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  • 251.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Trinajstic, Katherine M.
    Mirone, Alessandro
    Tafforeau, Paul
    Three-Dimensional Synchrotron Virtual Paleohistology: A New Insight into the World of Fossil Bone Microstructures2012Ingår i: Microscopy and Microanalysis, ISSN 1431-9276, E-ISSN 1435-8115, Vol. 18, nr 5, s. 1095-1105Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The recent developments of phase-contrast synchrotron imaging techniques have been of great interest for paleontologists, providing three-dimensional (3D) tomographic images of anatomical structures, thereby leading to new paleobiological insights and the discovery of new species. However, until now, it has not been used on features smaller than 57 mu m voxel size in fossil bones. Because much information is contained within the 3D histological architecture of bone, including an ontogenetic record, crucial for understanding the paleobiology of fossil species, the application of phase-contrast synchrotron tomography to bone at higher resolutions is potentially of great interest. Here we use this technique to provide new 3D insights into the submicron-scale histology of fossil and recent bones, based on the development of new pink-beam configurations, data acquisition strategies, and improved processing tools. Not only do the scans reveal by nondestructive means all of the major features of the histology at a resolution comparable to that of optical microscopy, they provide 3D information that cannot be obtained by any other method.

  • 252.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    de Ploeg, Gael
    Clément, Gael
    Ahlberg, Per Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    A new tool for determining degrees of mineralization in fossil amphibian skeletons: The example of the Late Palaeozoic branchiosaurid Apateon from the Autun Basin, France2010Ingår i: Comptes rendus. Palevol, ISSN 1631-0683, E-ISSN 1777-571X, Vol. 9, nr 6-7, s. 311-317Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Studying ontogenetic features of fossil tetrapods is of major interest for investigating the adaptive strategies of early tetrapods to their palaeoenvironments. To determine the degree of calcification of skeletal elements, biologists have until now relied on X-ray radiographs of organisms or isolated bones, or on thin sections. An X-ray tomographic scan of Apateon, a Carboniferous - Permian branchiosaurid from the Autun Basin, France, reveals distinct density properties related to different mineralized tissues (calcified cartilage versus bone). The rendering of Apateon as a "test individual" provides a 3D map of the degrees of ossification of the axial and cranial elements. The combination of these anatomical observations with histological information from classical thin sections made in limb bones of several other specimens of the same locality allows the detailed determination of their ontogenetic stage. A comparison with the well-known specimens of the Saar-Nahe Basin, Germany, makes it possible to investigate the influence of different palaeoenvironments on ontogenetic features.

  • 253.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Dupret, Vincent
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Ryll, Bettina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Trinajstic, Kate
    Curtin University, Western Australia.
    Wretman, Lovisa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Zylberberg, Louise
    Université Pierre et Marie Curie, UPMC, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Fossil bone histology revealed in 3D thanks to the synchrotron light: palaeobiological implications2011Konferensbidrag (Refereegranskat)
  • 254.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Dupret, Vincent
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Ryll, Bettina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Trinajstic, Kate
    Curti University, Western Australia.
    Wretman, Lovisa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Zylberberg, Louise
    Université Pierre et Marie Curie, UPMC, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Synchrotron virtual palaeohistology: a new tool for studying the evolution of bone microstructures in 3D2011Konferensbidrag (Refereegranskat)
  • 255.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Dupret, Vincent
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi.
    Tafforeau, Paul
    Trinajstic, Katherine M.
    Ryll, Bettina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Gouttenoire, Pierre-Jean
    Wretman, Lovisa
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Zylberberg, Louise
    Peyrin, Francoise
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    3D Microstructural Architecture of Muscle Attachments in Extant and Fossil Vertebrates Revealed by Synchrotron Microtomography2013Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, nr 2, s. e56992-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Background: Firm attachments binding muscles to skeleton are crucial mechanical components of the vertebrate body. These attachments (entheses) are complex three-dimensional structures, containing distinctive arrangements of cells and fibre systems embedded in the bone, which can be modified during ontogeny. Until recently it has only been possible to obtain 2D surface and thin section images of entheses, leaving their 3D histology largely unstudied except by extrapolation from 2D data. Entheses are frequently preserved in fossil bones, but sectioning is inappropriate for rare or unique fossil material.

    Methodology/Principal Findings: Here we present the first non-destructive 3D investigation, by propagation phase contrast synchrotron microtomography (PPC-SR mu CT), of enthesis histology in extant and fossil vertebrates. We are able to identify entheses in the humerus of the salamander Desmognathus from the organization of bone-cell lacunae and extrinsic fibres. Statistical analysis of the lacunae differentiates types of attachments, and the orientation of the fibres, reflect the approximate alignment of the muscle. Similar histological structures, including ontogenetically related pattern changes, are perfectly preserved in two 380 million year old fossil vertebrates, the placoderm Compagopiscis croucheri and the sarcopterygian fish Eusthenopteron foordi.

    Conclusions/Significance: We are able to determine the position of entheses in fossil vertebrates, the approximate orientation of the attached muscles, and aspects of their ontogenetic histories, from PPC-SRmCT data. Sub-micron microtomography thus provides a powerful tool for studying the structure, development, evolution and palaeobiology of muscle attachments.

  • 256.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Fernandez, Vincent
    Pierce, Stephanie E.
    Tafforeau, Paul
    Homogenization of sample absorption for the imaging of large and dense fossils with synchrotron microtomography2013Ingår i: Nature Protocols, ISSN 1754-2189, E-ISSN 1750-2799, Vol. 8, nr 9, s. 1708-1717Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Propagation phase-contrast synchrotron radiation microtomography (PPC-SR mu CT) has proved to be very successful for examining fossils. Because fossils range widely in taphonomic preservation, size, shape and density, X-ray computed tomography protocols are constantly being developed and refined. Here we present a 1-h procedure that combines a filtered high-energy polychromatic beam with long-distance PPC-SR mu CT (sample to detector: 4-16 m) and an attenuation protocol normalizing the absorption profile (tested on 13-cm-thick and 5.242 g cm(-3) locally dense samples but applicable to 20-cm-thick samples). This approach provides high-quality imaging results, which show marked improvement relative to results from images obtained without the attenuation protocol in apparent transmission, contrast and signal-to-noise ratio. The attenuation protocol involves immersing samples in a tube filled with aluminum or glass balls in association with a U-shaped aluminum profiler. This technique therefore provides access to a larger dynamic range of the detector used for tomographic reconstruction. This protocol homogenizes beam-hardening artifacts, thereby rendering it effective for use with conventional mu CT scanners.

  • 257.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Schoch, R. R.
    Bone Histology Reveals a High Environmental and Metabolic Plasticity as a Successful Evolutionary Strategy in a Long-Lived Homeostatic Triassic Temnospondyl2013Ingår i: Evolutionary biology, ISSN 0071-3260, E-ISSN 1934-2845, Vol. 40, nr 4, s. 627-647Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Evolutionary stasis (long-term stability of morphology in an evolving lineage) is a pattern for which explanations are usually elusive. The Triassic tetrapod Gerrothorax pulcherrimus, a gill-bearing temnospondyl, survived for 35 million years in the Germanic Basin of Central Europe persisting throughout the dinosaur-dominated Late Triassic period. This evolutionary stasis coincides with the occurrence of this species in a wide range of habitats and environmental conditions. By the combination of palaeoecological and palaeohistological analyses, we found great ecological flexibility in G. pulcherrimus and present substantial evidence of developmental and metabolic plasticity despite the morphological stasis. We conclude that G. pulcherrimus could show the capacity to settle in water bodies too harsh or unpredictable for most other tetrapods. This would have been made possible by a unique life history strategy that involved a wide reaction norm, permitting adjustment to fluctuating conditions such as salinity and level of nutrients. Growth rate, duration of juvenile period, age at maturity, and life span were all subject to broad variation within specimens of G. pulcherrimus in one single lake and in between different lakes. In addition to providing a better understanding of fossil ecosystems, this study shows the potential of such a methodology to encourage palaeobiologists and evolutionary biologists to consider the mechanisms of variation in extant and fossil organisms by using a similar time-scope reference.

  • 258.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Tafforeau, P.
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    The humerus of Eusthenopteron: a puzzling organization presaging the establishment of tetrapod limb bone marrow2014Ingår i: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 281, nr 1782, s. 20140299-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Because of its close relationship to tetrapods, Eusthenopteron is an important taxon for understanding the establishment of the tetrapod body plan. Notably, it is one of the earliest sarcopterygians in which the humerus of the pectoral fin skeleton is preserved. The microanatomical and histological organization of this humerus provides important data for understanding the evolutionary steps that built up the distinctive architecture of tetrapod limb bones. Previous histological studies showed that Eusthenopteron's long-bone organization was established through typical tetrapod ossification modalities. Based on a threedimensional reconstruction of the inner microstructure of Eusthenopteron's humerus, obtained from propagation phase-contrast X-ray synchrotron microtomography, we are now able to show that, despite ossification mechanisms and growth patterns similar to those of tetrapods, it also retains plesiomorphic characters such as a large medullary cavity, partly resulting from the perichondral ossification around a large cartilaginous bud as in actinopterygians. It also exhibits a distinctive tubular organization of bone-marrow processes. The connection between these processes and epiphyseal structures highlights their close functional relationship, suggesting that either bone marrow played a crucial role in the long-bone elongation processes or that trabecular bone resulting from the erosion of hypertrophied cartilage created a microenvironment for haematopoietic stem cell niches.

  • 259.
    Sanchez, Sophie
    et al.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. European Synchrotron Radiat Facil, 71 Ave Martyrs,CS 40220, F-38043 Grenoble, France..
    Tafforeau, Paul
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS 40220, F-38043 Grenoble, France..
    Clack, Jennifer A.
    Univ Cambridge, Univ Museum Zool, Dept Zool, Downing St, Cambridge CB2 3EJ, England..
    Ahlberg, Per E.
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Life history of the stem tetrapod Acanthostega revealed by synchrotron microtomography2016Ingår i: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 537, nr 7620, s. 408-+Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The transition from fish to tetrapod was arguably the most radical series of adaptive shifts in vertebrate evolutionary history. Data are accumulating rapidly for most aspects of these events(1-5), but the life histories of the earliest tetrapods remain completely unknown, leaving a major gap in our understanding of these organisms as living animals. Symptomatic of this problem is the unspoken assumption that the largest known Devonian tetrapod fossils represent adult individuals. Here we present the first, to our knowledge, life history data for a Devonian tetrapod, from the Acanthostega mass-death deposit of Stensio Bjerg, East Greenland(6,7). Using propagation phase-contrast synchrotron microtomography (PPC-SR mu CT)(8) to visualize the histology of humeri (upper arm bones) and infer their growth histories, we show that even the largest individuals from this deposit are juveniles. A long early juvenile stage with unossified limb bones, during which individuals grew to almost final size, was followed by a slow-growing late juvenile stage with ossified limbs that lasted for at least six years in some individuals. The late onset of limb ossification suggests that the juveniles were exclusively aquatic, and the predominance of juveniles in the sample suggests segregated distributions of juveniles and adults at least at certain times. The absolute size at which limb ossification began differs greatly between individuals, suggesting the possibility of sexual dimorphism, adaptive strategies or competition-related size variation.

  • 260.
    Schlebusch, Carina M.
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Prins, Frans
    Univ KwaZulu Natal, Sch Anthropol Gender & Hist Studies, Durban, South Africa..
    Lombard, Marlize
    Univ Johannesburg, Dept Anthropol & Dev Studies, Auckland Pk, ZA-2006 Johannesburg, South Africa..
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Soodyall, Himla
    Univ Witwatersrand, Fac Hlth Sci, Div Human Genet, Sch Pathol, Johannesburg, South Africa.;Natl Hlth Lab Serv, Johannesburg, South Africa..
    The disappearing San of southeastern Africa and their genetic affinities2016Ingår i: Human Genetics, ISSN 0340-6717, E-ISSN 1432-1203, Vol. 135, nr 12, s. 1365-1373Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Southern Africa was likely exclusively inhabited by San hunter-gatherers before similar to 2000 years ago. Around that time, East African groups assimilated with local San groups and gave rise to the Khoekhoe herders. Subsequently, Bantu-speaking farmers, arriving from the north (similar to 1800 years ago), assimilated and displaced San and Khoekhoe groups, a process that intensified with the arrival of European colonists similar to 350 years ago. In contrast to the western parts of southern Africa, where several Khoe-San groups still live today, the eastern parts are largely populated by Bantu speakers and individuals of non-African descent. Only a few scattered groups with oral traditions of Khoe-San ancestry remain. Advances in genetic research open up new ways to understand the population history of southeastern Africa. We investigate the genomic variation of the remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using similar to 2.2 million genetic markers, combined with comparative published data sets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the parallel to Xegwi San) and Bantu speakers. Specifically, we found that the Lake Chrissie San are closely related to the current southern San groups (i.e., the Karretjie people). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. This study illustrates how genetic tools can be used to assess hypotheses about the ancestry of people who seemingly lost their historic roots, only recalling a vague oral tradition of their origin.

  • 261.
    Schlebusch, Carina
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Malmström, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Günther, Torsten
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Sjödin, Per
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Coutinho, Alexandra
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Edlund, Hanna
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Munters, Arielle R.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Vicente, Mário
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Steyn, Maryna
    Human Variation and Identification Research Unit, School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, South Africa..
    Soodyall, Himla
    Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and National Health Laboratory Service, Johannesburg, South Africa..
    Lombard, Marlize
    Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa.; Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Marais Street, Stellenbosch, 7600, South Africa. .
    Jakobsson, Mattias
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Centre for Anthropological Research and Department of Anthropology and Development Studies, University of Johannesburg, Post Office Box 524, Auckland Park, 2006, South Africa..
    Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago2017Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 358, nr 6363, s. 652-655Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Southern Africa is consistently placed as a potential region for the evolution of Homo sapiens We present genome sequences, up to 13x coverage, from seven ancient individuals from KwaZulu-Natal, South Africa. The remains of three Stone Age hunter-gatherers (about 2000 years old) were genetically similar to current-day southern San groups, and those of four Iron Age farmers (300 to 500 years old) were genetically similar to present-day Bantu-language speakers. We estimate that all modern-day Khoe-San groups have been influenced by 9 to 30% genetic admixture from East Africans/Eurasians. Using traditional and new approaches, we estimate the first modern human population divergence time to between 350,000 and 260,000 years ago. This estimate increases the deepest divergence among modern humans, coinciding with anatomical developments of archaic humans into modern humans, as represented in the local fossil record.

  • 262.
    Scholze, Frank
    et al.
    TU Bergakad Freiberg, Geol Inst, Freiberg, Germany; Kazan Fed Univ, Inst Geol & Petr Technol, Kazan, Russia.
    Golubev, Valeriy K.
    Russian Acad Sci, Borissiak Paleontol Inst, Moscow, Russia; Kazan Fed Univ, Inst Geol & Petr Technol, Kazan, Russia.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Schneider, Joerg W.
    TU Bergakad Freiberg, Geol Inst, Freiberg, Germany; Kazan Fed Univ, Inst Geol & Petr Technol, Kazan, Russia.
    Sennikov, Andrey G.
    Russian Acad Sci, Borissiak Paleontol Inst, Moscow, Russia; Kazan Fed Univ, Inst Geol & Petr Technol, Kazan, Russia.
    Late Permian conchostracans (Crustacea, Branchiopoda) from continental deposits in the Moscow Syneclise, Russia2019Ingår i: Journal of Paleontology, ISSN 0022-3360, E-ISSN 1937-2337, Vol. 93, nr 1, s. 72-97Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Moscow Syneclise on the East European Platform is an important area for the study of the continental biota of late Permian to Early Triassic age in continuous sections. This study attempts a taxonomic description of the late Permian conchostracan fauna of this area. The rich, new material was collected, bed by bed, during geological and paleontological excavations of lacustrine and fluvial deposits of the Obnora Formation and Vokhma Formation of the late Permian Zhukovian Regional Stage near the towns of Vyazniki and Gorokhovets. The conchostracan fauna of the Zhukovian Regional Stage consists predominantly of Pseudestheria and less frequently of Palaeolimnadiopsis. In the earliest Triassic Vokhmian Regional Stage, a more diverse fauna including Euestheria, Magniestheria, Cornia, Palaeolimnadiopsis, and Rossolimnadiopsis was already recorded. The preliminary taxonomic determination of the pseudestheriids from the Zhukovian Regional Stage is intended to serve as a prerequisite for future studies of late Permian conchostracan biostratigraphy on the regional to interregional scale.

  • 263. Scholze, Frank
    et al.
    Golubev, Valeriy K.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Sennikov, Andrey G.
    Schneider, Joerg W.
    Silantiev, Vladimir V.
    Early Triassic Conchostracans (Crustacea: Branchiopoda) from the terrestrial Permian-Triassic boundary sections in the Moscow syncline2015Ingår i: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 429, s. 22-40Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Permian-Triassic boundary marks the greatest mass extinction in Earth's history. In order to understand the real causes of this severe extinction event, multidisciplinary investigations around the globe are required. Here, the terrestrial Permian-Triassic boundary sections in the Vladimir region, Central Russia, were sampled bed-by-bed for conchostracan study. In the Early Triassic intervals the following taxa were recognized for the first time: Cornia germari (Beyrich, 1857), Euestheria gutta (Lutkevitch, 1937), Magniestheria mangaliensis (Jones, 1862), Palaeolimnadiopsis vilujensis Varentsov, 1955, and Rossolimnadiopsis Novozhilov, 1958. The wide distribution of C germari demonstrates their high value for biostratigraphy, since this species was also reported from the Lower Buntsandstein Subgroup in the Germanic Basin as well as from Early Triassic deposits in Hungary, Greenland and Siberia. The assumption of an Early Triassic age of the studied sections is also supported by associated Tupilakosaurus bone fragments, which point to the Tupilakosaurus wedugensis Zone in the earliest Triassic.

  • 264.
    Sjödin, Per
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Population Genetic Nature of Copy Number Variation2012Ingår i: Genomic Strutural Variants: Methods and Protocols / [ed] Lars Feuk, Humana Press, 2012, 1, s. 209-223Kapitel i bok, del av antologi (Övrigt vetenskapligt)
    Abstract [en]

    Copy number variation has recently received considerable attention, and copy number variants (CNVs) have been shown to be both common in mammalian genomes and important for understanding genetic and phenotypic variation. As empirical knowledge and detection methods are quickly advancing, evolutionary theories about CNVs are rapidly updated and often revised. Here, we review recent progress on understanding CNVs, and we discuss some key issues for future research. In essence, we discuss four major forces in population genetics, recombination, mutation, selection, and demography, in relation to CNVs.

  • 265.
    Skawinski, Tomasz
    et al.
    Univ Wroclaw, Dept Evolutionary Biol & Conservat Vertebrates, Fac Biol Sci, Wroclaw, Poland..
    Ziegler, Maciej
    Glogowska 227c, PL-60111 Poznan, Poland..
    Czepinski, Lukasz
    Univ Warsaw, Dept Palaeobiol & Evolut, Fac Biol, Biol & Chem Res Ctr, Warsaw, Poland..
    Szermanski, Marcin
    Siemiradzkiego 19-23, PL-43300 Bielsko Biala, Poland..
    Talanda, Mateusz
    Univ Warsaw, Dept Palaeobiol & Evolut, Fac Biol, Biol & Chem Res Ctr, Warsaw, Poland..
    Surmik, Dawid
    Univ Silesia, Fac Earth Sci, Sosnowiec, Poland..
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    A re-evaluation of the historical "dinosaur' remains from the Middle-Upper Triassic of Poland2017Ingår i: Historical Biology, ISSN 0891-2963, E-ISSN 1029-2381, Vol. 29, nr 4, s. 442-472Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    The so-called historical Polish discoveries of Triassic dinosaurs' have been repeatedly cited in papers and popular science books. Here, we re-evaluate each historical and purported Triassic dinosaur find from Poland. Additionaly, we describe several supposed dinosaur' bones collected by Polish geologists but only briefly mentioned: in regional geological journals, on collection labels, or in field notes. We attempt to assign all investigated specimens to the least inclusive taxon possible. Our revision indicates that part of this material represents non-dinosaur archosauromorph taxa. Most of the analysed specimens are fragmentary bones or isolated teeth and are indistinguishable from skeletal elements described from other well-known Triassic archosauromorph taxa. We conclude that fossils of dinosauriforms are present in the Upper Triassic of Silesia and Holy Cross Mountains. New analysis of Velocipes guerichi von Huene, 1932 holotype specimen from Kocury shows that it is the proximal part of fibula of a medium-sized theropod (or even neotheropod). Formally undescribed part of dinosauriform limb bone from the Holy Cross Mountains and V. guerichi from Silesia are the only identifiable dinosauromorph skeletal remains recognised in the Polish Triassic discovered prior to the description of Silesaurus opolensis Dzik, 2003 from the Upper Carnian of Krasiejow.

  • 266.
    Skrzycki, Piotr
    et al.
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Talanda, Mateusz
    Univ Warsaw, Dept Palaeobiol & Evolut, Biol & Chem Res Ctr, Fac Biol, Zwirki & Wigury 101, PL-02089 Warsaw, Poland..
    Dipnoan remains from the Lower-Middle Triassic of the Holy Cross Mountains and northeastern Poland, with remarks on dipnoan palaeobiogeography2018Ingår i: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 496, s. 332-345Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Here we present a revision of dipnoans from the Middle-Upper Buntsandstein and the Lower Muschelkalk (Lower-Middle Triassic) of the Holy Cross Mountains (southeastern Poland) and from the Middle Buntsandstein of northeastern Poland. Two genera are identified: Arganodus and Ptychoceratodus. Specimens resemble synchronous species from the European part of Russia. It is the first Middle Triassic finding of Arganodus worldwide. Ptychoceratodus is reported for the first time from the Lower Triassic of Poland. It is its oldest known occurrence in Europe. The Holy Cross Mountains stands between the area of European Russia and the Central European Basin which were both inhabited by Arganodus and Ptychoceratodus in the Early-Middle Triassic. Resulting from a summary of palaeobiogeographic data of these two genera their distributional patterns are hypothesized herein. In the Early Triassic both genera often co-occurred in many regions. Starting from the Middle Triassic their ranges split into two almost separate ones. They reflect the palaeolatitudinal belts in the Late Triassic with Arganodus in the northern tropic belt and Ptychoceratodus along the palaeolatitudes 30 degrees.

  • 267.
    Somel, Mehmet
    et al.
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Kilinc, Gulsah Merve
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Ozer, Fusun
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Omrak, Ayca
    Stockholm Univ, Archaeol, Stockholm, Sweden..
    Yaka, Reyhan
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Donertas, Melike
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Dagtas, Nihan D.
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Yuncu, Eren
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Koptekin, Dilek
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Büyükkarakaya, Ali M.
    Hacettepe Univ, Anthropol, Stockholm, Sweden..
    Acan, Sinan C.
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Alkan, Can
    Bilkent Univ, Comp Sci, Ankara, Turkey..
    Hodder, Ian
    Stanford Univ, Anthropol, Stanford, CA 94305 USA..
    Haddow, Scott
    Stanford Univ, Anthropol, Stanford, CA 94305 USA..
    Knüsel, Christopher
    Univ Bordeaux, Prehist, Bordeaux, France..
    Larsen, Clark S.
    Ohio State Univ, Anthropol, Columbus, OH 43210 USA..
    Erdal, Yilmaz S.
    Hacettepe Univ, Anthropol, Stockholm, Sweden..
    Bicakci, Erhan
    Istanbul Univ, Prehist, Istanbul, Turkey..
    Baird, Douglas
    Univ Liverpool, Archaeol, Liverpool L69 3BX, Merseyside, England..
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Togan, Inci
    Middle E Tech Univ, Biol, Ankara, Turkey..
    Götherström, Anders
    Stockholm Univ, Archaeol, Stockholm, Sweden.
    Archaeogenomic analysis of ancient Anatolians: first genetic indication for Neolithic cultural diffusion in the Near East2016Ingår i: American Journal of Physical Anthropology, ISSN 0002-9483, E-ISSN 1096-8644, Vol. 159, nr Suppl. 62, s. 297-298Artikel i tidskrift (Övrigt vetenskapligt)
  • 268.
    Soussi, Mohamed
    et al.
    Univ Tunis El Manar, Fac Sci, Dept Geol, Tunis 2092, Tunisia..
    Niedźwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Talanda, Mateusz
    Univ Warsaw, Fac Biol, Dept Paleobiol & Evolut, Biol & Chem Res Ctr, Zwirki & Wigury 101, PL-02089 Warsaw, Poland..
    Drozdz, Dawid
    Univ Warsaw, Fac Biol, Dept Paleobiol & Evolut, Biol & Chem Res Ctr, Zwirki & Wigury 101, PL-02089 Warsaw, Poland.;Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Sulej, Tomasz
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Boukhalfa, Kamel
    Univ Tunis El Manar, Fac Sci, Dept Geol, Tunis 2092, Tunisia.;Univ Gabes, Fac Sci Gabes, Zerig 6029, Gabes, Tunisia..
    Mermer, Janusz
    Univ Warsaw, Fac Biol, Dept Paleobiol & Evolut, Biol & Chem Res Ctr, Zwirki & Wigury 101, PL-02089 Warsaw, Poland..
    Blazejowski, Blazej
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Middle Triassic (Anisian-Ladinian) Tejra red beds and Late Triassic (Carnian) carbonate sedimentary records of southern Tunisia, Saharan Platform: Biostratigraphy, sedimentology and implication on regional stratigraphic correlations2017Ingår i: MARINE AND PETROLEUM GEOLOGY, ISSN 0264-8172, Vol. 79, s. 222-256Artikel, forskningsöversikt (Refereegranskat)
    Abstract [en]

    The "red beds" of the Triassic succession outcropping at Tejra-Medenine (southern Tunisia, Saharan Platform) have yielded rich fossil assemblages of both freshwater and brackish-marine invertebrates and vertebrates. The new discovered fauna indicates an Anisian-Lower Ladinian age for the Tejra section. Its lowermost part is considered as equivalent of Ouled Chebbi Formation, while the medium and upper parts are considered as equivalent of the Kirchaou Formation. Both sedimentological characteristics and fossil assemblages indicate the increasing marine influences within the middle part of the section and the migration of brackish and freshwater fauna into the lacustrine/playa environment at the top. The marine fauna-rich interval of the Tejra section correlates well with the well-known Myophoria-rich carbonate stratigraphic marker confirming the Middle Triassic (Ladinian) major transgression well recorded eastward in the Tunisian Jeffara basin and in Libya. The use of this Ladinian stratigraphic event in addition to the Carnian carbonate transgressive events of the Jeffara escarpment outcrops was of great help for regional lithostratigraphic correlations between the Triassic outcropping series and those currently buried in Ghadames and Berkine basins. The age of the sandstones of "Trias Argilo-Greseux Inferieur" (TAGI) which forms the main oil and gas reservoir in the Saharan domain is attributed to the Anisian-Carnian and considered as coeval of Ouled Chebbi and Kirchaou Formations of the Dahar escarpment. An updated synthetic stratigraphic chart is proposed for the Triassic of Saharan Platform domain on the basis of the compilation of the new obtained results and the subsurface data taken from published literature.

  • 269.
    Sreedharan, Smitha
    et al.
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    Carlini, Valeria P
    Departamento de Farmacología, Universidad Nacional de Córdoba, Argentina.
    Jacobsson, Josefin A
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    Olszewski, Pawel K
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    Haitina, Tatjana
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Hammer, Joanna
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för immunologi, genetik och patologi, Genomik.
    Stephansson, Olga
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    Crona, Filip
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    Sommer, Wolfgang H
    Department of Psychopharmacology, Central institute of Mental Health, Mannheim, Germany.
    Riserus, Ulf
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för folkhälso- och vårdvetenskap, Klinisk nutrition och metabolism.
    Levine, Allen S
    Department of Food Science and Nutrition, Minnesota Obesity Center.
    Lannfelt, Lars
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för folkhälso- och vårdvetenskap, Geriatrik.
    Marcus, Claude
    Department for Clinical Science, Intervention and Technology, Karolinska Institute.
    Heilig, Marcus
    Laboratory of Clinical and Translational Studies, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Bethesda, MD, USA.
    de Barioglio, Susan R
    Departamento de Farmacología, Universidad Nacional de Córdoba, Argentina.
    Fredriksson, Robert
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    Schiöth, Helgi
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för neurovetenskap, Funktionell farmakologi.
    GPR162 is expressed in the hypothalamus and is involved in food intake related behaviour2011Artikel i tidskrift (Övrigt vetenskapligt)
    Abstract [en]

    The Rhodopsin family of G protein-coupled receptors (GPCRs) includes about 270 non-olfactory receptors and is the largest family of GPCRs. About sixty non-olfactory Rhodopsin GPCRs are still orphans without known ligands, and fairly little is known about their functions. In this study, we present molecular, neuroanatomical, genetic and behavioral data implicating a Rhodopsin family protein, GPR162, in the regulation of food intake-related behaviour and glucose homeostasis. The real-time PCR data show that GPR162 is predominantly expressed in the CNS. The in situ hybridization results confirmed significant expression of GPR162 in several hypothalamic sites, amygdala, substantia nigra and ventral tegmental area, among others regions. In line with the distribution of the GPR162 mRNA in the feeding circuitry, antisense oligo knockdown of GPR162 caused a significant reduction in food intake but no effect was observed towards reduction in body weight in rats. Our human genetics studies suggest that genetic variants of GPR162 affect glucose homeostasis. In conclusion, this study provides evidence linking the orphan GPR162 gene with the regulation of food intake-related behaviour.

  • 270.
    Sten, Sabine
    et al.
    Uppsala universitet, Humanistisk-samhällsvetenskapliga vetenskapsområdet, Historisk-filosofiska fakulteten, Institutionen för arkeologi och antik historia, Arkeologi.
    Lovén, Christian
    Riksarkivet,Box 12541, SE-10229 Stockholm, Sweden..
    Kjellström, Anna
    Stockholms Univ, Inst Arkeologi Antikens kultur, Osteologiska Skningslab, SE-10691 Stockholm, Sweden..
    Liden, Kerstin
    Stockholms Univ, Inst Arkeologi Antikens kultur, Arkeologiska Skningslabo, SE-10691 Stockholm, Sweden..
    Vretemark, Maria
    Västergotlands Museum, SE-53232 Skara, Sweden..
    Hongslo Vala, Cecilie
    Univ Goteborgs, Enheten Geriatrik Inst Medicin, Sahlgrenska Akademin, SE-40530 Gothenburg, Sweden..
    Ljunggren, Östen
    Uppsala universitet, Medicinska och farmaceutiska vetenskapsområdet, Medicinska fakulteten, Institutionen för medicinska vetenskaper, Endokrinologi och mineralmetabolism.
    Fjällstrom, Markus
    Uppsala Univ, Arkeol Forskningslab, SE-75185 Uppsala, Sweden..
    Shalabi, Adel
    Bild­ och funktionsmedicinskt centrum, Akademiska sjukhuset, Uppsala, Sweden..
    Duvernoy, Olov
    Bild­ och funktionsmedicinskt centrum, Akademiska sjukhuset, Uppsala, Sweden..
    Segelsjö, Monica
    Bild­ och funktionsmedicinskt centrum, Akademiska sjukhuset, Uppsala, Sweden..
    Malmström, Helena
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Jakobsson, Mattias
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Erik den heliges skelett2016Ingår i: Fornvännen, ISSN 0015-7813, E-ISSN 1404-9430, Vol. 111, nr 1, s. 27-40Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Saint Erik was King of Sweden for a few years up to 1160, when he was killed. A skeleton attributed to him is kept in Uppsala Cathedral. It underwent scientific reappraisal in 2014. The analyses included computer tomography, Xray absorptiometry, isotope analysis and DNA sampling. Radiocarbon confirms the alleged age of the bones. They belong to a 35-40-year-old man in excellent physical shape. The many wounds that he received in connection with his death fit surprisingly well with the saint's legend, whose preserved version was written 130 years after the event.

  • 271. Steyer, J. -Sebastien
    et al.
    Sanchez, Sophie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Debriette, Pierre J.
    Valli, Andrea M. F.
    Escuille, Francois
    Pohl, Burkhard
    Dechambre, Roger-Paul
    Vacant, Renaud
    Spence, Christopher
    de Ploeg, Gael
    A new vertebrate Lagerstatte from the Lower Permian of France (Franchesse, Massif Central): palaeoenvironmental implications for the Bourbon-l'Archambault basin2012Ingår i: Bulletin de la Société Géologique de France, ISSN 0037-9409, E-ISSN 1777-5817, Vol. 183, nr 6, s. 509-515Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A new vertebrate locality from the Lower Permian (Cisuralian) of the Bourbon-l'Archambault basin (Massif Central, France) is reported and its associated flora and fauna preliminarily described. This locality corresponds to a mass mortality assemblage deposited in an aquatic environment. Interestingly, it has yielded hundreds of exceptionally well preserved seymouriamorph specimens, all referred to Discosauriscus austriacus. This exquisite assemblage corresponds to the first seymouriamorph Lagerstatte and the first record of D. austriacus outside the Boskovice basin in Czechia. It enlarges the geographical distribution of the species during the Early Permian, and has new palaeoenvironmental implications regarding the Palaeozoic Bourbon-l'Archambault basin.

  • 272.
    Streng, Michael
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper, Paleobiologi.
    Mellbin, Barbro B.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Landing, Ed
    Keppie, J. Duncan
    Linguliform brachiopods from the terminal Cambrian and lowest Ordovician of the Oaxaquia microcontinent (Southern Mexico)2011Ingår i: Journal of Paleontology, ISSN 0022-3360, E-ISSN 1937-2337, Vol. 85, nr 1, s. 122-155Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Eighteen taxa of linguliform brachiopods, mainly represented by acrotretoids, are reported from the Upper Cambrian (Furongian, Stage 10) and Lower Ordovician (Tremadocian) Tinu Formation of Oaxaca State, Mexico. At the time of deposition, this area was part of Oaxaquia, which was either a microcontinent or an integral part of the Gondwanan margin. Whereas certain trilobites seem to indicate a Gondwanan affinity, the Tinu brachiopod faunas show a less definite paleogeographic relationship. Some taxa have previously only been reported from Laurentia (Eurytreta cf. fillmorensis, Eurytreta cf. campaniformis), and one taxon is best known from the Avalon microcontinent (Eurytreta cf. sabrinae). However, the relatively high percentage of new and potentially endemic taxa (Oaxaquiatreta labrifera n. gen. n. sp., Tapuritreta reclinata n. sp., Oaxaquiatreta sp., Eurytreta? n. sp., Acrotretidae n. gen. n. sp., Obolinae gen. and sp. indet.) and the lack of other typical Laurentian, Gondwanan, or Avalonian taxa suggest either a certain degree of insularity of Oaxaquia or reflects a more temperate, unrestricted marine environment during the Early Paleozoic. Other taxa reported from the Tinu Formation include Semitreta sp., Lingulella? spp., Obolinae gen. and sp. indet., Eoscaphelasma? sp., Ottenbyella? sp. A and sp. B, and Acrotretidae gen. and sp. indet. A, B, and C. Eurytreta and Semitreta are critically reviewed and several taxa previously assigned to them have been excluded. An emended diagnosis for the genus Eurytreta is presented. The presence of delthyrium and notothyrium-like structures in the siphonotretid Oaxaquiatreta n. gen. further strengthens the previously proposed relationship between the Siphonotretida and Paterinida.

  • 273.
    Strömberg, Susanna
    et al.
    Sven Lovens marina centrum, Tjärnö, Götegborgs Univesitet et.
    Östman, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Comparison of adult and larval cnidom in Lophelia pertusa (Linneaus, 1758)2013Konferensbidrag (Övrigt vetenskapligt)
  • 274.
    Strömberg, Susanna
    et al.
    Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden.
    Östman, Carina
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Larsson, Ann
    Department of Marine Sciences, Tjärnö Marine Laboratory, University of Gothenburg, Strömstad, Sweden.
    The cnidome and ultrastructural morphology of late planulae in Lophelia pertusa (Linnaeus, 1758) - With implications for settling competency2019Ingår i: Acta Zoologica (Stockholm), ISSN 0001-7272, E-ISSN 1463-6395, Vol. 100, nr 4, s. 431-450Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The larval pre-competency period and competency window are important in delimiting the potential dispersal distance for pelagic larvae of sessile marine fauna. Here, we provide evidence for morphological changes in the late planulae of Lophelia pertusa that have implications for their dispersal potential. Three weeks after spawning, the planulae gain functional cnidocysts, indicating that they are competent to settle at this time. Cnidae have been shown to be used for primary anchoring during settling, and before this time point, the larvae most probably do not have the ability to attach to a substrate in high flow conditions. The appearance of functional cnidae coincides with larvae gaining a flexible mouth that can be opened to the full width of the larva. The larval isorhizas differ the most from the adult polyps isorhizas, while the p- and b-mastigophores bear more resemblance to the adult homologues of similar size. The external and internal morphology of late planulae is further described with demonstration of long apical cilia and its effect on swimming agility, morphological changes of the ciliated cells in the larval mouth region and an internal nerve plexus. This study also indicates that L. pertusa planulae seek out cryptic spaces for settling.

  • 275.
    Sulej, Tomasz
    et al.
    PAS, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    An elephant-sized Late Triassic synapsid with erect limbs2019Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 363, nr 6422, s. 78-80Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Here, we describe the dicynodont Lisowicia bojani, from the Late Triassic of Poland, a gigantic synapsid with seemingly upright subcursorial limbs that reached an estimated length of more than 4.5 meters, height of 2.6 meters, and body mass of 9 tons. Lisowicia is the youngest undisputed dicynodont and the largest nondinosaurian terrestrial tetrapod from the Triassic. The lack of lines of arrested growth and the highly remodeled cortex of its limb bones suggest permanently rapid growth and recalls that of dinosaurs and mammals. The discovery of Lisowicia overturns the established picture of the Triassic megaherbivore radiation as a phenomenon restricted to dinosaurs and shows that stem-group mammals were capable of reaching body sizes that were not attained again in mammalian evolution until the latest Eocene.

  • 276. Swilo, Marlena
    et al.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Sulej, Tomasz
    Mammal-like tooth from the Upper Triassic of Poland2014Ingår i: Acta Palaeontologica Polonica, ISSN 0567-7920, E-ISSN 1732-2421, Vol. 59, nr 4, s. 815-820Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Recent Triassic discoveries have extended the record of near-mammals (Mammaliaformes) back to the Norian, about 215 Ma, and reveal a significant diversity of Late Triassic (Norian-Rhaetian) forms. We now add to this Late Triassic diversity a nearly complete double-rooted right lower molariform tooth (ZPAL V.33/734) from the Polish Upper Triassic that is significant because it comes from uppermost Norian–lower Rhaetian rocks and is the first discovery of a mammal-like tooth in the Mesozoic of Poland. The described tooth shows transitional dental morphology between advanced cynodonts and mammaliaforms and it appears to represent a basal mammaliaform (genus Hallautherium), probably belonging to Morganucodonta.

  • 277. Szrek, Piotr
    et al.
    Dec, Marek
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    The first placoderm fish from the Lower Devonian of Poland2015Ingår i: Journal of Vertebrate Paleontology, ISSN 0272-4634, E-ISSN 1937-2809, Vol. 35, nr 3, artikel-id e930471Artikel i tidskrift (Refereegranskat)
  • 278. Szrek, Piotr
    et al.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Dec, Marek
    Storm origin of bone-bearing beds in the Lower Devonian placoderm sandstone from Podlazie Hill (Holy Cross Mountains, central Poland)2014Ingår i: Geological Quarterly, ISSN 1641-7291, E-ISSN 2082-5099, Vol. 58, nr 4, s. 795-806Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The placoderm sandstone (Emsian, Holy Cross Mountains) exposed in the abandoned quarry at Podlazie Hill was revisited and excavated during fieldwork conducted in 2011–2013. Bone-bearing breccias were studied in details for the first time at this site and subjected to taphonomic analysis. Vertebrate remains are dominated by heterostracans, while true placoderm compose less than 20% of the total vertebrate assemblage. The high degree of fragmentation of the bones and low degree of abrasion indicate that the remains were reworked and transported be fore final burial. This is consistent with the mixed character of the bone accumulations, which comprise both open-shelf forms (acanthodians, chondrichthyans) as well as those related to marginal-marine environments (placoderms and sarcopterygians). The bone-bearing succession has been subdivided into five depositional facies attributed to a coastal lagoon influenced by stormy, possibly tidal conditions. The occurrence of the invertebrate trace fossil Ilmenichnus sp. accompanied by Lockeia and Monomorphichnus supports this interpretation.

  • 279. Szrek, Piotr
    et al.
    Salwa, Sylwester
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    A plant-root system in the Lower Devonian of the Holy Cross Mountains, Poland2015Ingår i: Estonian journal of earth sciences, ISSN 1736-4728, E-ISSN 1736-7557, Vol. 64, nr 1, s. 95-98Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The depositional environment of the Lower Devonian of the Holy Cross Mountains has only been studied and interpreted in part, particularly for the lower portion of the profile. Recent fieldwork findings suggest a considerable change with regard to earlier hypotheses. Apart from the sedimentological observations that indicate marginal marine and very shallow-water conditions, horizons with plant-root traces and layers interpreted as palaeosols showing different stages of pedogenesis have been documented. The presence of palaeosols in some areas of the Holy Cross Mountains is the first direct evidence for the existence of terrestrial conditions during the Lower Devonian in this area. This plant-root system is one of the oldest fossil records ever described globally.

  • 280.
    Szrek, Piotr
    et al.
    Polish Geol Inst, Natl Res Inst, Rakowiecka 4 St, PL-00075 Warsaw, Poland. Polish Geol Inst, Natl Res Inst, Holy Cross Mt Branch, Zgoda 21 St, PL-00075 Kielce, Poland..
    Salwa, Sylwester
    Holy Cross Mountains Branch of the Polish Geological Institute—National Research Institute, Zgoda 21 Street, 00-075 Kielce, Poland.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Dec, Marek
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Uchman, Alfred
    Jagiellonian Univ, Inst Geol Sci, Oleandry 2a, PL-30063 Krakow, Poland..
    A glimpse of a fish face: An exceptional fish feeding trace fossil from the Lower Devonian of the Holy Cross Mountains, Poland2016Ingår i: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 454, s. 113-124Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    An exceptionally well-preserved assemblage of numerous invertebrate and vertebrate trace fossils is described from the Lower Devonian of the Holy Cross Mountains, southern Poland. Two trace-bearing horizons occur in the shallow-marine sequence that is exposed in a small outcrop near Ujazd village. One of the trace fossils is preserved as a bilobate, generally elliptical, epichnial pit is described as Osculichnus tarnowskae isp. nov. and interpreted as a unique example of praedichnia. Neoichnologic experiments and observations indicate that the ichnogenus Osculichnus was produced by feeding fish. The fish producing O. tarnowskae probably hunted bivalves, polychaetes and arthropods, which are represented by invertebrate trace fossils in the same horizons. The overall shape and morphological details of O. tarnowskae suggest that it was made by a lungfish broadly similar to Dipnorhynchus. The trace provides the first direct evidence for Devonian lungfish feeding behaviour, as well as the first record of three-dimensional soft-tissue morphology of the snout area of an Emsian representative of this group. The trace fossils from Ujazd provide new insight into the palaeoecology and taphonomy of the Lower Devonian of the Holy Cross Mountains.

  • 281.
    Talanda, Mateusz
    et al.
    Univ Warsaw, Fac Biol, Dept Paleobiol & Evolut, Biol & Chem Res Ctr, Zwirki & Wigury 101, PL-02089 Warsaw, Poland..
    Bajdek, Piotr
    Aleja Najswietszej Maryi Panny 20-20A, PL-42200 Czestochowa, Poland..
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Sulej, Tomasz
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland..
    Upper Triassic freshwater oncoids from Silesia (southern Poland) and their microfossil biota2017Ingår i: Neues Jahrbuch für Geologie und Palaontologie - Abhandlungen, ISSN 0077-7749, Vol. 284, nr 1, s. 43-56Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Oncoids are rare components of Keuper sediments across Europe. The exceptions are localities linked to the Upper Triassic "Wozniki Limestone" (formally Limestone Member from Wozniki) in Silesia, southern Poland. Numerous oncoids occur in breccia-like deposits in the Lipie Slaskie clay pit at Lisowice. The oncoid-bearing level is underlying by organic-rich carbonaceous mudstone and siltstone and covered by non-carbonaceous sandstone and grey wacke sandstone-mudstone heterolithic deposits. The oncoids are of various shapes and are built by agglutinated or skeletal stromatolites composed of a rhythmically grown dendroid micropeloidal framework. The agglutinated stromatolites are poor in microfabrics. The oncoids consist of a smooth or granular outer part and distinct core (carbonate, carbon-rich or phosphate), which may be a fossil (bivalve shell, wood fragment, charcoal piece, carbon-rich coprolite or hone fragment). Dark laminae of the cortex are carbonate-rich, whereas the light ones are silica-rich. They exhibit remains of bacterial/cyanobacterial filaments, as well as some rare and not well-discernible palynomorphs. Ostracods (cf. Darwinula sp.), small fragments of vertebrate bones (mainly fish remains), fragments of wood, plant cuticles and fragments of unionoid bivalves are associated with the oncoid accumulations. Thus, they may have been formed in a shallow freshwater environment and were buried by rapid flood events or mud runoff.

  • 282. Telldahl, Ylva
    et al.
    Svensson, Emma
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Götherström, Anders
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för ekologi och genetik, Evolutionsbiologi.
    Storå, Jan
    Typing Late Prehistoric Cows and Bulls: Osteology and Genetics of Cattle at the Eketorp Ringfort on the Öland Island in Sweden2011Ingår i: PLOS ONE, ISSN 1932-6203, Vol. 6, nr 6, s. e20748-Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Human management of livestock and the presence of different breeds have been discussed in archaeozoology and animal breeding. Traditionally osteometrics has been the main tool in addressing these questions. We combine osteometrics with molecular sex identifications of 104 of 340 morphometrically analysed bones in order to investigate the use of cattle at the Eketorp ringfort on the Oland island in Sweden. The fort is dated to 300-1220/50 A. D., revealing three different building phases. In order to investigate specific patterns and shifts through time in the use of cattle the genetic data is evaluated in relation to osteometric patterns and occurrence of pathologies on cattle metapodia. Males were genotyped for a Y-chromosomal SNP in UTY19 that separates the two major haplogroups, Y1 and Y2, in taurine cattle. A subset of the samples were also genotyped for one SNP involved in coat coloration (MC1R), one SNP putatively involved in resistance to cattle plague (TLR4), and one SNP in intron 5 of the IGF-1 gene that has been associated to size and reproduction. The results of the molecular analyses confirm that the skeletal assemblage from Eketorp is dominated by skeletal elements from females, which implies that dairying was important. Pathological lesions on the metapodia were classified into two groups; those associated with the use as draught animals and those lesions without a similar aetiology. The results show that while bulls both exhibit draught related lesions and other types of lesions, cows exhibit other types of lesions. Interestingly, a few elements from females exhibit draught related lesions. We conclude that this reflects the different use of adult female and male cattle. Although we note some variation in the use of cattle at Eketorp between Iron Age and Medieval time we have found little evidence for the use of different types of animals for specific purposes. The use of specific (genetic) breeds seems to be a phenomenon that developed later than the Eketorp settlement.

  • 283.
    Toljagic, Olja
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för biologisk grundutbildning.
    Enigmatic basal archosauromorph from the Late Triassic of Poland2012Självständigt arbete på avancerad nivå (masterexamen), 20 poäng / 30 hpStudentuppsats (Examensarbete)
    Abstract [en]

    Choristodera, a lineage of basal archosauromorphs (Reptilia: Diapsida), first appeared in Early/Middle Jurassic (possibly Late Triassic; approximately 201 million years ago) and extended all the way into early Miocene (approximately 23 million years ago). Choristoderans are the only group of more basal archosauromorphs that survived after the Jurassic period, along with Archosauriformes (a more derived group of Archosauromorphs). The time of origin of the lineage is still speculative and preceded with long ghost lineages, a timespan when the animals were known to be alive, but are not represented in the fossil record. Unresolved phylogenetic position and inter-relationships, along with limited information about such an important group of early semi-aquatic reptiles, set choristodera in the focus of tetrapod evolution. In order to add information to gaps in the fossil records during the long temporal range of the group, new discoveries and descriptions of early choristoderan taxa are needed. Here, a description of long bones of a choristodere-like animal from the Late Triassic of Poland is presented adding information to the basal archosauromorpha and possibly shifting back the time of choristodera origin. Furthermore, bone histology analysis was conducted for the first time for choristodera, adding new information to the group. The other description of postcranial material of a possible early choristodere from Storrs et al. (1996) sets the origin of the group to Latest Triassic (Rhaetian, approximately 201 Mya). Description of newly discovered fossil material along with the histology sections of such an important group of tetrapods that are choristoders is of great significance, not only for the Triassic tetrapod communities, but for tetrapod evolution, development, ecology and life history in general.

  • 284. Trinajstic, Kate
    et al.
    Sanchez, Sophie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Dupret, Vincent
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Tafforeau, Paul
    Long, John
    Young, Gavin
    Senden, Tim
    Boisvert, Catherine
    Power, Nicola
    Ahlberg, Per Erik
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Fossil Musculature of the Most Primitive Jawed Vertebrates2013Ingår i: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 341, nr 6142, s. 160-164Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The transition from jawless to jawed vertebrates (gnathostomes) resulted in the reconfiguration of the muscles and skeleton of the head, including the creation of a separate shoulder girdle with distinct neck muscles. We describe here the only known examples of preserved musculature from placoderms (extinct armored fishes), the phylogenetically most basal jawed vertebrates. Placoderms possess a regionalized muscular anatomy that differs radically from the musculature of extant sharks, which is often viewed as primitive for gnathostomes. The placoderm data suggest that neck musculature evolved together with a dermal joint between skull and shoulder girdle, not as part of a broadly flexible neck as in sharks, and that transverse abdominal muscles are an innovation of gnathostomes rather than of tetrapods.

  • 285.
    Varshney, Gaurav K.
    et al.
    NHGRI, Dev Genom Sect, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA.;Oklahoma Med Res Fdn, Funct & Chem Genom Program, 825 NE 13th St, Oklahoma City, OK 73104 USA..
    Carrington, Blake
    NHGRI, Zebrafish Core, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Pei, Wuhong
    NHGRI, Dev Genom Sect, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Bishop, Kevin
    NHGRI, Zebrafish Core, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Chen, Zelin
    NHGRI, Dev Genom Sect, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Fan, Chunxin
    Shanghai Ocean Univ, Minist Educ, Key Lab Explorat & Utilizat Aquat Genet Resource, Shanghai, Peoples R China..
    Xu, Lisha
    NHGRI, Dev Genom Sect, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Jones, Marypat
    NHGRI, Canc Genet & Comparat Genom Branch, NIH, Bethesda, MD 20892 USA..
    LaFave, Matthew C.
    NHGRI, Dev Genom Sect, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA.;Synthet Genom, San Diego, CA USA..
    Ledin, Johan
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab.
    Sood, Raman
    NHGRI, Zebrafish Core, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    Burgess, Shawn M.
    NHGRI, Dev Genom Sect, Translat & Funct Genom Branch, NIH, Bethesda, MD 20892 USA..
    A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish2016Ingår i: Nature Protocols, ISSN 1754-2189, E-ISSN 1750-2799, Vol. 11, nr 12, s. 2357-2375Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The zebrafish is a popular model organism for studying development and disease, and genetically modified zebrafish provide an essential tool for functional genomic studies. Numerous publications have demonstrated the efficacy of gene targeting in zebrafish using CRISPR/Cas9, and they have included descriptions of a variety of tools and methods for guide RNA synthesis and mutant identification. However, most of the published techniques are not readily scalable to increase throughput. We recently described a CRISPR/Cas9-based high-throughput mutagenesis and phenotyping pipeline in zebrafish. Here, we present a complete workflow for this pipeline, including target selection; cloning-free single-guide RNA (sgRNA) synthesis; microinjection; validation of the target-specific activity of the sgRNAs; founder screening to identify germline-transmitting mutations by fluorescence PCR; determination of the exact lesion by Sanger or next-generation sequencing (including software for analysis); and genotyping in the F-1 or subsequent generations. Using these methods, sgRNAs can be evaluated in 3 d, zebrafish germline-transmitting mutations can be identified within 3 months and stable lines can be established within 6 months. Realistically, two researchers can target tens to hundreds of genes per year using this protocol.

  • 286. Varshney, Gaurav K.
    et al.
    Pei, Wuhong
    LaFave, Matthew C.
    Idol, Jennifer
    Xu, Lisha
    Gallardo, Viviana
    Carrington, Blake
    Bishop, Kevin
    Jones, MaryPat
    Li, Mingyu
    Harper, Ursula
    Huang, Sunny C.
    Prakash, Anupam
    Chen, Wenbiao
    Sood, Raman
    Ledin, Johan
    Uppsala universitet, Science for Life Laboratory, SciLifeLab. Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Burgess, Shawn M.
    High-throughput gene targeting and phenotyping in zebrafish using CRISPR/Cas92015Ingår i: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 25, nr 7, s. 1030-1042Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The use of CRISPR/Cas9 as a genome-editing tool in various model organisms has radically changed targeted mutagenesis. Here, we present a high-throughput targeted mutagenesis pipeline using CRISPR/Cas9 technology in zebrafish that will make possible both saturation mutagenesis of the genome and large-scale phenotyping efforts. We describe a cloning-free single-guide RNA (sgRNA) synthesis, coupled with streamlined mutant identification methods utilizing fluorescent PCR and multiplexed, high-throughput sequencing. We report germline transmission data from 162 loci targeting 83 genes in the zebrafish genome, in which we obtained a 99% success rate for generating mutations and an average germline transmission rate of 28%. We verified 678 unique alleles from 58 genes by high-throughput sequencing. We demonstrate that our method can be used for efficient multiplexed gene targeting. We also demonstrate that phenotyping can be done in the F-1 generation by inbreeding two injected founder fish, significantly reducing animal husbandry and time. This study compares germline transmission data from CRISPR/Cas9 with those of TALENs and ZFNs and shows that efficiency of CRISPR/Cas9 is sixfold more efficient than other techniques. We show that the majority of published "rules" for efficient sgRNA design do not effectively predict germline transmission rates in zebrafish, with the exception of a GG or GA dinucleotide genomic match at the 5' end of the sgRNA. Finally, we show that predicted off-target mutagenesis is of low concern for in vivo genetic studies.

  • 287.
    Vaskaninova, Valeria
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Charles Univ Prague, Fac Sci, Inst Geol & Palaeontol, Prague, Czech Republic..
    Ahlberg, Per E.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Unique diversity of acanthothoracid placoderms (basal jawed vertebrates) in the Early Devonian of the Prague Basin, Czech Republic: A new look at Radotina and Holopetalichthys2017Ingår i: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, nr 4, artikel-id e0174794Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The taxonomy of Early Devonian placoderm material from the Lochkovian and Pragian of the Prague basin, previously attributed to the genera Radotina and Holopetalichthys, is revised. The Pragian species Radotina tesselata Gross 1958 shares detailed similarities with the holotype of the Lochkovian Radotina kosorensis Gross 1950, which is also the holotype of the genus; the assignation of both species to Radotina is supported. However, the Lochkovian material previously attributed to Radotina kosorensis also contains two unrecognised taxa, distinguishable from Radotina at the generic level: these are here named Tlamaspis and Sudaspis. The disputed genus Holopetalichthys, synonymised with Radotina by some previous authors, is shown to be valid. Furthermore, whereas Radotina, Tlamaspis and Sudaspis can all be assigned to the group Acanthothoracii, on the basis of several features including possession of a projecting prenasal region of the endocranium, Holopetalichthys lacks such a region and is probably not an acanthothoracid. Skull roof patterns and other aspects of morphology vary greatly between these taxa. Radotina has a substantially tesselated skull roof, whereas the skull roofs of Tlamaspis and Holopetalichthys appear to lack tesserae altogether. Tlamaspis has an extremely elongated facial region and appears to lack a premedian plate. Sudaspis has a long prenasal region, but unlike Tlamaspis the postnasal face is not elongated. Past descriptions of the braincase of ' Radotina' and the skull roofs of ' Radotina' and ' Holopetalichthys' incorporate data from more than one taxon, giving rise to spurious characterisations including an apparently extreme degree of skull roof variability. These descriptions should all be disregarded.

  • 288.
    Voeten, Dennis F. A. E.
    et al.
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS-40220, F-38043 Grenoble, France.;Palacky Univ, Dept Zool, 17 Listopadu 50, Olomouc 77146, Czech Republic.;Palacky Univ, Lab Ornithol, 17 Listopadu 50, Olomouc 77146, Czech Republic..
    Cubo, Jorge
    Sorbonne Univ, CNRS INSU, Inst Sci Terre Paris, ISTeP UMR 7193, F-75005 Paris, France..
    de Margerie, Emmanuel
    Univ Rennes 1, Univ Caen Normandie, CNRS, Lab Ethol Anim & Humaine, 263 Ave Gen Leclerc, F-35042 Rennes, France..
    Roeper, Martin
    Burgermeister Muller Museum, Bahnhofstr 8, D-91807 Solnhofen, Germany.;Bayerische Staatssammlung Palaontol & Geol, Richard Wagner Str 10, D-80333 Munich, Germany..
    Beyrand, Vincent
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS-40220, F-38043 Grenoble, France.;Palacky Univ, Dept Zool, 17 Listopadu 50, Olomouc 77146, Czech Republic.;Palacky Univ, Lab Ornithol, 17 Listopadu 50, Olomouc 77146, Czech Republic..
    Bures, Stanislav
    Palacky Univ, Dept Zool, 17 Listopadu 50, Olomouc 77146, Czech Republic.;Palacky Univ, Lab Ornithol, 17 Listopadu 50, Olomouc 77146, Czech Republic..
    Tafforeau, Paul
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS-40220, F-38043 Grenoble, France..
    Sanchez, Sophie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi. Uppsala universitet, Science for Life Laboratory, SciLifeLab. European Synchrotron Radiat Facil, 71 Ave Martyrs,CS-40220, F-38043 Grenoble, France.
    Wing bone geometry reveals active flight in Archaeopteryx2018Ingår i: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 9, artikel-id 923Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Archaeopteryx is an iconic fossil taxon with feathered wings from the Late Jurassic of Germany that occupies a crucial position for understanding the early evolution of avian flight. After over 150 years of study, its mosaic anatomy unifying characters of both non-flying dinosaurs and flying birds has remained challenging to interpret in a locomotory context. Here, we compare new data from three Archaeopteryx specimens obtained through phase-contrast synchrotron microtomography to a representative sample of archosaurs employing a diverse array of locomotory strategies. Our analyses reveal that the architecture of Archaeopteryx's wing bones consistently exhibits a combination of cross-sectional geometric properties uniquely shared with volant birds, particularly those occasionally utilising short-distance flapping. We therefore interpret that Archaeopteryx actively employed wing flapping to take to the air through a more anterodorsally posteroventrally oriented flight stroke than used by modern birds. This unexpected outcome implies that avian powered flight must have originated before the latest Jurassic.

  • 289.
    Waldmann, Laura
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Haitina, Tatjana
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Characterization of synovial joint progenitor cells in zebrafish2017Ingår i: Characterization of synovial joint progenitor cells in zebrafish, 2017, s. 26-Konferensbidrag (Refereegranskat)
  • 290.
    Wretman, Lovisa
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Blom, Henning
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Kear, Benjamin P.
    Uppsala universitet, Enheten för musik och museer, Evolutionsmuseet.
    Resolution of the Early Jurassic actinopterygian fish Pachycormus and a dispersal hypothesis for Pachycormiformes2016Ingår i: Journal of Vertebrate Paleontology, ISSN 0272-4634, E-ISSN 1937-2809, Vol. 36, nr 5, artikel-id e1206022Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The Early Jurassic (Toarcian) actinopterygian Pachycormus is a basal taxon within Pachycormiformes, a Mesozoic marine neopterygian radiation that evolved an extreme ecomorph divergence between hyperspecialized billfish-like' macrocarnivores and gigantic suspension feeders, including the largest fish of all time. Current phylogenies place Pachycormus as an early member of the suspension-feeding lineage; however, species disparity renders character states uncertain and potential exists for considerable intraspecific variability. Given its importance for resolution of pachycormiform phylogenetic topology, we comprehensively reassessed Pachycormus fossils housed in collections across Europe and found that the proportional traits traditionally used to discriminate between species are actually consistent with an ontogenetic size morphocline. Our cladistic analyses further show that the monotypic senior synonym, Pachycormus macropterus, is a wildcard that manifests a mosaic of transitional states. This has significant implications for hypothesized Toarcian marine vertebrate provincialism because P. macropterus had a ubiquitous Boreal Tethyan distribution. Moreover, our tree-based palaeobiogeographical optimizations infer that the western Tethyan region was a pachycormiform dissemination center, with global dispersals occurring through transoceanic migration and invasion of epeiric basins.Citation for this article: Wretman, L., H. Blom, and B. P. Kear. 2016. Resolution of the Early Jurassic actinopterygian fish Pachycormus and a dispersal hypothesis for Pachycormiformes. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1206022.

  • 291.
    Wretman, Lovisa
    et al.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Kear, Benjamin P.
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Geovetenskapliga sektionen, Institutionen för geovetenskaper, Paleobiologi.
    Bite marks on an ichthyodectiform fish from Australia: possible evidence of trophic interaction in an Early Cretaceous marine ecosystem2014Ingår i: Alcheringa, ISSN 0311-5518, E-ISSN 1752-0754, Vol. 38, nr 2, s. 170-176Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A well-preserved fish skull from late Albian deposits of the Allaru Mudstone near Richmond in Queensland displays a conspicuous V-shaped pattern of indentations, punctures and depression fractures consistent with a vertebrate bite trace. This is the first direct evidence of trophic interaction between vertebrates within an Early Cretaceous marine ecosystem from Australia. The specimen is taxonomically referable to the largebodied (ca 1m snouttail length) ichthyodectiform Cooyoo australis, but the size and spacing of the tooth marks is incompatible with attack by a conspecific individual. The lack of osseous growths concordant with healing also suggests that the bite occurred shortly before or after the animals death. Comparison with the dentitions of other coeval vertebrates indicates compatible tooth arrangements in longirostrine amniote predators such as polycotylid plesiosaurians, ornithocheiroid pterosaurs and especially the ichthyosaurian Platypterygius. The implications of this as a potential predatorprey association are that Early Cretaceous actinopterygians occupied middle-level trophic niches and were in turn consumed by higher-level amniote carnivores, similar to many extant marine vertebrate communities of today.

  • 292.
    Xie, Meng
    et al.
    Karolinska Inst, Dept Physiol & Pharmacol, Stockholm.
    Gol'din, Pavel
    Stockholm Univ, Stockholm.
    Estsfa, Jordi
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi.
    Li, Lei
    Karolinska Inst, Dept Physiol & Pharmacol, Stockholm.
    Arregui, Irene Linares
    KTH, Dept Solid Mech, Stockholm.
    Gasser, Christian
    KTH, Dept Solid Mech, Stockholm.
    Medvedeva, Ekaterina
    Sechenov Med Univ, Moscow.
    Svetlana, Kotova
    Sechenov Med Univ, Moscow.
    Timashev, Peter
    Sechenov Med Univ, Moscow.
    Adameyko, Igor
    Karolinska Inst, Dept Physiol & Pharmacol, Stockholm.
    Eriksson, Anders
    KTH, Dept Mech, Stockholm.
    Sanchez, Sophie
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Chagin, Andrei
    Karolinska Inst, Dept Physiol & Pharmacol, Stockholm.
    Evolutional Separation of Epiphyseal and Articular Cartilage is a Bone Adaptation to Terrestrial Growth.2017Ingår i: Journal of Bone and Mineral Research, ISSN 0884-0431, E-ISSN 1523-4681, Vol. 32, nr S1, s. S328-S328, artikel-id Meeting Abstract: MO0490Artikel i tidskrift (Övrigt vetenskapligt)
  • 293. Xing, Li-Da
    et al.
    Niedzwiedzki, Grzegorz
    Uppsala universitet, Teknisk-naturvetenskapliga vetenskapsområdet, Biologiska sektionen, Institutionen för organismbiologi, Evolution och utvecklingsbiologi.
    Lockley, Martin G.
    Zhang, Jian-Ping
    Cai, Xiong-Fei
    Persons IV, W. Scott
    Ye, Yong
    Asianopodus-type footprints from the Hekou Group of Honggu District, Lanzhou City, Gansu, China and the “heel” of large theropod tracks2014Ingår i: Palaeoworld, ISSN 1871-174X, Vol. 23, nr 3-4, s. 304-313Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    An increasing number of dinosaur tracksites have been reported from the Cretaceous Hekou Group deposits of the Lanzhou-Minhe Basin in theGansu Province region. These include small sites such as the Huazhuang tracksite, from the Honggu District reported here, the Zhongpu tracksitewith multiple track levels but few well-preserved tracks, other small tracksites currently under investigation, and the large and diverse LiujixiaNational Dinosaur Geopark site at Yanguoxia, where intensive study is ongoing. Collectively these sites reveal that ichnofaunas in the HekouGroup are widespread and diverse. The Huazhuang tracksite yields a small assemblage of moderately well-preserved theropod tracks assigned toAsianopodus. This is the first report of Asianopodus from the Hekou Group. Huazhuang Asianopodus belongs to the Eubrontes morphotype. Thelarge theropod tracks from Lanzhou-Minhe Basin were left by large theropod trackmakers with the same general foot morphology. The specimensare described in detail and compared with other theropod track morphotypes from the Lower Cretaceous of China and elsewhere. In general,although the metatarsophalangeal pads of some Jurassic Eubrontes-type tracks are aligned with the axis of digit III, this feature appears mostcommon in the Early Cretaceous theropod (Eubrontes-type) tracks.

  • 294.
    Zaton, Michal