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Authors: Stoev et al. 2013 Data type: genomic The archive contains the following data: 1) fasta-Alignment as the basis for all analyses (.FASTA), 2) mega-file for the calculation of the genetic distances and the NJ tree (.MDSX), 3) NJ-tree in Newick format (.NWK), 4) graph of the TCS Software for the Statistical Parsimony method (.GRAPH) File: E_cavernicolus.rar

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.

Additional file 3: Summary of Zenodo view and download statistics, plus citations (CSV format) as of 28 April 2022 [235].

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.

Additional file 1: Summary of the NORMAN-SLE datasets (CSV format) as of 4 May 2022 [81].

Additional file 4: Summary of Zenodo citations plus DOIs per list (CSV format) as of 1 May 2022 [236].

Data and code for "Mohammed Taha, H., Aalizadeh, R., Alygizakis, N. et al. The NORMAN Suspect List Exchange (NORMAN-SLE): facilitating European and worldwide collaboration on suspect screening in high resolution mass spectrometry. Environ Sci Eur 34, 104 (2022). https://doi.org/10.1186/s12302-022-00680-6"

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.

Additional file 5: Authorship contributions and acknowledgements mapped to NORMAN-SLE lists (XLSX format).