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# Heatwave grazing kelp microbes sequences [https://doi.org/10.5061/dryad.vhhmgqns7](https://doi.org/10.5061/dryad.vhhmgqns7) We experimentally simulated ocean warming and marine heatwaves (MHWs) to quantify effects on two dominant temperate seaweed species and their microbiota, as well as grazing by a tropical herbivore. The kelp *Ecklonia radiata*’s microbiota in sustained warming and MHW treatments were enriched with microorganisms associated with seaweed disease and tissue degradation. In contrast, the fucoid *Sargassum linearifolium*’s microbiota was unaffected by temperature\*.\* Consumption by the tropical sea-urchin *Tripneustes gratilla* was greater on *Ecklonia* where the microbiota had been altered by higher temperatures, while *Sargassum*’s consumption was unaffected. Elemental traits (carbon, nitrogen), chemical defences (phenolics) and tissue bleaching of both seaweeds were generally unaffected by temperature. ## Description of the data and file structure Juvenile *Ecklonia radiata* (length \~15cm; N=140) and *Sargassum linearifolium* (length \~10cm; N=140) were collected haphazardly (>2m apart) at Cronulla rocky reef, Sydney, Australia. We exposed seaweeds to one of four temperature profiles over seven weeks: Ambient, Warming, marine heatwave MHW, MHW variable. After seven weeks of exposure to temperature treatments, a subset of individuals from each species/temperature treatment (*Ecklonia*: n=4-6; *Sargassum*: n=3) were randomly selected. Sterile cotton swabs were used to sample microbiota on algal surfaces, with the same area (20cm2) and swabbing time (30s) sampled for all individuals. Swabs were immediately stored in liquid nitrogen and transported to the University of New South Wales (UNSW, Sydney) and kept at -80°C until DNA extraction. DNA was extracted from swabs using the DNeasy PowerSoil Kit (Qiagen) and amplified using Polymerase Chain Reaction (PCR) primers 341F (5’-CCTACGGGNGGCWGCAG-3’) and 785R (5’-GACTACHVGGGTATCTAATCC-3’), targeting the 16S rRNA gene V3-V4 regions (bacteria and archaea), and were sequenced with a 2x250bp MiSeq reagent kit v2 on the Illumina MiSeq2000 Platform. The range-expansion of tropical herbivores due to ocean warming can profoundly alter temperate reef communities by overgrazing the seaweed forests that underpin them. Such ecological interactions may be mediated by changes to seaweed-associated microbiota in response to warming, but empirical evidence demonstrating this is rare. We experimentally simulated ocean warming and marine heatwaves (MHWs) to quantify effects on two dominant temperate seaweed species and their microbiota, as well as grazing by a tropical herbivore. The kelp Ecklonia radiata’s microbiotain sustained warming and MHW treatments were enriched with microorganisms associated with seaweed disease and tissue degradation. In contrast, the fucoid Sargassum linearifolium’s microbiota was unaffected by temperature. Consumption by the tropical sea-urchin Tripneustes gratilla was greater on Ecklonia where the microbiota had been altered by higher temperatures, while Sargassum’s consumption was unaffected. Elemental traits (carbon, nitrogen), chemical defences (phenolics) and tissue bleaching of both seaweeds were generally unaffected by temperature. Effects of warming and MHWs on seaweed holobionts (host plus its microbiota) are likely species-specific. The effect of increased temperature on Ecklonia’s microbiota and subsequent increased consumption suggest that changes to kelp microbiota may underpin kelp-herbivore interactions, providing novel insights into potential mechanisms driving change in species’ interactions in warming oceans.

Methane emissions from aquatic and terrestrial ecosystems play a crucial role in global warming, which is particularly affecting high-latitude ecosystems. As major contributors to methane emissions in natural environments, the microbial communities involved in methane production and oxidation deserve a special attention. Microbial diversity and activity are expected to be strongly affected by the already observed (and further predicted) temperature increase in high-latitude ecosystems, eventually resulting in disrupted feedback methane emissions. The METHANOBASE project has been designed to investigate the intricate relations between microbial diversity and methane emissions in Arctic, Subarctic and Subantarctic ecosystems, under natural (baseline) conditions and in response to simulated temperature increments. We report here a small subunit ribosomal RNA (16S rRNA) analysis of lake, peatland and mineral soil ecosystems.

Sample collection Samples of FWW were collected from 16 locations across its distribution range in China; 14 of these have previously been used for population genetics analysis using microsatellite markers (Cao et al., 2016). The other two newly collected populations were obtained from the expansion fronts of FWW in 2017-2018. Larvae of FWW were each sampled from different silk webs at each sampling location to reduce the chances of collecting siblings. In total, 306 larvae of FWW were obtained and used for DNA extraction, library construction, and genotyping, with 13-20 individuals per population. Library construction, SNP calling, and filtering Genomic DNA was isolated from larvae individually using a DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany). We used the ddRAD method to develop genome-wide SNPs for FWW (Peterson et al., 2012). Genomic DNA from each individual was digested by the restriction enzymes NlaIII and AciI for 3 hours at 37 °C (Aguilar et al., 1979; Li et al., 2018). Then we used 67.5 µl (1.5×) SpeedBeads (GE) to purify the digested DNA. A pair of uniquely modified Illumina P1 (5 bp) and P2 adapters (4 bp) were ligated to the digested DNA at 16 °C overnight. A heat-deactivation step was used to end the ligating reaction under conditions of 65 °C for 10 min and 22 cycles at 20 °C for 1 min. We pooled ligated products with a unique adapter into one library, followed by a purifying step using (1.5×) SpeedBeads (GE). Fragments of 420 - 540 bp were selected using BluePippin on a 2% gel cassette (Sage Sciences, Beverly, MA, USA) and then amplified using 12 PCR (polymerase chain reaction) amplification cycles. We used 64 µl 0.8× SpeedBeads to purify the amplified libraries. The quantity and quality of each library were evaluated using Qubit 3.0 and Agilent Bioanalyses 2100. The Illumina NovaSeq 6000 platform was used for sequencing to obtain 150-bp paired-end reads. We used Stacks version 2.52 to filter the low-quality sequencing data and call SNPs (Catchen et al., 2013). Raw sequencing reads were demultiplexed and trimmed using the process_radtags. Reads for each individual were mapped to the reference genome of FWW with a size of 510.5 Mb from NCBI (Assembly: GCA_003709505.1 ASM370950v1) (Wu et al., 2018) using Bowtie version 2.3.5.1 (Langmead et al., 2012). SNPs were called using a maximum likelihood framework and filtered with populations implemented in Stacks, VCFtools version 0.1.16 (Danecek et al., 2011), and the R package vcfR (Knaus et al., 2017) based on the following criteria: (a) samples with a mapping rate less than 80% were removed; (b) SNPs with a sequencing depth higher than eight and less than 500 were removed; (c) samples and SNPs with a missing rate higher than 10% in the corresponding dataset were removed; (d) SNPs with a minor allele count lower than 10 were removed; (e) SNPs with observed heterozygosity of > 0.75 across all populations were removed; (f) SNPs with a p-value of Hardy-Weinberg equilibrium (HWE) lower than 10-7 in all populations were removed to generate dataset of neutral SNPs. In order to reduce the influence of linkage on population structure inferences, we retained only SNPs separated by at least 1000 bp (Lowry et al., 2017). References Aguilar, J. D., & Riom, J. (1979). Nemoraea pellucida (Meigen), A new parasite of Hyphantria cunea (Drury) [France; fall webworm]. Bulletin De La Société Entomologique De France, 84, 204-207. Cao, L. J., Wei, S. J., Hoffmann, A. A., Wen, J. B., & Chen, M. (2016). Rapid genetic structuring of populations of the invasive fall webworm in relation to spatial expansion and control campaigns. Diversity and Distributions, 22, 1276-1287. Catchen, J., Hohenlohe, P. A., Bassham, S., Amores, A., & Cresko, W. A. (2013). Stacks: an analysis tool set for population genomics. Molecular Ecology, 22, 3124-3140. Danecek, P., Auton, A., Abecasis, G., Albers, C. A., anks, E. B., Depristo, M. A., . . . Sherry, S. T. (2011). The variant call format and VCFtools. Bioinformatics, 27, 2156-2158. Knaus, B. J., & Grünwald, N. J. (2017). VCFR: A package to manipulate and visualize variant call format data in R. Molecular Ecology Resources, 17, 44-53. Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357-359. Li, B. Y., Gao, Q., Cao, L. J., Hoffmann, A. A., Yang, Q., Zhu, J. Y., & Wei, S. J. (2018). Conserved profiles of digestion by double restriction endonucleases in insect genomes facilitate the design of ddRAD. Zoological Systematics, 43, 341-355. Lowry, D. B., Hoban, S., Kelley, J. L., Lotterhos, K. E., Reed, L. K., Antolin, M. F., & Storfer, A. (2017). Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation. Molecular Ecology Resources, 17, 142-152. Peterson, B. K., Weber, J. N., Kay, E. H., Fisher, H. S., & Hoekstra, H. E. (2012). Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PloS ONE, 7, e37135. Wu, N., Zhang, S., Li, X., Cao, Y., Liu, X., Wang, Q., . . . Zhan, S. (2018). Fall webworm genomes yield insights into rapid adaptation of invasive species. Nature Ecology and Evolution, 3, 105-115. Adaptive evolution following colonization can affect the impact of invasive species. The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. The well-recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. Based on genome-wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographic factors explained a similar proportion of the genetic variation across all populations compared to climatic factors. However, when the two population groups were analyzed separately, environmental factors explained more of the variation than geographic factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature-related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile. Here we provided VCF files generated and its population map generated in this study. Three VCF files were included. 1.fww_invariant+SNP_miss20_DP3.GQ20.vcf.gz, includes SNPs and invariant sites of all populations; 2.fww.ddRAD.all.vcf.gz, includes SNPs of all populations; 3.fww.4fds.vcf.gz, includes four degenerated SNPs of all populations; 4.fww_265_popmap.txt, includes a population map of all individuals. The three VCF files and a population map file can be opened by VCFtools and used as input files for population genetic diversity, population genetic structure, demographic inference, and outlier scanning analysis.

The paper "Blue Food policy objectives: an analysis of opportunities and trade-offs" integrates the findings of an initiative to assess the multiple roles of blue foods in food systems worldwide (https://www.bluefood.earth/) and translates them into four policy objectives aimed at realizing the contributions of aquatic foods to more nutritious, just, resilient and environmentally sustainable food systems. This dataset contains the variables used to assess conditions (at the level of nations) when blue food policy objectives are likely to be relevant. The R code used for Boolean analysis is available here: https://github.com/emmywas/BFA_Policy_analysis The paper "Blue Food policy objectives: an analysis of opportunities and trade-offs" is part of the Blue Food Assessment ( https://www.bluefood.earth/ ) a comprehensive examination of the role of aquatic foods in building healthy, sustainable, and equitable food systems. The assessment was supported by the Builders Initiative, the MAVA Foundation, the Oak Foundation, and the Walton Family Foundation. BC also thanks the Erling Persson Family Foundation. The data comes from publicly available (or published) datasets

Project: Coupled Model Intercomparison Project Phase 6 (CMIP6) datasets - These data have been generated as part of the internationally-coordinated Coupled Model Intercomparison Project Phase 6 (CMIP6; see also GMD Special Issue: http://www.geosci-model-dev.net/special_issue590.html). The simulation data provides a basis for climate research designed to answer fundamental science questions and serves as resource for authors of the Sixth Assessment Report of the Intergovernmental Panel on Climate Change (IPCC-AR6). CMIP6 is a project coordinated by the Working Group on Coupled Modelling (WGCM) as part of the World Climate Research Programme (WCRP). Phase 6 builds on previous phases executed under the leadership of the Program for Climate Model Diagnosis and Intercomparison (PCMDI) and relies on the Earth System Grid Federation (ESGF) and the Centre for Environmental Data Analysis (CEDA) along with numerous related activities for implementation. The original data is hosted and partially replicated on a federated collection of data nodes, and most of the data relied on by the IPCC is being archived for long-term preservation at the IPCC Data Distribution Centre (IPCC DDC) hosted by the German Climate Computing Center (DKRZ). The project includes simulations from about 120 global climate models and around 45 institutions and organizations worldwide. Summary: These data include the subset used by IPCC AR6 WGI authors of the datasets originally published in ESGF for 'CMIP6.ScenarioMIP.CSIRO.ACCESS-ESM1-5.ssp370' with the full Data Reference Syntax following the template 'mip_era.activity_id.institution_id.source_id.experiment_id.member_id.table_id.variable_id.grid_label.version'. The Australian Community Climate and Earth System Simulator Earth System Model Version 1.5 climate model, released in 2019, includes the following components: aerosol: CLASSIC (v1.0), atmos: HadGAM2 (r1.1, N96; 192 x 145 longitude/latitude; 38 levels; top level 39255 m), land: CABLE2.4, ocean: ACCESS-OM2 (MOM5, tripolar primarily 1deg; 360 x 300 longitude/latitude; 50 levels; top grid cell 0-10 m), ocnBgchem: WOMBAT (same grid as ocean), seaIce: CICE4.1 (same grid as ocean). The model was run by the Commonwealth Scientific and Industrial Research Organisation, Aspendale, Victoria 3195, Australia (CSIRO) in native nominal resolutions: aerosol: 250 km, atmos: 250 km, land: 250 km, ocean: 100 km, ocnBgchem: 100 km, seaIce: 100 km.

Growth parameters of Argopecten purpuratus and associated statisticsEstimation of growth parameters of Argopecten purpuratus using the ELEFAN_SA optimization procedure implemented in TropFishR. Ncohort: is the number of yearly repeating cohorts; Agemax: maximum age of the population; L∞ L asymptotic total length; K: von Bertalanffy growth constant; t_anchor: is the fraction of the year (ranging between 0 and 1) where yearly repeating growth curves cross length equal to zero; C: is a constant indicating the amplitude of the growth oscillation; ts is the fraction of a year where the sine wave oscillation begins; Φ´: growth performance index (see eq. 3); Rn_max: maximum possible score obtained during the fitness maximization process; ASP: available sum of peaks (for details see Mildenberger et al. 2017 [30]). CI: confidence intervals for growth parameters calculated with the jack knife technique [30]Dataset 1.xlsxP/B ratio of Argopecten purpuratus and environmental factorsAnnual changes in the production to biomass ratio of Argopecten purpuratus and environmental factors potentially affecting themDataset 2.xlsxPopulation parameters of Argopecten purpuratusMonthly estimation of population parameters of Argopecten purpuratus in Bahia independencia: Mean abundance (number of individuals per square meter); Individual mass (g ash-free dry mass estimated for a standard individual of 65 mm in shell length); body size (mm, mean, minimum, Q1 percentil, Q2 percentil and maximum)Dataset 3.xlsx The trophic flow of a species is considered a characteristic trait reflecting its trophic position and function in the ecosystem and its interaction with the environment. However, climate patterns are changing and we ignore how patterns of trophic flow are being affected. In the Humboldt Current ecosystem, arguably one of the most productive marine systems, El Niño-Southern Oscillation is the main source of interannual and longer-term variability. To assess the effect of this variability on trophic flow we built a 16-year series of mass-specific somatic production rate (P/B) of the Peruvian scallop (Argopecten purpuratus), a species belonging to a former tropical fauna that thrived in this cold ecosystem. A strong increase of the P/B ratio of this species was observed during nutrient-poor, warmer water conditions typical of El Niño, owing to the massive recruitment of fast-growing juvenile scallops. Trophic ecology theory predicts that when primary production is nutrient limited, the trophic flow of organisms occupying low trophic levels should be constrained (bottom-up control). For former tropical fauna thriving in cold, productive upwelling coastal zones, a short time of low food conditions but warm waters during El Niño could be sufficient to waken their ancestral biological features and display massive proliferations.

Aim: Climate change is transforming mountain summit plant communities worldwide, but we know little about such changes in the High Andes. Understanding large-scale patterns of vegetation changes across the Andes, and the factors driving these changes, is fundamental to predicting the effects of global warming. We assessed trends in vegetation cover, species richness (SR) and community-level thermal niches (CTN) and tested whether they are explained by summits’ climatic conditions and soil temperature trends. Location: High Andes Time period: Between 2011/2012 and 2017/2019 Major taxa studied: Vascular plants Methods: Using permanent vegetation plots placed on 45 mountain summits and soil temperature loggers situated along a ~6,800 km N-S gradient, we measured species and their percentage cover and estimated CTN in two surveys (intervals between 5-8 years). We then estimated the annual rate of changes for the three variables and used generalized linear models to assess their relationship with rates of change in the locally recorded soil temperatures, annual precipitation, and the minimum air temperatures of each summit. Results: Over time, there was an average loss of vegetation cover (mean = -0.26 %/yr), and a gain in SR across summits (mean = 0.38 species m2/yr), but most summits had significant increases in SR and vegetation cover. Changes in SR were positively related to minimum air temperature and soil temperature rate of change. Most plant communities experienced shifts in their composition by including greater abundances of species with broader thermal niches and higher optima. However, the measured changes in soil temperature did not explain the observed changes in CTN. Main conclusions: High-Andean vegetation is changing in cover and SR and is shifting towards species with wider thermal niche breadths. The weak relationship with soil temperature trends could have resulted from the short study period that only marginally captures changes in vegetation through time. (1) R-studio; (2) QGis For further information, users are advised to refer to the README document ("README_Dataset-compositional-changes_Andes.md") and the accompanying published article: Cuesta, F., Carilla, J., LLambí, L.D., Muriel, P., Lencinas, M. V., Meneses R.I., Feeley, K., Pauli, H., Aguirre, N., Beck, S., Bernardi, A., Cuello, Duchicela, S. A., Eguiguren, P., Gamez, L.E., Halloy, S., Hudson, L., Jaramillo, R., Peri, P.L., Ramírez, L. A., Rosero-Añazco, P., Thompson N., Yager, K., Tovar, C. Compositional shifts of alpine plant communities across the high Andes. Global Ecology and Biogeography. Accepted. DOI: 10.1111/geb.13721 The information reported here comes from two main sources: (1) Data collected on the field during vegetation surveys (between 2011/2012 and 2017/2019) on permanent vegetation plots plus soil temperature collected in dataloggers installed on each research site across the Andes. (2) Species records obtained from GBIF, TROPICOS, La Paz herbarium (LPB) and ULA -Merida herbarium. These records represent species in the permanent plots during the first and second surveys.

In birds little is known about the hormonal signals that communicate nutritional state to the brain and regulate appetitive behaviours. In mammals, the peptide hormones ghrelin and leptin elevate and inhibit consumption and food hoarding, respectively. In birds, administration of both ghrelin and leptin inhibit food consumption. The role of these hormones in the regulation of food hoarding in avian species has not been examined. To investigate this, we injected wild caught coal tits (Periparus ater) with leptin, high-dose ghrelin, low-dose ghrelin and a saline control in the laboratory. We then measured food hoarding and mass gain, as a proxy of food consumption, every 20 mins for two hours post-injection. Both high-dose ghrelin and leptin injections significantly reduced hoarding and mass gain compared with controls. Our results provide the first evidence that hoarding behaviour can be reduced by both leptin and ghrelin in a wild bird. These findings add to evidence that the hormonal control of food consumption and hoarding in avian species differs from that in mammals. Food hoarding and consumptive behaviours consistently show the same response to peripheral signals of nutritional state, suggesting that the hormonal regulation of food hoarding has evolved from the consumption regulatory system. DataBehavioural response to leptin and ghrelin treatment in coal tits.