@article{EppStoofTrauthetal.2010,
  author    = {Epp, Laura Saskia and Stoof, Kathleen R. and Trauth, Martin H. and Tiedemann, Ralph},
  title     = {Historical genetics on a sediment core from a Kenyan lake : intraspecific genotype turnover in a tropical rotifer is related to past environmental changes},
  issn      = {0921-2728},
  doi       = {10.1007/s10933-009-9379-7},
  year      = {2010},
  abstract  = {Using molecular genetic methods and an ancient DNA approach, we studied population and species succession of rotifers of the genus Brachionus in the Kenyan alkaline-saline crater lake Sonachi since the beginning of the 19th century as well as distribution of Brachionus haplotypes in recent and historic sediments of other lakes of the East African Rift System. The sediment core record of Lake Sonachi displays haplotypes of a distinct evolutionary lineage in all increments. Populations were dominated by a single mitochondrial haplotype for a period of 150 years, and two putatively intraspecific turnovers in dominance occurred. Both changes are concordant with major environmental perturbations documented by a profound visible change in sediment composition of the core. The first change was very abrupt and occurred after the deposition of volcanic ash at the beginning of the 19th century. The second change coincides with a major lake level lowstand during the 1940s. It was preceded by a period of successively declining lake level, in which two other haplotypes appeared in the lake. One of these putatively belongs to another species documented in historical and recent Kenyan lake sediments. The analysis of plankton population dynamics through historical time can reveal patterns of population persistence and turnover in relation to environmental changes.},
  language  = {en}
}
@article{StuckasStoofQuesadaetal.2009,
  author    = {Stuckas, Heiko and Stoof, Kathleen and Quesada, Humberto and Tiedemann, Ralph},
  title     = {Evolutionary implications of discordant clines across the Baltic Mytilus hybrid zone (Mytilus edulis and Mytilus trossulus)},
  issn      = {0018-067X},
  doi       = {10.1038/Hdy.2009.37},
  year      = {2009},
  abstract  = {It is well established that reproductive isolation often arises from genome incompatibilities and that genes encoding reproductive traits are less prone to introgression. Hybrid zones of Mytilus trossulus and Mytilus edulis provide an intriguing model to assess reproductive isolation. Although gene flow is restricted in North America, introgression is pervasive in the Baltic. This study aimed at analyzing the shape of multilocus clines across the Baltic contact zone between M. edulis and M. trossulus to infer mechanisms of restriction to gene flow. We use maximum likelihood methods to construct the best fitting individual clines for five markers located on biparentally inherited autosomes and paternally and maternally inherited mitochondrial DNA (mtDNA). Strong cline shape differences among markers suggest that reproductive isolation arising from genome-wide incompatibilities is weak, and that these discrepancies possibly result from genetic drift, hybrid zone movement or marker-specific selection. However, the finding of a common cline center for M7 lysin (involved in fertilization) and paternally transmitted mtDNA (causing nuclear-mitochondrial incompatibilities in hybrids) suggest that these loci may play a role in incomplete reproductive isolation.},
  language  = {en}
}
@article{StoofLeichsenringJungingerOlakaetal.2011,
  author    = {Stoof-Leichsenring, Kathleen Rosemarie and Junginger, Annett and Olaka, Lydia A. and Tiedemann, Ralph and Trauth, Martin H.},
  title     = {Environmental variability in Lake Naivasha, Kenya, over the last two centuries},
  series = {Journal of paleolimnolog},
  volume    = {45},
  journal   = {Journal of paleolimnolog},
  number    = {3},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0921-2728},
  doi       = {10.1007/s10933-011-9502-4},
  pages     = {353 -- 367},
  year      = {2011},
  abstract  = {Lake Naivasha, Kenya, is one of a number of freshwater lakes in the East African Rift System. Since the beginning of the twentieth century, it has experienced greater anthropogenic influence as a result of increasingly intensive farming of coffee, tea, flowers, and other horticultural crops within its catchment. The water-level history of Lake Naivasha over the past 200 years was derived from a combination of instrumental records and sediment data. In this study, we analysed diatoms in a lake sediment core to infer past lacustrine conductivity and total phosphorus concentrations. We also measured total nitrogen and carbon concentrations in the sediments. Core chronology was established by (210)Pb dating and covered a similar to 186-year history of natural (climatic) and human-induced environmental changes. Three stratigraphic zones in the core were identified using diatom assemblages. There was a change from littoral/epiphytic diatoms such as Gomphonema gracile and Cymbella muelleri, which occurred during a prolonged dry period from ca. 1820 to 1896 AD, through a transition period, to the present planktonic Aulacoseira sp. that favors nutrient-rich waters. This marked change in the diatom assemblage was caused by climate change, and later a strong anthropogenic overprint on the lake system. Increases in sediment accumulation rates since 1928, from 0.01 to 0.08 g cm(-2) year(-1) correlate with an increase in diatom-inferred total phosphorus concentrations since the beginning of the twentieth century. The increase in phosphorus accumulation suggests increasing eutrophication of freshwater Lake Naivasha. This study identified two major periods in the lake's history: (1) the period from 1820 to 1950 AD, during which the lake was affected mainly by natural climate variations, and (2) the period since 1950, during which the effects of anthropogenic activity overprinted those of natural climate variation.},
  language  = {en}
}
@article{EppStoofLeichsenringTrauthetal.2011,
  author    = {Epp, Laura Saskia and Stoof-Leichsenring, Kathleen Rosemarie and Trauth, Martin H. and Tiedemann, Ralph},
  title     = {Molecular profiling of diatom assemblages in tropical lake sediments using taxon-specific PCR and Denaturing High-Performance Liquid Chromatography (PCR-DHPLC)},
  series = {Molecular ecology resources},
  volume    = {11},
  journal   = {Molecular ecology resources},
  number    = {5},
  publisher = {Wiley-Blackwell},
  address   = {Hoboken},
  issn      = {1755-098X},
  doi       = {10.1111/j.1755-0998.2011.03022.x},
  pages     = {842 -- 853},
  year      = {2011},
  abstract  = {Here we present a protocol to genetically detect diatoms in sediments of the Kenyan tropical Lake Naivasha, based on taxon-specific PCR amplification of short fragments (approximately 100 bp) of the small subunit ribosomal (SSU) gene and subsequent separation of species-specific PCR products by PCR-based denaturing high-performance liquid chromatography (DHPLC). An evaluation of amplicons differing in primer specificity to diatoms and length of the fragments amplified demonstrated that the number of different diatom sequence types detected after cloning of the PCR products critically depended on the specificity of the primers to diatoms and the length of the amplified fragments whereby shorter fragments yielded more species of diatoms. The DHPLC was able to discriminate between very short amplicons based on the sequence difference, even if the fragments were of identical length and if the amplicons differed only in a small number of nucleotides. Generally, the method identified the dominant sequence types from mixed amplifications. A comparison with microscopic analysis of the sediment samples revealed that the sequence types identified in the molecular assessment corresponded well with the most dominant species. In summary, the PCR-based DHPLC protocol offers a fast, reliable and cost-efficient possibility to study DNA from sediments and other environmental samples with unknown organismic content, even for very short DNA fragments.},
  language  = {en}
}
@article{StoofLeichsenringEppTrauthetal.2012,
  author    = {Stoof-Leichsenring, Kathleen Rosemarie and Epp, Laura Saskia and Trauth, Martin H. and Tiedemann, Ralph},
  title     = {Hidden diversity in diatoms of Kenyan Lake Naivasha a genetic approach detects temporal variation},
  series = {Molecular ecology},
  volume    = {21},
  journal   = {Molecular ecology},
  number    = {8},
  publisher = {Wiley-Blackwell},
  address   = {Malden},
  issn      = {0962-1083},
  doi       = {10.1111/j.1365-294X.2011.05412.x},
  pages     = {1918 -- 1930},
  year      = {2012},
  abstract  = {This study provides insights into the morphological and genetic diversity in diatoms occurring in core sediments from tropical lakes in Kenya. We developed a genetic survey technique specific for diatoms utilizing a short region (7667 bp) of the ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (rbcL) gene as genetic barcode. Our analyses (i) validated the use of rbcL as a barcoding marker for diatoms, applied to sediment samples, (ii) showed a significant correlation between the results obtained by morphological and molecular data and (iii) indicated temporal variation in diatom assemblages on the inter- and intra-specific level. Diatom assemblages from a short core from Lake Naivasha show a drastic shift over the last 200 years, as littoral species (e.g. Navicula) are replaced by more planktonic ones (e.g. Aulacoseira). Within that same period, we detected periodic changes in the respective frequencies of distinct haplotype groups of Navicula, which coincide with wet and dry periods of Lake Naivasha between 1820 and 1938 AD. Our genetic analyses on historical lake sediments revealed inter- and intra-specific variation in diatoms, which is partially hidden behind single morphotypes. The occurrence of particular genetic lineages is probably correlated with environmental factors.},
  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}
}
@phdthesis{StoofLeichsenring2011,
  author    = {Stoof-Leichsenring, Kathleen Rosemarie},
  title     = {Genetic analysis of diatoms and rotifers in tropical Kenyan lake sediments},
  address   = {Potsdam},
  year      = {2011},
  language  = {en}
}
@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{ZimmermannRaschkeEppetal.2017,
  author    = {Zimmermann, Heike Hildegard and Raschke, Elena and Epp, Laura Saskia and Stoof-Leichsenring, Kathleen Rosemarie and Schwamborn, Georg and Schirrmeister, Lutz and Overduin, Pier Paul and Herzschuh, Ulrike},
  title     = {Sedimentary ancient DNA and pollen reveal the composition of plant organic matter in Late Quaternary permafrost sediments of the Buor Khaya Peninsula (north-eastern Siberia)},
  series = {Biogeosciences},
  volume    = {14},
  journal   = {Biogeosciences},
  number    = {3},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1726-4170},
  doi       = {10.5194/bg-14-575-2017},
  pages     = {575 -- 596},
  year      = {2017},
  abstract  = {Organic matter deposited in ancient, ice-rich permafrost sediments is vulnerable to climate change and may contribute to the future release of greenhouse gases; it is thus important to get a better characterization of the plant organic matter within such sediments. From a Late Quaternary permafrost sediment core from the Buor Khaya Peninsula, we analysed plant-derived sedimentary ancient DNA (sedaDNA) to identify the taxonomic composition of plant organic matter, and undertook palynological analysis to assess the environmental conditions during deposition. Using sedaDNA, we identified 154 taxa and from pollen and non-pollen palynomorphs we identified 83 taxa. In the deposits dated between 54 and 51 kyr BP, sedaDNA records a diverse low-centred polygon plant community including recurring aquatic pond vegetation while from the pollen record we infer terrestrial open-land vegetation with relatively dry environmental conditions at a regional scale. A fluctuating dominance of either terrestrial or swamp and aquatic taxa in both proxies allowed the local hydrological development of the polygon to be traced. In deposits dated between 11.4 and 9.7 kyr BP (13.4-11.1 cal kyr BP), sedaDNA shows a taxonomic turnover to moist shrub tundra and a lower taxonomic richness compared to the older samples. Pollen also records a shrub tundra community, mostly seen as changes in relative proportions of the most dominant taxa, while a decrease in taxonomic richness was less pronounced compared to sedaDNA. Our results show the advantages of using sedaDNA in combination with palynological analyses when macrofossils are rarely preserved. The high resolution of the sedaDNA record provides a detailed picture of the taxonomic composition of plant-derived organic matter throughout the core, and palynological analyses prove valuable by allowing for inferences of regional environmental conditions.},
  language  = {en}
}