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Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/283209
Dataset. 2020

MARINE BIOMONITORING WITH EDNA: CAN METABARCODING OF WATER SAMPLES CUT IT AS A TOOL FOR SURVEYING BENTHIC COMMUNITIES?

  • Antich, Adrià
  • Palacín, Cruz
  • Cebrian, Emma
  • Wangensteen, Owen S.
  • Golo, Raül
  • Turon, Xavier
In the marine realm, biomonitoring using eDNA of benthic communities requires destructive direct sampling or the setting-up of settlement structures. Comparatively much less effort is required to sample the water column, which can be accessed remotely. In this study we assess the feasibility of obtaining information from the eukaryotic benthic communities by sampling the adjacent water layer. We studied two different rocky-substrate benthic communities with a technique based on quadrat sampling. We also took replicate water samples at distances from a few centimetres to 20 m from the benthic habitat. Using as marker a fragment of the Cytochrome c oxidase subunit I gene with universal primers, we obtained a total of 3,543 molecular operational taxonomic units (MOTUs) from the samples. The structure obtained in the two environments was markedly different, with Metazoa, Archaeplastida Rhodophyta and Stramenopiles being the most diverse group in benthic samples, and HacrobiaAlveolata, Metazoa and Alveolata Rhizaria in the water. Only 265 MOTUs (7.5%) were shared between benthos and water samples, and of these 180 MOTUs (5.1%) were identified as benthic MOTUs that left their DNA in the water. Most of them were found immediately adjacent to the benthos, and their number decreased and The distribution of these benthic shared MOTUs showed a decrease both in number of MOTUs and in number of reads as we moved apart from the benthic habitat. It was concluded that water eDNA, even in the close vicinity of the benthos, was a poor proxy for the analysis of benthic structure, and that direct sampling methods are required for monitoring these complex benthic communities via metabarcoding., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/283242
Dataset. 2020

DATA FROM: SPONTANEOUS FOREST REGROWTH IN SOUTH-WEST EUROPE: CONSEQUENCES FOR NATURE’S CONTRIBUTIONS TO PEOPLE

  • Martín-Forés, Irene
  • Magro, Sandra
  • Bravo-Oviedo, Andrés
  • Alfaro-Sánchez, Raquel
  • Espelta, Josep Maria
  • Frei, Theresa
  • Valdés-Correcher, Elena
  • Rodríguez Fernández-Blanco, Carmen
  • Winkel, Georg
  • Gerzabek, Gabriel
  • Hampe, Arndt
  • Valladares Ros, Fernando
[Methods] The dataset was collected by four different teams who took part in the project. It consisted on four case studies of forest regrowth (including expansion and densification) after rural abandonment with contrasting ecological and societal contexts. The study took place in Spain and France. Two landscapes are located in rural areas undergoing human exodus and forest expansion and densification; the other two, in peri-urban areas with intense land use and forest densification but negligible expansion. For each forest plot, we estimated variables related to ten out of the 18 main Nature's contributions to people (NCP) defined by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services. Regulating and material NCP were addressed using variables measured in the field as proxies. Non-material NCP were studied through stakeholder interviews. Thus, this dataset contains data on NCP associated with forest regrowth of Juniperus thurifera L., Fagus sylvatica L., Quercus ilex L., and Quercus robur L stands. It includes a total of 65 study plots and 2,837 individual trees. The considered NCP included four regulating, three material, and three non-material NCP as well as one NCP common to all categories. The four regulating NCP were habitat creation and maintenance; pollination and dispersal of seeds and other propagules; regulation of climate through biological carbon (C) sequestration and storage; and regulation of detrimental organisms and biological processes. The two material NCP were energy; and medicinal, biochemical and genetic resources. The three non-material NCP were learning and inspiration; physical and psychological experience; and supporting identities. The NCP common to all categories was the maintenance of options, reflected in maintaining biodiversity (estimated in this case with the Shannon diversity index). The dataset contains information at both individual and plot level. Habitat creation and maintenance (NCP1) was calculated by computing the spatial connectivity of the plots in Q. ilex and Q. robur stands. It was inferred by calculating the percentage cover of broadleaved forest in a circular buffer (radius = 500 m) around each plot. Pollination and the dispersal of seeds and other propagules (NCP2) was estimated by counting all seedlings and saplings in each plot and divided them by the plot area to obtain the density of saplings per hectare. Climate regulation in terms of biological carbon (C) storage and sequestration (NCP4) was estimated by the overall C stock contained in the trees of the study plots. We calculated the total biomass per tree using species-specific allometric equations that combine the dbh and the height of the sampled trees. We also calculated the C stock per tree multiplying the obtained biomass by the percentage of C in each species. The regulation of detrimental organisms and biological processes (NCP10) was assessed using the percentage of invertebrate herbivory. For all except the J. thurifera case study, we determined herbivore damages by visually estimating the percentage of leaf area removed by invertebrates. Energy provision (NCP11) was understood as the production of biomass-based fuels such as fuelwood. We estimated biomass input from thick and medium branches (i.e. the tree parts normally employed as fuelwood) for each tree within plots. Biomass input from thick and medium branches was calculated from allometric equations specific for each species. The provision of medicinal, biochemical and genetic resources (NCP14) includes the production of plant genes and genetic information. In each plot we quantified gene diversity corrected for sample size as proxy for NCP14. The maintenance of options (NCP18) includes the benefits associated with species diversity. We scored woody species richness and abundance and computed the Shannon diversity index as proxy. Additionally, interviews regarding social perceptions related to learning and inspiration (NCP15), physical and psychological experiences (NCP16) and supporting identities (NCP17) were conducted at the case study level. Please notice that the social perception dataset is not uploaded to ensure data privacy policy. More information and detailed Methodology can be found in Martín-Forés et al. (2020) People and Nature, in both the main text and the Supplementary Material S1. [Usage Notes] Some values are missing because the methodology was adjusted according to each case study. For more information please read the detailed information provided by Martín-Forés et al. (2020) People and Nature, in both the main text and the Supplementary Material S1., [Context] European forests are expanding and becoming denser following the widespread abandonment of farmland and rural areas. Yet, little is known about the goods and services that spontaneous forest regrowth provide to people., [Aims] We assessed the changes in nature’s contributions to people (NCP) from spontaneous forest regrowth, i.e. forest expansion and densification, in South-West Europe., [Methods We investigated 65 forest plots in four different landscapes with contrasting ecological and societal contexts. Two landscapes are located in rural areas undergoing human exodus and forest expansion and densification; the other two, in peri-urban areas with intense land use and forest densification but negligible expansion. For each forest plot, we estimated variables related to ten out of the 18 main NCP defined by the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES). Regulating and material NCP were addressed using variables measured in the field as proxies. Non-material NCP were studied through stakeholder interviews., [Results] Our results show across the cases that forest expansion and densification is generally associated with greater climate regulation and energy provision. Changes in other NCP, especially in non-material ones, were strongly context-dependent. The social perception of spontaneous forest regrowth was primarily negative in rural areas and more positive in peri-urban landscapes., [Conclusion] Passive restoration through spontaneous forest expansion and densification can enhance regulating and material NCP, especially when adaptive management is applied. To optimise NCP and to increase the societal awareness of and interest in spontaneous forest regrowth, the effects of this process should be analysed in close coordination with local stakeholders to unveil and quantify the many and complex trade-offs involved in rural or peri-urban social perceptions., BiodivERsA, Award: BiodivERsA3-2015-58. Agencia Estatal de Investigación, Award: PCIN-2016-055. Ministerio de Economía, Industria y Competitividad, Gobierno de España, Award: CGL2017-83170-R. Deutsche Forschungsgemeinschaft. BiodivERsA, Award: BiodivERsA3-2015-58., Peer reviewed


Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/283251
Dataset. 2020

DATA FROM: SORPTION AND DESORPTION OF BICYCLOPYRONE ON SOILS

  • Spokas, K. A.
  • Gámiz, B.
  • Schneider, S. K.
  • Hall, K. E.
  • Chen, Wenlin
[Methods] Bicyclopyrone sorption was determined on each soil in triplicate using the batch equilibration method with radiolabeled compounds. The 14C spiking solution for BCP was prepared by diluting 14C-bicyclopyrone [pyridinyl-3-14C; specific activity = 95.3 µCi mg-1; 8,880 Bq mmol-1; 99.5% purity] with unlabeled BCP (Syngenta Crop Protection, LLC) to result in a stock solution of 10 mg L−1 with an overall activity of 1,090 Bq mL-1 (65,450 DPM mL-1). A 0.5 mL aliquot of this spiking solution was added to 9.5 mL of 0.01 M CaCl2 to achieve a 10 mL solution volume. This solution (0.5 mg L−1 BCP) was added to 1 g of soil in a 20 mL glass scintillation vial for a series of 25 different USDA soil series. Samples were then placed horizontally on a reciprocal shaker and allowed to equilibrate for 24 h (180 rev min-1) in the dark. Following centrifugation (20 min, 1500 × g), 2 mL of supernatant was removed and filtered (0.45 μm). Then a 1 mL aliquot of the filtered solution was mixed with 5 mL of scintillation cocktail [EcoLite(+)™; MP Biomedicals, LLC, Solon, OH] and analyzed for 14C by liquid scintillation counting (LSC) (HITACHI AccuFLEX LSC-8000, GMI Ramsey, MN, 10-minute counting window). No statistically significant sorption of the BCP to scintillation vials, syringes or syringe filters was observed (98-100% recovery, data not shown). The sorbed concentration of BCP on the soil was estimated by the following: Cs=Ci-CemV , where Ci is the initial concentration (mg L-1), Ce is the equilibrium concentration (mg L-1), V is the total volume of the liquid phase (L), and m is the mass of the soil (g). The equilibrium concentration was determined by the LSC of the liquid phase using the following equation: Ce=LSCe-Blank * CiLSCi , where LSCe is the disintegrations per minute of the sample following equilibration with the soil, Blank is the disintegrations per minute of the scintillation cocktail and vial alone, Ci is the liquid phase concentration of the initial standard (mg L-1), and LSCi are the disintegration of the corresponding BCP standards (without soil added). The partitioning coefficient (KD) is estimated by the following: KD= CSCe . Sorption Isotherms – Multiple Concentrations Sorption isotherms were generated for 7 selected soils which were selected based on the initial screening above for a range of observed KD values. The isotherm was determined utilizing initial BCP solution concentrations of 0.1, 0.5, 1, 2.5, 5, 10, and 20 mg L−1. Individual samples were run in duplicate using methods analogous to the single concentration batch KD determination described earlier. Equilibrium liquid (Ce) and solid (Cs) concentrations were then analyzed by fitting to different linear forms of four sorption models: Langmuir, Freundlich, Temkin, and the Dubinin-Radushkevich models (Horsfall, Spiff, & Abia, 2004; Hunt & He, 2015). [Usage Notes] Excel file with separate worksheets for the batch-isotherm (KD) and the multi-point isotherm datasets., Bicyclopyrone is a herbicide that is targeted for the control of herbicide-resistant weeds. However, there is a lack of extensive data on its sorption and factors that control its sorption in the soil system. In this study, we evaluated a series of 25 different soils, with a variety of soil properties to assess if an empirical relationship could be developed to predict the sorption coefficient for bicyclopyrone. Overall, there were no statistically significant relationships observed with organic carbon, cation exchange capacity, or clay content. There solely was a moderate negative correlation with soil pH (R=-0.65). Additionally, Freundlich isotherm analysis suggests that the KD could be adequate to characterize the sorption behavior for the range of soils evaluated here., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/283257
Dataset. 2022

DATA FROM: THE SOURCES OF VARIATION FOR INDIVIDUAL PREY-TO-PREDATOR SIZE RATIOS

  • Henriques, Jorge
  • Lacava, Mariángeles
  • Guzmán, Celeste
  • Gavín-Centol, M.P.
  • Ruiz-Lupión, Dolores
  • Mas, Eva de
  • Magalhães, S.
  • Moya-Laraño, Jordi
[Methods] Spider collection Individuals of Lycosa fasciiventris were collected from June 23rd to July 27th 2015 in four different localities within the Almeria province (South-East Spain), in dry temporal washes (“ramblas”): 1) around Paraje las Palmerillas, Estación Experimental de Cajamar (36.7917°N, 2.6891°O); 2) near Boca de los Frailes village (36.8036°N, 2.1386°O); 3) near Carboneras village (36.9667°N, 2.1019°O) and 4) near Almanzora river (37.3414°N, 2.0078°O). Individuals were then kept separately in the laboratory in a container (22 x 18 x 18 cm) with the bottom filled with 2-3 cm of soil collected from the sampling sites. Two wooden blocks (10 x 8 x 1 cm and 3 x 5 x 1 cm) were added to each tank to provide shelter. Only sub-adult virgin females were used to form the laboratory population. All individuals (adult and sub-adult males, and sub-adult females) were fed once a week with size-matched crickets (Gryllus assimilis; Fabricius 1775) purchased from a pet supply online store Exofauna, Spain (available in: https://exofauna.com). Spiders had access to water ad libitum through a 40 ml vial filled with water and covered with cotton. Tanks were placed in a climate chamber with simulated outdoor climatic conditions (day and night temperature cycles and photoperiod with light fluorescent tubes of 54 W, mimicking natural sunshine, and a relative humidity from 50 to 65%). Climatic conditions were adjusted to the preceding weekly average conditions in the Almeria province, with day-night temperature and light oscillations (temperature: 18.7-34.3 °C; light-dark photoperiod: 17:7-16:8 hours). Breeding design To assess genetic, maternal and environmental variation in individual prey-to-predator size ratio (PPSR), we performed a paternal half-sib split-brood design (Roff 1997; Lynch and Walsh 1998), in which 52 males (sires) were each mated with two virgin females (dams). Each week, offspring were provided with fruit flies (Drosophila melanogaster; Meigen, 1830) originated from cultures produced in the laboratory. Flies were fed with a nitrogen rich medium supplemented with high quality dogfood, which highly improves spider survival (Jensen et al. 2011). Maternal families were constituted by 12 offspring, split into two food availability treatments, varying in the number of flies provided. Thus, 3 out of 12 offspring from each maternal family were assigned to the rich environment, being given 3× the amount of food provided in the poor (or standard) environment. Initially, a single fly was offered to the spiders in the poor treatment and 3 flies in the richer treatment. This quantity was adjusted to 3 and 9 when individuals were approximately 6 months old due to higher food demand at that stage. After hatching, spiderlings of wolf spiders climb to the female back and, in L. fasciiventris, remain with it for a period of a few weeks (Parellada 1998). Due to logistic reasons, all spiderlings were removed from the female back within one week, that is approximately 42 ± 8 (mean ± SD) days after they hatched (age at isolation). To estimate and control for post-hatching common environmental effects occurring on the female back, the age at isolation was included in all models. This variable was never significant (data not shown). Spiderlings were carefully collected from the female back with the help of a paintbrush. We took 12 spiderlings from each female and placed them separately in cylindrical containers (5 cm height and 6 cm diameter). Each container had the bottom covered with filter paper, providing a substrate for both locomotion and absorption of excreta, inside the growth chamber. Filter papers were checked weekly and replaced if necessary. A plastic tip was inserted at the bottom of the container, filled with cotton connected to a reservoir, providing water ad libitum to spiders by capillarity (Moskalik and Uetz 2011). The 1248 spiderling containers were then randomly arranged within the growth chamber to ensure that individuals belonging to the same family were spatially interspersed. This allowed mitigating possible common environmental effects after spiderling isolation from their mothers. Morphometry Body components were divided between structural body size (carapace width; Hagstrum 1971) and body condition (residuals of abdomen width on carapace width; (Jakob et al. 1996). Body condition reflects energy and nutrient storage independently on the size of the spider and thus reflects hunger level (Moya-Laraño et al. 2008). Structural body size may reflect the strength to subdue prey (e.g., Moya-Laraño et al. 2002). Both carapace and abdomen width were measured at their widest point. Body size and body condition were measured in two instances: after individuals were taken from their mothers and isolated, and immediately before the trials for acceptance. Morphometric measurements were taken to the nearest 0.1 mm with a dissection microscope (Leica MZ125). While structural body size measured at the time of trial was needed to calculate prey-to-predator size ratio, body condition at the time of the trial was used to control for the hunger state of each spiderling (i.e. its motivational state). These traits were also measured early in life and used to calculate genetic and maternal correlations, to test how maternal investment in both offspring body size and condition could affect behavioural patterns of the spiders later in life. Prey acceptance This experiment aimed to measure the maximum relative size of a prey cricket (Gryllus assimilis) that a spider accepted, considering a range of cricket lengths (in mm) decreasing from 5× to 1× (in units of 1) the carapace width of the spider. For that, we placed them in experimental arenas where each spider was offered crickets in a decreasing order of relative size until it subdued and killed a cricket. The response variable, prey-to-predator size ratio (PPSR) is the ratio at which the spider attacks and kills the cricket. This measure corresponds to the maximum PPSR (PPSRmax) at which predators kill their prey and the larger the relative size of the prey killed, the higher the PPSR. Spiders were measured in blocks of 17 ± 5 (mean ± SD) individuals. Each block was defined as the experimental batch of individuals assessed in each day. Although this cricket species does not occur in the study site, L. fasciiventris is able to effectively prey on it, and a similar species with similar body size, Gryllus bimaculatus, is highly abundant in the collection area (Moya-laraño personal observation). As it was not feasible to collect G. bimaculatus in numbers enough to carry out this study, we used G. assimilis individuals from an established laboratory population. Note that this approach allowed testing the response of spiders that were naive to this prey, as all spiders had been fed with Drosophila to that point. Thus, this approach minimized environmental variation due to potential effects of previous experiences with cricket prey. In the trial, we used crickets with a length that differed from the target PPSR (5×, 4×, 3×, 2× or 1× of the width of the spider carapace) by less than 0.2 units. Crickets were weighted, and their length determined from a calibration curve, previously generated with the weight and length of 40 crickets: L = 3.22 + 0.32log(M); R2 = 0.99; p < 0.0001; where L is cricket body length (in mm) and M is cricket body mass (in mg). Mass was measured to the nearest 0.1 mg using a high precision scale (Mettler Toledo XP26). None of the crickets were used in more than one trial. To standardize hunger levels across individuals, spiders were left to starve for seven days before being tested, similarly to other studies (Persons and Rypstra 2000). As it was not possible to standardize age across trials, individuals were randomly assigned to each trial. Spider age at the time of each measurement (331 ± 30 days old, mean ± SD) was recorded and later controlled for in the statistical analysis as a covariate (see below). A single spider and one cricket were placed inside the arena (7.5 cm diameter), in opposite sides, within enclosed inverted plastic vials (3 cm diameter). Then, both vials were gently lifted simultaneously, and crickets and spiders were allowed to interact for 6 minutes. If the cricket was not captured and subdued, the spider was enclosed in the vial and the cricket was removed. Spiders were then left to recover in the vial for 30 minutes until a new cricket from the next immediately lower size was presented (lower PPSR). Trials ended as soon as the spider attacked and killed a cricket or if the spider did not catch the smallest (1×) cricket. [Usage Notes] Data used to assess the sources of variation of the maximum prey-to-predator size ratio (PPSRmax) in juveniles of the wolf spider Lycosa fasciiventris using a paternal half-sib split brood design., The relative body size at which predators are willing to attack prey, a key trait for predator-prey interactions, is usually considered invariant. However, this ratio can vary widely among individuals or populations. Identifying the range and origin of such variation is key to understanding the strength and constraints on selection in both predators and prey. Still, these sources of variation remain largely unknown. We filled this gap by measuring the genetic, maternal and environmental variation of the maximum prey-to-predator size ratio (PPSRmax) in juveniles of the wolf spider Lycosa fasciiventris using a paternal half-sib split brood design, in which each male was paired with two different females and the offspring reared in two different food environments: poor and rich. Each juvenile spider was then sequentially offered crickets of decreasing size and the maximum prey size killed was determined. We also measured body size and body condition of spiders upon emergence and just before the trial. We found low, but significant heritability (h2=0.069) and dominance and common environmental variance (d2+4c2=0.056). PPSRmax was also partially explained by body condition (during trial) but there was no effect of the rearing food environment. Finally, a maternal correlation between body size early in life and PPSRmax indicated that offspring born larger were less predisposed to feed on larger prey later in life. Therefore, PPSRmax, a central trait in ecosystems, can vary widely and this variation is due to different sources, with important consequences for changes in this trait in the short and long terms., Ministry of Education and Science, Award: Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation):PD/BD/106059/2015. Ministerio de Educación, Cultura y Deporte, Award: FPU13/04933. Ministerio de Economía y Competitividad, Award: CGL2015-66192-R., Peer reviewed


Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/283270
Dataset. 2021

EFFECTS OF EPISODIC NUTRIENTS ENRICHMENTS ON P-LIMITED PLANKTONIC COMMUNITIES: LAKE REDON ENEX 2013 EXPERIMENT

  • Catalán, Jordi
  • Felip, Marisol
  • Giménez-Grau, Pau
  • Zufiaurre, Aitziber
  • Camarero, Lluís
  • Pla Rabès, Sergi
[Methods] Analytical methods are described in the associated publication: Giménez-Grau, P., Felip, M., Zufiaurre, A., Pla-Rabès, S., Camarero, L. & Catalan, J. (2020) Homeostasis and non-linear changes in the stoichiometry of P limited planktonic communities. Ecosphere,11:e03249 [Usage Notes] Initial reference conditions in the lake water column were sampled during three dates. They are reported separately, but they should be amalgamated if used as initial experimental conditions. There are a few missing values across the biogeochemical data. Data from the enclosure water column and the sediment traps are reported in separated files., Planktonic communities are naturally subjected to episodic nutrient enrichments that may stress or redress the imbalances in limiting nutrients. Human-enhanced atmospheric nitrogen deposition has caused profound N:P imbalance in many remote oligotrophic lakes in which phosphorus has largely become limiting. These lakes offer an opportunity to investigate the planktonic community response to nutrient fluctuations in P-limited conditions. The ENEX experiment in Lake Redon (Pyrenees), performed during August 2013, aimed to investigate the structural and stoichiometric effects of pulse nutrient additions on P-limited planktonic communities. We performed P (PO43-), and N (NH4+ or NO3-) additions to the summer epilimnetic community of the ultraoligotrophic lake using self-filling ~100 L enclosures and analysed the response to varying P availability, N:P imbalance, and N source. The nutrient additions were gradients within the range of values seasonally found in the lake and other oligotrophic lakes of the Pyrenees, with a further P level typical of mesotrophic lakes to provided non-limiting conditions., Ministerio de Ciencia e Innovación, Award: CGL2010–19737. Ministerio de Ciencia e Innovación, Award: CGL2016–80124-C2-1-P. Generalitat de Catalunya, Award: 2017 SGR 910. Ministerio de Ciencia e Innovación, Award: FPI BES-2014-070196. Ministerio de Educación, Cultura y Deporte, Award: FPU AP2010-3596., Peer reviewed


Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/283288
Dataset. 2021

INFERRING INDIVIDUAL FATE FROM AQUATIC ACOUSTIC TELEMETRY DATA

  • Villegas Ríos, David
  • Freitas, Carla
  • Moland, Even
  • Huneide Thorbjørnsen, Susanna
  • Olsen, Esben Moland
[Methods] There are three types of data: - Detection data: 1-3 files per fish - Fish information data: includes all the relevant information for each individual, e.g. when it was tagged, transmitter type, etc... - Receiver array information: includes the location of the receivers [Usage Notes] Metadata of the dataset: Villegas Ríos, David et al. (2021), Inferring individual fate from aquatic acoustic telemetry data, Dryad, Dataset, https://doi.org/10.5061/dryad.2bvq83bn0 Detections data (all files starting with 9002 or 9004): Date and time: date and time of detection Receiver: name of the receiver Transmitter: ID of the transmitter Transmitter name: empty Transmitter serial: serial number of the transmitter Sensor value: depth measure Sensor units: units of the depth measure (meters) Station name: name of the station where the receiver is places Latitude: latitude of the station Longitude: longitude of the station fishinformation.csv: all the columns are self-explained except the following: MinDelaySec: minimum delay of the transmitter, in seconds. MaxDelaySec: maximum delay of the transmitter, in seconds. Release_lat_geo: release latitude, in geographic coordinates. Release_lon_geo: release longitude, in geographic coordinates. array_information.csv: all the columns are self-explained except the following: deploymentdatetime_timestamp: date of deployment of any particular receiver. recoverydatetime_timestamp: date of recovery of any particular receiver. lat_geo: latitude of the receiver location, in geographic coordinates. lon_geo: longitude of the receiver location, in geographic coordinates. lat_utm: latitude of the receiver location, in UTM. lon_utm: longitude of the receiver location, in UTM, Acoustic telemetry has become a popular means of obtaining individual behavioural data from a wide array of species in marine and freshwater systems. Fate information is crucial to understand important aspects of population dynamics such as mortality, predation or dispersal rates. Here we present a method to infer individual fate from acoustic telemetry arrays of receivers with overlapping detection ranges. Our method depends exclusively on information on animal movements and the characteristics and configuration of the telemetry equipment. By answering a limited number of simple questions, our method identifies six different fates: tagging mortality, natural mortality, fishing mortality, predation, dispersal and survival. Applying the method to a cod telemetry dataset, we were able to determine fate for 97% of the individuals. We validate the results using several external sources of information, such as recaptures from fishers and control fish with known fate. The method is readily applicable to a wide array of species with minimal adjustments, expanding the range of hypotheses that can be tested using telemetry data., H2020 Marie Skłodowska-Curie Actions, Award: 793627., Peer reviewed

Proyecto: EC/H2020/793627

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/283295
Dataset. 2021

PLANT COMMUNITY DATA FOR EUROPEAN ECOREGIONS

  • Capitán, José A.
  • Cuenda, Sara
  • Ordoñez, Alejandro
  • Alonso, David
[Methods] DATASETS: ABUN.Herba.csv: Plant community data were drawn from Atlas Florae Europaeae (AFE, Jalas & Suominen, 1964-1999). The distribution of flora is geographically described using equally-sized grid cells based on the Universal Transverse Mercator projection and the Military Grid Reference System. Each cell was assigned to a dominant habitat type based on the WWF Biomes of the World classification (Olson et al., 2001), which defines different ecoregions. We consider each cell in an ecoregion to represent a species aggregation. TRAIT.Herba.csv: Mean height values were obtained from the LEDA database (Kleyer et al., 2008) for as many species as there were available in the database. Most of the missing values were taken from (Ordonez et al., 2010), and some of them inferred using a MICE (Multivariate Imputation by Chained Equations) approach (Buuren & Groothuis-Oudshoorn, 2011). Based on plant growth forms, 2610 herbaceous species (aquatic, herbs, or graminoid) were considered in this dataset. MODIS_AET_mean.bil: Mean (annual) actual evapotranspiration maps were obtained from data estimated through remote sensing (Mu et al., 2011), which are publicly available in the MODIS project website (http://www.ntsg.umt.edu/project/modis/mod17.php). This data was put into a .bil format using QGIS. A map for European ecoregions is included in the file ecoregions.bil. CODE: Python code for replicability of the results is provided. randomize.py: performs randomization tests for each cell, by comparing with random samples taken from species in the corresponding ecoregion. It yields p-value distributions for each ecoregion, from which it is easy to compute height clustering indices. The variation of coexistence probabilities as function of competitive strengths can also be reproduced using the output file from this code. evapo_data.py: calculates ecoregional mean and std for actual evapotranspiration from MODIS data. Similar code can be used to obtain gross primary productivity averages. This code can be used to correlate AET with clustering indices and latitude. Note that this code can be easily adapted to obtain AET by cell instead of by ecoregion, using latitude and longitude defining each AFE cell., Patterns in macroecology are related to species occurrence across meaningful spatial and temporal scales. The dataset provided here reports species distribution data (presence-absence) for herbaceous plants across a number of European habitats (ecoregions). Species occurrence is accompanied by the corresponding plant's maximun stem height values. This dataset has been used to unveil patterns of herbaceous plant height clustering in mid-latitude European ecoregions. Presence-absence data for herbaceous plants were drawn from Atlas Florae Europaeae (Jalas & Suominen, 1964-1999). Associated to each species, a dominant habitat (ecoregion) was assigned according to the WWF Biomes of the World classification. Each herbaceous species in an ecoregion was characterized by its maximum stem height. Mean height values were obtained for different sources. In order to correlate clustering patterns with productivity measures, actual evapotranspiration (AET) data is also provided. AET maps were obtained from data estimated through remote sensing (Mu et al., 2011), which are publicly available in the MODIS project website (http://www.ntsg.umt.edu/project/modis/mod17.php). Plant distribution and trait data across Europe unveils a relation between plant height clustering and actual evapotranspiration. This clustering is most evident in mid-latitude ecoregions, where conditions for growth (reflected in actual evapotranspiration rates) are optimal. Away from this optimum, climate severity leads to non-significant height clustering in actual communities., Ministerio de Economia y Competitividad, Award: CGL2012-39964. Ministerio de Economia y Competitividad, Award: CGL2015-69043-P. Ministerio de Ciencia, Innovación y Universidades, Award: PGC2018-096577-B-I00. Banco Santander, Award: PR87/19-22582. Ministerio de Economia y Competitividad, Award: CGL2012-39964., Peer reviewed


Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/283313
Dataset. 2022

THE ORIGINS OF ASEXUAL BRINE SHRIMPS

  • Rode, Nicolas O.
  • Boyer, Loreleï
  • Flaven, E.
  • Hontoria, Francisco
  • Van Stappen, Gilbert
  • Dufresne, France
  • Haag, Christoph
  • Lenormand, Thomas
  • Jabbour-Zahab, Roula
[Methods] Flow cytometry of 147 individuals (+59 individuals from Nougué et al. 2015) COI sequencing of 336 individuals using primers 1/2COI_Fol-F and 1/2COI_Fol-R following the protocol of Muñoz et al. (2010). COI sequencing of 23 individuals using primers Co1APAR-F(5’-259 TTTGGAGCTTGAGCAGGAAT-3’) and Co1APAR-R(5’-260 TGCGGGATCAAAGAAAGAAG-3’). Genotyping of 432 individuals with a panel of 12 microsatellite markers (see Muñoz et al. 2008; Nougué et al. 2015 for details regarding markers and amplification protocol) [Usage Notes] See README files., Determining how and how often asexual lineages emerge within sexual species is central to our understanding of sex-asex transitions and the long-term maintenance of sex. Asexuality can arise “by transmission” from an existing asexual lineage to a new one, through different types of crosses. The occurrence of these crosses, cryptic sex, variation in ploidy and recombination within asexuals greatly complicates the study of sex-asex transitions, as they preclude the use of standard phylogenetic methods and genetic distance metrics. In this study we show how to overcome these challenges by developing new approaches to investigate the origin of the various asexual lineages of the brine shrimp Artemia parthenogenetica. We use a large sample of asexuals, including all known polyploids, and their sexual relatives. We combine flow cytometry with mitochondrial and nuclear DNA data. We develop new genetic distance measures and methods to compare various scenarios describing the origin of the different lineages. We find that all diploid and polyploid A. parthenogenetica likely arose within the last 80,000 years through successive and nested hybridization events that involved backcrosses with different sexual species. All A. parthenogenetica have the same common ancestor and therefore likely carry the same asexuality gene(s) and reproduce by automixis. These findings radically change our view of sex-asex transitions in this group, and show the importance of considering asexuality “by transmission” scenarios. The methods developed are applicable to many other asexual taxa., Peer reviewed

Proyecto: //

Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/283343
Dataset. 2022

FIRE FAVORS SEXUAL PRECOCITY IN A MEDITERRANEAN PINE

  • Guiote, Carmen
  • Pausas, J. G.
[Methods] We selected 13 sites dominated by Pinus halepensis trees in the Valencia region (eastern Spain) across a range of altitudes and climatic conditions. In each site, we established 4 transects, spaced by at least 100 m. In each transect, we haphazardly selected and georeferenced 10 trees, separated by at least 10 m. For each tree, we measured its basal diameter (10 cm above ground) and the distance to the two closest trees. Then, we compute the annual growth rate as the basal diameter (cm) divided by the age (years) and the average of the distances to the 2 closest trees. Afterward, we estimated the age of each tree by counting whorls. For reproductive trees, we also estimated the age of each cone following the same method of counting whorls (avoiding immature cone cohorts; i.e., the last or last two cohorts depending on the sampling season) and recorded whether they were open (non-serotinous), closed (serotinous cones), or from the last cohort considered (closed but serotiny unknown). The retention of branches and cones in this species allowed us to estimate the age of the young tree and its cones (even if they were open), and therefore the age at first reproduction (tree age - age of the first cone) and the total number of stored cones (i.e. closed cones; an estimation of the canopy seed bank) for each tree. Please see “materials and methods” section within the paper for more details., Wildfires are a natural disturbance in many ecosystems. Consequently, plant species have acquired traits that allow them to resist and regenerate in an environment with recurrent fires. A key trait in fire-prone ecosystems is the age at first reproduction (maturity age); populations of non-resprouting species cannot persist when fire interval is shorter than this age. Maturity age is variable among individuals, so we hypothesize that short fire intervals select for early seed production (precocity). We selected 13 plots with different fire regimes in eastern Spain, all dominated by Pinus halepensis (a non-resprouting serotinous species). Then, we evaluated the age at first reproduction and the size of the canopy seed bank of each individual pine. Our results show a significant effect of fire regime on the onset of reproduction in this species, suggesting a selection towards higher precocity in populations subject to shorter fire intervals. Due to this higher precocity, pines stored more cones, and therefore, increased their potential for post-fire regeneration. We provide the first field evidence that fire can act as a driver of precocity. Being precocious in fire-prone environments is adaptive because it increases the probability of having a significant seed bank when the next fire arrives., Ministerio de Ciencia e Innovación, Award: PGC2018-096569-B-I00. Ministerio de Ciencia e Innovación, Award: FPU16/06412., Peer reviewed


Digital.CSIC. Repositorio Institucional del CSIC
oai:digital.csic.es:10261/283348
Dataset. 2022

SALINITY EFFECTS ON SOIL P CYCLING

  • Hu, Minjie
  • Le, Yixun
  • Sardans, Jordi
  • Yan, Ruibing
  • Zhong, Yi
  • Sun, Dongyao
  • Tong, Chuan
  • Peñuelas, Josep
[Methods] The field experiments were conducted in the growing (July) and non-growing seasons (January) in both the freshwater and brackish C. malaccensis wetlands. Three 1 × 1 m quadrats (5 m apart) were randomly established at each site, and three soil cores (0–20 cm) were randomly collected in each quadrat and pooled into one sample. All samples were then stored in a portable refrigerator and immediately transported to the laboratory. The samples were homogenized and then split into two subsamples: one subsample was air-dried for the determination of P fractions and physicochemical parameters, and the other subsample was frozen at −80°C for DNA extraction. Plant biomasses were also collected during each season. We used the Hedley scheme of sequential extraction to estimate the fractions and availabilities of soil P (Hedley et al., 1982), which can effectively distinguish between Pi and Po. Briefly, soil samples were successively extracted using an anion-exchange resin (resin-P), 0.5 M NaHCO3 (NaHCO3-Pi and NaHCO3-Po), 0.1 M NaOH (NaOH-Pi and NaOH-Po), 0.1 M NaOH with sonication (NaOHs-Pi and NaOHs-Po), and 1 M HCl (HCl-Pi). The residual soils were then digested with 4 mL of H2SO4 and 1 mL of HClO4 (residual-P). The concentration of P was measured using a spectrophotometer. The P was further classified as labile P (resin-P, NaHCO3-Pi, and NaHCO3-Po), moderately labile P (NaOH-Pi and NaOH-Po), and stable P (NaOHs-Pi, NaOHs-Po, HCl-P, and residual-P) based on its availability to plants and microbes (Rodrigues et al., 2016). The salinity of the water was measured in situ using a salinometer (Oakton Instruments, Springfield, USA). Soil electric conductivity (EC) and pH were determined using a 2265FS EC meter (Spectrum Technologies Inc., Aurora, USA) and a pH meter (IQ Scientific Instruments, Carlsbad, USA), respectively. Soil moisture was evaluated by determining the amount of water lost at 105°C. Soil organic C (SOC) was analyzed using the dichromate oxidation method. Soil concentrations of total C (TC) and N (TN) were measured using an elemental analyzer (Elementar, Frankfurt, Germany). Soil concentrations of ammonium-N (NH4+-N) and nitrate-N (NO3−-N) were determined using flow-injection analysis (Skalar Analytical SAN++, Lachat, Netherland) and extraction with 2 M KCl. The soil texture was determined using a Mastersizer 2000 particle-size analyzer (Malvern Panalytical Ltd., Melvin, UK). Plant biomasses were measured by drying samples to constant weight at 70°C. Soil microbial DNA was extracted using an OMEGA DNA Kit following the manufacturer’s instructions. The quality and quantity of the extracted DNA were determined using a NanoDrop ND-1000 spectrophotometer (Thermo Fisher Scientific, Waltham, USA) and agarose gel electrophoresis, respectively. The extracted microbial DNA was processed, and metagenomic shotgun sequencing libraries were constructed with insert sizes of 400 bp using an Illumina TruSeq Nano DNA LT Library Preparation Kit. Each library was sequenced on an Illumina HiSeq X-ten platform (Illumina, San Diego, USA) using the PE150 strategy at Personal Biotechnology Co., Ltd. (Shanghai, China). Please refer to the Supporting Information for more detailed descriptions (Appendix I). We obtained a total of 931 million qualified sequences from 12 metagenomes, ranging from 69 million to 88 million sequences per sample for downstream analyses (Table S1). [Usage Notes] The dataset can be opened using regular Office software., Accelerated sea-level rise is expected to cause the salinization of freshwater wetlands, but the responses to salinity of the availability of soil phosphorus (P) and of microbial genes involved in the cycling and transformation of P remain unexplored. Our results suggest that the P-cycling microbial community abundance and P availability respond positively to moderate increases in salinity by promoting the microbial solubilization and mineralization of soil P in brackish wetlands. Changes in microbial communities and microbially mediated P cycling may represent microbial strategies to adapt to moderate salinity levels, which in turn control soil function and nutrient balance., National Natural Science Foundation of China. Natural Science Foundation of Fujian Province. Fundación Ramón Areces Project. Spanish Government. Catalan Government., Peer reviewed

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