DOI: 10.5061/dryad.6171j
title: Data from: Reconstructing long-term human impacts on plant communities: an ecological approach based on lake sediment DNA

description: Paleoenvironmental studies are essential to understand biodiversity
 changes over long timescales and to assess the relative importance of
 anthropogenic and environmental factors. Sedimentary ancient DNA (sedaDNA)
 is an emerging tool in the field of paleoecology and has proven to be a
 complementary approach to the use of pollen and macroremains for
 investigating past community changes. SedaDNA-based reconstructions of
 ancient environments often rely on indicator taxa or expert knowledge, but
 quantitative ecological analyses might provide more objective information.
 Here, we analysed sedaDNA to investigate plant community trajectories in
 the catchment of a high-elevation lake in the Alps over the last 6400
 years. We combined data on past and present plant species assemblages
 along with sedimentological and geochemical records to assess the relative
 impact of human activities through pastoralism, and abiotic factors
 (temperature and soil evolution). Over the last 6400 years, we identified
 significant variation in plant communities, mostly related to soil
 evolution and pastoral activities. An abrupt vegetational change
 corresponding to the establishment of an agropastoral landscape was
 detected during the Late Holocene, approximately 4500 years ago, with the
 replacement of mountain forests and tall-herb communities by heathlands
 and grazed lands. Our results highlight the importance of anthropogenic
 activities in mountain areas for the long-term evolution of local plant
 assemblages. SedaDNA data, associated with other paleoenvironmental
 proxies and present plant assemblages, appear to be a relevant tool for
 reconstruction of plant cover history. Their integration, in conjunction
 with classical tools, offers interesting perspectives for a better
 understanding of long-term ecosystem dynamics under the influence of
 human-induced and environmental drivers.
description: Sample_AgeThis file contains the age of each sample based on 14C measurements.Unfiltered sequencing data (fasta format)This fasta file contains unfiltered sequencing data (i.e. merged reads assigned to their original sample). Amplicons were amplified using the universal primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007). Sequences were obtained by a 2 x 100 bp paired-end sequencing on Illumina HiSeq 2500 platform. First processing steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) as follows: (i) Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (&gt;=40) (ii) Each merged sequence was assigned to its original sample using the tags information previously added to primers thanks to the ngsfilter program. For this step, only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. (iii) To reduce the file size, strictly identical sequences were merged together while keeping information about the origin of sequences.anterne_gh_raw_data_uniq.fastaUnfiltered sequencing data (table format)This table contains pre-filtered sequencing data (i.e. usable merged reads assigned to their original sample). Amplicons were amplified using the universal primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007). Sequences were obtained by a 2 x 100 bp paired-end sequencing on Illumina HiSeq 2500 platform. First processing steps were performed using the OBITOOLS software (http://metabarcoding.org/obitools) as follows: (i) Direct and reverse reads corresponding to the same sequence were aligned and merged thanks to the IlluminaPairEnd program. Only merged sequences with a high alignment quality score were retained (&gt;=40). (ii) Each merged sequence was assigned to its original sample using the tags information previously added to primers thanks to the ngsfilter program. For this step, only sequences containing both primers (with a maximum of 3 mismatches per primer) and exact tag sequences were selected. (iii) To reduce the file size, strictly identical sequences were merged together while keeping information about the origin of sequences. (iv) Sequences containing ambiguous nucleotides or shorter than 7 bp were discarded. (v) Pure singleton (sequences with 1 read among the whole dataset) were removed.ME_Pansu_AS2-1.txtFiltered sequencing dataThis table contains filtered sequences. Amplicons were amplified using the universal primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007). Sequences were obtained by a 2 x 100 bp paired-end sequencing on Illumina HiSeq 2500 platform. Data were filtered according to the filterering procedure described in Pansu et al. (2014) :'Reconstructing long-term human impacts on plant communities : an ecological approach based on lake sediment DNA'.ME_Pansu_AS1-1.xlsxAlpine reference database EMBL (gh)This file contains dereplicated sequences of alpine taxa extracted from the EMBL nucleic database release 117 using the ecopcr program (http://metabarcoding.org/obitools). Sequences have been extracted using the primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007). Then, only alpine taxa were selected.alpine_referenceDB_gh_embl.fastaGlobal reference database EMBL (gh)This file contains all dereplicated sequences of alpine taxa extracted from the EMBL nucleic database release 117 using the ecopcr program (http://metabarcoding.org/obitools). Sequences have been extracted using the primers “g” (5’-GGGCAATCCTGAGCCAA-3’) and “h” (5’-CCATTGAGTCTCTGCACCTATC-3’) (Taberlet et al. 2007).global_referenceDB_gh_embl.fasta.zip