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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Oboh, Eugene;

    The Biofilm grazer model is an agent based model (ABM) built upon the MESA ABM framework ( https://mesa.readthedocs.io/en/stable/ ). The model helps us understand the effects of nutrient, light and grazing on the spatio-temporal development of rivernine biofilm. Instructions from the README.md will help you set up the environment and run the model.

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    ZENODO
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    Authors: Buttigieg, Pier Luigi; Christoffersen, Shannon; Ingram, Rebekah; Manley, William; +11 Authors

    In this letter, we introduce The Polar Vocabularies and Semantics Working Group, originally established as a joint effort between the joint SAON/IASC Arctic Data Committee and the Data Management Collaboration Team of the Interagency Arctic Research Policy Committee. We Invite, communities of practice to actively engage with us in our activities (described below), to advance the state of semantics-based applications in polar activities (and to increase interoperability between stakeholders and rights holders within existing and emerging digital ecosystems).

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Lüdecke, Cornelia; Gazert, Volker;
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    Authors: Di Cintio, Antonio; Fernandes-Salvador, Jose Antonio; Puntila-Dodd, Riikka; Granado, Igor; +2 Authors

    A Bayesian network-based, user-friendly decision support tool modelling how different socioeconomic factors affect the effectiveness of a marine protected area. This is the model included in the paper "Socio-economic factors boosting the effectiveness of marine protected areas: a Bayesian network analysis".

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Chust, Guillem; Villarino, Ernesto; McLean, Matthew; Mieszkowska, Nova; +34 Authors

    cti_cross_region_taxon This repository provides the data and codes used in the manuscript: Guillem Chust, Ernesto Villarino, Matthew McLean, Nova Mieszkowska, Lisandro Benedetti-Cecchi, Fabio Bulleri, Chiara Ravaglioli, Angel Borja, Iñigo Muxika, José A. Fernandes-Salvador, Leire Ibaibarriaga, Ainhize Uriarte, Marta Revilla, Fernando Villate, Arantza Iriarte, Ibon Uriarte, Soultana Zervoudaki, Jacob Carstensen, Paul J. Somerfield, Ana M. Queirós , Andrea J. McEvoy, Arnaud Auber, Manuel Hidalgo, Marta Coll, Joaquim Garrabou, Daniel Gómez-Gras, Cristina Linares, Francisco Ramírez, Núria Margarit, Mario Lepage, Chloé Dambrine, Jérémy Lobry, Myron A. Peck, Paula de la Barra, Anieke van Leeuwen, Gil Rilov, Erez Yeruham, Anik Brind'Amour, and Martin Lindegren. Cross-basin and cross-taxa patterns of marine community tropicalization and deborealization in warming European seas. Nature Communications Please check the github repo cti_cross_region_taxon for updates. Abstract Ocean warming and acidification, decreases in dissolved oxygen concentrations, and changes in primary production are causing an unprecedented global redistribution of marine life. The identification of underlying ecological processes underpinning marine species turnover, particularly the prevalence of tropicalization over deborealization, has been recently debated in the context of ocean warming. Here, we track changes in the mean thermal affinity of marine communities across European seas by calculating the Community Temperature Index for 65 biodiversity time series collected over four decades and containing 1,817 species from different communities (zooplankton, coastal benthos, pelagic and demersal invertebrates and fish). We show most communities and sites have clearly responded to ongoing ocean warming via abundance increases of warm-water species (tropicalization; 54%) and decreases of cold-water species (deborealization; 18%). Tropicalization dominated Atlantic sites compared to semi-enclosed basins such as the Mediterranean and Baltic Seas, probably due to physical barrier constraints to connectivity and species colonization. Semi-enclosed basins appeared to be particularly vulnerable to ocean warming, experiencing the fastest rates of warming and biodiversity loss through deborealization. Keywords: climate change, community temperature index, CTI, ocean connectivity. Acknowledgements This study has been supported by the European Union's Horizon 2020 research and innovation programme under grant agreement No 869300 (FutureMARES project) (G.C., E.V., J.F-S., M.P., M.Lin., C.D., D.G-G., G.R., L.B., C.R., M.C., F.R., G.R., P.B., M.P., M.Lep., J.L., A.B., N.M., J.G., F.B., L.B.C, A.Q., F.V., A.I., and I.U.), and by the Urban Klima 2050 -- LIFE 18 IPC 000001 project, which has been received funding from European Union's LIFE programme (G.C., E.V., L.I., A.B., A.U., and M.R.). Additional financial support was obtained from the Basque Government (PIBA2020-1-0028 & IT1723-22). We thank the NOAA Climate Prediction Center for providing Sea Temperature data through the NCEP Global Ocean Data Assimilation System (GODAS) www.cpc.ncep.noaa.gov/products/GODAS. We also thank Ocean Biodiversity Information System (OBIS) for providing global occurrences of the biological group studied here. Data from the Basque Country were obtained from the Basque Water Agency (URA) monitoring network, through a Convention with AZTI. M.C., J.G., D.G.-G. and F.R. acknowledge the 'Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S). Authors M.H. and M.Lin. are grateful for the support from ICES Working Group on Comparative Ecosystem-based Analyses of Atlantic and Mediterranean marine systems (WGCOMEDA) for this research. This paper is contribution nº xxxx from AZTI, Marine Research, Basque Research and Technology Alliance (BRTA)

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    Authors: Maoum, Ahmadreza;

    These are the required files and the CLIMBER-X model coupeled with PDAF that was used to obtain the results that are presented in the paper "Paleoclimate Data Assimilation with CLIMBER-X: An ensemble Kalman filter for the Last Deglaciation". This paper will be published in PLOS ONE journal. For the original code of CLIMBER-X, see : (https://doi.org/10.5281/zenodo.6877358, Willeit, 2022) For PDAF source codes, see https://pdaf.awi.de/trac/wiki.

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    Authors: Haas, Christian; Happ, Lena; Landy, Jack; Krumpen, Thomas;
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    Authors: Boike, Julia; Stünzi, Simone Maria; Gottuk, Jannika; Bornemann, Niko; +1 Authors
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    Authors: Coon, Rachael E.; Tucker, Cassandra B.;

    Sub-acute ruminal acidosis (SARA), a disorder characterized by chronic low ruminal pH, occurs in feedlot cattle fed high-concentrate diets. Forages slow digestion and reduce acid production. Thus, we aimed to assess how motivated finishing cattle are to access forage (Sudan grass hay, SG) via their willingness to interact with an electrified barrier. Reticulorumen pH was measured to contextualize the results with digestive health. Twenty-eight animals fed a high-concentrate ration ad-libitum had access to 4 L one of two treatments (n=14/treatment) fed once a day behind a barrier: 1) SG, or 2) an additional offering of the normal ration (TMR). To access a treatment, the steer voluntarily pushed his muzzle against an electrified barrier. The electrical current was increased exponentially every 24 h (0, 156, 312, 625, 1250, 2500, 5000 µA) until the animal ceased accessing it. Visits to the treatment were recorded continuously 24 h/d and reticulorumen pH was measured every 10 min. Rumen pH averaged 3.0±1.2 and 2.3±0.9 h/d below 5.6, for SG and TMR, respectively, meeting the criterion for SARA. However, animals with access to SG were less likely to advance to the next current than TMR animals (P<0.01) and were approximately 3x less willing to interact with higher currents than TMR (mean maximum current touched: 469±169 and 1380±254 mA, respectively, mean±SE, P=0.01). Lower motivation to access SG was further demonstrated through fewer visits to the SG (2.4±0.4 vs 5.3±0.6 #/d, P<0.01), and less SG consumed than TMR (32.0±0.1 vs 74.0±0.0 %/d, P<0.01). Overall, finishing cattle valued the TMR more than SG, likely because of differences in the quantity offered, palatability, and familiarity. When rumen health was considered, SG animals visited more often (r=0.5, P=0.09) and showed fewer failed attempts (r=-0.5, P=0.06) to access forage as the severity and duration of pH depression below 5.6, for example, increased. There was no relationship between any measure of treatment use and pH depression for TMR animals (P≥0.3). These findings provide evidence that cattle are motivated for Sudan grass hay when experiencing chronic low reticulorumen pH. However, the findings also contribute to the mixed evidence about motivation for forage in this life stage, because, overall TMR was valued more highly than SG. Indeed, despite widespread pH depression, TMR cattle contrafreeloaded for additional concentrate, demonstrating unexpectedly high motivation for this resource. Please see the methods described in the associated research publication. Please see the information in the associated README file.

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    Authors: Lafferty, Kevin;

    Water samples were taken for eDNA at four sites known to contain tidewater gobies in the past: 16 samples Calleguas Creek (34 06' 42", 119 04' 54", Ventura County), 21 samples at Ormond Lagoon (34 8' 23", 119 11' 20", just west of NVBC), and 17 samples at Santa Clara River Mouth (34 4' 8", 119 15' 53", Ventura County). In addition, two samples were taken at Mugu Lagoon (34 5' 30", 119 7' 21", Ventura County) and 20 samples were taken at Devereux Slough (34 25' 4", 119 52' 27", Santa Barbara County). I used commercial aquatic eDNA kits from Jonah Ventures ® for US $90 each (this cost includes supplies, sequencing and bioinformatics). At all sites, nearshore water samples were taken for environmental DNA wearing latex gloves to reduce contamination with human DNA. Samples were then filtered through a 1-micron disk filter by pushing water through the filter with a 60cc luer-lock syringe until clogging (mean sample volume: 174 cc +/- 0.141 S.D.). Filter capsules were purged of water before filling with preservative (tris-EDTA) before refrigerating until they were express shipped back to Jonah Ventures ® for sequencing. Seines were taken at each water sampling site for one of the estuaries (Calleguas Creek) that was sampled for eDNA (tidewater gobies collection permit #PER0046428) and matched sites and effort. Seine hauls were 2.4 m wide by 6.4 m distance on average in 0.6 m water depth. Temperature was 21.2 C. conductivity was 32 (close to seawater), and DO (mg/L) was 8.3). Jonah Ventures' ® methods for qPCR and metabarcoding are summarized as follows. After the samples were received, DNA was extracted using the DNeasy Blood & Tissue Kit. Three qPCR replicates were run for a tidewater-goby-specific primer (Schmelzle & Kinziger 2016). Metabarcoding was done for the mitochondrial 12S ribosomal RNA (rRNA) gene which was PCR amplified from each genomic DNA sample using the MiFishUF and MiFishUR primers with spacer regions. Amplicon size and PCR efficiency were visually inspected and then cleaned by incubating. A second round of PCR was performed to complete the sequencing library construct. Final indexed amplicons from each sample were cleaned and normalized using SequalPrep Normalization Plates and then pooled. Sample library pools were sent for sequencing on an Illumina NovaSeq 6000 (San Diego, CA) at the Texas A&M Agrilife Genomics and Bioinformatics Sequencing Core facility using the SP Reagent Kit v1.5 (500 cycles) (cat# 20028402). Raw sequence data were then demultiplexed using pheniqs v2.10, primers were removed with Cutadapt v3.4, and read pairs were merged, denoised and chimeras were removed with vsearch v2.15.2. Exact sequence variants observed more than 7 times were assigned with a custom best-hits algorithm and a reference database that combined Genbank and a Jonah Ventures voucher sequence record, following a consensus taxonomy with all for any taxonomic level with > 90% agreement across top hits. Raw sequences were vouchered through NCBI SRA (SRP# PRJNA924783). Many studies have shown that environmental DNA (eDNA) sampling can be more sensitive than traditional sampling. For instance, past studies found a specific qPCR probe of a water sample is better than a seine for detecting the endangered tidewater goby, Eucyclogobius newberryi. Furthermore, a metabarcoding sample often detects more fish species than a seine detects. Less consideration has been given to sampling costs. To help managers choose the best sampling method for their budget, I estimated detectability and costs per sample to compare the cost-effectiveness of seining, qPCR and metabarcoding for detecting endangered tidewater gobies as well as the associated estuarine fish community in California. Five samples were enough for eDNA methods to confidently detect tidewater gobies, whereas seining required twice as many samples. Fixed program costs can be high for qPCR and seining, whereas metabarcoding had high per-sample costs, which led to changes in relative cost-effectiveness with the number of locations sampled. Under some circumstances (multiple locations visited or an already validated assay), qPCR was a bit more cost-effective than metabarcoding for detecting tidewater gobies. Under all assumptions, seining was the least cost-effective method for detecting tidewater gobies or other fishes. Metabarcoding was the most cost-effective sampling method for multiple species detection. Despite its advantages, metabarcoding still suffers from gaps in sequence databases, can yield vague results for some species, and can lead novices to serious errors. Seining is still the only way to rapidly assess densities, size distributions, and fine-scale spatial distributions. The manuscript relies on 8 separate data sets and an R file to analyze them. Each data file has an accompanying metadata file and information file. The subset of data used is provided in the data archive (Schmelzle&Kinziger_occupancy.csv) so that analyses can be reproduced but should be cited as Schmelzle, Molly C.; Kinziger, Andrew P. (2015). Data from: Using occupancy modeling to compare environmental DNA to traditional field methods for regional-scale monitoring of an endangered aquatic species [Dataset]. Dryad. https://doi.org/10.5061/dryad.6rs23 Funding provided by: United States Department of DefenseCrossref Funder Registry ID: https://ror.org/0447fe631Award Number: Q2 DAR-Q N6923222MP001XY

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    Authors: Oboh, Eugene;

    The Biofilm grazer model is an agent based model (ABM) built upon the MESA ABM framework ( https://mesa.readthedocs.io/en/stable/ ). The model helps us understand the effects of nutrient, light and grazing on the spatio-temporal development of rivernine biofilm. Instructions from the README.md will help you set up the environment and run the model.

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    Authors: Buttigieg, Pier Luigi; Christoffersen, Shannon; Ingram, Rebekah; Manley, William; +11 Authors

    In this letter, we introduce The Polar Vocabularies and Semantics Working Group, originally established as a joint effort between the joint SAON/IASC Arctic Data Committee and the Data Management Collaboration Team of the Interagency Arctic Research Policy Committee. We Invite, communities of practice to actively engage with us in our activities (described below), to advance the state of semantics-based applications in polar activities (and to increase interoperability between stakeholders and rights holders within existing and emerging digital ecosystems).

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    Authors: Lüdecke, Cornelia; Gazert, Volker;
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    Authors: Di Cintio, Antonio; Fernandes-Salvador, Jose Antonio; Puntila-Dodd, Riikka; Granado, Igor; +2 Authors

    A Bayesian network-based, user-friendly decision support tool modelling how different socioeconomic factors affect the effectiveness of a marine protected area. This is the model included in the paper "Socio-economic factors boosting the effectiveness of marine protected areas: a Bayesian network analysis".

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    Authors: Chust, Guillem; Villarino, Ernesto; McLean, Matthew; Mieszkowska, Nova; +34 Authors

    cti_cross_region_taxon This repository provides the data and codes used in the manuscript: Guillem Chust, Ernesto Villarino, Matthew McLean, Nova Mieszkowska, Lisandro Benedetti-Cecchi, Fabio Bulleri, Chiara Ravaglioli, Angel Borja, Iñigo Muxika, José A. Fernandes-Salvador, Leire Ibaibarriaga, Ainhize Uriarte, Marta Revilla, Fernando Villate, Arantza Iriarte, Ibon Uriarte, Soultana Zervoudaki, Jacob Carstensen, Paul J. Somerfield, Ana M. Queirós , Andrea J. McEvoy, Arnaud Auber, Manuel Hidalgo, Marta Coll, Joaquim Garrabou, Daniel Gómez-Gras, Cristina Linares, Francisco Ramírez, Núria Margarit, Mario Lepage, Chloé Dambrine, Jérémy Lobry, Myron A. Peck, Paula de la Barra, Anieke van Leeuwen, Gil Rilov, Erez Yeruham, Anik Brind'Amour, and Martin Lindegren. Cross-basin and cross-taxa patterns of marine community tropicalization and deborealization in warming European seas. Nature Communications Please check the github repo cti_cross_region_taxon for updates. Abstract Ocean warming and acidification, decreases in dissolved oxygen concentrations, and changes in primary production are causing an unprecedented global redistribution of marine life. The identification of underlying ecological processes underpinning marine species turnover, particularly the prevalence of tropicalization over deborealization, has been recently debated in the context of ocean warming. Here, we track changes in the mean thermal affinity of marine communities across European seas by calculating the Community Temperature Index for 65 biodiversity time series collected over four decades and containing 1,817 species from different communities (zooplankton, coastal benthos, pelagic and demersal invertebrates and fish). We show most communities and sites have clearly responded to ongoing ocean warming via abundance increases of warm-water species (tropicalization; 54%) and decreases of cold-water species (deborealization; 18%). Tropicalization dominated Atlantic sites compared to semi-enclosed basins such as the Mediterranean and Baltic Seas, probably due to physical barrier constraints to connectivity and species colonization. Semi-enclosed basins appeared to be particularly vulnerable to ocean warming, experiencing the fastest rates of warming and biodiversity loss through deborealization. Keywords: climate change, community temperature index, CTI, ocean connectivity. Acknowledgements This study has been supported by the European Union's Horizon 2020 research and innovation programme under grant agreement No 869300 (FutureMARES project) (G.C., E.V., J.F-S., M.P., M.Lin., C.D., D.G-G., G.R., L.B., C.R., M.C., F.R., G.R., P.B., M.P., M.Lep., J.L., A.B., N.M., J.G., F.B., L.B.C, A.Q., F.V., A.I., and I.U.), and by the Urban Klima 2050 -- LIFE 18 IPC 000001 project, which has been received funding from European Union's LIFE programme (G.C., E.V., L.I., A.B., A.U., and M.R.). Additional financial support was obtained from the Basque Government (PIBA2020-1-0028 & IT1723-22). We thank the NOAA Climate Prediction Center for providing Sea Temperature data through the NCEP Global Ocean Data Assimilation System (GODAS) www.cpc.ncep.noaa.gov/products/GODAS. We also thank Ocean Biodiversity Information System (OBIS) for providing global occurrences of the biological group studied here. Data from the Basque Country were obtained from the Basque Water Agency (URA) monitoring network, through a Convention with AZTI. M.C., J.G., D.G.-G. and F.R. acknowledge the 'Severo Ochoa Centre of Excellence' accreditation (CEX2019-000928-S). Authors M.H. and M.Lin. are grateful for the support from ICES Working Group on Comparative Ecosystem-based Analyses of Atlantic and Mediterranean marine systems (WGCOMEDA) for this research. This paper is contribution nº xxxx from AZTI, Marine Research, Basque Research and Technology Alliance (BRTA)

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    Authors: Maoum, Ahmadreza;

    These are the required files and the CLIMBER-X model coupeled with PDAF that was used to obtain the results that are presented in the paper "Paleoclimate Data Assimilation with CLIMBER-X: An ensemble Kalman filter for the Last Deglaciation". This paper will be published in PLOS ONE journal. For the original code of CLIMBER-X, see : (https://doi.org/10.5281/zenodo.6877358, Willeit, 2022) For PDAF source codes, see https://pdaf.awi.de/trac/wiki.

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