Raw and processed data for Regional endemism instead of unlimited gene flow: Phylogeography of nivicolous myxomycetes in the mountains of Eurasia

This ZIP file contains the raw and processed dataset for the following scientific article Title: Regional endemism instead of unlimited gene flow: Phylogeography of nivicolous myxomycetes in the mountains of Eurasia Associated Publication: Ecosphere (In revision) DOI: 10.5281/zenodo.17447097 Associated GenBank Data: 3751 newly sequenced data are available in the GenBank database under BioProject PRJNA1229858 (KIXC01000001-KIXC01003751; version KIXC00000000.1). Other sequences also can be found in NCBI GenBank. Each accession number is fully cataloged in the `01_Raw_Data/#all_records.csv` file. Associated Code Archive: The R scripts used for all statistical analyses are provided in a separate Zenodo Code Archive (DOI: https://doi.org/10.5281/zenodo.17593130). Funding: Funding for this study was provided in the frame of a PhD position for MI within the Research Training Group RESPONSE (RTG 2010) funded by the Deutsche Forschungsgemeinschaft (DFG); and a joint international project led by AR (grant no. 2020/39/I/NZ8/03262) and MS (SCHN 1080/6-1), co-funded by the National Science Centre (NCN), Poland and the DFG. Further support came from the state tasks of the Komarov Botanical Institute, Russian Academy of Science (124013100829-3 and 124020100148-3). About Data set: Abstract This data set includes the raw and processed dataset for the research paper titled "Regional endemism instead of unlimited gene flow: Phylogeography of nivicolous myxomycetes in the mountains of Eurasia". For this study, we collected nivicolous myxomycetes samples from eleven data sets of dark-spored nivicolous (snowbank) myxomycetes (protists: spore-dispersed members of the Amoebozoa) from different mountain regions of Eurasia (Jp: Central Honshu, Japan; SN: Sierra Nevada, Spain; Pyr: French Pyrénées, France; Cau: Northern Caucasus, Russia; Fr: French Alps, France; GAP: Bavarian Alps, Germany; B/V: Black Forest and Vosges Mountains, Germany/France; Tat: Tatra mountains, Poland/Slovakia; Kam: Kamchatka Peninsula, Russia; Nor: Central massif of Jotunheimen, Norway; Khi: Kola Peninsula, Russia; each region ca. \> 250 km away) to explore genetic structure in phylogeography. Using the raw data provided in this repository, we first delimited the myxomycete assemblage in three level of OTUs, unique 18S rDNA ribotype, cluster of RTs based on the genetic distance (ribogroup, RG), and clade based on the morphology and the maximum likelihood phylogenetic tree, utilizing for the all further analysis which was all conducted in R. The scripts for the analysis are provided separately in the associated Zenodo Code Archive (DOI: https://doi.org/10.5281/zenodo.17593130). This ZIP file only contains the raw data for analysis in R and the processed data files, including Excel spreadsheets and outputs from external platforms (e.g., Blast search on NCBI). Structure of this file This zip file hierarchically contains following folders: Folder: 01_Raw_Data/: All_records.csv: raw dataset for all analysis Related R scripts: 01_data_cleaning.R README_Data_Metadata.md: legend for the csv data, including voucher collection abbreviations Folder: 02_Processed_Data/: Blast_summary.xlsx: output of Blast Search and evaluation. See "Legend" sheet for details. 473RT_mafft.fas: alignment of 473 unique 18S rDNA ribotype, which was aligned using mafft 473RT_mafft.tree: phylogenetic tree data output from IQTree Related R scripts: 01_data_cleaning.R ASAP_details.xlsx: ASAP results for RG delimitation and visualization process. See "Legend" sheet for details. Folder: 03_Environmental_Data/ nc_data/: data from ERA5-Land 2001–2010 for 11 regions (.nc), downloaded on 30.07.2024 Related R scripts: 05_ecological_analysis.r wc2_30s/: 19 BioClim data in WorldClim version 2 (.tif) Related scripts: 05_ecological_analysis.r