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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: 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).

    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/ ZENODOarrow_drop_down
    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/
    ZENODO
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    ZENODO
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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/ ZENODOarrow_drop_down
      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/
      ZENODO
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      ZENODO
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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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    ZENODO
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      ZENODO
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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: 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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    ZENODO
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    ZENODO
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      ZENODO
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      ZENODO
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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: 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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      ZENODO
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    Authors: Kalhori, Aram; Wille, Christian; Pia, Gottschalk; Li, Zhan; +3 Authors

    Rewetting drained peatlands is recognized as a leading and effective natural solution to curb greenhouse gas emissions. However, rewetting creates novel ecosystems whose emission behaviors are not adequately captured by currently used emission factors. These emission factors are applied immediately after rewetting, thus do not reflect the temporal dynamics of greenhouse gas emissions during the period wherein there is a transition to a rewetted steady-state. Here, we provide long-term data showing a mismatch between actual emissions and default emission factors and revealing the temporal patterns of annual carbon dioxide and methane fluxes in a rewetted peatland site in northeastern Germany. We show that site-level annual emissions of carbon dioxide and methane approach the IPCC default emission factors and those suggested for the German national inventory report only between 13 to 16 years after rewetting. Over the entire study period, we observed a source-to-sink transition of annual carbon dioxide fluxes with a decreasing trend of −0.36 t CO2-C ha−1 yr−1 and a decrease in annual methane emissions of −23.6 kg CH4 ha−1 yr−1. Our results indicate that emission factors should represent the temporally dynamic nature of peatlands post-rewetting and consider the effect of site characteristics to better estimate associated annual emissions. This project is supported by the WET HORIZONS project.

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      ZENODO
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    Authors: Opdal, Anders Frugård; Lindemann, Christian; Andersen, Tom; Hessen, Dag Olav; +2 Authors

    Andenes surface temperature The monthly mean sea surface temperature (C°) from the Andenes lighthouse (69.3 °N, 16.1 °E) for the years 1868 to 1963 where drawn from two sources. For the period 1868-1945, temperatures where drawn directly from the publication Means and extremes of sea temperature by the Norwegian coast tables 291a and 291b (pages 61-62) by E. Frogner (1948, Geofysiske publikasjoner Vol. XV Issue 3 Pages 5-74). The raw data consisted of 8-hourly to daily observations, but are processed to monthly means by E: Frogner, without uncertainty. The wherabouts of the raw data is unknown. For the period 1946-1963, monthly mean temperatures where made available upon request to the The Norwegian Meteorological Institute (www.met.no). NEA cod catch statistics 1877-2021 Weekly resolved commercial landings of NEA cod and NEA cod-roe between 1877 and 2022 were drawn from the Official Fisheries Statistics of Norway via two pathways. For the period 1877 to 2014 these recordnings are available both as printed books and scanned copies available at a digital repository managed by the Norwegian Directorate of Fisheries. The name of the report, the report-series and the publisher changes through the years, and include the following titles. 1863-1878: Om Lofotfiskeriet aar [year], Årsberetning vedkommende Norges fiskerier,Departement for det indre 1879-1899: Lofotfiskeriet [year], Årsberetning vedkommende Norges fiskerier, Departement for det indre 1900-1905: Lofotfiskeriet [year], Årsberetning vedkommende Norges fiskerier, Norges fiskeristyrelse 1906-1922: Lofotfiskeriet [year], Årsberetning vedkommende Norges fiskerier, Fiskeridirektøren 1923-2000: Lofotfisket [year], Årsberetning vedkommende Norges fiskerier, Fiskeridirektøren 2001-2014: Melding fra utvalgsformannen for Lofotfisket. Meldingsåret [year], Årsberetning vedkommende Norges fiskerier, Fiskeridirektoratet For a partly overlapping period 2000-2022 these data have been digitized and made available by the Norwegian Directorate of fisheries at this website, described in Hopland & Aasheim (2023). Litterature The publication by E. Frogner (1948) and the data documentation for the 2000-2022 catsch statistics by Hopland & Aasheim (2023) have also been uploaded. At high latitudes, the suitable window for timing reproductive events is particularly narrow, promoting tight synchrony between trophic levels. Climate change may disrupt this synchrony due to diverging responses to temperature between e.g. the early life stages of higher trophic levels and their food resources. Evidence for this is equivocal, and the role of compensatory mechanisms are poorly understood. Here, we show how a combination of ocean warming and coastal water darkening drive long-term changes in phytoplankton spring bloom timing in Lofoten Norway, and how spawning time of Northeast Arctic cod responds in synchrony. Spring bloom timing was derived from hydrographical observations dating back to 1936, while cod spawning time was estimated from weekly fisheries catch and roe landing data since 1877. Our results suggest that land use change causing coastal water darkening has gradually delayed the spring bloom up to 1990 after which ocean warming has caused it to advance. The cod appear to track phytoplankton dynamics by timing gonadal development and spawning to maximize overlap between offspring hatch date and predicted resource availability. This finding emphasises the importance of land-ocean coupling for coastal ecosystem functioning, and the potential for fish to adapt through phenotypic plasticity. Funding provided by: The Research Council of NorwayCrossref Funder Registry ID: https://ror.org/00epmv149Award Number: 287490

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    Authors: Zapata-Hernández, Germán; Gajardo-Rojas, Martina; Calderón-Seguel, Matías; Muñoz, Ariel A.; +5 Authors

    Advances and knowledge gaps on climate change impacts on honey bees and beekeeping: A systematic review

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    Authors: Bald, Carlos; Domínguez, Haizea; Iñarra, Bruno;

    Aquaculture has grown exponentially during the last decades, even overcoming traditional fishing in volume since2012 (Iñarra et al, 2018). The rise of the production of fish involves the rise of fish by-products, that in case ofbeing disposed could suppose an environmental risk. Fish viscera are part of the by-products used to producefishmeal and are the 10-18 % of the whole fish weight.Fish silage or acid autolysis is commonly used in areas with high fisheries rates and consists of liquefactionand stabilization of minced fish at room temperature, normally adding formic acid until reaching a pH between3.5 and 4.5 to prevent microbial growth. Hydrolysis of proteins occurs thanks to the endogenous acid proteasesthat are located at the fish viscera, which enable to get low molecular weight peptides and amino acids (Toppe etal, 2018). The resulting protein hydrolysates could be used as fertilisers. However, silage can take several days toachieve a high hydrolysis degree. In this work, autolysis has been carried out simulating the conditions ofenzymatic hydrolysis but only working with the endogenous enzymes from fish viscera with the aim ofaccelerating a typical silage to get free amino acids while saving costs derived from the use of commercialenzymes

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    Authors: Schnetz, Lisa; Dunne, Emma; Feichtinger, Iris; Butler, Richard; +2 Authors

    The Paleozoic represents a key time interval in the origins and early diversification of chondrichthyans (cartilaginous fishes), but their diversity and macroevolution are largely obscured by heterogenous spatial and temporal sampling. The predominantly cartilaginous skeletons of chondrichthyans pose an additional limitation on their preservation potential and hence on the quality of their fossil record. Here, we use a newly compiled genus-level dataset and the application of sampling standardization methods to analyze global total-chondrichthyan diversity dynamics through time from their first appearance in the Ordovician through to the end of the Permian. Subsampled estimates of chondrichthyan genus richness were initially low in the Ordovician and Silurian but increased substantially in the early Devonian. Richness reached its maximum in the middle Carboniferous before dropping across the Carboniferous/Permian boundary and gradually decreasing throughout the Permian. Sampling is higher in both the Devonian and Carboniferous compared with the Silurian and most of the Permian stages. Shark-like scales from the Ordovician are too limited to allow for some of the subsampling techniques. Our results detect two Paleozoic radiations in chondrichthyan diversity: the first in the earliest Devonian, led by acanthodians (stem-group chondrichthyans), which then decline rapidly by the late Devonian, and the second in the earliest Carboniferous, led by holocephalans, which increase greatly in richness across the Devonian-Carboniferous boundary. Dispersal of chondrichthyans, specifically holocephalans, into deeper water environments may reflect a niche expansion following the faunal displacement in the aftermath of the Hangenberg extinction event at the end of the Devonian. Funding provided by: Natural Environment Research CouncilCrossref Funder Registry ID: https://ror.org/02b5d8509Award Number: NE/L002493/1 Funding provided by: SYNTHESYS project*Crossref Funder Registry ID: Award Number: All information on data collection as well as specific details can be found in the Methods section of the manuscript. Please also see the README file for additional data & method information.

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    Authors: Brandt, Peter; Körner, Mareike;

    Code and data to reproduce the analysis and figures in "Synchronous drivers of equatorial Atlantic productivity" by Brandt et al.

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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: 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: 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: Kalhori, Aram; Wille, Christian; Pia, Gottschalk; Li, Zhan; +3 Authors

    Rewetting drained peatlands is recognized as a leading and effective natural solution to curb greenhouse gas emissions. However, rewetting creates novel ecosystems whose emission behaviors are not adequately captured by currently used emission factors. These emission factors are applied immediately after rewetting, thus do not reflect the temporal dynamics of greenhouse gas emissions during the period wherein there is a transition to a rewetted steady-state. Here, we provide long-term data showing a mismatch between actual emissions and default emission factors and revealing the temporal patterns of annual carbon dioxide and methane fluxes in a rewetted peatland site in northeastern Germany. We show that site-level annual emissions of carbon dioxide and methane approach the IPCC default emission factors and those suggested for the German national inventory report only between 13 to 16 years after rewetting. Over the entire study period, we observed a source-to-sink transition of annual carbon dioxide fluxes with a decreasing trend of −0.36 t CO2-C ha−1 yr−1 and a decrease in annual methane emissions of −23.6 kg CH4 ha−1 yr−1. Our results indicate that emission factors should represent the temporally dynamic nature of peatlands post-rewetting and consider the effect of site characteristics to better estimate associated annual emissions. This project is supported by the WET HORIZONS project.

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