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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

Citation

Zimmermann, Heike H. et al. (2020), 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, Dryad, Dataset, https://doi.org/10.5061/dryad.866t1g1p5

Abstract

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.

Methods

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).

Usage Notes

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).