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  • 301. Dalen, Love
    et al.
    Nystrom, Veronica
    Valdiosera, Cristina
    Germonpre, Mietje
    Sablin, Mikhail
    Turner, Elaine
    Angerbjorn, Anders
    Arsuaga, Juan Luis
    Gotherstrom, Anders
    Ancient DNA reveals lack of postglacial habitat tracking in the arctic fox2007In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 104, no 16, p. 6726-6729Article in journal (Refereed)
  • 302. Dalen, Love
    et al.
    Orlando, Ludovic
    Shapiro, Beth
    Brandstrom-Durling, Mikael
    Quam, Rolf
    Gilbert, M. Thomas P.
    Diez Fernandez-Lomana, J. Carlos
    Willerslev, Eske
    Luis Arsuaga, Juan
    Goetherstrom, Anders
    Partial Genetic Turnover in Neandertals: Continuity in the East and Population Replacement in the West2012In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 29, no 8, p. 1893-1897Article in journal (Refereed)
  • 303. Dalerum, F.
    et al.
    Freire, S.
    Angerbjorn, A.
    Lecomte, N.
    Lindgren, A.
    Meijer, T.
    Pecnerova, P.
    Dalen, L.
    Exploring the diet of arctic wolves (Canis lupus arctos) at their northern range limit2018In: Canadian Journal of Zoology, ISSN 0008-4301, E-ISSN 1480-3283, Vol. 96, no 3, p. 277-281Article in journal (Refereed)
  • 304. Dalerum, Fredrik
    et al.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Frojd, Christina
    Lecomte, Nicolas
    Lindgren, Asa
    Meijer, Tomas
    Pecnerova, Patricia
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Angerbjorn, Anders
    Spatial variation in Arctic hare (Lepus arcticus) populations around the Hall Basin2017In: Polar Biology, ISSN 0722-4060, E-ISSN 1432-2056, Vol. 40, no 10, p. 2113-2118Article in journal (Refereed)
  • 305. Dalerum, Fredrik
    et al.
    Hellström, Peter
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Miranda, Maria
    Nyström, Jesper
    Ekenstedt, Johan
    Angerbjörn, Anders
    Network topology of stable isotope interactions in a sub-arctic raptor guild2016In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 182, no 2, p. 511-518Article in journal (Refereed)
    Abstract [en]

    Predation is an ecologically important process, and intra-guild interactions may substantially influence the ecological effects of predator species. Despite a rapid expansion in the use of mathematical graph theory to describe trophic relations, network approaches have rarely been used to study interactions within predator assemblages. Assemblages of diurnal raptors are subject to substantial intra- and interspecific competition. Here we used the novel approach of applying analyzes based on network topology to species-specific data on the stable isotopes 13C and 15N in feathers to evaluate patterns of relative resource utilization within a guild of diurnal raptors in northern Sweden. Our guild consisted of the golden eagle (Aquila chrysaetos), the gyrfalcon (Falco rusticolus), the peregrine falcon (Falco peregrinus) and the rough-legged buzzard (Buteo lagopus). We found a modular trophic interaction structure within the guild, but the interactions were less nested than expected by chance. These results suggest low redundancy and hence a strong ecological importance of individual species. Our data also suggested that species were less connected through intra-guild interactions than expected by chance. We interpret our results as a convergence on specific isotope niches, and that body size and different hunting behaviour may mediate competition within these niches. We finally highlight that generalist predators could be ecologically important by linking specialist predator species with disparate dietary niches.

  • 306. Dalsätt, J
    et al.
    Zhou, Z
    Zhang, F
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Food remains in Confuciusornis sanctus suggest a fish diet.2006In: Die Naturwissenschaften, ISSN 0028-1042, E-ISSN 1432-1904, Vol. 93, no 9, p. 444-6Article in journal (Refereed)
    Abstract [en]

    Despite hundreds of excellent fossils of Confuciusornis, the most abundant group of birds in the Early Cretaceous, 'Jehol Biota' in China, there is yet no indication of the food choice of these birds. Here, we describe fish remains preserved in the alimentary system of a specimen of Confuciusornis sanctus from the Jiufotang Formation. This find is about five million years younger than all previously published confuciusornithid birds from the Yixian Formation. Although it is unknown how common fish was in the diet of Confuciusornis, the find does not support previous hypotheses that it fed on plants or grain.

  • 307.
    Dalsätt, Johan
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Mörs, Thomas
    Swedish Museum of Natural History, Department of Paleobiology.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Fossil birds from the Miocene and Pliocene of Hambach (NW Germany)2006In: Palaeontographica. Abteilung A, Palaozoologie, Stratigraphie, ISSN 0375-0442, Vol. 277, no 1-6, p. 113-+Article in journal (Refereed)
  • 308.
    D'Aniello, Salvatore
    et al.
    Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn.
    Delroisse, Jérôme
    Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons.
    Valero-Garcia, Alberto
    Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn.
    Lowe, Elijah
    Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn.
    Byrne, Maria
    Schools of Medical and Biological Sciences, The University of Sydney.
    Cannon, Johanna
    Swedish Museum of Natural History, Department of Zoology.
    Halanych, Kenneth
    Auburn University, Department of Biological Sciences.
    Elphick, Maurice
    School of Biological & Chemical Sciences, Queen Mary University of London.
    Mallefet, Jerome
    Laboratory of Marine Biology, Earth and Life Institute, Université Catholique de Louvain.
    Kaul-Strehlow, Sabrina
    Department of Molecular Evolution and Development, University of Vienna.
    Lowe, Christopher
    Hopkins Marine Station of Stanford University.
    Flammang, Patrick
    Biology of Marine Organisms and Biomimetics, Research Institute for Biosciences, University of Mons.
    Ullrich-Lutter, Esther
    Museum fuer Naturkunde Berlin.
    Wanniger, Andreas
    Department of Integrative Zoology, University of Vienna.
    Arnone, Maria Ina
    Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn.
    Opsin evolution in the AmbulacrariaIn: Marine Genomics, ISSN 1874-7787, E-ISSN 1876-7478Article in journal (Refereed)
    Abstract [en]

    Opsins — G-protein coupled receptors involved in photoreception — have been extensively studied in the animal kingdom. The present work provides new insights into opsin-based photoreception and photoreceptor cell evo- lution with a first analysis of opsin sequence data for a major deuterostome clade, the Ambulacraria. Systematic data analysis, including for the first time hemichordate opsin sequences and an expanded echinoderm dataset, led to a robust opsin phylogeny for this cornerstone superphylum. Multiple genomic and transcriptomic resources were surveyed to cover each class of Hemichordata and Echinodermata. In total, 119 ambulacrarian opsin sequences were found, 22 new sequences in hemichordates and 97 in echinoderms (including 67 new sequences). We framed the ambulacrarian opsin repertoire within eumetazoan diversity by including selected reference opsins from non-ambulacrarians. Our findings corroborate the presence of all major ancestral bilaterian opsin groups in Ambulacraria. Furthermore, we identified two opsin groups specific to echinoderms. In conclu- sion, a molecular phylogenetic framework for investigating light-perception and photobiological behaviors in marine deuterostomes has been obtained. 

  • 309.
    Danielsson, Sara
    et al.
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Benskin, Jonathan
    Department of Environmental Science and Analytical Chemistry, Stockholm University.
    Bignert, Anders
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Bizkarguenaga, Ekhine
    Department of Environmental Science and Analytical Chemistry, Stockholm University..
    de Wit, Cynthia
    Department of Environmental Science and Analytical Chemistry, Stockholm University..
    Egebäck, Anna-Lena
    Department of Environmental Science and Analytical Chemistry, Stockholm University..
    Eriksson, Ulla
    Department of Environmental Science and Analytical Chemistry, Stockholm University..
    Faxneld, Suzanne
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Hjelmquist, Pär
    Department of Environmental Science and Analytical Chemistry, Stockholm University..
    Johansson, Ann-Marie
    Department of Environmental Science and Analytical Chemistry, Stockholm University..
    Jones, Douglas
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Kruså, Martin
    Department of Environmental Science and Analytical Chemistry, Stockholm University..
    Kylberg, Eva
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Mechedal, Jan
    Department of Environmental Science and Analytical Chemistry, Stockholm University..
    Nyberg, Elisabeth
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Sundbom, Marcus
    Department of Environmental Science and Analytical Chemistry, Stockholm University..
    Distribution and conversions of metal- and POP concentrations among various tissues in herring2018Report (Other academic)
  • 310.
    Danielsson, Sara
    et al.
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Ek, Caroline
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Faxneld, Suzanne
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Pütz Winkens, Kerstin
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    The Swedish National Monitoring Programme for Contaminants in marine biota (until 2017 year's data) - Temporal trends and spatial variations.2019Report (Other academic)
  • 311.
    Danielsson, Sara
    et al.
    Swedish Museum of Natural History, Department of.
    Faxneld, Suzanne
    Swedish Museum of Natural History, Department of.
    Bignert, Anders
    Swedish Museum of Natural History, Department of.
    Dahlgren, Henrik
    Swedish Museum of Natural History, Department of.
    Kylberg, Eva
    Swedish Museum of Natural History, Department of.
    Jones, Douglas
    Swedish Museum of Natural History, Department of.
    Sundbom, Marcus
    Stockholms universitet.
    Carbon and nitrogen stable isotopes within the Swedish national monitoring of contaminants in marine biota2015Report (Other academic)
  • 312.
    Danielsson, Sara
    et al.
    Swedish Museum of Natural History, Department of.
    Faxneld, Suzanne
    Swedish Museum of Natural History, Department of.
    Nyberg, Elisabeth
    Swedish Museum of Natural History, Department of.
    Vasileiou, Maria
    Swedish Museum of Natural History, Department of.
    Bignert, Anders
    Swedish Museum of Natural History, Department of.
    Contaminants in fish from potentially polluted sitesalong the Swedish coast with the nationalmonitoring programme as reference2014Report (Other academic)
  • 313.
    Daume, Stefan
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. University of Göttingen; Stockholm Resilience Centre.
    Mining Twitter to monitor Invasive Alien Species – An analytical framework and sample information topologies2016In: Ecological Informatics, ISSN 1574-9541, E-ISSN 1878-0512, Vol. 31, p. 70-82Article in journal (Refereed)
    Abstract [en]

    Social online media increasingly emerge as important informal information sources that can contribute to the detection of trends and early warnings in critical fields such as public health monitoring or emergency management. In the face of global environmental challenges the utilization of this information in ecological monitoring contexts has been called for, but examples remain sparse. This can be attributed to the significant technical challenges in processing this data and concerns about the quality, reliability and applicability of information mined from social media to the ecological domain. Here the strength and weaknesses of social media mining for ecological monitoring are assessed using the micro-blogging service Twitter and invasive alien species (IAS) monitoring as an example. The assessment is based on a manual analysis of 2842 Tweets sampled from Twitter data with potential direct or descriptive references to IAS impacting forest ecosystems, which was collected over a period of nearly three years. The results are presented as information topologies for Twitter messages of observational and non-observational character for three IAS with distinctive characteristics (Oak Processionary Moth, Emerald Ash Borer, Eastern Grey Squirrel). The results show that the social media channel Twitter is a rich source of primary and secondary observational biodiversity information. It also provides useful insights in the topical landscape of public communications on IAS as well as the public perception of IAS and IAS management. The analysis suggests broad application opportunities in IAS monitoring and management, and points at applications for related environmental questions. The results highlight that social media mining for ecological monitoring needs to be approached with the same best practices as ecological monitoring in general, requiring a good understanding of the monitored subjects and specific monitoring questions. The challenges in utilizing this information for operational systems are of technical rather than conceptual nature and include extending the degree of automation, especially with regard to image recognition and the automatic provisioning of location information.

  • 314.
    Daume, Stefan
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. University Göttingen, Germany.
    Albert, Matthias
    Northwest German Forest Research Institute.
    Gadow, von, Klaus
    University Göttingen, Germany.
    Assessing citizen science opportunities in forest monitoring using probabilistic topic modelling2014In: Forest Ecosystems, ISSN 2197-5620, Vol. 1, no 11, p. 1-12Article in journal (Refereed)
    Abstract [en]

    Background

    With mounting global environmental, social and economic pressures the resilience and stability of forests and thus the provisioning of vital ecosystem services is increasingly threatened. Intensified monitoring can help to detect ecological threats and changes earlier, but monitoring resources are limited. Participatory forest monitoring with the help of “citizen scientists” can provide additional resources for forest monitoring and at the same time help to communicate with stakeholders and the general public. Examples for citizen science projects in the forestry domain can be found but a solid, applicable larger framework to utilise public participation in the area of forest monitoring seems to be lacking. We propose that a better understanding of shared and related topics in citizen science and forest monitoring might be a first step towards such a framework.

    Methods

    We conduct a systematic meta-analysis of 1015 publication abstracts addressing “forest monitoring” and “citizen science” in order to explore the combined topical landscape of these subjects. We employ ‘topic modelling’, an unsupervised probabilistic machine learning method, to identify latent shared topics in the analysed publications.

    Results

    We find that large shared topics exist, but that these are primarily topics that would be expected in scientific publications in general. Common domain-specific topics are under-represented and indicate a topical separation of the two document sets on “forest monitoring” and “citizen science” and thus the represented domains. While topic modelling as a method proves to be a scalable and useful analytical tool, we propose that our approach could deliver even more useful data if a larger document set and full-text publications would be available for analysis.

    Conclusions

    We propose that these results, together with the observation of non-shared but related topics, point at under-utilised opportunities for public participation in forest monitoring. Citizen science could be applied as a versatile tool in forest ecosystems monitoring, complementing traditional forest monitoring programmes, assisting early threat recognition and helping to connect forest management with the general public. We conclude that our presented approach should be pursued further as it may aid the understanding and setup of citizen science efforts in the forest monitoring domain.

  • 315.
    Daume, Stefan
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. University of Göttingen; Stockholm Resilience Centre.
    Galaz, Victor
    Stockholm Resilience Centre, Stockholm University.
    “Anyone Know What Species This Is?” – Twitter Conversations as Embryonic Citizen Science Communities2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3Article in journal (Refereed)
    Abstract [en]

    Social media like blogs, micro-blogs or social networks are increasingly being investigated and employed to detect and predict trends for not only social and physical phenomena, but also to capture environmental information. Here we argue that opportunistic biodiversity observations published through Twitter represent one promising and until now unexplored example of such data mining. As we elaborate, it can contribute to real-time information to traditional ecological monitoring programmes including those sourced via citizen science activities. Using Twitter data collected for a generic assessment of social media data in ecological monitoring we investigated a sample of what we denote biodiversity observations with species determination requests (N = 191). These entail images posted as messages on the micro-blog service Twitter. As we show, these frequently trigger conversations leading to taxonomic determinations of those observations. All analysed Tweets were posted with species determination requests, which generated replies for 64% of Tweets, 86% of those contained at least one suggested determination, of which 76% were assessed as correct. All posted observations included or linked to images with the overall image quality categorised as satisfactory or better for 81% of the sample and leading to taxonomic determinations at the species level in 71% of provided determinations. We claim that the original message authors and conversation participants can be viewed as implicit or embryonic citizen science communities which have to offer valuable contributions both as an opportunistic data source in ecological monitoring as well as potential active contributors to citizen science programmes.

  • 316. Davies, Thomas G.
    et al.
    Rahman, Imran A.
    Lautenschlager, Stephan
    Cunningham, John A.
    Swedish Museum of Natural History, Department of Paleobiology. University of Bristol.
    Asher, Robert J.
    Barrett, Paul M.
    Bates, Karl T.
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Benson, Roger B. J.
    Boyer, Doug M.
    Braga, José
    Bright, Jen A.
    Claessens, Leon P. A. M.
    Cox, Philip G.
    Dong, Xi-Ping
    Evans, Alistair R.
    Falkingham, Peter L.
    Friedman, Matt
    Garwood, Russell J.
    Goswami, Anjali
    Hutchinson, John R.
    Jeffery, Nathan S.
    Johanson, Zerina
    Lebrun, Renaud
    Martínez-Pérez, Carlos
    Marugán-Lobón, Jesús
    O’Higgins, Paul M.
    Metscher, Brian
    Orliac, Maeva
    Rowe, Timothy B.
    Rücklin, Martin
    Sánchez-Villagra, Marcelo R.
    Shubin, Neil H.
    Smith, Selena Y.
    Starck, J. Matthias
    Stringer, Chris
    Summers, Adam P.
    Sutton, Mark D.
    Walsh, Stig A.
    Weisbecker, Vera
    Witmer, Lawrence M.
    Wroe, Stephen
    Yin, Zongjun
    Rayfield, Emily J.
    Donoghue, Philip C.J.
    University of Bristol.
    Open data and digital morphology.2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1852, p. 1-10Article in journal (Refereed)
    Abstract [en]

    Over the past two decades, the development of methods for visualizing and analysing specimens digitally, in three and even four dimensions, has transformed the study of living and fossil organisms. However, the initial promise that the widespread application of such methods would facilitate access to the underlying digital data has not been fully achieved. The underlying datasets for many published studies are not readily or freely available, introducing a barrier to verification and reproducibility, and the reuse of data. There is no current agreement or policy on the amount and type of data that should be made available alongside studies that use, and in some cases are wholly reliant on, digital morphology. Here, we propose a set of recommendations for minimum standards and additional best practice for three-dimensional digital data publication, and review the issues around data storage, management and accessibility.

  • 317. de Faria, Aparecida Donisete
    et al.
    Pirani, Jóse Rubens
    Lahoz da Silva Ribeiro, José E.
    Nylinder, Stephan
    Terra-Araujo, Mário H.
    Vieira, Pedro P.
    Swenson, Ulf
    Swedish Museum of Natural History, Department of Botany.
    Towards a natural classification of Sapotaceae subfamily Chrysophylloideae in the Neotropics2017In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 185, p. 27-55Article in journal (Refereed)
    Abstract [en]

    Generic limits of Chrysophyllum and Pouteria (Chrysophylloideae, Sapotaceae) have been found to be untenable. We here search for natural lineages in Neotropical Chrysophylloideae by sampling 101 terminals for molecular sequences of nuclear ribosomal DNA (external and internal transcribed spacer), the nuclear gene RPB2 and 17 morphological characters. Data were analysed with Bayesian inference and parsimony jackknifing. Morphological traits were finally optimized onto the tree to identify the most coherent characters. The resulting phylogenetic tree suggests that the limits of the well-known genera Chrysophyllum and Pouteria must be amended. Diploon, Ecclinusa and Elaeoluma can be maintained and Chrysophyllum sections Ragala section Prieurella and the satellite gen- era Achrouteria, Cornuella, Martiusella and Nemaluma merit generic resurrection. Lucuma may be restored if the type species belongs to the clade. The accepted genera Chromolucuma, Pradosia and Sarcaulus gain strong clade support, but are embedded in a core clade of Pouteria and may be relegated to the subgeneric level if morphologi- cal studies cannot provide evidence concurring with narrow generic concepts. Circumscriptions of Micropholis and Chrysophyllum sections Chrysophyllum and Villocuspis remain unclear and must be explored by using an extended taxon sampling. We predict that yet-to-be-analysed species of Pouteria sections Franchetella, Gayella, Oxythece and Pouteria and members of the currently accepted genera Chromolucuma, Pradosia and Sarcaulus will fall inside the core clade of Pouteria when analysed. 

  • 318.
    de Jong, Yde
    et al.
    University of Amsterdam.
    Kouwenberg, Juiana
    Boumans, Louis
    Hussey, Charles
    Hyam, Roger
    Nicolson, Nicola
    Kirk, Paul
    Paton, Alan
    Michel, Ellinor
    Guiry, Michael D,
    Boegh, Phillip S.
    Aerenlund Pedersen, Henrik
    Enghoff, Henrik
    von Raab-Straube, Eckhard
    Güntsch, Anton
    Geoffroy, Marc
    Müller, Andreas
    Kohlbecker, Andreas
    Berendsohn, Walter
    Appeltans, Ward
    Arvantidis, Christos
    Vanhoorne, Bart
    Declerck, Joram
    Vandepitte, Leen
    Hernandez, Francisco
    Nash, Róisín
    Costello, Mark John
    Ouvrard, David
    Bezard-Falgas, Pascale
    Bourgoin, Thierry
    Wetzel, Florian Tobias
    Glöckler, Falko
    Korb, Günther
    Ring, Caroline
    Hagedorn, Gregor
    Häuser, Christoph
    Aktaç, Nihat
    Asan, Ahmet
    Ardelean, Adorian
    Vieira Borges, Paulo Alexandre
    Dhora, Dhimiter
    Khachatryan, Hasmik
    Malicky, Michael
    Ibrahimov, Shaig
    Tuzikov, Alexander
    De Wever, Aike
    Moncheva, Snejana
    Spassov, Nikolai
    Chobot, Karel
    Popov, Alexei
    Borsíc, Igor
    Sfenthourakis, Spyros
    Köljalg, Urmas
    Uotila, Pertti
    Olivier, Gargominy
    Dauvin, Jean-Claude
    Tarkhnishvili, David
    Chaladze, Giorgi
    Tuerkay, Michael
    Legakis, Anastasios
    Peregovits, LáslZó
    Gudmundsson, Gudmundur
    Ólafsson, Erling
    Lysaght, Liam
    Galil, Bella Sarah
    Raimondo, Francesco M.
    Domina, Gianniantonio
    Stoch, Fabio
    Minelli, Alessandro
    Spungis, Voldemars
    Budrys, Eduardas
    Olenin, Sergei
    Turpel, Armand
    Walisch, Tania
    Krpach, Vladimir
    Gambin, Marie Therese
    Ungureano, Laurentia
    Karaman, Gordan
    Kleukers, Roy M. J. C.
    Stur, Elisabeth
    Aagaard, Kaare
    Valland, Nils
    Loennechen Moen, Tori
    Bogdanowicz, Wieslaw
    Tykarski, Piotr
    Wieslawski, Jan Marcin
    Kedra, Monika
    de frias Martins, ntonio M.
    Domingos Abreu, António
    Silva, Ricardo
    Medvedev, Sergei
    Ryss, Alexander
    Simic, Smilijka
    Marhold, Karel
    Stloukal, Eduard
    Tome, Davorin
    Ramos, Marian A.
    Valdés, Benito
    Pina, Francisco
    Kullander, Sven
    Swedish Museum of Natural History, Department of Zoology.
    Anders, Telenius
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Gonseth, Yves
    Tschudin, Pascal
    Sergeyeva, Oleksandra
    Vladymyrov, Volodymyr
    Bogdanovych Rizun, Volodymyr
    Raper, Chris
    Lear, Dan
    Stoev, Pavel
    Penev, Lyubomir
    Casino Rubio, Ana
    Backeljau, Thierry
    Saarenmaa, Hannu
    Ullenberg, Sandrine
    PESI - a taxonomic backbone for Europe2015In: Biodiversity Data Journal, ISSN 1314-2836, E-ISSN 1314-2828, Vol. 3, p. 1-51, article id e5848Article in journal (Refereed)
    Abstract [en]

    Reliable taxonomy underpins communication in all of biology, not least nature conservation and sustainable use of ecosystem resources. The flexibility of taxonomic interpretations, however, presents a serious challenge for end-users of taxonomic concepts. Users need standardised and continuously harmonised taxonomic reference systems, as well as high-quality and complete taxonomic data sets, but these are generally lacking for non-specialists. The solution is in dynamic, expertly curated web-based taxonomic tools.

    The Pan-European Species-directories Infrastructure (PESI) worked to solve this key issue by providing a taxonomic e-infrastructure for Europe. It strengthened the relevant social (expertise) and information (standards, data and technical) capacities of five major community networks on taxonomic indexing in Europe, which is essential for proper biodiversity assessment and monitoring activities. The key objectives of PESI were: 1) standardisation in taxonomic reference systems, 2) enhancement of the quality and completeness of taxonomic data sets and 3) creation of integrated access to taxonomic information.

    This paper describes the results of PESI and its future prospects, including the involvement in major European biodiversity informatics initiatives and programs.

  • 319.
    De La Rosa, Nathaly
    et al.
    Lunds universitet.
    Kristiansson, Per
    Lunds universitet.
    Nilsson, Charlotta
    Lunds universitet.
    Ros, Linus
    Lunds universitet.
    Pallon, Jan
    Lunds universitet.
    Skogby, Henrik
    Swedish Museum of Natural History, Department of Geology.
    Quantification of lithium at ppm level in geological samples using nuclear reaction analysis2018In: Journal of Radioanalytical and Nuclear Chemistry, ISSN 0236-5731, E-ISSN 1588-2780, Vol. 317, p. 253-259Article in journal (Refereed)
  • 320.
    de Sousa, Filipe
    et al.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Bertrand, Yann J. K.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Nylinder, Nylinder
    Swedish Museum of Natural History, Department of Botany.
    Oxelman, Bengt
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Eriksson, Jonna S.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Pfeil, Bernard E.
    Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden.
    Phylogenetic Properties of 50 Nuclear Loci in Medicago (Leguminosae) Generated Using Multiplexed Sequence Capture and Next-Generation Sequencing2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 10Article in journal (Refereed)
    Abstract [en]

    Next-generation sequencing technology has increased the capacity to generate molecular data for plant biological research,including phylogenetics, and can potentially contribute to resolving complex phylogenetic problems. The evolutionaryhistory of Medicago L. (Leguminosae: Trifoliae) remains unresolved due to incongruence between published phylogenies.Identification of the processes causing this genealogical incongruence is essential for the inference of a correct speciesphylogeny of the genus and requires that more molecular data, preferably from low-copy nuclear genes, are obtainedacross different species. Here we report the development of 50 novel LCN markers in Medicago and assess the phylogeneticproperties of each marker. We used the genomic resources available for Medicago truncatula Gaertn., hybridisation-basedgene enrichment (sequence capture) techniques and Next-Generation Sequencing to generate sequences. This alternativeproves to be a cost-effective approach to amplicon sequencing in phylogenetic studies at the genus or tribe level andallows for an increase in number and size of targeted loci. Substitution rate estimates for each of the 50 loci are provided,and an overview of the variation in substitution rates among a large number of low-copy nuclear genes in plants ispresented for the first time. Aligned sequences of major species lineages of Medicago and its sister genus are made availableand can be used in further probe development for sequence-capture of the same markers.

  • 321.
    de Vries, Bernard
    et al.
    Stockholms universitet.
    Skogby, Henrik
    Swedish Museum of Natural History, Department of Geology.
    Waters, L.B.F.M.
    University of Amsterdam.
    Min, M
    University of Amsterdam.
    Laboratory mid-IR spectra of equilibrated and igneous meteorites. Searching for observables of planetesimal debris2018In: Icarus (New York, N.Y. 1962), ISSN 0019-1035, E-ISSN 1090-2643, Vol. 307, p. 400-416Article in journal (Refereed)
  • 322. Decombeix, Anne-Laure
    et al.
    Bomfleur, Benjamin
    Swedish Museum of Natural History, Department of Paleobiology.
    Taylor, Edith
    Taylor, Thomas
    New data on the anatomy and systematic affinities of corystosperm wood from the Triassic of Antarctica2014In: Review of Palaeobotany and Palynology, ISSN 0034-6667, E-ISSN 1879-0615, Vol. 203, no 1, p. 22-34Article in journal (Refereed)
    Abstract [en]

    Anatomically preserved trunks and young stems of corystosperm seed ferns are described from the Triassic of Fremouw Peak, Beardmore Glacier area, Antarctica. Based on characters of the primary and secondary vascular system, these new specimens are assigned to Kykloxylon, a genus that was established based on young stems with attached Dicroidium leaf bases. The largest specimens illustrate how some secondary growth characters, such as unequal cambial activity, appeared during later development, which enables a better comparison of Kykloxylon with trunks assigned to other corystosperm genera. Jeffersonioxylon from the Gordon Valley, Antarctica, and Cuneumxylon from South America show strong similarities with the newly described larger Kykloxylon trunks from Fremouw Peak, and might be considered congeneric. Our results provide further support for the presence of two anatomically and morphologically distinct kinds of Dicroidium-bearing trees in the Triassic vegetation of Gondwana, one with a palm-like habit and Rhexoxylon stems and the other with a more Ginkgo-like habit and Kykloxylon/Cuneumxylon-type stems

  • 323. Deegan, F.M.
    et al.
    Troll, V.R.
    Whitehouse, Martin J.
    Swedish Museum of Natural History, Department of Geology.
    Jolis, E.M.
    Freda, C.
    Boron isotope fractionation in magma via crustal carbonate dissolution.2016In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 30774Article in journal (Refereed)
    Abstract [en]

    Carbon dioxide released by arc volcanoes is widely considered to originate from the mantle and from subducted sediments. Fluids released from upper arc carbonates, however, have recently been proposed to help modulate arc CO2 fluxes. Here we use boron as a tracer, which substitutes for carbon in limestone, to further investigate crustal carbonate degassing in volcanic arcs. We performed laboratory experiments replicating limestone assimilation into magma at crustal pressure-temperature conditions and analysed boron isotope ratios in the resulting experimental glasses. Limestone dissolution and assimilation generates CaO-enriched glass near the reaction site and a CO2-dominated vapour phase. The CaO-rich glasses have extremely low δ11B values down to −41.5‰, reflecting preferential partitioning of 10B into the assimilating melt. Loss of 11B from the reaction site occurs via the CO2 vapour phase generated during carbonate dissolution, which transports 11B away from the reaction site as a boron-rich fluid phase. Our results demonstrate the efficacy of boron isotope fractionation during crustal carbonate assimilation and suggest that low δ11B melt values in arc magmas could flag shallow-level additions to the subduction cycle.

  • 324. Deegan, F.M.
    et al.
    Whitehouse, Martin J.
    Swedish Museum of Natural History, Department of Geology.
    Troll, V.R.
    Budd, D.A.
    Harris, C.
    Geiger, H.
    Hålenius, U.
    Swedish Museum of Natural History, Department of Geology.
    Pyroxene standards for SIMS oxygen isotope analysis and their application to Merapi volcano, Sunda arc, Indonesia2016In: Chemical Geology, ISSN 0009-2541, E-ISSN 1872-6836, Vol. 447, p. 1-10Article in journal (Refereed)
    Abstract [en]

    Measurement of oxygen isotope ratios in common silicate minerals such as olivine, pyroxene, feldspar, garnet, and quartz is increasingly performed by Secondary Ion Mass Spectrometry (SIMS). However, certain mineral groups exhibit solid solution series, and the large compositional spectrum of these mineral phases will result in matrix effects during SIMS analysis. These matrix effects must be corrected through repeated analysis of compositionally similar standards to ensure accurate results. In order to widen the current applicability of SIMS to solid solution mineral groups in common igneous rocks, we performed SIMS homogeneity tests on new augite (NRM-AG-1) and enstatite (NRM-EN-2) reference materials sourced from Stromboli, Italy and Webster, North Carolina, respectively. Aliquots of the standard minerals were analysed by laser fluorination (LF) to establish their δ18O values. Repeated SIMS measurements were then performed on randomly oriented fragments of the same pyroxene crystals, which yielded a range in δ18O less than ± 0.42 and ± 0.58‰ (2σ) for NRM-AG-1 and NRM-EN-2, respectively. Homogeneity tests verified that NRM-AG-1 and NRM-EN-2 do not show any crystallographic orientation bias and that they are sufficiently homogeneous on the 20 μm scale to be used as routine mineral standards for SIMS δ18O analysis. We subsequently tested our new standard materials on recently erupted pyroxene crystals from Merapi volcano, Indonesia. The δ18O values for Merapi pyroxene obtained by SIMS (n = 204) agree within error with the LF-derived δ18O values for Merapi pyroxene but differ from bulk mineral and whole-rock data obtained by conventional fluorination. The bulk samples are offset to higher δ18O values as a result of incorporation of mineral and glass inclusions that in part reflects crustal contamination processes. The Merapi pyroxene SIMS data, in turn, display a frequency peak at 5.8‰, which allows us to estimate the δ18O value of the primary mafic magma at Merapi to ~ 6.1‰ when assuming closed system differentiation.

  • 325.
    Dekov, Vesselin
    et al.
    University of Sofia.
    Boycheva, Tanya
    University of Sofia.
    Hålenius, Ulf
    Swedish Museum of Natural History, Department of Geology.
    Billström, Kjell
    Swedish Museum of Natural History, Department of Geology.
    Kamenov, George D.
    University of Florida.
    Shanks, Wayne C.
    U.S. Geological Survey, Denver.
    Stummeyer, Jens
    Bundesanstalt für Geowissenschaften, Hannover.
    Mineralogical and geochemical evidence for recent hydrothermal activity at the west wall of 12°50´N core complex (Mid-Atlantic Ridge): a new ultramafic-hosted seafloor hydrothermal deposit?2011In: Marine Geology, ISSN 0025-3227, E-ISSN 1872-6151, Vol. 288, p. 90-102Article in journal (Refereed)
  • 326.
    Dekov, Vesselin
    et al.
    University of Sofia.
    Boycheva, Tanya
    University of Sofia.
    Hålenius, Ulf
    Swedish Museum of Natural History, Department of Geology.
    Petersen, Sven
    Leibiz-Institut für Meeresforschung, IFM-GEOMAR.
    Billström, Kjell
    Swedish Museum of Natural History, Department of Geology.
    Stummeyer, Jens
    Bundesanstalt für Geowissenschaften und Rohstoffe, Hannover.
    Kamenov, George
    University of Florida.
    Shanks, Wayne
    U.S. Geological Survey, Denver.
    Atacamite and paratacamite from the ultramafic-hosted Logatchev seafloor vent field (14°45´ N, Mid-Atlantic Ridge)2011In: Chemical Geology, ISSN 0009-2541, E-ISSN 1872-6836, Vol. 286, p. 169-184Article in journal (Refereed)
  • 327.
    Dekov, Vesselin M.
    et al.
    University of Sofia.
    Hålenius, Ulf
    Swedish Museum of Natural History, Department of Geology.
    Billström, Kjell
    Swedish Museum of Natural History, Department of Geology.
    Kamenov, George D.
    University of Florida.
    Munnik, Frans
    Forschungszentrum Dresden-Rossendorf.
    Eriksson, Lars
    Stockholms universitet.
    Dyer, Alan
    University of Salford.
    Schmidt, Mark
    Leibniz-Institut für Meeresforschung, IFM-GEOMAR.
    Botz, Reiner
    Universität Kiel.
    Native Sn-Pb droplets in a zeolitic amygdale (Isle of Mull, Inner Hebrides)2009In: Geochimica et Cosmochimica Acta, ISSN 0016-7037, E-ISSN 1872-9533, Vol. 73, p. 2907-2919Article in journal (Refereed)
  • 328.
    Dekov, Vesselin M.
    et al.
    IFREMER.
    Rouxel, Olivier
    Woods Hole Oceanographic Institution.
    Asael, Dan
    IFREMER.
    Hålenius, Ulf
    Swedish Museum of Natural History, Department of Geology.
    Munnik, Frans
    Helmoholz-Zentrum Dresden-Rossendorf.
    Native Cu from the oceanic crust: Isotopic insights into native metal origin2013In: Chemical Geology, ISSN 0009-2541, E-ISSN 1872-6836, Vol. 359, p. 136-149Article in journal (Refereed)
  • 329. Dekov, Vesselin
    et al.
    Vanlierde, E.
    Billström, Kjell
    Swedish Museum of Natural History, Department of Geology.
    Garbe-Schönberg, C-D.
    Weiss, D.J.
    Gatto Rotondo, G.
    Van Mee, K.
    Kuzmann, E.
    Fortin, D.
    Darchuk, L.
    Van Grieken, R.
    Ferrihydrite precipitation in goundwater-fed river systems (Nete and Demer river basins, Belgium): Insights from a combined Fe-Zn-Sr-Nd-Pb-isotope study.2014In: Chemical Geology, ISSN 0009-2541, E-ISSN 1872-6836, Vol. 386, p. 1-15Article in journal (Refereed)
    Abstract [en]

    Two groundwater-fed river systems (Nete and Demer, Belgium) carry red suspended material that settles on the river bed forming red sediments. The local aquifer that feeds these river systems is a glauconite-rich sand, which provides most of the dissolved Fe to the rivers. The solid component of these systems, i.e., the red suspended material and sediments, has a simple mineralogy (predominantly ferrihydrite), but shows a complex geochemistry pointing out the different processes contributing to the river chemistry: (1) the red sediments have higher transition metal (excluding Cu) and detrital element (e.g., Si, Al, K, Rb, etc.) concentrations than the red suspended matter because of their longer residence time in the river and higher contribution of the background (aquifer) component, respectively; (2) the red suspended material and sediments have inherited their rare earth element (REE) patterns from the aquifer; (3) the origin of Sr present in the red suspended matter and red sediments is predominantly marine (i.e., Quaternary calcareous rocks), but a small amount is geogenic (i.e., from detrital rocks); (4) Pb in both solids originates mostly from anthropogenic and geogenic sources; (5) all of the anthropogenic Pb in the red suspended material and sediments is hosted by the ferrihydrite; (6) Nd budget of the red riverine samples is controlled by the geogenic source and shows little anthropogenic component; (7) the signi- ficant Fe- and Zn-isotope fractionations are in line with the previous studies. Their fractionation patterns do not correlate, suggesting that the processes controlling the isotope geochemistry of Fe and Zn are different: oxidation/reduction most likely governs the Fe-isotope fractionation, whereas adsorption/desorption or admixing of anthropogenic sources controls the isotope fractionation of Zn.

  • 330.
    Delling, Bo
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Palm, Stefan
    Palkopoulou, Eleftheria
    Prestegaard, Tore
    Genetic signs of multiple colonization events in Baltic ciscoes with radiation into sympatric spring- and autumnspawners confined to early postglacial arrival2014In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 4, no 22, p. 4346-4360Article in journal (Refereed)
    Abstract [en]

    Presence of sympatric populations may reflect local diversification or secondary contact of already distinct forms. The Baltic cisco (Coregonus albula) normally spawns in late autumn, but in a few lakes in Northern Europe sympatric autumn and spring- or winter-spawners have been described. So far, the evolutionary relationships and taxonomic status of these main life history forms have remained largely unclear. With microsatellites and mtDNA sequences, we analyzed extant and extinct spring- and autumn-spawners from a total of 23 Swedish localities, including sympatric populations. Published sequences from Baltic ciscoes in Germany and Finland, and Coregonus sardinella from North America were also included together with novel mtDNA sequences from Siberian C. sardinella. A clear genetic structure within Sweden was found that included two population assemblages markedly differentiated at microsatellites and apparently fixed for mtDNA haplotypes from two distinct clades. All sympatric Swedish populations belonged to the same assemblage, suggesting parallel evolution of spring-spawning rather than secondary contact. The pattern observed further suggests that postglacial immigration to Northern Europe occurred from at least two different refugia. Previous results showing that mtDNA in Baltic cisco is paraphyletic with respect to North American C. sardinella were confirmed. However, the inclusion of Siberian C. sardinella revealed a more complicated pattern, as these novel haplotypes were found within one of the two main C. albula clades and were clearly distinct from those in North American C. sardinella. The evolutionary history of Northern Hemisphere ciscoes thus seems to be more complex than previously recognized.

  • 331.
    Delmonte, B
    et al.
    University Milano-Bicocca, Milano, Italy.
    Paleari, C. I.
    University Milano-Bicocca, Milano, Italy.
    Andò, S
    University Milano-Bicocca, Milano, Italy.
    Garzantini, E
    University Milano-Bicocca, Milano, Italy.
    Andersson, Per Sune
    Swedish Museum of Natural History, Department of Geology.
    Petit, J.R.
    University of Grenobles, Grenoble, France.
    Crosta, X
    Unversity of Bordeaux, St Hilaire, France.
    Narcisi, B
    ENEA, Rome, Italy.
    Baroni, C
    University of Pisa, Pisa, Italy.
    Salvatore, M.C.
    University of Pisa, Pisa, Italy.
    Baccolo, G.
    University Milano-Bicocca, Milano, Italy.
    Maggi, Valter
    University Milano-Bicocca, Milano, Italy.
    Causes of dust size variability in central East Antarctica (Dome B):Atmospheric transport from expanded South American sources during Marine Isotope Stage 22017In: Quaternary Science Reviews, ISSN 0277-3791, E-ISSN 1873-457X, Vol. 168, p. 55-68Article in journal (Refereed)
    Abstract [en]

    We here investigate the spatial and temporal variability of eolian dust particle sorting recorded in the Dome B (77 05 S, 94 55 E) ice core, central East Antarctica, during Marine Isotope Stage (MIS) 2. We address the question whether such changes reflect variable transport pathways from a unique source area or rather a variable apportionment from diverse Southern Hemisphere sources transported at different elevation in the troposphere. The Sr-Nd radiogenic isotope composition of glacial dust samples as well as single-particle Raman mineralogy support the hypothesis of a single dust provenance both for coarse and fine mode dust events at Dome B. The southern South American provenance of glacial dust in Antarctica deduced from these results indicate a dust composition coherent with a mixture of volcanic material and minerals derived from metamorphic and plutonic rocks. Additionally, Dome B glacial samples contain aragonite particles along with diatom valves of marine benthic/epiphytic species and freshwater species living today in the northern Antarctic Peninsula and southern South America. These data suggest contribution from the exposed Patagonian continental shelf and glacial outwash plains of southern Patagonia at the time when sea level reached its minimum. Our results confirm that dust sorting is controlled by the relative intensity of the two main patterns of tropospheric dust transport onto the inner Plateau, i.e. fast low-level advection and long-range high-altitude transport including air subsidence over Antarctica.

  • 332. Deng, Jun
    et al.
    Wang, Changming
    Bagas, Leon
    Selvaraja, Vikraman
    Jeon, Heejin
    Wu, Bin
    Yang, Lifei
    Insights into ore genesis of the Jinding Zn–Pb deposit, Yunnan Province, China: Evidence from Zn and in-situ S isotopes2017In: Ore Geology Reviews, Vol. 90, p. 943-957Article in journal (Refereed)
  • 333. Deng, Kai
    et al.
    Yang, Shouye
    Lei, Bi
    Chang, Yuan-Pin
    Su, Ni
    Frings, Patrick J
    Swedish Museum of Natural History, Department of Geology.
    Xie, Xiaolei
    Small dynamic mountainous rivers in Taiwan exhibit large sedimentary geochemical and provenance heterogeneity over multi-spatial scales2019In: Earth and Planetary Science Letters, ISSN 0012-821X, E-ISSN 1385-013X, Vol. 505, p. 96-109Article in journal (Refereed)
    Abstract [en]

    Taiwan rivers are characterized by extremely rapid mass wasting and sediment transfer due to active tectonics and frequent typhoons. Various methods have been applied to constrain processes affecting their sediment source-to-sink routing. In most cases, the sediment at the outlet is considered to be a representative average of the whole upstream basin due to the short sediment routes (<200 km). However, this assumption may be inappropriate because huge compositional heterogeneity can exist even within such small dynamic river systems. To reveal their intra-station and basin-wide geochemical heterogeneity, we collected sediment samples along the Zhuoshui and Liwu Rivers in Taiwan. Multiple samples deposited in different locations or with different grain-sizes were collected at each station, and the <63 μm fractions were measured for their elemental and Sr–Nd isotopic compositions. Elemental ratios and dimension-reducing technique were firstly applied to discriminate the sediment provenances. They show that the large elemental heterogeneity exists between samples at the same station and also between stations along each river, explainable by variable sediment mixing and local lithological heterogeneity. When combining our Sr–Nd isotopic data with literature data from Taiwan rivers, five discrete clusters of river sediments can be distinguished, reflecting the inter-catchment heterogeneity of sediment provenance in Taiwan Island. We also applied a Sr–Nd isotopic mixing model coupled with Monte-Carlo simulations to quantify the provenance heterogeneity in both rivers. The sediment contribution of the Western Foothills/Tailuko Belt to the Zhuoshui/Liwu downstream can vary by a factor of ∼2 between sediment samples that were considered as spatial or temporal replicates. Combined with field in-situ observations, we propose that fast-changing sediment transport modes cause the provenance heterogeneity in small dynamic mountainous rivers attacked by frequent heavy storms or typhoons. Sediments transported during different events and with different provenances can be preserved at each station, which leads to the intra-station and basin-wide geochemical heterogeneity. This study shows that “small” dynamic mountainous rivers can exhibit “large” geochemical and provenance heterogeneity over multi-spatial scales, and thus the common assumption that “let nature do the averaging” should be treated cautiously in this kind of river. Therefore, we propose several effective sediment sampling approaches on small mountainous rivers for reference. Future studies relying on detrital sediments, e.g. applying cosmogenic nuclides or Li isotopes, should also be aware of the heterogeneous nature in small mountainous rivers, because fast-changing provenances can simultaneously bias the weathering and erosion signals and lead to unrepresentative results.

  • 334. Denk, Thomas
    Palaeoecological interpretation of the late Miocene landscapes and vegetation of northern Greece: a comment to Merceron et al., 2016 (Geobios, doi:10.1016/j.geobios.2016.01.004).2016In: Geobios, ISSN 0016-6995, E-ISSN 1777-5728, Vol. 49, p. 135-146Article in journal (Refereed)
  • 335. Denk, Thomas
    Zohner, Constantin M. (Contributor)
    Renner, Susanne S.
    Plant fossils reveal major biomes occupied by the late Miocene Old-World Pikermian fauna2018In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, p. 1864-1870Article in journal (Refereed)
  • 336. Denk, Thomas
    et al.
    Grimm, Guido W.
    Manos, Paul S.
    Deng, Min
    Hipp, Andrew S.
    An updated infrageneric classification of the oaks: review of previous taxonomic schemes and synthesis of evolutionary patterns2017In: Oaks Physiological Ecology. Exploring the Functional Diversity of Genus Quercus / [ed] Gil-Peregrin, E., Peguero-Pina, J.J., Sancho-Knapik, D., Cham, Switzerland: Springer, 2017, 1, p. 13-38Chapter in book (Refereed)
    Abstract [en]

    In this chapter, we review major classification schemes proposed for oaksby John Claudius Loudon, Anders Sandøe Ørsted, William Trelease, Otto Karl AntonSchwarz, Aimée Antoinette Camus, Yuri Leonárdovich Menitsky, and Kevin C.Nixon. Classifications of oaks (Fig. 2.1) have thus far been based entirely on morphologicalcharacters. They differed profoundly from each other because each taxonomistgave a different weight to distinguishing characters; often characters that arehomoplastic in oaks. With the advent of molecular phylogenetics our view hasconsiderably changed. One of the most profound changes has been the realisation thatthe traditional split between the East Asian subtropical to tropical subgenusCyclobalanopsis and the subgenus Quercus that includes all other oaks is artificial.The traditional concept has been replaced by that of two major clades, each comprisingthree infrageneric groups: a Palearctic-Indomalayan clade including GroupIlex (Ilex oaks), Group Cerris (Cerris oaks) and Group Cyclobalanopsis (cycle-cupoaks), and a predominantly Nearctic clade including Group Protobalanus (intermediateor golden cup oaks), Group Lobatae (red oaks) and Group Quercus (white oaks, with most species in America and some 30 species in Eurasia). In addition, recentphylogenetic studies identified two distinct clades within a wider group of white oaks: the Virentes oaks of North America and a clade with two disjunct endemic species inwestern Eurasia and western North America, Quercus pontica and Q. sadleriana. Themain morphological feature characterising these phylogenetic lineages is pollenmorphology, a character overlooked in traditional classifications. This realisation,along with the now available (molecular-)phylogenetic framework, opens new avenuesfor biogeographic, ecological and evolutionary studies and a re-appraisal of thefossil record. We provide an overview about recent advances in these fields andoutline how the results of these studies contribute to the establishment of a unifyingsystematic scheme of oaks. Ultimately, we propose an updated classification ofQuercus recognising two subgenera with eight sections. This classification considersmorphological traits, molecular-phylogenetic relationships, and the evolutionaryhistory of one of the most important temperate woody plant genera.

  • 337. Denk, Thomas
    et al.
    Güner, H. T.
    Grimm, G. W.
    From mesic to arid: Leaf epidermal features suggest preadaptation in Miocene dragon trees (Dracaena)2014In: Review of Palaeobotany and Palynology, Vol. 200, p. 211-228Article in journal (Refereed)
  • 338.
    Denk, Thomas
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Güner, Tuncay H.
    , Istanbul University, Istanbul, Turkey.
    Kvaček, Zlatko
    Charles University, Prague, Czech Republic.
    Bouchal, Johannes M.
    Swedish Museum of Natural History, Department of Paleobiology. johannes.bouchal@nrm.se.
    The early Miocene flora of Güvem (Central Anatolia, Turkey): a window into early Neogene vegetation and environments in the Eastern Mediterranean2017In: Acta Palaeobotanica, ISSN 0001-6594, E-ISSN 1427-6402, Vol. 57, no 2, p. 237-338Article in journal (Refereed)
    Abstract [en]

    The early Burdigalian (MN3) plant assemblage of the Güvem area (northwestern Central Anatolia) is preserved in lacustrine sediments of the Dereköy pyroclastics. Its age is well constrained by radiometric dates of basaltic rocks bracketing the pyroclastics, making the Güvem flora one of the extremely few precisely dated early Miocene floras in the Mediterranean region. The rich assemblage of impression fossils comprises ferns and fern allies (2 species), gymnosperms (12 spp.) and angiosperms (129 spp.). Ilex miodipyrena sp. nov. is described as a new fossil-species. The most diverse families in the assemblage are the Fagaceae with 12 taxa and the Fabaceae with 12 leaf morphotypes and one fruit taxon. Aquatic plants are represented by seven taxa, riparian (including palms) and swamp forest elements by >35 taxa, and lianas by three taxa (Smilax spp., Chaneya). The relatively large number of aquatic and riparian/swamp elements is congruent with the rich fish, amphibian and reptile record of the Güvem area. Another characteristic feature of the plant assemblage is the presence of various lobed leaves which show similarities with modern species of different families (e.g. Alangium, various Malvales). Trees and shrubs growing on well-drained soils and forming closed-canopy and open-canopy forests are the most diversified group (>70 taxa). In terms of number of specimens in the collection and based on field observations, by far the most abundant leaf fossils belong to evergreen oaks of Quercus drymeja and Q. mediterranea and to various types of foliage that cannot be assigned to a particular extant or extinct genus of Fagaceae. These sclerophyllous trees must have covered vast areas surrounding the wetlands that developed during the early Miocene in the Güvem Basin. Based on a recent reassessment of the ecology and taxonomic affinity of these trees, they are considered to reflect humid temperate climatic conditions but with a brief drier season during the winter months. These forests are more similar to the laurel forests of the southeastern United States and those stretching in a narrow belt south of the Himalayas to eastern central China. The large number of Fabaceae may indicate the presence of warm subtropical environments but this is difficult to assess, as they are known for having wide ecological ranges today and in the past. All in all, a larger part of the plant taxa point to forested vegetation. This is in agreement with previous palynological studies which detected only small amounts of herbaceous and grass pollen. Open patches of vegetation may have been restricted to river banks and to rocky areas in a volcanic landscape. The biogeographic patterns detected for the early Miocene of the Güvem assemblage are manifold; most taxa are widespread Northern Hemispheric elements. A substantial part of the species migrated from Asia into Europe during the (late) Paleogene and reached Anatolia during the early Miocene (Fagus, Paliurus, Chaneya, Ailanthus, Quercus kubinyii, Davallia haidingeri, Acer angustilobum, A. palaeosaccharinum). Fewer taxa may have been in Anatolia before they migrated to Europe (e.g. Nerium, Smilax miohavanensis, Quercus sosnowskyi). Finally, very few taxa are Anatolian endemics (e.g. Ilex miodipyrena).

  • 339. Denk, Thomas
    et al.
    Tekleva, Maria V.
    Pollen morphology and ultrastructure of Quercus with focus on Group Ilex (=Quercus Subgenus Heterobalanus (Oerst.) Menitsky): implications for oak systematics and evolution2014In: Grana, ISSN 0017-3134, E-ISSN 1651-2049, Vol. 53, p. 255-282Article in journal (Refereed)
  • 340.
    Denk, Thomas
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Velitzelos, Dimitrios
    National and Kapodistrian University of Athens, Faculty of Geology and Geoenvironment, Department of Historical Geology and Paleontology, Panepistimiopolis, Athens 15784, Greece.
    Güner, Tuncay H.
    Istanbul University, Faculty of Forestry, Department of Forest Botany, 34473 Bahceköy, Istanbul, Turkey.
    Bouchal, Johannes M.
    Swedish Museum of Natural History, Department of Paleobiology.
    Grímsson, F.
    University of Vienna, Department of Palaeontology, 1090 Vienna, Austria.
    Grimm, Guido
    Department für Paläontologie, Universität Wien, Wien, Austria.
    Taxonomy and palaeoecology of two widespread western Eurasian Neogene sclerophyllous oak species: Quercus drymeja Unger and Q. mediterranea Unger2017In: Review of Palaeobotany and Palynology, ISSN 0034-6667, E-ISSN 1879-0615, ISSN 0034-6667, Vol. 241, p. 98-128Article in journal (Refereed)
    Abstract [en]

    Sclerophyllous oaks (genus Quercus) play important roles in Neogene ecosystems of south-western Eurasia. Modern analogues (‘nearest living relatives’) for these oaks have been sought among five of six infrageneric lineages of Quercus, distributed across the entire Northern Hemisphere. A revision of leaf fossils from lower Miocene to Pliocene deposits suggests that morphotypes of the Quercus drymeja complex are very similar to a number of extant Himalayan, East Asian, and Southeast Asian species of Quercus Group Ilex and may indicate subtropical, relatively humid conditions. Quercus mediterranea comprises leaf morphotypes that are encountered in modern Mediterranean species of Quercus Group Ilex, but also in Himalayan and East Asian members of this group indicating fully humid or summer-wet conditions. The fossil taxa Quercus drymeja and Q. mediterranea should be treated as morphotype complexes, which possibly comprised different biological species at different times. Quercus mediterranea, although readily recognizable as a distinct morphotype in early to late Miocene plant assemblages, may in fact represent small leaves of the same plants that constitute the Quercus drymeja complex. Based on the available evidence, the taxa [GG1] forming the Q. drymeja complex and Q. mediterranea thrived in fully humid or summer-wet climates. The onset of the modern vegetational context of Mediterranean sclerophyllous oaks is difficult to trace, but may have been during the latest Pliocene/early Pleistocene.

  • 341.
    Denk, Thomas
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Zohner, Constantin M.
    Institute of Integrative Biology, ETH Zurich (Swiss Federal Institute of Technology), Zurich, Switzerland..
    Grimm, Guido W.
    unaffiliated.
    Renner, Susanne S.
    Plant fossils reveal major biomes occupied by the late Miocene Old-World Pikermian fauna2018In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, p. 1864-1870Article in journal (Refereed)
    Abstract [en]

    Reconstruction of palaeobiomes, ancient communities that exhibit a physiognomic and functional structure controlled by their environment, depends on proxies from different disciplines. Based on terrestrial mammal fossils, the late Miocene vegetation from China to the eastern Mediterranean and East Africa has been reconstructed as a single cohesive biome with increasingly arid conditions, with modern African savannahs the surviving remnant. Here, we test this reconstruction using plant fossils spanning 14–4 million years ago from sites in Greece, Bulgaria, Turkey, the Tian Shan Mountains and Baode County in China, and East Africa. The western Eurasian sites had a continuous forest cover of deciduous or evergreen angiosperms and gymnosperms, with 15% of 1,602 fossil occurrences representing conifers, which were present at all but one of the sites. Raup–Crick analyses reveal high floristic similarity between coeval eastern Mediterranean and Chinese sites, and low similarity between Eurasian and African sites. The disagreement between plant-based reconstructions, which imply that late Miocene western Eurasia was covered by evergreen needleleaf forests and mixed forests, and mammal-based reconstructions, which imply a savannah biome, throws into doubt the approach of inferring Miocene precipitation and open savannah habitats solely from mammalian dental traits. Organismal communities are constantly changing in their species composition, and neither animal nor plant traits by themselves are sufficient to infer entire ancient biomes. The plant fossil record, however, unambiguously rejects the existence of a cohesive savannah biome from eastern Asia to northeast Africa.

  • 342.
    Deprá, Gabriel C.
    et al.
    Universidade Estadual de Maringá.
    Kullander, Sven O.
    Swedish Museum of Natural History, Department of Zoology.
    Pavanelli, Carla S,
    Universidade Estadual de Maringá.
    da Graça, Wefterson J.
    Universidade Estadual de Maringá.
    A new colorful species of Geophagus (Teleostei: Cichlidae), endemic to the rio Aripuanã in the Amazon basin of Brazil2014In: Neotropical Ichthyology, ISSN 1679-6225, E-ISSN 1982-0224, Vol. 12, no 4, p. 737-746Article in journal (Refereed)
    Abstract [en]

    Geophagus mirabilis, new species, is endemic to the rio Aripuanã drainage upstream from Dardanelos/Andorinhas falls.The new species is distinguished from all other species of the genus by the presence of one to five large black spots arrangedlongitudinally along the middle of the flank, in addition to the black midlateral spot that is characteristic of species in thegenus and by a pattern of iridescent spots and lines on the head in living specimens. It is further distinguished from allcongeneric species, except G. camopiensis and G. crocatus, by the presence of seven (vs. eight or more) scale rows in thecircumpeduncular series below the lateral line (7 in G. crocatus; 7-9 in G. camopiensis). Including the new species, five cichlids and 11 fish species in total are known only from the upper rio Aripuanã, and 15 fish species in total are known only from the rio Aripuanã drainage

  • 343. Devaere, Lea
    et al.
    Skovsted, Christian
    Swedish Museum of Natural History, Department of Paleobiology.
    New early Cambrian sclerites of Lapworthella schodakensis from NE Greenland: advancements in knowledge of lapworthellid taxonomy, sclerite growth and scleritome organization2017In: Geological Magazine, ISSN 0016-7568, E-ISSN 1469-5081, Vol. 154, no 5, p. 1061-1072Article in journal (Refereed)
    Abstract [en]

    The Cambrian Stage 4 upper Bastion Formation of Albert Heim Bjerge and CH Ostenfeld Nunatak, NE Greenland, yielded 34 excellently preserved sclerites of Lapworthella schodackensis among other small shelly fossils. Lapworthellids have been interpreted as members of the camenellans,a basal tommotiid group. Little is known about this group although the morphological andultrastructural features of their sclerites allow a potential reconstruction of a lophophorate body plan.The exquisite material from Greenland provides significant new data for the revision of the species taxonomy, but also for the comprehension of the scleritome structure of lapworthellids and the modeof formation of their sclerites. Two morphotypes of L. schodackensis sclerites are identified: one with asimple apex, occurring in sinistral and dextral forms; and one bilaterally symmetrical sclerite with twoapices. All bear a similar ornamentation constructed of repeated growth sets consisting of a reticulate inter-rib groove with tubercles, a densely denticulate rib and a striated sub-rib area. The new data onthe ornamentation and observations of the laminar shell microstructure of L. schodackensis enable us to improve the reconstruction of growth in lapworthellids. Finally, the morphological features of the two types of sclerites provide new information for the reconstruction of the bilaterally symmetrical multi-component lapworthellid scleritome with evidence of the fusion of adjacent sclerites duringearly ontogeny.

  • 344. Dias, Arildo S.
    et al.
    Santos, Karin
    Swedish Museum of Natural History, Department of Botany.
    Maës dos Santos, Flavio Antonio
    Martins, Fernando R.
    How liana loads alter tree allometry intropical forests2016In: Plant Ecology, ISSN 1385-0237, E-ISSN 1573-5052Article in journal (Refereed)
    Abstract [en]

    Intense competition with lianas (woodclimbers) can limit tree growth, reproduction, andsurvival. However, the negative effects of liana loadson tree allometry have not yet been addressed. Weinvestigated the hypothesis that liana loading on treecrown alters tree’s allometry, expressed throughslenderness (height–diameter ratio). The relationshipbetween trunk slenderness and percentage of treecrown covered by lianas was investigated for 12 treespecies from 10 fragments of the SemideciduousSeasonal Forest in Southeastern Brazil. We also testedwhether the relationship between slenderness andwood density differ between trees without lianas andtrees heavily infested. Liana loads significantly alteredtree allometry by decreasing slenderness, even whenlianas covered less than 25% of tree crown. Heavywoodspecies decreased their trunk slenderness in agreater ratio than light-wood species. Our findingsindicate that liana infestation shifts tree allometry, andthese effects are stronger on heavy-wood tree species.

  • 345. Dickinson, Edward C
    et al.
    Ericson, Per G P
    Swedish Museum of Natural History, Research Division.
    Systematic notes on Asian birds 32: The type locality of Hirundo daurica Laxmann, 17692002In: Zoologische Verhandelingen Leiden, ISSN 0024-1652, Vol. 340, p. 205-206Article in journal (Refereed)
    Abstract [en]

    The restricted type locality suggested by Brooke (1974) for Hirundo daurica Laxmann, 1769 was apparently made without a translation of the original Swedish description. With this in hand we find it necessary to correct that restriction and move the type locality some 2500 km west.

  • 346. Dickinson, Edward C.
    et al.
    Schodde, Richard
    Australian Biological Resources Study.
    Kullander, Sven
    Swedish Museum of Natural History, Department of Zoology.
    Chrochet, Pierre André
    Centre d'Ecologie Fonctionnelle et Evolutive.
    Elliott, Andy
    Lynx Edicions.
    Kirwan, Guy M
    Field Museum of Natural History.
    Correcting the "correct" name for the Asian Brown Flycatcher (Aves: Passeriformes, Muscicapidae, Muscicapa)2014In: Zootaxa, ISSN 1175-5326, E-ISSN 1175-5334, Vol. 3869, no 3, p. 343-347Article in journal (Refereed)
    Abstract [en]

    Muscicapa dauurica Pallas, 1811 is shown to be an available name and the oldest available name for the Asian Brown Flycatcher

  • 347. Dickison, William C.
    et al.
    Lundberg, Johannes
    Swedish Museum of Natural History, Department of Botany.
    Paracryphiaceae2016In: Flowering Plants. Eudicots: Aquifoliales, Boraginales, Bruniales, Dipsacales, Escalloniales, Garryales, Paracryphiales, Solanales (except Convolvulaceae), Icacinaceae, Metteniusaceae, Vahliaceae / [ed] Kadereit, Joachim W., Bittrich, Volker, Springer, 2016, p. 281-285Chapter in book (Refereed)
    Abstract [en]

    Shrubs to medium-sized trees, some vines. Leaves alternate to almost verticillate (Paracryphia), simple, margins finely serrate or sometimes entire; stipules absent; dense pubescence on young leaves, absent on mature foliage. Flowers in axillary or terminal racemes or compound spikes, bisexual or unisexual (plants andromonoecious); perianth differentiated into 4–5 sepals and 4–5 white, free, deciduous petals (Quintinia), or with undifferentiated perianth of 4 caducous, decussate, concave, free, imbricate segments (Paracryphia); stamens 4–5 (Quintinia) or ca. 8 (Paracryphia) in a single whorl; anthers basifixed, tetrasporangiate, with longitudinal dehiscence; ovary superior (Paracryphia) or inferior (Quintinia); 8–15- (Paracryphia) or 3–5-locular (Quintinia), ovules 4 per locule (Paracryphia) or numerous; style elongated with 3–5-lobed stigma (Quintinia), or absent (Paracryphia). Fruit capsular, septicidal; seeds small, winged in Paracryphia and mostQuintina, copiously endospermic.

  • 348. Diederich, P.
    et al.
    Millanes, A.M.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Tremella umbilicariae (Tremellomycetes, Basidiomycota), a new lichenicolous species on Umbilicaria from Peru2015In: Bulletin de la Société des Naturalistes Luxembourgeois, Vol. 115, p. 167-172Article in journal (Refereed)
  • 349. Diederich, P.
    et al.
    Millanes, A.M.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Tremella umbilicariae (Tremellomycetes, Basidiomycota), a new lichenicolous species on Umbilicaria from Peru2014In: Bulletin de la Société des Naturalistes Luxembourgeois, Vol. 115, p. 167-172Article in journal (Refereed)
  • 350. Diez-del-Molino, David
    et al.
    Sanchez-Barreiro, Fatima
    Barnes, Ian
    Gilbert, M. Thomas P.
    Dalen, Love
    Quantifying Temporal Genomic Erosion in Endangered Species2018In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 33, no 3, p. 176-185Article in journal (Refereed)
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