@article{HerzschuhBoehmerLietal.2022,
  author    = {Herzschuh, Ulrike and B{\"o}hmer, Thomas and Li, Chenzhi and Cao, Xianyong and H{\´e}bert, Rapha{\"e}l and Dallmeyer, Anne and Telford, Richard J. and Kruse, Stefan},
  title     = {Reversals in temperature-precipitation correlations in the Northern Hemisphere extratropics during the Holocene},
  series = {Geophysical research letters},
  volume    = {49},
  journal   = {Geophysical research letters},
  number    = {22},
  publisher = {American Geophysical Union},
  address   = {Washington},
  issn      = {0094-8276},
  doi       = {10.1029/2022GL099730},
  pages     = {11},
  year      = {2022},
  abstract  = {Future precipitation levels remain uncertain because climate models have struggled to reproduce observed variations in temperature-precipitation correlations. Our analyses of Holocene proxy-based temperature-precipitation correlations and hydrological sensitivities from 2,237 Northern Hemisphere extratropical pollen records reveal a significant latitudinal dependence and temporal variations among the early, middle, and late Holocene. These proxy-based variations are largely consistent with patterns obtained from transient climate simulations (TraCE21k). While high latitudes and subtropical monsoon areas show mainly stable positive correlations throughout the Holocene, the mid-latitude pattern is temporally and spatially more variable. In particular, we identified a reversal from positive to negative temperature-precipitation correlations in the eastern North American and European mid-latitudes from the early to mid-Holocene that mainly related to slowed down westerlies and a switch to moisture-limited convection under a warm climate. Our palaeoevidence of past temperature-precipitation correlation shifts identifies those regions where simulating past and future precipitation levels might be particularly challenging.},
  language  = {en}
}
@article{KruseHerzschuh2022,
  author    = {Kruse, Stefan and Herzschuh, Ulrike},
  title     = {Regional opportunities for tundra conservation in the next 1000 years},
  series = {eLife},
  volume    = {11},
  journal   = {eLife},
  publisher = {eLife Sciences Publications},
  address   = {Cambridge},
  issn      = {2050-084X},
  doi       = {10.7554/eLife.75163},
  pages     = {24},
  year      = {2022},
  abstract  = {The biodiversity of tundra areas in northern high latitudes is threatened by invasion of forests under global warming. However, poorly understood nonlinear responses of the treeline ecotone mean the timing and extent of tundra losses are unclear, but policymakers need such information to optimize conservation efforts. Our individual-based model LAVESI, developed for the Siberian tundra-taiga ecotone, can help improve our understanding. Consequently, we simulated treeline migration trajectories until the end of the millennium, causing a loss of tundra area when advancing north. Our simulations reveal that the treeline follows climate warming with a severe, century-long time lag, which is overcompensated by infilling of stands in the long run even when temperatures cool again. Our simulations reveal that only under ambitious mitigation strategies (relative concentration pathway 2.6) will ~30\% of original tundra areas remain in the north but separated into two disjunct refugia.},
  language  = {en}
}
@article{vanGeffenHeimBriegeretal.2022,
  author    = {van Geffen, Femke and Heim, Birgit and Brieger, Frederic and Geng, Rongwei and Shevtsova, Iuliia A. and Schulte, Luise and Stuenzi, Simone M. and Bernhardt, Nadine and Troeva, Elena and Pestryakova, Luidmila A. and Zakharov, Evgenii S. and Pflug, Bringfried and Herzschuh, Ulrike and Kruse, Stefan},
  title     = {SiDroForest: a comprehensive forest inventory of Siberian boreal forest investigations including drone-based point clouds, individually labeled trees, synthetically generated tree crowns, and Sentinel-2 labeled image patches},
  series = {Earth system science data},
  volume    = {14},
  journal   = {Earth system science data},
  number    = {11},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1866-3508},
  doi       = {10.5194/essd-14-4967-2022},
  pages     = {4967 -- 4994},
  year      = {2022},
  abstract  = {The SiDroForest (Siberian drone-mapped forest inventory) data collection is an attempt to remedy the scarcity of forest structure data in the circumboreal region by providing adjusted and labeled tree-level and vegetation plot-level data for machine learning and upscaling purposes. We present datasets of vegetation composition and tree and plot level forest structure for two important vegetation transition zones in Siberia, Russia; the summergreen-evergreen transition zone in Central Yakutia and the tundra-taiga transition zone in Chukotka (NE Siberia). The SiDroForest data collection consists of four datasets that contain different complementary data types that together support in-depth analyses from different perspectives of Siberian Forest plot data for multi-purpose applications. i. Dataset 1 provides unmanned aerial vehicle (UAV)-borne data products covering the vegetation plots surveyed during fieldwork (Kruse et al., 2021, ). The dataset includes structure-from-motion (SfM) point clouds and red-green-blue (RGB) and red-green-near-infrared (RGN) orthomosaics. From the orthomosaics, point-cloud products were created such as the digital elevation model (DEM), canopy height model (CHM), digital surface model (DSM) and the digital terrain model (DTM). The point-cloud products provide information on the three-dimensional (3D) structure of the forest at each plot. Dataset 2 contains spatial data in the form of point and polygon shapefiles of 872 individually labeled trees and shrubs that were recorded during fieldwork at the same vegetation plots (van Geffen et al., 2021c, ). The dataset contains information on tree height, crown diameter, and species type. These tree and shrub individually labeled point and polygon shapefiles were generated on top of the RGB UVA orthoimages. The individual tree information collected during the expedition such as tree height, crown diameter, and vitality are provided in table format. This dataset can be used to link individual information on trees to the location of the specific tree in the SfM point clouds, providing for example, opportunity to validate the extracted tree height from the first dataset. The dataset provides unique insights into the current state of individual trees and shrubs and allows for monitoring the effects of climate change on these individuals in the future. Dataset 3 contains a synthesis of 10 000 generated images and masks that have the tree crowns of two species of larch ( and ) automatically extracted from the RGB UAV images in the common objects in context (COCO) format (van Geffen et al., 2021a, ). As machine-learning algorithms need a large dataset to train on, the synthetic dataset was specifically created to be used for machine-learning algorithms to detect Siberian larch species. Larix gmeliniiLarix cajanderiDataset 4 contains Sentinel-2 (S-2) Level-2 bottom-of-atmosphere processed labeled image patches with seasonal information and annotated vegetation categories covering the vegetation plots (van Geffen et al., 2021b, ). The dataset is created with the aim of providing a small ready-to-use validation and training dataset to be used in various vegetation-related machine-learning tasks. It enhances the data collection as it allows classification of a larger area with the provided vegetation classes. The SiDroForest data collection serves a variety of user communities. <br /> The detailed vegetation cover and structure information in the first two datasets are of use for ecological applications, on one hand for summergreen and evergreen needle-leaf forests and also for tundra-taiga ecotones. Datasets 1 and 2 further support the generation and validation of land cover remote-sensing products in radar and optical remote sensing. In addition to providing information on forest structure and vegetation composition of the vegetation plots, the third and fourth datasets are prepared as training and validation data for machine-learning purposes. For example, the synthetic tree-crown dataset is generated from the raw UAV images and optimized to be used in neural networks. Furthermore, the fourth SiDroForest dataset contains S-2 labeled image patches processed to a high standard that provide training data on vegetation class categories for machine-learning classification with JavaScript Object Notation (JSON) labels provided. The SiDroForest data collection adds unique insights into remote hard-to-reach circumboreal forest regions.},
  language  = {en}
}
@article{JiaAnslanChenetal.2022,
  author    = {Jia, Weihan and Anslan, Sten and Chen, Fahu and Cao, Xianyong and Dong, Hailiang and Dulias, Katharina and Gu, Zhengquan and Heinecke, Liv and Jiang, Hongchen and Kruse, Stefan and Kang, Wengang and Li, Kai and Liu, Sisi and Liu, Xingqi and Liu, Ying and Ni, Jian and Schwalb, Antje and Stoof-Leichsenring, Kathleen R. and Shen, Wei and Tian, Fang and Wang, Jing and Wang, Yongbo and Wang, Yucheng and Xu, Hai and Yang, Xiaoyan and Zhang, Dongju and Herzschuh, Ulrike},
  title     = {Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: overview and prospects},
  series = {Quaternary science reviews : the international multidisciplinary research and review journal},
  volume    = {293},
  journal   = {Quaternary science reviews : the international multidisciplinary research and review journal},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0277-3791},
  doi       = {10.1016/j.quascirev.2022.107703},
  pages     = {14},
  year      = {2022},
  abstract  = {Alpine ecosystems on the Tibetan Plateau are being threatened by ongoing climate warming and intensified human activities. Ecological time-series obtained from sedimentary ancient DNA (sedaDNA) are essential for understanding past ecosystem and biodiversity dynamics on the Tibetan Plateau and their responses to climate change at a high taxonomic resolution. Hitherto only few but promising studies have been published on this topic. The potential and limitations of using sedaDNA on the Tibetan Plateau are not fully understood. Here, we (i) provide updated knowledge of and a brief introduction to the suitable archives, region-specific taphonomy, state-of-the-art methodologies, and research questions of sedaDNA on the Tibetan Plateau; (ii) review published and ongoing sedaDNA studies from the Tibetan Plateau; and (iii) give some recommendations for future sedaDNA study designs. Based on the current knowledge of taphonomy, we infer that deep glacial lakes with freshwater and high clay sediment input, such as those from the southern and southeastern Tibetan Plateau, may have a high potential for sedaDNA studies. Metabarcoding (for microorganisms and plants), metagenomics (for ecosystems), and hybridization capture (for prehistoric humans) are three primary sedaDNA approaches which have been successfully applied on the Tibetan Plateau, but their power is still limited by several technical issues, such as PCR bias and incompleteness of taxonomic reference databases. Setting up high-quality and open-access regional taxonomic reference databases for the Tibetan Plateau should be given priority in the future. To conclude, the archival, taphonomic, and methodological conditions of the Tibetan Plateau are favorable for performing sedaDNA studies. More research should be encouraged to address questions about long-term ecological dynamics at ecosystem scale and to bring the paleoecology of the Tibetan Plateau into a new era.},
  language  = {en}
}
@article{MiesnerHerzschuhPestryakovaetal.2022,
  author    = {Miesner, Timon and Herzschuh, Ulrike and Pestryakova, Luidmila Agafyevna and Wieczorek, Mareike and Zakharov, Evgenii S. and Kolmogorov, Alexei I. and Davydova, Paraskovya V. and Kruse, Stefan},
  title     = {Forest structure and individual tree inventories of northeastern Siberia along climatic gradients},
  series = {Earth system science data : ESSD},
  volume    = {14},
  journal   = {Earth system science data : ESSD},
  number    = {12},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1866-3508},
  doi       = {10.5194/essd-14-5695-2022},
  pages     = {5695 -- 5716},
  year      = {2022},
  abstract  = {We compile a data set of forest surveys from expeditions to the northeast of the Russian Federation, in Krasnoyarsk Krai, the Republic of Sakha (Yakutia), and the Chukotka Autonomous Okrug (59-73 degrees N, 97-169 degrees E), performed between the years 2011 and 2021. The region is characterized by permafrost soils and forests dominated by larch (Larix gmelinii Rupr. and Larix cajanderi Mayr). Our data set consists of a plot database describing 226 georeferenced vegetation survey plots and a tree database with information about all the trees on these plots. The tree database, consisting of two tables with the same column names, contains information on the height, species, and vitality of 40 289 trees. A subset of the trees was subject to a more detailed inventory, which recorded the stem diameter at base and at breast height, crown diameter, and height of the beginning of the crown. We recorded heights up to 28.5 m (median 2.5 m) and stand densities up to 120 000 trees per hectare (median 1197 ha(-1)), with both values tending to be higher in the more southerly areas. Observed taxa include Larix Mill., Pinus L., Picea A. Dietr., Abies Mill., Salix L., Betula L., Populus L., Alnus Mill., and Ulmus L. In this study, we present the forest inventory data aggregated per plot. Additionally, we connect the data with different remote sensing data products to find out how accurately forest structure can be predicted from such products. Allometries were calculated to obtain the diameter from height measurements for every species group. For Larix, the most frequent of 10 species groups, allometries depended also on the stand density, as denser stands are characterized by thinner trees, relative to height. The remote sensing products used to compare against the inventory data include climate, forest biomass, canopy height, and forest loss or disturbance. We find that the forest metrics measured in the field can only be reconstructed from the remote sensing data to a limited extent, as they depend on local properties. This illustrates the need for ground inventories like those data we present here. The data can be used for studying the forest structure of northeastern Siberia and for the calibration and validation of remotely sensed data.},
  language  = {en}
}
@article{KruseStuenziBoikeetal.2022,
  author    = {Kruse, Stefan and St{\"u}nzi, Simone Maria and Boike, Julia and Langer, Moritz and Gloy, Josias and Herzschuh, Ulrike},
  title     = {Novel coupled permafrost-forest model (LAVESI-CryoGrid v1.0) revealing the interplay between permafrost, vegetation, and climate across eastern Siberia},
  series = {Geoscientific model development : GMD ; an interactive open access journal of the European Geosciences Union},
  volume    = {15},
  journal   = {Geoscientific model development : GMD ; an interactive open access journal of the European Geosciences Union},
  number    = {6},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1991-959X},
  doi       = {10.5194/gmd-15-2395-2022},
  pages     = {2395 -- 2422},
  year      = {2022},
  abstract  = {Boreal forests of Siberia play a relevant role in the global carbon cycle. However, global warming threatens the existence of summergreen larch-dominated ecosystems, likely enabling a transition to evergreen tree taxa with deeper active layers. Complex permafrost-vegetation interactions make it uncertain whether these ecosystems could develop into a carbon source rather than continuing atmospheric carbon sequestration under global warming. Consequently, shedding light on the role of current and future active layer dynamics and the feedbacks with the apparent tree species is crucial to predict boreal forest transition dynamics and thus for aboveground forest biomass and carbon stock developments. Hence, we established a coupled model version amalgamating a one-dimensional permafrost multilayer forest land-surface model (CryoGrid) with LAVESI, an individual-based and spatially explicit forest model for larch species (Larix Mill.), extended for this study by including other relevant Siberian forest species and explicit terrain. <br /> Following parameterization, we ran simulations with the coupled version to the near future to 2030 with a mild climate-warming scenario. We focus on three regions covering a gradient of summergreen forests in the east at Spasskaya Pad, mixed summergreen-evergreen forests close to Nyurba, and the warmest area at Lake Khamra in the southeast of Yakutia, Russia. Coupled simulations were run with the newly implemented boreal forest species and compared to runs allowing only one species at a time, as well as to simulations using just LAVESI. Results reveal that the coupled version corrects for overestimation of active layer thickness (ALT) and soil moisture, and large differences in established forests are simulated. We conclude that the coupled version can simulate the complex environment of eastern Siberia by reproducing vegetation patterns, making it an excellent tool to disentangle processes driving boreal forest dynamics.},
  language  = {en}
}
@article{ZimmermannStoofLeichsenringKruseetal.2021,
  author    = {Zimmermann, Heike and Stoof-Leichsenring, Kathleen R. and Kruse, Stefan and N{\"u}rnberg, Dirk and Tiedemann, Ralf and Herzschuh, Ulrike},
  title     = {Sedimentary ancient DNA from the subarctic North Pacific},
  series = {Paleoceanography and paleoclimatology},
  volume    = {36},
  journal   = {Paleoceanography and paleoclimatology},
  number    = {4},
  publisher = {Wiley},
  address   = {Hoboken, NJ},
  issn      = {2572-4517},
  doi       = {10.1029/2020PA004091},
  pages     = {18},
  year      = {2021},
  abstract  = {We traced diatom composition and diversity through time using diatom-derived sedimentary ancient DNA (sedaDNA) from eastern continental slope sediments off Kamchatka (North Pacific) by applying a short, diatom-specific marker on 63 samples in a DNA metabarcoding approach. The sequences were assigned to diatoms that are common in the area and characteristic of cold water. SedaDNA allowed us to observe shifts of potential lineages from species of the genus Chaetoceros that can be related to different climatic phases, suggesting that pre-adapted ecotypes might have played a role in the long-term success of species in areas of changing environmental conditions. These sedaDNA results complement our understanding of the long-term history of diatom assemblages and their general relationship to environmental conditions of the past. Sea-ice diatoms (Pauliella taeniata [Grunow] Round \& Basson, Attheya septentrionalis [ostrup] R. M. Crawford and Nitzschia frigida [Grunow]) detected during the late glacial and Younger Dryas are in agreement with previous sea-ice reconstructions. A positive correlation between pennate diatom richness and the sea-ice proxy IP25 suggests that sea ice fosters pennate diatom richness, whereas a negative correlation with June insolation and temperature points to unfavorable conditions during the Holocene. A sharp increase in proportions of freshwater diatoms at similar to 11.1 cal kyr BP implies the influence of terrestrial runoff and coincides with the loss of 42\% of diatom sequence variants. We assume that reduced salinity at this time stabilized vertical stratification which limited the replenishment of nutrients in the euphotic zone.},
  language  = {en}
}
@article{LiuStoofLeichsenringKruseetal.2020,
  author    = {Liu, Sisi and Stoof-Leichsenring, Kathleen Rosemarie and Kruse, Stefan and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {Holocene vegetation and plant diversity changes in the north-eastern Siberian treeline region from pollen and sedimentary ancient DNA},
  series = {Frontiers in Ecology and Evolution},
  volume    = {8},
  journal   = {Frontiers in Ecology and Evolution},
  publisher = {Frontiers Media},
  address   = {Lausanne},
  issn      = {2296-701X},
  doi       = {10.3389/fevo.2020.560243},
  pages     = {17},
  year      = {2020},
  abstract  = {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.},
  language  = {en}
}
@article{KruseKolmogorovPestryakovaetal.2020,
  author    = {Kruse, Stefan and Kolmogorov, Aleksey I. and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {Long-lived larch clones may conserve adaptations that could restrict treeline migration in northern Siberia},
  series = {Ecology and evolution},
  volume    = {10},
  journal   = {Ecology and evolution},
  number    = {18},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.6660},
  pages     = {10017 -- 10030},
  year      = {2020},
  abstract  = {The occurrence of refugia beyond the arctic treeline and genetic adaptation therein play a crucial role of largely unknown effect size. While refugia have potential for rapidly colonizing the tundra under global warming, the taxa may be maladapted to the new environmental conditions. Understanding the genetic composition and age of refugia is thus crucial for predicting any migration response. Here, we genotype 194 larch individuals from an similar to 1.8 km(2)area in northcentral Siberia on the southern Taimyr Peninsula by applying an assay of 16 nuclear microsatellite markers. For estimating the age of clonal individuals, we counted tree rings at sections along branches to establish a lateral growth rate that was then combined with geographic distance. Findings reveal that the predominant reproduction type is clonal (58.76\%) by short distance spreading of ramets. One outlier of clones 1 km apart could have been dispersed by reindeer. In clonal groups and within individuals, we find that somatic mutations accumulate with geographic distance. Clonal groups of two or more individuals are observed. Clonal age estimates regularly suggest individuals as old as 2,200 years, which coincides with a major environmental change that forced a treeline retreat in the region. We conclude that individuals with clonal growth mode were naturally selected as it lowers the likely risk of extinction under a harsh environment. We discuss this legacy from the past that might now be a maladaptation and hinder expansion under currently strongly increasing temperatures.},
  language  = {en}
}
@article{ZimmermannStoofLeichsenringKruseetal.2020,
  author    = {Zimmermann, Heike Hildegard and Stoof-Leichsenring, Kathleen Rosemarie and Kruse, Stefan and M{\"u}ller, Juliane and Stein, Ruediger and Tiedemann, Ralf and Herzschuh, Ulrike},
  title     = {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},
  series = {Ocean science},
  volume    = {16},
  journal   = {Ocean science},
  number    = {5},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1812-0784},
  doi       = {10.5194/os-16-1017-2020},
  pages     = {1017 -- 1032},
  year      = {2020},
  abstract  = {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.},
  language  = {en}
}