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  • 301.
    Eriksson, Tage
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Fridborg, Gunnar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Physiological Botany.
    Fysiologisk botanik vid Uppsala universitet: En historik2008Book (Other academic)
  • 302.
    Erixon, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Phylogenetic Support and Chloroplast Genome Evolution in Sileneae (Caryophyllaceae)2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Evolutionary biology is dependent on accurate phylogenies. In this thesis two branch support methods, Bayesian posterior probablities and bootstrap frequencies, were evaluated with simulated data and empirical data from the chloroplast genome. Bayesian inference was found to be more powerful and less conservative than maximum likelihood bootstrapping, but considerably more sensitive to choice of parameters. Bayesian inference increased in power when data were underparameterized, but the associated increase in type I error was comparatively larger.

    The chloroplast DNA phylogeny of the tribe Sileneae (Caryophyllaceae) was inferred by analysis of 33,149 aligned nucleotide bases representing 24 taxa. The position of the SW Anatolian taxa Silene cryptoneura and S. sordida strongly disagreed with previous studies on nuclear DNA sequence data, and indicate a possible case of homoploid hybrid origin. Silene atocioides and S. aegyptiaca formed a sister group to Lychnis and remaining Silene, thus suggesting that Silene may be paraphyletic, despite recent revisions based on molecular data. Several nodes in the phylogeny remained poorly supported, despite large amounts of data. Additional sequence sampling is not expected to solve this problem. The main reason for poor resolution is probably a combination of rapid radiation and substitution rate hererogeneity. Apparent incongruent patterns between different regions of the chloroplast genome are evaluated with ancient interspecific chloroplast recombination as explanatory model.

    Extremely elevated substitution rates in the exons of the plastid clpP gene was documented in Oenothera and three separate lineages of Sileneae. Introns have been lost in some of the lineages, but where present, intron sequences have a markedly slower substitution rate, similar to the rates found in other introns of their genomes. Three branches in the phylogeny show significant whole gene positive selection. In two of the lineages multiple partial copies of the gene were found.

    List of papers
    1. Reliability of Bayesian Posterior Probabilities and Bootstrap Frequencies in Phylogenetics
    Open this publication in new window or tab >>Reliability of Bayesian Posterior Probabilities and Bootstrap Frequencies in Phylogenetics
    2003 (English)In: Systematic Biology, ISSN 1063-5157, Vol. 52, no 5, p. 665-673Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-94917 (URN)
    Available from: 2006-09-28 Created: 2006-09-28 Last updated: 2009-04-02Bibliographically approved
    2. The effect of under-parameterization and character dependency on Bayesian posterior probabilities and maximum likelihood bootstrap frequencies on empirical data
    Open this publication in new window or tab >>The effect of under-parameterization and character dependency on Bayesian posterior probabilities and maximum likelihood bootstrap frequencies on empirical data
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-94918 (URN)
    Available from: 2006-09-28 Created: 2006-09-28 Last updated: 2010-01-14Bibliographically approved
    3. Reticulate or treelike chloroplast DNA evolution in Sileneae (Caryophyllaceae)?
    Open this publication in new window or tab >>Reticulate or treelike chloroplast DNA evolution in Sileneae (Caryophyllaceae)?
    2008 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 1, p. 313-325Article in journal (Refereed) Published
    Abstract [en]

    Despite sampling of up to 25 kb of chloroplast DNA sequence from 24 species in Sileneae a number of nodes in the phylogeny remain poorly supported and it is not expected that additional sequence sampling will converge to a reliable phylogenetic hypothesis in these parts of the tree. The main reason for this is probably a combination of rapid radiation and substitution rate heterogeneity. Poor resolution among closely related species are often explained by low levels of variation in chloroplast data, but the problem with our data appear to be high levels of homoplasy. Tree-like cpDNA evolution cannot be rejected, but apparent incongruent patterns between different regions are evaluated with the possibility of ancient interspecific chloroplast recombination as explanatory model. However, several major phylogenetic relationships, previously not recognized, are confidently resolved, e.g. the grouping of the two SW Anatolian taxa S. cryptoneura and S. sordida strongly disagrees with previous studies on nuclear DNA sequence data, and indicate a possible case of homoploid hybrid origin. The closely related S. atocioides and S. aegyptiaca form a sister group to Lychnis and the rest of Silene, thus suggesting that Silene may be paraphyletic, despite recent revisions based on molecular data.

    Keywords
    Sileneae, cpDNA, chloroplast recombination, incongruence, indel characters
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-94919 (URN)10.1016/j.ympev.2008.04.015 (DOI)000257275200027 ()
    Available from: 2006-09-28 Created: 2006-09-28 Last updated: 2017-12-14Bibliographically approved
    4. Elevated substitution rates, putative positive selection, duplications, and intron evolution in the plastid clpP gene in Oenothera and Sileneae
    Open this publication in new window or tab >>Elevated substitution rates, putative positive selection, duplications, and intron evolution in the plastid clpP gene in Oenothera and Sileneae
    (English)Manuscript (preprint) (Refereed)
    Identifiers
    urn:nbn:se:uu:diva-94920 (URN)
    Available from: 2006-09-28 Created: 2006-09-28 Last updated: 2010-01-14Bibliographically approved
  • 303.
    Erixon, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Elevated substitution rates, putative positive selection, duplications, and intron evolution in the plastid clpP gene in Oenothera and SileneaeManuscript (preprint) (Refereed)
  • 304.
    Erixon, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Reticulate or treelike chloroplast DNA evolution in Sileneae (Caryophyllaceae)?2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 48, no 1, p. 313-325Article in journal (Refereed)
    Abstract [en]

    Despite sampling of up to 25 kb of chloroplast DNA sequence from 24 species in Sileneae a number of nodes in the phylogeny remain poorly supported and it is not expected that additional sequence sampling will converge to a reliable phylogenetic hypothesis in these parts of the tree. The main reason for this is probably a combination of rapid radiation and substitution rate heterogeneity. Poor resolution among closely related species are often explained by low levels of variation in chloroplast data, but the problem with our data appear to be high levels of homoplasy. Tree-like cpDNA evolution cannot be rejected, but apparent incongruent patterns between different regions are evaluated with the possibility of ancient interspecific chloroplast recombination as explanatory model. However, several major phylogenetic relationships, previously not recognized, are confidently resolved, e.g. the grouping of the two SW Anatolian taxa S. cryptoneura and S. sordida strongly disagrees with previous studies on nuclear DNA sequence data, and indicate a possible case of homoploid hybrid origin. The closely related S. atocioides and S. aegyptiaca form a sister group to Lychnis and the rest of Silene, thus suggesting that Silene may be paraphyletic, despite recent revisions based on molecular data.

  • 305.
    Erixon, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    The effect of under-parameterization and character dependency on Bayesian posterior probabilities and maximum likelihood bootstrap frequencies on empirical dataManuscript (Other (popular science, discussion, etc.))
  • 306.
    Erixon, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Whole-Gene Positive Selection, Elevated Synonymous Substitution Rates, Duplication, and Indel Evolution of the Chloroplast clpP1 Gene2008In: PLoS ONE, ISSN 1932-6203, Vol. 3, no 1, p. e1386-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Synonymous DNA substitution rates in the plant chloroplast genome are generally relatively slow and lineage dependent. Non-synonymous rates are usually even slower due to purifying selection acting on the genes. Positive selection is expected to speed up non-synonymous substitution rates, whereas synonymous rates are expected to be unaffected. Until recently, positive selection has seldom been observed in chloroplast genes, and large-scale structural rearrangements leading to gene duplications are hitherto supposed to be rare. METHODOLOGY/PRINCIPLE FINDINGS: We found high substitution rates in the exons of the plastid clpP1 gene in Oenothera (the Evening Primrose family) and three separate lineages in the tribe Sileneae (Caryophyllaceae, the Carnation family). Introns have been lost in some of the lineages, but where present, the intron sequences have substitution rates similar to those found in other introns of their genomes. The elevated substitution rates of clpP1 are associated with statistically significant whole-gene positive selection in three branches of the phylogeny. In two of the lineages we found multiple copies of the gene. Neighboring genes present in the duplicated fragments do not show signs of elevated substitution rates or positive selection. Although non-synonymous substitutions account for most of the increase in substitution rates, synonymous rates are also markedly elevated in some lineages. Whereas plant clpP1 genes experiencing negative (purifying) selection are characterized by having very conserved lengths, genes under positive selection often have large insertions of more or less repetitive amino acid sequence motifs. CONCLUSIONS/SIGNIFICANCE: We found positive selection of the clpP1 gene in various plant lineages to correlated with repeated duplication of the clpP1 gene and surrounding regions, repetitive amino acid sequences, and increase in synonymous substitution rates. The present study sheds light on the controversial issue of whether negative or positive selection is to be expected after gene duplications by providing evidence for the latter alternative. The observed increase in synonymous substitution rates in some of the lineages indicates that the detection of positive selection may be obscured under such circumstances. Future studies are required to explore the functional significance of the large inserted repeated amino acid motifs, as well as the possibility that synonymous substitution rates may be affected by positive selection.

  • 307.
    Erixon, Per
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Svennblad, Bodil
    Britton, Tom
    Oxelman, Bengt
    Reliability of Bayesian Posterior Probabilities and Bootstrap Frequencies in Phylogenetics2003In: Systematic Biology, ISSN 1063-5157, Vol. 52, no 5, p. 665-673Article in journal (Refereed)
  • 308.
    Ettema, Thijs J. G.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Ahmed, Hatim
    Geerling, Ans C. M.
    van der Oost, John
    Siebers, Bettina
    The non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPN) of Sulfolobus solfataricus: a key-enzyme of the semi-phosphorylative branch of the Entner-Doudoroff pathway2008In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 12, no 1, p. 75-88Article in journal (Refereed)
    Abstract [en]

    Archaea utilize a branched modification of the classical Entner-Doudoroff (ED) pathway for sugar degradation. The semi-phosphorylative branch merges at the level of glyceraldehyde 3-phosphate (GAP) with the lower common shunt of the Emden-Meyerhof-Parnas pathway. In Sulfolobus solfataricus two different GAP converting enzymes-classical phosphorylating GAP dehydrogenase (GAPDH) and the non-phosphorylating GAPDH (GAPN)-were identified. In Sulfolobales the GAPN encoding gene is found adjacent to the ED gene cluster suggesting a function in the regulation of the semi-phosphorylative ED branch. The biochemical characterization of the recombinant GAPN of S. solfataricus revealed that-like the well-characterized GAPN from Thermoproteus tenax-the enzyme of S. solfataricus exhibits allosteric properties. However, both enzymes show some unexpected differences in co-substrate specificity as well as regulatory fine-tuning, which seem to reflect an adaptation to the different lifestyles of both organisms. Phylogenetic analyses and database searches in Archaea indicated a preferred distribution of GAPN (and/or GAP oxidoreductase) in hyperthermophilic Archaea supporting the previously suggested role of GAPN in metabolic thermoadaptation. This work suggests an important role of GAPN in the regulation of carbon degradation via modifications of the EMP and the branched ED pathway in hyperthermophilic Archaea.

  • 309.
    Ettema, Thijs J. G.
    et al.
    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.
    The alpha-proteobacteria: the Darwin finches of the bacterial world2009In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 5, no 3, p. 429-432Article in journal (Refereed)
    Abstract [en]

    The alpha-proteobacteria represent one of the most diverse bacterial subdivisions, displaying extreme variations in lifestyle, geographical distribution and genome size. Species for which genome data are available have been classified into a species tree based on a conserved set of vertically inherited core genes. By mapping the variation in gene content onto the species tree, genomic changes can be associated with adaptations to specific growth niches. Genes for adaptive traits are mostly located in 'plasticity zones' in the bacterial genome, which also contain mobile elements and are highly variable across strains. By physically separating genes for information processing from genes involved in interactions with the surrounding environment, the rate of evolutionary change can be substantially enhanced for genes underlying adaptation to new growth habitats, possibly explaining the ecological success of the alpha-proteobacterial subdivision.

  • 310. Farah, Mohamed
    et al.
    Olsson, Sten
    Bate, Jenny
    Lindquist, Marie
    Edwards, Ralph
    Simmonds, Monique
    Leon, Christine
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Botanical Nomenclature in Pharmacovigilance and a Recommendation for Standardisation2006In: Drug Safety, ISSN 0114-5916, Vol. 29, p. 1023-1029Article in journal (Refereed)
    Abstract [en]

    Nomenclature of plants in pharmacology can be presented by pharmaceutical

    names or scientific names in the form of Linnaean binomials. In this paper,

    positive and negative aspects of both systems are discussed in the context of the

    scientific nomenclatural framework and the systems’ practical applicability. The

    Uppsala Monitoring Centre (UMC) runs the WHO Programme for International

    Drug Monitoring and is responsible for the WHO Adverse Drug Reaction (ADR)

    database that currently contains 3.6 million records WHO Adverse Drug Reaction

    database. In order for the UMC to monitor pharmacovigilance through ADRs to

    herbal medicine products the following species nomenclatural criteria are important:

    (i) the name should indicate only one species of plant; (ii) the source for this

    name must be authoritative; (iii) the name should indicate which part of the plant

    is used. Based on these criteria, the UMC investigated four options: (i) adopt main

    names used in recognised (inter-) national pharmacopoeias or authoritative publications;

    (ii) adopt option 1, but cite the publication for all names in abbreviated

    form; (iii) three-part pharmaceutical names consisting of Latinised part name plus

    Latinised genus name, plus Latinised specific epithet; (iv) scientific binomial

    names, optionally with author and plant part used. The UMC has selectedchosen

    for the latter option and willas its adoption utilizes the scientific botanical

    nomenclature as defined by the International Code of Botanical Nomenclature.

  • 311. Fiore-Donno, Anna Maria
    et al.
    Meyer, Marianne
    Baldauf, Sandra L
    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.
    Pawlowski, Jan
    Evolution of dark-spored Myxomycetes (slime-molds): Molecules versus morphology.2008In: Mol Phylogenet Evol, ISSN 1055-7903Article in journal (Refereed)
  • 312.
    Flagstad, Ö.
    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.
    Hedmark, E.
    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.
    Landa, A.
    Bröseth, H.
    Persson, J.
    Andersen, R.
    Segerström, P.
    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.
    Colonization history and non-invasive monitoring of a re-established wolverine (Gulo gulo) population.2004In: Conservation Biology, no 18, p. 676-688Article in journal (Refereed)
  • 313. Flagstad, Øystein
    et al.
    Hedmark, Eva
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Landa, Arild
    Brøseth, Henrik
    Persson, Jens
    Andersen, Roy
    Segerström, Peter
    Ellegren, Hans
    Colonization history and noninvasive monitoring of a reestablished wolverine population2004In: Conservation Biology, ISSN 0888-8892, Vol. 18, no 3, p. 676-688Article in journal (Refereed)
  • 314.
    Florin, Ann-Britt
    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.
    Gyllenstrand, Niclas
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Isolation and characterization of polymorphic microsatellite markers in the blowflies Lucilia illustris and Lucilia sericata2002In: Molecular Ecology Notes, Vol. 2, p. 113-116Article in journal (Refereed)
  • 315.
    Fogelqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Genetic structure and dispersal in plant populations2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on the spatial structure and methods to identify spatial structure in plants.

    Methods that investigate genetic structure can mainly be divided into equilibrium methods that reveal summed dispersal over many generations, and cluster methods, that reveal more recent dispersal events. Depending on the spatial level, local or global, suitable methods are different.

    The thesis consists of four papers.

    The first explores the spatial genetic structure in two epiphytic bryophytes that have different dispersal strategies (Orthotrichum speciosum and O. obtusifolium) using three different approaches based on pairwise kinship coefficients assessed from AFLP data. The spatial kinship structure was detected with both autocorrelation analysis and generalized additive models, but linear regression failed to detect any structure in O. speciosum.

    In the second paper the spatial genetic structure in marginal populations of the forest tree Quercus robur is investigated at both local and regional scales. At the local scale, dispersal kernels as estimated using maximum likelihood parentage methods showed to be comparable to results acquired in central located populations. At the regional scale the degree of isolation at the margin of the distribution is shown.

    The third paper compares a number of sibship clustering methods. It was found that the performances of the sibship reconstruction algorithms are strongly dependent on fulfilling the assumptions of the model and that using an overly simple model produced very unreliable results. The amount of information included in the model affected the results; models including all the available information outperformed the models using only a subset of the information.

    In the last paper we show that the number of clusters as estimated by the software Structurama depends on sample size. At high number of subpopulations, the estimated number of clusters tends to be grossly underestimated when the number of sampled individuals per subpopulation is low.

    List of papers
    1. Spatial genetic structure in two congeneric epiphytes with different dispersal strategies analysed by three different methods
    Open this publication in new window or tab >>Spatial genetic structure in two congeneric epiphytes with different dispersal strategies analysed by three different methods
    2004 In: Molecular Ecology, ISSN 0962-1083, Vol. 13, no 8, p. 2109-2119Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-97458 (URN)
    Available from: 2008-09-04 Created: 2008-09-04Bibliographically approved
    2. Genetic variation and dispersal at the northern limit of the Quercus robur natural range
    Open this publication in new window or tab >>Genetic variation and dispersal at the northern limit of the Quercus robur natural range
    In: Tree Genetics & GenomesArticle in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-97459 (URN)
    Available from: 2008-09-04 Created: 2008-09-04Bibliographically approved
    3. Algorithms for reconstruction of full-sibs families from molecular markers: a comparison study
    Open this publication in new window or tab >>Algorithms for reconstruction of full-sibs families from molecular markers: a comparison study
    In: HeredityArticle in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-97460 (URN)
    Available from: 2008-09-04 Created: 2008-09-04Bibliographically approved
    4. Cryptic population genetic structure: the number of inferred clusters depends on sample size
    Open this publication in new window or tab >>Cryptic population genetic structure: the number of inferred clusters depends on sample size
    Show others...
    2010 (English)In: Molecular Ecology Resources, ISSN 1755-098X, Vol. 10, no 2, p. 314-323Article in journal (Refereed) Published
    Abstract [en]

    Clustering methods have been used extensively to unravel cryptic population genetic structure. We investigated the effect of the number of individuals sampled in each location on the resulting number of clusters. Our study was motivated by recent results in Arabidopsis thaliana: studies in which more than one individual was sampled per location apparently have led to a much higher number of clusters than studies where only one individual was sampled in each location, as is generally done in this species. We show, using computer simulations and microsatellite data in A. thaliana, that the number of sampled individuals indeed has a strong impact on the number of resulting clusters. This effect is smaller if the sampled populations have a hierarchical structure. In most cases, sampling 5-10 individuals per population should be enough. The results argue for abandoning the concept of 'accessions' in partially selfing organisms.

    Keywords
    Arabidopsis thaliana, Population structure, Sampling, STRUCTURE
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-97461 (URN)10.1111/j.1755-0998.2009.02756.x (DOI)000274325400008 ()
    Available from: 2008-09-04 Created: 2008-09-04 Last updated: 2017-01-25Bibliographically approved
  • 316.
    Fogelqvist, Johan
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Mortier, Frédéric
    Gerber, Sophie
    Lascoux, Martin
    Algorithms for reconstruction of full-sibs families from molecular markers: a comparison studyIn: HeredityArticle in journal (Refereed)
  • 317.
    Fogelqvist, Johan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Niittyvuopio, Anne
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Savolainen, Outi
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Cryptic population genetic structure: the number of inferred clusters depends on sample size2010In: Molecular Ecology Resources, ISSN 1755-098X, Vol. 10, no 2, p. 314-323Article in journal (Refereed)
    Abstract [en]

    Clustering methods have been used extensively to unravel cryptic population genetic structure. We investigated the effect of the number of individuals sampled in each location on the resulting number of clusters. Our study was motivated by recent results in Arabidopsis thaliana: studies in which more than one individual was sampled per location apparently have led to a much higher number of clusters than studies where only one individual was sampled in each location, as is generally done in this species. We show, using computer simulations and microsatellite data in A. thaliana, that the number of sampled individuals indeed has a strong impact on the number of resulting clusters. This effect is smaller if the sampled populations have a hierarchical structure. In most cases, sampling 5-10 individuals per population should be enough. The results argue for abandoning the concept of 'accessions' in partially selfing organisms.

  • 318.
    Fogelqvist, Johan
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Parducci, Laura
    Lascoux, Martin
    Genetic variation and dispersal at the northern limit of the Quercus robur natural rangeIn: Tree Genetics & GenomesArticle in journal (Refereed)
  • 319. Ford, Caroline S.
    et al.
    Ayres, Karen L.
    Toomey, Nicola
    Haider, Nadia
    Stahl, Jonathan Van Alphen
    Kelly, Laura J.
    Wikström, Niklas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Hollingsworth, Peter M.
    Duff, R. Joel
    Hoot, Sarah B.
    Cowan, Robyn S.
    Chase, Mark W.
    Wilkinson, Mike J.
    Selection of candidate coding DNA barcoding regions for use on land plants2009In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 159, no 1, p. 1-11Article in journal (Refereed)
    Abstract [en]

    An in silico screen of 41 of the 81 coding regions of the Nicotiana plastid genome generated a shortlist of 12 candidates as DNA barcoding loci for land plants. These loci were evaluated for amplification and sequence variation against a reference set of 98 land plant taxa. The deployment of multiple primers and a modified multiplexed tandem polymerase chain reaction yielded 85-94% amplification across taxa, and mean sequence differences between sister taxa of 6.1 from 156 bases of accD to 22 from 493 bases of matK. We conclude that loci should be combined for effective diagnosis, and recommend further investigation of the following six loci: matK, rpoB, rpoC1, ndhJ, ycf5 and accD.

  • 320.
    Forshage, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Revision of the Eucoila/Trybliographa complex (Hymenoptera: Cynipoidea: Figitidae: Eucoilinae)Manuscript (preprint) (Other academic)
    Abstract [en]

    Eucoiline wasps are parasitoids of Diptera larvae in various microhabitats. They are by far the most species-rich subfamily of the Figitidae but they are poorly studied in general and the classification in particular is chaotic. Here, a taxonomic revision is provided of one of the more enigmatic eucoiline groups, the Eucoila/Trybliographa complex. This group is spread over the world, but significantly one of the most abundant groups of Eucoilinae in the Holarctic.

    This complex includes rather large genus Trybliographa Förster, the type genus of the subfamily, Eucoila Westwood, and the two small genera Bothrochacis Cameron and Linoeucoila Lin. In the present work, more than 500 species-level names are considered, which have at some time or another been placed in this group, and it is concluded that 156 of them truly belong to the group. The circumscriptions of these genera are emended according to phylogenetic concerns. Eucoila is restricted to the species-poor "crassinerva group", a Holarctic group comprising large species attacking various calyptrate flies in dung and similar microhabitats. Bothrochacis is extended to accomodate all the Paleotropic species previously considered to be part of Eucoila; their biology is similar to that of Eucoila. Linoeucoila was previously believed to be endemic to Taiwan, but one new species is described from South Africa, extending the distribution range of the group considerably. The species-rich genus Trybliographa was previously considered to be Holarctic and exclusively parasitising Anthomyiidae, but here it is demonstrated that the genus occurs globally, and includes species attacking other calyptrate flies. It is extended to include all the morphologically transitional forms which were previously classified in Eucoila, the "floralis group".

    All the known species are treated, and many are redescribed in full-length. 19 species are described as new to science: Eucoila primorskensis from the Russian Far East, Bothrochacis malaisei from South East Asia, B. iberica from south Europe, Linoeucoila laterostriata from South Africa, Trybliographa eofloralis from the Russian Far East, T. coprophila from northern Europe, T. merdaria from central Asia, T. dislocata from South America, T. longicella from South East Asia, T. bovina from Europe, T. ferruginea from North America, T. chrestosemoida from the Himalayas, T. pymi from Europe, T. japonica from Japan, T. vandynae from Europe, T. pedunculata from Europe, T. scandica from northern Europe, T. emblematica from northern Europe, and T. ptilicola from northern Europe.

    A large number of new combinations and new synonymies are made. Inside the Eucoila/Trybliographa complex, 3 new genus-level synonymies are made (Pentaplastidia Weld, Psilodoropsis Hedicke and Lenobria Belizin are new synonyms of Trybliographa), plus 45 new species-level synonymies, and 26 new combinations, while one species is removed from synonymy. An additional 142 new combinations are made of the names considered that were found not to belong within this group. Furthermore, one new genus-level synonymy (Tetramerocera Ashmead as new synonym of Ganaspis Förster) and seven new species-level synonymies are made, and six new replacement names (nomina nova) proposed; even though such nomenclatural acts have not been part of the primary scope of the paper.

  • 321.
    Forshage, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Systematics of Eucoilini: Exploring the diversity of a poorly known group of Cynipoid parasitic wasps2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Many animal species are still undiscovered, even in Sweden. This thesis deals with the wasps of the subfamily Eucoilinae (of Figitidae, Cynipoidea), a poorly known group of small parasitoids of Dipteran flies. In this group, old classifications are chaotic, knowledge of old taxa is scant, phylogenetic work has recently started, and many new taxa remain to be described.

    In this thesis, an identification key is given to the European genera of Eucolinae, and a tribal classification of the subfamily is reintroduced, based on recent phylogenetic results. Most of the thesis focuses on the tribe Eucoilini. That tribe is analyzed phylogenetically in two analyses, one based on a large morphological dataset, the other on two molecular markers, ribosomal 28S and mitochondrial Cytochrome B.

    The monophyletic core group of Eucoilini is the Eucoila/Trybliographa complex. It is treated in a big taxonomic revision, based on studies of several hundred possibly relevant type specimens and several thousands of other specimens, and on the phylogenetic analyses.

    More than 500 names of possible members of this group are investigated, and many new combinations are proposed, of species found not to belong within the group, as well as those that did, including some which are transferred to other genera in accordance with the new phylogenetic results. The new genus Quasimodoana is erected, and 20 new species described (8 from Northern Europe, 12 from elsewhere). More than 180 new combinations, more than 50 new species-level synonyms and ca 10 genus-level synonyms, are proposed.

    Within this complex, the basal split is found to have been between a Paleotropic, specis-poor lineage (Bothrochacis), and a species-rich and largely Holarctic lineage, dominated by Trybliographa but also including the small genera Eucoila and Linoeucoila. The three are not satisfactorily resolved in the analysis, but still maintained as separate genera for pragmatic reasons. It is hypothesized that this group originated in Asia during the Eocene or Oligocene, attacking calyptrate flies in herbivore dung. Then it separated in a tropical branch retaining the ancestral life history mode, and a Holarctic branch, where some lineages specialised in Anthomyiidae and colonised the microhabitats of fungi and plants, speciating extensively in the boreal forests.

    List of papers
    1. Revision of the Eucoila/Trybliographa complex (Hymenoptera: Cynipoidea: Figitidae: Eucoilinae)
    Open this publication in new window or tab >>Revision of the Eucoila/Trybliographa complex (Hymenoptera: Cynipoidea: Figitidae: Eucoilinae)
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    Eucoiline wasps are parasitoids of Diptera larvae in various microhabitats. They are by far the most species-rich subfamily of the Figitidae but they are poorly studied in general and the classification in particular is chaotic. Here, a taxonomic revision is provided of one of the more enigmatic eucoiline groups, the Eucoila/Trybliographa complex. This group is spread over the world, but significantly one of the most abundant groups of Eucoilinae in the Holarctic.

    This complex includes rather large genus Trybliographa Förster, the type genus of the subfamily, Eucoila Westwood, and the two small genera Bothrochacis Cameron and Linoeucoila Lin. In the present work, more than 500 species-level names are considered, which have at some time or another been placed in this group, and it is concluded that 156 of them truly belong to the group. The circumscriptions of these genera are emended according to phylogenetic concerns. Eucoila is restricted to the species-poor "crassinerva group", a Holarctic group comprising large species attacking various calyptrate flies in dung and similar microhabitats. Bothrochacis is extended to accomodate all the Paleotropic species previously considered to be part of Eucoila; their biology is similar to that of Eucoila. Linoeucoila was previously believed to be endemic to Taiwan, but one new species is described from South Africa, extending the distribution range of the group considerably. The species-rich genus Trybliographa was previously considered to be Holarctic and exclusively parasitising Anthomyiidae, but here it is demonstrated that the genus occurs globally, and includes species attacking other calyptrate flies. It is extended to include all the morphologically transitional forms which were previously classified in Eucoila, the "floralis group".

    All the known species are treated, and many are redescribed in full-length. 19 species are described as new to science: Eucoila primorskensis from the Russian Far East, Bothrochacis malaisei from South East Asia, B. iberica from south Europe, Linoeucoila laterostriata from South Africa, Trybliographa eofloralis from the Russian Far East, T. coprophila from northern Europe, T. merdaria from central Asia, T. dislocata from South America, T. longicella from South East Asia, T. bovina from Europe, T. ferruginea from North America, T. chrestosemoida from the Himalayas, T. pymi from Europe, T. japonica from Japan, T. vandynae from Europe, T. pedunculata from Europe, T. scandica from northern Europe, T. emblematica from northern Europe, and T. ptilicola from northern Europe.

    A large number of new combinations and new synonymies are made. Inside the Eucoila/Trybliographa complex, 3 new genus-level synonymies are made (Pentaplastidia Weld, Psilodoropsis Hedicke and Lenobria Belizin are new synonyms of Trybliographa), plus 45 new species-level synonymies, and 26 new combinations, while one species is removed from synonymy. An additional 142 new combinations are made of the names considered that were found not to belong within this group. Furthermore, one new genus-level synonymy (Tetramerocera Ashmead as new synonym of Ganaspis Förster) and seven new species-level synonymies are made, and six new replacement names (nomina nova) proposed; even though such nomenclatural acts have not been part of the primary scope of the paper.

    National Category
    Biological Systematics
    Research subject
    Entomology; Systematic Zoology
    Identifiers
    urn:nbn:se:uu:diva-109393 (URN)
    Available from: 2009-10-15 Created: 2009-10-14 Last updated: 2010-01-14
    2. Identification key to European genera of Eucoilinae (Hymenoptera, Cynipoidea, Figitidae)
    Open this publication in new window or tab >>Identification key to European genera of Eucoilinae (Hymenoptera, Cynipoidea, Figitidae)
    2008 (English)In: Insect Systematics & Evolution, ISSN 1399-560X, E-ISSN 1876-312X, Vol. 39, no 3, p. 341-359Article in journal (Refereed) Published
    Abstract [en]

    A key is presented to the European genera of Eucoilinae, for the first time after these genera have been circumscribed based on type studies and phylogenetic concerns. The key is illustrated with drawings based on SEM pictures. A generic catalogue with full synonymy of the European eucoiline genera is presented. The following new synonymies on the generic level are proposed: Trichoplasta Benoit, 1956 (Armigerina Belizin, 1968 syn.n.), Eucoila Westwood,1833 (Lenobria Belizin, 1968 syn.n.), Kleidotoma Westwood, 1833 (Nesokleidotoma Beardsley, 1990 syn.n., Octameris Belizin, 1973 syn.n., Polbourdouxia Dessart, 1977 syn.n., Pentakleidota Weld, 1951 syn.n.). One species level synonymy is proposed: Eucoila floralis Dahlbom, 1846 (Lenobria bidentata Belizin, 1968 syn.n.) A tribal classification of the subfamily is utilised, recognizing the following tribes: Diglyphosemini Belizin, 1961 stat.n.,Kleidotomini Hellén, 1960 stat.n. (Cothonaspini Belizin, 1961 syn.n.), Ganaspini Belizin,1961 stat.n. (Dieucoilini Belizin, 1961 syn.n., Glauraspidiini Belizin, 1961 syn.n.),Trichoplastini Kovalev, 1989 and Eucoilini Thomson, 1862.

    Keywords
    Eucoilinae, Cynipoidea, Hymenoptera, identification key, classification, nomenclature
    National Category
    Biological Systematics
    Research subject
    Entomology; Systematic Zoology
    Identifiers
    urn:nbn:se:uu:diva-109390 (URN)000260808600007 ()
    Available from: 2009-10-14 Created: 2009-10-14 Last updated: 2017-12-12Bibliographically approved
    3. Quasimodoana, a new Holarctic genus of eucoiline wasps (Hymenoptera, Cynipoidea, Figitidae), with a phylogenetic analysis of related genera
    Open this publication in new window or tab >>Quasimodoana, a new Holarctic genus of eucoiline wasps (Hymenoptera, Cynipoidea, Figitidae), with a phylogenetic analysis of related genera
    2008 (English)In: Systematic Entomology, ISSN 0307-6970, E-ISSN 1365-3113, Vol. 33, no 2, p. 301-318Article in journal (Refereed) Published
    Abstract [en]

    A new Holarctic genus, Quasimodoana gen.n. is described for the Palearctic eucoiline wasp Eucoila decipiens Förster, 1869, as Quasimodoana decipiens comb.n. A lectotype is designated for this species. A new North American species is described here as Quasimodoana gibba sp.n. As the new genus has similarities with several eucoiline genera, belonging to two related but distinct lineages, a phylogenetic analysis was carried out, based on 83 morphological characters. The two lineages included in the analysis are referred to here under the tribal names of Eucoilini and Trichoplastini stat.nov. We discuss reasons for adopting available tribal names (rather than 'informal genus groups'), and Trichoplastini is removed from synonymy with Eucoilini. The phylogenetic analysis places Quasimodoana unambiguously within Eucoilini, as a sistergroup to the Trybliographa complex. However, there is only weak support for the monophyly of Eucoilini and for the hypothesized sistergroup relationship between Eucoilini and Trichoplastini.

    Keywords
    Eucoilini, Eucoilinae, Figitidae, Cynipoidea, Hymenoptera, phylogenetics, classification, taxonomy, weighting schemes in phylogenetics, Quasimodoana
    National Category
    Biological Sciences
    Research subject
    Entomology; Systematic Zoology
    Identifiers
    urn:nbn:se:uu:diva-109374 (URN)10.1111/j.1365-3113.2007.00415.x (DOI)000253981300005 ()
    Available from: 2009-10-14 Created: 2009-10-14 Last updated: 2017-12-12Bibliographically approved
    4. Molecular phylogeny of the Eucoila/Trybliographa complex (Hymenoptera: Cynipoidea: Figitidae)
    Open this publication in new window or tab >>Molecular phylogeny of the Eucoila/Trybliographa complex (Hymenoptera: Cynipoidea: Figitidae)
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

    The Eucoilinae are small parasitic wasps attacking larvae of Diptera. Some species are important biological control agents; others are popular model organisms. One of the most species-rich groups in the Holarctic is the Eucoila/Trybliographa complex, which has previously been in a state of major classificatory disorder. One of the reasons for this has been the lack of knowledge of phylogenetic relationships. To address this, we have made a molecular phylo-genetic analysis of 51 taxa, comprising a representative sample of taxa of the complex, based on 28S nuclear ribosomal and CytB mitochondrial sequences. The analysis clearly shows the Eucoila/Trybliographa complex to be a monophyletic group. Within this group, there is a basal division between a Paleotropic, species-poor branch, identified as the genus Bothrochacis, and a species-rich, largely Holarctic branch comprising the remainder of the complex. A basal lineage within the latter corresponds to the genus Eucoila, and another to the small genus Linoeucoila from Taiwan. However, their exact relationships to each other and to basal lineages of the big genus Trybliographa, which comprises the remainder of the clade, remains uncertain. Within Trybliographa, several interesting relationships are suggested, but the result is not robust or comprehensive enough at this point for a major reclassification of the genus.

    Keywords
    Eucoila, Trybliographa, Eucoilini, Eucoilinae, Figitidae, Cynipoidea, Hymenoptera, phylogenetic analysis
    National Category
    Biological Systematics
    Research subject
    Entomology; Systematic Zoology
    Identifiers
    urn:nbn:se:uu:diva-109391 (URN)
    Available from: 2009-10-15 Created: 2009-10-14 Last updated: 2010-01-14
  • 322.
    Forshage, Mattias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Nordlander, Göran
    Department of Ecology, Swedish University of Agricultural Sciences.
    Identification key to European genera of Eucoilinae (Hymenoptera, Cynipoidea, Figitidae)2008In: Insect Systematics & Evolution, ISSN 1399-560X, E-ISSN 1876-312X, Vol. 39, no 3, p. 341-359Article in journal (Refereed)
    Abstract [en]

    A key is presented to the European genera of Eucoilinae, for the first time after these genera have been circumscribed based on type studies and phylogenetic concerns. The key is illustrated with drawings based on SEM pictures. A generic catalogue with full synonymy of the European eucoiline genera is presented. The following new synonymies on the generic level are proposed: Trichoplasta Benoit, 1956 (Armigerina Belizin, 1968 syn.n.), Eucoila Westwood,1833 (Lenobria Belizin, 1968 syn.n.), Kleidotoma Westwood, 1833 (Nesokleidotoma Beardsley, 1990 syn.n., Octameris Belizin, 1973 syn.n., Polbourdouxia Dessart, 1977 syn.n., Pentakleidota Weld, 1951 syn.n.). One species level synonymy is proposed: Eucoila floralis Dahlbom, 1846 (Lenobria bidentata Belizin, 1968 syn.n.) A tribal classification of the subfamily is utilised, recognizing the following tribes: Diglyphosemini Belizin, 1961 stat.n.,Kleidotomini Hellén, 1960 stat.n. (Cothonaspini Belizin, 1961 syn.n.), Ganaspini Belizin,1961 stat.n. (Dieucoilini Belizin, 1961 syn.n., Glauraspidiini Belizin, 1961 syn.n.),Trichoplastini Kovalev, 1989 and Eucoilini Thomson, 1862.

  • 323.
    Forshage, Mattias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Nordlander, Göran
    Department of Ecology, Swedish University of Agricultural Sciences.
    Ronquist, Fredrik
    Department of Entomology, Swedish Museum of Natural History.
    Quasimodoana, a new Holarctic genus of eucoiline wasps (Hymenoptera, Cynipoidea, Figitidae), with a phylogenetic analysis of related genera2008In: Systematic Entomology, ISSN 0307-6970, E-ISSN 1365-3113, Vol. 33, no 2, p. 301-318Article in journal (Refereed)
    Abstract [en]

    A new Holarctic genus, Quasimodoana gen.n. is described for the Palearctic eucoiline wasp Eucoila decipiens Förster, 1869, as Quasimodoana decipiens comb.n. A lectotype is designated for this species. A new North American species is described here as Quasimodoana gibba sp.n. As the new genus has similarities with several eucoiline genera, belonging to two related but distinct lineages, a phylogenetic analysis was carried out, based on 83 morphological characters. The two lineages included in the analysis are referred to here under the tribal names of Eucoilini and Trichoplastini stat.nov. We discuss reasons for adopting available tribal names (rather than 'informal genus groups'), and Trichoplastini is removed from synonymy with Eucoilini. The phylogenetic analysis places Quasimodoana unambiguously within Eucoilini, as a sistergroup to the Trybliographa complex. However, there is only weak support for the monophyly of Eucoilini and for the hypothesized sistergroup relationship between Eucoilini and Trichoplastini.

  • 324.
    Forshage, Mattias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Stigenberg, Julia
    Department of Entomology, Swedish Museum of Natural History.
    Molecular phylogeny of the Eucoila/Trybliographa complex (Hymenoptera: Cynipoidea: Figitidae)Manuscript (preprint) (Other academic)
    Abstract [en]

    The Eucoilinae are small parasitic wasps attacking larvae of Diptera. Some species are important biological control agents; others are popular model organisms. One of the most species-rich groups in the Holarctic is the Eucoila/Trybliographa complex, which has previously been in a state of major classificatory disorder. One of the reasons for this has been the lack of knowledge of phylogenetic relationships. To address this, we have made a molecular phylo-genetic analysis of 51 taxa, comprising a representative sample of taxa of the complex, based on 28S nuclear ribosomal and CytB mitochondrial sequences. The analysis clearly shows the Eucoila/Trybliographa complex to be a monophyletic group. Within this group, there is a basal division between a Paleotropic, species-poor branch, identified as the genus Bothrochacis, and a species-rich, largely Holarctic branch comprising the remainder of the complex. A basal lineage within the latter corresponds to the genus Eucoila, and another to the small genus Linoeucoila from Taiwan. However, their exact relationships to each other and to basal lineages of the big genus Trybliographa, which comprises the remainder of the clade, remains uncertain. Within Trybliographa, several interesting relationships are suggested, but the result is not robust or comprehensive enough at this point for a major reclassification of the genus.

  • 325.
    Foster, KR
    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.
    Ratnieks, FLW
    Gyllenstrand, N
    Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Thoren, PA
    Colony kin structure and male production in Dolichovespula wasps2001In: MOLECULAR ECOLOGY, ISSN 0962-1083, Vol. 10, no 4, p. 1003-1010Article in journal (Refereed)
    Abstract [en]

    In annual hymenopteran societies headed by a single outbred queen, paternity (determined by queen mating frequency and sperm use) is the sole variable affecting colony kin structure and is therefore a key predictor of colony reproductive characteristics.

  • 326. Foucault, C
    et al.
    La Scola, B.
    Lindroos, Hillevi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Raoult, D.
    Multispacer typing technique for sequence-based typing of Bartonella quintana2005In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 43, no 1, p. 41-48Article in journal (Refereed)
    Abstract [en]

    Bartonella quintana is a worldwide fastidious bacterium of the Alphaproteobacteria responsible for bacillary angiomatosis, trench fever, chronic lymphadenopathy, and culture-negative endocarditis. The recent genome sequencing of a B. quintana isolate allowed us to propose a genome-wide sequence-based typing method. To ensure sequence discrimination based on highly polymorphic areas, we amplified and sequenced 34 spacers in a large collection of B. quintana isolates. Six of these exhibited polymorphisms and allowed the characterization of 4 genotypes. However, the strain variants suggested by the noncoding sequences did not correlate with the results of pulsed-field gel electrophoresis (PFGE), which suggested a higher degree of variability. Modification of the PFGE profile of one isolate after nine subcultures confirmed that rearrangement frequencies are high in this species, making PFGE unreliable for epidemiological purposes. The low extent of sequence heterogeneity in the species suggests a recent emergence of this bacterium as a human pathogen. Direct typing of natural samples allowed the identification of a fifth genotype in the DNA extracted from a human body louse collected in Burundi. We have named the typing technique herein described multispacer typing.

  • 327. Foucault, C.
    et al.
    LaScola, Bernard
    Lindroos, Hillevi
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics.
    Andersson, Siv G. E.
    Raoult, Didier
    Multi-Spacer-Typing (MST) for sequence-based typing of Bartonella quintana2005In: Journal of Clinical Microbiology, ISSN 0095-1137, Vol. 43, no 1, p. 41-48Article in journal (Refereed)
  • 328. Fox-Dobbs, Kena
    et al.
    Leonard, Jennifer A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Koch, Paul L.
    Pleistocene megafauna from eastern Beringia: paleoecological and paleoenvironmental interpretations of stable carbon and nitrogen isotope and radiocarbon records2008In: Palaeogeography, Palaeoclimatology, Palaeoecology, ISSN 0031-0182, E-ISSN 1872-616X, Vol. 261, no 1-2, p. 30-46Article in journal (Refereed)
    Abstract [en]

    Late Pleistocene eastern Beringia is a model paleo-ecosystem for the study of potential and realized species interactions within a diverse mammalian fauna. Beringian paleontological records store a wealth of information that can be used to investigate how predator-prey and competitive interactions among consumers shifted in response to past episodes of environmental change. Two such recent periods of rapid climate change are the Last Glacial Maximum (LGM) and the end of glacial conditions at the beginning of the Holocene. Here we assemble carbon and nitrogen stable isotope, and AMS C-14 data collected from bone collagen of late Pleistocene carnivores and megafaunal prey species from the interior of eastern Beringia (Alaska), and reconstruct the diets of ancient Alaskan carnivores and herbivores. We are able to account for the relative influences of diet versus changing environmental conditions on variances in consumer isotope values, to identify species hiatuses in the fossil record, and to draw conclusions about paleoenvironmental conditions from faunal chronologies. Our isotopic results suggest that there was dietary niche overlap among some Beringian herbivore species, and partitioning among other species. We rely upon delta C-13 and delta N-15 values of modem Alaskan C-3 plant types to infer Beringian herbivore dietary niches. Horse, bison, yak, and mammoth primarily consumed grasses, sedges, and herbaceous plant species. Caribou and woodland muskox focused upon tundra plants, including lichen, fungi, and mosses. The network of Beringian carnivore interaction was complex and dynamic, some species (wolves) persisted for long periods of time, while others were only present during specific timeframes (large felids and ursids). Beringian carnivore diets included all measured herbivore species, although mammoth and muskox only appeared in carnivore diets during specific times in the late Pleistocene. We identified the potential presence of unmeasured diet sources that may have included forest-dwelling cervids and/or plant materials. None of the large-bodied carnivore species we analyzed (except short-faced bear) were specialized predators of a single prey species during the late Pleistocene. Differences in carnivore diet and dietary breadth between time periods either reflect changes in the relative abundances of prey on the Beringian landscape, or changes in competitive interactions among Beringian carnivore species

  • 329.
    Frajman, Bozo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae) – a multigene phylogenetic approach  with  Relative Dating2009In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 58, no 3, p. 328-345Article in journal (Refereed)
    Abstract [en]

    We used four potentially unlinked nuclear DNA regions from the gene   family encoding the second largest subunit of the RNA polymerases, as   well as the psbE-petG spacer and the rps16 intron from the chloroplast   genome, to evaluate the origin of and relationships within Heliosperma   (Sileneae, Caryophyllaceae). Relative dates of divergence times are   used to discriminate between hybridization and gene duplication/loss as   alternative explanations for topological conflicts between gene trees.   The observed incongruent relationships among the three major lineages   of Heliosperma are better explained by homoploid hybridization than by   gene duplication/losses because species branching events exceed gene   coalescence times under biologically reasonable population sizes and   generation times, making lineage sorting an unlikely explanation. The  origin of Heliosperma is complex and the gene trees likely reflect both reticulate evolution and sorting events. At least two lineages have   been involved in the origin of Heliosperma, one most closely related to   the ancestor of Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.

  • 330.
    Frajman, Bozo
    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.
    Jogan, Nec
    Oxelman, Bengt
    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.
    Heliosperma insulare Trinajstic' (Caryophyllaceae, Sileneae), a neglected species from the island Mljet (Croatia).2004In: Book of Abstracts.: Croatian Botanical Society, Zagreb, 2004, p. 110-111Conference paper (Other scientific)
  • 331.
    Frajman, Bozo
    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.
    Oxelman, Bengt
    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.
    Phylogeny of Heliosperma based on chloroplast and nuclear DNA sequences.2004In: Plant evolution in Mediterranean Climate Zones.: IXth IOPB Meeting, Valencia, 2004, p. 66-Conference paper (Other scientific)
  • 332.
    Frajman, Božo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Proposal to reject the name Cucubalus quadrifidus (Heliosperma quadrifidum, Silene quadrifida) (Caryophyllaceae, Sileneae)2007In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 1, p. 260-261Article in journal (Refereed)
  • 333.
    Frajman, Božo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Taxonomy and Reticulate Phylogeny of Heliosperma and Related Genera (Sileneae, Caryophyllaceae)2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Heliosperma (nom. cons prop.) comprises 15—20 taxa, most of them endemic to the Balkan Peninsula. DNA sequences from the chloroplast (rps16 intron, psbE-petG spacer) and the nuclear genome (ITS and four putatively unlinked RNA polymerase genes) are used to elucidate phylogenetic relationships within Heliosperma, and its position within Sileneae. Three main lineages are found within Heliosperma: Heliosperma alpestre, H. macranthum and the H. pusillum-clade. The relationships among the lineages differ between the plastid and the nuclear trees. Relative dates are used to discriminate among inter- and intralineage processes causing such incongruences, and ancient homoploid hybridisation is the most likely explanation.

    The chloroplast data strongly support two, geographically correlated clades in the H. pusillum-group, whereas the relationships appear poorly resolved by the ITS data, when analysed under a phylogenetic tree model. However, a network analysis finds a geographic structuring similar to that in the chloroplast data. Ancient vicariant divergence followed by hybridisation events best explains the observed pattern. The morphological and taxonomical diversity in the H. pusillum-group is possibly ecology-induced, and is not correlated with the molecular data.

    Phylogenetic patterns regarding the origin of Heliosperma are complicated, probably influenced by reticulate and sorting events. At least two ancient lineages have been involved in its evolution, one most closely related to Viscaria/Atocion and the other to Eudianthe/Petrocoptis.

    Atocion and Viscaria are sister genera, most species-rich on the Balkans, and including six/three species. Phylogenies do not support their traditional classification, and provide a framework for a taxonomic revision. Atocion compactum is found in three different positions in the chloroplast tree, and in a single clade in the nuclear gene trees. Using relative dates we demonstrate that hybridisation with subsequent chloroplast capture is a feasible explanation for the pattern observed. This, and other observed reticulate patterns, highlights the importance of hybridisation in plant evolution.

    List of papers
    1. Proposal to conserve the name Heliosperma against Ixoca (Caryophyllaceae, Sileneae)
    Open this publication in new window or tab >>Proposal to conserve the name Heliosperma against Ixoca (Caryophyllaceae, Sileneae)
    2006 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 55, no 3, p. 807-808Article in journal (Refereed) Published
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-96101 (URN)
    Available from: 2007-09-05 Created: 2007-09-05 Last updated: 2017-12-14Bibliographically approved
    2. Proposal to reject the name Cucubalus quadrifidus (Heliosperma quadrifidum, Silene quadrifida) (Caryophyllaceae, Sileneae)
    Open this publication in new window or tab >>Proposal to reject the name Cucubalus quadrifidus (Heliosperma quadrifidum, Silene quadrifida) (Caryophyllaceae, Sileneae)
    2007 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 1, p. 260-261Article in journal (Refereed) Published
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96102 (URN)
    Available from: 2007-09-05 Created: 2007-09-05 Last updated: 2017-12-14Bibliographically approved
    3. Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences
    Open this publication in new window or tab >>Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences
    2007 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 43, no 1, p. 140-155Article in journal (Refereed) Published
    Abstract [en]

    The Balkan Peninsula is known to be one of the most diverse and species-rich parts of Europe, but its biota has gained much less attention in phylogenetic and evolutionary studies compared to other southern European mountain systems. We used nuclear ribosomal internal transcribed spacer (ITS) sequences and intron sequences of the chloroplast gene rps16 to examine phylogenetic and biogeographical patterns within the genus Heliosperma (Sileneae, Caryophyllaceae). The ITS and rps16 intron sequences both support monophyly of Heliosperma, but the data are not conclusive with regard to its exact origin. Three strongly supported clades are found in both data sets, corresponding to Heliosperma alpestre, Heliosperma macranthum and the Heliosperma pusillum clade, including all other taxa. The interrelationships among these three differ between the nuclear and the plastid data sets. Hierarchical relationships within the H. pusillum clade are poorly resolved by the ITS data, but the rps16 intron sequences form two well-supported clades which are geographically, rather than taxonomically, correlated. A similar geographical structure is found in the ITS data, when analyzed with the NeighbourNet method. The apparent rate of change within Heliosperma is slightly higher for rps16 as compared to ITS. In contrast, in the Sileneae outgroup, ITS substitution rates are more than twice as high as those for rps16, a situation more in agreement with what has been found in other rate comparisons of noncoding cpDNA and ITS. Unlike most other Sileneae ITS sequences, the H. pusillum group sequences display extensive polymorphism. A possible explanation to these patterns is extensive hybridization and gene flow within Heliosperma, which together with concerted evolution may have eradicated the ancient divergence suggested by the rps16 data. The morphological differentiation into high elevation, mainly widely distributed taxa, and low elevation narrow endemics is not correlated with the molecular data, and is possibly a result of ecological differentiation.

    Keywords
    Heliosperma, Ixoca, Balkan biogeography, ITS, rps16, Reticulate evolution
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96103 (URN)10.1016/j.ympev.2006.11.003 (DOI)000245936000011 ()17188521 (PubMedID)
    Available from: 2007-09-05 Created: 2007-09-05 Last updated: 2017-12-14Bibliographically approved
    4. Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae) – a multigene phylogenetic approach  with  Relative Dating
    Open this publication in new window or tab >>Hybrid origins and homoploid reticulate evolution within Heliosperma (Sileneae, Caryophyllaceae) – a multigene phylogenetic approach  with  Relative Dating
    2009 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 58, no 3, p. 328-345Article in journal (Refereed) Published
    Abstract [en]

    We used four potentially unlinked nuclear DNA regions from the gene   family encoding the second largest subunit of the RNA polymerases, as   well as the psbE-petG spacer and the rps16 intron from the chloroplast   genome, to evaluate the origin of and relationships within Heliosperma   (Sileneae, Caryophyllaceae). Relative dates of divergence times are   used to discriminate between hybridization and gene duplication/loss as   alternative explanations for topological conflicts between gene trees.   The observed incongruent relationships among the three major lineages   of Heliosperma are better explained by homoploid hybridization than by   gene duplication/losses because species branching events exceed gene   coalescence times under biologically reasonable population sizes and   generation times, making lineage sorting an unlikely explanation. The  origin of Heliosperma is complex and the gene trees likely reflect both reticulate evolution and sorting events. At least two lineages have   been involved in the origin of Heliosperma, one most closely related to   the ancestor of Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.

    Keywords
    BEAST, homoploid hybridization, incongruence, lineage sorting, PATHd8, r8s, relative dating, RPA2, RPB2, RPD2
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95252 (URN)10.1093/sysbio/syp030 (DOI)000270004400004 ()
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2017-12-14Bibliographically approved
    5. Phylogenetic relationships of Atocion and Viscaria (Sileneae, Caryophyllaceae) inferred from chloroplast, nuclear ribosomal, and low-copy gene DNA sequences
    Open this publication in new window or tab >>Phylogenetic relationships of Atocion and Viscaria (Sileneae, Caryophyllaceae) inferred from chloroplast, nuclear ribosomal, and low-copy gene DNA sequences
    2009 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 58, no 3, p. 811-824Article in journal (Refereed) Published
    Abstract [en]

    Atocion and Viscaria are two of seven small genera recognised in the   tribe Sileneae on the basis of molecular phylogenies. The aim of the   present study is to infer phylogenetic relationships among their  subordinate taxa, using chloroplast (rps16 intron,psbE-petG spacer   region) and nuclear (ITS and the RNA polymerase gene family) DNA   sequences. Relative dating was used to discriminate among intralineage   and interlineage processes that cause incongruence among different   gene-tree topologies. Atocion asterias is demonstrated to belong to   Viscaria, which contains three species: V vulgaris (incl. V   atropurpurea), V alpina, and V asterias. Infraspecific differentiation   of V alpina is not supported by the sequence data. The traditional   sectional delimitation of Atocion taxa within Silene is not supported   phylogenetically, and Silene tatarinowii as well as S. hoefftiana do   not belong to Atocion, as classified previously. Atocion contains six   species: A. armeria, A. compactum, A. lerchenfeldianum, A. reuterianum,   A. rupestre, and A. scythicinum (not included in our study). With this   circumscription, Atocion and Viscaria, respectively, form monophyletic   groups in the cpDNA, ITS, RPD2a and RPD2b trees, but not in the RPA2   tree, where such relationships were possibly distorted by ancient   hybridisation. Hybridisation with subsequent chloroplast capture is   likely to have taken place in the evolutionary history of A. compactum.   Three novel nomenclatural combinations are made: Atocion reuterianum,  A. scythicinum and Viscaria asterias.

    Keywords
    BEAST, Lychnis sect. Viscaria, RPA2, RPD2a, RPD2b, Silene sect. Compactae, Silene sect. Rupifraga
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96105 (URN)000269774900010 ()
    Available from: 2007-09-05 Created: 2007-09-05 Last updated: 2017-12-14Bibliographically approved
    6. Taxonomic revision of Atocion and Viscaria (Sileneae, Caryophyllaceae)
    Open this publication in new window or tab >>Taxonomic revision of Atocion and Viscaria (Sileneae, Caryophyllaceae)
    2013 (English)In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 173, no 2, p. 194-210Article in journal (Refereed) Published
    Abstract [en]

    A species-level taxonomic revision of Atocion and Viscaria, based on a recent phylogenetic study, is presented. Atocion includes six species (A. armeria, A. compactum, A. lerchenfeldianum, A. reuterianum, A. rupestre and A. scythicinum), and Viscaria includes three species (V. alpina, V. asterias and V. vulgaris). The highest species diversity is found on the Balkan Peninsula. Species descriptions based on a study of morphological characters and generated using the Prometheus description model are provided and are also available in the Sileneae online database. Complete synonymy, notes on the ecology and geographical distribution of the taxa and an identification key are provided. Lectotypes for nine names (Lychnis helvetica, L. suecica, Silene armeria var. angustifolia, S. berdaui, S. lituanica, S. compacta, S. orientalis, S. reuteriana and Viscaria media) and a neotype for one name (S. lerchenfeldiana) are assigned.

    Keywords
    Europe, Lychnis, Middle East, Silene, taxonomy, typification
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96106 (URN)10.1111/boj.12090 (DOI)000324095100003 ()
    Funder
    Swedish Research Council
    Available from: 2007-09-05 Created: 2007-09-05 Last updated: 2017-12-14Bibliographically approved
  • 334.
    Frajman, Božo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Heidari, Nahid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Biology.
    Phylogenetic relationships of Atocion and Viscaria (Sileneae, Caryophyllaceae) inferred from chloroplast, nuclear ribosomal, and low-copy gene DNA sequences2009In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 58, no 3, p. 811-824Article in journal (Refereed)
    Abstract [en]

    Atocion and Viscaria are two of seven small genera recognised in the   tribe Sileneae on the basis of molecular phylogenies. The aim of the   present study is to infer phylogenetic relationships among their  subordinate taxa, using chloroplast (rps16 intron,psbE-petG spacer   region) and nuclear (ITS and the RNA polymerase gene family) DNA   sequences. Relative dating was used to discriminate among intralineage   and interlineage processes that cause incongruence among different   gene-tree topologies. Atocion asterias is demonstrated to belong to   Viscaria, which contains three species: V vulgaris (incl. V   atropurpurea), V alpina, and V asterias. Infraspecific differentiation   of V alpina is not supported by the sequence data. The traditional   sectional delimitation of Atocion taxa within Silene is not supported   phylogenetically, and Silene tatarinowii as well as S. hoefftiana do   not belong to Atocion, as classified previously. Atocion contains six   species: A. armeria, A. compactum, A. lerchenfeldianum, A. reuterianum,   A. rupestre, and A. scythicinum (not included in our study). With this   circumscription, Atocion and Viscaria, respectively, form monophyletic   groups in the cpDNA, ITS, RPD2a and RPD2b trees, but not in the RPA2   tree, where such relationships were possibly distorted by ancient   hybridisation. Hybridisation with subsequent chloroplast capture is   likely to have taken place in the evolutionary history of A. compactum.   Three novel nomenclatural combinations are made: Atocion reuterianum,  A. scythicinum and Viscaria asterias.

  • 335.
    Frajman, Božo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 43, no 1, p. 140-155Article in journal (Refereed)
    Abstract [en]

    The Balkan Peninsula is known to be one of the most diverse and species-rich parts of Europe, but its biota has gained much less attention in phylogenetic and evolutionary studies compared to other southern European mountain systems. We used nuclear ribosomal internal transcribed spacer (ITS) sequences and intron sequences of the chloroplast gene rps16 to examine phylogenetic and biogeographical patterns within the genus Heliosperma (Sileneae, Caryophyllaceae). The ITS and rps16 intron sequences both support monophyly of Heliosperma, but the data are not conclusive with regard to its exact origin. Three strongly supported clades are found in both data sets, corresponding to Heliosperma alpestre, Heliosperma macranthum and the Heliosperma pusillum clade, including all other taxa. The interrelationships among these three differ between the nuclear and the plastid data sets. Hierarchical relationships within the H. pusillum clade are poorly resolved by the ITS data, but the rps16 intron sequences form two well-supported clades which are geographically, rather than taxonomically, correlated. A similar geographical structure is found in the ITS data, when analyzed with the NeighbourNet method. The apparent rate of change within Heliosperma is slightly higher for rps16 as compared to ITS. In contrast, in the Sileneae outgroup, ITS substitution rates are more than twice as high as those for rps16, a situation more in agreement with what has been found in other rate comparisons of noncoding cpDNA and ITS. Unlike most other Sileneae ITS sequences, the H. pusillum group sequences display extensive polymorphism. A possible explanation to these patterns is extensive hybridization and gene flow within Heliosperma, which together with concerted evolution may have eradicated the ancient divergence suggested by the rps16 data. The morphological differentiation into high elevation, mainly widely distributed taxa, and low elevation narrow endemics is not correlated with the molecular data, and is possibly a result of ecological differentiation.

  • 336.
    Frajman, Božo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Rabeler, Richard
    Proposal to conserve the name Heliosperma against Ixoca (Caryophyllaceae, Sileneae)2006In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 55, no 3, p. 807-808Article in journal (Refereed)
  • 337.
    Frank, A. Carolin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Alsmark, Cecilia
    Mikael, Thollesson
    Functional divergence and horizontal transfer of type IV secretion systems2005In: Molecular Biology and Evolution, ISSN 1537-1719, Vol. 22, no 5, p. 1325-1336Article in journal (Refereed)
  • 338.
    Frank, A. Carolin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Amiri, Haleh
    Andersson, Siv G. E.
    Gene deterioration: loss of repeated sequences and accumulation of junk DNA2002In: Genetica, ISSN 0016-6707, Vol. 115, no 1, p. 1-12Article in journal (Refereed)
  • 339.
    Frank, A. Carolin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Eva, Berglund
    Olga, Vinnere
    Eriksson, Ann-Sofie
    Näslund, Kristina
    Holmberg, Martin
    Andersson, Siv G.E.
    Genome sequence of Bartonella grahamii, an environmental isolate from a Swedish wood mouseManuscript (Other academic)
  • 340.
    Frank, A. Carolin
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Mikael, Thollesson
    Andersson, Siv G. E.
    Recombination of pilus components in a Bartonella Type-IV secretion systemArticle in journal (Refereed)
  • 341.
    Frank, Anna Carolin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Lifestyle and Genome Evolution in Vector-Borne Bacteria: A Comparison of Three Bartonella Species2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Bacterial genomes provide records of the molecular processes associated with emergence and evolution of different bacterial lifestyles. This thesis is based on whole-genome comparisons within the genus Bartonella, an excellent model system for studies of host- and vector-specificity and infection outcome in animal-associated bacteria. The louse-borne human specialist and trench fever agent Bartonella quintana was contrasted to the flea-borne generalist relatives Bartonella henselae and Bartonella grahamii, which cause asymptomatic infection in cat and mouse respectively. While B. henselae is commonly isolated from humans, and causes cat scratch disease, there is only one reported case of B. grahamii human infection.

    The gene complements of the three species are nested like Russian dolls with the smaller genome (B. quintana) being entirely contained in the medium sized (B. henselae), which in turned is contained in the largest (B. grahamii). Size differences reflect differences in the horizontally and vertically acquired gene content, and in the number of genus- and species- specific genes, owing to differential impact of bacteriophages and plasmids, and to different degrees of genome decay. These processes can be attributed to the three distinct lifestyles.

    Comparisons with other alpha-proteobacteria suggest that the Bartonella genus as a whole evolved from plant-associated species, and that horizontal transfer, in particular of genes involved in interaction with the host, played a key role in the transition to animal intracellular lifestyle. The long-term genome decay associated with this lifestyle is most advanced in the host-restricted B. quintana. The broad host-range species B. grahamii has the largest genome and the largest proportion of auxiliary DNA of the three, probably because it has access to a larger gene pool. In encodes all the known pathogenicity determinants found in the genomes of B. henselae and B. quintana, suggesting that these genes primarily evolved to facilitate colonization in the reservoir host.

    List of papers
    1. Gene deterioration: loss of repeated sequences and accumulation of junk DNA
    Open this publication in new window or tab >>Gene deterioration: loss of repeated sequences and accumulation of junk DNA
    2002 In: Genetica, ISSN 0016-6707, Vol. 115, no 1, p. 1-12Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93415 (URN)
    Available from: 2005-09-09 Created: 2005-09-09Bibliographically approved
    2. The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae
    Open this publication in new window or tab >>The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae
    Show others...
    2004 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 101, no 26, p. 9716-9721Article in journal (Refereed) Published
    Abstract [en]

    We present the complete genomes of two human pathogens, Bartonella quintana (1,581,384 bp) and Bartonella henselae (1,931,047 bp). The two pathogens maintain several similarities in being transmitted by insect vectors, using mammalian reservoirs, infecting similar cell types (endothelial cells and erythrocytes) and causing vasculoproliferative changes in immunocompromised hosts. A primary difference between the two pathogens is their reservoir ecology. Whereas B. quintana is a specialist, using only the human as a reservoir, B. henselae is more promiscuous and is frequently isolated from both cats and humans. Genome comparison elucidated a high degree of overall similarity with major differences being B. henselae specific genomic islands coding for filamentous hemagglutinin, and evidence of extensive genome reduction in B. quintana, reminiscent of that found in Rickettsia prowazekii. Both genomes are reduced versions of chromosome I from the highly related pathogen Brucella melitensis. Flanked by two rRNA operons is a segment with similarity to genes located on chromosome II of B. melitensis, suggesting that it was acquired by integration of megareplicon DNA in a common ancestor of the two Bartonella species. Comparisons of the vector-host ecology of these organisms suggest that the utilization of host-restricted vectors is associated with accelerated rates of genome degradation and may explain why human pathogens transmitted by specialist vectors are outnumbered by zoonotic agents, which use vectors of broad host ranges.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-91600 (URN)10.1073/pnas.0305659101 (DOI)
    Available from: 2004-04-13 Created: 2004-04-13 Last updated: 2017-12-14Bibliographically approved
    3. Computational inference of scenarios for alpha-proteobacterial genome evolution
    Open this publication in new window or tab >>Computational inference of scenarios for alpha-proteobacterial genome evolution
    2004 In: Proceedings of the national academy of sciences USA, ISSN 1091-6490, Vol. 101, no 26, p. 9722-9727Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93417 (URN)
    Available from: 2005-09-09 Created: 2005-09-09Bibliographically approved
    4. Functional divergence and horizontal transfer of type IV secretion systems
    Open this publication in new window or tab >>Functional divergence and horizontal transfer of type IV secretion systems
    2005 In: Molecular Biology and Evolution, ISSN 1537-1719, Vol. 22, no 5, p. 1325-1336Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93418 (URN)
    Available from: 2005-09-09 Created: 2005-09-09Bibliographically approved
    5. Recombination of pilus components in a Bartonella Type-IV secretion system
    Open this publication in new window or tab >>Recombination of pilus components in a Bartonella Type-IV secretion system
    Article in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-93419 (URN)
    Available from: 2005-09-09 Created: 2005-09-09Bibliographically approved
    6. Genome sequence of Bartonella grahamii, an environmental isolate from a Swedish wood mouse
    Open this publication in new window or tab >>Genome sequence of Bartonella grahamii, an environmental isolate from a Swedish wood mouse
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-93420 (URN)
    Available from: 2005-09-09 Created: 2005-09-09 Last updated: 2010-01-13Bibliographically approved
  • 342.
    Frank, Carolin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Alsmark, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Thollesson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Andersson, Siv
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Functional divergence and horizontal transfer of type IV secretion systems2005In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 22, no 5, p. 1325-36Article in journal (Refereed)
    Abstract [en]

    The type IV secretion system (TFSSs) is a multifunctional family of translocation pathways that mediate the transfer of DNA among bacteria and deliver DNA and proteins to eukaryotic cells during bacterial infections. Horizontal transmission has dominated the evolution of the TFSS, as demonstrated here by a lack of congruence between the tree topology inferred from components of the TFSS and the presumed bacterial species divergence pattern. A parsimony analysis suggests that conjugation represents the ancestral state and that the divergence from conjugation to secretion of effector molecules has occurred independently at multiple sites in the tree. The result shows that the nodes at which functional shifts have occurred coincide with those of horizontal gene transfers among distantly related bacteria. We suggest that it is the transfer between species that paved the way for the divergence of the TFSSs and discuss the general role of horizontal gene transfers for the evolution of novel gene functions.

  • 343. Franzen, Oscar
    et al.
    Jerlström-Hultqvist, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Castro, Elsie
    Sherwood, Ellen
    Ankarklev, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Reiner, David S.
    Palm, Daniel
    Andersson, Jan O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics.
    Andersson, Björn
    Svärd, Staffan G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Draft genome sequencing of Giardia intestinalis assemblage B isolate GS: is human giardiasis caused by two different species?2009In: PLoS Pathogens, ISSN 1553-7366, Vol. 5, no 8, p. e1000560-Article in journal (Refereed)
    Abstract [en]

    Giardia intestinalis is a major cause of diarrheal disease worldwide and two major Giardia genotypes, assemblages A and B, infect humans. The genome of assemblage A parasite WB was recently sequenced, and the structurally compact 11.7 Mbp genome contains simplified basic cellular machineries and metabolism. We here performed 454 sequencing to 16 x coverage of the assemblage B isolate GS, the only Giardia isolate successfully used to experimentally infect animals and humans. The two genomes show 77% nucleotide and 78% amino-acid identity in protein coding regions. Comparative analysis identified 28 unique GS and 3 unique WB protein coding genes, and the variable surface protein (VSP) repertoires of the two isolates are completely different. The promoters of several enzymes involved in the synthesis of the cyst-wall lack binding sites for encystation-specific transcription factors in GS. Several synteny-breaks were detected and verified. The tetraploid GS genome shows higher levels of overall allelic sequence polymorphism (0.5 versus <0.01% in WB). The genomic differences between WB and GS may explain some of the observed biological and clinical differences between the two isolates, and it suggests that assemblage A and B Giardia can be two different species.

  • 344.
    Fredga, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Reconstruction of postglacial colonization of Sorex araneus into northern Scandinavia based on karyotype studies, and the subdivision of the Abisko race into three2007In: Russian Journal of Theriology, Vol. 6, p. 85-96Article in journal (Refereed)
  • 345. Friis, Ib
    et al.
    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. Avd f systematisk botanik.
    Adsersen, Henning
    Buerger, Anne-Marie
    Patterns of plant diversity and endemism in the Horn of Africa2005In: Biologiske Skrifter, ISSN 0366-3612, Vol. 55, p. 289-314Article in journal (Refereed)
  • 346.
    Fuxelius, Hans-Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Methods and Applications in Comparative Bacterial Genomics2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Comparative studies of bacterial genomes, now counting in the hundreds, generate massive amounts of information. In order to support a systematic and efficient approach to genomic analyses, a database driven system with graphic visualization of genomic properties was developed - GenComp. The software was applied to studies of obligate intracellular bacteria. In all studies, ORFs were extracted and grouped into ORF-families. Based on gene order synteny, orthologous clusters of core genes and variable spacer ORFs were identified and extracted for alignments and computation of substitution frequencies.

    The software was applied to the genomes of six Chlamydia trachomatis strains to identify the most rapidly evolving genes. Five genes were chosen for genotyping, and close to a 3-fold higher discrimination capacity was achieved than that of serotypes.

    With GenComp as the backbone, a massive comparative analysis were performed on the variable gene set in the Rickettsiaceae, which includes Rickettsia prowazekii and Orientia tsutsugamushi, the agents of epidemic and scrub typhus, respectively. O. tsutsugamushi has the most exceptional bacterial genome identified to date; the 2.2 Mb genome is 200-fold more repeated than the 1.1 Mb R. prowazekii genome due to an extensive proliferation of conjugative type IV secretion systems and associated genes. GenComp identified 688 core genes that are conserved across 7 closely related Rickettsia genomes along with a set of 469 variably present genes with homologs in other species. The analysis indicates that up to 70% of the extensively degraded and variably present genes represent mobile genetic elements and genes putatively acquired by horizontal gene transfer. This explains the paradox of the high pseudogene load in the small Rickettsia genomes. This study demonstrates that GenComp provides an efficient system for pseudogene identification and may help distinguish genes from spurious ORFs in the many pan-genome sequencing projects going on worldwide.

    List of papers
    1. Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction
    Open this publication in new window or tab >>Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction
    2008 (English)In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 9, no 2, p. R42-Article in journal (Refereed) Published
    Abstract [en]

    Background: Pseudogenes reveal ancestral gene functions. Some obligate intracellular bacteria, such as Mycobacterium leprae and Rickettsia spp., carry substantial fractions of pseudogenes. Until recently, horizontal gene transfers were considered to be rare events in obligate host-associated bacteria. Results: We present a visualization tool that displays the relationships and positions of degraded and partially overlapping gene sequences in multiple genomes. With this tool we explore the origin and deterioration patterns of the Rickettsia pseudogenes and find that variably present genes and pseudogenes tend to have been acquired more recently, are more divergent in sequence, and exhibit a different functional profile compared with genes conserved across all species. Overall, the origin of only one-quarter of the variable genes and pseudogenes can be traced back to the common ancestor of Rickettsia and the outgroup genera Orientia and Wolbachia. These sequences contain only a few disruptive mutations and show a broad functional distribution profile, much like the core genes. The remaining genes and pseudogenes are extensively degraded or solely present in a single species. Their functional profile was heavily biased toward the mobile gene pool and genes for components of the cell wall and the lipopolysaccharide. Conclusion: Reductive evolution of the vertically inherited genomic core accounts for 25% of the predicted genes in the variable segments of the Rickettsia genomes, whereas 75% stems from the flux of the mobile gene pool along with genes for cell surface structures. Thus, most of the variably present genes and pseudogenes in Rickettsia have arisen from recent acquisitions.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96596 (URN)10.1186/gb-2008-9-2-r42 (DOI)000254659300022 ()
    Available from: 2008-01-10 Created: 2008-01-10 Last updated: 2017-12-14Bibliographically approved
    2. The genomic and metabolic diversity of Rickettsia
    Open this publication in new window or tab >>The genomic and metabolic diversity of Rickettsia
    Show others...
    2007 (English)In: Research in Microbiology, ISSN 0923-2508, E-ISSN 1769-7123, Vol. 158, no 10, p. 745-753Article in journal (Refereed) Published
    Abstract [en]

    Comparative genomics of Rickettsia and Orientia has revealed an exciting interplay between reductive evolutionary forces acting on metabolic genes in all species and proliferation of mobile genetic elements in some species. These contradictory evolutionary forces highlight the influence of chance, adaptation and host-cell exploitation during the evolution of intracellular bacteria.

    Keywords
    mobile elements, Orientia, reductive evolution, Rickettsia, type IV secretion systems
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96597 (URN)10.1016/j.resmic.2007.09.008 (DOI)000252370300004 ()18031998 (PubMedID)
    Available from: 2008-01-10 Created: 2008-01-10 Last updated: 2017-12-18Bibliographically approved
    3. Intracellular pathogens go extreme: genome evolution in the Rickettsiales
    Open this publication in new window or tab >>Intracellular pathogens go extreme: genome evolution in the Rickettsiales
    Show others...
    2007 (English)In: Trends in Genetics, ISSN 0168-9525, E-ISSN 1362-4555, Vol. 23, no 10, p. 511-520Article, review/survey (Refereed) Published
    Abstract [en]

    The Rickettsiales, a genetically diverse group of the α-Proteobacteria, include major mammalian pathogens, such as the agents of epidemic typhus, scrub typhus, ehrlichioses and heartwater disease. Sequenced genomes of this bacterial order have provided exciting insights into reductive genome evolution, antigenic variation and host cell manipulation. Recent results suggest that human pathogens emerged relatively late in the evolution of the Rickettsiales. Surprisingly, there is no association between pathogenicity and the acquisition of novel virulence genes. Here, we explore the genomic differences between members of the Rickettsiales and ask what are the changes that enable infectious agents to emerge from seemingly harmless bacteria.

    Keywords
    Bacteria, Pathogenicity, Genome, Rickettsiales, Molecular evolution, Intracellular
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96598 (URN)10.1016/j.tig.2007.08.002 (DOI)000250636600008 ()17822801 (PubMedID)
    Available from: 2008-01-10 Created: 2008-01-10 Last updated: 2017-12-14Bibliographically approved
    4. The journey to smORF-land
    Open this publication in new window or tab >>The journey to smORF-land
    2003 In: Comparative and Functional Genomics, Vol. 4, p. 537-541Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-96599 (URN)
    Available from: 2008-01-10 Created: 2008-01-10Bibliographically approved
    5. The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host–cell interaction genes
    Open this publication in new window or tab >>The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host–cell interaction genes
    Show others...
    2007 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 104, no 19, p. 7981-7986Article in journal (Refereed) Published
    Abstract [en]

    Scrub typhus is caused by the obligate intracellular rickettsia Orientia tsutsugamushi (previously called Rickettsia tsutsugamushi). The bacterium is maternally inherited in trombicuid mites and transmitted to humans by feeding larvae. We report here the 2,127,051-bp genome of the Boryong strain, which represents the most highly repeated bacterial genome sequenced to date. The repeat density of the scrub typhus pathogen is 200-fold higher than that of its close relative Rickettsia prowazekii, the agent of epidemic typhus. A total of 359 tra genes for components of conjugative type IV secretion systems were identified at 79 sites in the genome. Associated with these are >200 genes for signaling and host–cell interaction proteins, such as histidine kinases, ankyrin-repeat proteins, and tetratrico peptide-repeat proteins. Additionally, the O. tsutsugamushi genome contains >400 transposases, 60 phage integrases, and 70 reverse transcriptases. Deletions and rearrangements have yielded unique gene combinations as well as frequent pseudogenization in the tra clusters. A comparative analysis of the tra clusters within the genome and across strains indicates sequence homogenization by gene conversion, whereas complexity, diversity, and pseudogenization are acquired by duplications, deletions, and transposon integrations into the amplified segments. The results suggest intragenomic duplications or multiple integrations of a massively proliferating conjugative transfer system. Diversifying selection on host–cell interaction genes along with repeated population bottlenecks may drive rare genome variants to fixation, thereby short-circuiting selection for low complexity in bacterial genomes.

    Keywords
    Bacterial genome, Duplication, Repeats
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-14984 (URN)10.1073/pnas.0611553104 (DOI)000246461500046 ()17483455 (PubMedID)
    Available from: 2008-02-01 Created: 2008-02-01 Last updated: 2017-12-11Bibliographically approved
    6. High-resolution genotyping of Chlamydia trachomatis strains by multilocus sequence analysis
    Open this publication in new window or tab >>High-resolution genotyping of Chlamydia trachomatis strains by multilocus sequence analysis
    Show others...
    2007 (English)In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 45, no 5, p. 1410-1414Article in journal (Refereed) Published
    Abstract [en]

    Genotyping of Chlamydia trachomatis is limited by the low sequence variation in the genome, and no adequatemethod is available for analysis of the spread of chlamydial infections in the community. We have developeda multilocus sequence typing (MLST) system based on five target regions and compared it with analysis ofompA, the single gene most extensively used for genotyping. Sequence determination of 16 reference strains,comprising all major serotypes, serotypes A to L3, showed that the number of genetic variants in the fiveseparate target regions ranged from 8 to 16. The genetic variation in 47 clinical C. trachomatis isolates ofrepresentative serotypes (14 serotype D, 12 serotype E, 11 serotype G, and 10 serotype K strains) was analyzed;and the MLST system detected 32 variants, whereas 12 variants were detected by using ompA analysis.Specimens of the predominant serotype, serotype E, were differentiated into seven genotypes by MLST but intoonly two by ompA analysis. The MLST system was applied to C. trachomatis specimens from a population ofmen who have sex with men and was able to differentiate 10 specimens of one predominant ompA genotype Gvariant into four distinct MLST variants. To conclude, our MLST system can be used to discriminate C.trachomatis strains and can be applied to high-resolution molecular epidemiology.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-13844 (URN)10.1128/JCM.02301-06 (DOI)000246600300005 ()17329456 (PubMedID)
    Available from: 2008-12-03 Created: 2008-12-03 Last updated: 2017-12-11Bibliographically approved
    7. The complete genome sequence of Francisella tularensis, the causative agent of tularemia
    Open this publication in new window or tab >>The complete genome sequence of Francisella tularensis, the causative agent of tularemia
    Show others...
    2005 In: Nature Genetics, ISSN 1061-4036, Vol. 37, no 2, p. 153-9Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-96602 (URN)
    Available from: 2008-01-10 Created: 2008-01-10Bibliographically approved
  • 347.
    Fuxelius, Hans-Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Darby, Alistair C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Cho, N. H.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Visualization of pseudogenes in intracellular bacteria reveals the different tracks to gene destruction2008In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 9, no 2, p. R42-Article in journal (Refereed)
    Abstract [en]

    Background: Pseudogenes reveal ancestral gene functions. Some obligate intracellular bacteria, such as Mycobacterium leprae and Rickettsia spp., carry substantial fractions of pseudogenes. Until recently, horizontal gene transfers were considered to be rare events in obligate host-associated bacteria. Results: We present a visualization tool that displays the relationships and positions of degraded and partially overlapping gene sequences in multiple genomes. With this tool we explore the origin and deterioration patterns of the Rickettsia pseudogenes and find that variably present genes and pseudogenes tend to have been acquired more recently, are more divergent in sequence, and exhibit a different functional profile compared with genes conserved across all species. Overall, the origin of only one-quarter of the variable genes and pseudogenes can be traced back to the common ancestor of Rickettsia and the outgroup genera Orientia and Wolbachia. These sequences contain only a few disruptive mutations and show a broad functional distribution profile, much like the core genes. The remaining genes and pseudogenes are extensively degraded or solely present in a single species. Their functional profile was heavily biased toward the mobile gene pool and genes for components of the cell wall and the lipopolysaccharide. Conclusion: Reductive evolution of the vertically inherited genomic core accounts for 25% of the predicted genes in the variable segments of the Rickettsia genomes, whereas 75% stems from the flux of the mobile gene pool along with genes for cell surface structures. Thus, most of the variably present genes and pseudogenes in Rickettsia have arisen from recent acquisitions.

  • 348.
    Fuxelius, Hans-Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Darby, Alistair
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Min, Chan-Ki
    Cho, Nam-Hyuk
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    The genomic and metabolic diversity of Rickettsia2007In: Research in Microbiology, ISSN 0923-2508, E-ISSN 1769-7123, Vol. 158, no 10, p. 745-753Article in journal (Refereed)
    Abstract [en]

    Comparative genomics of Rickettsia and Orientia has revealed an exciting interplay between reductive evolutionary forces acting on metabolic genes in all species and proliferation of mobile genetic elements in some species. These contradictory evolutionary forces highlight the influence of chance, adaptation and host-cell exploitation during the evolution of intracellular bacteria.

  • 349. Fuxelius, Hans-Henrik
    et al.
    Davids, Wagied
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Molecular Evolution.
    Gumaelius, Gustav
    Andersson, Siv
    To code or not to code: Sequence evolution in RickettsiaManuscript (Other academic)
  • 350. Galtier, N.
    et al.
    Nabholz, Benoit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Biology.
    Glemin, S.
    Hurst, G. D. D.
    Mitochondrial DNA as a marker of molecular diversity: a reappraisal2009In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 18, no 22, p. 4541-4550Article, review/survey (Refereed)
    Abstract [en]

    Over the last three decades, mitochondrial DNA has been the most popular marker of molecular diversity, for a combination of technical ease-of-use considerations, and supposed biological and evolutionary properties of clonality, near-neutrality and clock-like nature of its substitution rate. Reviewing recent literature on the subject, we argue that mitochondrial DNA is not always clonal, far from neutrally evolving and certainly not clock-like, questioning its relevance as a witness of recent species and population history. We critically evaluate the usage of mitochondrial DNA for species delineation and identification. Finally, we note the great potential of accumulating mtDNA data for evolutionary and functional analysis of the mitochondrial genome.

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