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Data from: Phylogenetic diversity and environment form assembly rules for Arctic diatom genera—a study on recent and ancient sedimentary DNA

Cite this dataset

Stoof-Leichsenring, Kathleen R.; Pestryakova, Luidmila A.; Epp, Laura S.; Herzschuh, Ulrike (2020). Data from: Phylogenetic diversity and environment form assembly rules for Arctic diatom genera—a study on recent and ancient sedimentary DNA [Dataset]. Dryad.



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.


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.


Arctic freshwater diatoms.


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).


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.


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.


Federal Ministry of Education and Research, Award: 5.2711.2017/4.6

Russian Foundation for Basic Research, Award: 18‐45‐140053