@article{TrauthFoersterJungingeretal.2018,
  author    = {Trauth, Martin H. and Foerster, Verena and Junginger, Annett and Asrat, Asfawossen and Lamb, Henry F. and Sch{\"a}bitz, Frank},
  title     = {Abrupt or gradual?},
  series = {Quaternary research : an interdisciplinary journal},
  volume    = {90},
  journal   = {Quaternary research : an interdisciplinary journal},
  number    = {2},
  publisher = {Cambridge Univ. Press},
  address   = {New York},
  issn      = {0033-5894},
  doi       = {10.1017/qua.2018.30},
  pages     = {321 -- 330},
  year      = {2018},
  abstract  = {We used a change point analysis on a late Pleistocene-Holocene lake-sediment record from the Chew Bahir basin in the southern Ethiopian Rift to determine the amplitude and duration of past climate transitions. The most dramatic changes occurred over 240 yr (from similar to 15,700 to 15,460 yr) during the onset of the African Humid Period (AHP), and over 990 yr (from similar to 4875 to 3885 yr) during its protracted termination. The AHP was interrupted by a distinct dry period coinciding with the high-latitude Younger Dryas stadial, which had an abrupt onset (less than similar to 100 yr) at similar to 13,260 yr and lasted until similar to 11,730 yr. Wet-dry-wet transitions prior to the AHP may reflect the high-latitude Dansgaard-Oeschger cycles, as indicated by cross-correlation of the potassium record with the NorthGRIP ice core record between similar to 45-20 ka. These findings may contribute to the debates regarding the amplitude, and duration and mechanisms of past climate transitions, and their possible influence on the development of early modern human cultures.},
  language  = {en}
}
@article{BorchardtTrauth2012,
  author    = {Borchardt, Sven and Trauth, Martin H.},
  title     = {Remotely-sensed evapotranspiration estimates for an improved hydrological modeling of the early holocene mega-lake Suguta, northern Kenya Rift},
  series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences},
  volume    = {361},
  journal   = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences},
  number    = {22},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0031-0182},
  doi       = {10.1016/j.palaeo.2012.07.009},
  pages     = {14 -- 20},
  year      = {2012},
  abstract  = {The actual evapotranspiration is an important, but difficult to determine, element in the water balance of lakes and their catchment areas. Reliable data on evapotranspiration are not available for most lake basins for which paleoclimate reconstructions and modeling have been performed, particularly those in remote parts of Africa. We have used thermal infrared multispectral data for 14 ASTER scenes from the TERRA satellite to estimate the actual evapotranspiration in the 12,800 km(2) catchment of the Suguta Valley, northern Kenya Rift Evidence from sediments and paleo-shorelines indicates that, during the African Humid Period (AHP, 14.8 to 5.5 kyrs BP), this valley contained a large lake, 280 m deep and covering similar to 2200 km(2), which has now virtually disappeared. Evapotranspiration estimates for the Suguta Basin were generated using the Surface Energy Balance Algorithm for Land (SEBAL). Climate data required for the model were extracted from a high-resolution gridded dataset obtained from the Climatic Research Unit (East Anglia, UK). Results suggest significant spatial variations in evapotranspiration within the catchment area (ranging from 450 mm/yr in the basin to the north to 2000 mm/yr in more elevated areas) and precipitation that was similar to 20\% higher during the AHP than in recent times. These results are in agreement with other estimates of paleo-precipitation in East Africa. The extreme response of the lake system (similar to 280 m greater water depth than today, and a lake surface area of 2200 km(2)) to only moderately higher precipitation illustrates the possible sensitivity of this area to future climate change.},
  language  = {en}
}
@article{BorchardtTrauth2021,
  author    = {Borchardt, Sven and Trauth, Martin H.},
  title     = {Erratum to: Borchardt, Sven, Trauth, Martin H.: Remotely-sensed evapotranspiration estimates for an improved hydrological modeling of the early Holocene mega-lake Suguta, northern Kenya Rift. - (Palaeogeography, Palaeoclimatology, Palaeoecology. - Volumes 361-362 (2012), S. 14 - 20. - doi.org/10.1016/j.palaeo.2012.07.009)},
  series = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences},
  volume    = {571},
  journal   = {Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0031-0182},
  doi       = {10.1016/j.palaeo.2019.109540},
  pages     = {1},
  year      = {2021},
  language  = {en}
}
@book{Trauth2022,
  author    = {Trauth, Martin H.},
  title     = {Python Recipes for Earth Sciences},
  series = {Springer Textbooks in Earth Sciences, Geography and Environment},
  journal   = {Springer Textbooks in Earth Sciences, Geography and Environment},
  publisher = {Springer},
  address   = {Cham},
  isbn      = {978-3-031-07719-7},
  issn      = {2510-1307},
  doi       = {10.1007/978-3-031-07719-7},
  pages     = {453},
  year      = {2022},
  abstract  = {Python is used in a wide range of geoscientific applications, such as in processing images for remote sensing, in generating and processing digital elevation models, and in analyzing time series. This book introduces methods of data analysis in the geosciences using Python that include basic statistics for univariate, bivariate, and multivariate data sets, time series analysis, and signal processing; the analysis of spatial and directional data; and image analysis. The text includes numerous examples that demonstrate how Python can be used on data sets from the earth sciences. The supplementary electronic material (available online through Springer Link) contains the example data as well as recipes that include all the Python commands featured in the book.},
  language  = {en}
}
@article{Trauth2021,
  author    = {Trauth, Martin H.},
  title     = {Spectral analysis in quaternary sciences},
  series = {Quaternary science reviews : the international multidisciplinary research and review journal},
  volume    = {270},
  journal   = {Quaternary science reviews : the international multidisciplinary research and review journal},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0277-3791},
  doi       = {10.1016/j.quascirev.2021.107157},
  pages     = {13},
  year      = {2021},
  abstract  = {Spectral analysis is a technique of time-series analysis that decomposes signals into linear combinations of harmonic components. Rooted in the 19th century, spectral analysis gained popularity in palaeoclimatology since the early 1980s. This was partly due to the availability of long time series of past climates, but also the development of new, partly adapted methods and the increasing spread of affordable personal computers. This paper reviews the most important methods of spectral analysis for palaeoclimate time series and discusses the prerequisites for their application as well as advantages and disadvantages. The paper also offers an overview of suitable software, as well as computer code for using the methods on synthetic examples.},
  language  = {en}
}
@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{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{KruegerFoersterTrauthetal.2021,
  author    = {Kr{\"u}ger, Johanna and Foerster, Verena Elisabeth and Trauth, Martin H. and Hofreiter, Michael and Tiedemann, Ralph},
  title     = {Exploring the Past Biosphere of Chew Bahir/Southern Ethiopia: Cross-Species Hybridization Capture of Ancient Sedimentary DNA from a Deep Drill Core},
  series = {Frontiers in Earth Science},
  journal   = {Frontiers in Earth Science},
  publisher = {Frontiers in Earth Science},
  address   = {Lausanne, Schweiz},
  issn      = {2296-6463},
  doi       = {10.3389/feart.2021.683010},
  pages     = {1 -- 20},
  year      = {2021},
  abstract  = {Eastern Africa has been a prime target for scientific drilling because it is rich in key paleoanthropological sites as well as in paleolakes, containing valuable paleoclimatic information on evolutionary time scales. The Hominin Sites and Paleolakes Drilling Project (HSPDP) explores these paleolakes with the aim of reconstructing environmental conditions around critical episodes of hominin evolution. Identification of biological taxa based on their sedimentary ancient DNA (sedaDNA) traces can contribute to understand past ecological and climatological conditions of the living environment of our ancestors. However, sedaDNA recovery from tropical environments is challenging because high temperatures, UV irradiation, and desiccation result in highly degraded DNA. Consequently, most of the DNA fragments in tropical sediments are too short for PCR amplification. We analyzed sedaDNA in the upper 70 m of the composite sediment core of the HSPDP drill site at Chew Bahir for eukaryotic remnants. We first tested shotgun high throughput sequencing which leads to metagenomes dominated by bacterial DNA of the deep biosphere, while only a small fraction was derived from eukaryotic, and thus probably ancient, DNA. Subsequently, we performed cross-species hybridization capture of sedaDNA to enrich ancient DNA (aDNA) from eukaryotic remnants for paleoenvironmental analysis, using established barcoding genes (cox1 and rbcL for animals and plants, respectively) from 199 species that may have had relatives in the past biosphere at Chew Bahir. Metagenomes yielded after hybridization capture are richer in reads with similarity to cox1 and rbcL in comparison to metagenomes without prior hybridization capture. Taxonomic assignments of the reads from these hybridization capture metagenomes also yielded larger fractions of the eukaryotic domain. For reads assigned to cox1, inferred wet periods were associated with high inferred relative abundances of putative limnic organisms (gastropods, green algae), while inferred dry periods showed increased relative abundances for insects. These findings indicate that cross-species hybridization capture can be an effective approach to enhance the information content of sedaDNA in order to explore biosphere changes associated with past environmental conditions, enabling such analyses even under tropical conditions.},
  language  = {en}
}