@article{KruseWieczorekJeltschetal.2016,
  author    = {Kruse, Stefan and Wieczorek, Mareike and Jeltsch, Florian and Herzschuh, Ulrike},
  title     = {Treeline dynamics in Siberia under changing climates as inferred from an individual-based model for Larix},
  series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog},
  volume    = {338},
  journal   = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0304-3800},
  doi       = {10.1016/j.ecolmodel.2016.08.003},
  pages     = {101 -- 121},
  year      = {2016},
  language  = {en}
}
@phdthesis{Kruse2017,
  author    = {Kruse, Stefan},
  title     = {Larix treeline dynamics in northern Siberia inferred from population genetics and individual-based modelling},
  school      = {Universit{\"a}t Potsdam},
  pages     = {181},
  year      = {2017},
  language  = {en}
}
@article{WieczorekKruseEppetal.2017,
  author    = {Wieczorek, Mareike and Kruse, Stefan and Epp, Laura Saskia and Kolmogorov, Alexei and Nikolaev, Anatoly N. and Heinrich, Ingo and Jeltsch, Florian and Pestryakova, Luidmila Agafyevna and Zibulski, Romy and Herzschuh, Ulrike},
  title     = {Dissimilar responses of larch stands in northern Siberia to increasing temperatures-a field and simulation based study},
  series = {Ecology : a publication of the Ecological Society of America},
  volume    = {98},
  journal   = {Ecology : a publication of the Ecological Society of America},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0012-9658},
  doi       = {10.1002/ecy.1887},
  pages     = {2343 -- 2355},
  year      = {2017},
  abstract  = {Arctic and alpine treelines worldwide differ in their reactions to climate change. A northward advance of or densification within the treeline ecotone will likely influence climate-vegetation feedback mechanisms. In our study, which was conducted in the Taimyr Depression in the North Siberian Lowlands, w present a combined field-and model-based approach helping us to better understand the population processes involved in the responses of the whole treeline ecotone, spanning from closed forest to single-tree tundra, to climate warming. Using information on stand structure, tree age, and seed quality and quantity from seven sites, we investigate effects of intra-specific competition and seed availability on the specific impact of recent climate warming on larch stands. Field data show that tree density is highest in the forest-tundra, and average tree size decreases from closed forest to single-tree tundra. Age-structure analyses indicate that the trees in the closed forest and forest-tundra have been present for at least similar to 240 yr. At all sites except the most southerly ones, past establishment is positively correlated with regional temperature increase. In the single-tree tundra, however, a change in growth form from krummholz to erect trees, beginning similar to 130 yr ago, rather than establishment date has been recorded. Seed mass decreases from south to north, while seed quantity increases. Simulations with LAVESI (Larix Vegetation Simulator) further suggest that relative density changes strongly in response to a warming signal in the forest-tundra while intra-specific competition limits densification in the closed forest and seed limitation hinders densification in the single-tree tundra. We find striking differences in strength and timing of responses to recent climate warming. While forest-tundra stands recently densified, recruitment is almost non-existent at the southern and northern end of the ecotone due to autecological processes. Palaeo-treelines may therefore be inappropriate to infer past temperature changes at a fine scale. Moreover, a lagged treeline response to past warming will, via feedback mechanisms, influence climate change in the future.},
  language  = {en}
}
@article{WieczorekKolmogorovKruseetal.2017,
  author    = {Wieczorek, Mareike and Kolmogorov, Alexei and Kruse, Stefan and Jacobsen, Inga and Nitze, Ingmar and Nikolaev, Anatoly N. and Heinrich, Ingo and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {Disturbance-effects on treeline larch-stands in the lower Kolyma River area (NE Siberia)},
  series = {Silva Fennica : a quarterly journal for forest science},
  volume    = {51},
  journal   = {Silva Fennica : a quarterly journal for forest science},
  number    = {3},
  publisher = {The Finnish Society of Forest Science},
  address   = {Helsinki},
  issn      = {0037-5330},
  doi       = {10.14214/sf.1666},
  pages     = {20},
  year      = {2017},
  abstract  = {Tree stands in the boreal treeline ecotone are, in addition to climate change, impacted by disturbances such as fire, water-related disturbances and logging. We aim to understand how these disturbances affect growth, age structure, and spatial patterns of larch stands in the north-eastern Siberian treeline ecotone (lower Kolyma River region), an insufficiently researched region. Stand structure of Larix cajanderi Mayr was studied at seven sites impacted by disturbances. Maximum tree age ranged from 44 to 300 years. Young to medium-aged stands had, independent of disturbance type, the highest stand densities with over 4000 larch trees per ha. These sites also had the highest growth rates for tree height and stem diameter. Overall lowest stand densities were found in a polygonal field at the northern end of the study area, with larches growing in distinct " tree islands". At all sites, saplings are significantly clustered. Differences in fire severity led to contrasting stand structures with respect to tree, recruit, and overall stand densities. While a low severity fire resulted in low-density stands with high proportions of small and young larches, high severity fires resulted in high-density stands with high proportions of big trees. At waterdisturbed sites, stand structure varied between waterlogged and drained sites and latitude. These mixed effects of climate and disturbance make it difficult to predict future stand characteristics and the treeline position.},
  language  = {en}
}
@article{KruseGerdesKathetal.2018,
  author    = {Kruse, Stefan and Gerdes, Alexander and Kath, Nadja J. and Herzschuh, Ulrike},
  title     = {Implementing spatially explicit wind-driven seed and pollen dispersal in the individual-based larch simulation model},
  series = {Geoscientific model development : an interactive open access journal of the European Geosciences Union},
  volume    = {11},
  journal   = {Geoscientific model development : an interactive open access journal of the European Geosciences Union},
  number    = {11},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1991-959X},
  doi       = {10.5194/gmd-11-4451-2018},
  pages     = {4451 -- 4467},
  year      = {2018},
  abstract  = {It is of major interest to estimate the feedback of arctic ecosystems to the global warming we expect in upcoming decades. The speed of this response is driven by the potential of species to migrate, tracking their climate optimum. For this, sessile plants have to produce and disperse seeds to newly available habitats, and pollination of ovules is needed for the seeds to be viable. These two processes are also the vectors that pass genetic information through a population. A restricted exchange among subpopulations might lead to a maladapted population due to diversity losses. Hence, a realistic implementation of these dispersal processes into a simulation model would allow an assessment of the importance of diversity for the migration of plant species in various environments worldwide. To date, dynamic global vegetation models have been optimized for a global application and overestimate the migration of biome shifts in currently warming temperatures. We hypothesize that this is caused by neglecting important fine-scale processes, which are necessary to estimate realistic vegetation trajectories. Recently, we built and parameterized a simulation model LAVESI for larches that dominate the latitudinal treelines in the northernmost areas of Siberia. In this study, we updated the vegetation model by including seed and pollen dispersal driven by wind speed and direction. The seed dispersal is modelled as a ballistic flight, and for the pollination of ovules of seeds produced, we implemented a wind-determined and distance-dependent probability distribution function using a von Mises distribution to select the pollen donor. A local sensitivity analysis of both processes supported the robustness of the model's results to the parameterization, although it highlighted the importance of recruitment and seed dispersal traits for migration rates. This individual-based and spatially explicit implementation of both dispersal processes makes it easily feasible to inherit plant traits and genetic information to assess the impact of migration processes on the genetics. Finally, we suggest how the final model can be applied to substantially help in unveiling the important drivers of migration dynamics and, with this, guide the improvement of recent global vegetation models.},
  language  = {en}
}
@misc{KruseGerdesKathetal.2018,
  author    = {Kruse, Stefan and Gerdes, Alexander and Kath, Nadja J. and Herzschuh, Ulrike},
  title     = {Implementing spatially explicit wind-driven seed and pollen dispersal in the individual-based larch simulation model},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {929},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-44597},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-445978},
  pages     = {4451 -- 4467},
  year      = {2018},
  abstract  = {It is of major interest to estimate the feedback of arctic ecosystems to the global warming we expect in upcoming decades. The speed of this response is driven by the potential of species to migrate, tracking their climate optimum. For this, sessile plants have to produce and disperse seeds to newly available habitats, and pollination of ovules is needed for the seeds to be viable. These two processes are also the vectors that pass genetic information through a population. A restricted exchange among subpopulations might lead to a maladapted population due to diversity losses. Hence, a realistic implementation of these dispersal processes into a simulation model would allow an assessment of the importance of diversity for the migration of plant species in various environments worldwide. To date, dynamic global vegetation models have been optimized for a global application and overestimate the migration of biome shifts in currently warming temperatures. We hypothesize that this is caused by neglecting important fine-scale processes, which are necessary to estimate realistic vegetation trajectories. Recently, we built and parameterized a simulation model LAVESI for larches that dominate the latitudinal treelines in the northernmost areas of Siberia. In this study, we updated the vegetation model by including seed and pollen dispersal driven by wind speed and direction. The seed dispersal is modelled as a ballistic flight, and for the pollination of ovules of seeds produced, we implemented a wind-determined and distance-dependent probability distribution function using a von Mises distribution to select the pollen donor. A local sensitivity analysis of both processes supported the robustness of the model's results to the parameterization, although it highlighted the importance of recruitment and seed dispersal traits for migration rates. This individual-based and spatially explicit implementation of both dispersal processes makes it easily feasible to inherit plant traits and genetic information to assess the impact of migration processes on the genetics. Finally, we suggest how the final model can be applied to substantially help in unveiling the important drivers of migration dynamics and, with this, guide the improvement of recent global vegetation models.},
  language  = {en}
}
@misc{EppKruseKathetal.2018,
  author    = {Epp, Laura Saskia and Kruse, Stefan and Kath, Nadja J. and Stoof-Leichsenring, Kathleen Rosemarie and Tiedemann, Ralph and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1052},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-46835},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-468352},
  pages     = {11},
  year      = {2018},
  abstract  = {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.},
  language  = {en}
}
@article{KruseEppWieczoreketal.2018,
  author    = {Kruse, Stefan and Epp, Laura Saskia and Wieczorek, Mareike and Pestryakova, Luidmila Agafyevna and Stoof-Leichsenring, Kathleen Rosemarie and Herzschuh, Ulrike},
  title     = {High gene flow and complex treeline dynamics of Larix Mill. stands on the Taymyr Peninsula (north-central Siberia) revealed by nuclear microsatellites},
  series = {Tree Genetics \& Genomes},
  volume    = {14},
  journal   = {Tree Genetics \& Genomes},
  number    = {2},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {1614-2942},
  doi       = {10.1007/s11295-018-1235-3},
  pages     = {14},
  year      = {2018},
  abstract  = {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.},
  language  = {en}
}
@article{EppKruseKathetal.2018,
  author    = {Epp, Laura Saskia and Kruse, Stefan and Kath, Nadja J. and Stoof-Leichsenring, Kathleen Rosemarie and Tiedemann, Ralph and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {Temporal and spatial patterns of mitochondrial haplotype and species distributions in Siberian larches inferred from ancient environmental DNA and modeling},
  series = {Scientific reports},
  volume    = {8},
  journal   = {Scientific reports},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2045-2322},
  doi       = {10.1038/s41598-018-35550-w},
  pages     = {9},
  year      = {2018},
  abstract  = {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.},
  language  = {en}
}
@misc{BriegerHerzschuhPestryakovaetal.2019,
  author    = {Brieger, Frederic and Herzschuh, Ulrike and Pestryakova, Luidmila Agafyevna and Bookhagen, Bodo and Zakharov, Evgenii S. and Kruse, Stefan},
  title     = {Advances in the derivation of Northeast Siberian forest metrics using high-resolution UAV-based photogrammetric point clouds},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1337},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-47331},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-473318},
  pages     = {24},
  year      = {2019},
  abstract  = {Forest structure is a crucial component in the assessment of whether a forest is likely to act as a carbon sink under changing climate. Detailed 3D structural information about the tundra-taiga ecotone of Siberia is mostly missing and still underrepresented in current research due to the remoteness and restricted accessibility. Field based, high-resolution remote sensing can provide important knowledge for the understanding of vegetation properties and dynamics. In this study, we test the applicability of consumer-grade Unmanned Aerial Vehicles (UAVs) for rapid calculation of stand metrics in treeline forests. We reconstructed high-resolution photogrammetric point clouds and derived canopy height models for 10 study sites from NE Chukotka and SW Yakutia. Subsequently, we detected individual tree tops using a variable-window size local maximum filter and applied a marker-controlled watershed segmentation for the delineation of tree crowns. With this, we successfully detected 67.1\% of the validation individuals. Simple linear regressions of observed and detected metrics show a better correlation (R2) and lower relative root mean square percentage error (RMSE\%) for tree heights (mean R2 = 0.77, mean RMSE\% = 18.46\%) than for crown diameters (mean R2 = 0.46, mean RMSE\% = 24.9\%). The comparison between detected and observed tree height distributions revealed that our tree detection method was unable to representatively identify trees <2 m. Our results show that plot sizes for vegetation surveys in the tundra-taiga ecotone should be adapted to the forest structure and have a radius of >15-20 m to capture homogeneous and representative forest stands. Additionally, we identify sources of omission and commission errors and give recommendations for their mitigation. In summary, the efficiency of the used method depends on the complexity of the forest's stand structure.},
  language  = {en}
}
@article{ZimmermannHarmsEppetal.2019,
  author    = {Zimmermann, Heike Hildegard and Harms, Lars and Epp, Laura Saskia and Mewes, Nick and Bernhardt, Nadine and Kruse, Stefan and Stoof-Leichsenring, Kathleen Rosemarie and Pestryakova, Luidmila Agafyevna and Wieczorek, Mareike and Trense, Daronja and Herzschuh, Ulrike},
  title     = {Chloroplast and mitochondrial genetic variation of larches at the Siberian tundrataiga ecotone revealed by de novo assembly},
  series = {PLoS one},
  volume    = {14},
  journal   = {PLoS one},
  number    = {7},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0216966},
  pages     = {21},
  year      = {2019},
  abstract  = {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.},
  language  = {en}
}
@article{BriegerHerzschuhPestryakovaetal.2019,
  author    = {Brieger, Frederic and Herzschuh, Ulrike and Pestryakova, Luidmila Agafyevna and Bookhagen, Bodo and Zakharov, Evgenii S. and Kruse, Stefan},
  title     = {Advances in the Derivation of Northeast Siberian Forest Metrics Using High-Resolution UAV-Based Photogrammetric Point Clouds},
  series = {Remote sensing},
  volume    = {11},
  journal   = {Remote sensing},
  number    = {12},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2072-4292},
  doi       = {10.3390/rs11121447},
  pages     = {24},
  year      = {2019},
  abstract  = {Forest structure is a crucial component in the assessment of whether a forest is likely to act as a carbon sink under changing climate. Detailed 3D structural information about the tundra-taiga ecotone of Siberia is mostly missing and still underrepresented in current research due to the remoteness and restricted accessibility. Field based, high-resolution remote sensing can provide important knowledge for the understanding of vegetation properties and dynamics. In this study, we test the applicability of consumer-grade Unmanned Aerial Vehicles (UAVs) for rapid calculation of stand metrics in treeline forests. We reconstructed high-resolution photogrammetric point clouds and derived canopy height models for 10 study sites from NE Chukotka and SW Yakutia. Subsequently, we detected individual tree tops using a variable-window size local maximum filter and applied a marker-controlled watershed segmentation for the delineation of tree crowns. With this, we successfully detected 67.1\% of the validation individuals. Simple linear regressions of observed and detected metrics show a better correlation (R2) and lower relative root mean square percentage error (RMSE\%) for tree heights (mean R2 = 0.77, mean RMSE\% = 18.46\%) than for crown diameters (mean R2 = 0.46, mean RMSE\% = 24.9\%). The comparison between detected and observed tree height distributions revealed that our tree detection method was unable to representatively identify trees <2 m. Our results show that plot sizes for vegetation surveys in the tundra-taiga ecotone should be adapted to the forest structure and have a radius of >15-20 m to capture homogeneous and representative forest stands. Additionally, we identify sources of omission and commission errors and give recommendations for their mitigation. In summary, the efficiency of the used method depends on the complexity of the forest's stand structure.},
  language  = {en}
}
@article{KruseGerdesKathetal.2019,
  author    = {Kruse, Stefan and Gerdes, Alexander and Kath, Nadja J. and Epp, Laura Saskia and Stoof-Leichsenring, Kathleen Rosemarie and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {Dispersal distances and migration rates at the arctic treeline in Siberia - a genetic and simulation-based study},
  series = {Biogeosciences},
  volume    = {16},
  journal   = {Biogeosciences},
  number    = {6},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1726-4170},
  doi       = {10.5194/bg-16-1211-2019},
  pages     = {1211 -- 1224},
  year      = {2019},
  abstract  = {A strong temperature increase in the Arctic is expected to lead to latitudinal treeline shift. This tundra-taiga turnover would cause a positive vegetation-climate feedback due to albedo decrease. However, reliable estimates of tree migration rates are currently lacking due to the complex processes involved in forest establishment, which depend strongly on seed dispersal. We aim to fill this gap using LAVESI, an individual-based and spatially explicit Larix vegetation simulator. LAVESI was designed to simulate plots within homogeneous forests. Here, we improve the implementation of the seed dispersal function via field-based investigations. We inferred the effective seed dispersal distances of a typical open-forest stand on the southern Taymyr Peninsula (northern central Siberia) from genetic parentage analysis using eight nuclear microsatellite markers. The parentage analysis gives effective seed dispersal distances (median similar to 10 m) close to the seed parents. A comparison between simulated and observed effective seed dispersal distances reveals an overestimation of recruits close to the releasing tree and a shorter dispersal distance generally. We thus adapted our model and used the newly parameterised version to simulate south-to-north transects; a slow-moving treeline front was revealed. The colonisation of the tundra areas was assisted by occasional long-distance seed dispersal events beyond the treeline area. The treeline (similar to 1 tree ha(-1)) advanced by similar to 1.6 m yr(-1), whereas the forest line (similar to 100 trees ha(-1)) advanced by only similar to 0.6 m yr(-1). We conclude that the treeline in northern central Siberia currently lags behind the current strong warming and will continue to lag in the near future.},
  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}
}
@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 = {Springer},
  address   = {Tokyo},
  pages     = {16},
  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}
}
@misc{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 = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {5},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-52515},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-525154},
  pages     = {18},
  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}
}
@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.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{GluecklerHerzschuhKruseetal.2021,
  author    = {Gl{\"u}ckler, Ramesh and Herzschuh, Ulrike and Kruse, Stefan and Andreev, Andrei and Vyse, Stuart Andrew and Winkler, Bettina and Biskaborn, Boris and Pestryakova, Luidmila Agafyevna and Dietze, Elisabeth},
  title     = {Wildfire history of the boreal forest of south-western Yakutia (Siberia) over the last two millennia documented by a lake-sediment charcoal record},
  series = {Biogeosciences : BG / European Geosciences Union},
  volume    = {18},
  journal   = {Biogeosciences : BG / European Geosciences Union},
  number    = {13},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1726-4170},
  doi       = {10.5194/bg-18-4185-2021},
  pages     = {4185 -- 4209},
  year      = {2021},
  abstract  = {Wildfires, as a key disturbance in forest ecosystems, are shaping the world's boreal landscapes. Changes in fire regimes are closely linked to a wide array of environmental factors, such as vegetation composition, climate change, and human activity. Arctic and boreal regions and, in particular, Siberian boreal forests are experiencing rising air and ground temperatures with the subsequent degradation of permafrost soils leading to shifts in tree cover and species composition. Compared to the boreal zones of North America or Europe, little is known about how such environmental changes might influence long-term fire regimes in Russia. The larch-dominated eastern Siberian deciduous boreal forests differ markedly from the composition of other boreal forests, yet data about past fire regimes remain sparse. Here, we present a high-resolution macroscopic charcoal record from lacustrine sediments of Lake Khamra (southwest Yakutia, Siberia) spanning the last ca. 2200 years, including information about charcoal particle sizes and morphotypes. Our results reveal a phase of increased charcoal accumulation between 600 and 900 CE, indicative of relatively high amounts of burnt biomass and high fire frequencies. This is followed by an almost 900-year-long period of low charcoal accumulation without significant peaks likely corresponding to cooler climate conditions. After 1750 CE fire frequencies and the relative amount of biomass burnt start to increase again, coinciding with a warming climate and increased anthropogenic land development after Russian colonization. In the 20th century, total charcoal accumulation decreases again to very low levels despite higher fire frequency, potentially reflecting a change in fire management strategies and/or a shift of the fire regime towards more frequent but smaller fires. A similar pattern for different charcoal morphotypes and comparison to a pollen and non-pollen palynomorph (NPP) record from the same sediment core indicate that broad-scale changes in vegetation composition were probably not a major driver of recorded fire regime changes. Instead, the fire regime of the last two millennia at Lake Khamra seems to be controlled mainly by a combination of short-term climate variability and anthropogenic fire ignition and suppression.},
  language  = {en}
}
@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{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{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{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 Agafyevna 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{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{HeimLisovskiWieczoreketal.2022,
  author    = {Heim, Birgit and Lisovski, Simeon and Wieczorek, Mareike and Morgenstern, Anne and Juhls, Bennet and Shevtsova, Iuliia and Kruse, Stefan and Boike, Julia and Fedorova, Irina and Herzschuh, Ulrike},
  title     = {Spring snow cover duration and tundra greenness in the Lena Delta, Siberia},
  series = {Environmental research letters},
  volume    = {17},
  journal   = {Environmental research letters},
  number    = {8},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1748-9326},
  doi       = {10.1088/1748-9326/ac8066},
  pages     = {18},
  year      = {2022},
  abstract  = {The Lena Delta in Siberia is the largest delta in the Arctic and as a snow-dominated ecosystem particularly vulnerable to climate change. Using the two decades of MODerate resolution Imaging Spectroradiometer satellite acquisitions, this study investigates interannual and spatial variability of snow-cover duration and summer vegetation vitality in the Lena Delta. We approximated snow by the application of the normalized difference snow index and vegetation greenness by the normalized difference vegetation index (NDVI). We consolidated the analyses by integrating reanalysis products on air temperature from 2001 to 2021, and air temperature, ground temperature, and the date of snow-melt from time-lapse camera (TLC) observations from the Samoylov observatory located in the central delta. We extracted spring snow-cover duration determined by a latitudinal gradient. The 'regular year' snow-melt is transgressing from mid-May to late May within a time window of 10 days across the delta. We calculated yearly deviations per grid cell for two defined regions, one for the delta, and one focusing on the central delta. We identified an ensemble of early snow-melt years from 2012 to 2014, with snow-melt already starting in early May, and two late snow-melt years in 2004 and 2017, with snow-melt starting in June. In the times of TLC recording, the years of early and late snow-melt were confirmed. In the three summers after early snow-melt, summer vegetation greenness showed neither positive nor negative deviations. Whereas, vegetation greenness was reduced in 2004 after late snow-melt together with the lowest June monthly air temperature of the time series record. Since 2005, vegetation greenness is rising, with maxima in 2018 and 2021. The NDVI rise since 2018 is preceded by up to 4 degrees C warmer than average June air temperature. The ongoing operation of satellite missions allows to monitor a wide range of land surface properties and processes that will provide urgently needed data in times when logistical challenges lead to data gaps in land-based observations in the rapidly changing Arctic.},
  language  = {en}
}
@article{StuenziKruseBoikeetal.2022,
  author    = {Stuenzi, Simone Maria and Kruse, Stefan and Boike, Julia and Herzschuh, Ulrike and Oehme, Alexander and Pestryakova, Luidmila A. and Westermann, Sebastian and Langer, Moritz},
  title     = {Thermohydrological impact of forest disturbances on ecosystem-protected permafrost},
  series = {Journal of geophysical research : Biogeosciences},
  volume    = {127},
  journal   = {Journal of geophysical research : Biogeosciences},
  number    = {5},
  publisher = {American Geophysical Union},
  address   = {Washington},
  issn      = {2169-8953},
  doi       = {10.1029/2021JG006630},
  pages     = {24},
  year      = {2022},
  abstract  = {Boreal forests cover over half of the global permafrost area and protect underlying permafrost. Boreal forest development, therefore, has an impact on permafrost evolution, especially under a warming climate. Forest disturbances and changing climate conditions cause vegetation shifts and potentially destabilize the carbon stored within the vegetation and permafrost. Disturbed permafrost-forest ecosystems can develop into a dry or swampy bush- or grasslands, shift toward broadleaf- or evergreen needleleaf-dominated forests, or recover to the pre-disturbance state. An increase in the number and intensity of fires, as well as intensified logging activities, could lead to a partial or complete ecosystem and permafrost degradation. We study the impact of forest disturbances (logging, surface, and canopy fires) on the thermal and hydrological permafrost conditions and ecosystem resilience. We use a dynamic multilayer canopy-permafrost model to simulate different scenarios at a study site in eastern Siberia. We implement expected mortality, defoliation, and ground surface changes and analyze the interplay between forest recovery and permafrost. We find that forest loss induces soil drying of up to 44\%, leading to lower active layer thicknesses and abrupt or steady decline of a larch forest, depending on disturbance intensity. Only after surface fires, the most common disturbances, inducing low mortality rates, forests can recover and overpass pre-disturbance leaf area index values. We find that the trajectory of larch forests after surface fires is dependent on the precipitation conditions in the years after the disturbance. Dryer years can drastically change the direction of the larch forest development within the studied period.},
  language  = {en}
}