DOI: 10.5061/dryad.h18931zg9
title: Data from: Phylogenetic diversity and environment form assembly rules for Arctic diatom genera—a study on recent and ancient sedimentary DNA

description: Aim This study investigates taxonomic and phylogenetic diversity in diatom
 genera to evaluate assembly rules for eukaryotic microbes across the
 Siberian treeline. We first analysed how phylogenetic distance relates to
 taxonomic richness and turnover. Second, we used relatedness indices to
 evaluate if environmental filtering or competition influences the
 assemblies in space and through time. Third, we used distance-based
 ordination to test which environmental variables shape diatom turnover.
 Location Yakutia and Taymyria, Russia: we sampled 78 surface sediments and
 a sediment core, extending to 7000 years before present, to capture the
 forest–tundra transition in space and time, respectively. Taxon Arctic
 freshwater diatoms. Methods We applied metabarcoding to retrieve diatom
 diversity from surface and core sedimentary DNA. The taxonomic assignment
 binned sequence types (lineages) into genera and created taxonomic
 (abundance of lineages within different genera) and phylogenetic datasets
 (phylogenetic distances of lineages within different genera). Results
 Contrary to our expectations, we find a unimodal relationship between
 phylogenetic distance and richness in diatom genera. We discern a positive
 relationship between phylogenetic distance and taxonomic turnover in
 spatially and temporally distributed diatom genera. Further, we reveal
 positive relatedness indices in diatom genera across the spatial
 environmental gradient and predominantly in time-slices at a single
 location, with very few exceptions assuming effects of competition.
 Distance-based ordination of taxonomic and phylogenetic turnover indicates
 that lake environment variables, like HCO3– and water depth, largely
 explain diatom turnover. Main conclusion Phylogenetic and abiotic assembly
 rules are important in understanding the regional assembly of diatom
 genera across lakes in the Siberian treeline ecotone. Using a space–time
 approach we are able to exclude the influence of geography and elucidate
 that lake environmental variables primarily shape the assemblies. We
 conclude that some diatom genera have greater capabilities to adapt to
 environmental changes, whereas others will be putatively replaced or lost
 due to the displacement of the Arctic tundra biome under recent global
 warming.
description: The raw sequencing data has been produced on two runs on an
 Economy lane of a HiSeq Illumina device (2x125bp, output~2.5 GB). The runs
 HUA-1/KD050 and HUA-3/KD079 are stored as zipped .fastq files. The raw
 sequencing data was trimmed with the bioinformatic pipeline OBITools
 (Boyer et al. 2016). See documentation of the pipeline
 in the files (Bioinformatic_pipeline_HUA-1_KD050.txt
 and Bioinformatic_pipeline_HUA-1_KD079.txt). To re run
 the pipeline we provide two tagfiles (tagfile_KD050.txt and
 tagfile_KD079.txt) needed for demultiplexing the data. In the tag files,
 "EB" indicate Extraction blanks and "NTC" indicate No
 Template controls of the PCRs. An description of the tagfile is also
 provided in a .xlsx file (Tag_files_KD050_KD079.xlsx).
 The final taxaonomic assigment of the filtered raw sequence data
 is provided in the files:
 pairedend_KD050_assigned_uniq_10_clean_embl127.txt and
 pairedend_KD079_assigned_uniq_10_clean_embl127.txt. The
 final genus data sets are provided as .xlsx files:
 KD079_50_all_diatom_genera_surface_samples.xlsx and
 KD079_50_all_diatom_genera_core_samples.xlsx and These files include read
 count and fasta file of the genera retrieved from sediment surface and
 core samples.