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  • 201.
    Oliveira, Marta Bastos
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer and Vascular Biology.
    Liedholm, Simon Eckerström
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Lopez, Jordi Estefa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Lochte, Annalena A.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Pazio, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Martin, Jesus Pena
    Uppsala University.
    Mörch, Patrik Rödin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Salakka, Seela
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    York, Julia
    Uppsala University.
    Yoshimoto, Andrew
    Uppsala University.
    Janssen, Ralf
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Expression of arthropod distal limb-patterning genes in the onychophoran Euperipatoides kanangrensis2014In: Development, Genes and Evolution, ISSN 0949-944X, E-ISSN 1432-041X, Vol. 224, no 2, p. 87-96Article in journal (Refereed)
    Abstract [en]

    A current hypothesis states that the ancestral limb of arthropods is composed of only two segments. The proximal segment represents the main part of the modern leg, and the distal segment represents the tarsus and claw of the modern leg. If the distal part of the limb is an ancestral feature, one would expect conserved regulatory gene networks acting in distal limb development in all arthropods and possibly even their sister group, the onychophorans. We investigated the expression patterns of six genes known to function during insect distal limb development in the onychophoran Euperipatoides kanangrensis, i.e., clawless (cll), aristaless (al), spineless (ss), zinc finger homeodomain 2 (zfh2), rotund (rn), and Lim1. We find that all investigated genes are expressed in at least some of the onychophoran limbs. The expression patterns of most of these genes, however, display crucial differences to the known insect patterns. The results of this study question the hypothesis of conserved distal limb evolution in arthropods and highlight the need for further studies on arthropod limb development.

  • 202.
    Onsbring Gustafson, Henning
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Haitina, Tatjana
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Divergent expression patterns of teleost specific gene duplicates during the development of craniofacial tendons and ligaments2015Conference paper (Refereed)
  • 203. Owocki, K.
    et al.
    Niedźwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sennikov, A. G.
    Golubev, V. K.
    Janiszewska, K.
    Sulej, T.
    Upper permian vertebrate coprolites from Vyazniki and Gorokhovets, Vyatkian regional stage, Russian platform2013In: Palaios, ISSN 0883-1351, E-ISSN 1938-5323, Vol. 27, no 11-12, p. 867-877Article in journal (Refereed)
    Abstract [en]

    Numerous coprolites have been found in the Vyazniki and Gorokhovets localities of European Russia. Five identified coprolite-bearing horizons occur in the upper Permian deposits of the Vyatkian Regional Stage. Coprolites were collected from mudstone with a coprolite breccia-like layer and also from intraformational conglomerates that were deposited in a floodplain and overbank environment. Two coprolite morphotypes (A and B) are recognized from size and shape analysis of 32 specimens. Morphotype A has long, nonsegmented feces. Smaller, cylindrical or tubular-shaped coprolites of morphotype B are commonly segmented. SEM images of the coprolite matrix show spheres and thin-walled vesicles with diameters 0.5-4 μm. Electron Micro Probe (EMP) analyses of polished thin sections show microcrystalline carbonate-fluoride-bearing calcium phosphate with small amounts of calcium replaced in the crystal lattice. Optical microscopy and EMP investigations show that iron and manganese oxides are responsible for elevated iron and manganese concentrations in the bulk mass of coprolites. Other metals (V, Ni) can be associated with oxides forming spheroids with diameters 3-10 μm. REEs (rare earth elements, U, and other trace element concentrations suggest significant eolian sediment input to the burial environment of the coprolites. The scats contain fish scales and bones of tetrapods (amphibians or reptiles). In one large-sized coprolite, a small fragment of therapsid bone was also found. Both morphotypes are matched to carnivorous taxa within the Archosaurus rossicus zone of the Eastern Europe. The size and shape of the best-preserved specimens suggest that they were possibly produced by a large therapsid, anthracosaur, or early archosauromorph predator.

  • 204.
    Pan, Zhaohui
    et al.
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Beijing 100049, Peoples R China..
    Zhu, Min
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.;Univ Chinese Acad Sci, Beijing 100049, Peoples R China..
    Zhu, You-an
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China.
    Jia, Liantao
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, POB 643, Beijing 100044, Peoples R China..
    A new antiarch placoderm from the Emsian (Early Devonian) of Wuding, Yunnan, China2018In: Alcheringa, ISSN 0311-5518, E-ISSN 1752-0754, Vol. 42, no 1, p. 10-21Article in journal (Refereed)
    Abstract [en]

    Wufengshania magniforaminis, a new genus and species of the Euantiarcha (Placodermi: Antiarcha), is described from the late Emsian (Early Devonian) of Wuding, Yunnan, southwestern China. The referred specimens were three-dimensionally preserved in black shales, allowing a high-resolution computed tomography reconstruction of anatomical details. The new euantiarch is characterized by a large orbital fenestra, an arched exoskeletal band around the orbital fenestra and a developed obtected nuchal area of the skull roof. Maximum parsimony analysis, using a revised data-set of antiarchs with 44 taxa and 66 characters, resolves Wufengshania gen. nov. as a member of the Bothriolepididae, which is characterized by the presence of the infraorbital sensory canal diverging on the lateral plate, and the nuchal plate with orbital facets. New analysis supports a sister group relationship between Dianolepis and the Bothriolepididae. Luquanolepis, a coeval euantiarch from the neighboring site of the new form, is referred to the Asterolepidoidei and represents the basalmost and earliest member of the Asterolepidoidei.

  • 205.
    Pardo, Jason D.
    et al.
    Univ Calgary, Dept Comparat Biol & Expt Med, 3330 Hosp Dr, Calgary, AB T2N 4N1, Canada..
    Szostakiwskyj, Matt
    Univ Calgary, Dept Biol Sci, 2500 Univ Dr, Calgary, AB T2N 1N4, Canada..
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Anderson, Jason S.
    Univ Calgary, Dept Comparat Biol & Expt Med, 3330 Hosp Dr, Calgary, AB T2N 4N1, Canada..
    Hidden morphological diversity among early tetrapods2017In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 546, no 7660, p. 642-645Article in journal (Refereed)
    Abstract [en]

    Phylogenetic analysis of early tetrapod evolution has resulted in a consensus across diverse data sets(1-3) in which the tetrapod stem group is a relatively homogenous collection of medium-to large-sized animals showing a progressive loss of 'fish' characters as they become increasingly terrestrial(4,5), whereas the crown group demonstrates marked morphological diversity and disparity(6). The oldest fossil attributed to the tetrapod crown group is the highly specialized astopod Lethiscus stocki(7,8), which shows a small size, extreme axial elongation, loss of limbs, spool-shaped vertebral centra, and a skull with reduced centres of ossification, in common with an otherwise disparate group of small animals known as lepospondyls. Here we use micro-computed tomography of the only known specimen of Lethiscus to provide new information that strongly challenges this consensus. Digital dissection reveals extremely primitive cranial morphology, including a spiracular notch, a large remnant of the notochord within the braincase, an open ventral cranial fissure, an anteriorly restricted parasphenoid element, and Meckelian ossifications. The braincase is elongate and lies atop a dorsally projecting septum of the parasphenoid bone, similar to stem tetrapods such as embolomeres. This morphology is consistent in a second astopod, Coloraderpeton, although the details differ. Phylogenetic analysis, including critical new braincase data, places astopods deep on the tetrapod stem, whereas another major lepospondyl lineage is displaced into the amniotes. These results show that stem group tetrapods were much more diverse in their body plans than previously thought. Our study requires a change in commonly used calibration dates for molecular analyses, and emphasizes the importance of character sampling for early tetrapod evolutionary relationships.

  • 206.
    Piechowski, Rafal
    et al.
    Polish Acad Sci, Inst Paleobiol, Warsaw, Poland;Univ Warsaw, Dept Palaeobiol & Evolut, Biol & Chem Res Ctr, Fac Biol, Warsaw, Poland.
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Talanda, Mateusz
    Univ Warsaw, Dept Palaeobiol & Evolut, Biol & Chem Res Ctr, Fac Biol, Warsaw, Poland.
    Unexpected bird-like features and high intraspecific variation in the braincase of the Triassic relative of dinosaurs2019In: Historical Biology, ISSN 0891-2963, E-ISSN 1029-2381, Vol. 31, no 8, p. 1065-1081Article in journal (Refereed)
    Abstract [en]

    Silesaurus opolensis Dzik, 2003 from the Late Triassic (late Carnian) of Poland is a key taxon for understanding the evolution of early dinosaurs. High intraspecific variation observed in the S. opolensis braincase brings caution in taxonomic and diversity studies of early dinosauromorphs. The external and internal osteology of three almost complete braincases of S. opolensis show that this taxon shares several similarities with other early dinosauriforms, which supports a close relationship among these forms. However, the paroccipital processes of S. opolensis are directed ventrally like in birds, reaching the level of the ventral margin of the basioccipital condyle. In dinosauromorphs, these processes usually have an almost horizontal orientation (presumed to be the plesiomorphic condition). Modifications observed in birds and S. opolensis have resulted in the dorsoventral expansion of M. complexus and M. depressor mandibulae, which occupy the dorsolateral part of the posterior side of the skull. In adult birds, these muscles act strongly on the initial upstroke of the head during drinking. Therefore, the inferred condition of these muscles in S. opolensis may imply that Silesauridae evolved toward bird-like feeding behaviour.

  • 207. Pierce, Stephanie E.
    et al.
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Hutchinson, John R.
    Molnar, Julia L.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tafforeau, Paul
    Clack, Jennifer A.
    Vertebral architecture in the earliest stem tetrapods2013In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 494, no 7436, p. 226-229Article in journal (Refereed)
    Abstract [en]

    The construction of the vertebral column has been used as a key anatomical character in defining and diagnosing early tetrapod groups(1). Rhachitomous vertebrae(2)-in which there is a dorsally placed neural arch and spine, an anteroventially placed intercentrum and paired, posterodorsally placed pleurocentra have long been considered the ancestral morphology for tetrapods(1,3-6). Nonetheless, very little is known about vertebral anatomy in the earliest stem tetrapods, because most specimens remain trapped in surrounding matrix, obscuring Important anatomical features(7-9). Here we describe the three-dimensional vertebral architecture of the Late Devonian stem tetrapod Ichthyostega using propagation phase-contrast X-ray synchrotron. microtomography. Our scans reveal a diverse array of new morphological, and associated developmental and functional, characteristics, including a possible posterior-to-anterior vertebral ossification sequence and the first evolutionary appearance of ossified sternal elements. One of the most intriguing features relates to the positional relationships between the vertebral elements, with the pleurocentra being unexpectedly sutured or fused to the intercentra that directly succeed them, indicating a 'reverse' rhachitomous design(10). Comparison of Ichthyostega with two other stem tetrapods, Acanthostegi and Pederpess, shows that reverse rhachitomous vertebrae may be the ancestral condition for limbed vertebrates. This study fundamentally revises our current understanding' of vertebral column evolution in the earliest tetrapods and raises questions about the presumed vertebral architecture of tetrapodomorph fish(12,13) and later, more crownward, tetrapods.

  • 208.
    Pinto da Silva, André
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Lisbon, CE3c, Fac Ciencias, Lisbon, Portugal..
    Curveira-Santos, Gonçalo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Lisbon, CE3c, Fac Ciencias, Lisbon, Portugal..
    Kilshaw, Kerry
    Univ Oxford, Recanti Kaplan Ctr, Wildlife Conservat Res Unit, Dept Zool, Tubney, Oxon, England..
    Newman, Chris
    Univ Oxford, Recanti Kaplan Ctr, Wildlife Conservat Res Unit, Dept Zool, Tubney, Oxon, England..
    Macdonald, David W.
    Univ Oxford, Recanti Kaplan Ctr, Wildlife Conservat Res Unit, Dept Zool, Tubney, Oxon, England..
    Simões, Luciana G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Univ Lisbon, CE3c, Fac Ciencias, Lisbon, Portugal..
    Rosalino, Luis M.
    Univ Lisbon, CE3c, Fac Ciencias, Lisbon, Portugal.;Univ Aveiro, CESAM, Aveiro, Portugal.;Univ Aveiro, Dept Biol, Aveiro, Portugal..
    Climate and anthropogenic factors determine site occupancy in Scotland's Northern-range badger population: implications of context-dependent responses under environmental change2017In: Diversity & distributions: A journal of biological invasions and biodiversity, ISSN 1366-9516, E-ISSN 1472-4642, Vol. 23, no 6, p. 627-639Article in journal (Refereed)
    Abstract [en]

    Aim: In the light of human-induced rapid environmental change (HIREC), populations are exposed to ever-greater bioclimatic stress at the edge of a species' historic range. The distribution dynamics of European badgers (Meles meles) at their southern edge are linked tightly to climatic variability. We contribute critical data on how climatic context and local factors determine site occupancy in a northern-range population.

    Location: Eleven study areas (averaging similar to 21.3km(2)) spread over similar to 50,000km(2) in Northern Scotland.

    Methods: While accounting for heterogeneous detectability, we applied single-season occupancy models to broad-scale camera-trapping data (168 stations) to evaluate how Autumn-Winter weather conditions interact with land-cover type (including agricultural land) and human disturbance to determine badger occupancy.

    Results: Mean minimum daily winter temperature and elevation influenced inter-site occupancy. When clustering study areas into two distinct topo-climatic types, badger occupancy was associated with agriculture in areas with lower mean minimum winter temperatures (<0.3 degrees C) at higher elevation (>246m). In areas with higher mean minimum winter temperature (>1.2 degrees C) at lower elevation (<133m), badgers selected sites further away from human infrastructures (settlements and main roads). Climatic factors and human disturbance interact in intricate, context-dependent patterns to determine badger site occupancy.

    Main Conclusions: The UKCP09 Medium Emissions Scenario projects a winter mean minimum temperature increase of between 1 and 3 degrees C (central estimate) for Northern Scotland by the 2050s. Although warmer weather should benefit badger occupancy, this may be counteracted by up to a predicted 5% human population increase in the Scottish highlands, by 2037, which is likely to disturb badgers. We show that even in instances where species' regional responses to climate change are positive, these effects can be neutralized by other anthropogenic pressures. Our findings add to the growing body of evidence advocating that interactive effects should be taken into account when planning conservation management.

  • 209.
    Poelstra, Jelmer W.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bossu, Christen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Lantz, Henrik
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ryll, Bettina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Müller, Inge
    Max Planck Institute for Ornithology, Radolfzell.
    Baglione, Vittorio
    Universidad de Valladolid.
    Unneberg, Per
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wikelski, Martin
    Max Planck Institute for Ornithology, Radolfzell.
    Grabherr, Manfred
    Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wolf, Jochen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The architecture of genomic and phenotypic divergence across the European crow hybrid zoneManuscript (preprint) (Other academic)
  • 210.
    Poelstra, Jelmer W.
    et al.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Bossu, Christen M.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Lantz, Henrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ryll, Bettina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Mueller, I.
    Baglione, V.
    Unneberg, P.
    Wikelski, M.
    Grabherr, Manfred G.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Wolf, Jochen B. W.
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The genomic landscape underlying phenotypic integrity in the face of gene flow in crows2014In: Science, ISSN 0036-8075, E-ISSN 1095-9203, Vol. 344, no 6190, p. 1410-1414Article in journal (Refereed)
    Abstract [en]

    The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception-a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

  • 211.
    Poelstra, Jelmer W.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Vijay, Nagarjun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Müller, Inge
    Max Planck Institute for Ornithology, Radolfzell.
    Ryll, Bettina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Baglione, Vittorio
    Universidad de Valladolid.
    Wikelski, Martin
    Max Planck Institute for Ornithology, Radolfzell.
    Wolf, Jochen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    The genetics of colouration patterning and divergence in carrion and hooded crows as inferred from transcriptome-wide gene expression profilesManuscript (preprint) (Other academic)
  • 212.
    Qiao, Tuo
    et al.
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing, Peoples R China..
    King, Benedict
    Flinders Univ S Australia, Sch Biol Sci, Adelaide, SA, Australia..
    Long, John A.
    Flinders Univ S Australia, Sch Biol Sci, Adelaide, SA, Australia..
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Zhu, Min
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Beijing, Peoples R China..
    Early Gnathostome Phylogeny Revisited: Multiple Method Consensus2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 9, article id e0163157Article in journal (Refereed)
    Abstract [en]

    A series of recent studies recovered consistent phylogenetic scenarios of jawed vertebrates, such as the paraphyly of placoderms with respect to crown gnathostomes, and antiarchs as the sister group of all other jawed vertebrates. However, some of the phylogenetic relationships within the group have remained controversial, such as the positions of Entelognathus, ptyctodontids, and the Guiyu-lineage that comprises Guiyu, Psarolepis and Achoania. The revision of the dataset in a recent study reveals a modified phylogenetic hypothesis, which shows that some of these phylogenetic conflicts were sourced from a few inadvertent miscodings. The interrelationships of early gnathostomes are addressed based on a combined new dataset with 103 taxa and 335 characters, which is the most comprehensive morphological dataset constructed to date. This dataset is investigated in a phylogenetic context using maximum parsimony (MP), Bayesian inference (BI) and maximum likelihood (ML) approaches in an attempt to explore the consensus and incongruence between the hypotheses of early gnathostome interrelationships recovered from different methods. Our findings consistently corroborate the paraphyly of placoderms, all 'acanthodians' as a paraphyletic stem group of chondrichthyans, Entelognathus as a stem gnathostome, and the Guiyu-lineage as stem sarcopterygians. The incongruence using different methods is less significant than the consensus, and mainly relates to the positions of the placoderm Wuttagoonaspis, the stem chondrichthyan Ramirosuarezia, and the stem osteichthyan Lophosteus D the taxa that are either poorly known or highly specialized in character complement. Given that the different performances of each phylogenetic approach, our study provides an empirical case that the multiple phylogenetic analyses of morphological data are mutually complementary rather than redundant.

  • 213.
    Qu, Qingming
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    3D Histological Architecture And Ontogeny In Two Early Osteichthyan Scales: the Origin Of Cosmine And A Reconsideration Of The Phylogenetic Application Of Paleohistology Data2013Conference paper (Other academic)
    Abstract [en]

    The histology of early osteichthyan scales have been extensively studied using thin sections and acid-etched ground surfaces, and it is known that these rhombic scales are composed of multiple odontodes (tooth-like denticles) in the crown and bony tissues in the base. However, the 2D nature of the ground sections does not allow us to know the 3D morphology and distribution of the odontodes, which contain the ontogenetic history of the scales. To compensate the traditional study based on ground sections, we used Propagation phase contrast X-ray Synchrotron microtomography (PPC-SRµCT) to examine body scales of two early osteichthyans Andreolepis and Psarolepis, both of which are important taxa to understand the origin of osteichthyan crown group.

     

    The reconstructed 3D models of the histological architecture provide novel data of the ontogenetic history of the scales. The crown of Andreolepis scale is constructed two distinct type of growth patterns: a linear polarized pattern in the initial stage and a gap-filling pattern in the later stage. In the crown of Psarolepis scale the second odontode is most peculiar, with a the enamel covering penetrated by several pores, while the primordia odontode is almost morphologically identical with that of Andreolepis scale. A developmental shift following the formation of the primordia odontode may be the key step of the evolution of cosmoid scales, and Psarolepis scale is explained as a transitional form between the Andreolepis-type scale and the typical cosmoid scales in more derived sarcopterygians such as Osteolepis. Comparison of the entire canal system among Andreolepis, Psarolepis and more derived sarcopterygians show that the pore-canal system and cosmine-like construction are already present in Psarolepis scales, although the construction is different from typical cosmine as in Osteolepis. A stepwise scenario of the origin of pore-canal system and cosmine is proposed according to the new data.

     

    New characters are composed based on the in situ 3D data and could be incorporated into phylogenetic analysis in the future when more taxa have been studied using similar imaging method and 3D histology obtained. The 3D histology study of skeletal fossils using PPC-SRµCT could provide more informative and reliable phylogenetic data.

  • 214.
    Qu, Qingming
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    What is a pore-canal system?2011In: Abstracts: The 2nd Wiman meeting : Carl Wiman's Legacy : 100 years of Swedish Palaeontology : Uppsala 17–18 November 2011 / [ed] Benjamin P. Kear and Michael Streng, 2011, p. 20-21Conference paper (Other academic)
    Abstract [en]

    The pore-canal system is part of the defining ‘comsine’ structure of early sarcopterygians. It lies in the upper dentinous region of the dermal skeleton and has abundant external openings connected by horizontal ‘Maschenkanäle' to a deeper canal system in the thickened spongia layer – the ‘Unter-Maschenkanäle'. A similar horizontal canal system is also present in early actinopterygians but is not generally considered homologous. We generated 3D reconstructions of scale canals in three early osteichthyans: Lophosteus, Andreolepis, and Psarolepis, the latter being a basal sarcopterygian. Well-developed horizontal canal-systems were found in all of the sampled taxa, although their morphology was more regular in Psarolepis. In addition, Psarolepis possesses a less regular canal system at slightly deeper levels within the bony tissues, which might correspond to the ‘Unter-Maschenkanäle' of crown sarcopterygians (e.g. Porolepis). Conversely, the dentinal canals in Psarolepis appear to arise from both the lower canal system and horizontal ‘Maschenkanäle'. This feature represents a potential link between actinopterygians and sarcopterygians, thus rendering the horizontal canal system (probably part of the vascularization of the scale) potentially homologous across early osteichthyans.

  • 215.
    Qu, Qingming
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Zhu, Min
    Li, Gang
    What is a pore-canal system?2011In: Program and Abstracts: 71st Annual Meeting Society of Vertebrate Paleontology, Philadelphia: Society of Vertebrate Paleontology , 2011, p. 177-177Conference paper (Other academic)
  • 216.
    Qu, Qingming
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Three-dimensional virtual histology of silurian osteostracan scales revealed by synchrotron radiation microtomography2015In: Journal of morphology (1931. Print), ISSN 0362-2525, E-ISSN 1097-4687, Vol. 276, no 8, p. 873-888Article in journal (Refereed)
  • 217.
    Qu, Qingming
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Haitina, Tatjana
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Zhu, Min
    Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences.
    Ahlberg, Per Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    New genomic and fossil data illuminate the origin of enamel2015In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 526, no 7571, p. 108-120Article in journal (Refereed)
    Abstract [en]

    Enamel, the hardest vertebrate tissue, covers the teeth of almost all sarcopterygians (lobe-finned bony fishes and tetrapods) as well as the scales and dermal bones of many fossil lobe-fins(1-5). Enamel deposition requires an organic matrix containing the unique enamel matrix proteins (EMPs) amelogenin (AMEL), enamelin (ENAM) and ameloblastin (AMBN)(6). Chondrichthyans (cartilaginous fishes) lack both enamel and EMP genes(7,8). Many fossil and a few living non-teleost actinopterygians (ray-finned bony fishes) such as the gar, Lepisosteus, have scales and dermal bones covered with a proposed enamel homologue called ganoine(1,9). However, no gene or transcript data for EMPs have been described from actinopterygians(10,11). Here we show that Psarolepis romeri, a bony fish from the the Early Devonian period, combines enamel-covered dermal odontodes on scales and skull bones with teeth of naked dentine, and that Lepisosteus oculatus (the spotted gar) has enam andambn genes that are expressed in the skin, probably associated with ganoine formation. The genetic evidence strengthens the hypothesis that ganoine is homologous with enamel. The fossil evidence, further supported by the Silurian bony fish Andreolepis, which has enamel-covered scales but teeth and odontodes on its dermal bones made of naked dentine(12-16), indicates that this tissue originated on the dermal skeleton, probably on the scales. It subsequently underwent heterotopic expansion across two highly conserved patterning boundaries (scales/head-shoulder and dermal/oral) within the odontode skeleton.

  • 218.
    Qu, Qingming
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tafforeau, Paul
    Ahlberg, Per Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Scales and Tooth Whorls of Ancient Fishes Challenge Distinction between External and Oral 'Teeth'2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 8, p. e71890-Article in journal (Refereed)
    Abstract [en]

    The debate about the origin of the vertebrate dentition has been given fresh fuel by new fossil discoveries and developmental studies of extant animals. Odontodes (teeth or tooth-like structures) can be found in two distinct regions, the 'internal' oropharyngeal cavity and the 'external' skin. A recent hypothesis argues that regularly patterned odontodes is a specific oropharyngeal feature, whereas odontodes in the external skeleton lack this organization. However, this argument relies on the skeletal system of modern chondrichthyans (sharks and their relatives), which differ from other gnathostome (jawed vertebrate) groups in not having dermal bones associated with the odontodes. Their external skeleton is also composed of monoodontode 'placoid scales', whereas the scales of most early fossil gnathostomes are polyodontode, i.e. constructed from several odontodes on a shared bony base. Propagation phase contrast X-ray Synchrotron microtomography (PPC-SRmCT) is used to study the polyodontode scales of the early bony fish Andreolepis hedei. The odontodes constructing a single scale are reconstructed in 3D, and a linear and regular growth mechanism similar to that in a gnathostome dentition is confirmed, together with a second, gap-filling growth mechanism. Acanthodian tooth whorls are described, which show that ossification of the whorl base preceded and probably patterned the development of the dental lamina, in contrast to the condition in sharks where the dental lamina develops early and patterns the dentition. The new findings reveal, for the first time, how polyodontode scales grow in 3D in an extinct bony fish. They show that dentition-like odontode patterning occurs on scales and that the primary patterning unit of a tooth whorl may be the bony base rather than the odontodes it carries. These results contradict the hypothesis that oropharyngeal and external odontode skeletons are fundamentally separate and suggest that the importance of dermal bone interactions to odontode patterning has been underestimated.

  • 219.
    Qu, Qingming
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. European Synchrotron Radiat Facil, 71 Ave Martyrs, F-38043 Grenoble 09, France.
    Zhu, Min
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Xiwaidajie 142, Beijing 100044, Peoples R China.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per E
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The origin of novel features by changes in developmental mechanisms: ontogeny and three-dimensional microanatomy of polyodontode scales of two early osteichthyans2017In: Biological Reviews, ISSN 1464-7931, E-ISSN 1469-185X, Vol. 92, no 2, p. 1189-1212Article in journal (Refereed)
    Abstract [en]

    Recent advances in synchrotron imaging allow us to study the three-dimensional (3D) histology of vertebrate fossils, including microfossils (e.g. teeth and scales) of early jawed vertebrates. These microfossils can often be scanned at submicron resolution (<1 µm) because of their small size. The resulting voxel (3D pixel) stacks can be processed into virtual thin sections revealing almost every internal detail of the samples, comparable to traditional thin sections. In addition, 3D models of the internal microanatomical structures, such as embedded odontodes and vasculature, can be assembled and examined in situ. Scales of two early osteichthyans, Psarolepis romeri from the Early Devonian of China and Andreolepis hedei from the Late Silurian of Sweden, were scanned using propagation phase-contrast synchrotron X-ray microtomography (PPC-SRµCT), and 3D models of internal canal systems and buried odontodes were created from the scans. Based on these new data, we review the evolutionary origin of cosmine and its associated pore-canal system, which has been long recognized as a synapomorphy of sarcopterygians. The first odontode that appeared during growth shows almost identical morphology in the two scales, but the second odontode of the Psarolepis scale shows a distinctive morphology with several pores on the surface. It is suggested that a shift from ridge-like odontode to pore-bearing odontode was the key step in the origin of cosmine, which was then elaborated further in more-derived sarcopterygians. We perform a detailed comparison between the two scales and propose a primary homology framework to generate microanatomical characters, which can be used in the phylogenetic analysis of early osteichthyans when more 3D data become available. Our results highlight the importance of 3D data for the study of histology and ontogeny of the dermal skeleton of early jawed vertebrates, especially scales of the polyodontode type. The traditional microvertebrate collection is not only useful for biostratigraphic studies, but also preserves invaluable biological information about the growth of vertebrate hard tissues. Today, we are only beginning to understand the biological meaning of the new 3D data. The increasing availability of such data will enable, and indeed require, a complete revision of traditional palaeohistological studies on early vertebrates.

  • 220.
    Qu, Qingming
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Zhu, Min
    Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tafforeau, Paul
    European Synchrotron Radiation Facility.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The origin of novel features by changes in developmental mechanisms: a 3D virtual paleohistology study on polyodontode scales of primitive osteichthyans2015Manuscript (preprint) (Other academic)
  • 221.
    Qu, Qingming
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Zhu, Min
    Wang, Wei
    Scales and Dermal Skeletal Histology of an Early Bony Fish Psarolepis romeri and Their Bearing on the Evolution of Rhombic Scales and Hard Tissues2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 4, p. e61485-Article in journal (Refereed)
    Abstract [en]

    Recent discoveries of early bony fishes from the Silurian and earliest Devonian of South China (e. g. Psarolepis, Achoania, Meemannia, Styloichthys and Guiyu) have been crucial in understanding the origin and early diversification of the osteichthyans (bony fishes and tetrapods). All these early fishes, except Guiyu, have their dermal skeletal surface punctured by relatively large pore openings. However, among these early fishes little is known about scale morphology and dermal skeletal histology. Here we report new data about the scales and dermal skeletal histology of Psarolepis romeri, a taxon with important implications for studying the phylogeny of early gnathostomes and early osteichthyans. Seven subtypes of rhombic scales with similar histological composition and surface sculpture are referred to Psarolepis romeri. They are generally thick and show a faint antero-dorsal process and a broad peg-and-socket structure. In contrast to previously reported rhombic scales of osteichthyans, these scales bear a neck between crown and base as in acanthodian scales. Histologically, the crown is composed of several generations of odontodes and an irregular canal system connecting cylindrical pore cavities. Younger odontodes are deposited on older ones both superpositionally and areally. The bony tissues forming the keel of the scale are shown to be lamellar bone with plywood-like structure, whereas the other parts of the base are composed of pseudo-lamellar bone with parallel collagen fibers. The unique tissue combination in the keel (i.e., extrinsic Sharpey's fibers orthogonal to the intrinsic orthogonal sets of collagen fibers) has rarely been reported in the keel of other rhombic scales. The new data provide insights into the early evolution of rhombic (ganoid and cosmoid) scales in osteichthyans, and add to our knowledge of hard tissues of early vertebrates.

  • 222.
    Qvarnström, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tyrannosaurid-like osteophagy by a Triassic archosaur2019In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 9, article id 925Article in journal (Refereed)
    Abstract [en]

    Here we present evidence for osteophagy in the Late Triassic archosaur Smok wawelski Niedzwiedzki, Sulej and Dzik, 2012, a large theropod-like predator from Poland. Ten medium to large-sized coprolites are matched, by their dimensions and by association with body fossils and footprints, to S. wawelski. The coprolites contain fragments of large serrated teeth as well as up to 50 percent by volume of bone fragments, with distinct fragmentation and angularity, from several prey taxa. This suggests pronounced osteophagy. Further evidence for bone-crushing behaviour is provided by isolated worn teeth, bone-rich regurgitalites (fossil regurgitates) and numerous examples of crushed or bite-marked dicynodont bones, all collected from the same bone-bearing beds in the Lipie Slaskie clay-pit. Several of the anatomical characters related to osteophagy, such as a massive head and robust body, seem to be shared by S. wawelski and the tyrannosaurids, despite their wide phylogenetic separation. These large predators thus provide evidence of convergence driven by similar feeding ecology at the beginning and end of the age of dinosaurs.

  • 223.
    Qvarnström, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Anagnostakis, Stavros
    Nikolaou Plastira 3, Thessaloniki 57500, Greece.
    Lindskog, Anders
    Lund Univ, Dept Geol, Solvegatan 12, S-22362 Lund, Sweden.
    Scheer, Udo
    Sat Matasaru 93, RO-137295 Com Matasaru, Romania.
    Vajda, Vivi
    Swedish Museum Nat Hist, Dept Palaeobiol, SE-10405 Stockholm, Sweden.
    Rasmussen, Bo W.
    Geomuseum Faxe, Ostervej 2, DK-4640 Faxe, Denmark.
    Lindgren, Johan
    Lund Univ, Dept Geol, Solvegatan 12, S-22362 Lund, Sweden.
    Eriksson, Mats E.
    Lund Univ, Dept Geol, Solvegatan 12, S-22362 Lund, Sweden.
    Multi-proxy analyses of Late Cretaceous coprolites from Germany2019In: Lethaia: an international journal of palaeontology and stratigraphy, ISSN 0024-1164, E-ISSN 1502-3931, Vol. 52, no 4, p. 550-569Article in journal (Refereed)
    Abstract [en]

    A total of 462 coprolites from three localities exposing Upper Cretaceous deposits in the Munster Basin, northwestern Germany, have been subjected to an array of analytical techniques, with the aim of elucidating ancient trophic structures and predator-prey interactions. The phosphatic composition, frequent bone inclusions, size and morphology collectively suggest that most, if not all, coprolites were produced by carnivorous (predatory or scavenging) vertebrates. The bone inclusions further indicate that the coprolite producers preyed principally upon fish. Putative host animals include bony fish, sharks and marine reptiles - all of which have been previously recorded from the Munster Basin. The presence of borings and other traces on several coprolites implies handling by coprophagous organisms. Remains of epibionts are also common, most of which have been identified as the encrusting bivalve Atreta. Palynological analyses of both the coprolites and host rocks reveal a sparse assemblage dominated by typical Late Cretaceous dinoflagellates, and with sub-ordinate fern spores, conifer pollen grains and angiosperm pollen grains. The dinoflagellate key taxon Exochosphaeridium cenomaniense corroborates a Cenomanian age for the Plenus Marl, from which most studied coprolites derive. The findings of this study highlight the potential of a multi-proxy approach when it comes to unravelling the origin, composition and importance of coprolites in palaeoecosystem analyses.

  • 224.
    Qvarnström, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Tafforeau, Paul
    European Synchrotron Radiation Facility.
    Zigaite, Zivile
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    3D – visualization of vertebrate coprolites through phase contrast synchrotron imaging unravel new aspects of paleoecological relations2017In: 77th Annual Meeting of the Society of Vertebrate Paleontology, Abstract book, 2017, p. 181-Conference paper (Refereed)
  • 225.
    Qvarnström, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tafforeau, Paul
    European Synchrotron Radiat Facil, 71 Ave Martyrs,CS40200, F-38043 Grenoble, France..
    Zigaite, Zivile
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Synchrotron phase-contrast microtomography of coprolites generates novel palaeobiological data2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 2723Article in journal (Refereed)
    Abstract [en]

    Coprolites (fossil faeces) reveal clues to ancient trophic relations, and contain inclusions representing organisms that are rarely preserved elsewhere. However, much information is lost by classical techniques of investigation, which cannot find and image the inclusions in an adequate manner. We demonstrate that propagation phase-contrast synchrotron microtomography (PPC-SR mu CT) permits high-quality virtual 3D-reconstruction of coprolite inclusions, exemplified by two coprolites from the Upper Triassic locality Krasiejow, Poland; one of the coprolites contains delicate beetle remains, and the other one a partly articulated fish and fragments of bivalves.

  • 226.
    Qvarnström, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Zigaite, Zivile
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Vertebrate coprolites (fossil faeces): An underexplored Konservat-Lagerstatte2016In: Earth-Science Reviews, ISSN 0012-8252, E-ISSN 1872-6828, Vol. 162, p. 44-57Article, review/survey (Refereed)
    Abstract [en]

    Fossilized soft tissues of animals (e.g. muscles, hair and feathers) are valuable sources of palaeobiological information, but a poor preservation potential makes them undesirably scarce in the fossil record. The aim of this review is to summarize main findings, current progress and the analytical constraints of detecting fossilized soft tissues in coprolites from, mainly, freshwater and terrestrial carnivorous vertebrates. We conclude that soft-tissue inclusions in coprolites are sources of two important lines of information: the fossils can be put in a direct palaeoecological context, and characters of extinct taxa are more likely preserved in the phosphate-rich taphonomic microenvironment of coprolites than elsewhere. As a result, it is possible to unravel the deep-time origins of host-parasite relations, to understand ancient trophic food webs and detect new soft-tissue characters of different animal groups. Examples of the latter include muscle tissues from a tyrannosaurid prey, tapeworm eggs (including a developing embryo) in a Permian shark coprolite, as well as hair from multituberculates and, probably, from stem-mammals (Therapsids). Additionally, the use of coprolites in an archaeological context is briefly reviewed with focus on key aspects that may become implemented in studies of pre-Quaternary specimens as well. In summary, there is a wide range of information that can be extracted from coprolites, which has not yet been fully explored in palaeontological studies.

  • 227.
    Qvarnström, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Niedźwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    A new charophyte flora from the Upper Triassic of Skane (Sweden) and implications on biostratigraphy, taphonomy and the palaeoenvironment2018In: Review of Palaeobotany and Palynology, ISSN 0034-6667, E-ISSN 1879-0615, Vol. 249, p. 61-79Article in journal (Refereed)
    Abstract [en]

    The record of fossil charophytes from Sweden was previously restricted to the Ladinian-earliest Carnian Falsterbo Formation. Here, we present a charophyte assemblage from the Upper Triassic KAgerod Formation exposed at the Balteberga Gorge (Sickle, southern Sweden) from the perspectives of taxonomy, taphonomy, palaeoecology and biostratigraphy. The microfossils originate from an interval of reddish sandy mudstone and are represented by rare fossil thalli, calcium carbonate encrustations of thalli and numerous calcified fructifications, called gyrogonites. The assemblage is relatively diverse, comprising six species belonging to four genera of the family Porocharaceae (Auerbachichara cf. rhaetica, Porochara sp., Stellatochara germanica, Stellatochara aff. subsphaerica, Stenochara aff. donetziana, Stenochara aff. kisielevskyi). Both the sedimentological context and the preservation of the charophyte remains point to an autochthonous origin for the charophyte-bearing strata. An autochthonous origin together with the habitat of modern charophytes, infer that the charophyte interval was deposited in shallow ephemeral pond or lake in a terrestrial setting. Their occurrence is also indicative of low amount of nutrients and the numerous thalli encrustations suggest a rather alkaline water composition. Some of the described species (Auerbachichara cf. rhaetica and Stellatochara aff. subsphaerica) are useful for biostratigraphical correlations which attributes the assemblage to the Auerbachichara rhaetica Range zone (sensu Bilan, 1991) in the proposed Germanic Triassic charophyte zonation. This range zone is assigned to a latest Carnian to late Norian age, strengthened by an interlayering with rocks containing a characteristic assemblage of palynomorphs (Corollina meyeriana subzone a and b) in the Upper Triassic of the Polish part of the Germanic Basin. The findings of the first Triassic thalli further strengthen the suggestion that the early Mesozoic fossil record of charophytes is not solely composed of oospores and gyrogonites. A better understanding of vegetative fossil remains (silicified thalli and encrustations) of charophytes may provide important future palaeoecological implications and links between recent and extinct forms. Our findings also provide evidence that charophyte occurrences in the ICagerod Formation are strictly controlled by palaeoenvironmental factors. (C) 2017 Elsevier B.V. All rights reserved.

  • 228.
    Qvarnström, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Szrek, Piotr
    Natl Res Inst, Polish Geol Inst, Rakowiecka 4 St, PL-00075 Warsaw, Poland..
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Non-marine palaeoenvironment associated to the earliest tetrapod tracks2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 1074Article in journal (Refereed)
    Abstract [en]

    Opinions differ on whether the evolution of tetrapods (limbed vertebrates) from lobe-finned fishes was directly linked to terrestrialization. The earliest known tetrapod fossils, from the Middle Devonian (approximately 390 million years old) of Zachelmie Quarry in Poland, are trackways made by limbs with digits; they document a direct environmental association and thus have the potential to help answer this question. However, the tetrapod identity of the tracks has recently been challenged, despite their well-preserved morphology, on account of their great age and supposedly shallow marine (intertidal or lagoonal) depositional environment. Here we present a new palaeoenvironmental interpretation of the track-bearing interval from Zachelmie, showing that it represents a succession of ephemeral lakes with a restricted and non-marine biota, rather than a marginal marine environment as originally thought. This context suggests that the trackmaker was capable of terrestrial locomotion, consistent with the appendage morphology recorded by the footprints, and thus provides additional support for a tetrapod identification.

  • 229.
    Qvarnström, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Vikberg Wernström, Joel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Piechowski, Rafal
    Polish Acad Sci, Inst Paleobiol, Twarda 51-55, PL-00818 Warsaw, Poland;Univ Warsaw, Dept Palaeobiol & Evolut, Fac Biol, Biol & Chem Res Ctr, Zwirki & Wigury 101, PL-02089 Warsaw, Poland.
    Talanda, Mateusz
    Univ Warsaw, Dept Palaeobiol & Evolut, Fac Biol, Biol & Chem Res Ctr, Zwirki & Wigury 101, PL-02089 Warsaw, Poland.
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Beetle-bearing coprolites possibly reveal the diet of a Late Triassic dinosauriform2019In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 6, no 3, article id 181042Article in journal (Refereed)
    Abstract [en]

    Diets of extinct animals can be difficult to analyse if no direct evidence, such as gut contents, is preserved in association with body fossils. Inclusions from coprolites (fossil faeces), however, may also reflect the diet of the host animal and become especially informative if the coprolite producer link can be established. Here we describe, based on propagation phase-contrast synchrotron microtomography (PPC-SRμCT), the contents of five morphologically similar coprolites collected from two fossil-bearing intervals from the highly fossiliferous Upper Triassic locality at Krasiejow in Silesia, Poland. Beetle remains, mostly elytra, and unidentified exoskeleton fragments of arthropods are the most conspicuous inclusions found in the coprolites. The abundance of these inclusions suggests that the coprolite producer deliberately targeted beetles and similar small terrestrial invertebrates as prey, but the relatively large size of the coprolites shows that it was not itself a small animal. The best candidate from the body fossil record of the locality is the dinosauriform Silesaurus opolensis Dzik, 2003, which had an anatomy in several ways similar to those of bird-like neotheropod dinosaurs and modern birds. We hypothesize that the beak-like jaws of S. opolensis were used to efficiently peck small insects off the ground, a feeding behaviour analogous to some extant birds.

  • 230.
    Radomska, Katarzyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Functional studies of the Quaking gene: Focus on astroglia and neurodevelopment2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The RNA-binding protein Quaking (QKI) plays a fundamental role in post-transcriptional gene regulation during mammalian nervous system development. QKI is well known for advancing oligodendroglia differentiation and myelination, however, its functions in astrocytes and embryonic central nervous system (CNS) development remain poorly understood. Uncovering the complete spectrum of QKI molecular and functional repertoire is of additional importance in light of growing evidence linking QKI dysfunction with human disease, including schizophrenia and glioma. This thesis summarizes my contribution to fill this gap of knowledge. 

           In a first attempt to identify the QKI-mediated molecular pathways in astroglia, we studied the effects of QKI depletion on global gene expression in the human astrocytoma cell line. This work revealed a previously unknown role of QKI in regulating immune-related pathways. In particular, we identified several putative mRNA targets of QKI involved in interferon signaling, with possible implications in innate cellular antiviral defense, as well as tumor suppression. We next extended these investigations to human primary astrocytes, in order to more accurately model normal brain astrocytes. One of the most interesting outcomes of this analysis was that QKI regulates expression of transcripts encoding the Glial Fibrillary Acidic Protein, an intermediate filament protein that mediates diverse biological functions of astrocytes and is implicated in numerous CNS pathologies. We also characterized QKI splice variant composition and subcellular expression of encoded protein isoforms in human astrocytes. Finally, we explored the potential use of zebrafish as a model system to study neurodevelopmental functions of QKI in vivo. Two zebrafish orthologs, qkib and qki2, were identified and found to be widely expressed in the CNS neural progenitor cell domains. Furthermore, we showed that a knockdown of qkib perturbs the development of both neuronal and glial populations, and propose neural progenitor dysfunction as the primary cause of the observed phenotypes.

           To conclude, the work presented in this thesis provides the first insight into understanding the functional significance of the human QKI in astroglia, and introduces zebrafish as a novel tool with which to further investigate the importance of this gene in neural development.

    List of papers
    1. QKI-7 regulates expression of interferon-related genes in human astrocyte glioma cells
    Open this publication in new window or tab >>QKI-7 regulates expression of interferon-related genes in human astrocyte glioma cells
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    2010 (English)In: PloS one, ISSN 1932-6203, Vol. 5, no 9, p. e13079-Article in journal (Refereed) Published
    Abstract [en]

    BACKGROUND: The human QKI gene, called quaking homolog, KH domain RNA binding (mouse), is a candidate gene for schizophrenia encoding an RNA-binding protein. This gene was shown to be essential for myelination in oligodendrocytes. QKI is also highly expressed in astrocytes, but its function in these cells is not known. METHODS/PRINCIPAL FINDINGS: We studied the effect of small interference RNA (siRNA)-mediated QKI depletion on global gene expression in human astrocyte glioma cells. Microarray measurements were confirmed with real-time quantitative polymerase chain reaction (qPCR). The presence of QKI binding sites (QRE) was assessed by a bioinformatic approach. Viability and cell morphology were also studied. The most significant alteration after QKI silencing was the decreased expression of genes involved in interferon (IFN) induction (P = 6.3E-10), including IFIT1, IFIT2, MX1, MX2, G1P2, G1P3, GBP1 and IFIH1. All eight genes were down-regulated after silencing of the splice variant QKI-7, but were not affected by QKI-5 silencing. Interestingly, four of them were up-regulated after treatment with the antipsychotic agent haloperidol that also resulted in increased QKI-7 mRNA levels. CONCLUSIONS/SIGNIFICANCE: The coordinated expression of QKI-7 splice variant and IFN-related genes supports the idea that this particular splice variant has specific functions in astrocytes. Furthermore, a role of QKI-7 as a regulator of an inflammatory gene pathway in astrocytes is suggested. This hypothesis is well in line with growing experimental evidence on the role of inflammatory components in schizophrenia.

    National Category
    Biological Sciences Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-132707 (URN)10.1371/journal.pone.0013079 (DOI)000282269400026 ()20927331 (PubMedID)
    Available from: 2010-10-25 Created: 2010-10-25 Last updated: 2014-05-20Bibliographically approved
    2. RNA-binding protein QKI regulates Glial fibrillary acidic protein expression in human astrocytes
    Open this publication in new window or tab >>RNA-binding protein QKI regulates Glial fibrillary acidic protein expression in human astrocytes
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    2013 (English)In: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 22, no 7, p. 1373-1382Article in journal (Refereed) Published
    Abstract [en]

    Linkage, association and expression studies previously pointed to the human QKI, KH domain containing, RNA-binding (QKI) as a candidate gene for schizophrenia. Functional studies of the mouse orthologue Qk focused mainly on its role in oligodendrocyte development and myelination, while its function in astroglia remained unexplored. Here, we show that QKI is highly expressed in human primary astrocytes and that its splice forms encode proteins targeting different subcellular localizations. Uncovering the role of QKI in astrocytes is of interest in light of growing evidence implicating astrocyte dysfunction in the pathogenesis of several disorders of the central nervous system. We selectively silenced QKI splice variants in human primary astrocytes and used RNA sequencing to identify differential expression and splice variant composition at the genome-wide level. We found that an mRNA expression of Glial fibrillary acidic protein (GFAP), encoding a major component of astrocyte intermediate filaments, was down-regulated after QKI7 splice variant silencing. Moreover, we identified a potential QKI-binding site within the 3 untranslated region of human GFAP. This sequence was not conserved between mice and humans, raising the possibility that GFAP is a target for QKI in humans but not rodents. Haloperidol treatment of primary astrocytes resulted in coordinated increases in QKI7 and GFAP expression. Taken together, our results provide the first link between QKI and GFAP, two genes with alterations previously observed independently in schizophrenic patients. Our findings for QKI, together with its well-known role in myelination, suggest that QKI is a hub regulator of glia function in humans.

    National Category
    Natural Sciences Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-198376 (URN)10.1093/hmg/dds553 (DOI)000316297000009 ()
    Available from: 2013-04-15 Created: 2013-04-15 Last updated: 2017-12-06Bibliographically approved
    3. The zebrafish qkib is essential for nervous system development
    Open this publication in new window or tab >>The zebrafish qkib is essential for nervous system development
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    (English)Manuscript (preprint) (Other academic)
    National Category
    Neurosciences
    Identifiers
    urn:nbn:se:uu:diva-223331 (URN)
    Available from: 2014-04-17 Created: 2014-04-17 Last updated: 2018-01-11
  • 231.
    Radomska, Katarzyna J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Halvardson, Jonatan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Genomics.
    Reinius, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Carlström, Eva Lindholm
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Emilsson, Lina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Feuk, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Genomics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    RNA-binding protein QKI regulates Glial fibrillary acidic protein expression in human astrocytes2013In: Human Molecular Genetics, ISSN 0964-6906, E-ISSN 1460-2083, Vol. 22, no 7, p. 1373-1382Article in journal (Refereed)
    Abstract [en]

    Linkage, association and expression studies previously pointed to the human QKI, KH domain containing, RNA-binding (QKI) as a candidate gene for schizophrenia. Functional studies of the mouse orthologue Qk focused mainly on its role in oligodendrocyte development and myelination, while its function in astroglia remained unexplored. Here, we show that QKI is highly expressed in human primary astrocytes and that its splice forms encode proteins targeting different subcellular localizations. Uncovering the role of QKI in astrocytes is of interest in light of growing evidence implicating astrocyte dysfunction in the pathogenesis of several disorders of the central nervous system. We selectively silenced QKI splice variants in human primary astrocytes and used RNA sequencing to identify differential expression and splice variant composition at the genome-wide level. We found that an mRNA expression of Glial fibrillary acidic protein (GFAP), encoding a major component of astrocyte intermediate filaments, was down-regulated after QKI7 splice variant silencing. Moreover, we identified a potential QKI-binding site within the 3 untranslated region of human GFAP. This sequence was not conserved between mice and humans, raising the possibility that GFAP is a target for QKI in humans but not rodents. Haloperidol treatment of primary astrocytes resulted in coordinated increases in QKI7 and GFAP expression. Taken together, our results provide the first link between QKI and GFAP, two genes with alterations previously observed independently in schizophrenic patients. Our findings for QKI, together with its well-known role in myelination, suggest that QKI is a hub regulator of glia function in humans.

  • 232.
    Radomska, Katarzyna J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sager, Jonathan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Farnsworth, Bryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tellgren-Roth, Åsa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tuveri, Giulia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Peuckert, Christiane
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Kettunen, Petronella
    Univ Gothenburg, Sahlgrenska Acad, Inst Neurosci & Physiol, Dept Psychiat & Neurochem, Gothenburg, Sweden.;Univ Oxford, John Radcliffe Hosp, Nuffield Dept Clin Neurosci, Dept Neuropathol, Oxford OX3 9DU, England..
    Jazin, Elena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Emilsson, Lina S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Characterization and Expression of the Zebrafish qki Paralogs2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 1, article id e0146155Article in journal (Refereed)
    Abstract [en]

    Quaking (QKI) is an RNA-binding protein involved in post-transcriptional mRNA processing. This gene is found to be associated with several human neurological disorders. Early expression of QKI proteins in the developing mouse neuroepithelium, together with neural tube defects in Qk mouse mutants, suggest the functional requirement of Qk for the establishment of the nervous system. As a knockout of Qk is embryonic lethal in mice, other model systems like the zebrafish could serve as a tool to study the developmental functions of qki. In the present study we sought to characterize the evolutionary relationship and spatiotemporal expression of qkia, qki2, and qkib; zebrafish homologs of human QKI. We found that qkia is an ancestral paralog of the single tetrapod Qk gene that was likely lost during the fin-to-limb transition. Conversely, qkib and qki2 are orthologs, emerging at the root of the vertebrate and teleost lineage, respectively. Both qki2 and qkib, but not qkia, were expressed in the progenitor domains of the central nervous system, similar to expression of the single gene in mice. Despite having partially overlapping expression domains, each gene has a unique expression pattern, suggesting that these genes have undergone subfunctionalization following duplication. Therefore, we suggest the zebrafish could be used to study the separate functions of qki genes during embryonic development.

  • 233.
    Rajagopalan, Aparna
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Schweizer, Nadine
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Nordenankar, Karin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Jahan, Sultana Nilufar
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Emilsson, Lina
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Wallen-Mackenzie, Åsa
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Reduced Gene Expression Levels of Munc13-1 and Additional Components of the Presynaptic Exocytosis Machinery Upon Conditional Targeting of Vglut2 in the Adolescent Mouse2014In: Synapse, ISSN 0887-4476, E-ISSN 1098-2396, Vol. 68, no 12, p. 624-633Article in journal (Refereed)
    Abstract [en]

    Presynaptic proteins orchestrate an intricate interplay of dynamic interactions in order to regulate quantal exocytosis of transmitter-filled vesicles, and their dysregulation might cause neurological and neuropsychiatric dysfunction. Mice carrying a spatiotemporal restriction in the expression of the Vesicular glutamate transporter 2 (Vglut2; aka Slc17a6) in the cortex, amygdala and hippocampal subiculum from the third postnatal week show a strong anxiolytic phenotype and certain behavioral correlates of schizophrenia. To further understand the molecular consequences of this targeted deletion of Vglut2, we performed an unbiased microarray analysis comparing gene expression levels in the subiculum of these conditional Vglut2 knockout mice (Vglut2(f/f;CamKII) cKO) to those in control littermates. Expression of Unc13C (Munc13-3), a member of the Unc/Munc family, previously shown to be important for glutamatergic transmission, was identified to be significantly down-regulated. Subsequent analysis by quantitative RT-PCR revealed a 50% down-regulation of Munc 13-1, the gene encoding the Unc/Munc subtype described as an essential component in the majority of glutamtergic synapses in the hippocampus. Genes encoding additional components of the presynaptic machinery were also found regulated, including Rab3A, RIM1, as well as Syntaxin1 and Synaptobrevin. Altered expression levels of these genes were further found in the amygdala and in the retrosplenial group of the cortex, additional regions in which Vglut2 was conditionally targeted. These findings suggest that expression levels of Vglut2 might be important for the maintenance of gene expression in the presynaptic machinery in the adult mouse brain. Synapse 68:624-633, 2014.

  • 234.
    Reinius, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sexually Dimorphic Gene Expression in the Mammalian Brain2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In recent times, major advances have been made towards understanding sexual dimorphism in the brain on a molecular basis. This thesis summarises my modest contributions to these endeavours. Sexual dimorphisms are manifested throughout the spectrum of biological complexity, and can be studied by numerous approaches. The approach of this thesis is to explore sex-biased gene expression in mammalian somatic tissues. Paper I describes an evolutionarily conserved sexual gene expression pattern in the primate brain. Conserved sex-biased genes may underlie important sex differences in neurobiology. In Paper II, Y-chromosome genes expressed across several regions of the human male brain during mid-gestation are identified. Such genes may play male-specific roles during brain development. The studies of Papers III and IV explore sex-biased gene expression in several somatic tissues from mouse. The amount of genes with sex-biased expression varied in different brain regions. The striatum was particularly interesting, with an order of magnitude increase in the number of sex-biased genes as compared to the other included brain regions. Of potentially wider significance are my observations regarding the transcriptional regulation of domains that escape X-chromosome inactivation (XCI). Specifically, I provide the first evidence that long non-coding RNAs (lncRNAs) transcribe together with protein-coding genes in XCI-escaping domains. This raises the possibility that lncRNAs mediate the transcriptional regulation of XCI-escaping domains. I also present evidence that the mouse X-chromosome has undergone both feminisation and de-masculinisation during evolution, as indicated by the sex-skewed regulation of genes on this chromosome. This finding is relevant for understanding the selective forces that shaped the mammalian X-chromosome. In the final chapter, Paper V, the generation of a novel transgenic mouse line, Gpr101-Cre, is described. Its progeny can be used for functional studies of striatum, a brain structure with major sexual dimorphism, as is further demonstrated in the Papers of this thesis.

    List of papers
    1. Prenatal sex differences in the human brain
    Open this publication in new window or tab >>Prenatal sex differences in the human brain
    2009 (English)In: Molecular Psychiatry, ISSN 1359-4184, E-ISSN 1476-5578, Vol. 14, no 11, p. 988-989Article in journal, Letter (Refereed) Published
    Place, publisher, year, edition, pages
    London, UK: Nature Publishing Group, 2009
    Keywords
    sex, brain, gene expression, sex differences, sexual dimorphism, human, Y, Y chromosome, Y-chromosome
    National Category
    Developmental Biology
    Research subject
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-112066 (URN)10.1038/mp.2009.79 (DOI)000271022100001 ()
    Available from: 2010-01-08 Created: 2010-01-08 Last updated: 2017-12-12Bibliographically approved
    2. mRNA expression of Y-linked transcripts in 12 regions of the prenatal human male brain (Featured Image)
    Open this publication in new window or tab >>mRNA expression of Y-linked transcripts in 12 regions of the prenatal human male brain (Featured Image)
    2009 (English)In: Molecular Psychiatry, ISSN 1359-4184, E-ISSN 1476-5578, Vol. 14, no 11, p. 987-Article in journal (Refereed) Published
    Place, publisher, year, edition, pages
    London, UK: Nature Publishing Group, 2009
    National Category
    Developmental Biology
    Research subject
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-112069 (URN)10.1038/mp.2009.114 (DOI)
    Note
    Featured ImageAvailable from: 2010-01-08 Created: 2010-01-08 Last updated: 2017-12-12Bibliographically approved
    3. A new mouse line based on the Gpr101 promoter drives expression of Cre in medium spiny neurons of the striatum.
    Open this publication in new window or tab >>A new mouse line based on the Gpr101 promoter drives expression of Cre in medium spiny neurons of the striatum.
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    A novel transgenic mouse that expresses the Cre recombinase in striatal medium spiny neurons was generated. To create the line, we have used the promoter of the X-linked gene Gpr101 and a Bacterial Artificial Chromosome recombineering strategy. When the Gpr101-Cre mouse was bred to the tdTomato Ai14 [1] reporter line, we observed strong fluorescence in medium-size spiny neurons (MSNs) of the striatum. In addition, Gpr101-Cre was detected in hippocampal pyramidal neurons and sparse cerebellar purkinje cells. Interestingly, Gpr101-Cre expression in this mouse line differs from the endogenous Gpr101 gene expression, which is highest in amygdala and hypothalamus and not detected in striatum in adult mice, as shown by in situ hybridization. The tdTomato Ai14 reporter marks any cell lineages in which Gpr101-Cre has, at any time, been expressed. Our results show that the Gpr101-Cre gene construct had lost the original ability of the Gpr101 promotor to drive expression of the Gpr101 gene in the amygdala and the hypothalamus. Second, the Gpr101-Cre gene construct either acquired a novel capability to express in striatum, or more probably, Gpr101 is expressed transiently in striatum during development. In addition, a small subpopulation of astrocytes (GFAP positive cells) was labelled in several regions of the central nervous system, allowing for specific follow-up studies of these cells. We envision that the newly created Cre-line will contribute to numerous studies, particularly related to the development and differentiation of cellular networks in the brain.

    Identifiers
    urn:nbn:se:uu:diva-156638 (URN)
    Available from: 2011-08-04 Created: 2011-08-04 Last updated: 2012-02-24
    4. Large-scale sex-bias expression analysis of somatic tissues reveals de-masculinisation of the mouse X-chromosome.
    Open this publication in new window or tab >>Large-scale sex-bias expression analysis of somatic tissues reveals de-masculinisation of the mouse X-chromosome.
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-156639 (URN)