Ancient sedimentary DNA shows rapid post-glacial colonisation of Iceland followed by relatively stable vegetation until the Norse settlement (Landnám) AD 870

Alsos, Inger Greve; Lammers, Youri; Kjellman, Sofia E.; Merkel, Marie Kristine Føreid; Bender, Emma M.; Rouillard, Alexandra; Erlendsson, Egill; Guðmundsdóttir, Esther Ruth; Benediktsson, Ívar Örn; Farnsworth, Wesley R.; Brynjólfsson, Skafti; Gísladóttir, Guðrún; Eddudóttir, Sigrún Dögg; Schomacker, Anders

doi:10.1016/j.quascirev.2021.106903

Cited by 37 publications

(60 citation statements)

References 75 publications

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“…With 366 identi ed plant taxa, Sulsseewli yields the richest single record studied to date with sedaDNA using an exact match. This is 2-3 times as many taxa as found in any previous study of ancient plant sedaDNA 7,8,28,29 , and highlights the advantage of using a region-wide comprehensive, rather than global and incomplete reference databases 9,30,31 . Our sedaDNA results uncover a hidden diversity of taxa that are unrepresented by pollen analysis [32][33][34] , including many insect-pollinated plants normally underrepresented by pollen, and highlights the importance of forbs in Subalpine communities 35 .…”

Section: Discussionmentioning

confidence: 69%

“…Singleton sequences and those shorter than 10 bp were removed and putative artifactual sequences were identi ed and removed from the dataset. 29 Previous metabarcoding studies of the Alps that targeted the trnL P6 loop have relied on global databases with a sparse representation of the Alpine ora resulting in limited, and potentially inaccurate, identi cations 9,30,31 . Here we generated a local DNA reference library.…”

Section: Database Construction and Sedimentary Ancient Dna Data Analysismentioning

confidence: 99%

“…The same approach was also used for the PhyloNorway genome skim database 29,83 , and the global EMBL rl143 database.…”

Section: Database Construction and Sedimentary Ancient Dna Data Analysismentioning

confidence: 99%

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High resolution ancient sedimentary DNA shows that alpine plant biodiversity is a result of human land use

Garcés-Pastor¹,

Coissac²,

Lavergne³

et al. 2021

Preprint

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Alpine areas are well known biodiversity hotspots, but their future may be threatened by expanding forest and changing human land use. Here, we reconstructed past vegetation, climate, and livestock over the past ~ 12,000 years from Lake Sulsseewli (European Alps), based on sedimentary ancient DNA, pollen, spores, chironomids, and microcharcoal. We assembled a highly-complete local DNA reference library (PhyloAlps, 3,923 plant species), and used this to obtain an exceptionally rich sedaDNA record of 366 plant taxa. The vegetation mainly responded to temperature during the first half of the Holocene, while human activity drove changes from 6 ka onwards. Land-use shifted from episodic grazing (Neolithic, Bronze Age) to agropastoral intensification (Medieval Age). This prompted a coexistence of species typically found at different elevational belts, thereby increasing plant richness to levels that characterise present-day alpine diversity. Our results indicate that traditional agropastoral activities should be maintained to prevent reforestation and preserve alpine plant biodiversity.

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Section: Discussionmentioning

confidence: 69%

Section: Database Construction and Sedimentary Ancient Dna Data Analysismentioning

confidence: 99%

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High resolution ancient sedimentary DNA shows that alpine plant biodiversity is a result of human land use

Garcés-Pastor¹,

Coissac²,

Lavergne³

et al. 2021

Preprint

Self Cite

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“…DNA extraction followed protocols followed Alsos et al . [ 63 ] using the QIAGEN DNeasy Powersoil Kit but adapted for smaller input volume of < 0.35mg and was performed in a dedicated ancient DNA laboratory at the University of Southampton. PCR amplification used generic primers of the trnL P6 loop of the plant chloroplast genome and exact PCR procedure followed Alsos et al .…”

Section: Methodsmentioning

confidence: 99%

Life before Stonehenge: The hunter-gatherer occupation and environment of Blick Mead revealed by sedaDNA, pollen and spores

et al. 2022

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The Neolithic and Bronze Age construction and habitation of the Stonehenge Landscape has been extensively explored in previous research. However, little is known about the scale of pre-Neolithic activity and the extent to which the later monumental complex occupied an ‘empty’ landscape. There has been a long-running debate as to whether the monumental archaeology of Stonehenge was created in an uninhabited forested landscape or whether it was constructed in an already partly open area of pre-existing significance to late Mesolithic hunter-gatherers. This is of significance to a global discussion about the relationship between incoming farmers and indigenous hunter-gatherer societies that is highly relevant to both Old and New World archaeology. Here we present the results of plant sedaDNA, palynological and geoarchaeological analysis at the Late hunter-gatherer site complex of Blick Mead at the junction of the drylands of Salisbury Plain and the floodplain of the River Avon, on the edge of the Stonehenge World Heritage Site. The findings are placed within a chronological framework built on OSL, radiocarbon and relative archaeological dating. We show that Blick Mead existed in a clearing in deciduous woodland, exploited by aurochsen, deer and hunter-gatherers for approximately 4000 years. Given its rich archaeology and longevity this strongly supports the arguments of continuity between the Late Mesolithic hunter-gatherers activity and Neolithic monument builders, and more specifically that this was a partially open environment important to both groups. This study also demonstrates that sediments from low-energy floodplains can provide suitable samples for successful environmental assaying using sedaDNA, provided they are supported by secure dating and complementary environmental proxies.

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“…Accurate identification of plant taxa is integral to many molecular studies and has been used in studies including the identification of plants from pollen for hay fever forecasting [1], for detecting adulteration in herbal medicine [2], and authenticating wood samples for commercially traded timber trees [3]. Plants can also be molecularly identified from ancient sedimentary DNA (sedaDNA) samples to reconstruct past vegetation [4,5], environmental DNA (eDNA) samples such as water for water quality assessments [6], faeces for diet authentication of grazing livestock [7] or to reveal new ecological information about animals' diet [8], and soil for biodiversity monitoring [9,10]. Accurate identification is essential for biodiversity monitoring studies as conservation efforts are dependent on obtaining species distribution information.…”

Section: Introductionmentioning

confidence: 99%

Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants

Chua

Leerhøi

Langkjær

et al. 2021

Preprint

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Recently, there has been a push towards the extended barcode concept of utilising chloroplast genomes (cpGenome) and nuclear ribosomal DNA (nrDNA) sequences for molecular identification of plants instead of the standard barcode regions. These extended barcodes has a wide range of applications, including biodiversity monitoring and assessment, primer design, and evolutionary studies. However, these extended barcodes are not well represented in global reference databases. To fill this gap, we generated cpGenomes and nrDNA reference data from genome skims of 184 plant species collected in Denmark. We further explored the application of our generated reference data for molecular identifications of plants in an environmental DNA metagenomics study. We assembled partial cpGenomes for 82.1% of sequenced species and full or partial nrDNA sequences for 83.7% of species. We added all assemblies to GenBank, of which chloroplast reference data from 101 species and nuclear reference data from 6 species were not previously represented. On average, we recovered 45 genes per species. The rate of recovery of standard barcodes was higher for nuclear barcodes (>89%) than chloroplast barcodes (< 60%). Extracted DNA yield did not affect assembly outcome, whereas high GC content did so negatively. For the in silico simulation of metagenomic reads, taxonomic assignments using the reference data generated had better species resolution (94.9%) as compared to GenBank (18.1%) without any identification errors. Genome skimming generates reference data of both standard barcodes and other loci, contributing to the global DNA reference database for plants.

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Ancient sedimentary DNA shows rapid post-glacial colonisation of Iceland followed by relatively stable vegetation until the Norse settlement (Landnám) AD 870

Cited by 37 publications

References 75 publications

High resolution ancient sedimentary DNA shows that alpine plant biodiversity is a result of human land use

High resolution ancient sedimentary DNA shows that alpine plant biodiversity is a result of human land use

Life before Stonehenge: The hunter-gatherer occupation and environment of Blick Mead revealed by sedaDNA, pollen and spores

Towards the extended barcode concept: Generating DNA reference data through genome skimming of danish plants

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