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Data for: Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia)

Citation

Zimmermann, Heike et al. (2020), Data for: Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia) , Dryad, Dataset, https://doi.org/10.5061/dryad.mgqnk98xk

Abstract

Organic matter deposited in ancient, ice-rich permafrost sediments is vulnerable to climate change and may contribute to the future release of greenhouse gases; it is thus important to get a better characterization of the plant organic matter within such sediments. From a Late Quaternary permafrost sediment core from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter, and undertook palynological analysis to assess the environmental conditions during deposition. Using sedaDNA, we identified 154 taxa and from pollen and non-pollen palynomorphs we identified 83 taxa. In the deposits dated between 54 and 51 kyr BP, sedaDNA records a diverse low-centred polygon plant community including recurring aquatic pond vegetation while from the pollen record we infer terrestrial open-land vegetation with relatively dry environmental conditions at a regional scale. A fluctuating dominance of either terrestrial or swamp and aquatic taxa in both proxies allowed the local hydrological development of the polygon to be traced. In deposits dated between 11.4 and 9.7 kyr BP (13.4–11.1 cal kyr BP), sedaDNA shows a taxonomic turnover to moist shrub tundra and a lower taxonomic richness compared to the older samples. Pollen also records a shrub tundra community, mostly seen as changes in relative proportions of the most dominant taxa, while a decrease in taxonomic richness was less pronounced compared to sedaDNA. Our results show the advantages of using sedaDNA in combination with palynological analyses when macrofossils are rarely preserved. The high resolution of the sedaDNA record provides a detailed picture of the taxonomic composition of plant-derived organic matter throughout the core, and palynological analyses prove valuable by allowing for inferences of regional environmental conditions.

Methods

From a Late Quaternary permafrost sediment core (BK-8) from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter. Total DNA was extracted from 54 samples which were processed in 5 batches of up to 11 samples and one negative control. The PCR reactions were performed with the trnL g and h primers (Taberlet et al., 2007). Both primers were modified on the 5end by unique 8 bp tags which varied from each other in at least five base pairs to distinguish samples after sequencing (Binladen et al., 2007) and were additionally elongated by NNN tagging to improve cluster detection on the sequencing platform (De Barba etal., 2014). For each sample, we pooled two positive PCR products for sequencing, under the condition that the associated NTCs and extraction blank were negative. The two pooled PCR products were purified using the MinElute PCRPurification Kit and subsequently the samples were pooled in equal concentrations. All extraction blanks and NTCs were included in the sequencing run, using a standardized volume of 10 μL, even though they were negative in the PCRs. Library preparation (HiSeq SBS Kit v4) and sequencing on the Illumina HiSeq 2500 platform Economy lane (2×125 bp, High Output, Index: ACTTGA) were performed by the Fasteris SA sequencing service (Switzerland).

Usage Notes

Here, we provide the raw paired-end sequencing data received from Fasteris as gz-compressed fastq files (forward reads: 150423_SND405_A_L001_HUT-1_R1.fastq.gz; reverse reads: 150423_SND405_A_L001_HUT-1_R2.fastq.gz).

Data processing, which includes assignment of the sequencing reads to the different samples with a tagfile (tagfile_BK8.txt), denoising and taxonomic assignment of reads, was performed with the OBITools pipeline (https://pythonhosted.org/OBITools/welcome.html). The script containing the commands used to process the data is provided (BK8.log). Furthermore, we provide the annotated obitools output as tab-separated txt-files (BK8_run2_Dez2015.clean.EMBL117_09_12_2015.txt, BK8_run2_Dez2015.clean.ET_arc_7_12_2015.txt).

Funding

German Federal Ministry of Education and Research (BMBF), Award: 03G0836B

German Federal Ministry of Education and Research (BMBF), Award: 03G0836F

German Federal Ministry of Education and Research (BMBF), Award: 03G0836B