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  • 301.
    Cortazar-Chinarro, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Yvone, Meyer-Lucht
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Van der Valk, Tom
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Ritcher-Boix, Alex
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Larila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Contrasting patterns of AMP nucleotide and peptide variation along a latitudinal gradient in two frog speciesManuscript (preprint) (Other academic)
  • 302.
    Cortés, Andres J,
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    On the origin of the Common Bean (Phaseolus vulgaris L.)2013In: American Journal of Plant Sciences, ISSN 2158-2742, E-ISSN 2158-2750, Vol. 4, no 10, p. 1998-2000Article in journal (Refereed)
    Abstract [en]

    Phylogeographic methods provide the tools to accurately access the geographic origin and diversification of crop species. In the present commentary, I urge the common bean community to face those methods and a tree-thinking mentality with regards to the long standing debate of the origin of common bean. Such efforts will ultimately bring back interest into wild bean studies and reinforce the uniqueness of this species as a system to study diversification, domestication and adaptive processes across the two most diverse hotspots in the world.

  • 303. Cossu, Rosa Maria
    et al.
    Casola, Claudio
    Giacomello, Stefania
    Vidalis, Amaryllis
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Zuccolo, Andrea
    LTR Retrotransposons Show Low Levels of Unequal Recombination and High Rates of Intraelement Gene Conversion in Large Plant Genomes2017In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 9, no 12, p. 3449-3462Article in journal (Refereed)
  • 304.
    Cowen, Matthew Bodle
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences.
    Oxygen Isotopes in Hybodont Shark Spines from the Triassic of Poland: Implications for Palaeobiology and Palaeoecology2019Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Hybodontiformes (hybodonts) were a clade of sharks with a high diversity during the Triassic and Jurassic. An extensive fossil record of freshwater hybodonts exists and is comprised of both adult and juvenile specimens, as well as egg cases found in fluvial and lacustrine deposits suggesting the group had the ability to tolerate a wide range of salinities. However, the extent to which hybodonts inhabited freshwater is not fully understood, largely due to limited knowledge of their life cycles. In this study geochemical analysis was performed on hybodont fin spines from the Late Triassic Keuper strata of southwestern Poland to investigate possible changes in the salinity of the water inhabited by the animals over the course of their lifetime. This understanding of hybodont migration also provides palaeogeographical insights regarding the inland basins bordering the Rhaetian Sea and Tethys Ocean. We also assess and comment upon the histology of the spines in order to better interpret the results of the Oxygen isotope analysis, by considering how the deposition of different osteodentine layers impacts the distribution of said isotopes throughout our specimens. Our results show that hybodonts likely inhabited increasingly saline conditions as they matured, as evidenced by enhanced δ 18O in ontogenically younger sections at the base of the spines relative to older sections closer to the tip. The results suggest that hybodonts migrated between freshwater and more saline environments, raising questions about the interconnectedness of the Rhaetian sea with terrestrial environments in the eastern Central European Basin.

    The full text will be freely available from 2024-09-09 00:00
  • 305.
    Craig, Rory J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Edinburgh, Sch Biol Sci, Inst Evolutionary Biol, Edinburgh, Midlothian, Scotland..
    Suh, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wang, Mi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis)2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 2, p. 476-492Article in journal (Refereed)
    Abstract [en]

    It is becoming increasingly clear that a significant proportion of the functional sequence within eukaryotic genomes is noncoding. However, since the identification of conserved elements (CEs) has been restricted to a limited number of model organisms, the dynamics and evolutionary character of the genomic landscape of conserved, and hence likely functional, sequence is poorly understood in most species. Moreover, identification and analysis of the full suite of functional sequence are particularly important for the understanding of the genetic basis of trait loci identified in genome scans or quantitative trait locus mapping efforts. We report that similar to 6.6% of the collared flycatcher genome (74.0Mb) is spanned by similar to 1.28 million CEs, a higher proportion of the genome but a lower total amount of conserved sequence than has been reported in mammals. We identified >200,000 CEs specific to either the archosaur, avian, neoavian or passeridan lineages, constituting candidates for lineage-specific adaptations. Importantly, no less than similar to 71% of CE sites were nonexonic (52.6Mb), and conserved nonexonic sequence density was negatively correlated with functional exonic density at local genomic scales. Additionally, nucleotide diversity was strongly reduced at nonexonic conserved sites (0.00153) relative to intergenic nonconserved sites (0.00427). By integrating deep transcriptome sequencing and additional genome annotation, we identified novel protein-coding genes, long noncoding RNA genes and transposon-derived (exapted) CEs. The approach taken here based on the use of a progressive cactus whole-genome alignment to identify CEs should be readily applicable to nonmodel organisms in general and help to reveal the rich repertoire of putatively functional noncoding sequence as targets for selection.

  • 306.
    Cramer, Emily R. A.
    et al.
    Univ Oslo, Nat Hist Museum, N-0318 Oslo, Norway.;Smithsonian Migratory Bird Ctr, POB 37012 MRC5503, Washington, DC 20008 USA.;Cornell Lab Ornithol, Ithaca, NY 14850 USA..
    Ålund, Murielle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    McFarlane, S. Eryn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Johnsen, Arild
    Univ Oslo, Nat Hist Museum, N-0318 Oslo, Norway..
    Qvarnström, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Females discriminate against heterospecific sperm in a natural hybrid zone2016In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 70, no 8, p. 1844-1855Article in journal (Refereed)
    Abstract [en]

    When hybridization is maladaptive, species-specific mate preferences are selectively favored, but low mate availability may constrain species-assortative pairing. Females paired to heterospecifics may then benefit by copulating with multiple males and subsequently favoring sperm of conspecifics. Whether such mechanisms for biasing paternity toward conspecifics act as important reproductive barriers in socially monogamous vertebrate species remains to be determined. We use a combination of long-term breeding records from a natural hybrid zone between collared and pied flycatchers (Ficedula albicollis and F. hypoleuca), and an in vitro experiment comparing conspecific and heterospecific sperm performance in female reproductive tract fluid, to evaluate the potential significance of female cryptic choice. We show that the females most at risk of hybridizing (pied flycatchers) frequently copulate with multiple males and are able to inhibit heterospecific sperm performance. The negative effect on heterospecific sperm performance was strongest in pied flycatcher females that were most likely to have been previously exposed to collared flycatcher sperm. We thus demonstrate that a reproductive barrier acts after copulation but before fertilization in a socially monogamous vertebrate. While the evolutionary history of this barrier is unknown, our results imply that there is opportunity for it to be accentuated via a reinforcement-like process.

  • 307.
    Cuthbertson, Robin S.
    et al.
    University of Calgary.
    Mallon, Jordan C.
    Canadian Museum of Nature.
    Campione, Nicolas E.
    Carleton Univ, Dept Earth Sci, Ottawa, Canada.
    Holmes, Robert B.
    University of Alberta.
    A new species of mosasaur (Squamata: Mosasauridae) from the Pierre Shale (lower Campanian) of Manitoba2007In: Canadian journal of earth sciences (Print), ISSN 0008-4077, E-ISSN 1480-3313, Vol. 44, no 5, p. 593-606Article in journal (Refereed)
    Abstract [en]

    Plioplatecarpus nichollsae, sp. nov., from the lower Campanian (Pembina Member, Pierre Shale Formation) is diagnosed by the following: a thickened ventral rim of the external naris, a short supratemporal fenestra, a frontal shield with well-developed posterolateral lappets that overlap the parietal dorsally, proximal rib shafts with an approximately circular (but not inflated) cross section, a scapula shaped as in other Plioplatecarpus species but approximately the same size (not larger) than the coracoid, and a moderately large parietal foramen that reaches the frontoparietal suture but does not invade the frontal. The last two characters require that the diagnosis of the genus Plioplatecarpus be emended. With other Plioplatecarpus species, P. nichollsae shares a robust humerus with a distal expansion at least as great as the total length of the bone, a rectangular preorbital frontal shield, a "peg and socket" postorbitofrontal-jugal articulation, a transversely directed ectopterygoid process of the pterygoid, a large, robust quadrate with a distinct eminence on the posterior surface of its shaft, an unossified gap in the ventral wall of the basioccipital, and at least 11 pygal vertebrae. P. nichollsae also shares primitive features with Platecarpus, as well as features apparently intermediate betweenPlatecarpus and Plioplatecarpus. Revision of the genus Platecarpus, currently hypothesized to be both paraphyletic and polyphyletic, as well as a better understanding of the early Campanian mosasaur fauna from the Morden area, are necessary before the phylogenetic significance of some of these characters, and therefore the relationships of Plioplatecarpus nichollsae, can be fully resolved.

  • 308.
    Cárdenas, Paco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Bergen, Dept Biol, N-5020 Bergen, Norway..
    Rapp, Hans Tore
    Univ Bergen, Dept Biol, N-5020 Bergen, Norway.;Univ Bergen, Ctr Geobiol, N-5007 Bergen, Norway.;Uni Environm, Uni Res, N-5006 Bergen, Norway..
    Demosponges from the Northern Mid-Atlantic Ridge shed more light on the diversity and biogeography of North Atlantic deep-sea sponges2015In: Journal of the Marine Biological Association of the United Kingdom, ISSN 0025-3154, E-ISSN 1469-7769, Vol. 95, no 7, p. 1475-1516Article in journal (Refereed)
    Abstract [en]

    In July-August 2004, the Mid-Atlantic Ridge Ecosystems (MAR-Eco) expedition collected Demospongiae (Porifera) from the Northern Mid-Atlantic Ridge (MAR) north of the Azores, between 41 degrees N and 61 degrees N. Demosponges were found at 10 stations, at depths ranging from 753 to 3046 m. Twenty-two species were identified: 17 Tetractinellida, one Polymastiida, one Suberitida, two Poecilosclerida and one Dendroceratida. The study of this material is an opportunity to revise the taxonomy and the North Atlantic distribution of each of these deep-sea species. Some species are particularly rare and poorly known (Tetilla longipilis, Tetilla sandalina, Craniella azorica, Polymastia corticata) and two are new to science: Forcepia (Forcepia) toxafera sp. nov. and Iotroata paravaridens sp. nov. This study suggests that the MAR is not a longitudinal barrier for the dispersal of deep-sea demosponges while on the contrary, the Charlie-Gibbs Fracture Zone (CGFZ) may be a latitudinal border for the dispersal of deep-sea demosponges, due to great depths and currents.

  • 309.
    Daskalaki, Evangelia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Archaeological Genetics - Approaching Human History through DNA Analysis2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    There are a variety of archaeological questions, which are difficult to assess by traditional archaeological methods. Similarly, there are genetic and population genetic questions about human evolution and migration that are difficult to assess by studying modern day genetic variation. Archaeological genetics can directly study the archaeological remains, allowing human history to be explored by means of genetics, and genetics to be expanded into historical and pre-historical times. Examples of archaeological questions that can be resolved by genetics are determining biological sex on archaeological remains and exploring the kinship or groups buried in close proximity. Another example is one of the most important events in human prehistory – the transition from a hunter-gatherer lifestyle to farming - was driven through the diffusion of ideas or with migrating farmers. Molecular genetics has the potential to contribute in answering all these questions as well as others of similar nature. However, it is essential that the pitfalls of ancient DNA, namely fragmentation, damage and contamination are handled during data collection and data analysis.

    Analyses of ancient DNA presented in this thesis are based on both mitochondrial DNA and nuclear DNA through the study of single nuclear polymorphisms (SNPs). I used pyrosequencing assays in order to identify the biological sex of archaeological remains as well as verifying if fragmented remains were human or from animal sources. I used a clonal assay approach in order to retrieve sequences for the HVRI of a small family-like burial constellation from the Viking age. By the use of low coverage shotgun sequencing I retrieved sequence data from 13 crew members from the 17th century Swedish man-of-war Kronan. This data was used to determine the ancestry of the crew, which in some cases was speculated to be of non-Scandinavian or non-European origin. However, I demonstrate that all individuals were of European ancestry. Finally, I retrieved sequence data from a Neolithic farmer from the Iberian Peninsula, which added one more facet of information in exploring the Neolithization process of Europe. The Neolithic Iberian individual was genetically similar to Scandinavian Neolithic farmers, indicating that the genetic variation of prehistoric Europe correlated with subsistence mode rather than with geography.

    List of papers
    1. Further developments in molecular sex assignment: a blind test of 18th and 19th century human skeletons
    Open this publication in new window or tab >>Further developments in molecular sex assignment: a blind test of 18th and 19th century human skeletons
    2011 (English)In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 38, no 6, p. 1326-1330Article in journal (Refereed) Published
    Abstract [en]

    The identification of sex in human remains recovered from archaeological locations is important in order to understand the social and biological structure of past societies, and to reconstruct past population demographic events. Sex determination is usually based on morphological traits of the skeletons, with the drawback that most methods do not apply to juveniles and require well preserved remains. In cases where morphological methods cannot be used, or are ambiguous, methods of molecular sexing systems are an alternative. In this methodological study we tested and validated the accuracy and usefulness of a molecular sexing method based on the amelogenin gene using pyrosequencing. We did this in a double blind study of documented 18th and 19th century human remains.

    Keywords
    Molecular sexing, Human, Ancient DNA, Pyrosequencing
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-154599 (URN)10.1016/j.jas.2011.01.009 (DOI)000290420300016 ()
    Available from: 2011-06-09 Created: 2011-06-08 Last updated: 2017-12-11Bibliographically approved
    2. Mitochondrial DNA reveals a lack of kin relations in a suspected Viking age family constellation from a Swedish proto-Christian burial site.
    Open this publication in new window or tab >>Mitochondrial DNA reveals a lack of kin relations in a suspected Viking age family constellation from a Swedish proto-Christian burial site.
    (English)Manuscript (preprint) (Other academic)
    Keywords
    ancient DNA, genetics, mtDNA, kinskip, Sweden, Viking, Estrid, aDNA
    National Category
    Archaeology Genetics
    Identifiers
    urn:nbn:se:uu:diva-211151 (URN)
    Available from: 2013-11-20 Created: 2013-11-20 Last updated: 2014-04-29
    3. Genomic analysis of biogeographic ancestry of 15 crewmembers from the 300 year-old Swedish man-of-war Kronan
    Open this publication in new window or tab >>Genomic analysis of biogeographic ancestry of 15 crewmembers from the 300 year-old Swedish man-of-war Kronan
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    Marine archaeology, Kronan, ancient DNA, genetics
    National Category
    Archaeology Genetics Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-211152 (URN)
    Available from: 2013-11-20 Created: 2013-11-20 Last updated: 2014-04-29
    4. A late Neolithic Iberian farmer exhibits genetic affinity to Neolithic Scandinavian farmers and a Bronze Age central European  farmer
    Open this publication in new window or tab >>A late Neolithic Iberian farmer exhibits genetic affinity to Neolithic Scandinavian farmers and a Bronze Age central European  farmer
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    ancient DNA, neolithization, Iberia, Portalon, aDNA, SNP
    National Category
    Archaeology Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-211155 (URN)
    Available from: 2013-11-20 Created: 2013-11-20 Last updated: 2014-04-29
  • 310.
    Daskalaki, Evangelia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Skoglund, Pontus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Einarson, Lars
    Kalmars läns museum.
    Kjellström, Anna
    Stockholm University.
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Götherström, Anders
    Stockholm University.
    Genomic analysis of biogeographic ancestry of 15 crewmembers from the 300 year-old Swedish man-of-war KronanManuscript (preprint) (Other academic)
  • 311. Davis, Simon J. M.
    et al.
    Svensson, Emma M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Albarella, Umberto
    Detry, Cleia
    Götherström, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Pires, Ana Elisabete
    Ginja, Catarina
    Molecular and osteometric sexing of cattle metacarpals: a case study from 15th century AD Beja, Portugal2012In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 39, no 5, p. 1445-1454Article in journal (Refereed)
    Abstract [en]

    In the course of a zooarchaeological survey of Holocene sites in southern Portugal, a substantial size increase of cattle bones was noted following the Christian reconquista of the 11th-13th centuries AD. A size increase in the course of time within a lineage of domestic livestock is usually considered to represent animal improvement. However several other factors including sex may influence the average size of a sample of mammal bones - cattle exhibit considerable sexual size dimorphism, with bulls being larger than cows. A histogram of the distal widths of a large (n = 44) sample of cattle metacarpals from 15th century Beja (Alentejo, Portugal), revealed a bimodal distribution. It was assumed that the large measurements belonged to males and the small to females. In order to rule out the possibility of a post-Moslem change in the sex ratio of cattle, a sub-sample of 21 cattle metacarpals from Beja was selected and we used genetic markers to identify the sex of the animals to which these metacarpals belonged. The ancient DNA sex of all specimens agreed with the previously assumed sex as determined osteometrically. We conclude that the two nearly separated peaks for the metacarpal distal width measurements do indeed indicate sex. A similar bimodal distribution was obtained from another large but earlier sample of cattle metacarpals from Moslem Alcacova de Santarem (9th-12th century AD). Although these have not been molecularly sexed and since osteometric sexing has now been validated, we conclude that both small (female) and large (male) peaks are smaller than the 15th century ones and that there was an overall size increase or improvement of cattle in this region. Why the Christians improved cattle is unclear, but a selection for larger beeves for meat is one possibility as is the selection of more robust cattle for power. The spread of the quadrangular or chariot plough in Iberia is known to have occurred at this time. We then use the genetically sexed metacarpals to determine which measurements provide reasonable distinction between the sexes. Both the distal width (BFd; as already noted by Svensson et al., 2008; in Swedish medieval cattle) and the width of the lateral condyle (WCL) offer the best distinction. We also used them as a reference 'collection' to sex the medieval and post-medieval cattle metacarpals from Launceston Castle in England. This re-visit of the Launceston data corroborates other evidence indicating increased specialisation (milk and veal) in post-medieval cattle husbandry in England.

  • 312.
    Den Boer, Wendy
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Kear, Benjamin P.
    Uppsala University, Music and Museums, Museum of Evolution.
    Is the fossil rat-kangaroo Palaeopotorous priscus the most basally branching stem macropodiform?2018In: Journal of Vertebrate Paleontology, ISSN 0272-4634, E-ISSN 1937-2809, Vol. 38, no 2, article id e1428196Article in journal (Refereed)
  • 313.
    Dharamshi, Jennah
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Abundant and diverse novel bacteria in the deep-sea.2015Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 314.
    Dirks-Mulder, Anita
    et al.
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Butot, Roland
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands..
    van Schaik, Peter
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Wijnands, Jan Willem P. M.
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    van den Berg, Roel
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Krol, Louie
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    Doebar, Sadhana
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    van Kooperen, Kelly
    Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands..
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Oslo, Nat Hist Museum, POB 1172 Blindern, N-0318 Oslo, Norway..
    Kramer, Elena M.
    Harvard Univ, Dept Organism & Evolutionary Biol, 16 Div Ave, Cambridge, MA 02138 USA..
    Smets, Erik F.
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Katholieke Univ Leuven, Ecol Evolut & Biodivers Conservat cluster, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium..
    Vos, Rutger A.
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Amsterdam, Inst Biodivers & Ecosyst Dynam, Sci Pk 904, NL-1098 XH Amsterdam, Netherlands..
    Vrijdaghs, Alexander
    Katholieke Univ Leuven, Ecol Evolut & Biodivers Conservat cluster, Kasteelpark Arenberg 31, B-3001 Leuven, Belgium..
    Gravendeel, Barbara
    Naturalis Biodivers Ctr, Endless Forms Grp, Vondellaan 55, NL-2332 AA Leiden, Netherlands.;Univ Appl Sci Leiden, Fac Sci & Technol, Zernikedreef 11, NL-2333 CK Leiden, Netherlands.;Leiden Univ, Inst Biol, Sylviusweg 72, NL-2333 BF Leiden, Netherlands..
    Exploring the evolutionary origin of floral organs of Erycina pusilla, an emerging orchid model system2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 89Article in journal (Refereed)
    Abstract [en]

    Background: Thousands of flowering plant species attract pollinators without offering rewards, but the evolution of this deceit is poorly understood. Rewardless flowers of the orchid Erycina pusilla have an enlarged median sepal and incised median petal ('lip') to attract oil-collecting bees. These bees also forage on similar looking but rewarding Malpighiaceae flowers that have five unequally sized petals and gland-carrying sepals. The lip of E. pusilla has a 'callus' that, together with winged 'stelidia', mimics these glands. Different hypotheses exist about the evolutionary origin of the median sepal, callus and stelidia of orchid flowers. Results: The evolutionary origin of these organs was investigated using a combination of morphological, molecular and phylogenetic techniques to a developmental series of floral buds of E. pusilla. The vascular bundle of the median sepal indicates it is a first whorl organ but its convex epidermal cells reflect convergence of petaloid features. Expression of AGL6 EpMADS4 and APETALA3 EpMADS14 is low in the median sepal, possibly correlating with its petaloid appearance. A vascular bundle indicating second whorl derivation leads to the lip. AGL6 EpMADS5 and APETALA3 EpMADS13 are most highly expressed in lip and callus, consistent with current models for lip identity. Six vascular bundles, indicating a stamen-derived origin, lead to the callus, stelidia and stamen. AGAMOUS is not expressed in the callus, consistent with its sterilization. Out of three copies of AGAMOUS and four copies of SEPALLATA, EpMADS22 and EpMADS6 are most highly expressed in the stamen. Another copy of AGAMOUS, EpMADS20, and the single copy of SEEDSTICK, EpMADS23, are most highly expressed in the stelidia, suggesting EpMADS22 may be required for fertile stamens. Conclusions: The median sepal, callus and stelidia of E. pusilla appear to be derived from a sepal, a stamen that gained petal identity, and stamens, respectively. Duplications, diversifying selection and changes in spatial expression of different MADS-box genes shaped these organs, enabling the rewardless flowers of E. pusilla to mimic an unrelated rewarding flower for pollinator attraction. These genetic changes are not incorporated in current models and urge for a rethinking of the evolution of deceptive flowers.

  • 315.
    Djureinovic, Dijana
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Fagerberg, L.
    Hallstrom, B.
    Danielsson, A.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Lindskog Bergström, Cecilia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Uhlen, M.
    Pontén, Fredrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The human testis-specific proteome defined by transcriptomics and antibody-based profiling2014In: Molecular human reproduction, ISSN 1360-9947, E-ISSN 1460-2407, Vol. 20, no 6, p. 476-488Article in journal (Refereed)
    Abstract [en]

    The testis' function is to produce haploid germ cells necessary for reproduction. Here we have combined a genome-wide transcriptomics analysis with immunohistochemistry-based protein profiling to characterize the molecular components of the testis. Deep sequencing (RNA-Seq) of normal human testicular tissue from seven individuals was performed and compared with 26 other normal human tissue types. All 20 050 putative human genes were classified into categories based on expression patterns. The analysis shows that testis is the tissue with the most tissue-specific genes by far. More than 1000 genes show a testis-enriched expression pattern in testis when compared with all other analyzed tissues. Highly testis enriched genes were further characterized with respect to protein localization within the testis, such as spermatogonia, spermatocytes, spermatids, sperm, Sertoli cells and Leydig cells. Here we present an immunohistochemistry-based analysis, showing the localization of corresponding proteins in different cell types and various stages of spermatogenesis, for 62 genes expressed at > 50-fold higher levels in testis when compared with other tissues. A large fraction of these genes were unexpectedly expressed in early stages of spermatogenesis. In conclusion, we have applied a genome-wide analysis to identify the human testis-specific proteome using transcriptomics and antibody-based protein profiling, providing lists of genes expressed in a tissue-enriched manner in the testis. The majority of these genes and proteins were previously poorly characterised in terms of localization and function, and our list provides an important starting point to increase our molecular understanding of human reproductive biology and disease.

  • 316.
    Dombrowski, Nina
    et al.
    Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, NIOZ, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands;Univ Utrecht, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands;Univ Texas Austin, Marine Sci Inst, Dept Marine Sci, 750 Channel View Dr, Port Aransas, TX 78373 USA.
    Lee, Jun-Hoe
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Williams, Tom A.
    Univ Bristol, Sch Biol Sci, Life Sci Bldg,24 Tyndall Ave, Bristol BS8 1TQ, Avon, England.
    Offre, Pierre
    Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, NIOZ, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands;Univ Utrecht, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands.
    Spang, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Royal Netherlands Inst Sea Res, Dept Marine Microbiol & Biogeochem, NIOZ, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands;Univ Utrecht, POB 59,Landsdiep 4, NL-1790 AB Den Burg, Netherlands.
    Genomic diversity, lifestyles and evolutionary origins of DPANN archaea2019In: FEMS Microbiology Letters, ISSN 0378-1097, E-ISSN 1574-6968, Vol. 366, no 2, article id fnz008Article, review/survey (Refereed)
    Abstract [en]

    Archaea-a primary domain of life besides Bacteriahave for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery of a large diversity of archaea in non-extreme environments enabled by the use of cultivation-independent methods. These approaches have allowed the reconstruction of genomes of uncultivated microorganisms and revealed that archaea are diverse and broadly distributed in the biosphere and seemingly include a large diversity of putative symbiotic organisms, most of which belong to the tentative archaeal superphylum referred to as DPANN. This archaeal group encompasses at least 10 different lineages and includes organisms with extremely small cell and genome sizes and limited metabolic capabilities. Therefore, many members of DPANN may be obligately dependent on symbiotic interactions with other organisms and may even include novel parasites. In this contribution, we review the current knowledge of the gene repertoires and lifestyles of members of this group and discuss their placement in the tree of life, which is the basis for our understanding of the deep microbial roots and the role of symbiosis in the evolution of life on Earth.

  • 317. Doolittle, W F
    et al.
    Boucher, Y
    Nesbø, C L
    Douady, C J
    Andersson, Jan O
    Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, NS B3H 1X5, Canada .
    Roger, A J
    How big is the iceberg of which organellar genes in nuclear genomes are but the tip?2003In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 358, no 1429, p. 39-58; discussion 57Article in journal (Refereed)
    Abstract [en]

    As more and more complete bacterial and archaeal genome sequences become available, the role of lateral gene transfer (LGT) in shaping them becomes more and more clear. Over the long term, it may be the dominant force, affecting most genes in most prokaryotes. We review the history of LGT, suggesting reasons why its prevalence and impact were so long dismissed. We discuss various methods purporting to measure the extent of LGT, and evidence for and against the notion that there is a core of never-exchanged genes shared by all genomes, from which we can deduce the "true" organismal tree. We also consider evidence for, and implications of, LGT between prokaryotes and phagocytic eukaryotes.

  • 318.
    Dordevic, Mirko
    et al.
    Univ Belgrade, Inst Biol Res, Dept Evolutionary Biol, Despota Stefana Blvd 142, Belgrade 11060, Serbia..
    Stojkovic, Biljana
    Univ Belgrade, Inst Biol Res, Dept Evolutionary Biol, Despota Stefana Blvd 142, Belgrade 11060, Serbia.;Univ Belgrade, Fac Biol, Inst Zool, Studentskitrg 16, Belgrade 11000, Serbia..
    Savkovic, Uros
    Univ Belgrade, Inst Biol Res, Dept Evolutionary Biol, Despota Stefana Blvd 142, Belgrade 11060, Serbia..
    Immonen, Elina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Tucic, Nikola
    Univ Belgrade, Inst Biol Res, Dept Evolutionary Biol, Despota Stefana Blvd 142, Belgrade 11060, Serbia..
    Lazarevic, Jelica
    Univ Belgrade, Inst Biol Res, Dept Insect Physiol & Biochem, Despota Stefana Blvd 142, Belgrade 11060, Serbia..
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Sex-specific mitonuclear epistasis and the evolution of mitochondrial bioenergetics, ageing, and life history in seed beetles2017In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 71, no 2, p. 274-288Article in journal (Refereed)
    Abstract [en]

    The role of mitochondrial DNA for the evolution of life-history traits remains debated. We examined mitonuclear effects on the activity of the multisubunit complex of the electron transport chain (ETC) involved in oxidative phosphorylation (OXPHOS) across lines of the seed beetle Acanthoscelides obtectus selected for a short (E) or a long (L) life for more than >160 generations. We constructed and phenotyped mitonuclear introgression lines, which allowed us to assess the independent effects of the evolutionary history of the nuclear and the mitochondrial genome. The nuclear genome was responsible for the largest share of divergence seen in ageing. However, the mitochondrial genome also had sizeable effects, which were sex-specific and expressed primarily as epistatic interactions with the nuclear genome. The effects of mitonuclear disruption were largely consistent with mitonuclear coadaptation. Variation in ETC activity explained a large proportion of variance in ageing and life-history traits and this multivariate relationship differed somewhat between the sexes. In conclusion, mitonuclear epistasis has played an important role in the laboratory evolution of ETC complex activity, ageing, and life histories and these are closely associated. The mitonuclear architecture of evolved differences in life-history traits and mitochondrial bioenergetics was sex-specific.

  • 319.
    Dougherty, Liam R.
    et al.
    Univ Western Australia, Sch Biol Sci, Ctr Evolutionary Biol, Australia..
    van Lieshout, Emile
    Univ Western Australia, Sch Biol Sci, Ctr Evolutionary Biol, Australia..
    McNamara, Kathryn B.
    Univ Western Australia, Sch Biol Sci, Ctr Evolutionary Biol, Crawley, Australia..
    Moschilla, Joe A.
    Univ Western Australia, Sch Biol Sci, Ctr Evolutionary Biol, Australia..
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Simmons, Leigh W.
    Univ Western Australia, Sch Biol Sci, Ctr Evolutionary Biol, Australia..
    Sexual conflict and correlated evolution between male persistence and female resistance traits in the seed beetle Callosobruchus maculatus2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1855, article id 20170132Article in journal (Refereed)
    Abstract [en]

    Traumatic mating (or copulatory wounding) is an extreme form of sexual conflict whereby male genitalia physically harm females during mating. In such species females are expected to evolve counter-adaptations to reduce male-induced harm. Importantly, female counter-adaptations may include both genital and non-genital traits. in this study, we examine evolutionary associations between harmful male genital morphology and female reproductive tract morphology and immune function across 13 populations of the seed beetle Callosobruchus maculatus. We detected positive correlated evolution between the injuriousness of male genitalia and putative female resistance adaptations across populations. Moreover, we found evidence for a negative relationship between female immunity and population productivity, which suggests that investment in female resistance may be costly due to the resource trade-offs that are predicted between immunity and reproduction. Finally, the degree of female tract scarring (harm to females) was greater in those populations with both longer aedeagal spines and a thinner female tract lining. Our results are thus consistent with a sexual arms race, which is only apparent when both male and female traits are taken into account. Importantly, our study provides rare evidence for sexually antagonistic coevolution of male and female traits at the within-species level.

  • 320. Dreiss, A N
    et al.
    Antoniazza, S
    Burri, Reto
    Fumagalli, L
    Sonnay, C
    Frey, C
    Goudet, J
    Roulin, Alexandre
    Local adaptation and matching habitat choice in female barn owls with respect to melanic coloration.2012In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 25, no 1, p. 103-114Article in journal (Refereed)
    Abstract [en]

    Local adaptation is a major mechanism underlying the maintenance of phenotypic variation in spatially heterogeneous environments. In the barn owl (Tyto alba), dark and pale reddish-pheomelanic individuals are adapted to conditions prevailing in northern and southern Europe, respectively. Using a long-term dataset from Central Europe, we report results consistent with the hypothesis that the different pheomelanic phenotypes are adapted to specific local conditions in females, but not in males. Compared to whitish females, reddish females bred in sites surrounded by more arable fields and less forests. Colour-dependent habitat choice was apparently beneficial. First, whitish females produced more fledglings when breeding in wooded areas, whereas reddish females when breeding in sites with more arable fields. Second, cross-fostering experiments showed that female nestlings grew wings more rapidly when both their foster and biological mothers were of similar colour. The latter result suggests that mothers should particularly produce daughters in environments that best match their own coloration. Accordingly, whiter females produced fewer daughters in territories with more arable fields. In conclusion, females displaying alternative melanic phenotypes bred in habitats providing them with the highest fitness benefits. Although small in magnitude, matching habitat selection and local adaptation may help maintain variation in pheomelanin coloration in the barn owl.

  • 321.
    Dunlap, Paul V
    et al.
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Ast, Jennifer C
    University of Michigan, Department of Ecology and Evolutionary Biology.
    Kimura, Seishi
    Fisheries Research Laboratory, Mie University, Shima, Mie, Japan.
    Fukui, Atsushi
    School of Fisheries and Marine Technology, Tokai University, Shimizu-Orido, Shizuoka, Japan.
    Yoshino, Tetsuo
    Department of Marine Sciences, University of the Ryukyus, Nishihara, Okinawa, Japan.
    Endo, Hiromitsu
    Laboratory of Marine Biology, Kochi University, Kochi, Japan.
    Phylogenetic analysis of host–symbiont specificity and codivergence in bioluminescent symbioses2007In: Cladistics, ISSN 0748-3007, E-ISSN 1096-0031, Vol. 23, no 5, p. 507-532Article in journal (Refereed)
  • 322.
    Dupret, Vincent
    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.
    Goujet, Daniel
    Muséum National D'Histoire Naturelle, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Being Romundina stellina Ørvig, 1975 (Vertebrate, Placodermi, Acanthothoraci): itracranial anatomy of one of the deepest gnathostomes revealed by synchrotron tomograpy in phase contrast protocole2012In: / [ed] Malvesy, T., Gauthrot, M., Fuchs, C., Berthoz, A., Blieck, A., Becker, D., Buffetaut, E., Mazin, J. -M.,, Montbéliard, 2012, p. 19-19Conference paper (Refereed)
    Abstract [en]

    Dans la peau de Romundina stellina Ørvig, 1975 (Vertebrata, Placodermi, Acanthothoraci)

    Anatomie crânienne d'un des premiers gnathostomes révélée par tomographie synchrotron en contraste de phase

     Being Romundina stellina Ørvig, 1975  (Vertebrata, Placodermi, Acanthothoraci)

    Intracranial anatomy of one of the deepest gnathostomes revealed by synchrotron tomography in phase contrast protocole

     

     

    The acanthothoracid placoderms (armored fishes) are the most basal and primitive gnathostomes (jawed vertebrates; 1). However, their endocranial morphology is poorly understood, and only one genus (Brindabellaspis) has been described thoroughly (2).

    Here we present the 3D reconstruction of a subcomplete skull of Romundina stellina Ørvig, 3, from the Lochkovian of Prince of Wales Island, Canadian Arctic Archipelago. The specimen was imaged in 3D with propagation phase contrast microtomography (4) on the ID19 beamline of the ESRF, using a 7.45 µm isotropic voxel size.

    Most features are properly preserved and most of the missing structures can be virtually rebuilt by symmetry. Another advantage of this virtual approach is the possibility of connecting with certainty all the external foramina to the blood and nerve canals and the central/internal structures, and hence to identify accurate homologies without destroying the specimen. Ørvig’s original assumptions can now be checked with confidence.

    The vasculature of the dermal bones, rendered in detail, allowed a better understanding of plate growth. It permits the visualization of dermal bone establishment over perichondral bone (5).

    The high level of details of this model reveals that between the trigeminal and vagus nerve (and the inner ears), the perichondral bone wrapping the endocranial cavity shows a “lace” pattern, unknown so far in vertebrates (presumably because of the lack of data). The significance of this character is unclear, but it is definitely not an artifact of taphonomy or scanning.

     

    References

    1          Janvier, P. Early Vertebrates. Clarendon Press edn, Vol. 1 (Oxford Science Publications, 1996).

    2          Young, G. C. A new Early Devonian placoderm from New South Wales, Australia, with a discussion of placoderm phylogeny. Palaeontographica (A) 167, 10–76 (1980).

    3          Ørvig, T. Description, with special reference to the dermal skeleton, of a new Radotinid arthrodire from the Gedinnian of Arctic Canada. Extrait des Colloques internationaux du Centre National de la Recherche Scientifique - Problèmes actuels de Paléontologie - Evolution des Vertébrés 218, 41–71 (1975).

    4          Tafforeau, P. et al. Applications of X-ray synchrotron microtomography for non-destructive 3D studies of paleontological specimens. Applied Physics A - Materials Science & Processing 83, 195–202 (2006).

    5          Dupret, V., Sanchez, S., Goujet, D., Tafforeau, P. & Ahlberg, P. Bone vascularization and growth in placoderms (Vertebrata): the example of the premedian plate of Romundina stellina Ørvig, 1975 Comptes Rendus Palevol 9, 369–375 (2010).

     

     

  • 323.
    Dupret, Vincent
    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.
    Goujet, Daniel
    Muséum National D'Histoire Naturelle, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Fossil early vertebrates shed lights on the origin of the gnathostome face2013In: Program and Abstracts of the 10th International Congress of Vertebrate Morphology, Barcelona, Spain, 2013, p. 245-245Conference paper (Refereed)
    Abstract [en]

    Jawless cyclostomes and jawed gnathostomes show very different face patterns. Cyclostomes have a single median nasohypophysial duct, an anterior hypophysis and a short telencephalon, while gnathostomes have a pair of nasal sacs opening externally, a more posterior separate hypophysis open in the palate and a longer telencephalon.

    Embryonic processes differ as well. In cyclostomes, premandibular crest cells migrate forwards either side of the nasohypophysial placode to form the upper lip; in gnathostomes they migrate between the hypophysial and nasal placodes to form the trabecular region. Supraoptic neural crest remains posterior to the nasohypophysial duct in cyclostomes; it moves forward to create the nasal capsules in gnathostomes.

    Some fossil forms illustrate a transition between these two patterns.

    The jawless galeaspid Shuyu (-430 Ma) has a nasohypophysial duct, short telencephalon, and anteriorly oriented hypophysis, but the paired nasal sacs and hypophysis are separated by a rudimentary trabecula.

    The jawed primitive placoderm Romundina (-415 Ma) shows a cranial cavity reminiscent of that of Shuyu (anteriorly directed hypophysis, very short telencephalon). The trabecular region is long and wide, the nasal capsule is small and located far behind the tip of the snout but just in front of the orbits. We interpret these features as uniquely primitive among gnathostomes. The premandibular crest of Romundina formed a trabecular region extending as anteriorly as the tip of the snout (like in extant cyclostome and the fossil Shuyu). The position of the nasal capsule suggests that the supraoptic crest had not migrated forwards.

    We suggest that the evolutionary sequence for the creation of the extant gnathostome face from a cyclostome pattern involved 1) separation of the nasal and hypophysial placodes (galeaspids), 2) loss of the nasohypophysial duct (placoderms), and 3) lengthening of the telencephalon and the migration of the nasal capsules to the snout tip.

  • 324.
    Dupret, Vincent
    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.
    Goujet, Daniel
    Muséum National D'Histoire Naturelle, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Fossils of early vertebrates and the evolution of the gnathostome face revealed by Synchrotron imaging2013In: Programme and Abstracts / [ed] Stig Walsh, Nick Fraser, Stephen Brusatte, Jeff Liston, Vicen Carrió, Edinburgh, U.K., 2013, p. 21-21Conference paper (Refereed)
    Abstract [en]

    Cyclostomes and gnathostomes have distinct face patterns. Cyclostomes possess a median nasohypophysial duct, an anterior hypophysis and a short telencephalon, contra gnathostomes possessing a pair of nasal sacs opening externally, a separate posterior hypophysis opening onto the palate and a long telencephalon. Embryonic development also differs. In cyclostomes, premandibular crest cells migrate forwards either side of the nasohypophysial placode, forming an upper lip; in gnathostomes they migrate between the hypophysial and nasal placodes forming the trabecular region. Supraoptic neural crest remains posterior to the nasohypophysial duct in cyclostomes but moves forward to create the nasal capsules in gnathostomes. Fossil stem gnathostomes illustrate a transitional sequence between these two patterns: 1) The galeaspid Shuyu (jawless stem gnathostome): nasohypophysial duct, short telencephalon, and anteriorly oriented hypophysis as in a cyclostome, but paired nasal sacs and hypophysis separated by a rudimentary trabecula. 2) The primitive placoderm Romundina (jawed stem gnathostome): short telencephalon, anteriorly directed hypophysis, trabecular region long and wide, nasal capsule located far behind the tip of the snout but just in front of the orbits. These features are interpreted as uniquely primitive among gnathostomes. The trabeculae of Romundina form an extensive precerebral region resembling the upper lip of extant cyclostomes and Shuyu. The position of the nasal capsule suggests that the supraoptic crest had not migrated forwards. 3) The arthrodire Kujdanowiapsis (a more derived placoderm): short telencephalon and vertically oriented hypophysis. The trabecula has been shortened anteriorly, making the nasal capsule terminal. These positional relationships are maintained in crown gnathostomes.

  • 325.
    Dupret, Vincent
    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.
    Goujet, Daniel
    Muséum National D'Histoire Naturelle, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Internal structures of the skull of Romundina stellina Ørvig 1975 (Vertebrata, Placodermi, Acanthothoraci) revealed by phase contrast synchrotron scanning2011In: CAVEPS Perth 2011: Conference on Australasian Vertebrate Evolution Palaeontology and Systematics, Perth, April 27th-30th : programme, abstracts / [ed] Geological Survey of Western Australia, East Perth, W.A: Geological Survey of Western Australia , 2011, p. 30-30Conference paper (Refereed)
  • 326.
    Dupret, Vincent
    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.
    Goujet, Daniel
    Muséum National D'Histoire Naturelle, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Intracranial anatomy of Romundina stellina Ørvig 1975 (Vertebrata, Placodermi, Acanthothoraci) revealed by phase contrast synchrotron imaging2011In: Abstracts: The 2nd Wiman meeting Carl Wiman's Legacy: 100 years of Swedish Palaeontology: Uppsala 17–18 November 2011 / [ed] Benjamin P. Kear, Michael Streng, 2011, p. 6-6Conference paper (Other academic)
    Abstract [en]

    Acanthothoracid placoderms are considered amongst the most basal of primitive gnathostomes. However, their endocranial morphology is poorly understood, and only one genus (Brindabellaspis) has been described in detail. Here we present a synchrotrongenerated 3D reconstruction of a nearly complete skull of Romundina stellina, a taxon established in 1975 by the Norwegian-born Swedish palaeontologist Tor Ørvig based on remains from the Lochkovian (Lower Devonian) of Prince of Wales Island, Canadian Arctic Archipelago. The specimen was imaged with propagation phase contrast microtomography on the ID19 beamline of the ESRF, using a 7.45 µm isotropic voxel size. Most structural features of the fossil are very well preserved, allowing missing elements to be virtually rebuilt by symmetry. This permitted reconnection of the external foramina and blood vessel/nerve canals, and alignment of the central/internal structures. Expanding on Ørvig’s original interpretations, our virtual models show the vasculature of the skull bones, and indicate establishment of successive dermal over perichondral bone layers. The perichondral bone wrapping the endocranial cavity, in between the trigeminal and vagus nerve (and the inner ears), shows a “lace” pattern, which is otherwise unknown in vertebrates (presumably because of the lack of data). The significance of this trait is unclear but it is not an artifact of taphonomy or scanning.

  • 327.
    Dupret, Vincent
    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.
    Goujet, Daniel
    Muséum National D'Histoire Naturelle, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Structures intra-crâniennes de Romundina stellina Ørvig 1975 (Vertebrata, Placodermi, Acanthothoraci) révélé par tomographie synchrotron en contraste de phase2012Conference paper (Refereed)
    Abstract [fr]

    Les placodermes acanthothoracides sont parmi les vertébrés gnathostomes les plus basaux phylogénetiquement et morphologiquement. Néanmoins, une bonne connaissance anatomie crânienne fait défaut, et à ce jour un seul genre (Brindabellaspis) a été décrit en détails. Nous présentons le modèle en 3 dimensions d’un crâne presque complet de Romundina stellina, un petit acanthothoracide du Dévonien inférieur de l’Archipel Arctique Canadien, décrit originellement par Ørvig (1975). Le spécimen a été microtomographié sur la ligne de faisceau ID 19 de l’ESRF de Grenoble (European Synchrotron Radiation Facility), en protocole de contraste de phase, avec un voxel isotrope de 7,45 micromètres.

    Malgré une cassure oblique, la plupart des structures peuvent être reconstruites par symétrie. Chaque nerf crânien peut être suivi entre la cavité encéphalique et les murs du neurocrâne composés d’os périchondral. Il en est de même pour les vaisseaux sanguins. La détermination des homologies en est donc facilitée, tout en assurant la non destruction du spécimen. Les hypothèses d’homologies formulées par Ørvig peuvent être traitées en toute confidence.

    La couche d’os périchondrale entourant la cavité encéphalique n’est pas homogène mais présente un aspect en dentelle entre les nerfs trijumeaux (V) et vague (X) ; il en est de même pour les oreilles internes, dont les canaux semi-circulaires ne sont pas ossifiés du tout latéralement et dorsalement. Cet aspect en dentelle n’est ni un artefact de fossilisation, de préservation ou de modélisation, et n’a jamais été retrouvé sur aucun autre vertébré (mais l’échantillonnage à cette résolution fait encore cruellement défaut).

    Les canalicules nerveux reliés aux neuromastes de la ligne latérale permettent de retracer leur origine à une branche du nerf facial (VII). Les deux oreilles internes ont été reconstruites avec précision et montrent une morphologie primitive.

    Le réseau vasculaire de l’os dermique a été reconstruit en détails, et permet de mettre en évidence les limites de plaques du toit crânien, invisibles autrement. Ce réseau vasculaire est relié à des veines drainant la bordure de la boîte crânienne ou à une branche de la veine jugulaire. La courbure de ces vaisseaux autour de l’oreille interne pourrait démarquer la limite entre la capsule otique et l’arc hyoïdien qui s’y attachait.

    D’un point de vue général, la morphologie de la boîte crânienne et de ses structures associées paraît moins primitive (et moins extrême) que celle de Brindabellaspis, mais rappelle au contraire plus les structures observées chez le placoderme arthrodire Kujdanowiaspis, plus dérivé.

    Ces différences mettent en lumière les premiers stades de l’évolution du crâne des placodermes, donc des gnathostomes. 

  • 328.
    Dupret, Vincent
    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.
    Goujet, Daniel
    Muséum National D'Histoire Naturelle, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The origin of the jawed vertebrate face: new insights from a synchrotron scanned skull of the primituve placoderm Romundina2013In: Program and abstracts / [ed] Maxwell, E., Miller-Camp, J., Anemone, R.,, Los Angeles, U.S.A., 2013, p. 118-118Conference paper (Other academic)
    Abstract [en]

    Jawless cyclostomes and jawed gnathostomes show very different face patterns.Cyclostomes have a single median nasohypophysial duct, an anterior hypophysis and ashort telencephalon, while gnathostomes have a pair of nasal sacs opening externally, amore posterior separate hypophysis opening in the palate and a longer telencephalon.Embryonic processes differ as well. In cyclostomes, infraorbital premandibular crest cellsmigrate forwards either side of the nasohypophysial placode to form the upper lip; ingnathostomes they migrate between the hypophysial and nasal placodes to form thetrabecular-ethmoid region. Supraoptic neural crest remains posterior to thenasohypophysial duct in cyclostomes; it moves forward to create the nasal capsules ingnathostomes. Some fossil forms illustrate a sequenced transition between these twopatterns. The Silurian galeaspid (jawless stem gnathostome) Shuyu has a nasohypophysialduct, a short telencephalon, and an anteriorly oriented hypophysis, but the paired nasalsacs and hypophysis are separated by a rudimentary trabecula. A synchrotron scannedskull of the primitive Early Devonian placoderm (jawed stem gnathostome) Romundinashows a cranial cavity reminiscent of that of Shuyu (anteriorly directed hypophysis, veryshort telencephalon). The trabecular-ethmoid region is long and wide, extending anteriorto the small nasal capsule which is located just in front of the orbits. We interpret thesefeatures as uniquely primitive among gnathostomes. In size and position the trabecularethmoidregion of Romundina resembles the upper lip of cyclostomes and Shuyu,suggesting a cyclostome-like pattern of proliferation coupled with a gnathostome-likemigration path for the premandibular crest. The position of the nasal capsule suggests thatthe supraoptic crest had not migrated forwards. A new phylogenetic analysis suggeststhat the evolutionary sequence for the creation of the extant gnathostome face from acyclostome ancestral pattern involved 1) separation of the nasal and hypophysialplacodes (galeaspids: Shuyu), 2) loss of the nasohypophysial duct (basal placoderms:antiarchs, Brindabellaspis, Romundina), 3) shortening and narrowing of the trabecularethmoidregion, the nasal capsule becoming anterior (derived placoderms such asarthrodires); 4) lengthening of the telencephalon (crown gnathostomes). Galeaspid facialanatomy appears closer to gnathostomes than that of osteostracans, but it is unclearwhether osteostracans are primitive or autapomorphic in this respect.

  • 329.
    Dupret, Vincent
    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.
    Goujet, Daniel
    Muséum National D'Histoire Naturelle, Paris, France.
    Tafforeau, Paul
    European Synchrotron Radiation Facility, Grenoble, France.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The Placoderm Romundina and the Origin of the Gnathostome Face2013Conference paper (Refereed)
    Abstract [en]

    Facial anatomy differs fundamentally between extant jawless and jawed vertebrates (cyclostomes and gnathostomes). Cyclostomes have a median nasohypophysial duct; gnathostomes have separate nasal sacs opening externally, and a palatal hypophysis. Premandibular crest cells migrate forwards either side of the nasohypophysial placode to form the upper lip in cyclostomes, but between the hypophysial and nasal placodes to form the trabecular region in gnathostomes1,2. Supraoptic neural crest remains posterior to the nasohypophysial duct in cyclostomes but moves forward to create the nasal capsules of gnathostomes1,2. In cyclostomes the telencephalon is much shorter than in gnathostomes and the hypophysis is relatively anterior. The galeaspid Shuyu, a 430 million year old jawless vertebrate, partly bridges the gap between these facial architectures3. Shuyu has a nasohypophysial duct, short telencephalon, and anteriorly oriented hypophysis, but the nasal sacs and hypophysis are separated by a rudimentary trabecul. Here we present the placoderm Romundina, a 415 million year old jawed vertebrate that represents a further transitional step. Its cranial cavity is similar to that of Shuyu, with an anteriorly directed hypophysis and very short telencephalon. The trabecular region is exceptionally long and wide whereas the nasal capsule (demarcated by a fissure) is small and located far behind the tip of the snout. The upper jaw articulates with the side of the trabecular region to its anterior end, without contacting the nasal capsule. We interpret these features as uniquely primitive among gnathostomes. The premandibular crest of Romundina formed a trabecular region, but like the upper lip of cyclostomes and Shuyu it was a large structure reaching the tip of the snout. The position of the nasal capsule suggests that the supraoptic crest had not migrated forwards. We suggest that during the creation of the gnathostome face, separation of the nasal and hypophysial placodes was followed by loss of the nasohypophysial duct, with lengthening of the telencephalon and migration of the nasal capsules to the snout tip as the final step.

     

    1. Kuratani, S. et al. Phil. Trans. R. Soc. Lond. B 356, 1615-1632 (2001).

    2. Kuratani, S. et al. Nature (in press, doi:10.1038/nature11794).

    3. Gai, Z. et al. Nature 476, 324-327 (2011).

  • 330.
    Dupret, Vincent
    et al.
    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, Xizhimenwai Dajie 142, Beijing 100044, Peoples R China.;Australian Natl Univ, Res Sch Phys & Engn, Dept Appl Math, Mills Rd, Acton, ACT 2601, Australia..
    Zhu, Min
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Xizhimenwai Dajie 142, Beijing 100044, Peoples R China..
    Wang, Jun-Qing
    Chinese Acad Sci, Inst Vertebrate Paleontol & Paleoanthropol, Key Lab Vertebrate Evolut & Human Origins, Xizhimenwai Dajie 142, Beijing 100044, Peoples R China..
    Redescription of Szelepis Liu, 1981 (Placodermi, Arthrodira), from the Lower Devonian of China2017In: Journal of Vertebrate Paleontology, ISSN 0272-4634, E-ISSN 1937-2809, Vol. 37, no 2, article id e1312422Article in journal (Refereed)
    Abstract [en]

    The skull roof of the species Szelepis yunnanensis (Liu, 1979) from the Early Devonian of Yunnan is redescribed, as well as other Szelepis material previously published. It appears that only the holotype of S. yunnanensis can be confidently assigned to this genus. The fusion of the preorbital plates into one plate strongly suggests the assignment of Szelepis yunnanensis to the monophyletic family Actinolepididae Gross, 1940, sensu stricto (comprising Actinolepis Agassiz, 1884, and Bollandaspis Schmidt, 1979). This is confirmed by a phylogenetic analysis. Hence, Szelepis constitutes the most ancient occurrence of the family but not the sister group to the remaining members.

  • 331.
    Dussutour, Audrey
    et al.
    Toulouse Univ, CNRS, Res Ctr Anim Cognit CRCA, Ctr Integrat Biol CBI,UPS, F-31062 Toulouse, France.
    Ma, Qi
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Sumpter, David J. T.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Applied Mathematics and Statistics.
    Phenotypic variability predicts decision accuracy in unicellular organisms2019In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 286, no 1896, article id 20182825Article in journal (Refereed)
    Abstract [en]

    When deciding between different options, animals including humans face the dilemma that fast decisions tend to be erroneous, whereas accurate decisions tend to be relatively slow. Recently, it has been suggested that differences in the efficacy with which animals make a decision relate closely to individual behavioural differences. In this paper, we tested this hypothesis in a unique unicellular organism, the slime mould Physarum polycephalum. We first confirmed that slime moulds differed consistently in their exploratory behaviour from 'fast' to 'slow' explorers. Second, we showed that slow explorers made more accurate decisions than fast explorers. Third, we demonstrated that slime moulds integrated food cues in time and achieved higher accuracy when sampling time was longer. Lastly, we showed that in a competition context, fast explorers excelled when a single food source was offered, while slow explorers excelled when two food sources varying in quality were offered. Our results revealed that individual differences in accuracy were partly driven by differences in exploratory behaviour. These findings support the hypothesis that decision-making abilities are associated with behavioural types, even in unicellular organisms.

  • 332.
    Dutoit, Ludovic
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Determinants of genomic diversity in the collared flycatcher (Ficedula albicollis)2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Individuals vary from each other in their genetic content. Genetic diversity is at the core of the evolutionary theory. Rooted in a solid theoretical framework developed as early as the 1930s, current empirical observations of genomic diversity became possible due to technological advances. These measurements, originally based on a few gene sequences from several individuals, are becoming possible at the genome scale for entire populations. We can now explore how evolutionary forces shape diversity levels along different parts of the genome. In this thesis, I focus on the variation in levels of diversity within genomes using avian systems and in particular that of the collared flycatcher (Ficedula albicollis). First, I describe the variation in genetic diversity along the genome of the collared flycatcher and compare it to the amount of variation in diversity across individuals within the population. I provide guidelines on how a small number of makers can capture the extent of variability in a population. Second, I investigate the stability of the local levels of diversity in the genome across evolutionary time scales by comparing collared flycatcher to the hooded crow (Corvus (corone) corone). Third, I study how selection can maintain variation through pervasive evolutionary conflict between sexes. Lastly, I explore how shifts in genome-wide variant frequencies across few generations can be utilised to estimate the effective size of population.

    List of papers
    1. Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome
    Open this publication in new window or tab >>Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome
    Show others...
    2017 (English)In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 4, p. 586-597Article in journal (Refereed) Published
    Abstract [en]

    Properly estimating genetic diversity in populations of nonmodel species requires a basic understanding of how diversity is distributed across the genome and among individuals. To this end, we analysed whole-genome resequencing data from 20 collared flycatchers (genome size approximate to 1.1 Gb; 10.13 million single nucleotide polymorphisms detected). Genomewide nucleotide diversity was almost identical among individuals (mean = 0.00394, range = 0.00384-0.00401), but diversity levels varied extensively across the genome (95% confidence interval for 200-kb windows = 0.0013-0.0053). Diversity was related to selective constraint such that in comparison with intergenic DNA, diversity at fourfold degenerate sites was reduced to 85%, 3' UTRs to 82%, 5' UTRs to 70% and nondegenerate sites to 12%. There was a strong positive correlation between diversity and chromosome size, probably driven by a higher density of targets for selection on smaller chromosomes increasing the diversity-reducing effect of linked selection. Simulations exploring the ability of sequence data from a small number of genetic markers to capture the observed diversity clearly demonstrated that diversity estimation from finite sampling of such data is bound to be associated with large confidence intervals. Nevertheless, we show that precision in diversity estimation in large out-bred population benefits from increasing the number of loci rather than the number of individuals. Simulations mimicking RAD sequencing showed that this approach gives accurate estimates of genomewide diversity. Based on the patterns of observed diversity and the performed simulations, we provide broad recommendations for how genetic diversity should be estimated in natural populations.

    Keywords
    genetic markers, nucleotide diversity, population genomics, recombination
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-327358 (URN)10.1111/1755-0998.12602 (DOI)000403258900002 ()
    Available from: 2017-08-22 Created: 2017-08-22 Last updated: 2018-02-22Bibliographically approved
    2. Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
    Open this publication in new window or tab >>Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting
    Show others...
    2017 (English)In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1849, article id 20162756Article in journal (Refereed) Published
    Abstract [en]

    Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird speciescollared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome). From analyses of whole-genome resequencing data in large population samples of both species we found nucleotide diversity in 200 kb windows to be well correlated (Spearman's rho = 0.407). The correlation remained highly similar after excluding coding sequences. To explain this covariation, we suggest that a stable avian karyotype and a conserved landscape of recombination rate variation render the diversity-reducing effects of linked selection similar in divergent bird lineages. Principal component regression analysis of several potential explanatory variables driving heterogeneity in flycatcher diversity levels revealed the strongest effects from recombination rate variation and density of coding sequence targets for selection, consistent with linked selection. It is also possible that a stable karyotype is associated with a conserved genomic mutation environment contributing to covariation in diversity levels between lineages. Our observations imply that genetic diversity is to some extent predictable.

    Place, publisher, year, edition, pages
    ROYAL SOC, 2017
    Keywords
    nucleotide diversity, linked selection, recombination rate, birds
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-320453 (URN)10.1098/rspb.2016.2756 (DOI)000395893200017 ()
    Available from: 2017-04-26 Created: 2017-04-26 Last updated: 2018-02-22Bibliographically approved
    3. Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome
    Open this publication in new window or tab >>Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome
    Show others...
    2018 (English)In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 18, p. 3572-3581Article in journal (Other academic) Published
    Abstract [en]

    Theoretical work suggests that sexual conflict should promote the maintenance of genetic diversity by the opposing directions of selection on sexually antagonistic mutations in males and females. This prediction, so far not been empirically tested on a genome-wide scale, could potentially contribute towards genomic heterogeneity in levels of genetic diversity. We used large-scale population genomic and transcriptomic data from the collared flycatcher (Ficedula albicollis) to analyse how sex-biased gene expression – one outcome of sexual conflict – relates to genetic variability. Here, we demonstrate that the extent of sex-biased gene expression of both male-biased and female-biased genes is significantly correlated with levels of nucleotide diversity in gene sequences and that this correlation extends to the overall levels of genomic diversity. We find evidence for balancing selection in sex-biased genes, suggesting that sex-biased gene expression could be seen as a component counteracting the diversity-reducing effects of linked positive and purifying selection. The observation of significant genetic differentiation between males and females for male-biased genes indicates ongoing sexual conflict and sex-specific viability selection, potentially driven by sexual selection. Our results thus provide a new perspective on the long-standing question in evolutionary biology of how genomes can remain so genetically variable in face of strong natural and sexual selection.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-331832 (URN)10.1111/mec.14789 (DOI)000444577100002 ()30055065 (PubMedID)
    Funder
    Knut and Alice Wallenberg FoundationSwedish Research Council
    Available from: 2017-10-18 Created: 2017-10-18 Last updated: 2018-11-15Bibliographically approved
    4. Estimation of contemporary effect population size in an island population of the collared flycatcher (Ficedula albicollis) using large-scale genome data
    Open this publication in new window or tab >>Estimation of contemporary effect population size in an island population of the collared flycatcher (Ficedula albicollis) using large-scale genome data
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Due to its central importance to many aspects of evolutionary biology and population genetics, the long-term effective population size (Ne) has been estimated for numerous species and populations. However, estimating contemporary Ne is difficult and in practice this parameter is often not known. In principle, contemporary Ne can be estimated using either analyses of temporal changes in allele frequencies or the extent of linkage disequilibrium (LD) between unlinked markers. We applied these approaches for contemporary Ne estimation of a relatively recently founded island population of collared flycatchers (Ficedula albicollis). We sequenced the genomes of 85 birds sampled in 1993 and 2015, and used a method of Jorde & Ryman (2007) to estimate Ne to ≈5,000 based on the amount of genetic drift observed between the two cohorts. This corresponds to an effective size/census size (Ne/Nc) ratio of ≈0.5. An approach based on LD applied to each cohort could not separate from Ne infinity. When individuals from the two cohorts were pooled, Ne was estimated to 10,000-25,000, but these estimates may be sensitive to biases. We conclude that whole-genome sequence data offer new possibilities for estimation of contemporary Ne, but also note that such estimation remains difficult. 

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-331916 (URN)
    Note

    Dutoit L and Nadachowska-Brzyska K contributed equally.

    Available from: 2017-10-19 Created: 2017-10-19 Last updated: 2017-10-19
  • 333.
    Dutoit, Ludovic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Burri, Reto
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nater, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mugal, Carina F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Hans, Ellegren
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 4, p. 586-597Article in journal (Refereed)
    Abstract [en]

    Properly estimating genetic diversity in populations of nonmodel species requires a basic understanding of how diversity is distributed across the genome and among individuals. To this end, we analysed whole-genome resequencing data from 20 collared flycatchers (genome size approximate to 1.1 Gb; 10.13 million single nucleotide polymorphisms detected). Genomewide nucleotide diversity was almost identical among individuals (mean = 0.00394, range = 0.00384-0.00401), but diversity levels varied extensively across the genome (95% confidence interval for 200-kb windows = 0.0013-0.0053). Diversity was related to selective constraint such that in comparison with intergenic DNA, diversity at fourfold degenerate sites was reduced to 85%, 3' UTRs to 82%, 5' UTRs to 70% and nondegenerate sites to 12%. There was a strong positive correlation between diversity and chromosome size, probably driven by a higher density of targets for selection on smaller chromosomes increasing the diversity-reducing effect of linked selection. Simulations exploring the ability of sequence data from a small number of genetic markers to capture the observed diversity clearly demonstrated that diversity estimation from finite sampling of such data is bound to be associated with large confidence intervals. Nevertheless, we show that precision in diversity estimation in large out-bred population benefits from increasing the number of loci rather than the number of individuals. Simulations mimicking RAD sequencing showed that this approach gives accurate estimates of genomewide diversity. Based on the patterns of observed diversity and the performed simulations, we provide broad recommendations for how genetic diversity should be estimated in natural populations.

  • 334.
    Dutoit, Ludovic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Mugal, Carina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bolivar, Paulina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wang, Mi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nadachowska-Brzyska, Krystyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Smeds, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 18, p. 3572-3581Article in journal (Other academic)
    Abstract [en]

    Theoretical work suggests that sexual conflict should promote the maintenance of genetic diversity by the opposing directions of selection on sexually antagonistic mutations in males and females. This prediction, so far not been empirically tested on a genome-wide scale, could potentially contribute towards genomic heterogeneity in levels of genetic diversity. We used large-scale population genomic and transcriptomic data from the collared flycatcher (Ficedula albicollis) to analyse how sex-biased gene expression – one outcome of sexual conflict – relates to genetic variability. Here, we demonstrate that the extent of sex-biased gene expression of both male-biased and female-biased genes is significantly correlated with levels of nucleotide diversity in gene sequences and that this correlation extends to the overall levels of genomic diversity. We find evidence for balancing selection in sex-biased genes, suggesting that sex-biased gene expression could be seen as a component counteracting the diversity-reducing effects of linked positive and purifying selection. The observation of significant genetic differentiation between males and females for male-biased genes indicates ongoing sexual conflict and sex-specific viability selection, potentially driven by sexual selection. Our results thus provide a new perspective on the long-standing question in evolutionary biology of how genomes can remain so genetically variable in face of strong natural and sexual selection.

  • 335.
    Dutoit, Ludovic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nadachowska-Brzyska, Krystyna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Linnéa, Smeds
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gustafsson, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Estimation of contemporary effect population size in an island population of the collared flycatcher (Ficedula albicollis) using large-scale genome dataManuscript (preprint) (Other academic)
    Abstract [en]

    Due to its central importance to many aspects of evolutionary biology and population genetics, the long-term effective population size (Ne) has been estimated for numerous species and populations. However, estimating contemporary Ne is difficult and in practice this parameter is often not known. In principle, contemporary Ne can be estimated using either analyses of temporal changes in allele frequencies or the extent of linkage disequilibrium (LD) between unlinked markers. We applied these approaches for contemporary Ne estimation of a relatively recently founded island population of collared flycatchers (Ficedula albicollis). We sequenced the genomes of 85 birds sampled in 1993 and 2015, and used a method of Jorde & Ryman (2007) to estimate Ne to ≈5,000 based on the amount of genetic drift observed between the two cohorts. This corresponds to an effective size/census size (Ne/Nc) ratio of ≈0.5. An approach based on LD applied to each cohort could not separate from Ne infinity. When individuals from the two cohorts were pooled, Ne was estimated to 10,000-25,000, but these estimates may be sensitive to biases. We conclude that whole-genome sequence data offer new possibilities for estimation of contemporary Ne, but also note that such estimation remains difficult. 

  • 336. Dylus, David Viktor
    et al.
    Czarkwiani, Anna
    Stångberg, Josefine
    Ortega-Martinez, Olga
    Dupont, Sam
    Oliveri, Paola
    Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks.2016In: EvoDevo, ISSN 2041-9139, E-ISSN 2041-9139, Vol. 7, article id 2Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The evolutionary mechanisms involved in shaping complex gene regulatory networks (GRN) that encode for morphologically similar structures in distantly related animals remain elusive. In this context, echinoderm larval skeletons found in brittle stars and sea urchins provide an ideal system. Here, we characterize for the first time the development of the larval skeleton in the ophiuroid Amphiura filiformis and compare it systematically with its counterpart in sea urchin.

    RESULTS: We show that ophiuroids and euechinoids, that split at least 480 Million years ago (Mya), have remarkable similarities in tempo and mode of skeletal development. Despite morphological and ontological similarities, our high-resolution study of the dynamics of genetic regulatory states in A. filiformis highlights numerous differences in the architecture of their underlying GRNs. Importantly, the A.filiformis pplx, the closest gene to the sea urchin double negative gate (DNG) repressor pmar1, fails to drive the skeletogenic program in sea urchin, showing important evolutionary differences in protein function. hesC, the second repressor of the DNG, is co-expressed with most of the genes that are repressed in sea urchin, indicating the absence of direct repression of tbr, ets1/2, and delta in A. filiformis. Furthermore, the absence of expression in later stages of brittle star skeleton development of key regulatory genes, such as foxb and dri, shows significantly different regulatory states.

    CONCLUSION: Our data fill up an important gap in the picture of larval mesoderm in echinoderms and allows us to explore the evolutionary implications relative to the recently established phylogeny of echinoderm classes. In light of recent studies on other echinoderms, our data highlight a high evolutionary plasticity of the same nodes throughout evolution of echinoderm skeletogenesis. Finally, gene duplication, protein function diversification, and cis-regulatory element evolution all contributed to shape the regulatory program for larval skeletogenesis in different branches of echinoderms.

  • 337. Dyrhage, K.
    et al.
    Seeger, C.
    Mahajan, M.
    Andersson, S.G.E.
    Comparative proteomics identify the core proteome of growing bacterial cells of the family Gemmataceae2019Manuscript (preprint) (Other (popular science, discussion, etc.))
  • 338.
    Dyrhage, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Bioinformatic Analysis of Genomic and Proteomic Data from Gemmata2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Members of the bacterial phylum Planctomycetes have been claimed to have a

    compartmentalised cell plan, with cell walls lacking peptidoglycan despite being free-living.

    These theories have been challenged in recent years, and the nature of the planctomycete cell

    structure is currently under debate. Yet it remains clear that the planctomycete membranes

    have unique properties, and are thus likely localisations of evolutional innovation. In this

    study, proteomes and genomes of four planctomycete species from the Gemmata/Tuwongella

    clade were investigated with the aim to find candidate genes for functional characterisation.

    Analysis based on full genome sequencing and mass spectrometry revealed 21 proteins unique

    to the Gemmata/Tuwongella clade that were present in the proteomes of all four species. The

    gene coding for one of these was found to be organised in an operon, containing an additional

    four clade-specific genes, likely related to type II secretion. A planctomycete-specific cell

    surface signal peptide previously not seen in Gemmata was identified in all four species, with

    proteins found to have the motif indicating that their cell surface has a strong negative charge.

    Lastly, the study has revealed evidence suggesting that the planctomycetes have a traditional

    gram-negative cell wall, contradicting the previously proposed proteinaceous cell wall model.

  • 339.
    Dölfors, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Växters effektorutlösta försvars funktionoch evolution: Ett uthålligt skydd mot patogener?2014Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The diversity among genes conferring resistance (R) against infectious diseases is very high in the plant kingdom, especially in the effector triggered class of defense. This article describes the interactions between the plant effector triggered immunity and pathogen effectors and examines the evolutionary and genetic mechanisms for the emergence of new resistance. R gene products have a typical domain structure and interacts both directly and indirectly with pathogen effectors. Upon contact with an effector a defense response is triggered that may prevent the further pathogen growth. Multiple genetic mechanisms act simultaneously on the R-genes, which results in a rapid diversification of novel R variants. The intimate co-evolution of many existing plant-pathogen systems form the evolutionary pattern of R genes. Diversifying positive selection via the biological arms race model and conservative negative frequency-dependent selection are both important coevolutionary processes. This article indicates that the plant immune system is adaptive and robust, but also highlights the lack of knowledge in plant resistance research.

  • 340.
    Eckerström Liedholm, Simon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Brain size does not affect reproductive behaviour in male guppies (Poecilia reticulata)2014Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The processes and mechanisms that govern brain size evolution remain a widely discussed topic in evolutionary biology. How relative brain size relates to animal behaviour and cognition is even more controversial. Recent comparative and experimental studies have shown a positive relationship between relative brain size and complexity of behaviour. Some of the most important behaviours that have direct consequences for an individual’s fitness are reproductive behaviours, and they sometimes require quite complex behavioural repertoires. Selection for complex behaviour might therefore induce an expansion of brain size to allow for cognitively demanding tasks during courtship and mating. In the present study we investigated the effect of relative brain size on reproductive behaviour in male guppies (Poecilia reticulata), using fish from a recently established brain size artificial selection experiment. Females were paired with either a large- or a small-brained male, and we collected data on a suite of male courtship behaviours including sneak copulation attempts, courtship display, gonopodial swings and time spent following the female. Although the extent of orange colouration, a trait that varies across large- and small-brained males, affected male behaviour, we were not able to detect any difference in reproductive behaviour between the brain size selection lines. These results suggest that there is no strong association between male mating behaviour and relative brain size, and future studies will examine this question further. But currently, our results indicate that relative brain size might not be linked to reproductive behaviour to any significant extent, at least not in the guppy.

  • 341.
    Edelaar, Pim
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Siepielski, Adam M.
    Clobert, Jean
    Matching habitat choice causes directed gene flow: A neglected dimension in evolution and ecology2008In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 62, p. 2462-2472Article in journal (Refereed)
    Abstract [en]

    Gene flow among populations is typically thought to be antagonistic to population differentiation and local adaptation. However,this assumes that dispersing individuals disperse randomly with respect to their ability to use the environment. Yet dispersingindividuals often sample and compare environments and settle in those environments that best match their phenotype, causingdirected gene flow, which can in fact promote population differentiation and adaptation. We refer to this process as “matchinghabitat choice.” Although this process has been acknowledged by several researchers, no synthesis or perspective on its potentiallywidespread importance exists. Here we synthesize empirical and theoretical studies, and offer a new perspective that matchinghabitat choice can have significant effects on important and controversial topics. We discuss the potential implications of matchinghabitat choice for the degree and rate of local adaptation, the evolution of niche width, adaptive peak shifts, speciation in thepresence of gene flow, and on our view and interpretation of measures of natural selection. Because of its potential importance forsuch a wide range of topics, we call for heightened empirical and theoretical attention for this neglected dimension in evolutionaryand ecological studies.

  • 342. Edvardsson, M
    et al.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Copulatory courtship and cryptic female choice in red flour beetles Tribolium castaneum2000In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 267, no 1443, p. 559-563Article in journal (Refereed)
  • 343. Ehrlen, Johan
    et al.
    Morris, William F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Predicting changes in the distribution and abundance of species under environmental change2015In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 18, no 3, p. 303-314Article, review/survey (Refereed)
    Abstract [en]

    Environmental changes are expected to alter both the distribution and the abundance of organisms. A disproportionate amount of past work has focused on distribution only, either documenting historical range shifts or predicting future occurrence patterns. However, simultaneous predictions of abundance and distribution across landscapes would be far more useful. To critically assess which approaches represent advances towards the goal of joint predictions of abundance and distribution, we review recent work on changing distributions and on effects of environmental drivers on single populations. Several methods have been used to predict changing distributions. Some of these can be easily modified to also predict abundance, but others cannot. In parallel, demographers have developed a much better understanding of how changing abiotic and biotic drivers will influence growth rate and abundance in single populations. However, this demographic work has rarely taken a landscape perspective and has largely ignored the effects of intraspecific density. We advocate a synthetic approach in which population models accounting for both density dependence and effects of environmental drivers are used to make integrated predictions of equilibrium abundance and distribution across entire landscapes. Such predictions would constitute an important step forward in assessing the ecological consequences of environmental changes.

  • 344.
    Einarsson, Elin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Ástvaldsson, Ásgeir
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Hultenby, Kjell
    Karolinska Inst, Dept Lab Med, Stockholm, Sweden.
    Andersson, Jan O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Svärd, Staffan G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Jerlstrom-Hultqvist, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Comparative cell biology and evolution of Annexins in Diplomonads2016In: MSphere, ISSN 2379-5042, Vol. 1, no 2, article id e00032-15Article in journal (Refereed)
    Abstract [en]

    Annexins are multifunctional, calcium-binding proteins found in organisms across all kingdoms. Most studies of annexins from single-celled eukaryotes have focused on the alpha-giardins, proteins assigned to the group E annexins, expressed by the diplomonad Giardia intestinalis. We have characterized the annexin gene family in another diplomonad parasite, Spironucleus salmonicida, by phylogenetic and experimental approaches. We constructed a comprehensive phylogeny of the diplomonad group E annexins and found that they are abundant across the group with frequent gene duplications and losses. The annexins of S. salmonicida were found to be related to alpha-giardins but with better-preserved type II Ca2+ coordination sites. Two annexins were confirmed to bind phospholipids in a Ca2+-dependent fashion but with different specificities. Superresolution and confocal microscopy of epitope-tagged S. salmonicida annexins revealed localization to distinct parts of the cytoskeleton and membrane. The ultrastructural details of the localization of several annexins were determined by proximity labeling and transmission electron microscopy. Two annexins localize to a novel cytoskeletal structure in the anterior of the cell. Our results show that the annexin gene family is expanded in diplomonads and that these group E annexins are associated mostly with cytoskeletal and membrane structures. IMPORTANCE Annexins are proteins that associate with phospholipids in a Ca2+-dependent fashion. These proteins have been intensely studied in animals and plants because of their importance in diverse cellular processes, yet very little is known about annexins in single-celled eukaryotes, which represent the largest diversity of organisms. The human intestinal parasite Giardia intestinalis is known to have more annexins than humans, and they contribute to its pathogenic potential. In this study, we investigated the annexin complement in the salmon pathogen Spironucleus salmonicida, a relative of G. intestinalis. We found that S. salmonicida has a large repertoire of annexins and that the gene family has expanded separately across diplomonads, with members showing sequence diversity similar to that seen across kingdom-level groups such as plants and animals. S. salmonicida annexins are prominent components of the cytoskeleton and membrane. Two annexins are associated with a previously unrecognized structure in the anterior of the cell.

  • 345.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Smeds, Linnea
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria2014In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 15, p. 467-Article in journal (Refereed)
    Abstract [en]

    Background: Genome and transcriptome sequencing applications that rely on variation in sequence depth can be negatively affected if there are systematic biases in coverage. We have investigated patterns of local variation in sequencing coverage by utilising ultra-deep sequencing (>100,000X) of mtDNA obtained during sequencing of two vertebrate genomes, wolverine (Gulo gulo) and collared flycatcher (Ficedula albicollis). With such extreme depth, stochastic variation in coverage should be negligible, which allows us to provide a very detailed, fine-scale picture of sequence dependent coverage variation and sequencing error rates. Results: Sequencing coverage showed up to six-fold variation across the complete mtDNA and this variation was highly repeatable in sequencing of multiple individuals of the same species. Moreover, coverage in orthologous regions was correlated between the two species and was negatively correlated with GC content. We also found a negative correlation between the site-specific sequencing error rate and coverage, with certain sequence motifs "CCNGCC" being particularly prone to high rates of error and low coverage. Conclusions: Our results demonstrate that inherent sequence characteristics govern variation in coverage and suggest that some of this variation, like GC content, should be controlled for in, for example, RNA-Seq and detection of copy number variation.

  • 346.
    Ekblom, Robert
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A field guide to whole-genome sequencing, assembly and annotation2014In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 7, no 9, p. 1026-1042Article in journal (Refereed)
    Abstract [en]

    Genome sequencing projects were long confined to biomedical model organisms and required the concerted effort of large consortia. Rapid progress in high-throughput sequencing technology and the simultaneous development of bioinformatic tools have democratized the field. It is now within reach for individual research groups in the eco-evolutionary and conservation community to generate de novo draft genome sequences for any organism of choice. Because of the cost and considerable effort involved in such an endeavour, the important first step is to thoroughly consider whether a genome sequence is necessary for addressing the biological question at hand. Once this decision is taken, a genome project requires careful planning with respect to the organism involved and the intended quality of the genome draft. Here, we briefly review the state of the art within this field and provide a step-by-step introduction to the workflow involved in genome sequencing, assembly and annotation with particular reference to large and complex genomes. This tutorial is targeted at scientists with a background in conservation genetics, but more generally, provides useful practical guidance for researchers engaging in whole-genome sequencing projects.

  • 347.
    Ekebom, Nicklas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Mälardalens Högskola UKK.
    Loss of parental care in a sympatric three-spine stickleback system of southern Sweden2018Data set
  • 348.
    Elgh, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Pterosaur Ichnites from the Late Jurassic of Poland: Morphometrical comparisons with body fossils2018Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
  • 349.
    Elgh, Erik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Pienkowski, Grzegorz
    Natl Res Inst, Polish Geol Inst, Ul Rakowiecka 4, PL-00975 Warsaw, Poland.
    Niedzwiedzki, Grzegorz
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Pterosaur track assemblages from the Upper Jurassic (lower Kimmeridgian) intertidal deposits of Poland: Linking ichnites to potential trackmakers2019In: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 530, p. 32-48Article in journal (Refereed)
    Abstract [en]

    Two distinct tetrapod track assemblages, dominated by pterosaur traces, are reported from Upper Jurassic (lower Kimmeridgian, Hypselocyclum Zone) tidal flat carbonate deposits exposed in Wierzbica Quarry, 20 km south of Radom, Poland. The pterosaur tracks, tentatively assigned to Pteraichnus isp. are well preserved as a positive hyporelief in intertidal facies. Some are preserved with anatomical details (e.g., skin, claw or digital pad impressions) and quality sufficient to make preliminary ichnotaxonomic assignment. Nearly all collected specimens are larger than most other pterosaurian ichnites of the Late Jurassic age, thus adding to the growing diversity of pterosaur traces known from this time period. Morphometrical and anatomical analyses show that ctenochasmatoids or possibly non-pterydactyloid monofenestratans or rhamphorhynchids were most likely the trackmakers. Anatomical comparisons give new insights into the morphology of the pes of pterydactyloids and the most closely related non-pterodactyloids which may be correlated with a niche expansion into marginal marine and lacustrine environments by Middle and Late Jurassic pterosaurs. The palaeoenvironmental interpretation as tidal flat is confirmed by presence of vertically accreted tidal bundles, each representing deposition in one tidal cycle. Most likely then, this was one of the environments frequented by these pterosaurs and other small tetrapods. The wider palaeoecological significance of the tracks is evaluated in the context of other similar reports from the Late Jurassic of Europe, Africa and North America.

  • 350.
    Ellegaard, Kirsten Maren
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Genome Evolution and Niche Differentiation of Bacterial Endosymbionts2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Most animals contain chronic microbial infections that inflict no harm on their hosts. Recently, the gut microflora of humans and other animals have been characterized. However, little is known about the forces that shape the diversity of these bacterial communities. In this work, comparative genomics was used to investigate the evolutionary dynamics of host-adapted bacterial communities, using Wolbachia infecting arthropods and Lactobacteria infecting bees as the main model systems.

    Wolbachia are maternally inherited bacteria that cause reproductive disorders in arthropods, such as feminization, male killing and parthenogenesis. These bacteria are difficult to study because they cannot be cultivated outside their hosts. We have developed a novel protocol employing multiple displacement amplification to isolate and sequence their genomes. Taxonomically, Wolbachia is classified into different supergroups. We have sequenced the genomes of Wolbachia strain wHa and wNo that belong to supergroup A and B, respectively, and are present as a double-infection in the fruit-fly Drosophila simulans. Together with previously published genomes, a supergroup comparison of strains belonging to supergroups A and B indicated rampant homologous recombination between strains that belong to the same supergroup but were isolated from different hosts. In contrast, we observed little recombination between strains of different supergroups that infect the same host.

    Likewise, phylogenetically distinct members of Lactic acid bacteria co-exist in the gut of the honeybee, Apis mellifera, without transfer of genes between phylotypes. Nor did we find any evidence of co-diversification between symbionts and hosts, as inferred from a study of 13 genomes of Lactobacillus kunkeei isolated from diverse bee species and different geographic origins. Although Lactobacillus kunkeii is the most frequently isolated strain from the honey stomach, we hypothesize that the primary niche is the beebread where the bacteria are likely to contribute to the fermentation process.

    In the human gut, the microbial community has been shown to interact with the immune system, and likewise the microbial communities associated with insects are thought to affect the health of their host. Therefore, a better understanding of the role and evolution of endosymbiotic communities is important for developing strategies to control the health of their hosts.

    List of papers
    1. Comparative Genomics of Wolbachia and the Bacterial Species Concept
    Open this publication in new window or tab >>Comparative Genomics of Wolbachia and the Bacterial Species Concept
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    2013 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 9, no 4, p. e1003381-Article in journal (Refereed) Published
    Abstract [en]

    The importance of host-specialization to speciation processes in obligate host-associated bacteria is well known, as is also the ability of recombination to generate cohesion in bacterial populations. However, whether divergent strains of highly recombining intracellular bacteria, such as Wolbachia, can maintain their genetic distinctness when infecting the same host is not known. We first developed a protocol for the genome sequencing of uncultivable endosymbionts. Using this method, we have sequenced the complete genomes of the Wolbachia strains wHa and wNo, which occur as natural double infections in Drosophila simulans populations on the Seychelles and in New Caledonia. Taxonomically, wHa belong to supergroup A and wNo to supergroup B. A comparative genomics study including additional strains supported the supergroup classification scheme and revealed 24 and 33 group-specific genes, putatively involved in host-adaptation processes. Recombination frequencies were high for strains of the same supergroup despite different host-preference patterns, leading to genomic cohesion. The inferred recombination fragments for strains of different supergroups were of short sizes, and the genomes of the co-infecting Wolbachia strains wHa and wNo were not more similar to each other and did not share more genes than other A- and B-group strains that infect different hosts. We conclude that Wolbachia strains of supergroup A and B represent genetically distinct clades, and that strains of different supergroups can co-exist in the same arthropod host without converging into the same species. This suggests that the supergroups are irreversibly separated and that barriers other than host-specialization are able to maintain distinct clades in recombining endosymbiont populations. Acquiring a good knowledge of the barriers to genetic exchange in Wolbachia will advance our understanding of how endosymbiont communities are constructed from vertically and horizontally transmitted genes.

    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-200821 (URN)10.1371/journal.pgen.1003381 (DOI)000318073300004 ()
    Available from: 2013-06-04 Created: 2013-06-04 Last updated: 2017-12-06Bibliographically approved
    2. Testing the Reproducibility of Multiple Displacement Amplification on Genomes of Clonal Endosymbiont Populations
    Open this publication in new window or tab >>Testing the Reproducibility of Multiple Displacement Amplification on Genomes of Clonal Endosymbiont Populations
    2013 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 11, p. e82319-Article in journal (Refereed) Published
    Abstract [en]

    The multiple displacement amplification method has revolutionized genomic studies of uncultured bacteria, where the extraction of pure DNA in sufficient quantity for next-generation sequencing is challenging. However, the method is problematic in that it amplifies the target DNA unevenly, induces the formation of chimeric reads and also amplifies contaminating DNA. Here, we have tested the reproducibility of the multiple displacement amplification method using serial dilutions of extracted genomic DNA and intact cells from the cultured endosymbiont Bartonella australis. The amplified DNA was sequenced with the Illumina sequencing technology, and the results were compared to sequence data obtained from unamplified DNA in this study as well as from a previously published genome project. We show that artifacts such as the extent of the amplification bias, the percentage of chimeric reads and the relative fraction of contaminating DNA increase dramatically for the smallest amounts of template DNA. The pattern of read coverage was reproducibly obtained for samples with higher amounts of template DNA, suggesting that the bias is non-random and genome-specific. A re-analysis of previously published sequence data obtained after amplification from clonal endosymbiont populations confirmed these predictions. We conclude that many of the artifacts associated with the use of the multiple displacement amplification method can be alleviated or much reduced by using multiple cells as the template for the amplification. These findings should be particularly useful for researchers studying the genomes of endosymbionts and other uncultured bacteria, for which a small clonal population of cells can be isolated.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-214040 (URN)10.1371/journal.pone.0082319 (DOI)000327652100111 ()
    Available from: 2014-01-07 Created: 2014-01-07 Last updated: 2017-12-06Bibliographically approved
    3. Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut
    Open this publication in new window or tab >>Extensive intra-phylotype diversity in lactobacilli and bifidobacteria from the honeybee gut
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    2015 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 16, article id 284Article in journal (Refereed) Published
    Abstract [en]

    Background: In the honeybee Apis mellifera, the bacterial gut community is consistently colonized by eight distinct phylotypes of bacteria. Managed bee colonies are of considerable economic interest and it is therefore important to elucidate the diversity and role of this microbiota in the honeybee. In this study, we have sequenced the genomes of eleven strains of lactobacilli and bifidobacteria isolated from the honey crop of the honeybee Apis mellifera. Results: Single gene phylogenies confirmed that the isolated strains represent the diversity of lactobacilli and bifidobacteria in the gut, as previously identified by 16S rRNA gene sequencing. Core genome phylogenies of the lactobacilli and bifidobacteria further indicated extensive divergence between strains classified as the same phylotype. Phylotype-specific protein families included unique surface proteins. Within phylotypes, we found a remarkably high level of gene content diversity. Carbohydrate metabolism and transport functions contributed up to 45% of the accessory genes, with some genomes having a higher content of genes encoding phosphotransferase systems for the uptake of carbohydrates than any previously sequenced genome. These genes were often located in highly variable genomic segments that also contained genes for enzymes involved in the degradation and modification of sugar residues. Strain-specific gene clusters for the biosynthesis of exopolysaccharides were identified in two phylotypes. The dynamics of these segments contrasted with low recombination frequencies and conserved gene order structures for the core genes. Hits for CRISPR spacers were almost exclusively found within phylotypes, suggesting that the phylotypes are associated with distinct phage populations. Conclusions: The honeybee gut microbiota has been described as consisting of a modest number of phylotypes; however, the genomes sequenced in the current study demonstrated a very high level of gene content diversity within all three described phylotypes of lactobacilli and bifidobacteria, particularly in terms of metabolic functions and surface structures, where many features were strain-specific. Together, these results indicate niche differentiation within phylotypes, suggesting that the honeybee gut microbiota is more complex than previously thought.

    Keywords
    Lactic acid bacteria, Lactobacillus spp, Firmicutes, Bifidobacteria, Comparative genomics, Phosphotransferase systems, Niche specialization
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-256855 (URN)10.1186/s12864-015-1476-6 (DOI)000355302300001 ()25880915 (PubMedID)
    External cooperation:
    Note

    De två förstaförfattarna delar förstaförfattarskapet.

    Available from: 2015-06-26 Created: 2015-06-26 Last updated: 2017-12-04Bibliographically approved
    4. Comparative Genomics of Lactobacillus kunkeii indicates Selection for Rapid Growth in the Beebread
    Open this publication in new window or tab >>Comparative Genomics of Lactobacillus kunkeii indicates Selection for Rapid Growth in the Beebread
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Research subject
    Biology with specialization in Molecular Evolution
    Identifiers
    urn:nbn:se:uu:diva-217720 (URN)
    Available from: 2014-02-04 Created: 2014-02-04 Last updated: 2014-04-29
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