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Supplement to: Callbeck, Cameron; Lavik, Gaute; Ferdelman, Timothy G; Fuchs, Bernhard M; Gruber-Vodicka, Harald R; Hach, Philipp F; Littmann, Sten; Schoffelen, Niels J; Kalvelage, Tim; Thomsen, Soeren; Schunck, Harald; Löscher, Carolin R; Schmitz, Ruth A; Kuypers, Marcel MM (2018): Oxygen minimum zone cryptic sulfur cycling sustained by offshore transport of key sulfur oxidizing bacteria. The data set includes, sulfide and sulfur concentrations, SUP05 cell densities, as well as denitrification and carbon fixation rates (based on 15N- and 13C-labelled in situ incubation experiments). The transect extends from the sulfidic upper shelf into the sulfide-free offshore oxygen minimum zone.

This dataset contains hydrochemistry and absorption measurements from surface water bodies (standing and flowing water) from Herschel Island, Yukon, Canada collected in 2016 and Cape Bounty Arctic Watershed Observatory, Nunavut, Canada collected in 2017.The detailed methods will be found in the accompanying manuscript.

edelman2019_lepidopteraAlignmentThis is the full multi-species whole genome alignment generated by ProgressiveCactus.fasta alignments and newick trees of loci used for species tree reconstructionA number of different datasets were used to generate species tree estimates in this paper. This file includes alignments (in fasta format) and locus-by-locus gene trees (in newick format). The datasets include fully-aligned coding and non-coding blocks among all heliconiini species included here (Agraulis vanillae, Eueides tales, Heliconius melpomene, H. cydno, H. timareta, H. pardalinus, H. numata, H. besckei, H. doris, H. erato, H. himera, H. erato x H. himera F1 hybrid, H. hecalesia, H. telesiphe, H. demeter, and H. sara), as well as blocks among the Heliconiini species + lepidopteran outgroups (Plutella xytostella, Bombyx mori, Melitea cinxia, Danaus plexippus, Larema accius, Papilio polytes, and Bicyclus anynana). In addition to these blocks, we have alignments and trees for genes extracted based on the H. melpomene reference annotation.phylogeny_trees_fastas_2.tar.gzeratoClade_HeraRef_5KB_all.tarThese fasta files were used to calculate fd and to generate trees for our branch length test. This is the full dataset, which was subset in various ways for testing as detailed in the paper.eratoClade.phyloNetFastas.tarfasta files from which samples were extracted to run phyloNet for the erato clademelpomene_phyloNetFastas.tarfasta files from which samples were extracted to run phyloNet for the melpomene cladeProgressive Cactus FilesThis archive contains the configuration files used to generate the full lepidoptera progressiveCactus alignment.progressiveCactusFiles.ziperatoClade.50KBSliding.toHeraGenometree file used for figure 2A - trees of erato clade genomes in 50KB sliding windows made from the H. erato demophoon reference coordinates.eratoClade_50KBSliding.allTrees.toHmelGenometrees of erato clade genomes in 50KB sliding windows made from the H. melpomene v2.5 reference coordinates.melpomeneClade.50KBSliding.allTrees.nwktrees of melpomene clade genomes in 50KB sliding windows made from the H. melpomene v2.5 reference coordinates.repeatsrepeatMasker output for all genomes in hal alignmenteratoGenomeInfoThis archive contains information on local recombination rate (for specified 10 kb windows) as well as general positional information for the locations of scaffolds on chromosomeseratoClade_10KBAbutting_HeraRef.ge2kb.treeserato clade trees made from 10 kb abutting windows constructed from the H. erato demophoon reference coordinates. These trees were used for the recombination rate analyses in the paper. We probe the history of rapidly radiating Heliconius butterflies by means of 20 new genome assemblies and employ them to investigate the genomic architecture of gene flow among lineages. By developing a test to distinguish incomplete lineage sorting from introgression, we demonstrate that histories of loci that differ from the species tree arose mostly through introgression. Moreover, these loci are underrepresented in low recombination and gene-rich regions, consistent with the purging of introgressed alleles tightly linked with incompatibility loci. Additionally, our analysis identifies an inversion that captures a color pattern switch locus which was transferred between lineages via introgression and is convergent with a similar rearrangement in another part of the genus. This analysis of multiple de novo genome sequences enables an improved understanding of the importance of introgression and selective processes in adaptive radiation.

The data publication contains supplementary data to the article "Supplementary Dataset to: The catastrophic thermokarst lake drainage events of 2018 in northwestern Alaska: Fast-forward into the future" This data publication includes four datasets: 1. Lake change datasets for 1999-2014 and 2017-2018 based on Landsat and Sentinel-1 data as Polygon Shapefiles 2. Lake change datasets for 2017 and 2018 based on high-temporal resolution PlanetScope imagery as Polygon Shapefiles and csv. 3. Lake ice simulations for the study area for 1980-2018. 4. Study sites in two versions: a) including seawater and b) clipped to land area. Files are Polygon Shapefiles. The datasets cover the land area of the Baldwin Peninsula and northern Seward Peninsula in north-western Alaska. The datasets are (#1) remote sensing based observations and (#3) modelled data. Methods are described in detail in the original manuscript (open access). Dataset #4 is the extent of the study site in two versions, a) full extent including seawater and b) land only including lakes. The land boundary was clipped with the “Global Self-consistent, Hierarchical, High-resolution Geography Database” (GSHHG; Wessel and Smith, 1996) dataset in scale “h”. The datasets cover different temporal periods and have a different temporal resolution. Data were collected to measure the extent of a rapid and widespread thermokarst lake drainage event in northwestern Alaska in 2018 and to compare the affected number of lakes and area to previous periods. Lake-ice model data were calculated to simulate lake-ice conditions since 1980 and to put the lake-ice and weather conditions in 2017/2018 into context.

Narrowing uncertainties about carbon cycling is important in the Arctic where rapid environmental changes contribute to enhanced mobilization of carbon. Here we quantify soil organic carbon (SOC) contents of permafrost soils along the Yukon Coastal Plain and determine the annual fluxes from erosion. Different terrain units are assessed based on surficial geology, morphology, and ground ice conditions. To account for the volume of wedge ice and massive ice in a unit, sample SOC contents are reduced by 19% and sediment contents by 16%. The SOC content in a 1 m**2 column of soil varies according to the height of the bluff, ranging from 30 to 662 kg, with a mean value of 183 kg. Forty-four per cent of the SOC is within the top 1 m of soil and values vary based on surficial materials, ranging from 30 to 53 kg C/m**3, with a mean of 41 kg. Eighty per cent of the shoreline is erosive with a mean annual rate of change is 0.7 m/a. This results in a SOC flux per meter of shoreline of 131 kg C/m/a, and a total flux for the entire Yukon coast of 35.5 10**6 kg C/a (0.036 Tg C/a). The mean flux of sediment per meter of shoreline is 5.3 10**3 kg/m/a, with a total flux of 1,832.0 10**6 kg/a (1.832 Tg/a). Sedimentation rates indicate that approximately 13% of the eroded carbon is sequestered in nearshore sediments, where the overwhelming majority of organic carbon is of terrestrial origin. Supplement to: Couture, Nicole; Irrgang, Anna Maria; Pollard, Wayne H; Lantuit, Hugues; Fritz, Michael (2018): Coastal Erosion of Permafrost Soils Along the Yukon Coastal Plain and Fluxes of Organic Carbon to the Canadian Beaufort Sea. Journal of Geophysical Research: Biogeosciences

We produced carbon and nitrogen isoscapes across the entire Southern Ocean (>40°S) using surface particulate organic matter isotope data, collected over the past 50 years. We used Integrated Nested Laplace Approximation -based approaches to predict mean annual isoscapes and four seasonal isoscapes using a suite of environmental data as predictor variables.

The present data publication provides permanent links to original and updated versions of validated data files. The data files include properties of seawater, particulate matter and dissolved matter that were measured from discrete water samples collected with Niskin bottles during the 2009-2013 Tara Oceans expedition. Properties include pigment concentrations from HPLC analysis (10 depths per vertical profile, 25 pigments per depth), the carbonate system (Surface and 400m; pH (total scale), CO2, pCO2, fCO2, HCO3, CO3, Total alkalinity, Total carbon, OmegaAragonite, OmegaCalcite, and dosage Flags), nutrients (10 depths per vertical profile; NO2, PO4, N02/NO3, SI, quality Flags), DOC, CDOM, and dissolved oxygen isotopes. The Service National d'Analyse des Paramètres Océaniques du CO2, at the Université Pierre et Marie Curie, determined CT and AT potentiometrically (Edmond 1970; DOE 1994) on samples preserved according to Dickson et al. (2007). More than 250 vertical profiles of these properties were made across the world ocean. DOC, CDOM and dissolved oxygen isotopes are available only for the Arctic Ocean and Arctic Seas (2013).

The potential interactive effects of iron (Fe) limitation and Ocean Acidification in the Southern Ocean (SO) are largely unknown. Here we present results of a long-term incubation experiment investigating the combined effects of CO2 and Fe availability on natural phytoplankton assemblages from the Weddell Sea, Antarctica. Active Chl a fluorescence measurements revealed that we successfully cultured phytoplankton under both Fe-depleted and Fe-enriched conditions. Fe treatments had significant effects on photosynthetic efficiency (Fv/Fm; 0.3 for Fe-depleted and 0.5 for Fe-enriched conditions), non-photochemical quenching (NPQ), and relative electron transport rates (rETR). pCO2 treatments significantly affected NPQ and rETR, but had no effect on Fv/Fm. Under Fe limitation, increased pCO2 had no influence on C fixation whereas under Fe enrichment, primary production increased with increasing pCO2 levels. These CO2-dependent changes in productivity under Fe-enriched conditions were accompanied by a pronounced taxonomic shift from weakly to heavily silicified diatoms (i.e. from Pseudo-nitzschia sp. to Fragilariopsis sp.). Under Fe-depleted conditions, this functional shift was absent and thinly silicified species dominated all pCO2 treatments (Pseudo-nitzschia sp. and Synedropsis sp. for low and high pCO2, respectively). Our results suggest that Ocean Acidification could increase primary productivity and the abundance of heavily silicified, fast sinking diatoms in Fe-enriched areas, both potentially leading to a stimulation of the biological pump. Over much of the SO, however, Fe limitation could restrict this possible CO2 fertilization effect. In order to allow full comparability with other ocean acidification data sets, the R package seacarb (Lavigne et al, 2014) was used to compute a complete and consistent set of carbonate system variables, as described by Nisumaa et al. (2010). In this dataset the original values were archived in addition with the recalculated parameters (see related PI). The date of carbonate chemistry calculation is 2014-09-16. Supplement to: Hoppe, Clara Jule Marie; Hassler, Christel S; Payne, Christopher D; Tortell, Philippe Daniel; Rost, Björn; Trimborn, Scarlett (2013): Iron limitation modulates ocean acidification effects in Southern Ocean phytoplankton communities. PLoS ONE, 8(11), e79890

We present results from a field study of inorganic carbon (C) acquisition by Ross Sea phytoplankton during Phaeocystis-dominated early season blooms. Isotope disequilibrium experiments revealed that HCO3- was the primary inorganic C source for photosynthesis in all phytoplankton assemblages. From these experiments, we also derived relative enhancement factors for HCO3-/CO2 interconversion as a measure of extracellular carbonic anhydrase activity (eCA). The enhancement factors ranged from 1.0 (no apparent eCA activity) to 6.4, with an overall mean of 2.9. Additional eCA measurements, made using membrane inlet mass spectrometry (MIMS), yielded activities ranging from 2.4 to 6.9 U/[mg chl a] (mean 4.1). Measurements of short-term C-fixation parameters revealed saturation kinetics with respect to external inorganic carbon, with a mean half-saturation constant for inorganic carbon uptake (K1/2) of ~380 mM. Comparison of our early springtime results with published data from late-season Ross Sea assemblages showed that neither HCO3- utilization nor eCA activity was significantly correlated to ambient CO2 levels or phytoplankton taxonomic composition. We did, however, observe a strong negative relationship between surface water pCO2 and short-term 14C-fixation rates for the early season survey. Direct incubation experiments showed no statistically significant effects of pCO2 (10 to 80 Pa) on relative HCO3- utilization or eCA activity. Our results provide insight into the seasonal regulation of C uptake by Ross Sea phytoplankton across a range of pCO2 and phytoplankton taxonomic composition. Supplement to: Tortell, Philippe Daniel; Trimborn, Scarlett; Li, Y; Rost, Björn; Payne, Christopher D (2010): Inorganic carbon utilization by Ross Sea phytoplankton across natural and experimental CO2 gradients. Journal of Phycology, 46(3), 433-443