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  • 1. Andersson, Ki
    et al.
    Norman, David
    Werdelin, Lars
    Swedish Museum of Natural History, Department of Paleobiology.
    Sabertoothed carnivores and the killing of large prey2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 10, p. e24971-Article in journal (Refereed)
    Abstract [en]

    Sabre-like canines clearly have the potential to inflict grievous wounds leading to massive blood loss and rapid death. Hypotheses concerning sabretooth killing modes include attack to soft parts such as the belly or throat, where biting deep is essential to generate strikes reaching major blood vessels. Sabretoothed carnivorans are widely interpreted as hunters of larger and more powerful prey than that of their present-day nonsabretoothed relatives. However, the precise functional advantage of the sabretooth bite, particularly in relation to prey size, is unknown. Here, we present a new point-to-point bite model and show that, for sabretooths, depth of the killing bite decreases dramatically with increasing prey size. The extended gape of sabretooths only results in considerable increase in bite depth when biting into prey with a radius of less than ~10 cm. For sabretooths, this size-reversed functional advantage suggests predation on species within a similar size range to those attacked by present-day carnivorans, rather than “megaherbivores” as previously believed. The development of the sabretooth condition appears to represent a shift in function and killing behaviour, rather than one in predator-prey relations. Furthermore, our results demonstrate how sabretoothed carnivorans are likely to have evolved along a functionally continuous trajectory: beginning as an extension of a jaw-powered killing bite, as adopted by present-day pantherine cats, followed by neck-powered biting and thereafter shifting to neck-powered shear-biting. We anticipate this new insight to be a starting point for detailed study of the evolution of pathways that encompass extreme specialisation, for example, understanding how neck-powered biting shifts into shear-biting and its significance for predator-prey interactions. We also expect that our model for point-to-point biting and bite depth estimations will yield new insights into the behaviours of a broad range of extinct predators including therocephalians (gorgonopsian + cynodont, sabretoothed mammal-like reptiles), sauropterygians (marine reptiles) and theropod dinosaurs.

  • 2.
    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.

  • 3.
    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.

  • 4. DOGUZHAEVA, Larisa
    et al.
    BENGTSON, Stefan
    REGUERO, Marcelo
    Mörs, Thomas
    Swedish Museum of Natural History, Department of Paleobiology.
    An Eocene orthocone from Antarctica shows convergent evolution of internally shelled cephalopods2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 3, article id e0172169Article in journal (Refereed)
    Abstract [en]

    Background

    The Subclass Coleoidea (Class Cephalopoda) accommodates the diverse present-day internally shelled cephalopod mollusks (Spirula, Sepia and octopuses, squids, Vampyroteuthis) and also extinct internally shelled cephalopods. Recent Spirula represents a unique coleoid retaining shell structures, a narrow marginal siphuncle and globular protoconch that signify the ancestry of the subclass Coleoidea from the Paleozoic subclass Bactritoidea. This hypothesis has been recently supported by newly recorded diverse bactritoid-like coleoids from the Carboniferous of the USA, but prior to this study no fossil cephalopod indicative of an endochochleate branch with an origin independent from subclass Bactritoidea has been reported.

    Methodology/Principal findings

    Two orthoconic conchs were recovered from the Early Eocene of Seymour Island at the tip of the Antarctic Peninsula, Antarctica. They have loosely mineralized organic-rich chitin-compatible microlaminated shell walls and broadly expanded central siphuncles. The morphological, ultrustructural and chemical data were determined and characterized through comparisons with extant and extinct taxa using Scanning Electron Microscopy/Energy Dispersive Spectrometry (SEM/EDS).

    Conclusions/Significance

    Our study presents the first evidence for an evolutionary lineage of internally shelled cephalopods with independent origin from Bactritoidea/Coleoidea, indicating convergent evolution with the subclass Coleoidea. A new subclass Paracoleoidea Doguzhaeva n. subcl. is established for accommodation of orthoconic cephalopods with the internal shell associated with a broadly expanded central siphuncle. Antarcticerida Doguzhaeva n. ord., Antarcticeratidae Doguzhaeva n. fam., Antarcticeras nordenskjoeldi Doguzhaeva n. gen., n. sp. are described within the subclass Paracoleoidea. The analysis of organic-rich shell preservation of A. nordenskjoeldi by use of SEM/EDS techniques revealed fossilization of hyposeptal cameral soft tissues. This suggests that a depositional environment favoring soft-tissue preservation was the factor enabling conservation of the weakly mineralized shell of A. nordenskjoeldi.

  • 5. Díez, Beatriz
    et al.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. BILS.
    Ininbergs, Karolina
    Dupont, Christopher L
    Allen, Andrew E
    Yooseph, Shibu
    Rusch, Douglas B
    Bergman, Birgitta
    Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 5Article in journal (Refereed)
    Abstract [en]

    Unicellular cyanobacteria are ubiquitous photoautotrophic microbes that contribute substantially to global primary production. Picocyanobacteria such as Synechococcus and Prochlorococcus depend on chlorophyll a-binding protein complexes to capture light energy. In addition, Synechococcus has accessory pigments organized into phycobilisomes, and Prochlorococcus contains chlorophyll b. Across a surface water transect spanning the sparsely studied tropical Indian Ocean, we examined Synechococcus and Prochlorococcus occurrence, taxonomy and habitat preference in an evolutionary context. Shotgun sequencing of size fractionated microbial communities from 0.1 μm to 20 μm and subsequent phylogenetic analysis indicated that cyanobacteria account for up to 15% of annotated reads, with the genera Prochlorococcus and Synechococcus comprising 90% of the cyanobacterial reads, even in the largest size fraction (3.0-20 mm). Phylogenetic analyses of cyanobacterial light-harvesting genes (chl-binding pcb/isiA, allophycocyanin (apcAB), phycocyanin (cpcAB) and phycoerythin (cpeAB)) mostly identified picocyanobacteria clades comprised of overlapping sequences obtained from Indian Ocean, Atlantic and/or Pacific Oceans samples. Habitat reconstructions coupled with phylogenetic analysis of the Indian Ocean samples suggested that large Synechococcus-like ancestors in coastal waters expanded their ecological niche towards open oligotrophic waters in the Indian Ocean through lineage diversification and associated streamlining of genomes (e.g. loss of phycobilisomes and acquisition of Chl b); resulting in contemporary small celled Prochlorococcus. Comparative metagenomic analysis with picocyanobacteria populations in other oceans suggests that this evolutionary scenario may be globally important.

  • 6. El Albani, Abderrazak
    et al.
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Canfield, Donald E.
    Riboulleau, Armelle
    Rollion Bard, Claire
    Macchiarelli, Roberto
    Ngombi Pemba, Lauriss
    Hammarlund, Emma
    Meunier, Alain
    Moubiya Mouele, Idalina
    Benzerara, Karim
    Bernard, Sylvain
    Boulvais, Philippe
    Chaussidon, Marc
    Cesari, Christian
    Fontaine, Claude
    Chi-Fru, Ernest
    Garcia Ruiz, Juan Manuel
    Gauthier-Lafaye, François
    Mazurier, Arnaud
    Pierson-Wickmann, Anne Catherine
    Rouxel, Olivier
    Trentesaux, Alain
    Vecoli, Marco
    Versteegh, Gerard J. M.
    White, Lee
    Whitehouse, Martin
    Swedish Museum of Natural History, Department of Geology.
    Bekker, Andrey
    The 2.1 Ga old Francevillian biota: biogenicity, taphonomy and biodiversity.2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 6:e99438, p. 1-18Article in journal (Refereed)
    Abstract [en]

    The Paleoproterozoic Era witnessed crucial steps in the evolution of Earth’s surface environments following the first appreciable rise of free atmospheric oxygen concentrations ~2.3 to 2.1 Ga ago, and concomitant shallow ocean oxygenation. While most sedimentary successions deposited during this time interval have experienced thermal overprinting from burial diagenesis and metamorphism, the ca. 2.1 Ga black shales of the Francevillian B Formation (FB2) cropping out in southeastern Gabon have not. The Francevillian Formation contains centimeter-sized structures interpreted as organized and spatially discrete populations of colonial organisms living in an oxygenated marine ecosystem. Here, new material from the FB2 black shales is presented and analyzed to further explore its biogenicity and taphonomy. Our extended record comprises variably sized, shaped, and structured pyritized macrofossils of lobate, elongated, and rodshaped morphologies as well as abundant non-pyritized disk-shaped macrofossils and organic-walled acritarchs. Combined microtomography, geochemistry, and sedimentary analysis suggest a biota fossilized during early diagenesis. The emergence of this biota follows a rise in atmospheric oxygen, which is consistent with the idea that surface oxygenation allowed the evolution and ecological expansion of complex megascopic life.

  • 7. Heinrichs, Jochen
    et al.
    Scheben, Armin
    Bechteler, Julia
    Lee, Gaik Ee
    Schäfer-Verwimp, Alfons
    Hedenäs, Lars
    Swedish Museum of Natural History, Department of Botany.
    Singh, Hukam
    Pócs, Tamas
    Nascimbene, Paul C.
    Peralta, Denilson F.
    Renner, Matt
    Schmidt, Alexander R.
    Crown group Lejeuneaceae and pleurocarpous mosses in Early Eocene (Ypresian) Indian amber2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 5, p. 1-15, article id e156301Article in journal (Refereed)
  • 8.
    Ivarsson, Magnus
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Bengtson, Stefan
    Skogby, Henrik
    Lazor, Peter
    Broman, Curt
    Belivanova, Veneta
    Marone, Federica
    A fungal-prokaryotic consortium at the basalt-zeolite interface in subseafloor igneous crust2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203Article in journal (Refereed)
  • 9. Ivarsson, Magnus
    et al.
    Broman, Curt
    Håkan, Gustafsson
    Holm, Nils
    Biogenic Mn-oxides in subseafloor basalts2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203Article in journal (Refereed)
  • 10.
    Ivarsson, Magnus
    et al.
    Swedish Museum of Natural History, Department of Paleobiology. University of Southern Denmark, Department of Biology and Nordic Center for Earth Evolution, Campusvej 55, Odense M, DK-5230, Denmark.
    Skogby, Henrik
    Swedish Museum of Natural History, Department of Geology.
    Phichaikamjornwut, Bongkot
    Gems and Jewelry Program, Faculty of Science, Srinakharinwirot University, Bangkok, Thailand .
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Siljeström, Sandra
    RISE Research Institutes of Sweden, Bioscience and Materials/Chemistry and Materials, Stockholm, Sweden.
    Ounchanum, Prayote
    Department of Geological Sciences, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.
    Boonsong, Apichet
    Department of Geological Sciences, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.
    Kruachanta, M
    Department of Geological Sciences, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand .
    Marone, Federica
    Swiss Light Source, Paul Scherrer Institute, Villigen, Switzerland.
    Belivanova, Veneta
    Swedish Museum of Natural History, Department of Paleobiology.
    Sara, Holmström
    Stockholm University, Department of Geological Sciences, Stockholm, Sweden.
    Intricate tunnels in garnets from soils and rivere sediments in Thailand - possible endolithic microborings2018In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 13, no 8, article id e0200351Article in journal (Refereed)
    Abstract [en]

    Garnets from disparate geographical environments and origins such as oxidized soils and river sediments in Thailand host intricate systems of microsized tunnels that significantly decrease the quality and value of the garnets as gems. The origin of such tunneling has previously been attributed to abiotic processes. Here we present physical and chemical remains of endolithic microorganisms within the tunnels and discuss a probable biological origin of the tunnels. Extensive investigations with synchrotron-radiation X-ray tomographic microscopy (SRXTM) reveal morphological indications of biogenicity that further support a euendolithic interpretation. We suggest that the production of the tunnels was initiated by a combination of abiotic and biological processes, and that at later stages biological processes came to dominate. In environments such as river sediments and oxidized soils garnets are among the few remaining sources of bio-available Fe2+, thus it is likely that microbially mediated boring of the garnets has trophic reasons. Whatever the reason for garnet boring, the tunnel system represents a new endolithic habitat in a hard silicate mineral otherwise known to be resistant to abrasion and chemical attack.

  • 11.
    Johansson, Ulf S.
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Pasquet, Eric
    Irestedt, Martin
    The New Zealand: Thrush: An extinct Oriole2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 9, article id e24317Article in journal (Refereed)
  • 12.
    Jondelius, Ulf
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Meyer-Wachsmuth, Inga
    Swedish Museum of Natural History, Department of Zoology.
    Hyper-cryptic marine meiofauna: species complexes in Nemertodermatida2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 9, article id e107688Article in journal (Refereed)
  • 13.
    Kiel, Steffen
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Hansen, Bent
    Cenozoic methane-seep faunas of the Caribbean region2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 10, article id e0140788Article in journal (Refereed)
    Abstract [en]

    We report new examples of Cenozoic cold-seep communities from Colombia, Cuba, the Dominican Republic, Trinidad, and Venezuela, and attempt to improve the stratigraphic dating of Cenozoic Caribbean seep communities using strontium isotope stratigraphy. Two seep faunas are distinguished in Barbados: the late Eocene mudstone-hosted ‘Joes River fauna’ consists mainly of large lucinid bivalves and tall abyssochrysoid gastropods, and the early Miocene carbonate-hosted ‘Bath Cliffs fauna’ containing the vesicomyid Pleurophopsis, the mytilid Bathymodiolus and small gastropods. Two new Oligocene seep communities from the Sinú River basin in Colombia consist of lucinid bivalves including Elongatolucina, thyasirid and solemyid bivalves, and Pleurophopsis. A new early Miocene seep community from Cuba includes Pleurophopsis and the large lucinid Meganodontia. Strontium isotope stratigraphy suggests an Eocene age for the Cuban Elmira asphalt mine seep community, making it the oldest in the Caribbean region. A new basal Pliocene seep fauna from the Dominican Republic is characterized by the large lucinid Anodontia (Pegophysema). In Trinidad we distinguish two types of seep faunas: the mudstone-hosted Godineau River fauna consisting mainly of lucinid bivalves, and the limestone-hosted Freeman’s Bay fauna consisting chiefly of Pleurophopsis, Bathymodiolus, and small gastropods; they are all dated as late Miocene. Four new seep communities of Oligocene to Miocene age are reported from Venezuela. They consist mainly of large globular lucinid bivalves including Meganodontia, and moderately sized vesicomyid bivalves. After the late Miocene many large and typical ‘Cenozoic’ lucinid genera disappeared from the Caribbean seeps and are today known only from the central Indo-Pacific Ocean. We speculate that the increasingly oligotrophic conditions in the Caribbean Sea after the closure of the Isthmus of Panama in the Pliocene may have been unfavorable for such large lucinids because they are only facultative chemosymbiotic and need to derive a significant proportion of their nutrition from suspended organic matter.

  • 14. Kuhn, Brian F.
    et al.
    Werdelin, Lars
    Swedish Museum of Natural History, Department of Paleobiology.
    Hartstone-Rose, Adam
    Lacruz, Rodrigo S.
    Berger, Lee R.
    Carnivoran remains from the Malapa hominin site, South Africa2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 11, p. e26940-Article in journal (Refereed)
    Abstract [en]

    Recent discoveries at the new hominin-bearing deposits of Malapa, South Africa, have yielded a rich faunal assemblage associated with the newly described hominin taxon Australopithecus sediba. Dating of this deposit using U-Pb and palaeomagnetic methods has provided an age of 1.977 Ma, being one of the most accurately dated, time constrained deposits in the Plio-Pleistocene of southern Africa. To date, 81 carnivoran specimens have been identified at this site including members of the families Canidae, Viverridae, Herpestidae, Hyaenidae and Felidae. Of note is the presence of the extinct taxon Dinofelis cf. D. barlowi that may represent the last appearance date for this species. Extant large carnivores are represented by specimens of leopard (Panthera pardus) and brown hyaena (Parahyaena brunnea). Smaller carnivores are also represented, and include the genera Atilax and Genetta, as well as Vulpes cf. V. chama. Malapa may also represent the first appearance date for Felis nigripes (Black-footed cat). The geochronological age of Malapa and the associated hominin taxa and carnivoran remains provide a window of research into mammalian evolution during a relatively unknown period in South Africa and elsewhere. In particular, the fauna represented at Malapa has the potential to elucidate aspects of the evolution of Dinofelis and may help resolve competing hypotheses about faunal exchange between East and Southern Africa during the late Pliocene or early Pleistocene.

  • 15.
    Kullander, Sven
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Rahman, MD. Mizanur
    University of Dhaka.
    Norén, Michael
    Swedish Museum of Natural History, Department of Zoology.
    Mollah, Abdur Rob
    University of Dhaka.
    Devario in Bangladesh: species diversity, sibling species, and introgression in danionin cyprinids (Teleostei: Cyprinidae: Danioninae2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, p. 1-37, article id 12(11): e0186895Article in journal (Refereed)
    Abstract [en]

    Four species of Devario are recorded from Bangladesh: D. aequipinnatus, D. anomalus, D. coxi, new species, and D. devario. Devario aequipinnatus has a wide distribution in northern India and Bangladesh. Devario coxi, from southeastern Bangladesh near Cox’s Bazar, differs from D. aequipinnatus in mtDNA (COI, p-distance 1.8%), colouration, proportional measurements, and meristics. The minor morphological differences and low frequency of overlapping meristics suggest relatively recent separation of D. coxi from other D. aequipinnatus. Devario anomalus occurs only in southeastern Bangladesh and is here reported from localities in addition to the type locality. It differs from the similar D. xyrops in adjacent Myanmar by slender body shape and by 2.3% p-distance in the COI gene. Specimens of D. anomalus from the Sangu River were found to have the mitochondrial genome of D. aequipinnatus from Bangladesh, but agree with other D. anomalus in the nuclear RAG1 gene. Devario devario has a wide distribution on the Indian Peninsula and border regions; in Bangladesh it is restricted in distribution to the Ganga, Brahmaputra, and Meghna drainages. Reports of D. assamensis and D. malabaricus from Bangladesh are misidentifications. Perilampus ostreographus M’Clelland, 1839, is tentatively synonymized with D. aequipinnatus. Phylogenetic analysis of 14 species of striped devarios based on the COI gene results in a polytomy with four unresolved clades. Devario deruptotalea from the Chindwin basin is the sister group of D. aequipinnatus+D. coxi. Devario devario is the sistergroup of D. xyrops+D. anomalus.

  • 16.
    Lah, Ljerka
    et al.
    University of Potsdam, Germany.
    Trense, Daronja
    University of Potsdam, Germany.
    Benke, Harald
    Deutches Meeremuseum, Stralsund, Germany.
    Berggren, Per
    Dove Marine Laboratory, School of Marine Science and Technology, Newcastle University, UK.
    Gunnlaugsson, Þorvaldur
    Marine Research Institute, Reykjavik, Iceland.
    Christina, Lockyer
    North Atlantic Marine Mammal Commission, Tromsö, Norway.
    Özturk, Ayaka
    Marine Biology Department, Istanbul University, Turkey.
    Pawliczka, Iwona
    Hel Marine Station, University of Gdansk, Poland.
    Roos, Anna
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Siebert, Ursula
    ITAW, Univ of Veterinary Medicine, Hannover Foundation, Busum, Germany.
    Skora, Krzysztof
    Hel Marine Station, Univ of Gansk, Poland.
    Vikingsson, Gisli
    Marine Research Institute, Reykjavik, Iceland.
    Ralph, Tiedemann
    Unit of Evolutionary Biology/Zooology, University of Potsdam, Germany.
    Spatially Explicit Analysis of Genome-Wide SNPs Detects Subtle Population Structure in a Mobile Marine Mammal, the Harbor Porpoise2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Plos, Vol. 11, no 10, p. e0162792-Article in journal (Refereed)
    Abstract [en]

    The population structure of the highly mobile marine mammal, the harbor porpoise (Phocoena phocoena), in the Atlantic shelf waters follows a pattern of significant isolation-bydistance. The population structure of harbor porpoises from the Baltic Sea, which is connected with the North Sea through a series of basins separated by shallow underwater ridges, however, is more complex. Here, we investigated the population differentiation of harbor porpoises in European Seas with a special focus on the Baltic Sea and adjacent waters, using a population genomics approach. We used 2872 single nucleotide polymorphisms (SNPs), derived from double digest restriction-site associated DNA sequencing (ddRAD-seq), as well as 13 microsatellite loci and mitochondrial haplotypes for the same set of individuals. Spatial principal components analysis (sPCA), and Bayesian clustering on a subset of SNPs suggest three main groupings at the level of all studied regions: the Black Sea, the North Atlantic, and the Baltic Sea. Furthermore, we observed a distinct separation of the North Sea harbor porpoises from the Baltic Sea populations, and identified splits between porpoise populations within the Baltic Sea. We observed a notable distinction between the Belt Sea and the Inner Baltic Sea sub-regions. Improved delineation of harbor porpoise population assignments for the Baltic based on genomic evidence is important for conservation management of this endangered cetacean in threatened habitats, particularly in the Baltic Sea proper. In addition, we show that SNPs outperform microsatellite markers and demonstrate the utility of RAD-tags from a relatively small, opportunistically sampled cetacean sample set for population diversity and divergence analysis.

  • 17. Lind, Tomas
    et al.
    Ekebom, Agneta
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Alm Kübler, Kerstin
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Östensson, Pia
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Bellander, Tom
    Lõhmus, Mare
    Pollen Season Trends (1973-2013) in Stockholm Area, Sweden2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 11, p. 1-12Article in journal (Refereed)
  • 18.
    Mikkelsen, Lonnie
    et al.
    Aarhus University, Denmark.
    Rigét, Frank F
    Kyhn, Line A
    Sveegaard, Signe
    Dietz, Rune
    Tougaard, Jakob
    Carlström, Julia A K
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Carlén, Ida
    Koblitz, Jens C
    Teilmann, Jonas
    Comparing Distribution of Harbour Porpoises (Phocoena phocoena) Derived from Satellite Telemetry and Passive Acoustic Monitoring.2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 7Article in journal (Refereed)
    Abstract [en]

    Cetacean monitoring is essential in determining the status of a population. Different monitoring methods should reflect the real trends in abundance and patterns in distribution, and results should therefore ideally be independent of the selected method. Here, we compare two independent methods of describing harbour porpoise (Phocoena phocoena) relative distribution pattern in the western Baltic Sea. Satellite locations from 13 tagged harbour porpoises were used to build a Maximum Entropy (MaxEnt) model of suitable habitats. The data set was subsampled to one location every second day, which were sufficient to make reliable models over the summer (Jun-Aug) and autumn (Sep-Nov) seasons. The modelled results were compared to harbour porpoise acoustic activity obtained from 36 static acoustic monitoring stations (C-PODs) covering the same area. The C-POD data was expressed as the percentage of porpoise positive days/hours (the number of days/hours per day with porpoise detections) by season. The MaxEnt model and C-POD data showed a significant linear relationship with a strong decline in porpoise occurrence from west to east. This study shows that two very different methods provide comparable information on relative distribution patterns of harbour porpoises even in a low density area.

  • 19.
    Neimanis, Aleksija
    et al.
    Department of Pathology and Wildlife Diseases, National Veterinary Institute, Uppsala, Sweden.
    Moraeus, Charlotta
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Bergman, Anders
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Bignert, Anders
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Höglund, Johan
    Department of Biomedical Science and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, Uppsala, Sweden .
    Lundström, Karl
    Department of Aquatic Resources, Swedish University of Agricultural Sciences, Lysekil, Sweden.
    Strömberg, Annika
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Bäcklin, Britt-Marie
    Swedish Museum of Natural History, Department of Environmental research and monitoring.
    Emergence of the Zoonotic Biliary Trematode Pseudamphistomum truncatum in Grey Seals (Halichoerus grypus) in the Baltic Sea2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 10, p. e0164782-Article in journal (Refereed)
    Abstract [en]

    The biliary trematode Pseudamphistomum truncatum parasitizes a wide range of fish-eating mammals, including humans. Here we report the emergence of this parasite in grey seals (Halichoerus grypus) in the Baltic Sea. One hundred eighty-three of 1 554 grey seals (11.9%) examined from 2002–2013 had detectable hepatobiliary trematode infection. Parasite identification was confirmed as P. truncatum by sequencing the ITS2 region of a pool of five to 10 trematodes from each of ten seals collected off the coast of seven different Swedish counties. The proportion of seals parasitized by P. truncatum increased significantly over time and with increasing age of seals. Males were 3.1 times more likely to be parasitized than females and animals killed in fishery interactions were less likely to be parasitized than animals found dead or hunted. There was no significant difference in parasitism of seals examined from the Gulf of Bothnia versus those examined from the Baltic Proper. Although the majority of infections were mild, P. truncatum can cause severe hepatobiliary disease and resulted in liver failure in at least one seal. Because cyprinid fish are the second intermediate host for opisthorchiid trematodes, diets of grey seals from the Baltic Sea were analysed regarding presence of cyprinids. The proportion of gastrointestinal tracts containing cyprinid remains was ten times higher in seals examined from 2008 to 2013 (12.2%) than those examined from 2002 to 2007 (1.2%) and coincided with a general increase of trematode parasitism in the host population. The emergence and relatively common occurrence of P. truncatum in grey seals signals the presence of this parasite in the Baltic Sea ecosystem and demonstrates how aquatic mammals can serve as excellent sentinels of marine ecosystem change. Investigation of drivers behind P. truncatum emergence and infection risk for other mammals, including humans, is highly warranted.

  • 20. Niemi, Marianna
    et al.
    Bläuer, Auli
    Iso-Touru, Terhi
    Harjula, Janne
    Nyström Edmark, Veronica
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Rannamäe, Eve
    Lõugas, Lembi
    Sajantila, Antti
    Lidén, Kerstin
    Taavitsainen, Jussi-Pekka
    Temporal Fluctuation in North East Baltic Sea Region Cattle Population Revealed by Mitochondrial and Y-Chromosomal DNA Analyses2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 5, article id e0123821Article in journal (Refereed)
  • 21.
    Prieto, Maria
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Dating the diversification of the major lineages of Ascomycota (Fungi)2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 6Article in journal (Refereed)
  • 22.
    Ronquist, Fredrik
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Nieves-Aldrey, José-Luis
    Buffington, Matthew L
    Liu, Zhiwei
    Liljeblad, Johan
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. BILS.
    Phylogeny, evolution and classification of gall wasps: the plot thickens.2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 5Article in journal (Refereed)
    Abstract [en]

    Gall wasps (Cynipidae) represent the most spectacular radiation of gall-inducing insects. In addition to true gall formers, gall wasps also include phytophagous inquilines, which live inside the galls induced by gall wasps or other insects. Here we present the first comprehensive molecular and total-evidence analyses of higher-level gall wasp relationships. We studied more than 100 taxa representing a rich selection of outgroups and the majority of described cynipid genera outside the diverse oak gall wasps (Cynipini), which were more sparsely sampled. About 5 kb of nucleotide data from one mitochondrial (COI) and four nuclear (28S, LWRh, EF1alpha F1, and EF1alpha F2) markers were analyzed separately and in combination with morphological and life-history data. According to previous morphology-based studies, gall wasps evolved in the Northern Hemisphere and were initially herb gallers. Inquilines originated once from gall inducers that lost the ability to initiate galls. Our results, albeit not conclusive, suggest a different scenario. The first gall wasps were more likely associated with woody host plants, and there must have been multiple origins of gall inducers, inquilines or both. One possibility is that gall inducers arose independently from inquilines in several lineages. Except for these surprising results, our analyses are largely consistent with previous studies. They confirm that gall wasps are conservative in their host-plant preferences, and that herb-galling lineages have radiated repeatedly onto the same set of unrelated host plants. We propose a revised classification of the family into twelve tribes, which are strongly supported as monophyletic across independent datasets. Four are new: Aulacideini, Phanacidini, Diastrophini and Ceroptresini. We present a key to the tribes and discuss their morphological and biological diversity. Until the relationships among the tribes are resolved, the origin and early evolution of gall wasps will remain elusive.

  • 23.
    Roos, Anna
    et al.
    Swedish Museum of Natural History, Department of.
    Ågren, Erik
    Statens Veterinärmedicinska Anstalt.
    High Prevalence of Proposed Müllerian Duct RemnantCysts on the Spermatic Duct in Wild Eurasian Otters (Lutra lutra) from Sweden2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 12, p. 1-5Article in journal (Refereed)
    Abstract [en]

    The spermatic ducts (vasa deferentia) of 235 otters (Lutra lutra) found dead between 1999 and 2012 in Sweden were examined for presence of paraductular cysts. Single or multiple elongated uni- or bilateral cysts parallel to the spermatic duct were noted in 72% of the examined males. The cysts were adjacent to, but did not communicate with the lumen of the spermatic duct, and were usually located within a few centimeters of the testis and epididymis. The cysts are proposed to be congenital Müllerian duct remnants. Other morphologic abnormalities in the reproductive organs were not noted within this study. Possible causes of the incomplete regression of the embryonic female gonadal duct are exposure to environmental contaminants such as elevated concentrations of estrogen-like compounds (endocrine disrupting chemicals), inbreeding, or a naturally occurring anatomic defect. No obvious geographical pattern was observed for otters with or without cysts. This is the first study and description of cysts on the spermatic duct in otters.

  • 24.
    Räikkönen, Jannikke
    et al.
    Swedish Museum of Natural History, Department of. Swedish Museum of Natural History, Department of Contaminant Research, Stockholm, Sweden.
    Vucetich, John A.
    School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA.
    Vucetich, Leah M.
    School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA.
    Peterson, Rolf O.
    School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA.
    Nelson, Michael P.
    Department of Forest Ecosystems and Society, Oregon State University, Corvallis, Oregon, USA.
    What the Inbred Scandinavian Wolf Population Tells Us about the Nature of Conservation2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 6Article in journal (Refereed)
  • 25.
    Réblová, Martina
    et al.
    Department of Taxonomy, Institute of Botany of the Czech Academy of Sciences, 252 43, Pruhonice, Czech Republic.
    Hubka, Vit
    Department of Botany, Faculty of Science, Charles University in Prague, Benatska 2, 128 01 Prague 2, Czech Republic.
    Thureborn, Olle
    Institutionen för ekologi miljö och botanik, Stockholms Universitet.
    Lundberg, Johannes
    Swedish Museum of Natural History, Department of Botany.
    Sallstedt, Therese
    Swedish Museum of Natural History, Department of Paleobiology. Nordic Center for Earth Evolution (NordCEE).
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Department of Paleobiology. Nordic Center for Earth Evolution (NordCEE).
    From the tunnels into the treetops: new lineages of black yeasts from biofilm in the Stockholm metro system and their relatives among ant-associated fungi in the Chaetothyriales2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 10, p. e0163396-, article id e0163396Article in journal (Refereed)
    Abstract [en]

    Rock-inhabiting fungi harbour species-rich, poorly differentiated, extremophilic taxa of polyphyletic origin. Their closest relatives are often well-known species from various biotopes with significant pathogenic potential. Speleothems represent a unique rock-dwelling habitat, whose mycobiota are largely unexplored. Isolation of fungi from speleothem biofilm covering bare granite walls in the Kungsträdgården metro station in Stockholm yielded axenic cultures of two distinct black yeast morphotypes. Phylogenetic analyses of DNA sequences from six nuclear loci, ITS, nuc18S and nuc28S rDNA, rpb1, rpb2 and β-tubulin, support their placement in the Chaetothyriales (Ascomycota). They are described as a new genus Bacillicladium with the type species Blobatum, and a new species Bradymyces graniticolaBacillicladium is distantly related to the known five chaetothyrialean families and is unique in the Chaetothyriales by variable morphology showing hyphal, meristematic and yeast-like growth in vitro. The nearest relatives of Bacillicladium are recruited among fungi isolated from cardboard-like construction material produced by arboricolous non-attine ants. Their sister relationship is weakly supported by the Maximum likelihood analysis, but strongly supported by Bayesian inference. The genus Bradymyces is placed amidst members of the Trichomeriaceae and is ecologically undefined; it includes an opportunistic animal pathogen while two other species inhabit rock surfaces. ITS rDNA sequences of three species accepted in Bradymyces and other undescribed species and environmental samples were subjected to phylogenetic analysis and in-depth comparative analysis of ITS1 and ITS2 secondary structures in order to study their intraspecific variability. Compensatory base change criterion in the ITS2 secondary structure supported delimitation of species in Bradymyces, which manifest a limited number of phenotypic features useful for species recognition. The role of fungi in the speleothem biofilm and relationships of Bacillicladium and Bradymyces with other members of the Chaetothyriales are discussed.

  • 26.
    Sandoval-Castellanos, Edson
    et al.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Palkopoulou, Eleftheria
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Dalen, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Back to BaySICS: A User-Friendly Program for Bayesian Statistical Inference from Coalescent Simulations2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 5Article in journal (Refereed)
    Abstract [en]

    Inference of population demographic history has vastly improved in recent years due to a number of technological and theoretical advances including the use of ancient DNA. Approximate Bayesian computation (ABC) stands among the most promising methods due to its simple theoretical fundament and exceptional flexibility. However, limited availability of user-friendly programs that perform ABC analysis renders it difficult to implement, and hence programming skills are frequently required. In addition, there is limited availability of programs able to deal with heterochronous data. Here we present the software BaySICS: Bayesian Statistical Inference of Coalescent Simulations. BaySICS provides an integrated and user-friendly platform that performs ABC analyses by means of coalescent simulations from DNA sequence data. It estimates historical demographic population parameters and performs hypothesis testing by means of Bayes factors obtained from model comparisons. Although providing specific features that improve inference from datasets with heterochronous data, BaySICS also has several capabilities making it a suitable tool for analysing contemporary genetic datasets. Those capabilities include joint analysis of independent tables, a graphical interface and the implementation of Markov-chain Monte Carlo without likelihoods.

  • 27.
    Stöhr, Sabine
    et al.
    Swedish Museum of Natural History, Department of Zoology.
    Martynov, Alexander V.
    Paedomorphosis as an evolutionary driving force: insights from deep-sea brittle stars2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, p. 1-24, article id e0164562Article in journal (Refereed)
  • 28.
    Tassia, Michael
    et al.
    Auburn University.
    Cannon, Johanna
    Swedish Museum of Natural History, Department of Zoology. Auburn University.
    Konikoff, Charlotte
    University of Washington.
    Shenkar, Noa
    University of Washington.
    Halanych, Kenneth
    Auburn University.
    Swalla, Billie
    The Global Diversity of Hemichordata2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 10, article id e0162564Article in journal (Refereed)
    Abstract [en]

    Phylum Hemichordata, composed of worm-like Enteropneusta and colonial Pterobranchia, has been reported to only contain about 100 species. However, recent studies of hemichordate phylogeny and taxonomy suggest the species number has been largely underestimated. One issue is that species must be described by experts, and historically few taxonomists have studied this group of marine invertebrates. Despite this previous lack of coverage, interest in hemichordates has piqued in the past couple of decades, as they are critical to understanding the evolution of chordates–as acorn worms likely resemble the deuterostome ancestor more closely than any other extant animal. This review provides an overview of our current knowledge of hemichordates, focusing specifically on their global biodiversity, geographic distribution, and taxonomy. Using information available in the World Register of Marine Species and published literature, we assembled a list of 130 described, extant species. The majority (83%) of these species are enteropneusts, and more taxonomic descriptions are forthcoming. Ptychoderidae contained the greatest number of species (41 species), closely followed by Harrimaniidae (40 species), of the recognized hemichordate families. Hemichordates are found throughout the world’s oceans, with the highest reported numbers by regions with marine labs and diligent taxonomic efforts (e.g. North Pacific and North Atlantic). Pterobranchs are abundant in Antarctica, but have also been found at lower latitudes. We consider this a baseline report and expect new species of Hemichordata will continue to be discovered and described as new marine habitats are characterized and explored.

  • 29. Thuy, Ben
    et al.
    Stöhr, Sabine
    Swedish Museum of Natural History, Department of Zoology.
    A New Morphological Phylogeny of the Ophiuroidea (Echinodermata) Accords with Molecular Evidence and Renders Microfossils Accessible for Cladistics2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 5, p. e0156140-Article in journal (Refereed)
  • 30.
    Todaro, M. Antonio
    et al.
    Department of Biology, University of Modena and Reggio Emilia, Modena, Italy.
    Dal Zotto, Matteo
    Department of Biology, University of Modena and Reggio Emilia, Modena, Italy.
    Jondelius, Ulf
    Swedish Museum of Natural History, Department of Zoology.
    Hochberg, Rick
    Department of Biology, University of Massachusetts Lowell, Lowell, MA 01854, USA.
    Hummon, William D.
    Department of Biological Sciences,Ohio University, Athens, Ohio, United States of America.
    Kånneby, Tobias
    Swedish Museum of Natural History, Department of Zoology.
    Rocha, Carlos E. F.
    Departamento de Zoologia, Instituto de Biocieˆncias, Universidade de Sa˜o Paulo, Sa˜o Paulo, Brazil.
    Gastrotricha: A Marine Sister for a Freshwater Puzzle2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 2, p. e31740-Article in journal (Refereed)
    Abstract [en]

    Within an evolutionary framework of Gastrotricha Marinellina flagellata and Redudasys fornerise bear special interest, as they are the only Macrodasyida that inhabit freshwater ecosystems. Notwithstanding, these rare animals are poorly known; found only once (Austria and Brazil), they are currently systematised as incertae sedis. Here we report on the rediscovery of Redudasys fornerise, provide an account on morphological novelties and present a hypothesis on its phylogenetic relationship based on molecular data. Specimens were surveyed using DIC microscopy and SEM, and used to obtain the 18 S rRNA gene sequence; molecular data was analyzed cladistically in conjunction with data from 42 additional species belonging to the near complete Macrodasyida taxonomic spectrum. Morphological analysis, while providing new information on taxonomically relevant traits (adhesive tubes, protonephridia and sensorial bristles), failed to detect elements of the male system, thus stressing the parthenogenetic nature of the Brazilian species. Phylogenetic analysis, carried out with ML, MP and Bayesian approaches, yielded topologies with strong nodal support and highly congruent with each other. Among the supported groups is the previously undocumented clade showing the alliance between Redudasys fornerise and Dactylopodola agadasys; other strongly sustained clades include the densely sampled families Thaumastodermatidae and Turbanellidae and most genera. A reconsideration of the morphological traits of Dactylopodola agadasys in light of the new information on Redudasys fornerise makes the alliance between these two taxa very likely. As a result, we create Anandrodasys gen. nov. to contain members of the previously described D. agadasys and erect Redudasyidae fam. nov. to reflect this novel relationship between Anandrodasys and Redudasys. From an ecological perspective, the derived position of Redudasys, which is deeply nested within the Macrodasyida clade, unequivocally demonstrates that invasion of freshwater by gastrotrichs has taken place at least twice, in contrast with the single event hypothesis recently put forward.

  • 31.
    Todaro, M. Antonio
    et al.
    Department of Biology, University of Modena and Reggio Emilia, Modena, Italy.
    Kånneby, Tobias
    Swedish Museum of Natural History, Department of Zoology.
    Dal Zotto, Matteo
    Department of Biology, University of Modena and Reggio Emilia, Modena, Italy.
    Jondelius, Ulf
    Swedish Museum of Natural History, Department of Zoology.
    Phylogeny of Thaumastodermatidae (Gastrotricha: Macrodasyida) Inferred from Nuclear and Mitochondrial Sequence Data2011In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 3, p. e17892-Article in journal (Refereed)
    Abstract [en]

    Background: Phylogenetic relationships within Gastrotricha are poorly known. Attempts to shed light on this subject using morphological traits have led to hypotheses lacking satisfactory statistical support; it seemed therefore that a different approach was needed.

    Methodology/Principal Findings: In this paper we attempt to elucidate the relationships within the taxonomically vast family Thaumastodermatidae (Macrodasyida) using molecular sequence data. The study includes representatives of all the extant genera of the family and for the first time uses a multi-gene approach to infer evolutionary liaisons within Gastrotricha. The final data set comprises sequences of three genes (18S, 28S rDNA and COI mtDNA) from 41 species, including 29 thaumastodermatids, 11 non-thaumastodermatid macrodasyidans and a single chaetonotidan. Molecular data was analyzed as a combined set of 3 genes and as individual genes, using Bayesian and maximum likelihood approaches. Two different outgroups were used: Xenotrichula intermedia (Chaetonotida) and members of the putative basal Dactylopodola (Macrodasyida). Thaumastodermatidae and all other sampled macrodasyidan families were found monophyletic except for Cephalodasyidae. Within Thaumastodermatidae Diplodasyinae and Thaumastodermatinae are monophyletic and so are most genera. Oregodasys turns out to be the most basal group within Thaumastodermatinae in analyses of the concatenated data set as well as in analyses of the nuclear genes. Thaumastoderma appears as the sister taxon to the remaining species. Surprisingly, Tetranchyroderma is non-monophyletic in our analyses as one group of species clusters with Ptychostomella while another appears as the sister group of Pseudostomella.

    Conclusions/Significance: Results in general agree with the current classification; however, a revision of the more derived thaumastodermatid taxa seems necessary. We also found that the ostensible COI sequences from several species do not conform to the general invertebrate or any other published mitochondrial genetic code; they may be mitochondrially derived nuclear genes (numts), or one or more modifications of the mitochondrial genetic code within Gastrotricha.

  • 32.
    Werdelin, Lars
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Lewis, Margaret E.
    Richard Stockton College of New Jersey.
    Temporal change in functional richness and evenness in the eastern African Plio-Pleistocene carnivoran guild2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 3, p. e57944-Article in journal (Refereed)
    Abstract [en]

    We analyze functional richness and functional evenness of the carnivoran guild in eastern Africa from 3.5 Ma to 1.5 Ma, and compare them to the present day. The data consist of characters of the craniodental apparatus of 76 species of fossil and extant carnivorans, divided into four 0.5 Ma time slices from 3.5 to 1.5 Ma, together with the modern fauna. Focus is on large (>21.5 kg) carnivores. Results show that the large carnivore guild has lost nearly 99% of its functional richness since 3.5 Ma, in a process starting prior to 2 Ma. Measurement of functional evenness shows the modern large carnivore guild to be unique in being randomly distributed in morphospace while in all past time slices there is significant clustering of species. The results are analyzed in the light of known changes to climate and environment in eastern Africa. We conclude that climate change is unlikely to explain all of the changes found and suggest that the evolution of early hominins into carnivore niche space, especially the evolution of derived dietary strategies after 2 Ma, played a significant part in the reduction of carnivore functional richness.

  • 33.
    Zepeda Mendoza, Marie Lisandra
    et al.
    Natural History Museum of Denmark.
    Lundberg, Johannes
    Swedish Museum of Natural History, Department of Botany.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Department of Paleobiology. Nordic Center for Earth Evolution (NordCEE).
    Campos, Paula
    University of Copenhagen.
    Nylander, Johan A. A.
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Sallstedt, Thereese
    Swedish Museum of Natural History, Department of Paleobiology. Nordic Center for Earth Evolution (NordCEE).
    Dalén, Love
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 3, p. 1-23, article id e015177Article in journal (Refereed)
    Abstract [en]

    Speleothems are secondary mineral deposits normally formed by water supersaturated with calcium carbonate percolating into underground caves, and are often associated with low-nutrient and mostly non-phototrophic conditions. Tjuv-Ante’s cave is a shallow-depth cave formed by the action of waves, with granite and dolerite as major components, and opal-A and calcite as part of the speleothems, making it a rare kind of cave. We generated two DNA shotgun sequencing metagenomic datasets from the interior of a speleothem from Tjuv-Ante’s cave representing areas of old and relatively recent speleothem formation. We used these datasets to perform i) an evaluation of the use of these speleothems as past biodiversity archives, ii) functional and taxonomic profiling of the speleothem’s different formation periods, and iii) taxonomic comparison of the metagenomic results to previous microscopic analyses from a nearby speleothem of the same cave. Our analyses confirm the abundance of Actinobacteria and fungi as previously reported by microscopic analyses on this cave, however we also discovered a larger biodiversity. Interestingly, we identified photosynthetic genes, as well as genes related to iron and sulphur metabolism, suggesting the presence of chemoautotrophs. Furthermore, we identified taxa and functions related to biomineralization. However, we could not confidently establish the use of this type of speleothems as biological paleoarchives due to the potential leaching from the outside of the cave and the DNA damage that we propose has been caused by the fungal chemical etching.

1 - 33 of 33
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