Bergsten J.,Swedish Museum of Natural History |
Nilsson A.N.,Umeå University |
Ronquist F.,Swedish Museum of Natural History
Systematic Biology | Year: 2013
We review Bayesian approaches to model testing in general and to the assessment of topological hypotheses in particular. We show that the standard way of setting up Bayes factor tests of the monophyly of a group, or the placement of a sample sequence in a known reference tree, can be misleading. The reason for this is related to the well-known dependency of Bayes factors on model-specific priors. Specifically, when testing tree hypotheses it is important that each hypothesis is associated with an appropriate tree space in the prior. This can be achieved by using appropriately constrained searches or by filtering trees in the posterior sample, but in a more elaborate way than typically implemented. If it is difficult to find the appropriate tree sets to be contrasted, then the posterior model odds may be more informative than the Bayes factor. We illustrate the recommended techniques using an empirical test case addressing the issue of whether two genera of diving beetles (Coleoptera: Dytiscidae), Suphrodytes and Hydroporus, should be synonymized. Our refined Bayes factor tests, in contrast to standard analyses, show that there is strong support for Suphrodytes nesting inside Hydroporus, and the genera are therefore synonymized. [Bayes factor; Coleoptera; Dytiscidae; marginal likelihood; model testing; posterior odds; reversible-jump MCMC; stepping-stone sampling.] © 2013 The Author(s). All rights reserved.
Whitehouse M.J.,Swedish Museum of Natural History
Geostandards and Geoanalytical Research | Year: 2013
High spatial resolution multiple sulfur isotope studies undertaken by multi-collector secondary ion mass spectrometry (SIMS) commonly use well-characterised sulfide reference materials that do not (or are assumed not to) exhibit mass-independent fractionation in 33S and 36S, taking advantage of the three-isotope plot to evaluate the extent of such fractionation in unknown targets. As a result, few studies to date have used a mass independently fractionated reference sulfide to demonstrate accuracy of measurement and/or data reduction procedures. This article evaluates two mass independently fractionated sulfides, a pyrite from the 3.7 Ga Isua greenstone belt and a pyrrhotite from a 2.7 Ga gold deposit in Minas Gerais, Brazil, which may be used to provide additional confidence in the obtained multiple sulfur isotope data. Additionally, the article presents a method for measuring quadruple sulfur isotopes by SIMS at a comparable spatial and volume resolution to that typically employed for triple sulfur isotopes. This method has been applied to the Isua pyrite as well as to a sample of 2.5 Ga pyrite from the Campbellrand, Transvaal, South Africa, previously investigated using SIMS for triple sulfur isotopes, illustrating its potential for quadruple sulfur investigations. © 2012 The Author. Geostandards and Geoanalytical Research © 2012 International Association of Geoanalysts.
Johansson A.,Swedish Museum of Natural History
Precambrian Research | Year: 2014
A refined model of the late Mesoproterozoic to Neoproterozoic supercontinent Rodinia is presented, with Baltica, Amazonia and West Africa attached to eastern Laurentia as in the SAMBA model (Johansson, 2009), and East Antarctica, Australia and India to western Laurentia in a SWEAT configuration (Moores, 1991). In such a model, the Proto-Andean margin of South America would form the conjugate margin of Laurentia's Grenville margin. With the Kalahari craton attached to SW Laurentia and East Antarctica, as proposed by Loewy et al. (2011), followed by the Congo and Tanzania cratons in Africa and the São Fransisco and Rio de la Plata cratons in South America, all these cratons would be part of Rodinia, but would still be separated from Amazonia by a wide Brasiliano (Clymene) ocean embayment. By rotating the African and eastern South American cratons ca. 90° counterclockwise around a pole located close to the Laurentia-Kalahari junction, and East Antarctica, Australia and India ca. 120° counterclockwise around a pole located inside the Kalahari craton, all relative to a fixed Laurentia, these cratons will move from a Rodinia to a Gondwana configuration. These rotations will open up the Proto-Pacific ocean, close the Brasiliano (Clymene) ocean, and both open and close the intervening Adamastor and Mozambique oceans, creating the various Brasiliano and Pan-African fold belts in the ensuing collisions. The maximum plate velocity, ca 7.5. cm/year (15,000. km in 200. m.y.), will occur along the outer periphery of this rotation, thereby explaining the formation of large amounts of juvenile Neoproterozoic continental crust within the oceanic Arabian-Nubian sector of the Pan-African Orogen. Rather than being an example of 'introversion' or 'extroversion', the change from Rodinia to Gondwana in this model would be more like the 90° 'orthoversion' model proposed by Mitchell et al. (2012). © 2013 Elsevier B.V.
McLoughlin S.,Swedish Museum of Natural History
Australian Journal of Botany | Year: 2011
Single, midrib-positioned galls and midrib-flanking oviposition scars are described from four species of Permian glossopterid foliage from Australia and South Africa. Several of these traces have been mistaken previously for glossopterid reproductive organs or fructification detachment scars. A single Early Triassic corystosperm leaf from Australia is reported bearing multiple disc-like galls on both the midrib and pinnules. A Middle Triassic taeniopterid gymnosperm leaf from Australia is described hosting oviposition scars between consecutive secondary veins flanking the midrib. These fossils attest to a much richer record of plantarthropod interactions in the late Palaeozoic and early Mesozoic of high-latitude Gondwana than previously reported, and indicate that herbivory and reproductive strategies involving galling and foliar ovipositioning were re-established relatively soon after the end-Permian mass extinction event that saw major turnovers in both the flora and insect fauna. © 2011 CSIRO.
Bomfleur B.,Swedish Museum of Natural History |
McLoughlin S.,Swedish Museum of Natural History |
Vajda V.,Lund University
Science | Year: 2014
Rapidly permineralized fossils can provide exceptional insights into the evolution of life over geological time. Here, we present an exquisitely preserved, calcified stem of a royal fern (Osmundaceae) from Early Jurassic lahar deposits of Sweden in which authigenic mineral precipitation from hydrothermal brines occurred so rapidly that it preserved cytoplasm, cytosol granules, nuclei, and even chromosomes in various stages of cell division. Morphometric parameters of interphase nuclei match those of extant Osmundaceae, indicating that the genome size of these reputed "living fossils" has remained unchanged over at least 180 million years - a paramount example of evolutionary stasis.
Ericson P.G.P.,Swedish Museum of Natural History
Journal of Biogeography | Year: 2012
Aim To reconstruct the biogeographical history of a large clade of mainly terrestrially adapted birds (coraciiform and piciform birds, owls, diurnal raptors, New World vultures, trogons, mousebirds, cuckoo-rollers, seriemas, parrots and passerines) to test the hypothesis of its Gondwanan origin. Location Global. Methods The phylogenetic tree used in the analysis was a family-level tree estimated from previously published nuclear DNA sequence data. Each family for which a thorough and taxonomically well-sampled phylogenetic analysis exists was subject to an initial dispersal-vicariance analysis in order to reconstruct ancestral areas for its two most basal lineages. Both basal lineages were then used to represent the family in the subsequent reconstruction of ancestral distributions for the entire radiation. Results The analysis showed that three reciprocally monophyletic groups of terrestrial birds have diversified in the Gondwanan land areas of Australia, South America and Africa, respectively. Although each of these three groups may also have originally included other groups, the only survivors today from the Australian radiation are the passerines and parrots, while the falcons and seriemas have survived from the South American radiation. The group of survivors from the African radiation is considerably more taxonomically diverse and includes all coraciiform and piciform birds, owls, diurnal raptors (except falcons), New World vultures, trogons, mousebirds and cuckoo-rollers. Main conclusions The outlined evolutionary scenario with three geographically isolated clades of terrestrial birds is consistent with the available estimates of Late Cretaceous to early Palaeogene dates for these radiations. The diversifications and ecological adaptations within each of the three groups most likely took place in isolation on the different continents. Many cases of convergently evolved adaptations may be revealed through the increased understanding of the phylogenetic relationships of terrestrial birds. © 2011 Blackwell Publishing Ltd.
Pott C.,Swedish Museum of Natural History
International Journal of Plant Sciences | Year: 2014
Premise of research. The concept of Wielandiella angustifolia, a shrub-sized bennettite from the Rhaetian of southern Sweden and East Greenland, became the standard interpretation of the habit and plant architecture of the Williamsoniaceae during the last 100 years. This concept, however, was never critically reinvestigated to evaluate the validity of the restoration. In addition, the new International Code of Nomenclature for algae, fungi, and plants (Melbourne Code) allows erecting fossil taxa for whole-plant concepts, wherefore Wielandiella angustifolia is an ideal candidate. Methodology. The excellently preserved plant fossils were reinvestigated using modern methods, such as cuticular analysis and light, fluorescence, and scanning electron microscopy. Pivotal results. The reinvestigation led to the rejection of the bisexual nature of the plant and provides deeper insights into the plant's nature, biology, and ecology. The rejection of the bisexual nature necessitated emendation of the diagnosis of Wielandiella. Conclusions. The revised diagnosis circumscribes a whole-plant concept that includes branched axes bearing leaves, immature seed cones, and monosporangiate, flowerlike reproductive structures. Good candidates for the hitherto-unidentified microsporangiate structure and the mature seed cone are Bennettistemon and Vardekloeftia, respectively. Discussion of the results concluded that Wielandiella definitely forms a separate genus within the Williamsoniaceae that is distinct from Williamsoniella and Williamsonia. © 2014 by The University of Chicago. All rights reserved.
Kalthoff D.C.,Swedish Museum of Natural History
Journal of Morphology | Year: 2011
A striking difference between xenarthrans and other mammals is the complete loss of tooth enamel in all members but the earliest armadillos. However, sloth and armadillo teeth show structured wear facets, which in all other mammals are formed by tooth enamel. How is that possible? Here, I report about an analysis of fossil and recent xenarthran dental hard tissue microstructure. It shows that osteodentine is not exclusive to fossil Cingulata, but also occurs in some recent taxa. Furthermore, I found profound modifications of orthodentine architecture in comparison to other mammals. Remarkable features are (a) a larger proportion of the highly mineralized, collagen-free peritubular dentine, and (b) a modified architecture of the odontoblastic process with frequent interconnections between the extensions and unusually intensive branching of the extensions forming a complex meshwork, penetrating the intertubular dentine matrix. The orthodentine microstructural build-up is unique in Folivora and Cingulata. © 2011 Wiley-Liss, Inc.
Hedenas L.,Swedish Museum of Natural History
Botanical Journal of the Linnean Society | Year: 2012
Global phylogeographic patterns in Sanionia uncinata are addressed based on information in internal transcribed spacer (ITS) (214 specimens) and the plastid markers trnL-trnF (221) and rpl16 (217). ITS suggests a monophyletic Sanionia and a paraphyletic S. uncinata; this was neither supported nor rejected by plastid data. Northern or Eastern Eurasia and Alaska appear important in the early evolution of Sanionia and some populations dispersed into the Southern Hemisphere relatively early. Some haplotypes or groups of haplotypes are morphologically and ecologically distinct, biologically meaningful units that correspond with S. orthothecioides, S. symmetrica and S. georgicouncinata s.l. The latter includes two species that are indistinguishable by morphology, S. georgicouncinata s.s. (Southern Hemisphere) and S. nivalis (Northern Hemisphere). Tropical African and South American S. uncinata populations have separate origins and the Southern Hemisphere was colonized at least twice. In the northern circum-Arctic region, the haplotype composition differs between the North Atlantic and Beringian areas. Eastern Eurasia has a higher S. uncinata haplotype diversity than other Holarctic regions, implying less devastating effects of recurrent glacial periods. For Eastern and Western Eurasia, North America and the Southern Hemisphere, most of the haplotype variation was found within the regions, but 14-18% can be referred to among region variation. Plastid haplotype diversity was lower in the Southern Hemisphere than in the Arctic to subarctic, possibly attributable to founder effects. © 2011 The Linnean Society of London.
Ivarsson M.,Swedish Museum of Natural History
Biogeosciences | Year: 2012
The oceanic crust is believed to host the largest potential habitat for microbial life on Earth, yet, still we lack substantial information about the abundance, diversity, and consequence of its biosphere. The last two decades have involved major research accomplishments within this field and a change in view of the ocean crust and its potential to harbour life. Here fossilised fungal colonies in subseafloor basalts are reported from three different seamounts in the Pacific Ocean. The fungal colonies consist of various characteristic structures interpreted as fungal hyphae, fruit bodies and spores. The fungal hyphae are well preserved with morphological characteristics such as hyphal walls, septa, thallic conidiogenesis, and hyphal tips with hyphal vesicles within. The fruit bodies consist of large (∼50-200 μm in diameter) body-like structures with a defined outer membrane and an interior filled with calcite. The fruit bodies have at some stage been emptied of their contents of spores and filled by carbonate-forming fluids. A few fruit bodies not filled by calcite and with spores still within support this interpretation. Spore-like structures (ranging from a few μm to ∼20 μm in diameter) are also observed outside of the fruit bodies and in some cases concentrated to openings in the membrane of the fruit bodies. The hyphae, fruit bodies and spores are all closely associated with a crust lining the vein walls that probably represent a mineralized biofilm. The results support a fungal presence in deep subseafloor basalts and indicate that such habitats were vital between ∼81 and 48 Ma. © 2012 Author(s).