@article{SchulteBernhardtStoofLeichsenringetal.2020, author = {Schulte, Luise and Bernhardt, Nadine and Stoof-Leichsenring, Kathleen Rosemarie and Zimmermann, Heike Hildegard and Pestryakova, Luidmila Agafyevna and Epp, Laura S. and Herzschuh, Ulrike}, title = {Hybridization capture of larch (Larix Mill.) chloroplast genomes from sedimentary ancient DNA reveals past changes of Siberian forest}, series = {Molecular ecology resources}, volume = {21}, journal = {Molecular ecology resources}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {1755-098X}, doi = {10.1111/1755-0998.13311}, pages = {801 -- 815}, year = {2020}, abstract = {Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.}, 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{DommainAndamaMcDonoughetal.2020, author = {Dommain, Ren{\´e} and Andama, Morgan and McDonough, Molly M. and Prado, Natalia A. and Goldhammer, Tobias and Potts, Richard and Maldonado, Jes{\´u}s E. and Nkurunungi, John Bosco and Campana, Michael G.}, title = {The Challenges of Reconstructing Tropical Biodiversity With 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.2020.00218}, pages = {26}, year = {2020}, abstract = {Sedimentary ancient DNA has been proposed as a key methodology for reconstructing biodiversity over time. Yet, despite the concentration of Earth's biodiversity in the tropics, this method has rarely been applied in this region. Moreover, the taphonomy of sedimentary DNA, especially in tropical environments, is poorly understood. This study elucidates challenges and opportunities of sedimentary ancient DNA approaches for reconstructing tropical biodiversity. We present shotgun-sequenced metagenomic profiles and DNA degradation patterns from multiple sediment cores from Mubwindi Swamp, located in Bwindi Impenetrable Forest (Uganda), one of the most diverse forests in Africa. We describe the taxonomic composition of the sediments covering the past 2200 years and compare the sedimentary DNA data with a comprehensive set of environmental and sedimentological parameters to unravel the conditions of DNA degradation. Consistent with the preservation of authentic ancient DNA in tropical swamp sediments, DNA concentration and mean fragment length declined exponentially with age and depth, while terminal deamination increased with age. DNA preservation patterns cannot be explained by any environmental parameter alone, but age seems to be the primary driver of DNA degradation in the swamp. Besides degradation, the presence of living microbial communities in the sediment also affects DNA quantity. Critically, 92.3\% of our metagenomic data of a total 81.8 million unique, merged reads cannot be taxonomically identified due to the absence of genomic references in public databases. Of the remaining 7.7\%, most of the data (93.0\%) derive from Bacteria and Archaea, whereas only 0-5.8\% are from Metazoa and 0-6.9\% from Viridiplantae, in part due to unbalanced taxa representation in the reference data. The plant DNA record at ordinal level agrees well with local pollen data but resolves less diversity. Our animal DNA record reveals the presence of 41 native taxa (16 orders) including Afrotheria, Carnivora, and Ruminantia at Bwindi during the past 2200 years. Overall, we observe no decline in taxonomic richness with increasing age suggesting that several-thousand-year-old information on past biodiversity can be retrieved from tropical sediments. However, comprehensive genomic surveys of tropical biota need prioritization for sedimentary DNA to be a viable methodology for future tropical biodiversity studies.}, language = {en} } @misc{DommainAndamaMcDonoughetal.2020, author = {Dommain, Ren{\´e} and Andama, Morgan and McDonough, Molly M. and Prado, Natalia A. and Goldhammer, Tobias and Potts, Richard and Maldonado, Jes{\´u}s E. and Nkurunungi, John Bosco and Campana, Michael G.}, title = {The Challenges of Reconstructing Tropical Biodiversity With Sedimentary Ancient DNA}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {970}, issn = {1866-8372}, doi = {10.25932/publishup-47430}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-474305}, pages = {28}, year = {2020}, abstract = {Sedimentary ancient DNA has been proposed as a key methodology for reconstructing biodiversity over time. Yet, despite the concentration of Earth's biodiversity in the tropics, this method has rarely been applied in this region. Moreover, the taphonomy of sedimentary DNA, especially in tropical environments, is poorly understood. This study elucidates challenges and opportunities of sedimentary ancient DNA approaches for reconstructing tropical biodiversity. We present shotgun-sequenced metagenomic profiles and DNA degradation patterns from multiple sediment cores from Mubwindi Swamp, located in Bwindi Impenetrable Forest (Uganda), one of the most diverse forests in Africa. We describe the taxonomic composition of the sediments covering the past 2200 years and compare the sedimentary DNA data with a comprehensive set of environmental and sedimentological parameters to unravel the conditions of DNA degradation. Consistent with the preservation of authentic ancient DNA in tropical swamp sediments, DNA concentration and mean fragment length declined exponentially with age and depth, while terminal deamination increased with age. DNA preservation patterns cannot be explained by any environmental parameter alone, but age seems to be the primary driver of DNA degradation in the swamp. Besides degradation, the presence of living microbial communities in the sediment also affects DNA quantity. Critically, 92.3\% of our metagenomic data of a total 81.8 million unique, merged reads cannot be taxonomically identified due to the absence of genomic references in public databases. Of the remaining 7.7\%, most of the data (93.0\%) derive from Bacteria and Archaea, whereas only 0-5.8\% are from Metazoa and 0-6.9\% from Viridiplantae, in part due to unbalanced taxa representation in the reference data. The plant DNA record at ordinal level agrees well with local pollen data but resolves less diversity. Our animal DNA record reveals the presence of 41 native taxa (16 orders) including Afrotheria, Carnivora, and Ruminantia at Bwindi during the past 2200 years. Overall, we observe no decline in taxonomic richness with increasing age suggesting that several-thousand-year-old information on past biodiversity can be retrieved from tropical sediments. However, comprehensive genomic surveys of tropical biota need prioritization for sedimentary DNA to be a viable methodology for future tropical biodiversity studies.}, language = {en} }