TY - JOUR A1 - Niemeyer, Bastian A1 - Epp, Laura Saskia A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline JF - Molecular ecology resources N2 - Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north-south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes. sedDNA metabarcoding recorded 114 plant taxa, about half of them to species level, while pollen analyses identified 43 taxa, both exceeding the 31 taxa found by vegetation field surveys. Increasing Larix percentages from north to south were consistently recorded by all three methods and principal component analyses based on percentage data of vegetation surveys and DNA sequences separated tundra from forested sites. Comparisons of the ordinations using procrustes and protest analyses show a significant fit among all compared pairs of records. Despite similarities of sedDNA and pollen records, certain idiosyncrasies, such as high percentages of Alnus and Betula in all pollen and high percentages of Salix in all sedDNA spectra, are observable. Our results from the tundra to single-tree tundra transition zone show that sedDNA analyses perform better than pollen in recording site-specific richness (i.e., presence/absence of taxa in the vicinity of the lake) and perform as well as pollen in tracing vegetation composition. KW - environmental DNA KW - metabarcoding KW - pollen KW - Siberia KW - trnL marker KW - vegetation Y1 - 2017 U6 - https://doi.org/10.1111/1755-0998.12689 SN - 1755-098X SN - 1755-0998 VL - 17 SP - e46 EP - e62 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Salleh, Faezah Mohd A1 - Ramos-Madrigal, Jazmin A1 - Penaloza, Fernando A1 - Liu, Shanlin A1 - Sinding, Mikkel-Holger S. A1 - Patel, Riddhi P. A1 - Martins, Renata A1 - Lenz, Dorina A1 - Fickel, Jörns A1 - Roos, Christian A1 - Shamsir, Mohd Shahir A1 - Azman, Mohammad Shahfiz A1 - Lim, Burton K. A1 - Rossiter, Stephen J. A1 - Wilting, Andreas A1 - Gilbert, M. Thomas P. T1 - An expanded mammal mitogenome dataset from Southeast Asia JF - Gigascience N2 - Background: Findings: Approximately 55 gigabases of raw sequence were generated. From this data we assembled 72 complete mitogenome sequences, with an average depth of coverage of 102.9x and 55.2x for modern samples and historical samples, respectively. This dataset represents 52 species, of which 30 species had no previous mitogenome data available. The mitogenomes were geotagged to their sampling location, where known, to display a detailed geographical distribution of the species. Conclusion: KW - invertebrate-derived (iDNA) KW - metabarcoding KW - GenBank KW - Taxonomic assignment Y1 - 2017 SN - 2047-217X VL - 6 IS - 8 SP - 1 EP - 19 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Wurzbacher, Christian A1 - Warthmann, Norman A1 - Bourne, Elizabeth Charlotte A1 - Attermeyer, Katrin A1 - Allgaier, Martin A1 - Powell, Jeff R. A1 - Detering, Harald A1 - Mbedi, Susan A1 - Großart, Hans-Peter A1 - Monaghan, Michael T. T1 - High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany) JF - MycoKeys N2 - Freshwater fungi are a poorly studied ecological group that includes a high taxonomic diversity. Most studies on aquatic fungal diversity have focused on single habitats, thus the linkage between habitat heterogeneity and fungal diversity remains largely unexplored. We took 216 samples from 54 locations representing eight different habitats in the meso-oligotrophic, temperate Lake Stechlin in North-East Germany. These included the pelagic and littoral water column, sediments, and biotic substrates. We performed high throughput sequencing using the Roche 454 platform, employing a universal eukaryotic marker region within the large ribosomal subunit (LSU) to compare fungal diversity, community structure, and species turnover among habitats. Our analysis recovered 1027 fungal OTUs (97% sequence similarity). Richness estimates were highest in the sediment, biofilms, and benthic samples (189-231 OTUs), intermediate in water samples (42-85 OTUs), and lowest in plankton samples (8 OTUs). NMDS grouped the eight studied habitats into six clusters, indicating that community composition was strongly influenced by turnover among habitats. Fungal communities exhibited changes at the phylum and order levels along three different substrate categories from littoral to pelagic habitats. The large majority of OTUs (> 75%) could not be classified below the order level due to the lack of aquatic fungal entries in public sequence databases. Our study provides a first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition. Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body. KW - Freshwater fungi KW - aquatic fungi KW - metabarcoding KW - LSU KW - GMYC KW - habitat specificity KW - Chytridiomycota KW - Cryptomycota KW - Rozellomycota KW - community ecology KW - lake ecosystem KW - biofilm KW - sediment KW - plankton KW - water sample KW - benthos KW - reed KW - fungal diversity Y1 - 2016 U6 - https://doi.org/10.3897/mycokeys.16.9646 SN - 1314-4057 SN - 1314-4049 VL - 41 SP - 17 EP - 44 PB - Pensoft Publ. CY - Sofia ER - TY - JOUR A1 - Liu, Sisi A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Kruse, Stefan A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - Holocene vegetation and plant diversity changes in the north-eastern Siberian treeline region from pollen and sedimentary ancient DNA JF - Frontiers in Ecology and Evolution N2 - Although sedimentary ancient DNA (sedaDNA) has been increasingly used to study paleoecological dynamics (Schulte et al., 2020), the approach has rarely been compared with the traditional method of pollen analysis for investigating past changes in the vegetation composition and diversity of Arctic treeline areas. Here, we provide a history of latitudinal floristic composition and species diversity based on a comparison ofsedaDNA and pollen data archived in three Siberian lake sediment cores spanning the mid-Holocene to the present (7.6-0 cal ka BP), from northern typical tundra to southern open larch forest in the Omoloy region. Our results show that thesedaDNA approach identifies more plant taxa found in the local vegetation communities, while the corresponding pollen analysis mainly captures the regional vegetation development and has its limitations for plant diversity reconstruction. Measures of alpha diversity were calculated based onsedaDNA data recovered from along a tundra to forest tundra to open larch forest gradient. Across all sites,sedaDNA archives provide a complementary record of the vegetation transition within each lake's catchment, tracking a distinct latitudinal vegetation type range from larch tree/alder shrub (open larch forest site) to dwarf shrub-steppe (forest tundra) to wet sedge tundra (typical tundra site). By contrast, the pollen data reveal an open landscape, which cannot distinguish the temporal changes in compositional vegetation for the open larch forest site and forest-tundra site. IncreasingLarixpollen percentages were recorded in the forest-tundra site in the last millenium although noLarixDNA was detected, suggesting that thesedaDNA approach performs better for tracking the local establishment ofLarix. Highest species richness and diversity are found in the mid-Holocene (before 4.4 ka) at the typical tundra site with a diverse range of vegetational habitats, while lowest species richness is recorded for the forest tundra where dwarf-willow habitats dominated the lake's catchment. During the late Holocene, strong declines in species richness and diversity are found at the typical tundra site with the vegetation changing to relatively simple communities. Nevertheless, plant species richness is mostly higher than at the forest-tundra site, which shows a slightly decreasing trend. Plant species richness at the open larch forest site fluctuates through time and is higher than the other sites since around 2.5 ka. Taken together, there is no evidence to suggest that the latitudinal gradients in species diversity changes are present at a millennial scale. Additionally, a weak correlation between the principal component analysis (PCA) site scores ofsedaDNA and species richness suggests that climate may not be a direct driver of species turnover within a lake's catchment. Our data suggest thatsedaDNA and pollen have different but complementary abilities for reconstructing past vegetation and species diversity along a latitude. KW - sedimentary ancient DNA KW - metabarcoding KW - pollen KW - Siberia KW - palaeovegetation KW - plant diversity KW - latitudinal gradient Y1 - 2020 U6 - https://doi.org/10.3389/fevo.2020.560243 SN - 2296-701X VL - 8 PB - Frontiers Media CY - Lausanne ER - TY - THES A1 - Huang, Sichao T1 - Past and present biodiversity in northeastern Siberia inferred from sedimentary DNA metabarcoding N2 - The arctic-boreal treeline is a transition zone from taiga to tundra covering a vast area in Siberia. It often features large environmental gradients and reacts sensitively to changes in the environment. For example, the expansion of shrubs and a northward movement of the treeline are observable in Siberia as a response to the warming climate. The changes in vegetation across the treeline are known to influence the water chemistry in the lakes. This causes further alteration to the composition and diversity of sensitive aquatic organisms such as diatoms and macrophytes. Despite the rising awareness of the complex climate-feedback mechanisms of terrestrial plants, the understanding of their assembly rules and about responses of aquatic biomes in the surrounding treeline lakes is still limited. The goal of this thesis is to examine the previous and present biodiversity of terrestrial and freshwater biomes from the Siberian treeline ecotone, as well as their reactions to environmental changes. In particular, this thesis attempts to examine the performance of applying sedimentary DNA metabarcoding in terrestrial plants, aquatic macrophytes and diatoms, their spatial patterns along the environmental gradients and their temporal patterns throughout the climate transition from the late Pleistocene to Holocene. Sedimentary DNA metabarcoding combined with next-generation sequencing is applied as a primary tool to explore the composition and diversity of terrestrial plants, diatoms and aquatic macrophytes. The main study area is located in Chukotka of northeastern Siberia in the Arctic, a biodiversity hotspot due to its continental location and the diverse habitats of the glacial refugium. The modern diatom diversity was assessed with a specific diatom metabarcoding marker and morphological identification. Both approaches agree to a dominance of Fragilariaceae and Aulacoseiraceae, as well as on the environmental influential indicators of the diatom community. The high diversity of Fragilariaceae identified in the thermokarst lakes is found to follow the vegetation gradient along the treeline, suggesting that diatom metabarcoding can decipher relationships between diatom assemblage shifts and the relevant environmental changes. In particular, the metabarcoding approach detects diversification of fragilarioids in glacial lakes which is not visible using morphology. Sedimentary ancient DNA records indicate a vegetation mosaic of forb-dominated steppe-tundra during 28-19 ka, followed by a shift to dwarf-shrub tundra during 19-14 ka. During the most recent 14 thousand years, the vegetation consists of deciduous shrublands, then a change to boreal forest is observed. Investigations on the alpha diversity of the vegetation show that species richness is unexpectedly highest during pre-LGM, which is likely related to the extensive area that allows for more taxa. The optimum Holocene warming during 9-6 ka is not accompanied by a high richness as widely believed, but with an evenly distributed community by the fulfilment of erect shrubs. Furthermore, changes in taxonomic and phylogenetic diversity show complementary results in understanding community diversity. The composition and richness in the modern macrophytes community from Siberian Arctic and Chinese alpine are best co-influenced by July temperature and electrical conductivity.. Past macrophyte turnover during the late Pleistocene-Holocene is less noticeable in Siberia, whereas a pronounced community change from emergent to submerged plants is detected from Chinese alpine regions at about 14 ka due to increasing temperature and varying water conductivity. Finally, sedimentary DNA metabarcoding is a cost-effective and powerful proxy for ecological application, whereas completeness of the reference library, coverage and resolution of the metabarcoding marker are the major limitations of sedimentary DNA based diversity monitoring. The composition and richness in modern vegetation and macrophytes across broad spatial gradients is constrained by environmental variables, suggesting a potential usage for environmental monitoring. Diatom distributions are driven by different water variables along the treeline. Past records indicate that the shrub coverage has a noticeable influence on the assemblies of both terrestrial plants and aquatic macrophytes, though the shift in macrophyte community is relatively minor in the past 28 thousand years. In the long-term, the shrub expansion may eventually result in a genetically more diverse vegetation community but reduced species richness. When exceeding the optimal temperatures, further warming may lead to a decrease and putative loss of macrophytes and diatoms. N2 - Die arktisch-boreale Baumgrenze ist eine Übergangszone von Taiga zu Tundra, die ein weites Gebiet in Sibirien abdeckt. Es weist häufig große Umweltgradienten auf und reagiert empfindlich auf Änderungen in der Umwelt. Beispielsweise sind in Sibirien als Reaktion auf das sich erwärmende Klima die Ausdehnung von Sträuchern und eine Bewegung der Baumgrenze nach Norden zu beobachten. Es ist bekannt, dass die Veränderungen der Vegetation entlang der Baumgrenze die Wasserchemie in den Seen beeinflussen. Dies führt zu einer weiteren Veränderung der Zusammensetzung und Vielfalt empfindlicher Wasserorganismen wie Kieselalgen und Makrophyten. Trotz des zunehmenden Bewusstseins für die komplexen Klimarückkopplungsmechanismen von Landpflanzen ist das Verständnis ihrer Zusammensetzung und der Reaktionen aquatischer Biome in den umliegenden Baumseen immer noch begrenzt. Ziel dieser Arbeit ist es, die bisherige und gegenwärtige Artenvielfalt von Land- und Süßwasserbiomen aus dem sibirischen Baumlinien-Ökoton sowie deren Reaktionen auf Umweltveränderungen zu untersuchen. In dieser Arbeit wird insbesondere versucht, die Leistung der Anwendung der sedimentären DNA-Metabarkodierung in Landpflanzen, aquatischen Makrophyten und Kieselalgen, ihre räumlichen Muster entlang der Umweltgradienten und ihre zeitlichen Muster während des Klimaübergangs vom späten Pleistozän zum Holozän zu untersuchen. Die metabolische DNA-Metabarkodierung in Kombination mit der “Next generation Sequencing” wird als primäres Instrument zur Untersuchung der Zusammensetzung und Vielfalt von Landpflanzen, Kieselalgen und aquatischen Makrophyten eingesetzt. Das Hauptuntersuchungsgebiet befindet sich in Chukotka im Nordosten Sibiriens in der Arktis, einem Hotspot für Artenvielfalt aufgrund seiner kontinentalen Lage und der vielfältigen Lebensräume des Gletscher-Refugiums. Die moderne Diatomeendiversität wurde mit einem spezifischen Diatom-Metabarcoding Marker und einer morphologischen Identifizierung bewertet. Beide Ansätze stimmen mit einer Dominanz von Fragilariaceae und Aulacoseiraceae sowie mit den umweltbeeinflussenden Indikatoren der Kieselalgengemeinschaft überein. Die hohe Vielfalt der in den Thermokarstseen identifizierten Fragilariaceae folgt dem Vegetationsgradienten entlang der Baumgrenze, was darauf hindeutet, dass die Metabarkodierung von Kieselalgen Beziehungen zwischen Verschiebungen der Kieselalgenassemblage und den relevanten Umweltveränderungen entschlüsseln kann. Insbesondere erkennt der Metabarcoding-Ansatz eine Diversifikation von Fragilarioiden in Gletscherseen, die unter Verwendung der Morphologie nicht sichtbar ist. Sedimentäre alte DNA-Aufzeichnungen weisen auf ein Vegetationsmosaik der von Forb dominierten Steppentundra zwischen 28 und 19 ka hin, gefolgt von einer Verschiebung in die Zwergstrauch-Tundra zwischen 19 und 14 ka. In den letzten 14.000 Jahren besteht die Vegetation aus Laubbäumen, dann wird eine Veränderung des borealen Waldes beobachtet. Untersuchungen zur Alpha-Diversität der Vegetation zeigen, dass der Artenreichtum vor der LGM unerwartet am höchsten ist, was wahrscheinlich mit dem ausgedehnten Gebiet zusammenhängt, das mehr Taxa zulässt. Die optimale Erwärmung des Holozäns während 9-6 ka geht nicht mit einem hohen Reichtum einher, wie allgemein angenommen wird, sondern mit einer gleichmäßig verteilten Gemeinschaft durch die Erfüllung aufrecht stehender Sträucher. Darüber hinaus zeigen Änderungen der taxonomischen und phylogenetischen Vielfalt komplementäre Ergebnisse für das Verständnis der Vielfalt in der Gemeinschaft. Die Zusammensetzung und der Reichtum der modernen Makrophytengemeinschaft aus der sibirischen Arktis und den chinesischen Alpen werden am besten von der Temperatur im Juli und der elektrischen Leitfähigkeit beeinflusst. Der vergangene Makrophytenumsatz während des späten Pleistozän-Holozäns ist in Sibirien weniger auffällig, während in chinesischen Alpenregionen bei etwa 14 ka aufgrund der steigenden Temperatur und der unterschiedlichen Wasserleitfähigkeit ein ausgeprägter Wechsel der Gemeinschaft von emergenten zu untergetauchten Pflanzen festgestellt wird. Schließlich ist die Sediment-DNA-Metabarkodierung ein kostengünstiger und leistungsfähiger Proxy für die ökologische Anwendung, während die Vollständigkeit der Referenzbibliothek, die Abdeckung und die Auflösung des Metabarkodierungsmarkers die Hauptbeschränkungen der auf Sediment-DNA basierenden Diversitätsüberwachung darstellen. Die Zusammensetzung und der Reichtum an moderner Vegetation und Makrophyten über breite räumliche Gradienten hinweg werden durch Umgebungsvariablen eingeschränkt, was auf eine mögliche Verwendung für die Umweltüberwachung hindeutet. Die Verteilung der Kieselalgen wird durch verschiedene Wasservariablen entlang der Baumgrenze gesteuert. Frühere Aufzeichnungen zeigen, dass die Strauchbedeckung einen spürbaren Einfluss auf die Ansammlungen von Landpflanzen und Wassermakrophyten hat, obwohl die Verschiebung der Makrophytengemeinschaft in den letzten 28.000 Jahren relativ gering ist. Langfristig kann die Strauchausdehnung letztendlich zu einer genetisch vielfältigeren Vegetationsgemeinschaft führen, die jedoch den Artenreichtum verringert. Wenn die optimalen Temperaturen überschritten werden, kann eine weitere Erwärmung zu einer Abnahme und einem mutmaßlichen Verlust von Makrophyten und Kieselalgen führen. KW - metabarcoding KW - plant diversity KW - iatom diversity KW - phylogenetic diversity KW - ancient DNA Y1 - 2021 ER - TY - GEN A1 - Bálint, Miklós A1 - Márton, Orsolya A1 - Schatz, Marlene A1 - Düring, Rolf-Alexander A1 - Grossart, Hans-Peter T1 - Proper experimental design requires randomization/balancing of molecular ecology experiments T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 616 KW - batch effect KW - bias KW - DNA extraction KW - environmental DNA KW - laboratory practice KW - lake community KW - metabarcoding KW - nondemonic intrusions KW - PCR KW - sediment Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-423878 SN - 1866-8372 IS - 616 ER - TY - JOUR A1 - Balint, Miklos A1 - Marton, Orsolya A1 - Schatz, Marlene A1 - Düring, Rolf-Alexander A1 - Grossart, Hans-Peter T1 - Proper experimental design requires randomization/balancing of molecular ecology experiments JF - Ecology and evolution N2 - Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results. KW - batch effect KW - bias KW - DNA extraction KW - environmental DNA KW - laboratory practice KW - lake community KW - metabarcoding KW - nondemonic intrusions KW - PCR KW - sediment Y1 - 2018 U6 - https://doi.org/10.1002/ece3.3687 SN - 2045-7758 VL - 8 IS - 3 SP - 1786 EP - 1793 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Minutillo, Serena A. A1 - Ruano-Rosa, David A1 - Abdelfattah, Ahmed A1 - Schena, Leonardo A1 - Malacrino, Antonino T1 - The fungal microbiome of wheat flour includes potential mycotoxin producers JF - Foods N2 - Consumers are increasingly demanding higher quality and safety standards for the products they consume, and one of this is wheat flour, the basis of a wide variety of processed products. This major component in the diet of many communities can be contaminated by microorganisms before the grain harvest, or during the grain storage right before processing. These microorganisms include several fungal species, many of which produce mycotoxins, secondary metabolites that can cause severe acute and chronic disorders. Yet, we still know little about the overall composition of fungal communities associated with wheat flour. In this study, we contribute to fill this gap by characterizing the fungal microbiome of different types of wheat flour using culture-dependent and -independent techniques. Qualitatively, these approaches suggested similar results, highlighting the presence of several fungal taxa able to produce mycotoxins. In-vitro isolation of fungal species suggest a higher frequency of Penicillium, while metabarcoding suggest a higher abundance of Alternaria. This discrepancy might reside on the targeted portion of the community (alive vs. overall) or in the specific features of each technique. Thus, this study shows that commercial wheat flour hosts a wide fungal diversity with several taxa potentially representing concerns for consumers, aspects that need more attention throughout the food production chain. KW - Penicillium KW - Alternaria KW - post-harvest KW - metabarcoding Y1 - 2022 U6 - https://doi.org/10.3390/foods11050676 SN - 2304-8158 VL - 11 IS - 5 PB - MDPI CY - Basel ER - TY - JOUR A1 - Zimmermann, Heike Hildegard A1 - Raschke, Elena A1 - Epp, Laura Saskia A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Schirrmeister, Lutz A1 - Schwamborn, Georg A1 - Herzschuh, Ulrike T1 - 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 JF - Genes N2 - 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. KW - sedaDNA KW - metabarcoding KW - trnL KW - single-nucleotide polymorphism (SNP) KW - treeline KW - MIS 5 to 1 KW - permafrost deposits KW - radiocarbon ages KW - palaeoenvironment KW - Larix Y1 - 2017 U6 - https://doi.org/10.3390/genes8100273 SN - 2073-4425 VL - 8 IS - 10 SP - 273 PB - MDPI CY - Basel ER - TY - JOUR A1 - Courtin, Jérémy A1 - Andreev, Andrei A1 - Raschke, Elena A1 - Bala, Sarah A1 - Biskaborn, Boris A1 - Liu, Sisi A1 - Zimmermann, Heike A1 - Diekmann, Bernhard A1 - Stoof-Leichsenring, Kathleen R. A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - Vegetation changes in Southeastern Siberia during the late pleistocene and the holocene JF - Frontiers in Ecology and Evolution N2 - Relationships between climate, species composition, and species richness are of particular importance for understanding how boreal ecosystems will respond to ongoing climate change. This study aims to reconstruct changes in terrestrial vegetation composition and taxa richness during the glacial Late Pleistocene and the interglacial Holocene in the sparsely studied southeastern Yakutia (Siberia) by using pollen and sedimentary ancient DNA (sedaDNA) records. Pollen and sedaDNA metabarcoding data using the trnL g and h markers were obtained from a sediment core from Lake Bolshoe Toko. Both proxies were used to reconstruct the vegetation composition, while metabarcoding data were also used to investigate changes in plant taxa richness. The combination of pollen and sedaDNA approaches allows a robust estimation of regional and local past terrestrial vegetation composition around Bolshoe Toko during the last similar to 35,000 years. Both proxies suggest that during the Late Pleistocene, southeastern Siberia was covered by open steppe-tundra dominated by graminoids and forbs with patches of shrubs, confirming that steppe-tundra extended far south in Siberia. Both proxies show disturbance at the transition between the Late Pleistocene and the Holocene suggesting a period with scarce vegetation, changes in the hydrochemical conditions in the lake, and in sedimentation rates. Both proxies document drastic changes in vegetation composition in the early Holocene with an increased number of trees and shrubs and the appearance of new tree taxa in the lake's vicinity. The sedaDNA method suggests that the Late Pleistocene steppe-tundra vegetation supported a higher number of terrestrial plant taxa than the forested Holocene. This could be explained, for example, by the "keystone herbivore" hypothesis, which suggests that Late Pleistocene megaherbivores were able to maintain a high plant diversity. This is discussed in the light of the data with the broadly accepted species-area hypothesis as steppe-tundra covered such an extensive area during the Late Pleistocene. KW - last glacial KW - Holocene KW - Lake Bolshoe Toko KW - paleoenvironments KW - sedimentary ancient DNA KW - metabarcoding KW - trnL KW - pollen Y1 - 2021 U6 - https://doi.org/10.3389/fevo.2021.625096 SN - 2296-701X VL - 9 PB - Frontiers Media CY - Lausanne ER -