@article{NiemeyerEppStoofLeichsenringetal.2017,
  author    = {Niemeyer, Bastian and Epp, Laura Saskia and Stoof-Leichsenring, Kathleen Rosemarie and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {A comparison of sedimentary DNA and pollen from lake sediments in recording vegetation composition at the Siberian treeline},
  series = {Molecular ecology resources},
  volume    = {17},
  journal   = {Molecular ecology resources},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1755-098X},
  doi       = {10.1111/1755-0998.12689},
  pages     = {e46 -- e62},
  year      = {2017},
  abstract  = {Reliable information on past and present vegetation is important to project future changes, especially for rapidly transitioning areas such as the boreal treeline. To study past vegetation, pollen analysis is common, while current vegetation is usually assessed by field surveys. Application of detailed sedimentary DNA (sedDNA) records has the potential to enhance our understanding of vegetation changes, but studies systematically investigating the power of this proxy are rare to date. This study compares sedDNA metabarcoding and pollen records from surface sediments of 31 lakes along a north-south gradient of increasing forest cover in northern Siberia (Taymyr peninsula) with data from field surveys in the surroundings of the lakes. sedDNA metabarcoding recorded 114 plant taxa, about half of them to species level, while pollen analyses identified 43 taxa, both exceeding the 31 taxa found by vegetation field surveys. Increasing Larix percentages from north to south were consistently recorded by all three methods and principal component analyses based on percentage data of vegetation surveys and DNA sequences separated tundra from forested sites. Comparisons of the ordinations using procrustes and protest analyses show a significant fit among all compared pairs of records. Despite similarities of sedDNA and pollen records, certain idiosyncrasies, such as high percentages of Alnus and Betula in all pollen and high percentages of Salix in all sedDNA spectra, are observable. Our results from the tundra to single-tree tundra transition zone show that sedDNA analyses perform better than pollen in recording site-specific richness (i.e., presence/absence of taxa in the vicinity of the lake) and perform as well as pollen in tracing vegetation composition.},
  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{BalintMartonSchatzetal.2018,
  author    = {Balint, Miklos and Marton, Orsolya and Schatz, Marlene and D{\"u}ring, Rolf-Alexander and Grossart, Hans-Peter},
  title     = {Proper experimental design requires randomization/balancing of molecular ecology experiments},
  series = {Ecology and evolution},
  volume    = {8},
  journal   = {Ecology and evolution},
  number    = {3},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {2045-7758},
  doi       = {10.1002/ece3.3687},
  pages     = {1786 -- 1793},
  year      = {2018},
  abstract  = {Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.},
  language  = {en}
}