DOI: 10.5061/dryad.866t1g1p5
title: Data from: The history of tree and shrub taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the last interglacial uncovered by sedimentary ancient DNA and pollen data

description: Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly
 coupled with climate and were spatially highly dynamic during past
 glacial-interglacial cycles. Only a few studies cover vegetation changes
 since the last interglacial, as most of the former landscapes are
 inundated and difficult to access. Using pollen analysis and sedimentary
 ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on
 Bol’shoy Lyakhovsky Island since the last interglacial from permafrost
 sediments. Last interglacial samples depict high levels of floral
 diversity with the presence of trees (Larix, Picea, Populus) and shrubs
 (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island.
 After the Last Glacial Maximum, Larix re-colonised the island but
 disappeared along with most shrub taxa. This was probably caused by
 Holocene sea-level rise, which led to increased oceanic conditions on the
 island. Additionally, we applied two newly developed larch-specific
 chloroplast markers to evaluate their potential for tracking past
 population dynamics from environmental samples. The novel markers were
 successfully re-sequenced and exhibited two variants of each marker in
 last interglacial samples. SedaDNA can track vegetation changes as well as
 genetic changes across geographic space through time and can improve our
 understanding of past processes that shape modern patterns.
description: In this study we analysed plant-derived sedimentary ancient DNA
 (sedaDNA) from permafrost cores L14-2, L14-3, L14-4 and L14-5 to
 investigate past vegetation change on Bol’shoy Lyakhovsky Island. A core
 barrel loss in the borehole prevented further drilling and four additional
 samples (hand-pieces) L14-04B were collected from the coastal bluff from
 layers resembling the upper part of core L14-04 while five additional
 samples L14-04C originated from ice-wedge casts resembling the lower part
 of the core. Total DNA was extracted from 72 samples
 and 8 negative controls. 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.
 Yet, for one sample (core L14-03, 5.13 m depth) only one positive
 amplification could be retrieved. The two pooled PCR products were
 purified using the MinElute PCR Purification 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) 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: 161028_SND405_A_L005_HUA-6_R1.fastq.gz; reverse
 reads: 161028_SND405_A_L005_HUA-6_R2.fastq.gz). Data processing, which includes
 assignment of the sequencing reads to the different samples with a tagfile
 (tagfile_L14.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 (log.L14.txt).
 Furthermore, we provide the annotated obitools output as tab-separated
 txt-files (L14_embl127gh_final.txt, L14_arc_gh_final.txt). To translate
 extraction labels to sample names with corresponding depth, we provide a
 table (sample_names.text).