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152 results for “Ancient DNA”
Arctic-boreal bryophyte dynamics since the last glacial from ancient DNA metabarcoding
<p>A total of 26 lake-sediment cores collected from 26 study sites spanning the glacial and interglacial transition are used in this study. These sites are distributed across Siberia, Beringia, and Alaska regions, with a gradient of vegetation types dominated by tundra in the northern region and transitioning to boreal forest in the southern extents. DNA samples from the sediment core were analysed with a standard sedimentary ancient DNA metabarcoding pipeline (see additional description), which resulted in a raw dataset of all DNA plant sequences, which were then filtered for Bryophytes (Bryophyte DNA dataset). The Bryophyte DNA dataset contains 120 unique ASV. Samples in the Bryophyte DNA dataset are then grouped into 1000-year time slices and are subsequently resampled to a base count of 500 read counts for each time slice. After that, a Bryophyte trait datastet is assigned to the Bryophyte DNA dataset. </p> <p> </p> <h3>Input files</h3> <ul> <li><strong>Excel file with all data used in the R-Script:</strong> "Bryophytes_data.xlsx"</li> <li><strong>WorldClim 2.0 dataset with mean temperatures of Warmest Quarter</strong> (https://www.worldclim.org/; Fick, S.E. and R.J. Hijmans, 2017. WorldClim 2: new 1km spatial resolution climate surfaces for global land areas. <a href="https://rmets.onlinelibrary.wiley.com/doi/abs/10.1002/joc.5086">International Journal of Climatology 37 (12): 4302-4315</a>): "wc2.1_30s_bio_10.tif"</li> </ul> <h3>R script</h3> <ul> <li><strong>R-Script:</strong> "2025-01-14_R-Script_ arctic_boreal_bryophyte_dynamics_DNA_metabarcoding.R"</li> </ul> <h3>R outputs</h3> <ul> <li><strong>resampled Bryophyte metabarcoding percentage dataset with ASV:</strong> "2025-01-14_bryophyta_resampled_percentages_mean_100runs_sequences.csv"</li> <li><strong>resampled Bryophyte metabarcoding percentage dataset with unique scientific names: </strong>"2025-01-14_bryophyta_resampled_percentages_mean_100runs_scientific_names.csv"</li> <li><strong>GBIF taxa occurrences with WorldClim temperature data: </strong>"2025-01-14_gbif_taxa_occurrences_seqtypes_climate.csv"</li> </ul> <p> </p>
The use of ancient DNA from sediment as a viable measure of Quaternary biodiversity within the Brecon Beacons National Park: a preliminary study
<p>Contains 3 files.</p> <ul> <li>One spreadsheet containing processed sequences -SM1_results_spreadsheets</li> <li>The other two containing Read 1 and Read 2 of the raw sequences (fastq).</li> </ul> <p>Abstract</p> <p>A major challenge in the study of Quaternary environments is the variable preservation of paleoenvironmental evidence at many locations. Using ancient DNA from sediment cores (sedaDNA) allows the reconstruction of past biodiversity patterns at locations where traditional techniques often only reveal a partial picture. To test the feasibility of this approach, we analysed a sediment core from a peat bog, Traeth Mawr, in the Brecon Beacons National Park. Plant DNA was extracted and subjected to DNA metabarcoding, combining the use of universal PCR primers with Next-Generation Sequencing, to analyse a 7-143bp segment of the chloroplast <em>trn</em>L gene in five temporally separated sections of the core. Pollen analyses, from sections of the core, provide a comparison between the sedaDNA results and more traditional methods for studying the paleoenvironment. Partial reconstruction of past environmental variation was possible with the recovery of 113,682 DNA sequences representing six plant families, adding complementary results to traditional pollen analysis. This study is the first in the UK to successfully report the sequencing of ancient plant DNA from terrestrial sediments (currently a peat bog) using a DNA metabarcoding approach and exemplifies a promising area of research for addressing a range of questions about Quaternary environmental change.</p>
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)
<p>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.</p>
Permafrost-thaw lake development in Central Yakutia: sedimentary ancient DNA and element analyses from a Holocene sediment record
<p>In Central Yakutia (Siberia) livelihoods of local communities depend on alaas (thermokarst depression) landscapes and the lakes within. Development and dynamics of these alaas lakes are closely connected to climate change, permafrost thawing, catchment conditions, and land use. To reconstruct lake development throughout the Holocene we analyze sedimentary ancient DNA (sedaDNA) and biogeochemistry from a sediment core from Lake Satagay, spanning the last c. 10,800 calibrated years before present (cal yrs BP). SedaDNA of diatoms and macrophytes and microfossil diatom analysis reveal lake formation earlier than 10,700 cal yrs BP. The sedaDNA approach detected 42 amplicon sequence variants (ASVs) of diatom taxa, one ASV of Eustigmatophyceae (Nannochloropsis), and 12 ASVs of macrophytes. We relate diatom and macrophyte community changes to climate-driven shifts in water level and mineral and organic input, which result in variable water conductivity, in-lake productivity, and sediment deposition. We detect a higher lake level and water conductivity in the Early Holocene (c. 10,700–7000 cal yrs BP) compared to other periods, supported by the dominance of Stephanodiscus sp. and Stuckenia pectinata. Further climate warming towards the Mid-Holocene (7000–4700 cal yrs BP) led to a shallowing of Lake Satagay, an increase of the submerged macrophyte Ceratophyllum, and a decline of planktonic diatoms. In the Late Holocene (c. 4700 cal yrs BP–present) stable shallow water conditions are confirmed by small fragilarioid and staurosiroid diatoms dominating the lake. Lake Satagay has not yet reached the final stage of alaas development, but satellite imagery shows an intensification of anthropogenic land use, which in combination with future warming will likely result in a rapid desiccation of the lake.</p>
Fig. 7 in Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)
Fig. 7. Rio Doce drainage with the distribution of Deuterodon pedri, southeastern Brazil. The star indicates the type locality.
Fig. 3 in Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)
Fig. 3 Two paralectotypes of Deuterodon pedri, MCZ 17510. a-c. Photograph and X-ray computed tomography of the paralectotype with 72.1 mm SL, showing the dentary teeth decreasing gradually in size, corresponding to D. pedri. b-d. Photograph and X-ray computed tomography of the paralectotype with 58.6 mm SL, showing the dentary teeth decreasing abruptly, corresponding to Astyanax intermedius.
Fig. 2 in Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)
Fig. 2. Neighbor Joining tree and Haplotype network showing high similarity between specimens collected at rio Santo Antônio basin and sequence of the lectotype of Deuterodon pedri. a. Neighbor joining tree with bootstrap values. b. Haplotype network of D. pedri clade. Numbers in each branch of the net refer to number of mutational steps between haplotypes.
Fig. 5 in Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)
Fig. 5. Detailed images of the dorsolateral series of scales in Deuterodon pedri, showing their pigmentation pattern, each scale showing an arched and well delineated strip at the distal margin of the free border that is either dark brown when chromatophores are expanded (a. MNRJ 38463, 51.18 mm SL) or translucent when chromatophores are contracted (b. MCN 19698, 85.70 mm SL).
Fig. 6 in Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)
Fig. 6. Recently collected specimens of Deuterodon pedri showing variability according to sex and body size: a, female, MCN 19697, 79.82 mm SL; b, female, MCN 19698, 85.70 mm SL; c, juvenile, MNRJ 38463, 51.18 mm SL; d, male, UFRGS 17543, 86.47 mm SL.
Fig. 4 in Using ancient DNA to unravel taxonomic puzzles: the identity of Deuterodon pedri (Ostariophysi: Characidae)
Fig. 4. Specimen of Astyanax hastatus from Santa Cruz, Rio de Janeiro (MCZ 20958, 33.0 mm SL), tentatively identified as
Ancient DNA glossary
<p>The ancient DNA field uses a collection of specialized terms, as well as a specific vocabulary to describe its purposes, methodologies, results, and interpretations, which may be unfamiliar and unclear/obscure to scientists of other disciplines, such as archaeologists, anthropologists, historians, etc. To this end, in order to fill the comprehension gap and enable easier multidisciplinary communication, the Ancient DNA Lab of IMBB-FORTH compiled a list of terms, frequently used in the ancient DNA field that can serve as a thesaurus for everybody.</p>
Figure 3 in Ancient DNA from the extinct New Zealand grayling (Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal
Figure 3. Median-joining haplotype networks of the Retropinnidae constructed from A, cytochrome b (1363 comparable sites) and B, 16s rRNA (575 comparable sites) alignments in POPART (for GenBank Accession numbers, see Supporting Information, Table S2). Haplotypes (circles) are proportional to frequency (numbers), with number of substitutions indicated by hatches along branches. Black circles represent undetected intermediary haplotypes, with colours corresponding to species.
Figure 1 in Ancient DNA from the extinct New Zealand grayling (Prototroctes oxyrhynchus) reveals evidence for Miocene marine dispersal
Figure 1. The extinct New Zealand grayling (Prototroctes oxyrhynchus). Artwork by Frank Edward Clarke. Annotations in figure contain a nomen nudum. Museum of New Zealand Te Papa Tongarewa CC BY-NC-ND 4.0.
Data and scripts for: Read length dominates phylogenetic placement accuracy of ancient DNA reads
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Tracing 600 years of long-distance Atlantic cod trade in medieval and post-medieval Oslo using stable isotopes and ancient DNA
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Ancient DNA reveals genetic admixture in China during tiger evolution
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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)
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Permafrost-thaw lake development in Central Yakutia: sedimentary ancient DNA and element analyses from a Holocene sediment record
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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
<p>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 (<span class="html-italic">s</span>edaDNA) 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 (<em><span class="html-italic">Larix</span></em>,<span class="html-italic"> <em>Picea</em></span>,<span class="html-italic"> <em>Populus</em></span>) and shrubs (<em><span class="html-italic">Alnus</span></em>, <em><span class="html-italic">Betula</span></em>, <em><span class="html-italic">Ribes</span></em>, <span class="html-italic"><em>Cornus</em>, </span>Saliceae) on the currently treeless island. After the Last Glacial Maximum, <em><span class="html-italic">Larix</span> </em>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.</p>
Phylogenetic diversity and environment form assembly rules for Arctic diatom genera – a study on recent and ancient sedimentary DNA
<p><span><b>Aim</b></span></p> <p><span>This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian treeline. We first analysed how phylogenetic distance relates to taxonomic richness and turnover. Second, we used relatedness indices to evaluate if environmental filtering or competition influences the assemblies in space and through time. Third, we used distance-based ordination to test which environmental variables shape diatom turnover.</span></p> <p><span><b>Location</b></span></p> <p><span>Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7000 years before present, to capture the forest–tundra transition in space and time, respectively. </span></p> <p><span><b>Taxon</b></span></p> <p><span>Arctic freshwater diatoms.</span></p> <p><span><b>Methods</b></span></p> <p><span>We applied metabarcoding to retrieve diatom diversity from surface and core sedimentary DNA. The taxonomic assignment binned sequence types (lineages) into genera and created taxonomic (abundance of lineages within different genera) and phylogenetic datasets (phylogenetic distances of lineages within different genera).</span></p> <p><span><b>Results</b></span></p> <p><span>Contrary to our expectations, we find a unimodal relationship between phylogenetic distance and richness in diatom genera. We discern a positive relationship between phylogenetic distance and taxonomic turnover in spatially and temporally distributed diatom genera. Further, we reveal positive relatedness indices in diatom genera across the spatial environmental gradient and predominantly in time-slices at a single location, with very few exceptions assuming effects of competition. Distance-based ordination of taxonomic and phylogenetic turnover indicates that lake environment variables, like HCO<sub>3</sub><sup>–</sup> and water depth, largely explain diatom turnover. </span></p> <p><span><b>Main conclusion</b></span></p> <p>Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian treeline ecotone. Using a space–time approach we are able to exclude the influence of geography and elucidate that lake environmental variables primarily shape the assemblies. We conclude that some diatom genera have greater capabilities to adapt to environmental changes, whereas others will be putatively replaced or lost due to the displacement of the Arctic tundra biome under recent global warming.</p>
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