uu.seUppsala University Publications
Change search
Refine search result
1 - 22 of 22
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 1.
    Ah-King, Malin
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Centre for Gender Research.
    Barron, Andrew B.
    Herberstein, Marie E.
    Genital Evolution: Why Are Females Still Understudied?2014In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 12, no 5, p. e1001851-Article in journal (Refereed)
    Abstract [en]

    The diversity, variability, and apparent rapid evolution of animal genitalia are a vivid focus of research in evolutionary biology, and studies exploring genitalia have dramatically increased over the past decade. These studies, however, exhibit a strong male bias, which has worsened since 2000, despite the fact that this bias has been explicitly pointed out in the past. Early critics argued that previous investigators too often considered only males and their genitalia, while overlooking female genitalia or physiology. Our analysis of the literature shows that overall this male bias has worsened with time. The degree of bias is not consistent between subdisciplines: studies of the lock-and-key hypothesis have been the most male focused, while studies of cryptic female choice usually consider both sexes. The degree of bias also differed across taxonomic groups, but did not associate with the ease of study of male and female genital characteristics. We argue that the persisting male bias in this field cannot solely be explained by anatomical sex differences influencing accessibility. Rather the bias reflects enduring assumptions about the dominant role of males in sex, and invariant female genitalia. New research highlights how rapidly female genital traits can evolve, and how complex coevolutionary dynamics between males and females can shape genital structures. We argue that understanding genital evolution is hampered by an outdated single-sex bias.

  • 2. Andersson, Marlene
    et al.
    Chen, Gefei
    Otikovs, Martins
    Landreh, Michael
    Nordling, Kerstin
    Kronqvist, Nina
    Westermark, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Molecular and Morphological Pathology.
    Jornvall, Hans
    Knight, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Ridderstrale, Yvonne
    Holm, Lena
    Meng, Qing
    Jaudzems, Kristaps
    Chesler, Mitchell
    Johansson, Jan
    Rising, Anna
    Carbonic Anhydrase Generates CO2 and H+ That Drive Spider Silk Formation Via Opposite Effects on the Terminal Domains2014In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 12, no 8, p. e1001921-Article in journal (Refereed)
    Abstract [en]

    Spider silk fibers are produced from soluble proteins (spidroins) under ambient conditions in a complex but poorly understood process. Spidroins are highly repetitive in sequence but capped by nonrepetitive N- and C-terminal domains (NT and CT) that are suggested to regulate fiber conversion in similar manners. By using ion selective microelectrodes we found that the pH gradient in the silk gland is much broader than previously known. Surprisingly, the terminal domains respond in opposite ways when pH is decreased from 7 to 5: Urea denaturation and temperature stability assays show that NT dimers get significantly stabilized and then lock the spidroins into multimers, whereas CT on the other hand is destabilized and unfolds into ThT-positive beta-sheet amyloid fibrils, which can trigger fiber formation. There is a high carbon dioxide pressure (pCO(2)) in distal parts of the gland, and a CO2 analogue interacts with buried regions in CT as determined by nuclear magnetic resonance (NMR) spectroscopy. Activity staining of histological sections and inhibition experiments reveal that the pH gradient is created by carbonic anhydrase. Carbonic anhydrase activity emerges in the same region of the gland as the opposite effects on NT and CT stability occur. These synchronous events suggest a novel CO2 and proton-dependent lock and trigger mechanism of spider silk formation.

  • 3.
    Bailey, Richard
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Animal Ecology.
    Schonrogge, Karsten
    Cook, M
    Melika, George
    Csoka, Gyoergy
    Thuroczy, Csaba
    Stone, Graham N.
    Host Niches and Defensive Extended Phenotypes Structure Parasitoid Wasp Communities2009In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 7, no 8, p. e1000179-Article in journal (Refereed)
    Abstract [en]

    Oak galls are spectacular extended phenotypes of gallwasp genes in host oak tissues and have evolved complex morphologies that serve, in part, to exclude parasitoid natural enemies. Parasitoids and their insect herbivore hosts have coevolved to produce diverse communities comprising about a third of all animal species. The factors structuring these communities, however, remain poorly understood. An emerging theme in community ecology is the need to consider the effects of host traits, shaped by both natural selection and phylogenetic history, on associated communities of natural enemies. Here we examine the impact of host traits and phylogenetic relatedness on 48 ecologically closed and species-rich communities of parasitoids attacking gall-inducing wasps on oaks. Gallwasps induce the development of spectacular and structurally complex galls whose species- and generation-specific morphologies are the extended phenotypes of gallwasp genes. All the associated natural enemies attack their concealed hosts through gall tissues, and several structural gall traits have been shown to enhance defence against parasitoid attack. Here we explore the significance of these and other host traits in predicting variation in parasitoid community structure across gallwasp species. In particular, we test the "Enemy Hypothesis,'' which predicts that galls with similar morphology will exclude similar sets of parasitoids and therefore have similar parasitoid communities. Having controlled for phylogenetic patterning in host traits and communities, we found significant correlations between parasitoid community structure and several gall structural traits (toughness, hairiness, stickiness), supporting the Enemy Hypothesis. Parasitoid community structure was also consistently predicted by components of the hosts' spatiotemporal niche, particularly host oak taxonomy and gall location (e.g., leaf versus bud versus seed). The combined explanatory power of structural and spatiotemporal traits on community structure can be high, reaching 62% in one analysis. The observed patterns derive mainly from partial niche specialisation of highly generalist parasitoids with broad host ranges (>20 hosts), rather than strict separation of enemies with narrower host ranges, and so may contribute to maintenance of the richness of generalist parasitoids in gallwasp communities. Though evolutionary escape from parasitoids might most effectively be achieved via changes in host oak taxon, extreme conservatism in this trait for gallwasps suggests that selection is more likely to have acted on gall morphology and location. Any escape from parasitoids associated with evolutionary shifts in these traits has probably only been transient, however, due to subsequent recruitment of parasitoid species already attacking other host galls with similar trait combinations.

  • 4. Benson, Roger B. J.
    et al.
    Campione, Nicolàs E.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Carrano, Matthew T.
    Mannion, Philip D.
    Sullivan, Corwin
    Upchurch, Paul
    Evans, David C.
    Rates of Dinosaur Body Mass Evolution Indicate 170 Million Years of Sustained Ecological Innovation on the Avian Stem Lineage2014In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 12, no 5, p. e1001853-Article in journal (Refereed)
    Abstract [en]

    Large-scale adaptive radiations might explain the runaway success of a minority of extant vertebrate clades. This hypothesis predicts, among other things, rapid rates of morphological evolution during the early history of major groups, as lineages invade disparate ecological niches. However, few studies of adaptive radiation have included deep time data, so the links between extant diversity and major extinct radiations are unclear. The intensively studied Mesozoic dinosaur record provides a model system for such investigation, representing an ecologically diverse group that dominated terrestrial ecosystems for 170 million years. Furthermore, with 10,000 species, extant dinosaurs (birds) are the most speciose living tetrapod clade. We assembled composite trees of 614-622 Mesozoic dinosaurs/birds, and a comprehensive body mass dataset using the scaling relationship of limb bone robustness. Maximum-likelihood modelling and the node height test reveal rapid evolutionary rates and a predominance of rapid shifts among size classes in early (Triassic) dinosaurs. This indicates an early burst niche-filling pattern and contrasts with previous studies that favoured gradualistic rates. Subsequently, rates declined in most lineages, which rarely exploited new ecological niches. However, feathered maniraptoran dinosaurs (including Mesozoic birds) sustained rapid evolution from at least the Middle Jurassic, suggesting that these taxa evaded the effects of niche saturation. This indicates that a long evolutionary history of continuing ecological innovation paved the way for a second great radiation of dinosaurs, in birds. We therefore demonstrate links between the predominantly extinct deep time adaptive radiation of non-avian dinosaurs and the phenomenal diversification of birds, via continuing rapid rates of evolution along the phylogenetic stem lineage. This raises the possibility that the uneven distribution of biodiversity results not just from large-scale extrapolation of the process of adaptive radiation in a few extant clades, but also from the maintenance of evolvability on vast time scales across the history of life, in key lineages.

  • 5.
    Berglund, Jonas
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Pollard, Katherine S.
    Webster, Matthew T.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Hotspots of biased nucleotide substitutions in human genes2009In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 7, no 1, p. e26-Article in journal (Refereed)
    Abstract [en]

    Genes that have experienced accelerated evolutionary rates on the human lineage during recent evolution are candidates for involvement in human-specific adaptations. To determine the forces that cause increased evolutionary rates in certain genes, we analyzed alignments of 10,238 human genes to their orthologues in chimpanzee and macaque. Using a likelihood ratio test, we identified protein-coding sequences with an accelerated rate of base substitutions along the human lineage. Exons evolving at a fast rate in humans have a significant tendency to contain clusters of AT-to-GC (weak-to-strong) biased substitutions. This pattern is also observed in noncoding sequence flanking rapidly evolving exons. Accelerated exons occur in regions with elevated male recombination rates and exhibit an excess of nonsynonymous substitutions relative to the genomic average. We next analyzed genes with significantly elevated ratios of nonsynonymous to synonymous rates of base substitution (dN/dS) along the human lineage, and those with an excess of amino acid replacement substitutions relative to human polymorphism. These genes also show evidence of clusters of weak-to-strong biased substitutions. These findings indicate that a recombination-associated process, such as biased gene conversion (BGC), is driving fixation of GC alleles in the human genome. This process can lead to accelerated evolution in coding sequences and excess amino acid replacement substitutions, thereby generating significant results for tests of positive selection.

  • 6. Church, Deanna M
    et al.
    Goodstadt, Leo
    Hillier, Ladeana W
    Zody, Michael C.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Goldstein, Steve
    She, Xinwe
    Bult, Carol J
    Agarwala, Richa
    Cherry, Joshua L
    DiCuccio, Michael
    Hlavina, Wratko
    Kapustin, Yuri
    Meric, Peter
    Maglott, Donna
    Birtle, Zoë
    Marques, Ana C
    Graves, Tina
    Zhou, Shiguo
    Teague, Brian
    Potamousis, Konstantinos
    Churas, Christopher
    Place, Michael
    Herschleb, Jill
    Runnheim, Ron
    Forrest, Daniel
    Amos-Landgraf, James
    Schwartz, David C
    Cheng, Ze
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Eichler, Evan E
    Ponting, Chris P
    Lineage-specific biology revealed by a finished genome assembly of the mouse2009In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 7, no 5, p. e1000112-Article in journal (Refereed)
    Abstract [en]

    The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer gaps and over 139 Mb more of novel sequence, compared with the earlier MGSCv3 draft genome assembly. In a comprehensive analysis of this revised genome sequence, we are now able to define 20,210 protein-coding genes, over a thousand more than predicted in the human genome (19,042 genes). In addition, we identified 439 long, non-protein-coding RNAs with evidence for transcribed orthologs in human. We analyzed the complex and repetitive landscape of 267 Mb of sequence that was missing or misassembled in the previously published assembly, and we provide insights into the reasons for its resistance to sequencing and assembly by whole-genome shotgun approaches. Duplicated regions within newly assembled sequence tend to be of more recent ancestry than duplicates in the published draft, correcting our initial understanding of recent evolution on the mouse lineage. These duplicates appear to be largely composed of sequence regions containing transposable elements and duplicated protein-coding genes; of these, some may be fixed in the mouse population, but at least 40% of segmentally duplicated sequences are copy number variable even among laboratory mouse strains. Mouse lineage-specific regions contain 3,767 genes drawn mainly from rapidly-changing gene families associated with reproductive functions. The finished mouse genome assembly, therefore, greatly improves our understanding of rodent-specific biology and allows the delineation of ancestral biological functions that are shared with human from derived functions that are not.

  • 7. Feng, Boya
    et al.
    Mandava, Chandra Sekhar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Guo, Qiang
    Wang, Jie
    Cao, Wei
    Li, Ningning
    Zhang, Yixiao
    Zhang, Yanqing
    Wang, Zhixin
    Wu, Jiawei
    Sanyal, Suparna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Lei, Jianlin
    Gao, Ning
    Structural and Functional Insights into the Mode of Action of a Universally Conserved Obg GTPase2014In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 12, no 5, p. e1001866-Article in journal (Refereed)
    Abstract [en]

    Obg proteins are a family of P-loop GTPases, conserved from bacteria to human. The Obg protein in Escherichia coli (ObgE) has been implicated in many diverse cellular functions, with proposed molecular roles in two global processes, ribosome assembly and stringent response. Here, using pre-steady state fast kinetics we demonstrate that ObgE is an anti-association factor, which prevents ribosomal subunit association and downstream steps in translation by binding to the 50S subunit. ObgE is a ribosome dependent GTPase; however, upon binding to guanosine tetraphosphate (ppGpp), the global regulator of stringent response, ObgE exhibits an enhanced interaction with the 50S subunit, resulting in increased equilibrium dissociation of the 70S ribosome into subunits. Furthermore, our cryo-electron microscopy (cryo-EM) structure of the 50S? ObgE? GMPPNP complex indicates that the evolutionarily conserved N-terminal domain (NTD) of ObgE is a tRNA structural mimic, with specific interactions with peptidyl-transferase center, displaying a marked resemblance to Class I release factors. These structural data might define ObgE as a specialized translation factor related to stress responses, and provide a framework towards future elucidation of functional interplay between ObgE and ribosome-associated (p) ppGpp regulators. Together with published data, our results suggest that ObgE might act as a checkpoint in final stages of the 50S subunit assembly under normal growth conditions. And more importantly, ObgE, as a (p) ppGpp effector, might also have a regulatory role in the production of the 50S subunit and its participation in translation under certain stressed conditions. Thus, our findings might have uncovered an under-recognized mechanism of translation control by environmental cues.

  • 8.
    Gentekaki, Eleni
    et al.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.;Mae Fah Luang Univ, Sch Sci, Chiang Rai, Thailand.;Mae Fah Luang Univ, Human Gut Microbiome Hlth Res Unit, Chiang Rai, Thailand..
    Curtis, Bruce A.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada..
    Stairs, Courtney W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada..
    Klimes, Vladimir
    Univ Ostrava, Dept Biol & Ecol, Fac Sci, Ostrava, Czech Republic..
    Elias, Marek
    Univ Ostrava, Dept Biol & Ecol, Fac Sci, Ostrava, Czech Republic..
    Salas-Leiva, Dayana E.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada..
    Herman, Emily K.
    Univ Alberta, Dept Cell Biol, Edmonton, AB, Canada..
    Eme, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada..
    Arias, Maria C.
    Univ Sci & Technol Lille, Unite Glycobiol Struct & Fonct, CNRS, UMR8576,Cite Sci, Villeneuve Dascq, France..
    Henrissat, Bernard
    Aix Marseille Univ, CNRS, UMR 7257, Marseille, France.;NRA, USC 1408, AFMB, Marseille, France.;King Abdulaziz Univ, Dept Biol Sci, Jeddah, Saudi Arabia..
    Hilliou, Frederique
    Univ Cote Azur, NRA, ISA, Sophia Antipolis, France..
    Klute, Mary J.
    Univ Alberta, Dept Cell Biol, Edmonton, AB, Canada..
    Suga, Hiroshi
    Prefectural Univ Hiroshima, Fac Life & Environm Sci, Nanatsuka 562, Shobara, Hiroshima, Japan..
    Malik, Shehre-Banoo
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada..
    Pightling, Arthur W.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;US FDA, Ctr Food Safety & Appl Nutr, College Pk, MD USA..
    Kolisko, Martin
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.;Czech Acad Sci, Inst Parasitol, Ctr Biol, Ceske Budejovice, Czech Republic..
    Rachubinski, Richard A.
    Schlacht, Alexander
    Soanes, Darren M.
    Univ Exeter, Coll Life & Environm Sci, Exeter, Devon, England..
    Tsaousis, Anastasios D.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.;Univ Kent, Lab Mol & Evolutionary Parasitol, RAPID Grp, Sch Biosci, Canterbury, Kent, England..
    Archibald, John M.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.;Canadian Inst Adv Res, CIFAR Program Integrated Microbial Biodivers, Toronto, ON, Canada..
    Ball, Steven G.
    Dacks, Joel B.
    Univ Alberta, Dept Cell Biol, Edmonton, AB, Canada..
    Clark, C. Graham
    London Sch Hyg & Trop Med, Fac Infect & Trop Dis, London, England..
    van der Giezen, Mark
    Univ Exeter, Biosci, Exeter, Devon, England..
    Roger, Andrew J.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS, Canada.;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.;Canadian Inst Adv Res, CIFAR Program Integrated Microbial Biodivers, Toronto, ON, Canada..
    Extreme genome diversity in the hyper-prevalent parasitic eukaryote Blastocystis2017In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 15, no 9, article id e2003769Article in journal (Refereed)
    Abstract [en]

    Blastocystis is the most prevalent eukaryotic microbe colonizing the human gut, infecting approximately 1 billion individuals worldwide. Although Blastocystis has been linked to intestinal disorders, its pathogenicity remains controversial because most carriers are asymptomatic. Here, the genome sequence of Blastocystis subtype (ST) 1 is presented and compared to previously published sequences for ST4 and ST7. Despite a conserved core of genes, there is unexpected diversity between these STs in terms of their genome sizes, guanine-cytosine (GC) content, intron numbers, and gene content. ST1 has 6,544 protein-coding genes, which is several hundred more than reported for ST4 and ST7. The percentage of proteins unique to each ST ranges from 6.2% to 20.5%, greatly exceeding the differences observed within parasite genera. Orthologous proteins also display extreme divergence in amino acid sequence identity between STs (i.e., 59%-61% median identity), on par with observations of the most distantly related species pairs of parasite genera. The STs also display substantial variation in gene family distributions and sizes, especially for protein kinase and protease gene families, which could reflect differences in virulence. It remains to be seen to what extent these inter-ST differences persist at the intra-ST level. A full 26% of genes in ST1 have stop codons that are created on the mRNA level by a novel polyadenylation mechanism found only in Blastocystis. Reconstructions of pathways and organellar systems revealed that ST1 has a relatively complete membrane-trafficking system and a near-complete meiotic toolkit, possibly indicating a sexual cycle. Unlike some intestinal protistan parasites, Blastocystis ST1 has near-complete de novo pyrimidine, purine, and thiamine biosynthesis pathways and is unique amongst studied stramenopiles in being able to metabolize alpha-glucans rather than beta-glucans. It lacks all genes encoding heme-containing cytochrome P450 proteins. Predictions of the mitochondrion-related organelle (MRO) proteome reveal an expanded repertoire of functions, including lipid, cofactor, and vitamin biosynthesis, as well as proteins that may be involved in regulating mitochondrial morphology and MRO/endoplasmic reticulum (ER) interactions. In sharp contrast, genes for peroxisome-associated functions are absent, suggesting Blastocystis STs lack this organelle. Overall, this study provides an important window into the biology of Blastocystis, showcasing significant differences between STs that can guide future experimental investigations into differences in their virulence and clarifying the roles of these organisms in gut health and disease.

  • 9.
    Günther, Torsten
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Svensson, Emma
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Omrak, Ayca
    Stockholm Univ, Dept Archaeol & Class Studies.
    Sanchez-Quinto, Federico
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Kilinc, Gülsah Merve
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.; Middle East Tech Univ, Dept Biol Sci, Ankara.
    Krzewińska, Maja
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Eriksson, Gunilla
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Fraser, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Arts, Department of Archaeology and Ancient History, Archaeology.
    Edlund, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Munters, Arielle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Coutinho, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Simões, Luciana G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Vicente, Mário
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution.
    Sjölander, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Sellevold, Berit Jansen
    Norwegian Inst Cultural Heritage Res, Oslo.
    Jørgensen, Roger
    Arctic Univ Norway, Univ Tromsø, Tromsø Univ Museum, Tromsø.
    Claes, Peter
    Katholieke Univ Leuven, Dept Elect Engn, Ctr Proc Speech & Images, Leuven.
    Shriver, Mark D.
    Penn State Univ, Dept Anthropol, State Coll, Pennsylvania.
    Valdiosera, Cristina
    La Trobe Univ, Dept Archaeol & Hist, Melbourne.
    Netea, Mihai G.
    Radboud Univ Nijmegen, Med Ctr, Dept Internal Med, Nijmegen; Radboud Univ Nijmegen, Med Ctr, Radboud Ctr Infect Dis, Nijmegen.
    Apel, Jan
    Lund Univ, Dept Archaeol & Ancient Hist, Lund.
    Liden, Kerstin
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Skar, Birgitte
    Norwegian Univ Sci & Technol Univ Museum, Trondheim.
    Storå, Jan
    Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.
    Götherström, Anders
    Uppsala University, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Archaeol & Class Studies, Stockholm.; SciLifeLab, Stockholm.
    Jakobsson, Mattias
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Human Evolution. SciLifeLab, Stockholm.
    Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation2018In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 16, no 1, article id e2003703Article in journal (Refereed)
    Abstract [en]

    Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57x coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500-6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east-west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans.

  • 10.
    Hilscher, Markus M.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics. Univ Fed Rio Grande do Norte, Inst Brain, Natal, RN, Brazil..
    Leão, Richardson N.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics. Univ Fed Rio Grande do Norte, Inst Brain, Natal, RN, Brazil..
    Edwards, Steven J.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Leão, Katarina E.
    Univ Fed Rio Grande do Norte, Inst Brain, Natal, RN, Brazil..
    Kullander, Klas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Chrna2-Martinotti Cells Synchronize Layer 5 Type A Pyramidal Cells via Rebound Excitation2017In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 15, no 2, article id e2001392Article in journal (Refereed)
    Abstract [en]

    Martinotti cells are the most prominent distal dendrite-targeting interneurons in the cortex, but their role in controlling pyramidal cell ( PC) activity is largely unknown. Here, we show that the nicotinic acetylcholine receptor alpha 2 subunit (Chrna2) specifically marks layer 5 (L5) Martinotti cells projecting to layer 1. Furthermore, we confirm that Chrna2-expressing Martinotti cells selectively target L5 thick-tufted type A PCs but not thin-tufted type B PCs. Using optogenetic activation and inhibition, we demonstrate how Chrna2-Martinotti cells robustly reset and synchronize type A PCs via slow rhythmic burst activity and rebound excitation. Moreover, using optical feedback inhibition, in which PC spikes controlled the firing of surrounding Chrna2-Martinotti cells, we found that neighboring PC spike trains became synchronized by Martinotti cell inhibition. Together, our results show that L5 Martinotti cells participate in defined cortical circuits and can synchronize PCs in a frequency-dependent manner. These findings suggest that Martinotti cells are pivotal for coordinated PC activity, which is involved in cortical information processing and cognitive control.

  • 11.
    Husby, Arild
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Visser, Marcel E.
    Kruuk, Loeske E. B.
    Speeding Up Microevolution: The Effects of Increasing Temperature on Selection and Genetic Variance in a Wild Bird Population2011In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 9, no 2, p. e1000585-Article in journal (Refereed)
    Abstract [en]

    The amount of genetic variance underlying a phenotypic trait and the strength of selection acting on that trait are two key parameters that determine any evolutionary response to selection. Despite substantial evidence that, in natural populations, both parameters may vary across environmental conditions, very little is known about the extent to which they may covary in response to environmental heterogeneity. Here we show that, in a wild population of great tits (Parus major), the strength of the directional selection gradients on timing of breeding increased with increasing spring temperatures, and that genotype-by-environment interactions also predicted an increase in additive genetic variance, and heritability, of timing of breeding with increasing spring temperature. Consequently, we therefore tested for an association between the annual selection gradients and levels of additive genetic variance expressed each year; this association was positive, but nonsignificant. However, there was a significant positive association between the annual selection differentials and the corresponding heritability. Such associations could potentially speed up the rate of micro-evolution and offer a largely ignored mechanism by which natural populations may adapt to environmental changes.

  • 12.
    Innocenti, Paolo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Morrow, Edward H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    The Sexually Antagonistic Genes of Drosophila melanogaster2010In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 8, no 3, p. e1000335-Article in journal (Refereed)
    Abstract [en]

    When selective pressures differ between males and females, the genes experiencing these conflicting evolutionary forces are said to be sexually antagonistic. Although the phenotypic effect of these genes has been documented in both wild and laboratory populations, their identity, number, and location remains unknown. Here, by combining data on sex-specific fitness and genome-wide transcript abundance in a quantitative genetic framework, we identified a group of candidate genes experiencing sexually antagonistic selection in the adult, which correspond to 8% of Drosophila melanogaster genes. As predicted, the X chromosome is enriched for these genes, but surprisingly they represent only a small proportion of the total number of sex-biased transcripts, indicating that the latter is a poor predictor of sexual antagonism. Furthermore, the majority of genes whose expression profiles showed a significant relationship with either male or female adult fitness are also sexually antagonistic. These results provide a first insight into the genetic basis of intralocus sexual conflict and indicate that genetic variation for fitness is dominated and maintained by sexual antagonism, potentially neutralizing any indirect genetic benefits of sexual selection.

  • 13. Mahmoudi, Salah
    et al.
    Henriksson, Sofia
    Weibrecht, Irene
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Smith, Stephen
    Söderberg, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Strömblad, Staffan
    Wiman, Klas G.
    Farnebo, Marianne
    WRAP53 Is Essential for Cajal Body Formation and for Targeting the Survival of Motor Neuron Complex to Cajal Bodies2010In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 8, no 11, p. e1000521-Article in journal (Refereed)
    Abstract [en]

    The WRAP53 gene gives rise to a p53 antisense transcript that regulates p53. This gene also encodes a protein that directs small Cajal body-specific RNAs to Cajal bodies. Cajal bodies are nuclear organelles involved in diverse functions such as processing ribonucleoproteins important for splicing. Here we identify the WRAP53 protein as an essential factor for Cajal body maintenance and for directing the survival of motor neuron (SMN) complex to Cajal bodies. By RNA interference and immunofluorescence we show that Cajal bodies collapse without WRAP53 and that new Cajal bodies cannot be formed. By immunoprecipitation we find that WRAP53 associates with the Cajal body marker coilin, the splicing regulatory protein SMN, and the nuclear import receptor importin beta, and that WRAP53 is essential for complex formation between SMN-coilin and SMN-importin beta. Furthermore, depletion of WRAP53 leads to accumulation of SMN in the cytoplasm and prevents the SMN complex from reaching Cajal bodies. Thus, WRAP53 mediates the interaction between SMN and associated proteins, which is important for nuclear targeting of SMN and the subsequent localization of the SMN complex to Cajal bodies. Moreover, we detect reduced WRAP53-SMN binding in patients with spinal muscular atrophy, which is the leading genetic cause of infant mortality worldwide, caused by mutations in SMN1. This suggests that loss of WRAP53-mediated SMN trafficking contributes to spinal muscular atrophy.

  • 14.
    Markljung, Ellen
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jiang, Lin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jaffe, Jacob D.
    Mikkelsen, Tarjei S.
    Wallerman, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Larhammar, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Zhang, Xiaolan
    Wang, Li
    Saenz-Vash, Veronica
    Gnirke, Andreas
    Lindroth, Anders M.
    Barrés, Romain
    Yan, Jie
    Strömberg, Sara
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    De, Sachinandan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Pontén, Fredrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Lander, Eric S.
    Carr, Steven A.
    Zierath, Juleen R.
    Kullander, Klas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Developmental Genetics.
    Wadelius, Claes
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Lindblad-Toh, Kerstin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Andersson, Göran
    Hjälm, Göran
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Andersson, Leif
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    ZBED6, a novel transcription factor derived from a domesticated DNA transposon regulates IGF2 expression and muscle growth2009In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 7, no 12, p. e1000256-Article in journal (Refereed)
    Abstract [en]

    A single nucleotide substitution in intron 3 of IGF2 in pigs abrogates a binding site for a repressor and leads to a 3-fold up-regulation of IGF2 in skeletal muscle. The mutation has major effects on muscle growth, size of the heart, and fat deposition. Here, we have identified the repressor and find that the protein, named ZBED6, is previously unknown, specific for placental mammals, and derived from an exapted DNA transposon. Silencing of Zbed6 in mouse C2C12 myoblasts affected Igf2 expression, cell proliferation, wound healing, and myotube formation. Chromatin immunoprecipitation (ChIP) sequencing using C2C12 cells identified about 2,500 ZBED6 binding sites in the genome, and the deduced consensus motif gave a perfect match with the established binding site in Igf2. Genes associated with ZBED6 binding sites showed a highly significant enrichment for certain Gene Ontology classifications, including development and transcriptional regulation. The phenotypic effects in mutant pigs and ZBED6-silenced C2C12 myoblasts, the extreme sequence conservation, its nucleolar localization, the broad tissue distribution, and the many target genes with essential biological functions suggest that ZBED6 is an important transcription factor in placental mammals, affecting development, cell proliferation, and growth.

  • 15. Maxwell, Christopher A.
    et al.
    Benitez, Javier
    Gomez-Baldo, Laia
    Osorio, Ana
    Bonifaci, Nuria
    Fernandez-Ramires, Ricardo
    Costes, Sylvain V.
    Guino, Elisabet
    Chen, Helen
    Evans, Gareth J. R.
    Mohan, Pooja
    Catala, Isabel
    Petit, Anna
    Aguilar, Helena
    Villanueva, Alberto
    Aytes, Alvaro
    Serra-Musach, Jordi
    Rennert, Gad
    Lejbkowicz, Flavio
    Peterlongo, Paolo
    Manoukian, Siranoush
    Peissel, Bernard
    Ripamonti, Carla B.
    Bonanni, Bernardo
    Viel, Alessandra
    Allavena, Anna
    Bernard, Loris
    Radice, Paolo
    Friedman, Eitan
    Kaufman, Bella
    Laitman, Yael
    Dubrovsky, Maya
    Milgrom, Roni
    Jakubowska, Anna
    Cybulski, Cezary
    Gorski, Bohdan
    Jaworska, Katarzyna
    Durda, Katarzyna
    Sukiennicki, Grzegorz
    Lubinski, Jan
    Shugart, Yin Yao
    Domchek, Susan M.
    Letrero, Richard
    Weber, Barbara L.
    Hogervorst, Frans B. L.
    Rookus, Matti A.
    Collee, J. Margriet
    Devilee, Peter
    Ligtenberg, Marjolijn J.
    van der Luijt, Rob B.
    Aalfs, Cora M.
    Waisfisz, Quinten
    Wijnen, Juul
    van Roozendaal, Cornelis E. P.
    Easton, Douglas F.
    Peock, Susan
    Cook, Margaret
    Oliver, Clare
    Frost, Debra
    Harrington, Patricia
    Evans, D. Gareth
    Lalloo, Fiona
    Eeles, Rosalind
    Izatt, Louise
    Chu, Carol
    Eccles, Diana
    Douglas, Fiona
    Brewer, Carole
    Nevanlinna, Heli
    Heikkinen, Tuomas
    Couch, Fergus J.
    Lindor, Noralane M.
    Wang, Xianshu
    Godwin, Andrew K.
    Caligo, Maria A.
    Lombardi, Grazia
    Loman, Niklas
    Karlsson, Per
    Ehrencrona, Hans
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Medical Genetics.
    von Wachenfeldt, Anna
    Barkardottir, Rosa Bjork
    Hamann, Ute
    Rashid, Muhammad U.
    Lasa, Adriana
    Caldes, Trinidad
    Andres, Raquel
    Schmitt, Michael
    Assmann, Volker
    Stevens, Kristen
    Offit, Kenneth
    Curado, Joao
    Tilgner, Hagen
    Guigo, Roderic
    Aiza, Gemma
    Brunet, Joan
    Castellsague, Joan
    Martrat, Griselda
    Urruticoechea, Ander
    Blanco, Ignacio
    Tihomirova, Laima
    Goldgar, David E.
    Buys, Saundra
    John, Esther M.
    Miron, Alexander
    Southey, Melissa
    Daly, Mary B.
    Schmutzler, Rita K.
    Wappenschmidt, Barbara
    Meindl, Alfons
    Arnold, Norbert
    Deissler, Helmut
    Varon-Mateeva, Raymonda
    Sutter, Christian
    Niederacher, Dieter
    Imyamitov, Evgeny
    Sinilnikova, Olga M.
    Stoppa-Lyonne, Dominique
    Mazoyer, Sylvie
    Verny-Pierre, Carole
    Castera, Laurent
    de Pauw, Antoine
    Bignon, Yves-Jean
    Uhrhammer, Nancy
    Peyrat, Jean-Philippe
    Vennin, Philippe
    Ferrer, Sandra Fert
    Collonge-Rame, Marie-Agnes
    Mortemousque, Isabelle
    Spurdle, Amanda B.
    Beesley, Jonathan
    Chen, Xiaoqing
    Healey, Sue
    Barcellos-Hoff, Mary Helen
    Vidal, Marc
    Gruber, Stephen B.
    Lazaro, Conxi
    Capella, Gabriel
    McGuffog, Lesley
    Nathanson, Katherine L.
    Antoniou, Antonis C.
    Chenevix-Trench, Georgia
    Fleisch, Markus C.
    Moreno, Victor
    Angel Pujana, Miguel
    Interplay between BRCA1 and RHAMM Regulates Epithelial Apicobasal Polarization and May Influence Risk of Breast Cancer2011In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 9, no 11, p. e1001199-Article in journal (Refereed)
    Abstract [en]

    Differentiated mammary epithelium shows apicobasal polarity, and loss of tissue organization is an early hallmark of breast carcinogenesis. In BRCA1 mutation carriers, accumulation of stem and progenitor cells in normal breast tissue and increased risk of developing tumors of basal-like type suggest that BRCA1 regulates stem/progenitor cell proliferation and differentiation. However, the function of BRCA1 in this process and its link to carcinogenesis remain unknown. Here we depict a molecular mechanism involving BRCA1 and RHAMM that regulates apicobasal polarity and, when perturbed, may increase risk of breast cancer. Starting from complementary genetic analyses across families and populations, we identified common genetic variation at the low-penetrance susceptibility HMMR locus (encoding for RHAMM) that modifies breast cancer risk among BRCA1, but probably not BRCA2, mutation carriers: n = 7,584, weighted hazard ratio ((w)HR) = 1.09 (95% CI 1.02-1.16), p(trend) = 0.017; and n = 3,965, (w)HR = 1.04 (95% CI 0.94-1.16), p(trend) = 0.43; respectively. Subsequently, studies of MCF10A apicobasal polarization revealed a central role for BRCA1 and RHAMM, together with AURKA and TPX2, in essential reorganization of microtubules. Mechanistically, reorganization is facilitated by BRCA1 and impaired by AURKA, which is regulated by negative feedback involving RHAMM and TPX2. Taken together, our data provide fundamental insight into apicobasal polarization through BRCA1 function, which may explain the expanded cell subsets and characteristic tumor type accompanying BRCA1 mutation, while also linking this process to sporadic breast cancer through perturbation of HMMR/RHAMM.

  • 16.
    Nordström, Karin
    et al.
    The University of Adelaide.
    Barnett, Paul D
    The University of Adelaide.
    O'Carroll, David C
    The University of Adelaide.
    Insect detection of small targets moving in visual clutter.2006In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 4, no 3, p. e54-Article in journal (Refereed)
    Abstract [en]

    Detection of targets that move within visual clutter is a common task for animals searching for prey or conspecifics, a task made even more difficult when a moving pursuer needs to analyze targets against the motion of background texture (clutter). Despite the limited optical acuity of the compound eye of insects, this challenging task seems to have been solved by their tiny visual system. Here we describe neurons found in the male hoverfly, Eristalis tenax, that respond selectively to small moving targets. Although many of these target neurons are inhibited by the motion of a background pattern, others respond to target motion within the receptive field under a surprisingly large range of background motion stimuli. Some neurons respond whether or not there is a speed differential between target and background. Analysis of responses to very small targets (smaller than the size of the visual field of single photoreceptors) or those targets with reduced contrast shows that these neurons have extraordinarily high contrast sensitivity. Our data suggest that rejection of background motion may result from extreme selectivity for small targets contrasting against local patches of the background, combined with this high sensitivity, such that background patterns rarely contain features that satisfactorily drive the neuron.

  • 17. Pawlowski, Jan
    et al.
    Audic, Stephane
    Adl, Sina
    Bass, David
    Belbahri, Lassaad
    Berney, Cedric
    Bowser, Samuel S.
    Cepicka, Ivan
    Decelle, Johan
    Dunthorn, Micah
    Fiore-Donno, Anna Maria
    Gile, Gillian H.
    Holzmann, Maria
    Jahn, Regine
    Jirku, Miloslav
    Keeling, Patrick J.
    Kostka, Martin
    Kudryavtsev, Alexander
    Lara, Enrique
    Lukes, Julius
    Mann, David G.
    Mitchell, Edward A. D.
    Nitsche, Frank
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Saunders, Gary W.
    Simpson, Alastair G. B.
    Smirnov, Alexey V.
    Spouge, John L.
    Stern, Rowena F.
    Stoeck, Thorsten
    Zimmermann, Jonas
    Schindel, David
    de Vargas, Colomban
    CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms2012In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 10, no 11, p. e1001419-Article in journal (Refereed)
  • 18. Reesink, Ger
    et al.
    Singer, Ruth
    Dunn, Michael
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Languages, Department of Linguistics and Philology.
    Explaining the Linguistic Diversity of Sahul Using Population Models2009In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 7, no 11Article in journal (Refereed)
  • 19. Richards, Stephen
    et al.
    Gibbs, Richard A.
    Gerardo, Nicole M.
    Moran, Nancy
    Nakabachi, Atsushi
    Stern, David
    Tagu, Denis
    Wilson, Alex C. C.
    Muzny, Donna
    Kovar, Christie
    Cree, Andy
    Chacko, Joseph
    Chandrabose, Mimi N.
    Dao, Marvin Diep
    Dinh, Huyen H.
    Gabisi, Ramatu Ayiesha
    Hines, Sandra
    Hume, Jennifer
    Jhangian, Shalini N.
    Joshi, Vandita
    Lewis, Lora R.
    Liu, Yih-shin
    Lopez, John
    Morgan, Margaret B.
    Nguyen, Ngoc Bich
    Okwuonu, Geoffrey O.
    Ruiz, San Juana
    Santibanez, Jireh
    Wright, Rita A.
    Fowler, Gerald R.
    Hitchens, Matthew E.
    Lozado, Ryan J.
    Moen, Charles
    Steffen, David
    Warren, James T.
    Zhang, Jingkun
    Nazareth, Lynne V.
    Chavez, Dean
    Davis, Clay
    Lee, Sandra L.
    Patel, Bella Mayurkumar
    Pu, Ling-Ling
    Bell, Stephanie N.
    Johnson, Angela Jolivet
    Vattathil, Selina
    Williams, Rex L., Jr.
    Shigenobu, Shuji
    Dang, Phat M.
    Morioka, Mizue
    Fukatsu, Takema
    Kudo, Toshiaki
    Miyagishima, Shin-ya
    Jiang, Huaiyang
    Worley, Kim C.
    Legeai, Fabrice
    Gauthier, Jean-Pierre
    Collin, Olivier
    Zhang, Lan
    Chen, Hsiu-Chuan
    Ermolaeva, Olga
    Hlavina, Wratko
    Kapustin, Yuri
    Kiryutin, Boris
    Kitts, Paul
    Maglott, Donna
    Murphy, Terence
    Pruitt, Kim
    Sapojnikov, Victor
    Souvorov, Alexandre
    Thibaud-Nissen, Francoise
    Camara, Francisco
    Guigo, Roderic
    Stanke, Mario
    Solovyev, Victor
    Kosarev, Peter
    Gilbert, Don
    Gabaldon, Toni
    Huerta-Cepas, Jaime
    Marcet-Houben, Marina
    Pignatelli, Miguel
    Moya, Andres
    Rispe, Claude
    Ollivier, Morgane
    Quesneville, Hadi
    Permal, Emmanuelle
    Llorens, Carlos
    Futami, Ricardo
    Hedges, Dale
    Robertson, Hugh M.
    Alioto, Tyler
    Mariotti, Marco
    Nikoh, Naruo
    McCutcheon, John P.
    Burke, Gaelen
    Kamins, Alexandra
    Latorre, Amparo
    Moran, Nancy A.
    Ashton, Peter
    Calevro, Federica
    Charles, Hubert
    Colella, Stefano
    Douglas, Angela
    Jander, Georg
    Jones, Derek H.
    Febvay, Gerard
    Kamphuis, Lars G.
    Kushlan, Philip F.
    Macdonald, Sandy
    Ramsey, John
    Schwartz, Julia
    Seah, Stuart
    Thomas, Gavin
    Vellozo, Augusto
    Cass, Bodil
    Degnan, Patrick
    Hurwitz, Bonnie
    Leonardo, Teresa
    Koga, Ryuichi
    Altincicek, Boran
    Anselme, Caroline
    Atamian, Hagop
    Barribeau, Seth M.
    de Vos, Martin
    Duncan, Elizabeth J.
    Evans, Jay
    Ghanim, Murad
    Heddi, Abdelaziz
    Kaloshian, Isgouhi
    Vincent-Monegat, Carole
    Parker, Ben J.
    Perez-Brocal, Vicente
    Rahbe, Yvan
    Spragg, Chelsea J.
    Tamames, Javier
    Tamarit, Daniel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Tamborindeguy, Cecilia
    Vilcinskas, Andreas
    Bickel, Ryan D.
    Brisson, Jennifer A.
    Butts, Thomas
    Chang, Chun-che
    Christiaens, Olivier
    Davis, Gregory K.
    Duncan, Elizabeth
    Ferrier, David
    Iga, Masatoshi
    Janssen, Ralf
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    Lu, Hsiao-Ling
    McGregor, Alistair
    Miura, Toru
    Smagghe, Guy
    Smith, James
    van der Zee, Maurijn
    Velarde, Rodrigo
    Wilson, Megan
    Dearden, Peter
    Edwards, Owain R.
    Gordon, Karl
    Hilgarth, Roland S.
    Rider, Stanley Dean, Jr.
    Srinivasan, Dayalan
    Walsh, Thomas K.
    Ishikawa, Asano
    Jaubert-Possamai, Stephanie
    Fenton, Brian
    Huang, Wenting
    Rizk, Guillaume
    Lavenier, Dominique
    Nicolas, Jacques
    Smadja, Carole
    Zhou, Jing-Jiang
    Vieira, Filipe G.
    He, Xiao-Li
    Liu, Renhu
    Rozas, Julio
    Field, Linda M.
    Ashton, Peter D.
    Campbell, Peter
    Carolan, James C.
    Douglas, Angela E.
    Fitzroy, Carol I. J.
    Reardon, Karen T.
    Reeck, Gerald R.
    Singh, Karam
    Wilkinson, Thomas L.
    Huybrechts, Jurgen
    Abdel-latief, Mohatmed
    Robichon, Alain
    Veenstra, Jan A.
    Hauser, Frank
    Cazzamali, Giuseppe
    Schneider, Martina
    Williamson, Michael
    Stafflinger, Elisabeth
    Hansen, Karina K.
    Grimmelikhuijzen, Cornelis J. P.
    Price, Daniel R. G.
    Caillaud, Marina
    van Fleet, Eric
    Ren, Qinghu
    Gatehouse, John A.
    Brault, Veronique
    Monsion, Baptiste
    Diaz, Jason
    Hunnicutt, Laura
    Ju, Ho-Jong
    Pechuan, Ximo
    Aguilar, Jose
    Cortes, Teresa
    Ortiz-Rivas, Benjamin
    Martinez-Torres, David
    Dombrovsky, Aviv
    Dale, Richard P.
    Davies, T. G. Emyr
    Williamson, Martin S.
    Jones, Andrew
    Sattelle, David
    Williamson, Sally
    Wolstenholme, Adrian
    Cottret, Ludovic
    Sagot, Marie France
    Heckel, David G.
    Hunter, Wayne
    Genome Sequence of the Pea Aphid Acyrthosiphon pisum2010In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 8, no 2, p. e1000313-Article in journal (Refereed)
    Abstract [en]

    Aphids are important agricultural pests and also biological models for studies of insect-plant interactions, symbiosis, virus vectoring, and the developmental causes of extreme phenotypic plasticity. Here we present the 464 Mb draft genome assembly of the pea aphid Acyrthosiphon pisum. This first published whole genome sequence of a basal hemimetabolous insect provides an outgroup to the multiple published genomes of holometabolous insects. Pea aphids are host-plant specialists, they can reproduce both sexually and asexually, and they have coevolved with an obligate bacterial symbiont. Here we highlight findings from whole genome analysis that may be related to these unusual biological features. These findings include discovery of extensive gene duplication in more than 2000 gene families as well as loss of evolutionarily conserved genes. Gene family expansions relative to other published genomes include genes involved in chromatin modification, miRNA synthesis, and sugar transport. Gene losses include genes central to the IMD immune pathway, selenoprotein utilization, purine salvage, and the entire urea cycle. The pea aphid genome reveals that only a limited number of genes have been acquired from bacteria; thus the reduced gene count of Buchnera does not reflect gene transfer to the host genome. The inventory of metabolic genes in the pea aphid genome suggests that there is extensive metabolite exchange between the aphid and Buchnera, including sharing of amino acid biosynthesis between the aphid and Buchnera. The pea aphid genome provides a foundation for post-genomic studies of fundamental biological questions and applied agricultural problems.

  • 20.
    Shafer, Aaron B. A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Northrup, Joseph M.
    Colorado State Univ, Dept Fish Wildlife & Conservat Biol, Ft Collins, CO 80523 USA..
    Wikelski, Martin
    Max Planck Inst Ornithol, Radolfzell am Bodensee, Germany.;Univ Konstanz, Biol, Constance, Germany..
    Wittemyer, George
    Colorado State Univ, Dept Fish Wildlife & Conservat Biol, Ft Collins, CO 80523 USA..
    Wolf, Jochen B. W.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Forecasting Ecological Genomics: High-Tech Animal Instrumentation Meets High-Throughput Sequencing2016In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 14, no 1, article id e1002350Article in journal (Refereed)
    Abstract [en]

    Recent advancements in animal tracking technology and high-throughput sequencing are rapidly changing the questions and scope of research in the biological sciences. The integration of genomic data with high-tech animal instrumentation comes as a natural progression of traditional work in ecological genetics, and we provide a framework for linking the separate data streams from these technologies. Such a merger will elucidate the genetic basis of adaptive behaviors like migration and hibernation and advance our understanding of fundamental ecological and evolutionary processes such as pathogen transmission, population responses to environmental change, and communication in natural populations.

  • 21.
    Suh, Alexander
    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.
    The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds2015In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 13, no 8, article id e1002224Article in journal (Refereed)
    Abstract [en]

    The diversification of neoavian birds is one of the most rapid adaptive radiations of extant organisms. Recent whole-genome sequence analyses have much improved the resolution of the neoavian radiation and suggest concurrence with the Cretaceous-Paleogene (K-Pg) boundary, yet the causes of the remaining genome-level irresolvabilities appear unclear. Here we show that genome-level analyses of 2,118 retrotransposon presence/absence markers converge at a largely consistent Neoaves phylogeny and detect a highly differential temporal prevalence of incomplete lineage sorting (ILS), i.e., the persistence of ancestral genetic variation as polymorphisms during speciation events. We found that ILS-derived incongruences are spread over the genome and involve 35% and 34% of the analyzed loci on the autosomes and the Z chromosome, respectively. Surprisingly, Neoaves diversification comprises three adaptive radiations, an initial near-K-Pg super-radiation with highly discordant phylogenetic signals from near-simultaneous speciation events, followed by two post-K-Pg radiations of core landbirds and core waterbirds with much less pronounced ILS. We provide evidence that, given the extreme level of up to 100% ILS per branch in super-radiations, particularly rapid speciation events may neither resemble a fully bifurcating tree nor are they resolvable as such. As a consequence, their complex demographic history is more accurately represented as local networks within a species tree.

  • 22.
    Suzuki, Toshitaka N.
    et al.
    Grad Univ Adv Studies, SOKENDAI, Dept Evolutionary Studies Biosyst, Hayama, Kanagawa, Japan.
    Wheatcroft, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Griesser, Michael
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland.
    Call combinations in birds and the evolution of compositional syntax2018In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 16, no 8, article id e2006532Article in journal (Refereed)
    Abstract [en]

    Syntax is the set of rules for combining words into phrases, providing the basis for the generative power of linguistic expressions. In human language, the principle of compositionality governs how words are combined into a larger unit, the meaning of which depends on both the meanings of the words and the way in which they are combined. This linguistic capability, i.e., compositional syntax, has long been considered a trait unique to human language. Here, we review recent studies on call combinations in a passerine bird, the Japanese tit (Parus minor), that provide the first firm evidence for compositional syntax in a nonhuman animal. While it has been suggested that the findings of these studies fail to provide evidence for compositionality in Japanese tits, this criticism is based on misunderstanding of experimental design, misrepresentation of the importance of word order in human syntax, and necessitating linguistic capabilities beyond those given by the standard definition of compositionality. We argue that research on avian call combinations has provided the first steps in elucidating how compositional expressions could have emerged in animal communication systems.

1 - 22 of 22
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf