BUSCADOR RECOLECTA

Maps and diagrams of reproduction 1, 2 and 3., Peer reviewed

Materials and methods: Identification of α-1,3-galactosyltransferase genes in bird microbiome. Determination of anti-α-Gal antibodies in eggs. Experimental Plasmodium infection of birds. Determination of anti-α-Gal Abs in sera samples. Quantification of α-Gal levels on different Plasmodium species., Peer reviewed

2 pages. -- Supplementary Table 1. Experiment husbandry schedule. Amount of daily feed offered, shading concentration (Nannochloropsis sp.) and recirculation flow changes with time are shown (Imentai, et al., 2020). -- Supplementary Table 2. Oligonucleotides used for QPCR., The present study investigates the effects of different feeding regimes with rotifers (Brachionus plicatilis) and Artemia salina on the gene expression and digestive enzymes in pikeperch (Sander lucioperca) larvae at 17 days post-hatch (DPH) over a period of 13 days. Five experimental feeding protocols were performed in four replicates. At 4 DPH, the larvae (total length= 5.62 ± 0.03 mm, body weight = 0.66 ± 0.16 mg) were divided into five experimental groups (2-L tanks) at initial density of 100 larvae per liter. Light intensity on the water surface was 90-100 lux and photoperiod was set at 13L: 11D (07:00 to 20:00 h). Water temperature, pH, and dissolved oxygen (DO) were measured before each feeding and the values were 17.8 ± 0.17°C, 7.3 ± 0.04 and 88.5 ± 2.53%. The fish larvae at 5 days post-hatch (DPH), were initially fed with rotifers (Brachionus plicatilis) for 3 days and from 8 to 17 DPH were fed with rotifers/Artemia for different time periods as follows: (A) only rotifers; (B) 8–13 DPH rotifers/14–17 DPH Artemia; (C) 8–10 DPH rotifers/11–17 DPH Artemia; (D) only Artemia; (E) a combination of rotifers and Artemia. Frozen paste of algae was added to the larval tanks twice a day (2 x 300,000 cells/mL). Rotifers and Artemia were provided as live feed to larvae three times a day with residual counts prior to each feeding. Feeding densities were steadily increased based on residual counts, performed prior to each feeding. The expression of genes related to intestinal development and maturation (aminopeptidase N, anpep; leucine aminopeptidase 3, lap3; intestinal-type alkaline phosphatase, alpi), together with key pancreatic digestive proenzymes (trypsinogen 1, try1; chymotrypsinogen b, ctrb; carboxyl ester lipase precursor, cel; phospholipase a2, pla2g1b; pancreatic alpha amylase, amy2a), were assessed. Additionally, the activity of six enzymes (trypsin, lipase, alkaline phosphatase, amino peptidase, amylase, and chymotrypsin) were determined. The highest expression of two genes related to intestine (lap3; anpep) were observed in the fish fed a combination of rotifers and Artemia from 8 DPH (Group E). The expression of amy2a, ctrb, pla2g1b, try1 was significantly lower in larvae fed rotifers until 14 DPH and replaced by Artemia afterwards (Group B). The specific activity of brush border membrane enzymes (alkaline phosphatase and aminopeptidase N) increased with combination of rotifers and Artemia in larval diet (Group E), indicating a more efficient functionality of digestive structures. The groups fed only with rotifers till 17 DPH (Group A) (38 ± 4.07%) and larvae fed with rotifers till 14 DPH followed by feeding with Artemia till 17 DPH (Group B) (36 ± 5.25%) showed significantly (P<0.05) lower survival rates than the other groups (54-67%). The group fed only with rotifers (Group A) showed significantly lower specific growth rate (SGR) than the other groups, and the highest SGR was found in the group fed with combination of rotifers and Artemia after 3 day rotifer feeding (Group E). The highest standard length (8.32 ± 0.48 mm) was obtained by combined feeding of rotifers and Artemia after 3 day of initial rotifer feeding. Combination of rotifers and Artemia from 8 DPH (Group E) could be considered a more appropriate diet for first feeding pikeperch larvae compared with later introduction of Artemia, as indicated by the higher expression of genes and activities of digestive enzymes. Our findings provide new insight into the effect of temporal sequence of rotifers and Artemia on the expression of genes and activities of digestive enzymes in pikeperch larvae., Peer reviewed

Table S1. Compounds studied and standard supplier. Table S2. LC-MS/MS conditions and quality parameters for the analysis of pharmaceuticals (ordered by retention time: R.T.), indicating quantification (Q) and confirmation (q) transitions, Collision Energy (C.E.), the response Factor (F) of the calibration curve, Instrument Detection Limit (IDL), Method Detection Limit (MDL), intra-day precision (%, n=5), inter-day precision (%, n=5) and percentage recovery with standard deviation (%R±SD). Coefficient of determination (R2) was 0.99 for all compounds over a concentration range of 0.001-0.6 ng/µL. Table S3. LC-MS/MS conditions and quality parameters for the analysis of pesticides and OPEs (*) (ordered by retention time: R.T.), indicating quantification (Q) and confirmation (q) transitions used, Collision Energy (C.E.), the response Factor (F) of the calibration curve, Instrument Detection Limit (IDL), Method Detection Limit (MDL), intra-day precision (%, n=5), inter-day precision (%, n=5) and percentage recovery with standard deviation (%R±SD). Coefficient of determination (R2) was 0.99 for all compounds over a concentration range of 0.001-0.6 ng/µL. Table S4. LC-MS/MS conditions and quality parameters for the analysis of PFAS (ordered by retention time: R.T.), indicating quantification (Q) and confirmation (q) transitions used, Collision Energy (C.E.), the response Factor (F) of the calibration curve, Instrument Detection Limit (IDL), Method Detection Limit (MDL), intra-day precision (%, n=5), inter-day precision (%, n=5) and percentage recovery with standard deviation (%R±SD). Coefficient of determination (R2) was 0.99 for all compounds over a concentration range of 0.001-0.6 ng/µL. Figure 1. UPLC-MS/MS chromatogram of a pharmaceuticals standard at 0.6 ng/µL. Figure 2. UPLC-MS/MS chromatogram of a pesticide and organophosphoshate ester standard at 0.6 ng/µL. Figure 3. UPLC-MS/MS chromatogram of a perfluoroalkyl substances standard at 0.6 ng/µL., Peer reviewed

Table S1a. Summary of main findings of the 34 studies reviewed that assessed the relationship between European Turtle Dove abundance (in the broad sense, including density, variation in numbers, etc.) and occurrence with habitat. Table S1b. Summary of main findings of the 34 studies reviewed that assessed the relationship between European Turtle Dove abundance (in the broad sense; some studies assessed density, others used measures of relative abundance, trends, etc.) and occurrence with habitat. Results of direct comparison between habitats, and favourable elements in each major habitat type. Table S2. Plant taxa whose seeds have been reported as ingested by turtle dove. Table S3. Relative importance of the 40 environmental predictors of the eight Species Distribution Models for Streptopelia turtur in the second European Breeding Bird Atlas, EBBA2 (Keller et al. 2020) and their weighted Ensemble Prediction. Variable importance ranges between 0 (no importance) to 100 %., Peer reviewed

3 pages. -- Figures and tables. -- Table S1. List of Posidonia oceanica rhizome samples analyzed for the different organic components of ultra-violet filters (UVFs) and paraben conservatives. -- Table S2. Limits of detection and quantification, and precision (relative standard deviation, RSD%) of the analyses of the different ultra-violet filters (UVFs) and paraben conservatives. -- Figure S1. Map of the study site indicating the location of the sampling points. -- Figure S2. Morphology of the seagrass Posidonia oceanica, detailing the structure of the peeled rhizome., Peer reviewed

Table A.1: Most important crops (> 1000 ha) in the V (mid-west) administrative region of Navarra (130,000 ha) in 2007, 2019 and their change (in ha and %) along the survey period, broken down by each crop’s rain-fed and irrigated surface. Table A.2: Number of irrigated and non-irrigated points sampled each year during the survey period. Figure A.1: Species-level occurrence probabilities: a) before irrigation (excluding control sampling locations); and b) after irrigation was implemented. Species are organized by habitat classification: farmland, shrubland, (R) rocky habitat specialist species, (Fo) forest habitat specialist species, (W) wetland habitats specialist species, (U) urban habitat specialist species, and non-specialist. The short horizontal black lines show means, the boxes show 50% credible intervals (CI) and the vertical lines show the 95% CI. Figure A.2: Effect of arable land surface on species occurrence probabilities organized by habitat classification: farmland, shurbland, (R) rocky habitat specialist species, (Fo) forest habitat specialist species, (W) wetland habitats specialist species, (U) urban habitat specialist species, and non-specialist. The short horizontal black lines show the mean value (across MCMC iterations), the boxes show the 50% credible intervals (CI), and the vertical lines delineate the 95% CI. Light grey indicates no effect of arable land on occurrence probability, orange (negative effect) and blue (positive effect) indicate that the 50% CI does not overlap zero but the 95% CI does overlap zero, and red (negative effect) and dark blue (positive effect) indicate that the 95% CI does not overlap zero. Figure A.3: Detection probability by: a) hour; and b) date. The black lines show the mean values across all species analysed (with shaded 50% and 95% credible intervals). Light grey lines show the detection probabilities of each species included in the analysis. JAGS model code: Multi-species hierarchical occurrence model with a BACI design., Peer reviewed

The datasets are reported in the supplementary material Tables S1-S4., Table S1. Summary of the distributions of the proportion of the population harvested each year and supporting data. Figure S1. Histogram and probability density of the estimated proportion of the population harvested each year, autocorrelation and trace plots. Table S2. Summary of the estimated distributions of abundance and supporting data at each site. The Geweke test was -0.557 (P=0.577) for the wild boar and 1.085 (P=0.278) for the red deer models. Figure S2. Histogram and probability density of the abundance estimated at each site, autocorrelation and trace plots of the Markov Chain Monte Carlo simulations. Table S3. Summary of the estimated distributions and supporting references for the sensitivity and specificity of the diagnostic tests. Figure S3. Histogram and probability density of the estimated sensitivity and specificity of the diagnostic tests employed, autocorrelation and trace plots of the Markov Chain Monte Carlo simulations. Table S4. Summary of the estimated distributions of the true prevalence by host species and supporting data at each study site. Figure S4. Histogram and probability density of the estimated true prevalence at each site, autocorrelation and trace plots of the Markov Chain Monte Carlo simulations. Figure S5. Histogram and probability density of the estimated probability of Mycobacterium tuberculosis complex excretion from infected wild boar and red deer, autocorrelation and trace plots of the Markov Chain Monte Carlo simulations. Table S5. Summary of the estimated distributions of the R0 by host species at each study site. Figure S6. Histogram and probability density of the estimated R0 by host species at each study site, autocorrelation and trace plots of the Markov Chain Monte Carlo simulations. For intelligibility, only R0 estimates <200 were plotted. Table S6. Probability of animal tuberculosis being a single-host or multi-host disease at each site. Probabilities derived from the 100,000 estimates of the R0 of Mycobacterium tuberculosis complex in each host species. Single maintenance host: only one species with R0>1; Obligatory multi-host: R0 both species<1; Facultative multi-host: R0 both species >1. Highest probability for each site is highlighted in bold. Figure S7. Diagnostic plots of the generalised linear models. Diagnostic plots for the wild boar, red deer, and multi-host models with the whole dataset and after removing one influential outlier (site 15). Table S7. Summary of the generalised linear model selection. Models with ΔAICc<2 from the most supported model. Figure S8. Basic reproduction number estimated for the wild boar and red deer in each of the study sites. Kernel density of 100 estimates of the R0 of Mycobacterium tuberculosis complex in the wild boar and red deer drawn randomly from the 100,000 estimates at each site. Axes in square root scale, R0=1 as blue horizontal and vertical lines., Peer reviewed

9 pages. -- Figure S1: SDS‐PAGE of the various APE1 variants. -- Figure S2: (A) Far‐UV spectra of the different APE1 variants: unlabelled (black), Cy3‐APE1 (magenta), Cy5‐APE1 (cyan) and doubly labelled (purple). The protein concentration was 4 mM in buffer 20 mM potassium phosphate pH 7.0, 50 mM NaCl, 5 mM MgCl2. (B) Thermal denaturation profiles as based on the change in ellipticity at 222 nm in the absence (solid line) and presence (broken line) of an equimolar amount of product DNA. The scan rate was 1ºC / min. -- Figure S3: Binding of labelled APE1 to the oligonucleotides mimicking the abasic product (P) and substrate (S). -- Figure S4: Incision kinetics of 2 mM substrate DNA by the various APE1 variants as followed by 18% polyacrylamide‐urea gel electrophoresis. -- Figure S5: Sequence of the oligonucleotides used as model of the abasic APE1 product (left) and substrate (right), highlighting the two labelled thymines. X stands for tetrahydrofurane. -- Figure S6: Original prediction as obtained with AlphaFold of human APE1 (UniProt entry P27695), represented as a cartoon, and aligned to the DNA part (grey sticks) of crystal structure 5DFF [17]. -- Figure S7: Emission spectra of doubly labelled APE1 (black line) and Cy5‐APE1 (cyan solid line) upon excitation at 547 nm. Spectrum of Cy5‐APE1 with exc 647 nm (cyan broken line). -- Figure S8: Charge distribution in full‐length APE1 bound to DNA., Peer reviewed

Supplementary contents: Appendix A: Additional results of carnivore environmental favourability in Andalusia. Appendix B: Data on drivers threatening terrestrial carnivores in Andalusia used in General Linear Modelling. Appendix C: Additional results of multiple drivers influence changes in carnivore environmental favourability in Andalusia. Supplementary references., Peer reviewed