DOI: 10.5061/dryad.mgqnk98xk
title: 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)

description: 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.
description: 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 5′end 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).
description: 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).