@article{ZimmermannRaschkeEppetal.2017, author = {Zimmermann, Heike Hildegard and Raschke, Elena and Epp, Laura Saskia and Stoof-Leichsenring, Kathleen Rosemarie and Schirrmeister, Lutz and Schwamborn, Georg and Herzschuh, Ulrike}, title = {The history of tree and shrub taxa on Bol'shoy Lyakhovsky Island (New Siberian Archipelago) since the Last Interglacial Uncovered by Sedimentary Ancient DNA and Pollen Data}, series = {Genes}, volume = {8}, journal = {Genes}, number = {10}, publisher = {MDPI}, address = {Basel}, issn = {2073-4425}, doi = {10.3390/genes8100273}, pages = {273}, year = {2017}, abstract = {Ecosystem boundaries, such as the Arctic-Boreal treeline, are strongly coupled with climate and were spatially highly dynamic during past glacial-interglacial cycles. Only a few studies cover vegetation changes since the last interglacial, as most of the former landscapes are inundated and difficult to access. Using pollen analysis and sedimentary ancient DNA (sedaDNA) metabarcoding, we reveal vegetation changes on Bol'shoy Lyakhovsky Island since the last interglacial from permafrost sediments. Last interglacial samples depict high levels of floral diversity with the presence of trees (Larix, Picea, Populus) and shrubs (Alnus, Betula, Ribes, Cornus, Saliceae) on the currently treeless island. After the Last Glacial Maximum, Larix re-colonised the island but disappeared along with most shrub taxa. This was probably caused by Holocene sea-level rise, which led to increased oceanic conditions on the island. Additionally, we applied two newly developed larch-specific chloroplast markers to evaluate their potential for tracking past population dynamics from environmental samples. The novel markers were successfully re-sequenced and exhibited two variants of each marker in last interglacial samples. SedaDNA can track vegetation changes as well as genetic changes across geographic space through time and can improve our understanding of past processes that shape modern patterns.}, language = {en} } @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{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} } @phdthesis{Schulte2022, author = {Schulte, Luise}, title = {Dynamics of Larix (Mill.) species in Siberia during the last 50,000 years inferred from sedimentary ancient DNA}, doi = {10.25932/publishup-55878}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-558782}, school = {Universit{\"a}t Potsdam}, pages = {xi, 121}, year = {2022}, abstract = {The deciduous needle tree larch (Larix Mill.) covers more than 80\% of the Asian boreal forests. Only a few Larix species constitute the vast forests and these species differ markedly in their ecological traits, most importantly in their ability to grow on and stabilize underlying permafrost. The pronounced dominance of the summergreen larches makes the Asian boreal forests unique, as the rest of the northern hemisphere boreal forests is almost exclusively dominated by evergreen needle-leaf forests. Global warming is impacting the whole world but is especially pronounced in the arctic and boreal regions. Although adapted to extreme climatic conditions, larch forests are sensitive to varying climatic conditions. By their sheer size, changes in Asian larch forests as range shifts or changes in species composition and the resulting vegetation-climate feedbacks are of global relevance. It is however still uncertain if larch forests will persist under the ongoing warming climate or if they will be replaced by evergreen forests. It is therefore of great importance to understand how these ecosystems will react to future climate warmings and if they will maintain their dominance. One step in the better understanding of larch dynamics is to study how the vast dominant forests developed and why they only established in northern Asia. A second step is to study how the species reacted to past changes in the climate. The first objective of this thesis was to review and identify factors promoting Asian larch dominance. I achieved this by synthesizing and comparing reported larch occurrences and influencing components on the northern hemisphere continents in the present and in the past. The second objective was to find a possibility to directly study past Larix populations in Siberia and specifically their genetic variation, enabling the study of geographic movements. For this, I established chloroplast enrichment by hybridization capture from sedimentary ancient DNA (sedaDNA) isolated from lake sediment records. The third objective was to use the established method to track past larch populations, their glacial refugia during the Last Glacial Maximum (LGM) around 21,000 years before present (ka BP), and their post-glacial migration patterns. To study larch promoting factors, I compared the present state of larch species ranges, areas of dominance, their bioclimatic niches, and the distribution on different extents and thaw depths of permafrost. The species comparison showed that the bioclimatic niches greatly overlap between the American and Asian species and that it is only in the extremely continental climates in which only the Asian larch species can persist. I revealed that the area of dominance is strongly connected to permafrost extent but less linked to permafrost seasonal thaw depths. Comparisons of the paleorecord of larch between the continents suggest differences in the recolonization history. Outside of northern Asia and Alaska, glacial refugial populations of larch were confined to the southern regions and thus recolonization could only occur as migration from south to north. Alaskan larch populations could not establish wide-range dominant forest which could be related to their own genetically depletion as separated refugial population. In Asia, it is still unclear whether or not the northern refugial populations contributed and enhanced the postglacial colonization or whether they were replaced by populations invading from the south in the course of climate warming. Asian larch dominance is thus promoted partly by adaptions to extremely continental climates and by adaptations to grow on continuous permafrost but could be also connected to differences in glacial survival and recolonization history of Larix species. Except for extremely rare macrofossil findings of fossilized cones, traditional methods to study past vegetation are not able to distinguish between larch species or populations. Within the scope of this thesis, I therefore established a method to retrieve genetic information of past larch populations to distinguish between species. Using the Larix chloroplast genome as target, I successfully applied the method of DNA target enrichment by hybridization capture on sedaDNA samples from lake records and showed that it is able to distinguish between larch species. I then used the method on samples from lake records from across Siberia dating back up to 50 ka BP. The results allowed me to address the question of glacial survival and post-glacial recolonization mode in Siberian larch species. The analyzed pattern showed that LGM refugia were almost exclusively constituted by L. gmelinii, even in sites of current L. sibirica distribution. For included study sites, L. sibirica migrated into its extant northern distribution area only in the Holocene. Consequently, the post-glacial recolonization of L. sibirica was not enhanced by northern glacial refugia. In case of sites in extant distribution area of L. gmelinii, the absence of a genetic turn-over point to a continuous population rather than an invasion of southern refugia. The results suggest that climate has a strong influence on the distribution of Larix species and that species may also respond differently to future climate warming. Because species differ in their ecological characteristics, species distribution is also relevant with respect to further feedbacks between vegetation and climate. With this thesis, I give an overview of present and past larch occurrences and evaluate which factors promote their dominance. Furthermore, I provide the tools to study past Larix species and give first important insights into the glacial history of Larix populations.}, language = {en} } @article{SchulteLiLisovskietal.2022, author = {Schulte, Luise and Li, Chenzhi and Lisovski, Simeon and Herzschuh, Ulrike}, title = {Forest-permafrost feedbacks and glacial refugia help explain the unequal distribution of larch across continents}, series = {Journal of biogeography}, volume = {49}, journal = {Journal of biogeography}, number = {10}, publisher = {Wiley}, address = {Hoboken}, issn = {0305-0270}, doi = {10.1111/jbi.14456}, pages = {1825 -- 1838}, year = {2022}, abstract = {Aim: The continental-scale distribution of plant functional types, such as evergreen and summergreen needle-leaf forest, is assumed to be determined by contemporary climate. However, the distribution of summergreen needle-leaf forest of larch (Larix Mill.) differs markedly between the continents, despite relatively similar climatic conditions. The reasons for these differences are little understood. Our aim is to identify potential triggers and drivers of the current distribution patterns by comparing species' bioclimatic niches, glacial refugia and postglacial recolonization patterns. Location: Northern hemisphere. Taxon: Species of the genus Larix (Mill.). Methods: We compare species distribution and dominance using species ranges and sites of dominance, as well as their occurrence on modelled permafrost extent, and active layer thickness (ALT). We compare the bioclimatic niches and calculate the niche overlap between species, using the same data in addition to modern climate data. We synthesize pollen, macrofossil and ancient DNA palaeo-evidence of past Larix occurrences of the last 60,000 years and track differences in distribution patterns through time. Results: Bioclimatic niches show large overlaps between Asian larch species and American Larix laricina. The distribution across various degrees of permafrost extent is distinctly different for Asian L. gmelinii and L. cajanderi compared to the other species, whereas the distribution on different depths of ALT is more similar among Asian and American species. Northern glacial refugia for Larix are only present in eastern Asia and Alaska. Main Conclusion: The dominance of summergreen larches in Asia, where evergreen conifers dominate most of the rest of the boreal forests, is dependent on the interaction of several factors which allows Asian L. gmelinii and L. cajanderi to dominate where these factors coincide. These factors include the early postglacial spread out of northern glacial refugia in the absence of competitors as well as a positive feedback mechanism between frozen ground and forest.}, language = {en} }