BUSCADOR RECOLECTA

We include information (raw Datasets) corresponding to the paper; Adaptation of Mediterranean forest species to climate: lessons from common garden experiments. Table Journal of Ecology Review.xls. Material used in the metaanalysis JoE Row data Common garden.xls. Raw data for survival and height used in the study. Multi-environment commong garden data for Pinus canariensis, P. halepensis, P. nigra, P. pinaster, Quercus ilex, and Q. suber. JoE Dataset4.xls. Data used for the analysis of local adaptation., Techcnial assitance in Data measurements: del Caño, F, Barba D, Chambel R. Data adquisiton was funded by the Spanish Ministry of Agriculture (AEG-17-048) and the Spanish Ministry of Science (RTI2018-094691-B-C32)., Peer reviewed

Longidorid nematodes comprise more than 500 species, and Longidorus and Xiphinema are the most diversified, abundant and cosmopolitan genera, which increases the risk of species misidentification. We conducted an integrative morphometric and genetic study on two longidorid species to elucidate the existence of new cases of cryptic speciation within the genera Longidorus and Xiphinema. Detailed morphological, morphometric, multivariate and genetic studies were carried out, as well as mitochondrial and nuclear haploweb analyses, to differentiate species within the L. iliturgiensis- and X. hispanum-complexes. Species delimitation using haplonet tools of L. iliturgiensis-species complex clearly separated L. tabernensis sp. nov. from L. iliturgiensis and L. indalus. Similarly, the haploweb analysis of X. subbaetense sp. nov. showed it as a unique and separate species from X. hispanum and X. adenohystherum. D2-D3 expansion domains of 28S rRNA, partial 18S rRNA, and partial coxI region were used for inferring phylogenetic relationships. The present study provides new insights into the diversity of Longidorus and Xiphinema species detected in southern Spain, and new evidence of cryptic speciation in both genera. These results support our hypothesis that the biodiversity of Longidoridae in southern Europe is higher than previously supposed and is still not fully clarified., Peer reviewed

This dataset was intended to describe schistosomiasis severity in a backcross cohort and to study the genetic linkage analysis with parasitological, pathological and immunological variables., [Description of methods used for collection/generation of data] F1BX mice were infected with 150 ± 5 S. mansoni cercariae each mouse and nine weeks post-infection were euthanized. We considered 20 variables: granulomas; affected liver surface (mm2/cm2); the number of adult male and female worms; eggs per gram of liver and small intestine; eggs in liver and small intestine per female; CD4, CD8, CD45, CD220 in blood or spleen; IgG, IgG1, IgG2a, IgM antibodies. Multivariate models (cluster and principal component analyses and K-means) identified four levels of infection intensity in the cohort. The genetic regions associated with severity were assessed by massive genotyping and genetic linkage analysis using 961 informative SNPs., [Methods for processing the data] Mean and standard error in each variable, Kolmogorov-Smirnov test. ANOVA and Tukey’ test or Student t-test. The Pearson correlation coefficient (r) and Student t-test for the statistical significance. Multivariant models considering sex influence in worm recovery, eggs in the liver and intestine, fecundity, granulomas and the affected liver surface. All the variables were standardized to 0 mean and standard deviation to 1. Cluster analysis, dendrogram, Principal components analysis and conglomerates by k-means were used to generate clusters. Median proportions were performed. SIMFIT statistical package for Windows version 7.3.7 were used Massive genotyping and geneticlinkage analysis using 961 informative SNPs: The genetic distance based on the recombination frequencies between markers in the F1BX cohort was compared with http://cgd.jax.org/mousemapconverter using maximum-likelihood mapping with HM algorithm. The Haldane function was used with a step size of 2.5 cM and a genotyping error of 0.001. We used the LOD-score to calculate the statistical significance of the linkage of the QTLs found. LOD-score higher than 1.4 suggested linkage. The Ensembl bioinformatics tool (https://www.ensembl.org/index.html) was used to identify syntenic regions between mouse and human., Here we present the dataset used in our study entitled "Identification of genomic regions implicated in susceptibility to Schistosoma mansoni infection in a murine genetic model (backcross)". Thus, we crossed the C57BL/6 mouse strain with the CBA one and then the F1B6CBA females (C57 x CBA) were backcrossed with CBA males generating the F1BX cohort of the study. The study consists of the identification of genetic markers of schistosomiasis. High infection levels and severe liver fibrosis in schistosomiasis appear only in a few highly susceptible infected people. Schistosomiasis could be a complex trait disease and it could be possible to identify genetic markers associated with severity. This study uses a genetically heterogeneous back-cross cohort with genetically unique mice. A backcross (F1BX) mouse cohort was generated after two stages; firstly, we crossed a mouse strain (CBA/2J) susceptible to schistosomiasis with a resistant one (C57BL/6J) to generate the F1B6CBA mice; secondly, the F1BX mice were generated by backcrossing. F1B6CBA female mice with CBA/2J males. F1BX mice were infected with 150 ± 5 S. mansoni cercariae each mouse and nine weeks post-infection were euthanized. We considered 20 variables: granulomas; affected liver surface (mm2/cm2); the number of adult male and female worms; eggs per gram of liver and small intestine; eggs in liver and small intestine per female; CD4, CD8, CD45, CD220 in blood or spleen; IgG, IgG1, IgG2a, IgM antibodies. Multivariate models (cluster and principal component analyses and K-means) identified four levels of infection intensity in the cohort. The genetic regions associated with severity were assessed by massive genotyping and genetic linkage analysis using 961 informative SNPs., The main research project is: Red de Investigación Colaborativa en Enfermedades Tropicales (RICET) Ref.: RD16/0027/0018., Peer reviewed

Exploiting metal-microbe applications to expand the circular economy (M2ex) GA no 861088, 1 Excel file, Digestate originating from anaerobic digestion of non-source-separated organic fraction of municipal solid waste (OFMSW) is produced abundantly worldwide and generally discarded in landfills. However, it can be a valuable resource for many bioeconomy strategies as land restoration, only if a consolidated understanding of the contaminants’ presence and behaviour in digestate-amended soil is achieved. This study aimed to investigate the fate of trace metals, namely Zn, Cu, Pb, and Cr found in the digestate, along the soil profile after digestate application on soil, and the influence that other contaminants as pharmaceutical compounds can have on their behaviour in the soil system. For that, a 90-day soil column experiment was conducted using a fine loamy sand soil topped with a layer of digestate-amended soil. Digestate-amended soil had a soil to digestate proportion of 14 to 1 (dry weight). Two experimental conditions were tested: soil amended with digestate, and soil amended with digestate spiked with the antidiabetic drug metformin. Soil samples were taken at 4 depths on days 1, 7, 21, 35 and 90, and total trace metals concentrations and fractionation was determined via atomic absorption spectroscopy. Results showed that Zn, Cu, Pb ad Cr initially present in the digestate were transferred from the digestate-amended soil layer to the underlying soil layer over time, although in low amounts. Nevertheless, no transfer was detected to the deeper soil layers. Trace metals in soil were predominantly in immobile and less bioavailable forms associated with clay and silicate mineral groups, whereas in the digestate-amended soil they were in more bioavailable forms, which could be related also to metals’ migration in the soil layers below. Results also show that the presence of metformin had no influence on trace metal behaviour, giving insight also on possible interactions with other potentially present contaminants as microplastics. The current study showed that OFMSW digestate can be a promising organic nutrient-rich matrix for land restoration even if it may contain high metals’ concentrations because low metal mobility along the soil profile can be expected., This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 861088., Peer reviewed

[Usage Notes] Puncher et al_Thunnus thynnus_95loci_723individuals_27samples Puncher et al_Thunnus thynnus_221loci_167individuals_9samples Puncher et al_Thunnus thynnus_384 SNPs with flanking sequences "Puncher et al_Thunnus thynnus_384 SNPs with flanking sequences.txt" contains the flanking sequences of 384 SNPs discovered using reduced representation sequence libraries, 221 of which passed quality criteria and 95 that were used for population structure analysis., The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genome-wide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n= 326) and from these 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST = 0.008, p=0.034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts., Peer reviewed

Quality is defined as the extent to which a product conforms to the design specifications and how it complies with the requirements of component functionality. For some industries, such as automotive and aeronautical, the quality of their parts is very important given the high requirements to which they are subject. However, difficulties arise from the fact that a measure of quality can only be evaluated ‘‘out-of-process”, resulting in losses because there is no alternative to removing defective parts from the production line. Therefore, it is necessary to apply Artificial Intelligence-based kits/solutions that provide in-process estimation to predict quality from some measured variables. The main goal of these datasets is to monitor the final quality of the manufactured components or parts by estimating surface roughness from vibration signals and cutting parameters information using Artificial Intelligence-based solutions. Surface roughness is an essential feature in quality control defined by the deviation in the direction of the normal vector of a real surface from its ideal form. Because the roughness measurement is an offline and post process procedure, being able to estimate this value online brings a series of benefits in terms of time and cost reduction in manufacturing lines, energy efficiency, unnecessary wear of tools and machines, etc. Once a part has been detected with a surface quality below what is desired, a series of corrective measures can be applied for the following operations, such as: reducing the feed rate percentage, increasing the percentage of spindle speed or reducing the axial depth per pass, etc., European Commission: KITT4SME - platform-enabled KITs of arTificial intelligence FOR an easy uptake by SMEs (952119)., Peer reviewed

Analysis of pheromone content in T2 generation of SPv1.0 plants., European Commission: ERA CoBioTech - Cofund on Biotechnologies (722361)., Peer reviewed

Dataset are structured following well-established data formats. Three files are provided., The first file (Don_biom_red-swamp-crayfish_ev_20230111) contains the information of each event (eventID, event date, geographical coordinates, sample effort, etc…); the second file (Don_ biom_red-swamp-crayfish _occ_20230111) contains the information of the occurrences of individuals recorded in each station and its taxonomic classification; and the third file (Don_ biom_red-swamp-crayfish _mof_20230111) provide information of biometric variables of individual crayfish recorded (total body length, cephalothorax length, cephalothorax width and weight)., The monitoring of biometric parameters (total body length, cephalothorax length, cephalothorax width and weight) of red-swamp crayfish (Procambarus clarkii) in Doñana wetlands was initiated in 2004 as part of the Monitoring Program of Natural Resources and Processes. The aim was to obtain a temporal and continuous series of data in the biometry of the species to analyze the evolution in these variables. Data were recorded annually between 2004-2022 by more than 2 members of the monitoring team which performed samplings in different locations twice per year in winter-spring and summer seasons when the study sites are flooded. The individuals were sampled at the 64 stations classified according to their location (on either aeolian sands or marshland). Modified commercial traps, similar to funnel traps, with 4 mm mesh size were used as sampling method, following the method by Bravo et. al., 1994. Between 5-9 traps were randomly distributed (until 50 cm of depth) in each location, depending of the flooded area and depth. The traps were left for 24 hours and emptied the content into white sorting pans. Individuals were counted and identified until the maximun taxonomic level in the field and realease. Each individual captured was weigthed using an electronic balance within 0.2 g accuracy. Cephalothorax length (from the tip of the rostrum to the tip of the cephalatorax) and cephalothorax width (maximum width of the cephalothorax) were measured using a slide caliper within 0.1 mm accuracy. Total body length (from the tip of the rostrum to the tip of the telson) were recorded using a ruler within 0.5 mm accuracy. Data recorded during the surveys also included sex and maturation stage (inmature, mature) of the organisms when possible, as well as the time and georreferenced data of the capture. Between 2004-2007 data was registered in Excel file and since 2008 data was recorded in CyberTracker sequence. The protocol used has been supervised by researchers and the data have been validated by the members who performed the sampling. Bravo, M. A.; Duarte, C. M. & Montes, C. (1994) Environmental factors controlling the life history of Procambarus clarkii (Decapoda, Cambaridae) in a temporary marsh of the Doñana National Park (SW Spain). January 1994. Limnology 25(4):2450-2453. Romaire, R. P. & Lutz, C. G., 1989 Population dynamics of Procambarus clarkii (Girard) and Procambarus acutus acutus (Girard) (Decapoda: Cambaridae) in commercial ponds. Aquaculture 81(3-4):253-274., National Parks Autonomous Agency (OAPN) between 2002-2007; Singular Scientific and Technical Infrastructures from the Spanish Science and Innovation Ministry (ICTS-MICINN); Ministry of Agriculture, Livestock, Fisheries and Sustainable Development from the Regional Government of Andalusia (CAGPDES-JA) since 2007; and Doñana Biological Station from the Spanish National Research Council (EBD-CSIC) since all the study period (2004)., 1. Don_biom_red-swamp-crayfish_ev_20230111: eventID, intitutionCode, institutionID, datasetName, eventDate, eventTime, continent, country, stateProvince, location, localityID, locality, decimalLatitude, decimalLongitude, habitat, sampleSizeValue, sampleSizeUnit, sampleSizeEffort. 2. Don_ biom_red-swamp-crayfish _occ_20230111: eventID, occurrenceID, occurenceTime, individualCount, basisOfRecord, sex lifestage, kingdom, phylum, class, family, genus, specificEpithet, scientificName, scientificNameAuthorship. 3. Don_ biom_red-swamp-crayfish _mof_20230111: ocurrenceID, measurementID, measurementValue, measurementUnit, measurementType, measurementAccuracy, measurementMethod., Peer reviewed

The purpose of this assay is to define the volatilome of SxPv1.0, v1.2 and WT Nicotiana benthamiana plant roots, focusing on the differences between them, by GC-MS., European Commission: ERA CoBioTech - Cofund on Biotechnologies (722361)., Peer reviewed

The purpose of this assay is to define the volatilome of SxPv1.0, v1.2 and WT Nicotiana benthamiana plant leaves, focusing on the differences between them, by GC-MS., European Commission: ERA CoBioTech - Cofund on Biotechnologies (722361)., Peer reviewed