cases. The groups were generated according to two aspects: (1) the geographical location of the units as determined by the administrative divisions of the city (10 areas, 33 regions, and 160 neighborhoods); and (2) the population of the units based on quantiles in order to obtain equal size groups. We considered specifically four different partition levels, resulting in 12, 25, 50, and 100 groups with about 900, 450, 225, and 100 units, respectively (from a total number of 11,247 units for the whole city). Groups of unequal size can introduce different statistical effects (it is not the same, for example, to calculate a mean value using 1000 or 10 elements). To compare quantities across groups it is therefore prudent to define groups with the same number of elements. In particular, this consideration becomes important for a large number of groups. Since the population density distribution (number of individuals per unit) is not uniform, groups defined with “equidistant” boundaries would exhibit very different numbers of elements.Given a unit u, we define its time series ({{{{{{bf{v}}}}}}}_{{{{{{bf{u}}}}}}}={{c}_{u}({t}_{1}),{c}_{u}({t}_{2}),…,{c}_{u}({t}_{f})}), where ({c}_{u}({t}_{i})) is the number of reported cases of dengue at time ({t}_{i}) (i = 1, 2, …f) (and the bold symbol is used to indicate a vector). Thus, the aggregated time series is given by$${{{{{{bf{V}}}}}}}_{{{{{{bf{g}}}}}}}=mathop{sum}limits_{uin g}{{{{{{bf{v}}}}}}}_{{{{{{bf{u}}}}}}}={{C}_{g}({t}_{1})=mathop{sum}limits_{uin g}{c}_{u}({t}_{1}),{C}_{g}({t}_{2})=mathop{sum}limits_{uin g}{c}_{u}({t}_{2}),…,{C}_{g}({t}_{f})=mathop{sum}limits_{uin g}{c}_{u}({t}_{f})},$$with (g=1,2,…,G). Then, for each ({{{{{{bf{V}}}}}}}_{{{{{{bf{g}}}}}}}) we computed the ratio between the sizes of the second and first DENV4 peaks, that is$${{{{{rm{peakrati}}}}}}{{{{{{rm{o}}}}}}}_{{{{{{rm{g}}}}}}}=frac{{ma}{x}_{tin {season}2}{{C}_{g}({t}_{1}),{C}_{g}({t}_{2}),…,{C}_{g}({t}_{f})}}{{ma}{x}_{tin {season}1}{{C}_{g}({t}_{1}),{C}_{g}({t}_{2}),…,{C}_{g}({t}_{f})}}$$
(1)
(Supplementary Fig. 2).The deterministic SIR modelAlthough dengue is a vector-borne disease, for simplicity we omitted the explicit representation of the dynamics of the mosquito population, and treated vector transmission via the seasonality of the transmission rate26. Thus, for each unit u, the deterministic SIR model is based on the following traditional differential equations:$$frac{d{S}_{u}}{{dt}}=mu {N}_{u}-beta {S}_{u}frac{{I}_{u}}{{N}_{u}}-mu {S}_{u}$$$$frac{d{I}_{u}}{{dt}}=beta {S}_{u}frac{{I}_{u}}{{N}_{u}}-gamma {I}_{u}-mu {I}_{u}$$
(2)
$$frac{d{R}_{u}}{{dt}}={gamma I}_{u}-mu {R}_{u},$$where ({S}_{u},{I}_{u},{R}_{u}), are, respectively, the number of susceptible, infected, and recovered individuals, and ({N}_{u}) the number of inhabitants, of the spatial unit u. Parameter (mu) is the mortality rate (equal to the birth rate), and (gamma) is the recovery rate. The seasonal transmission rate is specified as (beta (t)={beta }_{0}(1+delta {{sin }},(omega t+phi ))). The units are considered independent of each other, and the initial conditions establish that the whole population of each unit is susceptible to the virus (({S}_{u}(t=0)={N}_{u}) and ({I}_{u}left(t=0right)={R}_{u}left(t=0right)=0forall u)). Transmission begins with one infected individual at a time ({t}_{0u}ge t=0) where ({t}_{0u}) is obtained from the data.Since the goal of this model is to examine the representative dynamics of different population densities, we binned the units according to their population into 12 groups, and computed the mean value of their number of inhabitants ({N}_{g}=langle {N}_{uin g}rangle) and of their arrival times of the infection ({t}_{0g}sim langle {t}_{0uin g}rangle) (where g = 1, …, 12). We then simulated the system considering the 12 sets ({{N}_{g},{t}_{0g}}) as given.The stochastic modelSince units will suffer local extinction of transmission, a major component of a stochastic implementation is the description of the local reintroduction of the virus, namely the arrival of a ‘spark’ or imported infection, in analogy to fire spread. Because space is described by a highly-resolved lattice, we considered that well-mixed transmission applies within each unit. Moreover, in lieu of  explicit spatial coupling between units, we postulated  the importation of infection through the specification of a spark rate.For this purpose, we constructed a binary representation of the time series of cases per month by defining the spatial units either as positive or negative according to whether they reported cases or not (Supplementary Fig. 3). Then, to derive a spark rate we explored the dynamics of the number of positive units as follows,$${U}^{{{mbox{+}}}}(t+{dt})={U}^{{{mbox{+}}}}(t)+{U}_{{{{{{{mathrm{new}}}}}}}}^{{{mbox{+}}}}(t,t+{dt})-{U}_{{{{{{{mathrm{extinct}}}}}}}}^{{{mbox{+}}}}(t,t+{dt})$$
(3)
The number of positive units at time ({t+dt}) is equal to the number of positive units at time t, plus the number of units that have been infected ({{U}_{{{{{{{mathrm{new}}}}}}}}}^{{{mbox{+}}}}(t,t+{dt})) between t and t + dt, minus the number of units that were infected at t but are no longer infected at t + dt (i.e., the number of ‘extinctions’ between t and t + dt, ({{U}_{{{{{{{mathrm{extinct}}}}}}}}}^{{{mbox{+}}}}(t,t+{dt}))).Since uninfected units (i.e., negative units) require the arrival of a spark to become positive, the following equation specifies the mean of ({{U}_{{{{{{{mathrm{new}}}}}}}}}^{{{mbox{+}}}}(t,t+{dt})) under the assumption that a small unit is unlikely to receive more than a single spark in a period of time dt$${{langle }}{U}_{{{{{{{mathrm{new}}}}}}}}^{{+}}(t,t+{dt}){{rangle }}simeq {N}_{{{{{{{mathrm{sparks}}}}}}}}(t,t+{dt})frac{{U}^{{-}}(t)}{U},$$
(4)
where ({N}_{{{{{{{mathrm{sparks}}}}}}}}(t,t+{dt})) is the number of sparks produced between t and t + dt, ({U}^{{{{-}}}}(t)) is the number of negative units at a time t, and (U) is the total number of units in the city ((U={U}^{{{mbox{+}}}}+{U}^{{{{-}}}})).By introducing Eq. (4) into Eq. (3) we obtain,$${U}^{{{mbox{+}}}}(t+{dt})simeq {U}^{{{mbox{+}}}}(t)+{N}_{{{{{{{mathrm{sparks}}}}}}}}(t,t+{dt})frac{{U}^{{{{-}}}}(t)}{U}-{{U}_{{{{{{{mathrm{extinct}}}}}}}}}^{{{mbox{+}}}}(t,t+{dt})$$
(5)
From Eq. (5) we can now compute the spark rate per unit ({{sigma }_{u}}^{{emp}}(t,t+{dt})) from the high-resolution incidence data as$${{sigma }_{u}}^{{emp}}(t,t+{dt})=frac{{N}_{{{{{{{mathrm{sparks}}}}}}}}(t,t+{dt})}{U}simeq frac{{U}^{{{mbox{+}}}}(t+{dt})-{U}^{{{mbox{+}}}}(t)+{U}_{{{{{{{mathrm{extinct}}}}}}}}(t,t+{dt})}{{U}^{{{{-}}}}(t)}$$
(6)
In order to address the effects of human density on the spark rate, we binned the spatial units according to their population into G groups. To avoid statistical effects due to group size, we considered population quantiles. Then, by applying Eq. (6) to each of these groups, we obtained an empirical spark rate per unit that depends on human density,$${sigma }_{uin g}^{{emp}}(t,t+{dt})={sigma }_{u}^{{emp}}(t,t+{dt}{{{{{rm{;}}}}}}{N}_{g}),$$
(7)
where ({N}_{g}={{langle }}{N}_{uin g}{{rangle }}) with g = 1, 2, …, G.SimulationsThe associated differential equations of the stochastic model are those shown on Eq. (2) but the transmission component has now an additional term ({sigma }_{u}) to describe the importation of infections.$$frac{d{S}_{u}}{{dt}}=mu {N}_{u}-left(beta {S}_{u}frac{{I}_{u}}{{N}_{u}}+{sigma }_{u}right)-mu {S}_{u}$$$$frac{d{I}_{u}}{{dt}}=left(beta {S}_{u}frac{{I}_{u}}{{N}_{u}}+{sigma }_{u}right)-gamma {I}_{u}-mu {I}_{u}$$
(8)
$$frac{d{R}_{u}}{{dt}}={gamma I}_{u}-mu {R}_{u}$$Since the inferred spark rate from the data (Eq. (7)) is obtained from observed infections, we computed the spark rate ({sigma }_{u}) as:$${sigma }_{uin g}={{{{{{mathrm{Poisson}}}}}}}({{sigma }_{uin g}}^{{emp}}/rho )$$
(9)
where (rho) is the reporting rate.The model shown on Eq. (8) was formulated as stochastic by incorporating demographic noise (with the different events represented as Poisson processes). It was implemented in R with the package pomp50. We also considered measurement error by assuming that the observed number of cases ({{C}_{u}}^{{obs}}) during a period of time T is,$${{C}_{u}}^{{obs}}left(Tright)={{{{{{mathrm{binomial}}}}}}}left(rho ,{C}_{u}left(Tright)right),$$
(10)
where ({C}_{u}(T)) is the number of cases computed in the unit u. We simulated the 11,247 units that compose the city of Rio de Janeiro, and aggregated the resulting time series as for the empirical data (see Peak ratio section).The parameters of the model are given in Supplementary Table 1. We relied on parameters estimated for dengue transmission in Rio de Janeiro by ref. 26. Those estimates were obtained for the aggregated city and for the emergence of DENV1. We use these parameters here as a sufficiently realistic set for illustrating and exploring the behavior of the stochastic model with population density. Moreover, with the exception of the spark rate, the model parameters were considered the same for all units. In particular, we applied a uniform reporting rate because access to the nearest public healthcare clinic does not show a dependency on population density (see Supplementary Note 1).Reporting summaryFurther information on research design is available in the Nature Research Reporting Summary linked to this article. More

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Plant materials, growth conditions and salt treatmentsSoil samples were performed as in previous experiments with S. europaea25, seeds were collected at two maternal sites, the first of which represents natural salinity related to inland salt springs at the health resort of Ciechocinek (Cie) (52°53′N, 18°47′E) characterised by a high soil salinity of ca 100 dS m−1 (~ 1000 mM NaCl), and the second of which is associated with soda factory waste that affects the local environment in Inowrocław-Mątwy (Inw) (52°48′N, 18°15′E) and with a lower salinity of ca 55 dS m−1 (~ 550 mM NaCl). The complete soil description is reported in Piernik et al.51 and Szymanska et al.52,53. Populations are isolated by a distance of ca 40 km without any saline environment between them, however, they were somehow connected due to the presence of salt springs in the nineteenth century. The seeds came from one generation and were collected in early November 2018. The seeds were germinated and grown according to the same steps reported in Cárdenas-Pérez et al.25 with a slight modification in the number of salt treatments at 0, 200, 400, 600, 800 and 1000 mM NaCl. In total, 144 plants were cultivated, and, therefore, a complete randomised factorial design 26 was used, which included (12 plants × 6 treatments × 2 populations) with 14 response variables. After 2 months of development, anatomical analysis such as cell area (A), roundness (R) and maximum cell diameter (Cdiam) were estimated in 12 samples, whereas high and low methyl esterified pectins (HM-HGs and LM-HGs), proline (P), hydrogen peroxide (HP), total soluble protein (Prot), catalase activity (CAT), peroxidase activity (POD), chlorophyll a, b and total (Cha, Chb and TC), carotenoid (Carot) contents, as well as SeNHX1 and SeSOS1 gene expression, were all determined per triplicate (plants were randomly selected). The collection of plant material, comply with relevant institutional, national, and international guidelines and legislation, IUCN Policy Statement on Research Involving Species at Risk of Extinction and Convention on the Trade in Endangered Species of Wild Fauna and Flora. The voucher specimen of the plant material has been deposited in a publicly available herbarium of the Nicolaus Copernicus University in Toruń (Index Herbarium code TRN), deposition number not available (dr. hab. Agnieszka Piernik, prof. NCU undertook the formal identification of plant species, and permission to work with the seeds was provided by the Regional Director of Environmental Protection in Bydgoszcz, WOP.6400.12.2020.JC).Anatomical image analysisFrom the middle primary branch (fleshy segment shoot) of S. europaea plant treatments (0, 200, 400, 600, 800 and 1000 mM NaCl), slices of fresh tissue were obtained by cutting them with a sharp bi-shave blade. The thinner slices of approximately 0.5 mm were selected and used in the microstructure analysis. The size and shape of the stem-cortex cells from the fresh water-storing tissue were characterised by a light microscope (Olympus BX51, USA) connected to a digital camera (DP72 digital microscope camera) and digital acquisition software (DP2-BSW). The microscope images were captured at a magnification of 10 ×/0.30 in RGB scale and stored in TIFF format at 1280 × 1024 pixels. A total of 300 ± 50 cells from five individuals per treatment were analysed. Finally, the shape and size of the cells were obtained from the captured images. Cell image analysis (IA) was performed in ImageJ v. 1.47 (National Institutes of Health, Bethesda, MD, USA). The following anatomical parameters were obtained. Firstly, the cell area (A) was estimated as the number of pixels within the boundary. Secondly, the maximum cell’s diameter (Cdiam) was determined by the distance between the two points separated by the largest coordinates in different orientations, and the cell roundness (R) was obtained through the equation R = (4 A)/(π (Cdiam)2)—where a perfectly round cell has R = 1.0, while elongated cells will show an R → 0. Finally, the degree of succulence (S) in stem was calculated according to24 with slight change S = (Fresh Weight-Dry Weight)/stem Area, where the Area of the stem (As) was calculated as: As = π × r2, the diameter of the stems was obtained according to Cárdenas-Pérez et al.25.Immunolocalisation experimentsThe samples dissected from the middle segment of the shoot (3 individuals per treatment) were prepared for embedding in BMM resin (butyl methacrylate, methyl methacrylate, 0.5% benzoyl ethyl ether (Sigma) with 10 mM DDT (Thermo Fisher Scientific) according to Niedojadło et al.54. Next, specimens were cut on a Leica UCT ultramicrotome into serial semi-thin cross sections (1.5 µm) that were collected on Thermo Scientific Polysine adhesion microscope slides. Before immunocytochemical reaction, the resin was removed with two changes of acetone and washed in distilled water and PBS pH 7.2. After incubation with blocking solution containing 2% BSA (bovine serum albumin, Sigma) in PBS pH 7.2 for 30 min at room temperature, the sections were incubated with anti-pectin rat monoclonal primary antibody JIM7 (recognises partially methylesterified epitopes of homogalacturonan [HG] but does not bind to fully de-esterified HGs) or antibody LM19 (recognises partially methylesterified epitopes of HG and binds strongly to de-esterified HGs) (Plant Probes) diluted 1:50 in 0.2% BSA in PBS pH 7.2 overnight at 4 °C. After washing with PBS pH 7.2, the material was incubated with AlexaFluor 488-conjugated goat anti-rat secondary antibody (Thermo Fisher Scientific) diluted 1:1000 in 0.2% BSA in PBS pH 7.2 for 1 h at 37 °C. Finally, the sections were washed in PBS pH 7.2, dried at room temperature and covered with ProLongTMGold antifade reagent (Thermo Fisher Scientific). The control reactions were performed with the omission of incubation with primary antibodies. Semithin sections were analysed with an Olympus BX50 fluorescence microscope, with an UPlanFI 1009 (N.A. 1.3) oil immersion lens and narrow band filters (U-MNU, U-MNG). The results were recorded with an Olympus XC50 digital colour camera and CellB software (Olympus Soft Imaging Solutions GmbH, Germany).Fluorescence quantitative evaluationFor the quantitative measurement, each experiment was performed using consistent temperatures, incubation times and concentrations of antibodies. The aforementioned ImageJ (1.47v) software was used for image processing and analysis. The fluorescence intensity was measured for five semi-thin sections for each experimental population (Inowrocław and Ciechocinek) at the same magnification (100 ×) and the constant exposure time to ensure comparable results. The threshold fluorescence in the sample was established based on the autofluorescence of the control reaction. The level of signal intensity was expressed in arbitrary units (a.u.) as the mean intensity per μm2 according to Niedojadło et al.54.Biochemical analysisProline content (P) was measured according to Ábrahám et al.55. Five hundred milligrams of fresh stem material was minced on ice and homogenised with 3% aqueous sulfosalicylic acid solution (5 μl mg−1 fresh plant material), centrifuged at 18,000×g, 10 min at 4 °C, and the supernatant was collected. The reaction mixture: 100 μl of 3% sulphosalicylic acid, 200 μl of glacial acetic acid, 200 μl of acidic ninhydrin reagent and 100 μl of supernatant. Acidic ninhydrin reagent was prepared according to Bates et al.56. The standard curve for proline in the concentration range of 0 to 40 μg ml−1. The standard curve equation was y = 0.0467x − 0.0734, R2 = 0.963. P was expressed in mg of proline per gram of fresh weight. Hydrogen peroxide (HP) levels were determined according to the methods described by Velikova et al.57, and 500 mg of stem tissues were homogenised with 5 ml trichloroacetic acid 0.1% (w:v) in an ice bath. The homogenate was centrifuged (12,000×g, 4 °C, 15 min) and 0.5 ml of the supernatant was added to potassium phosphate buffer (0.5 ml) (10 mM, pH 7.0) and 2 ml of 1 M KI. The absorbance was read at 390 nm, and the HP content was given on a standard curve from 0 to 40 mM. The standard curve equation was y = 0.0188x + 0.046, R2 = 0.987. HP concentrations were expressed in nM per gram of fresh weight. Chlorophylls (Cha and Chb) and carotenoids were extracted from fresh plant stems (100 mg) using 80% acetone for 6 h in darkness, and then centrifuged at 10,000 rpm, 10 min. Supernatants were quantified spectrophotometrically. Absorbance was determined at 646, 663 and 470 nm and calculations were performed according to Lichtenthaler and Wellburn58, when 80% of acetone is used as dissolvent. Total chlorophyll content was calculated as the sum of chlorophyll a and b contents.Total CAT activity was determined spectrophotometrically by following the decline in A240 as H2O2 (ε = 39.9 M−1 cm−1) was catabolised, according to the method of Beers and Sizer59. Decrease in absorbance of the reaction at 240 nm was recorded after every 20 s. One unit CAT was defined as an absorbance change of 0.01 units min−1. Total POD activity was determined spectrophotometrically by monitoring the formation of tetraguaiacol (ε = 26.6 mM−1 cm−1) from guaiacol at A470 in the presence of H2O2 by the method of Chance and Maehly60. Increase in absorbance of the reaction solution at 470 nm was recorded after every 20 s. One unit of POD activity was defined as an absorbance change of 0.01 units min−1. Total soluble protein (Prot) content was measured according to Bradford61 using bovine serum albumin (BSA) as a protein standard. Fresh leaf samples (1 g) were homogenised with 4 ml Na-phosphate buffer (pH 7.2) and then centrifuged at 4 °C. Supernatant and dye were pipetted in spectrophotometer cuvettes and absorbances were measured using a UV–vis spectrophotometer (PG instruments T80) at 595 nm62. Prot was determined based on the standard curve y = 1.6565x + 0.0837, R2 = 0.982, for total soluble protein in the concentration range of 0 to 1.2 mg ml−1 BSA. Triplicates per treatment were used for each analysis.Total RNA isolationAfter 2 months of salt treatment, shoots of S. europaea plants (3 individuals per treatment) were washed several times with tap water and then three times with miliQ water. After drying, plant material was frozen in liquid nitrogen, and stored at − 80 °C. Total RNA isolation was performed using RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. The quality and quantity of RNA was checked on 1.5% agarose gels in TAE (Tris–HCl, acetic acid, EDTA, pH 8.3) buffer stained with ethidium bromide, and by spectrophotometric measurement (NanoDrop Lite, Thermo Fisher Scientific, Waltham, MA, USA).Cloning of SOS1 gene from S. europaea (SeSOS1)One microgram (1 µg) of total RNA isolated from shoots of S. europaea was primed with 0.5 µg of oligo (dT)20 primer for 5 min at 70 °C. Then 4 µl of ImProm-II 5 × reaction buffer, 2 mM MgCl2, 0.5 mM each dNTP, 20 U of recombinant RNasin ribonuclease inhibitor, and 1 µl of ImProm-II reverse transcriptase (Promega, Madison, WI, USA) were added to a final volume of 20 µl. The reaction was performed at 42 °C for 60 min. To design degenerate primers for SOS1, cDNA sequences from Arabidopsis thaliana (NM_126259.4), Lycopersicon esculentum (AJ717346.1), Mesembryanthemum crystallinum (EF207776.1), Oryza sativa (AY785147.1), Triticum aestivum (AY326952.3), Salicornia brachiata (EU879059.1) were obtained from NCBI GeneBank. The sequences were aligned using the Clustal Omega tool (https://www.ebi.ac.uk/Tools/msa/clustalo/) and three pairs of degenerate primes were designed (listed in Table 4). The PCR reaction mixture includes cDNA, 0.2 µM each primer, 0.2 mM each dNTP, 4 µl of 5 × HF buffer, and 0.5 U of Phusion High-Fidelity DNA polymerase (Thermo Fisher Scientific, Waltham, MA, USA) in a total volume of 20 µl. The thermal conditions were as follows: 98 °C for 30 s, 98 °C for 10 s, gradient between 48 °C and 56 °C for 20 s, 72 °C for 60 s, 32 cycle, final extension for 10 min at 72 °C. A pair of primers deg2_F and deg2_R yielded a PCR product with expected size. The PCR product was purified from agarose gel, cloned into pJET1.2 vector (Thermo Fisher Scientific, Waltham, MA, USA) according to manufacturer’s protocol and sequenced (Genomed, Warsaw, Poland). The obtained partial cDNA sequence was named SeSOS1 and deposited in NCBI GeneBank (acc. no. MZ707082).Table 4 Sequences of the primers used for cloning of SeSOS1 and quantitative real-time PCR.Full size tableReverse transcription reaction and quantitative real-time PCR (qPCR) SeNHX1 and SeSOS1 gene expression analysisPrior to reverse transcription reaction, RNA was treated with DNaseI (Thermo Fisher Scientific, Waltham, MA, USA). The cDNA was synthesised from 1.5 µg of total RNA using a mixture of 2.5 µM oligo(dT)20 primer and 0.2 µg of random hexamers with NG dART RT Kit (Eurx, Gdańsk, Poland) according to the manufacturer’s protocol. The reaction was performed at 25 °C for 10 min, followed by 50 min at 50 °C. The cDNA was stored at − 20 °C.The PCR reaction mixture includes 4 µl of 1/20 diluted cDNA, 0.5 µM gene-specific primers (Table 4) and 5 µl of LightCycler 480 SYBR Green I Master (Roche, Penzberg, Germany) in a total volume of 10 µl. Clathrin adaptor complexes (CAC) was used as a reference gene63. The reaction was performed in triplicate (technical replicates) in LightCycler 480 Instrument II (Roche, Penzberg, Germany). The thermal cycling conditions were as follows: 95 °C for 5 min, 95 °C for 10 s, 60 °C for 20 s, 72 °C for 20 s, 40 cycles. The SYBR Green I fluorescence signal was recorded at the end of the extension step in each cycle. The specificity of the assay was confirmed by the melt curve analysis i.e., increasing the temperature from 55 to 95 °C at a ramp rate 0.11 °C/s. The fold-change in gene expression was calculated using LightCycler 480 Software release 1.5.1.62 (Roche, Penzberg, Germany).Statistical and multivariate analysisIn order to determine the projection of the effect of salt treatment in plants we followed Cárdenas-Pérez et al.25 methodology. A principal component analysis (PCA) was developed using XLSTAT software version 2019.4.165. For this analysis, 14 variables were used, (A, Cdiam, R, Prot, CAT, POD, HM-HGs, LM-HGs, P, HP, Cha, Chb, TC, Carot), arranged in a matrix with the average values obtained from replicates of each treatment and population. A two-way ANOVA comparing treatments within populations and populations within treatments was conducted for all the results with the Holm–Sidak method. The data was fit with a modified three parameter exponential decay using SigmaPlot version 11.066. The relationships between variables were performed using a Pearson analysis, while a significance test (Kaisere Meyere Olkin) was performed in order to determine which variables had a significant correlation with each other (α = 0.05). Then, a 3D plot was developed using the three principal component factors according to the Kaiser criterion which stated that the factors below the unit are irrelevant. The three main factorial scores of the PCA from each sample were used to calculate the distance (D) between the two points (populations) under the same treatment P1 = (x1, y1, z1) and P2 = (x2, y2, z2) in 3D space of the PCA (Eq. 1).$$D ( {P_{1} ,, P_{2} } ) = sqrt {( {x_{2} – x_{1} } )^{2} + ( {y_{2} – y_{1} } )^{2} + ( {z_{2} – z_{1} } )^{2} }$$
(1)
where x, y, and z are the three main factorial scores in the PCA corresponding to the evaluated treatment in Inw and in Cie. Distances were used to evaluate and determine in which salt treatment the greatest differences between the populations were recorded. More

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Study islands and bird dataSystematic ringing in spring on Mediterranean islands has been promoted by the Piccole Isole project since 198826. Standard methods of the project involve ringing between 16th April and 15th May attempting to include the peak of the spring passage of long-distance migrants. Ringing is performed from dawn to nightfall using a constant number of nets within ringing stations placed at stable sites located at representative habitats in each island (Supplementary Table S1). The use of tape-lures is not allowed. We have compiled ringing data for all the Spanish Mediterranean islands that have been applying this methodology, with the exception of Mallorca and Menorca where the ringing stations were located in wetlands and captured a large percentage of local birds (Fig. 2, Table 1). The nine study islands are spread along a south-west to north-east gradient and, with the exception of Columbrets, they are distributed in pairs of similar longitude but different latitudes (Fig. 2). Ringing stations have been operating over a variable number of years (5–27 years), with the maximum number of ringing stations operating at the same time occurring between 2003 and 2010. To include between-year variation on islands that started ringing campaigns more recently we used data from the years 2003–2018.Figure 2Image source: Google Earth. Data SIO, NOAA, US Navy, NGA, GEBCO. Image Landsat/Copernicus.Geographical location of studied islands in the western Mediterranean.Full size imageTable 1 Period of activity of the ringing stations located on each island between the years 1992 and 2018.Full size tableThe ringing period within each spring also varied in most islands, owing to funding or logistic limitations; thus, to reduce the possible effects on migrant composition we only used data from the standard period of the Piccole Isole project and from years that included at least one week of ringing in the fortnight of each month within this interval. This procedure excluded the use of some years for several islands, and the final number of data years for islands ranged between 5 and 16 (Table 1).We used only data for trans-Saharan nocturnal migrant passerines, which form the bulk of species ringed on Mediterranean islands during the standard period. The standard ringing period only covers the tail end of the short-distance migrants’ passage; thus, these species were excluded as their contribution to composition of migrants could vary mainly due to between-year variation in migration phenology. Diurnal migrants, like hirundinids and fringillids, also represent a small fraction of birds ringed and may use different cues to select stopover islands. In addition, some of these species nest in some of the islands studied and birds ringed could include breeding birds. To avoid the distorting effect of species that are captured accidentally in very small numbers, we considered only the species that were ringed in at least five separate years, or on five different islands, which limited the species considered to 35 (Supplementary Table S2). This led to the exclusion of just two species (Ficedula semitorquata with three individuals ringed in two islands and Locustella luscinioides with one individual ringed in Aire island). In addition, we only considered the number of ringed birds, since the proportion of recaptures varies among islands, likely reflecting variation in the duration of stopovers21, which could bias the comparison of the patterns of migrant species composition.Island descriptorsWe obtained two groups of variables describing the characteristics of the study islands (Tables 2, 3): (1) Variables related to geographical location: latitude, longitude, straight distance and minimum distance to the North African coast, minimum distance to the closest large body of land (continent or large island) in any direction and to the closest large body of land situated in a southerly angle between SW and SE. (2) Variables related to the habitat characteristics of the islands: area, maximum altitude and Normalized Difference Vegetation Index (NDVI). We estimated NDVI from Landsat 8 Images taken during the standard ringing period in the years 2015 and 2016. Pixels containing shoreline were excluded and the average NDVI was calculated for the rest of the pixels.Table 2 Variables describing the characteristics of the islands that included the ringing stations studied.Full size tableTable 3 Values of the island descriptors (see Table 2) and two measures of temporal variability of migrant composition in each island: average local contribution of each island to beta diversity (LCBD) and beta diversity for each island (BDTi).Full size tableContinental abundance dataAbundance estimates for western Europe were obtained from the European Red List of Birds27. We used the mean of the minimum and maximum number of pairs estimated for the 27 EU Member States as a measure of continental abundance (Supplementary Table S2).Data analysisAll analyses were done using R 3.6.128. We built a matrix of island-year x species containing the number of individuals of each selected species ringed in the study period in each island and year. Average number of individuals of each species ringed at each island was calculated and was used (log-transformed) as a dependent variable in a linear model with continental abundance (log-transformed), island and their interaction as predictors. This model was simplified using AICc as criteria to identify the best model.To analyze variation of species composition, the matrix of island-year x species was transformed using the chord transformation29 with the function decostand in the vegan package30.Using the function beta.div of the adespatial package31 we calculated beta diversity, including temporal and between-island variability (BDI,T), as the total variance of the aforementioned transformed matrix (BDTotal in29), which varies between 0 and 1 when chord distance is used. Considering that yijk is the chord transformed abundance of the species j in the island i and year k and (overline{{y }_{j}}) is the mean for species j in all islands and years altogether, then:$${SS}_{Total}=sum_{i=1}^{n}sum_{j=1}^{p}{sum_{k=1}^{q}{({y}_{ijk}-{overline{y} }_{j})}^{2}}$$$$BD_{I,T} = , SS_{Total} /left( {N – 1} right)$$where N is the total number of samples. The function beta.div also provides an estimation of contribution of localities (LCBD) and species (SCBD) to beta diversity (Table 3). Yearly LCBD (log transformed because of skewed distribution) of each island were averaged and compared between islands using ANOVA and a post-hoc Tukey test.We partitioned the above sum of squares in several ways. First, we calculated a beta diversity that considered only between-island variability, excluding temporal variability (BDI), by averaging the chord transformed abundances of each species j in each island along study years (({overline{y} }_{ij})) and applying the same procedure, but using the number of studied islands (n):$${SS}_{I}=sum_{i=1}^{n}sum_{j=1}^{p}{{({overline{y} }_{ij}-{overline{y} }_{j})}^{2}}$$$$BD_{I} = SS_{I} /left( {n – 1} right)$$Second, we calculated a beta diversity due to inter-annual variation of migrant composition within islands (BDT) as:$${SS}_{Temp}=sum_{i=1}^{n}sum_{j=1}^{p}{sum_{k=1}^{q}{({y}_{ijk}-{overline{y} }_{ij})}^{2}}$$$$BD_{T} = SS_{Temp} /left( {Y – n} right)$$where Y is the total number of study years and n is the number of studied islands (9). We also calculated a temporal beta diversity for each island i (BDTi) as the sum of squares due to variation within the island divided by the number of the island study years (Yi) minus 1:$${SS}_{Temp,i}=sum_{j=1}^{p}sum_{k=1}^{q}{({y}_{ijk}-{overline{y} }_{ij})}^{2}$$$$BD_{Ti} = SS_{Temp,i} /left( {Y_{i} – 1} right)$$Differences in temporal variability between islands could be due to different predominance of species that are more or less variable between years. To check this, we calculated Spearman’s rank correlation between the percentage of captures of each species in the total ringed on each island and BDTi and LCDB indices, for species present on all islands.We tested for the existence of differences between islands in migrant species composition using Permutational Multivariate Analysis of Variance (PERMANOVA) using the function adonis2 in the vegan package. We performed a multivariate test of homogeneity of variances using the betadisper function (vegan package) with the adjustment for small sample bias, to test if temporal variability in species composition differed between islands. We made post-hoc comparisons between islands with False Discovery Rate (FDR) correction using the function pairwise.perm.manova of the package RVAideMemoire32.To identify gradients in migrant species composition and the island characteristics that were associated with them, we employed Redundancy Analysis using the rda function (vegan package). We used the chord transformed matrix of species x island-year as a response matrix. We used two explanatory matrices, one including variables of geographical location and the other the variables related to habitat characteristics of the islands. We evaluated the relative importance of each group of variables to explain migrant species composition by performing a variation partitioning analysis, using the varpart function (vegan package). For that analysis, we followed the steps and R scripts recommended in33.Variables describing island characteristics were transformed using natural logarithms and collinearity within each group was evaluated with variance inflation factor (VIF)34. All the habitat variables presented VIF  More

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