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  • 101. Batut, Jacques
    et al.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    O'Callaghan, David
    The evolution of chronic infection strategies in the α-proteobacteria2004In: Nature Reviews Microbiology, ISSN 1740-1526, E-ISSN 1740-1534, Vol. 2, p. 933-945Article, review/survey (Refereed)
    Abstract [en]

    Many of the -proteobacteria establish long-term, often chronic, interactions with higher eukaryotes. These interactions range from pericellular colonization through facultative intracellular multiplication to obligate intracellular lifestyles. A common feature in this wide range of interactions is modulation of host-cell proliferation, which sometimes leads to the formation of tumour-like structures in which the bacteria can grow. Comparative genome analyses reveal genome reduction by gene loss in the intracellular -proteobacterial lineages, and genome expansion by gene duplication and horizontal gene transfer in the free-living species. In this review, we discuss -proteobacterial genome evolution and highlight strategies and mechanisms used by these bacteria to infect and multiply in eukaryotic cells.

  • 102.
    Beier, Björn Axel
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Zoology. Systematisk botanik.
    Nylander, Johan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Zoology. Systematisk zoologi.
    Chase, Mark W
    Thulin, Mats
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Zoology. Systematisk botanik.
    Phylogenetic relationships and biogeography of the desert plant genus Fagonia (Zygophyllaceae), inferred by parsimony and Bayesian model averaging2004In: Molecular Phylogenetics and Evolution, Vol. 33, no 1, p. 91-108Article in journal (Refereed)
  • 103.
    Beier, Björn-Axel
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    A revision of the desert shrub Fagonia (Zygophyllaceae)2005In: Systematics and Biodiversity, Vol. 3, p. 221-263Article in journal (Refereed)
  • 104.
    Beier, Björn-Axel
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Avdelningen för systematisk botanik.
    Thulin, Mats
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Avdelningen för systematisk botanik.
    Proposal to conserve the name Tetraena against Petrusia (Zygophyllaceae)2004In: Taxon, Vol. 53, p. 1078-1079Article in journal (Refereed)
  • 105. Belle, Elise M S
    et al.
    Webster, Matthew T
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Eyre-Walker, Adam
    Why are young and old repetitive elements distributed differently in the human genome?2005In: J Mol Evol, ISSN 0022-2844, Vol. 60, no 3, p. 290-6Article in journal (Refereed)
    Abstract [en]

    Alu elements are not distributed homogeneously throughout the human genome: old elements are preferentially found in the GC-rich parts of the genome, while young Alus are more often found in the GC-poor parts of the genome. The process giving rise to this differential distribution remains poorly understood. Here we investigate whether this pattern could be due to a preferential degradation of Alu elements integrated in GC-poor regions by small indel mutations. We aligned 5.1 Mb of human and chimpanzee sequences and examined whether the rate of insertion and deletion inside Alu elements differed according to the base composition surrounding them. We found that Alu elements are not preferentially degraded in GC-poor regions by indel events. We also looked at whether very young L1 elements show the same change in distribution compared to older ones. This analysis indicated that L1 elements also show a shift in their distribution, although we could not assess it as precisely as for Alu elements. We propose that the differential distribution of Alu elements is likely to be due to a change in their pattern of insertion or their probability of fixation through evolutionary time.

  • 106.
    Bennett, Keith D.
    et al.
    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 Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Parducci, Laura
    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 Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    DNA from pollen: principles and potential2006In: The Holocene, ISSN 0959-6836, E-ISSN 1477-0911, Vol. 16, no 8, p. 1031-1034Article in journal (Refereed)
    Abstract [en]

    This paper describes our recent extraction of ancient DNA (aDNA) from Holocene pollen and discusses the potential of the technique for elucidating timescales of evolutionary change. We show that plastid DNA is recoverable and usable from pollen grains of Scots pine Pinus sylvestris from 10 ka and 100 years ago. Comparison of the ancient sequences with modern sequences, obtained from an extant population, establish a first genetic link between modern and fossil samples of Scots pine, providing a genetic continuity through time. One common haplotype is present in each of the three periods investigated, suggesting that it persisted near the lake throughout the postglacial. The retrieval of aDNA from pollen has major implications for palaeoecology by allowing (i) investigation of population-level dynamics in time and space, and (ii) tracing ancestry of populations and developing phylogenetic trees that include extinct as well as extant taxa. The method should work over the last glacial oscillation, thus giving access to ancestry of populations over a crucial period of time for the understanding of the relationship between speciation and climate change.

  • 107.
    Berg, LM
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Lascoux, M
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Neutral genetic differentiation in an island model with cyclical parthenogenesis2000In: JOURNAL OF EVOLUTIONARY BIOLOGY, ISSN 1010-061X, Vol. 13, no 3, p. 488-494Article in journal (Refereed)
    Abstract [en]

    Unusually high levels of genetic differentiation are often observed between populations of Daphnia (Crustacea: Cladocera) and other cladocerans. Selection and departure from migration-mutation-drift equilibrium have been invoked to explain this fact. Howe

  • 108.
    Berg, LM
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. CONSERVATION BIOLOGY AND GENETICS.
    Lascoux, M
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Pamilo, P
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    The infinite island model with sex-differentiated gene flow1998In: HEREDITY, ISSN 0018-067X, Vol. 81, p. 63-68Article in journal (Refereed)
    Abstract [en]

    Identity measures are derived for the infinite island model with separate sexes and sex-differentiated contribution to gene flow. The concept of effective migration rate, m(e), is introduced, which describes the genetically effective flow when sexes migra

  • 109.
    Berg, LM
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Biology, Department of Evolutionary Biology. Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. CONSERVATION BIOLOGY AND GENETICS.
    Palsson, S
    Lascoux, M
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Fitness and sexual response to population density in Daphnia pulex2001In: FRESHWATER BIOLOGY, ISSN 0046-5070, Vol. 46, no 5, p. 667-677Article in journal (Refereed)
    Abstract [en]

    1. The switch between asexual and sexual reproduction is an important fitness component in cyclically parthenogenetic populations as it is the key to persistence in unstable habitats and because it influences population genetic characteristics such as lin

  • 110.
    Berg, Otto G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Yu, Bao-Zhu
    Jain, Mahendra K.
    Thermodynamic Reciprocity of the Inhibitor Binding to the Active Site and the Interface Binding Region of IB Phospholipase A22009In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 48, no 14, p. 3209-3218Article in journal (Refereed)
    Abstract [en]

    Interfacial activation of pig pancreatic IB phospholipase A(2) (PLA2) is modeled in terms of the three discrete premicellar complexes (E-i(#), i = 1, 2, or 3) consecutively formed by the cooperative binding of a monodisperse amphiphile to the i-face (the interface binding region of the enzyme) without or with an occupied active site. Monodisperse PCU, the sn-2-amide analogue of the zwitterionic substrate, is a competitive inhibitor. PCU cooperatively binds to the i-face to form premicellar complexes ((E) over tilde (i), i = 1 or 2) and also binds to the active site of the premicellar complexes in the presence of calcium. In the (E) over tilde I-i complex formed in the presence of PCU and calcium, one inhibitor molecule is bound to the active site and a number of others are bound to the i-face. The properties of the (E) over tilde (i) complexes with PCU are qualitatively similar to those of E-i(#) formed with decylsulfate. Decylsulfate binds to the i-face but does not bind to the active site in the presence of calcium, nor does it interfere with the binding of PCU to the active site in the premicellar complexes. Due to the strong coupling between binding at the i-face and at the active site, it is difficult to estimate the primary binding constants for each site in these complexes. A model is developed that incorporates the above boundary conditions in relation to a detailed balance between the complexes. A key result is that a modest effect on cooperative amphiphile binding corresponds to a large change in the affinity of the inhibitor for the active site. We suggest that besides the binding to the active site, PCU also binds to another site and that full activation requires additional amphiphiles on the i-face. Thus, the activation of the inhibitor binding to the active site of the E-2(#) complex or, equivalently, the shift in the E-1(#) to E-2(#) equilibrium by the inhibitor is analogous to the allosteric activation of the substrate binding to the enzyme bound to the interface.

  • 111.
    Berg, Otto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Yu, Bao-Zhu
    Apitz-Castro, Rafael J.
    Jain, Mahendra K.
    Phosphatidylinositol-specific phospholipase C forms different complexes with monodisperse and micellar phosphatidylcholine2004In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 43, no 7, p. 2080-2090Article in journal (Refereed)
    Abstract [en]

    Phosphatidylinositol-specific phospholipase C (PI-PLC) from Bacillus cereus forms a premicellar complex E# with monodisperse diheptanoylphosphatidylcholine (DC7PC) that is distinguishable from the E* complex formed with micelles. Results are interpreted with the assumption that in both cases amphiphiles bind to the interfacial binding surface (i-face) of PI-PLC but not to the active site. Isothermal calorimetry and fluorescence titration results for the binding of monodisperse DC7PC give an apparent dissociation constant of K2 = 0.2 mM with Hill coefficient of 2. The gel-permeation, spectroscopic, and probe partitioning behaviors of E# are distinct from those of the E* complex. The aggregation and partitioning behaviors suggest that the acyl chains in E# but not in E* remain exposed to the aqueous phase. The free (E) and complexed (E# and E*) forms of PI-PLC, each with distinct spectroscopic signatures, readily equilibrate with changing DC7PC concentration. The underlying equilibria are modeled and their significance for the states of the PI-PLC under monomer kinetic conditions is discussed to suggest that the Michaelis−Menten complex formed with monodisperse DC7PC is likely to be E#S or its aggregate rather than the classical monodisperse ES complex.

  • 112.
    Berg, Otto
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Yu, Bao-Zhu
    Chang, Cherry
    Koehler, Karl A.
    Jain, Mahendra K.
    Cooperative binding of monodisperse anionic amphiphiles to the i-Face: Phospholipase A2-paradigm for interfacial binding2004In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 43, no 25, p. 7999-8013Article in journal (Refereed)
    Abstract [en]

    Equilibrium parameters for the binding of monodisperse alkyl sulfate along the i-face (the interface binding surface) of pig pancreatic IB phospholipase A2 (PLA2) to form the premicellar complexes (Ei#) are characterized to discern the short-range specific interactions. Typically, Ei# complexes are reversible on dilution. The triphasic binding isotherm, monitored as the fluorescence emission from the single tryptophan of PLA2, is interpreted as a cooperative equilibrium for the sequential formation of three premicellar complexes (Ei#, i = 1, 2, 3). In the presence of calcium, the dissociation constant K1 for the E1# complex of PLA2 with decyl sulfate (CMC = 4500 μM) is 70 μM with a Hill coefficient n1 = 2.1 ± 0.2; K2 for E2# is 750 μM with n2 = 8 ± 1, and K3 for E3# is 4000 μM with an n3 value of about 12. Controls show that (a) self-aggregation of decyl sulfate alone is not significant below the CMC; (b) occupancy of the active site is not necessary for the formation of Ei#; (c) Ki and ni do not change significantly due to the absence of calcium, possibly because alkyl sulfate does not bind to the active site of PLA2; (d) the Ei# complexes show a significant propensity for aggregation; and (e) PLA2 is not denatured in Ei#. The results are interpreted to elaborate the model for atomic level interactions along the i-face: The chain length dependence of the fit parameters suggests that short-range specific anion binding of the headgroup is accompanied by desolvation of the i-face of Ei#. We suggest that allosteric activation of PLA2 results from such specific interactions of the amphiplies and the desolvation of the i-face. The significance of these primary interfacial binding events and the coexistence of the E* and Ei# aggregates is discussed.

  • 113.
    Berggren Bremdal, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Evolution of MHC Genes and MHC Gene Expression2010Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Polymorphism in coding regions and regions controlling gene expression is the major determinant of adaptive differences in natural populations. Genes of the major histocompatibility complex (MHC) possess a high level of genetic variation, which is maintained by selection over long coalescence times. MHC genes encode antigen-presenting molecules in the adaptive immune system, which protects the host from infectious diseases. However, MHC molecules may also present self-peptides and for most autoimmune diseases there is a genetic factor associated with the MHC.

    MHC genes have been used to learn about the interplay of selection and historical population events. In domestic dogs and their progenitor, the wolf, I explored factors associated with domestication and breed formation and their influence not only on MHC coding regions but also on the haplotypic structure of the class II region. Polymorphism and strong selection was demonstrated in the proximal promoters of MHC genes in dogs and wolves. Hence, genetic variation associated with MHC gene expression may have at least equal importance for a well functioning immune system. Associations between promoter sequences and particular coding alleles suggested allele-specific expression patterns. SNP haplotypes of the MHC class II region revealed ancestral as well as convergent haplotypes, in which combinations of alleles are kept by selection. Interestingly, weaker allelic associations were found between different genes and between coding regions and promoters in dogs compared to wolves. Potentially, this could cause insufficient defense against infections and predispose dogs to autoimmune diseases. For example, I identified a site in the promoter region that showed a consistent difference between haplotypes conferring susceptibility and protection to diabetes in dogs, which should be investigated further.

    Furthermore, I investigated how selection and demographic changes associated with glacial and inter-glacial periods have affected MHC variation in European hedgehogs and extended the prevailing knowledge concerning their population history.

    List of papers
    1. Understanding the phylogeographic patterns of European hedgehogs, Erinaceus concolor and E. europaeus using the MHC.
    Open this publication in new window or tab >>Understanding the phylogeographic patterns of European hedgehogs, Erinaceus concolor and E. europaeus using the MHC.
    2005 (English)In: Heredity, ISSN 0018-067X, Vol. 95, no 1, p. 84-90Article in journal (Refereed) Published
    Abstract [en]

    The genome of the European hedgehog, Erinaceus concolor and E. europaeus, shows a strong signal of cycles of restriction to glacial refugia and postglacial expansion. Patterns of expansion, however, differ for mitochondrial DNA (mtDNA) and preliminary analysis of nuclear markers. In this study, we determine phylogeographic patterns in the hedgehog using two loci of the major histocompatibility complex (MHC), isolated for the first time in hedgehogs. These genes show long persistence times and high polymorphism in many species because of the actions of balancing selection. Among 84 individuals screened for variation, only two DQA alleles were identified in each species, but 10 DQB alleles were found in E. concolor and six in E. europaeus. A strong effect of demography on patterns of DQB variability is observed, with only weak evidence of balancing selection. While data from mtDNA clearly subdivide both species into monophyletic subgroups, the MHC data delineate only E. concolor into distinct subgroups, supporting the preliminary findings of other nuclear markers. Together with differences in variability, this suggests that the refugia history and/or expansion patterns of E. concolor and E. europaeus differ.

    Keywords
    Animals, DNA; Mitochondrial/*genetics, Europe, Genome, Geography, Hedgehogs/*classification/*genetics, Major Histocompatibility Complex, Movement, Phylogeny, Population Dynamics, Research Support; Non-U.S. Gov't, Selection (Genetics)
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-76386 (URN)16077505 (PubMedID)
    Available from: 2006-03-02 Created: 2006-03-02 Last updated: 2018-02-22
    2. MHC promoter polymorphism in grey wolves and domestic dogs.
    Open this publication in new window or tab >>MHC promoter polymorphism in grey wolves and domestic dogs.
    2005 (English)In: Immunogenetics, ISSN 0093-7711, Vol. 57, no 3-4, p. 267-72Article in journal (Refereed) Published
    Abstract [en]

    A functional immune system requires a tight control over major histocompatibility complex (MHC) gene transcription, as the abnormal MHC expression patterns of severe immunodeficiency and autoimmune diseases demonstrate. Although the regulation of MHC expression has been well documented in humans and mice, little is known in other species. In this study, we detail the level of polymorphism in wolf and dog MHC gene promoters. The promoter regions of the DRB, DQA and DQB locus were sequenced in 90 wolves and 90 dogs. The level of polymorphism was high in the DQB promoters, with variation found within functionally relevant regions, including binding sites for transcription factors. Clear associations between DQB promoters and exon 2 alleles were noted in wolves, indicating strong linkage disequilibrium in this region. Low levels of polymorphism were found within the DRB and DQA promoter regions. However, a variable site was identified within the T box, a TNF-alpha response element, of the DQA promoter. Furthermore, we identified a previously unrecognised 18-base-pair deletion within exon 1 of the DQB locus.

    Keywords
    Alleles, Animals, Base Sequence, Comparative Study, DNA/genetics, Dogs/*genetics/*immunology, Exons, Linkage Disequilibrium, Major Histocompatibility Complex, Molecular Sequence Data, Polymorphism; Genetic, Promoter Regions (Genetics), Research Support; Non-U.S. Gov't, Sequence Deletion, Sequence Homology; Nucleic Acid, Species Specificity, Variation (Genetics), Wolves/*genetics/*immunology
    National Category
    Genetics
    Identifiers
    urn:nbn:se:uu:diva-76387 (URN)15900498 (PubMedID)
    Available from: 2006-03-02 Created: 2006-03-02 Last updated: 2011-01-11
    3. Allelic combinations of promoter and exon 2 in DQB1 in dogs and wolves
    Open this publication in new window or tab >>Allelic combinations of promoter and exon 2 in DQB1 in dogs and wolves
    2008 (English)In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 67, no 1, p. 76-84Article in journal (Refereed) Published
    Abstract [en]

    Polymorphism of PBRs of the major histocompatibility complex (MHC) genes is well recognized, but the polymorphism also extends to proximal promoter regions. Examining DQB1 variability in dogs and wolves, we identified 7 promoter variants and 13 exon 2 alleles among 89 dogs, including a previously unknown DQB1 exon 2 allele, and 8 promoter variants and 9 exon 2 alleles among 85 wolves. As expected from previous studies and from a close chromosomal location, strong linkage disequilibrium was demonstrated in both wolves and dogs by having significantly fewer promoter/exon 2 combinations than expected from simulations of randomized data sets. Interestingly, we noticed weaker haplotypic associations in dogs than in wolves. Dogs had twice as many promoter/exon 2 combinations as wolves and an almost 2-fold difference in the number of exon 2 alleles per promoter variant. This difference was not caused by an admixture of breeds in our group of dogs because the high ratio of observed to expected number of haplotypes persisted within a single dog breed, the German Shepherd. Ewens-Watterson tests indicated that both the promoter and exon 2 are under the balancing selection, and both regions appear to be more recently derived in the dog than in the wolf. Hence, although reasons for the differences are unknown, they may relate to altered selection pressure on patterns of expression. Deviations from normal MHC expression patterns have been associated with autoimmune diseases, which occur frequently in several dog breeds. Further knowledge about these deviations may help us understand the source of such diseases.

    Keywords
    dog, DLA, DQB1, MHC, promoter, linkage disequilibrium, wolf
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-109175 (URN)10.1007/s00239-008-9126-0 (DOI)000258088000008 ()
    Available from: 2009-10-09 Created: 2009-10-09 Last updated: 2017-12-13Bibliographically approved
    4. Evolutionary history of DLA class II haplotypes in canine diabetes mellitus through single nucleotide polymorphism genotyping
    Open this publication in new window or tab >>Evolutionary history of DLA class II haplotypes in canine diabetes mellitus through single nucleotide polymorphism genotyping
    2010 (English)In: Tissue Antigens, ISSN 0001-2815, E-ISSN 1399-0039, Vol. 75, no 3, p. 218-226Article in journal (Refereed) Published
    Abstract [en]

    Strong linkage disequilibrium (LD) is a characteristic of the major histocompatibility complex (MHC) region, as well as the genome in general in dogs as a consequence of demographic changes with domestication. Disease association studies of MHC haplotypes may be affected by high LD and the resultant shared genetic backgrounds of haplotypes giving associations with linked but non-causative mutations, and also by convergent haplotypes, in which combinations of alleles have arisen independently. This study provides preliminary tools for dog leukocyte antigen (DLA) class II haplotype analysis with 102 single nucleotide polymorphisms (SNPs) identified in 14.6 kb and genotyping of 20 of these SNPs to tag haplotypes in 60 dogs with diabetes mellitus and in 49 non-diabetic dogs. The pattern of LD and analysis of SNP patterns indicated combinations of exon 2 alleles have arisen through both recombination and convergence. For exon 2 haplotypes associated with susceptibility or protection from diabetes mellitus, a region of fixed differences in SNPs across the DQ region was observed, suggesting a region outside exon 2 may be implicated in disease association. Four new DQB1 promoter alleles restricted to diabetic dogs were identified, as well as a substitution difference in the X1 box of the DQB1 promoter that will potentially modify the effect of the protective haplotypes within diabetic dogs

    Keywords
    canine major histocompatibility complex, diabetes mellitus, DLA, haplotypes
    National Category
    Genetics
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-122009 (URN)10.1111/j.1399-0039.2009.01426.x (DOI)000274336000004 ()20047645 (PubMedID)
    Available from: 2010-04-05 Created: 2010-04-05 Last updated: 2017-12-12Bibliographically approved
    5. Linkage disequilibrium and haplotype patterns of the MHC class II region - a comparison between wolves and dogs.
    Open this publication in new window or tab >>Linkage disequilibrium and haplotype patterns of the MHC class II region - a comparison between wolves and dogs.
    (English)Manuscript (preprint) (Other academic)
    Keywords
    major histocompatibility complex, MHC, DLA, linkage disequilibrium, haplotype, wolves, dogs
    National Category
    Genetics
    Research subject
    Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-122010 (URN)
    Available from: 2010-04-05 Created: 2010-04-05 Last updated: 2010-04-07
  • 114.
    Berggren, Karin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Ellegren, H
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Hewitt, G M
    Seddon, J M
    Understanding the phylogeographic patterns of European hedgehogs, Erinaceus concolor and E. europaeus using the MHC.2005In: Heredity, ISSN 0018-067X, Vol. 95, no 1, p. 84-90Article in journal (Refereed)
    Abstract [en]

    The genome of the European hedgehog, Erinaceus concolor and E. europaeus, shows a strong signal of cycles of restriction to glacial refugia and postglacial expansion. Patterns of expansion, however, differ for mitochondrial DNA (mtDNA) and preliminary analysis of nuclear markers. In this study, we determine phylogeographic patterns in the hedgehog using two loci of the major histocompatibility complex (MHC), isolated for the first time in hedgehogs. These genes show long persistence times and high polymorphism in many species because of the actions of balancing selection. Among 84 individuals screened for variation, only two DQA alleles were identified in each species, but 10 DQB alleles were found in E. concolor and six in E. europaeus. A strong effect of demography on patterns of DQB variability is observed, with only weak evidence of balancing selection. While data from mtDNA clearly subdivide both species into monophyletic subgroups, the MHC data delineate only E. concolor into distinct subgroups, supporting the preliminary findings of other nuclear markers. Together with differences in variability, this suggests that the refugia history and/or expansion patterns of E. concolor and E. europaeus differ.

  • 115.
    Berggren, Karin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Ellegren, Hans
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Hewitt, G. M.
    Seddon, J. M.
    Demographic effects have been more important than selection in shaping patterns of variation at MHC genes in European hedgehogs, Erinaceus europaeus and Erinaceus concolor.2005In: Heredity, no 85, p. 84-90Article in journal (Refereed)
  • 116.
    Berggren, Karin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Seddon, Jennifer
    University of Queensland.
    Linkage disequilibrium and haplotype patterns of the MHC class II region - a comparison between wolves and dogs.Manuscript (preprint) (Other academic)
  • 117.
    Berggren, Karin T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Seddon, Jennifer M.
    Allelic combinations of promoter and exon 2 in DQB1 in dogs and wolves2008In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 67, no 1, p. 76-84Article in journal (Refereed)
    Abstract [en]

    Polymorphism of PBRs of the major histocompatibility complex (MHC) genes is well recognized, but the polymorphism also extends to proximal promoter regions. Examining DQB1 variability in dogs and wolves, we identified 7 promoter variants and 13 exon 2 alleles among 89 dogs, including a previously unknown DQB1 exon 2 allele, and 8 promoter variants and 9 exon 2 alleles among 85 wolves. As expected from previous studies and from a close chromosomal location, strong linkage disequilibrium was demonstrated in both wolves and dogs by having significantly fewer promoter/exon 2 combinations than expected from simulations of randomized data sets. Interestingly, we noticed weaker haplotypic associations in dogs than in wolves. Dogs had twice as many promoter/exon 2 combinations as wolves and an almost 2-fold difference in the number of exon 2 alleles per promoter variant. This difference was not caused by an admixture of breeds in our group of dogs because the high ratio of observed to expected number of haplotypes persisted within a single dog breed, the German Shepherd. Ewens-Watterson tests indicated that both the promoter and exon 2 are under the balancing selection, and both regions appear to be more recently derived in the dog than in the wolf. Hence, although reasons for the differences are unknown, they may relate to altered selection pressure on patterns of expression. Deviations from normal MHC expression patterns have been associated with autoimmune diseases, which occur frequently in several dog breeds. Further knowledge about these deviations may help us understand the source of such diseases.

  • 118.
    Berggren, Karin T
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Seddon, Jennifer M
    MHC promoter polymorphism in grey wolves and domestic dogs.2005In: Immunogenetics, ISSN 0093-7711, Vol. 57, no 3-4, p. 267-72Article in journal (Refereed)
    Abstract [en]

    A functional immune system requires a tight control over major histocompatibility complex (MHC) gene transcription, as the abnormal MHC expression patterns of severe immunodeficiency and autoimmune diseases demonstrate. Although the regulation of MHC expression has been well documented in humans and mice, little is known in other species. In this study, we detail the level of polymorphism in wolf and dog MHC gene promoters. The promoter regions of the DRB, DQA and DQB locus were sequenced in 90 wolves and 90 dogs. The level of polymorphism was high in the DQB promoters, with variation found within functionally relevant regions, including binding sites for transcription factors. Clear associations between DQB promoters and exon 2 alleles were noted in wolves, indicating strong linkage disequilibrium in this region. Low levels of polymorphism were found within the DRB and DQA promoter regions. However, a variable site was identified within the T box, a TNF-alpha response element, of the DQA promoter. Furthermore, we identified a previously unrecognised 18-base-pair deletion within exon 1 of the DQB locus.

  • 119.
    Berglind, Sven-Åke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Area-sensitivity of the sand lizard and spider wasps in sandy pine heath forests – umbrella species for early successional biodiversity conservation?2004In: Ecological Bulletins, Vol. 51, p. 189-207Article in journal (Refereed)
  • 120.
    Berglind, Sven-Åke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Demography and management of relict sand lizard (Lacerta agilis) populations on the edge of extinction2000In: Ecological Bulletins, ISSN 0346-6868, Vol. 48, p. 123-142Article in journal (Refereed)
  • 121.
    Berglind, Sven-Åke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Habitat tracking and population dynamics of an early successional lizard in a changing pine forest landscapeManuscript (Other (popular science, discussion, etc.))
  • 122.
    Berglind, Sven-Åke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Population Dynamics and Conservation of the Sand Lizard (Lacerta agilis) on the Edge of its Range2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The sand lizard (Lacerta agilis) reaches the northern periphery of its distribution in south-central Sweden, where small, isolated relict populations occur in pine heath forests on sandy sediments. Modern forestry and fire suppression have reduced the amount of suitable open habitat for the species in this area and seem to be important for its decline. Main objectives of this thesis were to evaluate the efficiency of different management strategies, and if the sand lizard can function as an umbrella species for biodiversity conservation.

    Over a 16-year period, the estimated annual numbers of adult females in each of two study populations fluctuated between 23 and 3. Simulations of stochastic future population growth showed that the risk of extinction was highly dependent on population growth rate, which in turn was strongly affected by juvenile survival as indicated by elasticity analysis.

    Simulations of population growth for 50 years showed that the quasi-extinction risk (threshold ≤ 10 females) was > 56% for patches ≤ 1 ha; which is the observed average size of suitable habitat for inhabited patches during a 10-year period. In managed metapopulation networks with highly co-fluctuating local populations, among-population dispersal was not important to reduce extinction risks over a 50-year horizon.

    In the field the preferred microhabitat of sand lizards was successfully restored using tree felling and patch-soil scarification. The lizards gradually colonized the restored patches, and 16 years after restoration, sand lizards where mainly found there.

    Pine-heath area, and patch area within individual pine heaths, were of major importance for long-term population persistence at regional and landscape scales, respectively. Analyses of nested species subsets and an umbrella index suggest that the sand lizard can be a useful cross-taxonomic umbrella species on both scales for other red-listed species.

    List of papers
    1. Demography and management of relict sand lizard (Lacerta agilis) populations on the edge of extinction
    Open this publication in new window or tab >>Demography and management of relict sand lizard (Lacerta agilis) populations on the edge of extinction
    2000 (English)In: Ecological Bulletins, ISSN 0346-6868, Vol. 48, p. 123-142Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92922 (URN)
    Available from: 2005-04-22 Created: 2005-04-22 Last updated: 2009-04-01Bibliographically approved
    2. Sand lizard (Lacerta agilis) in Central Sweden: Modeling Juvenile Reintroduction and Spatial management Strategies for Metapopulation Establishment
    Open this publication in new window or tab >>Sand lizard (Lacerta agilis) in Central Sweden: Modeling Juvenile Reintroduction and Spatial management Strategies for Metapopulation Establishment
    2004 (English)In: Species Conservation and Management: Case Studies, 2004, p. 326-339Chapter in book (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-92923 (URN)0-19-516646-9 (ISBN)
    Available from: 2005-04-22 Created: 2005-04-22 Last updated: 2009-04-01Bibliographically approved
    3. Habitat tracking and population dynamics of an early successional lizard in a changing pine forest landscape
    Open this publication in new window or tab >>Habitat tracking and population dynamics of an early successional lizard in a changing pine forest landscape
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92924 (URN)
    Available from: 2005-04-22 Created: 2005-04-22 Last updated: 2010-01-14Bibliographically approved
    4. Area-sensitivity of the sand lizard and spider wasps in sandy pine heath forests – umbrella species for early successional biodiversity conservation?
    Open this publication in new window or tab >>Area-sensitivity of the sand lizard and spider wasps in sandy pine heath forests – umbrella species for early successional biodiversity conservation?
    2004 (English)In: Ecological Bulletins, Vol. 51, p. 189-207Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92925 (URN)
    Available from: 2005-04-22 Created: 2005-04-22 Last updated: 2009-04-01Bibliographically approved
  • 123.
    Berglind, Sven-Åke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Sand lizard (Lacerta agilis) in Central Sweden: Modeling Juvenile Reintroduction and Spatial management Strategies for Metapopulation Establishment2004In: Species Conservation and Management: Case Studies, 2004, p. 326-339Chapter in book (Other academic)
  • 124.
    Berglund, Eva C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Ehrenborg, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Vinnere Pettersson, Olga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Granberg, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Näslund, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Holmberg, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents2010In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, p. 152-Article in journal (Refereed)
    Abstract [en]

    Background: Rodents represent a high-risk reservoir for the emergence of new human pathogens. The recent completion of the 2.3 Mb genome of Bartonella grahamii, one of the most prevalent blood-borne bacteria in wild rodents, revealed a higher abundance of genes for host-cell interaction systems than in the genomes of closely related human pathogens. The sequence variability within the global B. grahamii population was recently investigated by multi locus sequence typing, but no study on the variability of putative host-cell interaction systems has been performed.

    Results: To study the population dynamics of B. grahamii, we analyzed the genomic diversity on a whole-genome scale of 27 B. grahamii strains isolated from four different species of wild rodents in three geographic locations separated by less than 30 km. Even using highly variable spacer regions, only 3 sequence types were identified. This low sequence diversity contrasted with a high variability in genome content. Microarray comparative genome hybridizations identified genes for outer surface proteins, including a repeated region containing the fha gene for filamentous hemaggluttinin and a plasmid that encodes a type IV secretion system, as the most variable. The estimated generation times in liquid culture medium for a subset of strains ranged from 5 to 22 hours, but did not correlate with sequence type or presence/absence patterns of the fha gene or the plasmid.

    Conclusion: Our study has revealed a geographic microstructure of B. grahamii in wild rodents. Despite near-identity in nucleotide sequence, major differences were observed in gene presence/absence patterns that did not segregate with host species. This suggests that genetically similar strains can infect a range of different hosts.

  • 125.
    Berglund, Eva C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Frank, A. Carolin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Calteau, Alexandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Vinnere Pettersson, Olga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Granberg, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Eriksson, Ann-Sofie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Näslund, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Holmberg, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Lindroos, Hillevi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii2009In: PLoS genetics, ISSN 1553-7404, Vol. 5, no 7, p. e1000546-Article in journal (Refereed)
    Abstract [en]

    The genus Bartonella comprises facultative intracellular bacteria adapted to mammals, including previously recognized and emerging human pathogens. We report the 2,341,328 bp genome sequence of Bartonella grahamii, one of the most prevalent Bartonella species in wild rodents. Comparative genomics revealed that rodent-associated Bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens. Many of these gene clusters are located in a highly dynamic region of 461 kb. Using hybridization to a microarray designed for the B. grahamii genome, we observed a massive, putatively phage-derived run-off replication of this region. We also identified a novel gene transfer agent, which packages the bacterial genome, with an over-representation of the amplified DNA, in 14 kb pieces. This is the first observation associating the products of run-off replication with a gene transfer agent. Because of the high concentration of gene clusters for host-adaptation proteins in the amplified region, and since the genes encoding the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize that these systems are driven by selection. We propose that the coupling of run-off replication with gene transfer agents promotes diversification and rapid spread of host-adaptability factors, facilitating host shifts in Bartonella.

  • 126.
    Berglund, Eva C
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Granberg, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Zhoupeng, Xie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Ellegaard, Kirsten
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Kosoy, Michael Y
    National Center for Infectious Diseases, Centers for Disease Control and Prevention.
    Birtles, Richard
    Centre for Comparative Infectious Diseases, University of Liverpool.
    Andersson, Siv GE
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Diversification by recombination in Bartonella grahamii from wild rodents in Asia contrasts with a clonal population structure in Northern Europe and AmericaManuscript (preprint) (Other academic)
  • 127.
    Berglund, Eva C.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Nystedt, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Computational Resources in Infectious Disease: Limitations and Challenges2009In: PloS Computational Biology, ISSN 1553-734X, E-ISSN 1553-7358, Vol. 5, no 10, p. e1000481-Article in journal (Refereed)
  • 128.
    Berglund, Eva Caroline
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Genome Evolution and Host Adaptation in Bartonella2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Bacteria of the genus Bartonella infect the red blood cells of a wide range of wild and domestic mammals and are transmitted between hosts by blood-sucking insects. Although most Bartonella infections are asymptomatic, the genus contains several human pathogens. In this work, host adaptation and host switches in Bartonella have been studied from a genomic perspective, with special focus on the acquisition and evolution of genes involved in host interactions.

    As part of this study, the complete genome of B. grahamii isolated from a Swedish wood mouse was sequenced. A genus-wide comparison revealed that rodent-associated Bartonella species, which have rarely been associated with human disease, have the largest genomes and the largest number of host-adaptability genes. Analysis of known and putative genes for host interactions identified several families of autotransporters as horizontally transferred to the Bartonella ancestor, with a possible role both during early host adaptation and subsequent host shifts.

    In B. grahamii, the association of a gene transfer agent (GTA) and phage-derived run-off replication of a large genomic segment was demonstrated for the first time. Among all acquisitions to the Bartonella ancestor, the only well conserved gene clusters are those that encode the GTA and contain the origin of the run-off replication. This conservation, along with a high density of host-adaptability genes in the amplified region suggest that the GTA provides a strong selective advantage, possibly by increasing recombination frequencies of host-adaptability genes, thereby facilitating evasion of the host immune system and colonization of new hosts.

    B. grahamii displays stronger geographic pattern and higher recombination frequencies than the cat-associated B. henselae, probably caused by different lifestyles and/or population sizes of the hosts. The genomic diversity of B. grahamii is markedly lower in Europe and North America than in Asia, possibly an effect of reduced host variability in these areas following the latest ice age.

    List of papers
    1. Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii
    Open this publication in new window or tab >>Run-off replication of host-adaptability genes is associated with gene transfer agents in the genome of mouse-infecting Bartonella grahamii
    Show others...
    2009 (English)In: PLoS genetics, ISSN 1553-7404, Vol. 5, no 7, p. e1000546-Article in journal (Refereed) Published
    Abstract [en]

    The genus Bartonella comprises facultative intracellular bacteria adapted to mammals, including previously recognized and emerging human pathogens. We report the 2,341,328 bp genome sequence of Bartonella grahamii, one of the most prevalent Bartonella species in wild rodents. Comparative genomics revealed that rodent-associated Bartonella species have higher copy numbers of genes for putative host-adaptability factors than the related human-specific pathogens. Many of these gene clusters are located in a highly dynamic region of 461 kb. Using hybridization to a microarray designed for the B. grahamii genome, we observed a massive, putatively phage-derived run-off replication of this region. We also identified a novel gene transfer agent, which packages the bacterial genome, with an over-representation of the amplified DNA, in 14 kb pieces. This is the first observation associating the products of run-off replication with a gene transfer agent. Because of the high concentration of gene clusters for host-adaptation proteins in the amplified region, and since the genes encoding the gene transfer agent and the phage origin are well conserved in Bartonella, we hypothesize that these systems are driven by selection. We propose that the coupling of run-off replication with gene transfer agents promotes diversification and rapid spread of host-adaptability factors, facilitating host shifts in Bartonella.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-108371 (URN)10.1371/journal.pgen.1000546 (DOI)000269219500042 ()19578403 (PubMedID)
    Available from: 2009-09-17 Created: 2009-09-17 Last updated: 2010-07-09Bibliographically approved
    2. Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents
    Open this publication in new window or tab >>Genome dynamics of Bartonella grahamii in micro-populations of woodland rodents
    Show others...
    2010 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 11, p. 152-Article in journal (Refereed) Published
    Abstract [en]

    Background: Rodents represent a high-risk reservoir for the emergence of new human pathogens. The recent completion of the 2.3 Mb genome of Bartonella grahamii, one of the most prevalent blood-borne bacteria in wild rodents, revealed a higher abundance of genes for host-cell interaction systems than in the genomes of closely related human pathogens. The sequence variability within the global B. grahamii population was recently investigated by multi locus sequence typing, but no study on the variability of putative host-cell interaction systems has been performed.

    Results: To study the population dynamics of B. grahamii, we analyzed the genomic diversity on a whole-genome scale of 27 B. grahamii strains isolated from four different species of wild rodents in three geographic locations separated by less than 30 km. Even using highly variable spacer regions, only 3 sequence types were identified. This low sequence diversity contrasted with a high variability in genome content. Microarray comparative genome hybridizations identified genes for outer surface proteins, including a repeated region containing the fha gene for filamentous hemaggluttinin and a plasmid that encodes a type IV secretion system, as the most variable. The estimated generation times in liquid culture medium for a subset of strains ranged from 5 to 22 hours, but did not correlate with sequence type or presence/absence patterns of the fha gene or the plasmid.

    Conclusion: Our study has revealed a geographic microstructure of B. grahamii in wild rodents. Despite near-identity in nucleotide sequence, major differences were observed in gene presence/absence patterns that did not segregate with host species. This suggests that genetically similar strains can infect a range of different hosts.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-108379 (URN)10.1186/1471-2164-11-152 (DOI)000276363100003 ()
    Available from: 2009-09-23 Created: 2009-09-17 Last updated: 2017-12-13Bibliographically approved
    3. Diversification by recombination in Bartonella grahamii from wild rodents in Asia contrasts with a clonal population structure in Northern Europe and America
    Open this publication in new window or tab >>Diversification by recombination in Bartonella grahamii from wild rodents in Asia contrasts with a clonal population structure in Northern Europe and America
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-108384 (URN)
    Available from: 2009-09-24 Created: 2009-09-17 Last updated: 2010-01-14
    4. Evolution of Host Adaptation Systems in  the Mammalian Blood Specialist Bartonella
    Open this publication in new window or tab >>Evolution of Host Adaptation Systems in  the Mammalian Blood Specialist Bartonella
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Bacteria of the genus Bartonella are facultative intracellular bacteria infecting the red blood cells of mammals. Bartonella isolates have now been reported from a wide range of mammalian host species, including humans, domestic animals such as pets and livestock, as well as many wild animals such as deer, moose, kangaroo, and whales. Here, we present the first major genus-wide investigation of host-adaptation systems in Bartonella, using 5 published and 5 draft genome sequences. The sampling includes both clinical and natural isolates, and represent well the major phylogenetic diversity of the genus. Our study reveals four distinct protein families of Type V Secretion Systems (T5SS) shared by all sequenced members of the genus. We also show that a recently identified gene transfer agent (GTA) consisting of a defective phage is, surprisingly, the most conserved gene cluster among all Bartonella-specific or imported genes, strongly emphasizing the functional importance of this system for the life-style and evolution of Bartonella.

    Keywords
    host adaptation, pathogen, secretion systems, flagella, gene transfer agent, evolution
    National Category
    Bioinformatics and Systems Biology
    Research subject
    Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-107784 (URN)
    Available from: 2009-08-26 Created: 2009-08-26 Last updated: 2010-01-14
    5. Low-coverage pyrosequencing reveals recombination and run-off replication in Bartonella henselae strains
    Open this publication in new window or tab >>Low-coverage pyrosequencing reveals recombination and run-off replication in Bartonella henselae strains
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Bartonella henselae is a natural intracellular colonizer of cats, and is transferred by blood-sucking insect vectors. It is also an opportunistic human pathogen. Two strains of B. henselae, thought to be representative of the diversity of the species, were selected for low-coverage 454 sequencing. The comparison of these two strains to the published Houston-1 reveals very high nucleotide identity and low substitution and recombination, with the remarkable exception of phages and host-interaction genes such as type IV and V secretion systems. Among the few variable genes of unknown function, BH14680, an alpha-Proteobacteria-specific gene, shows faster evolution in Bartonella compared to other alpha-Proteobacteria. Its 5’ end, which is likely coding for a domain exposed extracellularly, is under positive or very relaxed selection, and might be involved in host-interaction processes. Finally, we show that a simple genome coverage analysis reveal major genomic events such as duplications and unusual replication modes, such as the run-off replication. The latter, combined with a gene transfer agent, is thought to be a novel way to increase substitution and recombination frequencies. An extensive analysis of all bacterial pyrosequencing projects showed that it is probably Bartonella-specific.

    Keywords
    pathogen, recombination, run-off replication, phage, gene transfer agent, pyrosequencing, evolution
    National Category
    Bioinformatics and Systems Biology
    Research subject
    Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-107785 (URN)
    Available from: 2009-08-27 Created: 2009-08-26 Last updated: 2010-01-14
  • 129.
    Bergström, Rosita
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm , Ludwig Institute for Cancer Research. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Savary, Katia
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm , Ludwig Institute for Cancer Research.
    Morén, Anita
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm , Ludwig Institute for Cancer Research.
    Guibert, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Heldin, Carl-Henrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm , Ludwig Institute for Cancer Research.
    Ohlsson, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Moustakas, Aristidis
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Medicinska och farmaceutiska vetenskapsområdet, centrumbildningar mm , Ludwig Institute for Cancer Research.
    Transforming growth factor β promotes complexes between Smad proteins and the CCCTC-binding factor on the H19 imprinting control region chromatin2010In: Journal of Biological Chemistry, ISSN 0021-9258, E-ISSN 1083-351X, Vol. 285, no 26, p. 19727-19737Article in journal (Refereed)
    Abstract [en]

    Whether signal transduction pathways regulate epigenetic states in response to environmental cues remains poorly understood. We demonstrate here that Smad3, signaling downstream of transforming growth factor beta, interacts with the zinc finger domain of CCCTC-binding factor (CTCF), a nuclear protein known to act as "the master weaver of the genome." This interaction occurs via the Mad homology 1 domain of Smad3. Although Smad2 and Smad4 fail to interact, an alternatively spliced form of Smad2 lacking exon 3 interacts with CTCF. CTCF does not perturb well established transforming growth factor beta gene responses. However, Smads and CTCF co-localize to the H19 imprinting control region (ICR), which emerges as an insulator in cis and regulator of transcription and replication in trans via direct CTCF binding to the ICR. Smad recruitment to the ICR requires intact CTCF binding to this locus. Smad2/3 binding to the ICR requires Smad4, which potentially provides stability to the complex. Because the CTCF-Smad complex is not essential for the chromatin insulator function of the H19 ICR, we propose that it can play a role in chromatin cross-talk organized by the H19 ICR.

  • 130. Bergström, Sven
    et al.
    Olsen, Björn
    Burman, Nils
    Gothefors, Leif
    Jaenson, Thomas G.T.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Jonsson, Maria
    Mejlon, Hans
    Uppsala University, Music and Museums, Museum of Evolution.
    Molecular characterization of Borrelia burgdorferi isolated from Ixodes ricinus in northern Sweden.1992In: Scandinavian Journal of Infectious Diseases, ISSN 0036-5548, E-ISSN 1651-1980, Vol. 24, no 2, p. 181-188Article in journal (Refereed)
    Abstract [en]

    Ixodes ricinus ticks, harbouring Borrelia burgdorferi, were found in an area in northern Sweden, not thought to be endemic for Lyme borreliosis. This investigation took place at Norrbyskär, an island situated in the Bothnian Gulf, 63 degrees 33'N/19 degrees 52'E. One of 42 nymphal and 8/43 adult I. ricinus ticks collected carried spirochetes as seen by phase contrast microscopy. Pure bacterial cultures were obtained from 2 of the ticks. Western blot analysis using species-specific monoclonal antibodies showed that the isolated spirochetes were B. burgdorferi. The identity of the isolated spirochetes was confirmed by DNA amplification using B. burgdorferi OspA and flagellin gene specific oligonucleotides as well as partial DNA sequencing of the respective OspA and flagellin genes. The 2 isolated spirochaete populations were different as shown by their protein profiles in sodium dodecyl sulphate polyacrylamide gels. Moreover, the demonstration of Lyme borreliosis in a patient from the island of Norrbyskär indicates the need for clinical consideration of this disease in northern Sweden.

  • 131.
    Berlin, S.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Ellegren, H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Chicken W:: A genetically uniform chromosome in a highly variable genome.2004In: Proceedings of the National Academy of Sciences USA, no 101, p. 15967-15969Article in journal (Refereed)
  • 132.
    Berlin, S.
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Smith, N.G.
    Ellegren, H.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Do avian mitochondria recombine?2004In: Journal of Molecular Evolution, no 58, p. 163-167Article in journal (Refereed)
  • 133.
    Berlin, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    The Effects of Mutation and Selection on the Rate and Pattern of Molecular Evolution in Birds2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    By comparing sequence diversity and divergence on sex chromosomes one can study how the rate of evolution in affected by mutation and/or selection. The rate of mutation in male biased, meaning that relatively more mutations are created in the male germ line than in the female. Since the male mutation bias (αm) most likely is a consequence of the difference in cell divisions between male and female germ lines, life history characters that affect this difference should covary with αm. Indeed, we found a positive correlation between estimates of αm and increased generation times and increased intensity of sperm competition. We have also found that estimates of αm varied significantly between gametologous introns located on the sex chromosomes. This could be a consequence of the variation in substitution rates between loci.

    Population genetics theory predicts that both positive and negative selection reduce genetic diversity around a selected locus at a distance determined by the rate of recombination. Consequently, a non-recombining chromosome, like the female specific W chromosome in birds, selection is expected to have a large impact on sequence diversity. Indeed, in a large sequence screening we found only one segregating site among 7643 base pairs sequenced in 47 chicken females. Furthermore, we also found that deleterious substitutions are fixed in a higher rate for W- than Z-linked sequences, which is in agreement with the lack of recombination and strong genetic drift due to the low effective population size.

    Rarely non-synonymous mutations are beneficial for an individual, but when it happens, the mutation is positively selected and rapidly reaches fixation in a population. We have found that positive selection has been acting on the female reproductive protein, zona pellucida c in birds. This rapid evolution is likely a mechanism to prevent hybridisation.

    List of papers
    1. Life history and the male mutation bias.
    Open this publication in new window or tab >>Life history and the male mutation bias.
    Show others...
    2003 (English)In: Evolution, ISSN 0014-3820, Vol. 57, no 10, p. 2398-2406Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-92040 (URN)
    Available from: 2004-09-07 Created: 2004-09-07 Last updated: 2009-03-31Bibliographically approved
    2. Substitution rate heterogeneity and the male mutation bias.
    Open this publication in new window or tab >>Substitution rate heterogeneity and the male mutation bias.
    Show others...
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92041 (URN)
    Available from: 2004-09-07 Created: 2004-09-07 Last updated: 2010-01-14Bibliographically approved
    3. Accumulation of deleterious mutations on the female specific chromosome in birds.
    Open this publication in new window or tab >>Accumulation of deleterious mutations on the female specific chromosome in birds.
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92042 (URN)
    Available from: 2004-09-07 Created: 2004-09-07 Last updated: 2010-01-14Bibliographically approved
    4. Chicken W: a genetically uniform chromosome in a highly variable genome.
    Open this publication in new window or tab >>Chicken W: a genetically uniform chromosome in a highly variable genome.
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92043 (URN)
    Available from: 2004-09-07 Created: 2004-09-07 Last updated: 2010-01-14Bibliographically approved
    5. Adaptive evolution of ZPC, a female reproductive protein in diverse vertebrate species.
    Open this publication in new window or tab >>Adaptive evolution of ZPC, a female reproductive protein in diverse vertebrate species.
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-92044 (URN)
    Available from: 2004-09-07 Created: 2004-09-07 Last updated: 2010-01-14Bibliographically approved
  • 134.
    Berlin, Sofia
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Evolutionsbiologi.
    Brandström, Mikael
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Evolutionsbiologi.
    Backström, Niclas
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Evolutionsbiologi.
    Axelsson, Erik
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Evolutionsbiologi.
    Smith, Nick G C
    Ellegren, Hans
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Evolutionsbiologi.
    Substitution rate heterogeneity and the male mutation bias.2006In: Journal of Molecular Evolution, ISSN 0022-2844, Vol. 62, no 2, p. 226-33Article in journal (Refereed)
  • 135.
    Berlin, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Brandström, Mikael
    Backström, Niclas
    Axelsson, Erik
    Smith, Nick G.C.
    Ellegren, Hans
    Substitution rate heterogeneity and the male mutation bias.Manuscript (Other (popular science, discussion, etc.))
  • 136.
    Berlin, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Accumulation of deleterious mutations on the female specific chromosome in birds.Manuscript (Other (popular science, discussion, etc.))
  • 137.
    Berlin, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Chicken W: a genetically uniform chromosome in a highly variable genome.Manuscript (Other (popular science, discussion, etc.))
  • 138.
    Berlin, Sofia
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Ellegren, Hans
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Fast accumulation of nonsynonymous mutations on the female-specific W chromosome in birds.2006In: Journal of Molecular Evolution, ISSN 0022-2844, Vol. 62, no 1, p. 66-72Article in journal (Refereed)
  • 139.
    Berlin, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Qu, Lujiang
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Adaptive Evolution of Gamete-Recognition Proteins in Birds2008In: Journal of Molecular Evolution, ISSN 0022-2844, E-ISSN 1432-1432, Vol. 67, no 5, p. 488-496Article in journal (Refereed)
    Abstract [en]

    Gamete-recognition proteins have been shown to evolve by positive selection in diverse organism groups, such as marine invertebrates and mammals, although underlying evolutionary mechanisms driving this rapid divergence are poorly understood. However, several hypotheses have been put forward to explain the observed pattern, including different forms of sexual conflict and sperm competition. Because female gametes require more energy to produce than male gametes, female organisms suffer more when fertilisation goes wrong. One process that results in a failed mammalian fertilisation is polyspermy, when > 1 sperm fertilises the egg. However in birds, there is no such sexual conflict because multiple sperm typically bind and fuse with the egg. If sexual conflict driven by polyspermy avoidance is important for the evolution of gamete-recognition proteins in vertebrates, we expect to find positive selection in the genes to be less pronounced in birds. We therefore sequenced six genes (ZP1, ZP2, ZP4, ZPAX, CD9, and Acrosin) encoding gamete-recognition proteins in several bird species to test for positive selection. For comparison, we also analysed ortologous sequences in a set of mammalian species. We found no major differences in the occurrence of adaptive evolution and the strength of selection between bird and mammal orthologs. From this we conclude that polyspermy avoidance does not act as the main underlying evolutionary force shaping the rate of evolution in these genes. We discuss other possible processes that could explain positive selection of gamete-recognition proteins in birds and mammals, such as hybridisation avoidance, cryptic female choice, and postcopulatory sperm competition.

  • 140.
    Berlin, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Qu, Lujiang
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Li, Xianyao
    Yang, Ning
    Ellegren, Hans
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Positive diversifying selection in avian Mx genes2008In: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 60, no 11, p. 689-697Article in journal (Refereed)
    Abstract [en]

    Mx proteins are interferon-induced GTPases that confer antiviral activities against RNA viruses. We analysed the molecular evolution of the Mx gene in birds using data on interspecific divergence in anseriform and galliform birds, and on intraspecific diversity in commercial chicken lines, local Chinese chicken breeds as well as in the mallard. The overall ratio of non-synonymous to synonymous substitution was unusually high, 0.80, indicating relaxed constraint or positive selection. Evidence for the latter was provided by that a total of 11-18 codons were found to have evolved under positive selection. The great majority of these codons are located in a region unique to birds at the N-terminal end of the Mx protein. We found an excess of non-synonymous polymorphisms relative to synonymous variants in all comparisons. This, together with positive Tajima's D values in the local Chinese chicken breeds and in the mallard suggests that balancing selection is acting in avian Mx genes. As such, Mx mimics the major histocompatibility complex system, indicating that heterozygous individuals are better off withstanding pathogen attack.

  • 141.
    Berlin, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Quintela, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution, Population and Conservation Biology.
    A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus)2008In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 9, p. 89-Article in journal (Refereed)
    Abstract [en]

    Background: There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (similar to 10(-3)) and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (Lagopus lagopus) has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance.

    Results: We sequenced 18 autosomal protein coding loci from approximately 15-18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (pi(t)) was between 1.30 x 10(-4) and 7.66 x 10(-3) (average pi(t) = 2.72 x 10(-3) +/- 2.06 x 10(-3)) and silent nucleotide diversity varied between 4.20 x 10(-4) and 2.76 x 10(-2) (average pi(S) = 9.22 x 10(-3) +/- 7.43 x 10(-4)). The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 x 10(-3) (average pi(a) = 5.08 x 10(-4) +/- 7.43 x 10(3)), which suggest that purifying selection is strong in these genes. F-ST values based on synonymous SNP's varied between -5.60 x 10(-4) and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of F-ST = 0.03 (95% CI: 0.006 -0.057) over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low levels of linkage disequilibrium were observed within genes, with an average r(2) = 0.084 +/- 0.110, which is expected for a large outbred population with no population differentiation. The mean per site per generation recombination parameter (rho) was comparably high (0.028 +/- 0.018), indicating high recombination rates in these genes.

    Conclusion: We found unusually high levels of nucleotide diversity in the Scandinavian willow grouse as well as very little population structure among localities with up to 1647 km distance. There are also low levels of linkage disequilibrium within the genes and the population recombination rate is high, which is indicative of an old panmictic population, where recombination has had time to break up any haplotype blocks. The non-synonymous nucleotide diversity is low compared with the silent, which is in agreement with effective purifying selection, possibly due to the large effective population size.

  • 142.
    Berlin, Sofia
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionsbiologi.
    Smith, Nick G C
    Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test.2005In: BMC Evol Biol, ISSN 1471-2148, Vol. 5, p. 65-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive biology. We have attempted to apply this approach to the study of a female reproductive protein, zona pellucida C (ZPC), which has been previously shown by the use of likelihood ratio tests (LRTs) to be under positive selection in mammals. RESULTS: We tested for evidence of adaptive evolution of ZPC in 15 mammalian species, in 11 avian species and in six fish species using three different LRTs (M1a-M2a, M7-M8, and M8a-M8). The only significant findings of adaptive evolution came from the M7-M8 test in mammals and fishes. Since LRTs of adaptive evolution may yield false positives in some situations, we examined the properties of the LRTs by several different simulation methods. When we simulated data to test the robustness of the LRTs, we found that the pattern of evolution in ZPC generates an excess of false positives for the M7-M8 LRT but not for the M1a-M2a or M8a-M8 LRTs. This bias is strong enough to have generated the significant M7-M8 results for mammals and fishes. CONCLUSION: We conclude that there is no strong evidence for adaptive evolution of ZPC in any of the vertebrate groups we studied, and that the M7-M8 LRT can be biased towards false inference of adaptive evolution by certain patterns of non-adaptive evolution.

  • 143.
    Berlin, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Smith, Nick G.C.
    Adaptive evolution of ZPC, a female reproductive protein in diverse vertebrate species.Manuscript (Other (popular science, discussion, etc.))
  • 144.
    Berlin, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Tomaras, D.
    Charlesworth, B.
    Low mitochondrial variability in birds may indicate Hill-Robertson effects on the W chromosome2007In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 99, no 4, p. 389-396Article in journal (Refereed)
    Abstract [en]

    Interference among loci subject to selection ( the Hill Robertson effect) may considerably reduce levels of adaptation and variability in genomic regions that lack recombination. Y- or W chromosomes are particularly vulnerable to such effects, since they represent large, non-recombining blocks of genetic material. In birds, the W chromosome and mitochondrial genomes are both maternally transmitted, and hence fail to recombine with each other, whereas in mammals the Y chromosome is paternally transmitted. We show here that mitochondrial DNA sequence diversity is reduced in non-ratite birds compared with mammals. After considering possible confounding factors, such as differences in generation times, mutation rates and demography, we conclude that Hill-Robertson effects associated with the W chromosome provide the most likely explanation for this difference.

  • 145. Bermejo, Magdalena
    et al.
    Rodríguez-Teijeiro, José Domingo
    Illera, Germán
    Barroso, Alex
    Vila, Carles
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Biology. Evolutionary Biology.
    Walsh, Peter D
    Ebola outbreak killed 5000 gorillas.2006In: Science, ISSN 1095-9203, Vol. 314, no 5805, p. 1564-Article in journal (Refereed)
    Abstract [en]

    Over the past decade, the Zaire strain of Ebola virus (ZEBOV) has repeatedly emerged in Gabon and Congo. Each human outbreak has been accompanied by reports of gorilla and chimpanzee carcasses in neighboring forests, but both the extent of ape mortality and the causal role of ZEBOV have been hotly debated. Here, we present data suggesting that in 2002 and 2003 ZEBOV killed about 5000 gorillas in our study area. The lag between neighboring gorilla groups in mortality onset was close to the ZEBOV disease cycle length, evidence that group-to-group transmission has amplified gorilla die-offs.

  • 146.
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    The cell cycle of Sulfolobus2007In: Molecular Microbiology, ISSN 0950-382X, E-ISSN 1365-2958, Vol. 66, no 3, p. 557-562Article, review/survey (Refereed)
    Abstract [en]

    Much of the current information about the archaeal cell cycle has been generated through studies of the genus Sulfolobus. The overall organization of the cell cycle in these species is well understood, and information about the regulatory principles that govern cell cycle progression is rapidly accumulating. Exciting progress regarding the control and molecular details of the chromosome replication process is evident, and the first insights into the elusive crenarchaeal mitosis and cytokinesis machineries are within reach.

  • 147.
    Bernander, Rolf
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Lundgren, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Microbiology.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Comparative and functional analysis of the archaeal cell cycle2010In: Cell Cycle, ISSN 1538-4101, E-ISSN 1551-4005, Vol. 9, no 4, p. 795-806Article in journal (Refereed)
    Abstract [en]

    The temporal and spatial organization of the chromosome replication, genome segregation and cell division processes is less well understood in species belonging to the Archaea, than in those from the Bacteria and Eukarya domains. Novel insights into the regulation and key components of the Sulfolobus acidocaldarius cell cycle have been obtained through genome-wide analysis of cell cycle-specific gene expression, followed by cloning and characterization of gene products expressed at different cell cycle stages. Here, the results of the transcript profiling are further explored, and potential key players in archaeal cell cycle progression are highlighted in an evolutionary context, by comparing gene expression patterns and gene conservation between three selected microbial species from different domains of life. We draw attention to novel putative nucleases and helicases implicated in DNA replication, recombination and repair, as well as to potential genome segregation factors. Focus is also placed upon regulatory features, including transcription factors and protein kinases inferred to be involved in the execution of specific cell cycle stages, and regulation through metabolic coupling is discussed.

  • 148. Bize, Ariane
    et al.
    Karlsson, Erik A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Ekefjärd, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Quax, F.
    Pina, Mery
    Prevost, Marie-Christine
    Forterre, Patrick
    Tenaillon, Olivier
    Bernander, Rolf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Prangishvili, David
    A unique virus release mechanism in the Archaea2009In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 106, no 27, p. 11306-11311Article in journal (Refereed)
    Abstract [en]

    Little is known about the infection cycles of viruses infecting cells from Archaea, the third domain of life. Here, we demonstrate that the virions of the archaeal Sulfolobus islandicus rod-shaped virus 2 (SIRV2) are released from the host cell through a mechanism, involving the formation of specific cellular structures. Large pyramidal virus-induced protrusions transect the cell envelope at several positions, rupturing the S-layer; they eventually open out, thus creating large apertures through which virions escape the cell. We also demonstrate that massive degradation of the host chromosomes occurs because of virus infection, and that virion assembly occurs in the cytoplasm. Furthermore, intracellular viral DNA is visualized by flow cytometry. The results show that SIRV2 is a lytic virus, and that the host cell dies as a consequence of elaborated mechanisms orchestrated by the virus. The generation of specific cellular structures for a distinct step of virus life cycle is known in eukaryal virus-host systems but is unprecedented in cells from other domains.

  • 149.
    Björk, Lars
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Tunon, Håkan
    Framtidens växter2005In: Människan och floran: Etnobiologi i Sverige 2, Wahlstöm och Widstrand, Stockholm , 2005, p. 471-482Chapter in book (Other (popular scientific, debate etc.))
  • 150.
    Björnerfeldt, S
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Hailer, F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Nord, M.
    Vila, C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Assortative mating and fragmentation within dog breeds2008In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 8, p. 28-Article in journal (Refereed)
    Abstract [en]

    Background: There are around 400 internationally recognized dog breeds in the world today, with a remarkable diversity in size, shape, color and behavior. Breeds are considered to be uniform groups with similar physical characteristics, shaped by selection rooted in human preferences. This has led to a large genetic difference between breeds and a large extent of linkage disequilibrium within breeds. These characteristics are important for association mapping of candidate genes for diseases and therefore make dogs ideal models for gene mapping of human disorders. However, genetic uniformity within breeds may not always be the case. We studied patterns of genetic diversity within 164 poodles and compared it to 133 dogs from eight other breeds. Results: Our analyses revealed strong population structure within poodles, with differences among some poodle groups as pronounced as those among other well-recognized breeds. Pedigree analysis going three generations back in time confirmed that subgroups within poodles result from assortative mating imposed by breed standards as well as breeder preferences. Matings have not taken place at random or within traditionally identified size classes in poodles. Instead, a novel set of five poodle groups was identified, defined by combinations of size and color, which is not officially recognized by the kennel clubs. Patterns of genetic diversity in other breeds suggest that assortative mating leading to fragmentation may be a common feature within many dog breeds. Conclusion: The genetic structure observed in poodles is the result of local mating patterns, implying that breed fragmentation may be different in different countries. Such pronounced structuring within dog breeds can increase the power of association mapping studies, but also represents a serious problem if ignored. In dog breeding, individuals are selected on the basis of morphology, behaviour, working or show purposes, as well as geographic population structure.

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