TY - JOUR A1 - Epp, Laura Saskia A1 - Stoof, Kathleen R. A1 - Trauth, Martin H. A1 - Tiedemann, Ralph T1 - Historical genetics on a sediment core from a Kenyan lake : intraspecific genotype turnover in a tropical rotifer is related to past environmental changes N2 - Using molecular genetic methods and an ancient DNA approach, we studied population and species succession of rotifers of the genus Brachionus in the Kenyan alkaline-saline crater lake Sonachi since the beginning of the 19th century as well as distribution of Brachionus haplotypes in recent and historic sediments of other lakes of the East African Rift System. The sediment core record of Lake Sonachi displays haplotypes of a distinct evolutionary lineage in all increments. Populations were dominated by a single mitochondrial haplotype for a period of 150 years, and two putatively intraspecific turnovers in dominance occurred. Both changes are concordant with major environmental perturbations documented by a profound visible change in sediment composition of the core. The first change was very abrupt and occurred after the deposition of volcanic ash at the beginning of the 19th century. The second change coincides with a major lake level lowstand during the 1940s. It was preceded by a period of successively declining lake level, in which two other haplotypes appeared in the lake. One of these putatively belongs to another species documented in historical and recent Kenyan lake sediments. The analysis of plankton population dynamics through historical time can reveal patterns of population persistence and turnover in relation to environmental changes. Y1 - 2010 UR - http://www.springerlink.com/content/100294 U6 - https://doi.org/10.1007/s10933-009-9379-7 SN - 0921-2728 ER - TY - JOUR A1 - Stuckas, Heiko A1 - Stoof, Kathleen A1 - Quesada, Humberto A1 - Tiedemann, Ralph T1 - Evolutionary implications of discordant clines across the Baltic Mytilus hybrid zone (Mytilus edulis and Mytilus trossulus) N2 - It is well established that reproductive isolation often arises from genome incompatibilities and that genes encoding reproductive traits are less prone to introgression. Hybrid zones of Mytilus trossulus and Mytilus edulis provide an intriguing model to assess reproductive isolation. Although gene flow is restricted in North America, introgression is pervasive in the Baltic. This study aimed at analyzing the shape of multilocus clines across the Baltic contact zone between M. edulis and M. trossulus to infer mechanisms of restriction to gene flow. We use maximum likelihood methods to construct the best fitting individual clines for five markers located on biparentally inherited autosomes and paternally and maternally inherited mitochondrial DNA (mtDNA). Strong cline shape differences among markers suggest that reproductive isolation arising from genome-wide incompatibilities is weak, and that these discrepancies possibly result from genetic drift, hybrid zone movement or marker-specific selection. However, the finding of a common cline center for M7 lysin (involved in fertilization) and paternally transmitted mtDNA (causing nuclear-mitochondrial incompatibilities in hybrids) suggest that these loci may play a role in incomplete reproductive isolation. Y1 - 2009 UR - http://www.nature.com/hdy/archive/index.html U6 - https://doi.org/10.1038/Hdy.2009.37 SN - 0018-067X ER - TY - JOUR A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Junginger, Annett A1 - Olaka, Lydia A. A1 - Tiedemann, Ralph A1 - Trauth, Martin H. T1 - Environmental variability in Lake Naivasha, Kenya, over the last two centuries JF - Journal of paleolimnolog N2 - Lake Naivasha, Kenya, is one of a number of freshwater lakes in the East African Rift System. Since the beginning of the twentieth century, it has experienced greater anthropogenic influence as a result of increasingly intensive farming of coffee, tea, flowers, and other horticultural crops within its catchment. The water-level history of Lake Naivasha over the past 200 years was derived from a combination of instrumental records and sediment data. In this study, we analysed diatoms in a lake sediment core to infer past lacustrine conductivity and total phosphorus concentrations. We also measured total nitrogen and carbon concentrations in the sediments. Core chronology was established by (210)Pb dating and covered a similar to 186-year history of natural (climatic) and human-induced environmental changes. Three stratigraphic zones in the core were identified using diatom assemblages. There was a change from littoral/epiphytic diatoms such as Gomphonema gracile and Cymbella muelleri, which occurred during a prolonged dry period from ca. 1820 to 1896 AD, through a transition period, to the present planktonic Aulacoseira sp. that favors nutrient-rich waters. This marked change in the diatom assemblage was caused by climate change, and later a strong anthropogenic overprint on the lake system. Increases in sediment accumulation rates since 1928, from 0.01 to 0.08 g cm(-2) year(-1) correlate with an increase in diatom-inferred total phosphorus concentrations since the beginning of the twentieth century. The increase in phosphorus accumulation suggests increasing eutrophication of freshwater Lake Naivasha. This study identified two major periods in the lake's history: (1) the period from 1820 to 1950 AD, during which the lake was affected mainly by natural climate variations, and (2) the period since 1950, during which the effects of anthropogenic activity overprinted those of natural climate variation. KW - Lake sediments KW - Diatoms KW - Conductivity KW - Lake Naivasha KW - Human impact KW - Eutrophication Y1 - 2011 U6 - https://doi.org/10.1007/s10933-011-9502-4 SN - 0921-2728 VL - 45 IS - 3 SP - 353 EP - 367 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Epp, Laura Saskia A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Trauth, Martin H. A1 - Tiedemann, Ralph T1 - Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High-Performance Liquid Chromatography (PCR-DHPLC) JF - Molecular ecology resources N2 - Here we present a protocol to genetically detect diatoms in sediments of the Kenyan tropical Lake Naivasha, based on taxon-specific PCR amplification of short fragments (approximately 100 bp) of the small subunit ribosomal (SSU) gene and subsequent separation of species-specific PCR products by PCR-based denaturing high-performance liquid chromatography (DHPLC). An evaluation of amplicons differing in primer specificity to diatoms and length of the fragments amplified demonstrated that the number of different diatom sequence types detected after cloning of the PCR products critically depended on the specificity of the primers to diatoms and the length of the amplified fragments whereby shorter fragments yielded more species of diatoms. The DHPLC was able to discriminate between very short amplicons based on the sequence difference, even if the fragments were of identical length and if the amplicons differed only in a small number of nucleotides. Generally, the method identified the dominant sequence types from mixed amplifications. A comparison with microscopic analysis of the sediment samples revealed that the sequence types identified in the molecular assessment corresponded well with the most dominant species. In summary, the PCR-based DHPLC protocol offers a fast, reliable and cost-efficient possibility to study DNA from sediments and other environmental samples with unknown organismic content, even for very short DNA fragments. KW - diatoms KW - environmental DNA KW - lake sediments KW - PCR-DHPLC Y1 - 2011 U6 - https://doi.org/10.1111/j.1755-0998.2011.03022.x SN - 1755-098X VL - 11 IS - 5 SP - 842 EP - 853 PB - Wiley-Blackwell CY - Hoboken ER - TY - JOUR A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Epp, Laura Saskia A1 - Trauth, Martin H. A1 - Tiedemann, Ralph T1 - Hidden diversity in diatoms of Kenyan Lake Naivasha a genetic approach detects temporal variation JF - Molecular ecology N2 - This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (7667 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by morphological and molecular data and (iii) indicated temporal variation in diatom assemblages on the inter- and intra-specific level. Diatom assemblages from a short core from Lake Naivasha show a drastic shift over the last 200 years, as littoral species (e.g. Navicula) are replaced by more planktonic ones (e.g. Aulacoseira). Within that same period, we detected periodic changes in the respective frequencies of distinct haplotype groups of Navicula, which coincide with wet and dry periods of Lake Naivasha between 1820 and 1938 AD. Our genetic analyses on historical lake sediments revealed inter- and intra-specific variation in diatoms, which is partially hidden behind single morphotypes. The occurrence of particular genetic lineages is probably correlated with environmental factors. KW - diatoms KW - DNA barcoding KW - historical DNA KW - intra-specific variation KW - rbcL KW - tropical lake sediments Y1 - 2012 U6 - https://doi.org/10.1111/j.1365-294X.2011.05412.x SN - 0962-1083 VL - 21 IS - 8 SP - 1918 EP - 1930 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Zimmermann, Heike Hildegard A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Kruse, Stefan A1 - Müller, Juliane A1 - Stein, Ruediger A1 - Tiedemann, Ralf A1 - Herzschuh, Ulrike T1 - Changes in the composition of marine and sea-ice diatoms derived from sedimentary ancient DNA of the eastern Fram Strait over the past 30 000 years JF - Ocean science N2 - The Fram Strait is an area with a relatively low and irregular distribution of diatom microfossils in surface sediments, and thus microfossil records are scarce, rarely exceed the Holocene, and contain sparse information about past richness and taxonomic composition. These attributes make the Fram Strait an ideal study site to test the utility of sedimentary ancient DNA (sedaDNA) metabarcoding. Amplifying a short, partial rbcL marker from samples of sediment core MSM05/5-712-2 resulted in 95.7% of our sequences being assigned to diatoms across 18 different families, with 38.6% of them being resolved to species and 25.8% to genus level. Independent replicates show a high similarity of PCR products, especially in the oldest samples. Diatom sedaDNA richness is highest in the Late Weichselian and lowest in Mid- and Late Holocene samples. Taxonomic composition is dominated by cold-water and sea-ice-associated diatoms and suggests several reorganisations - after the Last Glacial Maximum, after the Younger Dryas, and after the Early and after the Mid-Holocene. Different sequences assigned to, amongst others, Chaetoceros socialis indicate the detectability of intra-specific diversity using sedaDNA. We detect no clear pattern between our diatom sedaDNA record and the previously published IP25 record of this core, although proportions of pennate diatoms increase with higher IP25 concentrations and proportions of Nitzschia cf. frigida exceeding 2% of the assemblage point towards past sea-ice presence. Y1 - 2020 U6 - https://doi.org/10.5194/os-16-1017-2020 SN - 1812-0784 VL - 16 IS - 5 SP - 1017 EP - 1032 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Zimmermann, Heike Hildegard A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Kruse, Stefan A1 - Müller, Juliane A1 - Stein, Ruediger A1 - Tiedemann, Ralf A1 - Herzschuh, Ulrike T1 - Changes in the composition of marine and sea-ice diatoms derived from sedimentary ancient DNA of the eastern Fram Strait over the past 30 000 years JF - Ocean Science N2 - The Fram Strait is an area with a relatively low and irregular distribution of diatom microfossils in surface sediments, and thus microfossil records are scarce, rarely exceed the Holocene, and contain sparse information about past richness and taxonomic composition. These attributes make the Fram Strait an ideal study site to test the utility of sedimentary ancient DNA (sedaDNA) metabarcoding. Amplifying a short, partial rbcL marker from samples of sediment core MSM05/5-712-2 resulted in 95.7 % of our sequences being assigned to diatoms across 18 different families, with 38.6 % of them being resolved to species and 25.8 % to genus level. Independent replicates show a high similarity of PCR products, especially in the oldest samples. Diatom sedaDNA richness is highest in the Late Weichselian and lowest in Mid- and Late Holocene samples. Taxonomic composition is dominated by cold-water and sea-ice-associated diatoms and suggests several reorganisations – after the Last Glacial Maximum, after the Younger Dryas, and after the Early and after the Mid-Holocene. Different sequences assigned to, amongst others, Chaetoceros socialis indicate the detectability of intra-specific diversity using sedaDNA. We detect no clear pattern between our diatom sedaDNA record and the previously published IP25 record of this core, although proportions of pennate diatoms increase with higher IP25 concentrations and proportions of Nitzschia cf. frigida exceeding 2 % of the assemblage point towards past sea-ice presence. KW - last glacial maximum KW - surface temperatures KW - species composition KW - greenland shelf KW - Disko Bay KW - phytoplankton KW - communities KW - variability KW - diversity KW - Svalbard Y1 - 2019 VL - 16 IS - 5 PB - Springer CY - Tokyo ER - TY - THES A1 - Stoof-Leichsenring, Kathleen Rosemarie T1 - Genetic analysis of diatoms and rotifers in tropical Kenyan lake sediments Y1 - 2011 CY - Potsdam 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 - Zimmermann, Heike Hildegard A1 - Raschke, Elena A1 - Epp, Laura Saskia A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Schwamborn, Georg A1 - Schirrmeister, Lutz A1 - Overduin, Pier Paul A1 - Herzschuh, Ulrike T1 - 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) JF - Biogeosciences N2 - 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. Y1 - 2017 U6 - https://doi.org/10.5194/bg-14-575-2017 SN - 1726-4170 SN - 1726-4189 VL - 14 IS - 3 SP - 575 EP - 596 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Kruse, Stefan A1 - Epp, Laura Saskia A1 - Wieczorek, Mareike A1 - Pestryakova, Luidmila Agafyevna A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Herzschuh, Ulrike T1 - High gene flow and complex treeline dynamics of Larix Mill. stands on the Taymyr Peninsula (north-central Siberia) revealed by nuclear microsatellites JF - Tree Genetics & Genomes N2 - Arctic treelines are facing a strong temperature increase as a result of recent global warming, causing possible changes in forest extent, which will alter vegetation-climate feedbacks. However, the mode and strength of the response is rather unclear, as potential changes are happening in areas that are very remote and difficult to access, and empirical data are still largely lacking. Here, we assessed the current population structure and genetic differentiation of Larix Mill. tree stands within the northernmost latitudinal treeline reaching ~ 72° N in the southern lowlands of the Taymyr Peninsula (~ 100° E). We sampled 743 individuals belonging to different height classes (seedlings, saplings, trees) at 11 locations along a gradient from ‘single tree’ tundra over ‘forest line’ to ‘dense forest’ stands and conducted investigations applying eight highly polymorphic nuclear microsatellites. Results suggest a high diversity within sub-populations (HE = 0.826–0.893), coupled, however, with heterozygote deficits in all sub-populations, but pronounced in ‘forest line’ stands. Overall, genetic differentiation of sub-populations is low (FST = 0.005), indicating a region-wide high gene flow, although ‘forest line’ stands harbour few rare and private alleles, likely indicating greater local reproduction. ‘Single tree’ stands, located beyond the northern forest line, are currently not involved in treeline expansion, but show signs of a long-term refuge, namely asexual reproduction and change of growth-form from erect to creeping growth, possibly having persisted for thousands of years. The lack of differentiation between the sub-populations points to a sufficiently high dispersal potential, and thus a rapid northward migration of the Siberian arctic treeline under recent global warming seems potentially unconstrained, but observations show it to be unexpectedly slow. KW - Larch KW - Population genetics KW - Boreal forests KW - Tundra-taiga transition KW - Range expansion Y1 - 2018 U6 - https://doi.org/10.1007/s11295-018-1235-3 SN - 1614-2942 SN - 1614-2950 VL - 14 IS - 2 PB - Springer CY - Heidelberg ER - TY - JOUR A1 - Epp, Laura Saskia A1 - Kruse, Stefan A1 - Kath, Nadja J. A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Tiedemann, Ralph A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling JF - Scientific reports N2 - Changes in species’ distributions are classically projected based on their climate envelopes. For Siberian forests, which have a tremendous significance for vegetation-climate feedbacks, this implies future shifts of each of the forest-forming larch (Larix) species to the north-east. However, in addition to abiotic factors, reliable projections must assess the role of historical biogeography and biotic interactions. Here, we use sedimentary ancient DNA and individual-based modelling to investigate the distribution of larch species and mitochondrial haplotypes through space and time across the treeline ecotone on the southern Taymyr peninsula, which at the same time presents a boundary area of two larch species. We find spatial and temporal patterns, which suggest that forest density is the most influential driver determining the precise distribution of species and mitochondrial haplotypes. This suggests a strong influence of competition on the species’ range shifts. These findings imply possible climate change outcomes that are directly opposed to projections based purely on climate envelopes. Investigations of such fine-scale processes of biodiversity change through time are possible using paleoenvironmental DNA, which is available much more readily than visible fossils and can provide information at a level of resolution that is not reached in classical palaeoecology. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-35550-w SN - 2045-2322 VL - 8 PB - Nature Publ. Group CY - London ER - TY - GEN A1 - Zimmermann, Heike Hildegard A1 - Raschke, Elena A1 - Epp, Laura Saskia A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Schwamborn, Georg A1 - Schirrmeister, Lutz A1 - Overduin, Pier Paul A1 - Herzschuh, Ulrike T1 - 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) T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 670 KW - NE Siberia KW - vegetation patterns KW - environmental DNA KW - Arctic vegetation KW - frozen sediments KW - lake-sediments KW - gas-production KW - carbon KW - polygon KW - climate Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-417130 SN - 1866-8372 IS - 670 ER - TY - GEN A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Pestryakova, Luidmila Agafyevna A1 - Epp, Laura Saskia A1 - Herzschuh, Ulrike T1 - Phylogenetic diversity and environment form assembly rules for Arctic diatom genera BT - a study on recent and ancient sedimentary DNA T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Aim This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian tree line. 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. Location Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7,000 years before present, to capture the forest-tundra transition in space and time respectively. Taxon Arctic freshwater diatoms. Methods 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). Results 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. Furthermore, 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 HCO3- and water depth, largely explain diatom turnover. Main conclusion Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian tree line 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. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1442 KW - ancient sedimentary DNA KW - Arctic lakes KW - assembly rules KW - climate change KW - diatoms KW - environmental filtering KW - phylogenetic diversity KW - Siberian tree line Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-515485 SN - 1866-8372 IS - 5 ER - TY - JOUR A1 - von Hippel, Barbara A1 - Stoof-Leichsenring, Kathleen R. A1 - Schulte, Luise A1 - Seeber, Peter Andreas A1 - Epp, Laura Saskia A1 - Biskaborn, Boris A1 - Diekmann, Bernhard A1 - Melles, Martin A1 - Pestryakova, Luidmila Agafyevna A1 - Herzschuh, Ulrike T1 - Long-term funguseplant covariation from multi-site sedimentary ancient DNA metabarcoding JF - Quaternary science reviews : the international multidisciplinary research and review journal N2 - Climate change has a major impact on arctic and boreal terrestrial ecosystems as warming leads to northward treeline shifts, inducing consequences for heterotrophic organisms associated with the plant taxa. To unravel ecological dependencies, we address how long-term climatic changes have shaped the co-occurrence of plants and fungi across selected sites in Siberia. We investigated sedimentary ancient DNA from five lakes spanning the last 47,000 years, using the ITS1 marker for fungi and the chloroplast P6 loop marker for vegetation metabarcoding. We obtained 706 unique fungal operational taxonomic units (OTUs) and 243 taxa for the plants. We show higher OTU numbers in dry forest tundra as well as boreal forests compared to wet southern tundra. The most abundant fungal taxa in our dataset are Pseudeurotiaceae, Mortierella, Sordariomyceta, Exophiala, Oidiodendron, Protoventuria, Candida vartiovaarae, Pseudeurotium, Gryganskiella fimbricystis, and Tricho-sporiella cerebriformis. The overall fungal composition is explained by the plant composition as revealed by redundancy analysis. The fungal functional groups show antagonistic relationships in their climate susceptibility. The advance of woody taxa in response to past warming led to an increase in the abun-dance of mycorrhizae, lichens, and parasites, while yeast and saprotroph distribution declined. We also show co-occurrences between Salicaceae, Larix, and Alnus and their associated pathogens and detect higher mycorrhizal fungus diversity with the presence of Pinaceae. Under future warming, we can expect feedbacks between fungus composition and plant diversity changes which will affect forest advance, species diversity, and ecosystem stability in arctic regions. KW - Ecosystem dynamics KW - Fungus -plant covariation KW - ITS marker KW - Metabarcoding KW - Sedimentary ancient DNA KW - Siberia KW - trnL P6 loop Y1 - 2022 U6 - https://doi.org/10.1016/j.quascirev.2022.107758 SN - 0277-3791 SN - 1873-457X VL - 295 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Pestryakova, Luidmila Agafyevna A1 - Epp, Laura Saskia A1 - Herzschuh, Ulrike T1 - Phylogenetic diversity and environment form assembly rules for Arctic diatom genera BT - a study on recent and ancient sedimentary DNA JF - Journal of Biogeography N2 - Aim This study investigates taxonomic and phylogenetic diversity in diatom genera to evaluate assembly rules for eukaryotic microbes across the Siberian tree line. 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. Location Yakutia and Taymyria, Russia: we sampled 78 surface sediments and a sediment core, extending to 7,000 years before present, to capture the forest-tundra transition in space and time respectively. Taxon Arctic freshwater diatoms. Methods 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). Results 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. Furthermore, 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 HCO3- and water depth, largely explain diatom turnover. Main conclusion Phylogenetic and abiotic assembly rules are important in understanding the regional assembly of diatom genera across lakes in the Siberian tree line 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. KW - ancient sedimentary DNA KW - Arctic lakes KW - assembly rules KW - climate change KW - diatoms KW - environmental filtering KW - phylogenetic diversity KW - Siberian tree line Y1 - 2020 U6 - https://doi.org/10.1111/jbi.13786 SN - 0305-0270 SN - 1365-2699 VL - 47 IS - 5 SP - 1166 EP - 1179 PB - Wiley-Blackwell CY - Oxford ER - 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 - Heinecke, Liv A1 - Epp, Laura Saskia A1 - Reschke, Maria A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Mischke, Steffen A1 - Plessen, Birgit A1 - Herzschuh, Ulrike T1 - Aquatic macrophyte dynamics in Lake Karakul (Eastern Pamir) over the last 29 cal ka revealed by sedimentary ancient DNA and geochemical analyses of macrofossil remains JF - Journal of paleolimnolog KW - Potamogeton/Stuckenia KW - Arid central Asia KW - Paleo-productivity KW - Submerged vegetation composition KW - Metabarcoding KW - Chara/Characeae Y1 - 2017 U6 - https://doi.org/10.1007/s10933-017-9986-7 SN - 0921-2728 SN - 1573-0417 VL - 58 SP - 403 EP - 417 PB - Springer CY - Dordrecht ER - TY - JOUR A1 - Stoof-Leichsenring, Kathleen R. A1 - Huang, Sichao A1 - Liu, Sisi A1 - Jia, Weihan A1 - Li, Kai A1 - Liu, Xingqi A1 - Pestryakova, Luidmila A. A1 - Herzschuh, Ulrike T1 - Sedimentary DNA identifies modern and past macrophyte diversity and its environmental drivers in high-latitude and high-elevation lakes in Siberia and China JF - Limnology and oceanography N2 - Arctic and alpine aquatic ecosystems are changing rapidly under recent global warming, threatening water resources by diminishing trophic status and changing biotic composition. Macrophytes play a key role in the ecology of freshwaters and we need to improve our understanding of long-term macrophytes diversity and environmental change so far limited by the sporadic presence of macrofossils in sediments. In our study, we applied metabarcoding using the trnL P6 loop marker to retrieve macrophyte richness and composition from 179 surface-sediment samples from arctic Siberian and alpine Chinese lakes and three representative lake cores. The surface-sediment dataset suggests that macrophyte richness and composition are mostly affected by temperature and conductivity, with highest richness when mean July temperatures are higher than 12 degrees C and conductivity ranges between 40 and 400 mu S cm(-1). Compositional turnover during the Late Pleistocene/Holocene is minor in Siberian cores and characterized by a less rich, but stable emergent macrophyte community. Richness decreases during the Last Glacial Maximum and rises during wetter and warmer climate in the Late-glacial and Mid-Holocene. In contrast, we detect a pronounced change from emergent to submerged taxa at 14 ka in the Tibetan alpine core, which can be explained by increasing temperature and conductivity due to glacial runoff and evaporation. Our study provides evidence for the suitability of the trnL marker to recover modern and past macrophyte diversity and its applicability for the response of macrophyte diversity to lake-hydrochemical and climate variability predicting contrasting macrophyte changes in arctic and alpine lakes under intensified warming and human impact. Y1 - 2022 U6 - https://doi.org/10.1002/lno.12061 SN - 0024-3590 SN - 1939-5590 VL - 67 IS - 5 SP - 1126 EP - 1141 PB - Wiley-Blackwell CY - Oxford [u.a.] ER - TY - JOUR A1 - Zimmermann, Heike Hildegard A1 - Harms, Lars A1 - Epp, Laura Saskia A1 - Mewes, Nick A1 - Bernhardt, Nadine A1 - Kruse, Stefan A1 - Stoof-Leichsenring, Kathleen Rosemarie A1 - Pestryakova, Luidmila Agafyevna A1 - Wieczorek, Mareike A1 - Trense, Daronja A1 - Herzschuh, Ulrike T1 - Chloroplast and mitochondrial genetic variation of larches at the Siberian tundrataiga ecotone revealed by de novo assembly JF - PLoS one N2 - Larix populations at the tundra-taiga ecotone in northern Siberia are highly under-represented in population genetic studies, possibly due to the remoteness of these regions that can only be accessed at extraordinary expense. The genetic signatures of populations in these boundary regions are therefore largely unknown. We aim to generate organelle reference genomes for the detection of single nucleotide polymorphisms (SNPs) that can be used for paleogenetic studies. We present 19 complete chloroplast genomes and mitochondrial genomic sequences of larches from the southern lowlands of the Taymyr Peninsula (northernmost range of Larix gmelinii (Rupr.) Kuzen.), the lower Omoloy River, and the lower Kolyma River (both in the range of Larix cajanderi Mayr). The genomic data reveal 84 chloroplast SNPs and 213 putatively mitochondrial SNPs. Parsimony-based chloroplast haplotype networks show no spatial structure of individuals from different geographic origins, while the mitochondrial haplotype network shows at least a slight spatial structure with haplotypes from the Omoloy and Kolyma populations being more closely related to each other than to most of the haplotypes from the Taymyr populations. Whole genome alignments with publicly available complete chloroplast genomes of different Larix species show that among official plant barcodes only the rcbL gene contains sufficient polymorphisms, but has to be sequenced completely to distinguish the different provenances. We provide 8 novel mitochondrial SNPs that are putatively diagnostic for the separation of L. gmelinii and L. cajanderi, while 4 chloroplast SNPs have the potential to distinguish the L. gmelinii/ L. cajanderi group from other Larix species. Our organelle references can be used for a targeted primer and probe design allowing the generation of short amplicons. This is particularly important with regard to future investigations of, for example, the biogeographic history of Larix by screening ancient sedimentary DNA of Larix. Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0216966 SN - 1932-6203 VL - 14 IS - 7 PB - PLoS CY - San Fransisco ER -