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  • 1.
    Capo, Eric
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Department of Marine Biology, Institut de Ciències del Mar, CSIC, Barcelona, Spain.
    Giguet-Covex, Charline
    Department Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204, CNRS, University Savoie Mont Blanc, Le Bourget du Lac, France.
    Rouillard, Alexandra
    Department of Geosciences, UiT the Arctic University of Norway, Tromsø, Norway; Section for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
    Nota, Kevin
    Department of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
    Heintzman, Peter D.
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway.
    Vuillemin, Aurèle
    Department of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany; GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany.
    Ariztegui, Daniel
    Department of Earth Sciences, University of Geneva, Geneva, Switzerland.
    Arnaud, Fabien
    Department Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204, CNRS, University Savoie Mont Blanc, Le Bourget du Lac, France.
    Belle, Simon
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Bertilsson, Stefan
    Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Bigler, Christian
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bindler, Richard
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Brown, Antony G.
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway; School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom.
    Clarke, Charlotte L.
    School of Geography and Environmental Science, University of Southampton, Southampton, United Kingdom.
    Crump, Sarah E.
    Institute of Arctic and Alpine Research, University of Colorado Boulder, CO, Boulder, United States.
    Debroas, Didier
    LMGE, UMR CNRS 6023, University Clermont Auvergne, Clermont-Ferrand, France.
    Englund, Göran
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Ficetola, Gentile Francesco
    Department of Environmental Science and Policy, University of Milan, Milan, Italy; Laboratoire d’Écologie Alpine (LECA), University Grenoble Alpes, CNRS, Grenoble, France.
    Garner, Rebecca E.
    Department of Biology, Concordia University, QC, Montréal, Canada; Groupe de Recherche Interuniversitaire en Limnologie, QC, Montréa, Canada.
    Gauthier, Joanna
    Groupe de Recherche Interuniversitaire en Limnologie, QC, Montréa, Canada; Department of Biology, University McGill, QC, Montréal, Canada.
    Gregory-Eaves, Irene
    Groupe de Recherche Interuniversitaire en Limnologie, QC, Montréa, Canada; Department of Biology, University McGill, QC, Montréal, Canada.
    Heinecke, Liv
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany; Institute for Mathematics, University of Potsdam, Potsdam, Germany.
    Herzschuh, Ulrike
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany; Institute for Environmental Sciences and Geography, University of Potsdam, Potsdam, Germany.
    Ibrahim, Anan
    Department of Biology, University of Konstanz, Konstanz, Germany.
    Kisand, Veljo
    Institute of Technology, University of Tartu, Tartu, Estonia.
    Kjær, Kurt H.
    Section for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
    Lammers, Youri
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway.
    Littlefair, Joanne
    School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom.
    Messager, Erwan
    Department Environment, Dynamics and Territories of the Mountains (EDYTEM), UMR 5204, CNRS, University Savoie Mont Blanc, Le Bourget du Lac, France.
    Monchamp, Marie-Eve
    Groupe de Recherche Interuniversitaire en Limnologie, QC, Montréa, Canada; Department of Biology, University McGill, QC, Montréal, Canada.
    Olajos, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Orsi, William
    Department of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, Munich, Germany; GeoBio-Center LMU, Ludwig-Maximilians-Universität München, Munich, Germany.
    Pedersen, Mikkel W.
    Section for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
    Rijal, Dilli P.
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway.
    Rydberg, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Spanbauer, Trisha
    Department of Environmental Sciences and Lake Erie Center, University of Toledo, OH, Toledo, United States.
    Stoof-Leichsenring, Kathleen R.
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany.
    Taberlet, Pierre
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway; Laboratoire d’Écologie Alpine (LECA), University Grenoble Alpes, CNRS, Grenoble, France.
    Talas, Liisi
    Institute of Technology, University of Tartu, Tartu, Estonia.
    Thomas, Camille
    Department of Earth Sciences, University of Geneva, Geneva, Switzerland.
    Walsh, David A.
    Department of Biology, Concordia University, QC, Montréal, Canada.
    Wang, Yucheng
    Section for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark; Department of Zoology, University of Cambridge, Cambridge, United Kingdom.
    Willerslev, Eske
    Section for Geogenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
    van Woerkom, Anne
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Zimmermann, Heike H.
    Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Potsdam, Germany.
    Coolen, Marco J. L.
    Western Australia Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, the Institute for Geoscience Research (TIGeR), Curtin University, Bentley, Australia.
    Epp, Laura S.
    Limnological Institute, Department of Biology, University of Konstanz, Konstanz, Germany.
    Domaizon, Isabelle
    INRAE, University Savoie Mont Blanc, CARRTEL, Thonon les bains, France; UMR CARRTEL, Pôle R&D ECLA, Thonon les bains, France.
    Alsos, Inger G.
    The Arctic University Museum of Norway, UiT the Arctic University of Norway, Tromsø, Norway.
    Parducci, Laura
    Department of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden; Department of Environmental Biology, Sapienza University of Rome, Rome, Italy.
    Lake sedimentary dna research on past terrestrial and aquatic biodiversity: Overview and recommendations2021In: Quaternary, E-ISSN 2571-550X, Vol. 4, no 1, article id 6Article, review/survey (Refereed)
    Abstract [en]

    The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.

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  • 2.
    Capo, Eric
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences. Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden.
    Spong, Göran
    Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden; Fisheries, Wildlife and Conservation Biology Program, Department of Forestry and Environmental Resources, North Carolina State University, NC, Raleigh, United States.
    Koizumi, Shuntaro
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Puts, Isolde
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Olajos, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Königsson, Helena
    Molecular Ecology Group, Department of Wildlife, Fish and Environmental Studies, SLU, Umeå, Sweden.
    Karlsson, Jan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Byström, Pär
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Droplet digital PCR applied to environmental DNA, a promising method to estimate fish population abundance from humic-rich aquatic ecosystems2021In: Environmental DNA, E-ISSN 2637-4943, Vol. 3, no 2, p. 343-352Article in journal (Refereed)
    Abstract [en]

    Measures of environmental DNA (eDNA) concentrations in water samples have the potential to be both a cost-efficient and a nondestructive method to estimate fish population abundance. However, the inherent temporal and spatial variability in abiotic and biotic conditions in aquatic systems have been suggested to be a major obstacle to determine relationships between fish eDNA concentrations and fish population abundance. Moreover, once water samples are collected, methodological biases are common, which introduces additional sources of variation to potential relationships between eDNA concentrations and fish population abundance. Here, we evaluate the performance of applying the droplet digital PCR (ddPCR) method to estimate fish population abundance in experimental enclosures. Using large-scale enclosure ecosystems that contain populations of nine-spined stickleback (Pungitius pungitius), we compared the concentrations of fish eDNA (COI mitochondrial region, 134 bp) obtained with the ddPCR method with high precision estimates of fish population abundance (i.e., number of individuals) and biomass. To evaluate the effects of contrasted concentrations of humic substances (potential PCR inhibitors) on the performance of ddPCR assays, we manipulated natural dissolved organic carbon (DOC) concentrations (range 4–11 mg/L) in the enclosures. Additionally, water temperature (+2°C) was manipulated in half of the enclosures. Results showed positive relationships between eDNA concentration and fish abundance and biomass estimates although unexplained variation remained. Still and importantly, fish eDNA estimates from high DOC enclosures were not lowered by potential inhibitory effects with our procedure. Finally, water temperature (although only 2°C difference) was neither detected as a significant factor influencing fish eDNA estimates. Altogether, our work highlights that ddPCR-based eDNA is a promising method for future quantification of fish population abundance in natural systems.

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  • 3.
    Englund, Göran
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Öhlund, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Olajos, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Finstad, Anders
    Bellard, Celine
    Hugueny, Bernard
    Holocene extinctions of a top predator: effects of time, habitat area and habitat subdivision2020In: Journal of Animal Ecology, ISSN 0021-8790, E-ISSN 1365-2656, Vol. 89, no 5, p. 1202-1215Article in journal (Refereed)
    Abstract [en]

    Loss of habitat and changes in the spatial configuration of habitats are major drivers of species extinctions, but the responses to these drivers differ between organisms. To advance theory on how extinction risk from different types of habitat alteration relates to species-specific traits, there is a need for studies of the long-term extinction dynamic of individual species. The goal of this study was to quantify how habitat area and the spatial configuration of habitats affect extinction rate of an aquatic top predator, the northern pike Esox lucius L. We recorded the presence/absence of northern pike in 398 isolated habitat fragments, each one consisting of a number of interconnected lakes. Time since isolation of the habitat fragments, caused by cut-off from the main dispersal source in the Baltic Sea, varied between 0 and 10,000 years. Using survival regression, we analysed how pike population survival was affected by time since isolation, habitat size and habitat subdivision. The approach builds on the assumptions that pike colonized all fragments before isolation and that current absences result from extinctions. We verified these assumptions by testing (a) if pike was present in the region throughout the entire time period when the lakes formed and (b) if pike typically colonize lakes that are formed today. We also addressed the likelihood that unrecorded anthropogenic introductions could bias our estimates of extinction rate. Our results supported the interpretation that current patterns of presence/absence in our study system are shaped by extinctions. Further, we found that time since isolation and fragment area had strong effects on pike population survival. In contrast, spatial habitat subdivision (i.e. if a fragment contained few large lakes or many small lakes) and other environmental covariates describing climate and productivity were unrelated to pike survival. Over all, extinction rate was high in young fragments and decreased sharply with increasing fragment age. Our study demonstrates how the link between extinction rate and habitat size and spatial structure can be quantified. More similar studies may help us find generalizations that can guide management of habitat size and connectivity.

  • 4.
    Kanbar, Hussein Jaafar
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Olajos, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Englund, Göran
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Holmboe, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Geochemical identification of potential DNA-hotspots and DNA-infrared fingerprints in lake sediments2020In: Applied Geochemistry, ISSN 0883-2927, E-ISSN 1872-9134, Vol. 122, article id 104728Article in journal (Refereed)
    Abstract [en]

    DNA preserved in sedimentary materials can be used to study past ecosystem changes, such as species' colonization and extinction. It is believed that minerals, especially clay minerals, enhance the preservation of DNA. However, the role of minerals, as well as organic matter, on DNA sorption in heterogeneous sediments is still not clear. In this study, we examined the effect of mineral and organic matter on DNA binding in lake sediments. Bulk and size-fractionated sediments (0–4, 4–16, 16–64, and >64 μm), having different mineral and organic composition, were used to test DNA sorption; similar experiments were also run after the removal of sedimentary organic matter. Additionally, diffuse reflectance infrared spectroscopy (DRIFT) was used to determine the chemical changes caused by DNA sorption and subsequently produce a DNA-infrared (IR) fingerprint. Clay minerals were the main minerals to sorb DNA in the different samples. Moreover, mica promoted DNA sorption in all size fractions, while chlorite promoted DNA sorption in size fractions greater than 16 μm; clay-mineral and organo-mineral complexes caused a preference of certain clay minerals over others. Sedimentary organic matter affected DNA sorption by covering as well as by amplifying potential DNA binding sites, yet DNA sorption did not change significantly. DNA sorption showed IR spectral modifications mainly at ~1640, 1416, and 1231 cm−1. Interestingly, the DNA-IR fingerprint in the heterogeneous sediments was evident by those peaks after spectral subtraction. Finally, we proposed a simple model, based on sediment geochemistry, that can be used to determine potential DNA-hotspots in sediments.

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  • 5.
    Kanbar, Hussein Jaafar
    et al.
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Tran Le, Thai
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Olajos, Fredrik
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Englund, Göran
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Holmboe, Michael
    Umeå University, Faculty of Science and Technology, Department of Chemistry.
    Tracking mineral and geochemical characteristics of Holocene lake sediments: the case of Hotagen, west-central Sweden2021In: Journal of Soils and Sediments, ISSN 1439-0108, E-ISSN 1614-7480, Vol. 21, no 9, p. 3150-3168Article in journal (Refereed)
    Abstract [en]

    Purpose: Intact lake sediments reflect the development of terrestrial ecosystems. This development can be understood by decoding mineral and geochemical information of sedimentary archives. Therefore, we characterized a Holocene lake sediment core and revealed bulk to micro-scale variations via a combination of geochemical techniques and statistical methods.

    Methods: A 2.3 m sediment core was collected from Hotagen, a lake in west-central Sweden; a sediment sample was collected every 5 cm. A part of each sediment sample was kept untreated (named bulk) and another part was size-fractionated into < 4, 4–16, 16–64, and > 64 µm subsamples. Characterization was then made with respect to grain size distribution (GSD), physico-chemical parameters, geochemical properties, organic composition, and mineralogy. The sediments were investigated at bulk, micro-, and elemental scales using powder X-ray diffraction (XRD), diffuse reflectance infrared Fourier transform spectroscopy (DRIFT), and scanning electron microscopy coupled to energy-dispersive X-ray spectroscopy (SEM–EDX).

    Results: The deepest sediment was identified as glacial till dating back to the Late Pleistocene. The bulk sediments showed a clear distinction between 0–195 cm (unit 1, U1) and 200–225 cm (unit 2, U2) depths. Quartz and feldspar minerals decreased and organic matter and clay minerals increased from the till towards the lower limit of U1. The development in the sedimentary properties marked the transformation of the terrestrial ecosystem from glacier-covered land to vegetated areas. This development was also well reflected by the appearance of X-ray amorphous materials and the formation of distinct organo-mineral aggregates; chlorite was the predominant clay mineral in these aggregates. The geochemical variation between U2 and U1 sediments was further established by resolving the DRIFT spectral components through multivariate curve resolution alternating least square (MCR-ALS). The U1 sediments settled over a period of ~ 7500 years and showed comparable mineral, geochemical, and organic composition. However, the size-fractionated sediments, mainly < 4 µm, showed diverse mineral and geochemical composition. Indeed, these sediments were distinct by containing relatively higher amounts of X-ray amorphous materials and clay minerals, the latter had variable Na, Mg, and K contents.

    Conclusion: The combined use of geochemical and statistical approaches used in this study followed the mineral and geochemical development of sediments that had settled during the Late Pleistocene and Early Holocene Epochs. Finally, the U2 sediments marked the terrestrial ecosystem development that occurred during the late glaciation, deglaciation, and post-glaciation periods. Graphical abstract: [Figure not available: see fulltext.]

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  • 6.
    Olajos, Fredrik
    et al.
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bokma, Folmer
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bartels, Pia
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Myrstener, Erik
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Rydberg, Johan
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Öhlund, Gunnar
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Bindler, Richard
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Wang, Xiao-Ru
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Zale, Rolf
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Englund, Göran
    Umeå University, Faculty of Science and Technology, Department of Ecology and Environmental Sciences.
    Estimating species colonization dates using DNA in lake sediment2018In: Methods in Ecology and Evolution, E-ISSN 2041-210X, Vol. 9, no 3, p. 535-543Article in journal (Refereed)
    Abstract [en]
    1. Detection of DNA in lake sediments holds promise as a tool to study processes like extinction, colonization, adaptation and evolutionary divergence. However, low concentrations make sediment DNA difficult to detect, leading to high false negative rates. Additionally, contamination could potentially lead to high false positive rates. Careful laboratory procedures can reduce false positive and negative rates, but should not be assumed to completely eliminate them. Therefore, methods are needed that identify potential false positive and negative results, and use this information to judge the plausibility of different interpretations of DNA data from natural archives.
    2. We developed a Bayesian algorithm to infer the colonization history of a species using records of DNA from lake-sediment cores, explicitly labelling some observations as false positive or false negative. We illustrate the method by analysing DNA of whitefish (Coregonus lavaretus L.) from sediment cores covering the past 10,000 years from two central Swedish lakes. We provide the algorithm as an R-script, and the data from this study as example input files.
    3. In one lake, Stora Lögdasjön, where connectivity with the proto-Baltic Sea and the degree of whitefish ecotype differentiation suggested colonization immediately after deglaciation, DNA was indeed successfully recovered and amplified throughout the post-glacial sediment. For this lake, we found no loss of detection probability over time, but a high false negative rate. In the other lake, Hotagen, where connectivity and ecotype differentiation suggested colonization long after deglaciation, DNA was amplified only in the upper part of the sediment, and colonization was estimated at 2,200 bp based on the assumption that successful amplicons represent whitefish presence. Here the earliest amplification represents a false positive with a posterior probability of 41%, which increases the uncertainty in the estimated time of colonization.
    4. Complementing careful laboratory procedures aimed at preventing contamination, our method estimates contamination rates from the data. By combining these results with estimates of false negative rates, our models facilitate unbiased interpretation of data from natural DNA archives.
1 - 6 of 6
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