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  • 101.
    Nordin, Anders
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Owe-Larsson, Björn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Aspicilia berntii, a new name for a poorly known species2008In: The Lichenologist, ISSN 0024 2829, Vol. 40, no 2, p. 127-133Article in journal (Other (popular science, discussion, etc.))
    Abstract [en]

    The new name Aspicilia berntii is proposed to accomodate Lecanora mastoidea Lynge in Aspicilia and a lectotype is designated. Additional characters are added to the species description and a comparison is made with similar species. The species is reported as new to Scandinavia with localities in northern Norway. An assessement of the phylogenetic relationships, based on a split network analysis of ITS sequences, places A. berntii close to A. verrucigera in the A. cinerea group

  • 102.
    Nordin, Anders
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology.
    Owe-Larsson, Björn
    Endocarpon moenium belongs in Acarosporaceae2009In: Graphis Scripta, ISSN 0901-7593, Vol. 21, no 1, p. 21-22Article in journal (Refereed)
    Abstract [en]

    ITS, LSU and mtSSU sequences indicate that Endocarpon moenium belongs in Acarosporaceae. The name Acarospora moenium (Vain.) Räsänen is available and could be adopted awaiting a more definite placement of the species.

  • 103.
    Oh, Il-Chan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Anderberg, A. -L.
    Schonenberger, J.
    Anderberg, A. A.
    Comparative seed morphology and character evolution in the genus Lysimachia (Myrsinaceae) and related taxa2008In: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110, Vol. 271, no 3-4, p. 177-197Article in journal (Refereed)
    Abstract [en]

    We investigated seed morphology in 34 species of the genus Lysimachia and in 14 species and two subspecies of six additional genera (Anagallis, Ardisiandra, Asterolinon, Glaux, Pelletiera, Trientalis), which have been shown to be closely related to, or are placed within Lysimachia in previous molecular studies. We studied seed shape, seed coat structure, and seed coat surface patterns. Three major types of seed shape were identified: (1) sectoroid, (2) polyhedral, and (3) coarsely rugose with concave hilar area. In addition, seeds may be keeled or winged. The outer layer of the seed coat is either sponge-like and adhering only loosely to the inner seed coat or it is thin and tightly adhering to the underlying tissue. Seed surface patterns can be divided into six main types: (1) reticulate, (2) tuberculate, (3) vesiculose, (4) colliculate, (5) undulate, or (6) poroid-alveolate. Seed surface patterns are mostly congruent with molecular phylogenetic relationships. A reticulate surface pattern is diagnostic of, e.g. Lysimachia subgenera Palladia and Hawaiian Lysimachiopsis. Mapping seed characters onto a recent phylogenetic tree, reveals that they provide potentially synapomorphic character states for various subclades of Lysimachia. Salient examples include a rugose seed shape, which turns out to be synapomorphic for the clade comprising the genus Pelletiera plus Asterolinon linum-stellatum and a sponge-like outer seed coat layer, which characterizes a clade with Lysimachia vulgaris, L. thyrsiflora, and L. terrestris, with an analogue that apparently evolved in parallel in Trientalis europaea. We also discuss possible habitat factors that may have favored the independent evolution of particular seed types such as winged seeds in various lineages.

  • 104. Owe-Larsson, Björn
    et al.
    Nordin, Anders
    Uppsala University, Music and Museums, Museum of Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Aspicilia2007In: Lichen Flora of the Greater Sonoran Desert Region: Volume 3: balance of the microlichens and the lichenicolous fungi / [ed] TH Nash III, C Gries, F Bungartz, Tempe: Lichens Unlimited, Arizona State University , 2007Chapter in book (Refereed)
  • 105. Oxelman, Bengt
    et al.
    Backlund, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Bremer, Birgitta
    Relationships of the Buddlejaceae s.l. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF andrbcL sequence data1999In: Systematic Botany, Vol. 24, no 2, p. 164-182Article in journal (Refereed)
  • 106.
    Oxelman, Bengt
    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.
    Kornhall, Per
    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.
    Norman, Eliane
    Buddlejaceae2004In: The families and genera of flowering plants, Springer-Verlag, Berlin , 2004, p. 39-44Chapter in book (Refereed)
  • 107. Oxelman, Bengt
    et al.
    Kornhall, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Olmstead, Richard G.
    Bremer, Birgitta
    Further disintegration of Scrophulariaceae.Manuscript (Other (popular science, discussion, etc.))
  • 108.
    Oxelman, Bengt
    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. Systematisk Botanik.
    Kornhall, Per
    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.
    Olmstead, Richard G.
    Bremer, Birgitta
    Further disintegration of Scrophulariaceae2005In: TAXON, Vol. 54, p. 411-425Article in journal (Refereed)
  • 109.
    Oxelman, Bengt
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Popp, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lazkov, Georgy
    Frajman, Bozo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Erixon, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Långström, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Rautenberg, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Heidari, Nahid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Treelike and reticulate phylogeny of Sileneae and its implications on taxonomy2005In: XVII International Botanical Congress: abstracts : Vienna, Austria, Europe, Austria Center Vienna 17-23 July 2005 : 100 Years after the II IBC in Vienna 1905, 2005, p. 11-11Conference paper (Other academic)
  • 110.
    Oxelman, Bengt
    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.
    Yoshikawa, Nori
    McConaughy, Betty L
    Luo, Jie
    Denton, Amy L
    Hall, Benjamin D
    RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids.2004In: Molecular Phylogenetics and Evolution, Vol. 32, no 2, p. 462-479Article in journal (Refereed)
    Abstract [en]

    Two, apparently functional, paralogues of the RPB2 gene, which encodes the second largest subunit of RNA polymerase II, are shown to be present in two major groups of asterid plants. Although all other land plants surveyed so far have been found to have only one of these two copies, the RPB2 gene phylogeny inferred from the 3' half of the gene for 35 angiosperm taxa and six other land plants indicates that the duplication of the RPB2 gene occurred earlier than the time for origin of the asterid group, probably near the origin of "core eudicots." The d copy is present in all plants which are unambiguously assigned to the core eudicots, whereas the I copy is retained only in the lamiid clade, Ericales, and Escallonia, all belonging to the asterid group of plants. Both parsimony and likelihood analyses of sequences from the 3' half of the gene give strong bootstrap support for these conclusions. There is no support for monophyly of the taxa having both copies. Thus, numerous losses of one of the copies must be inferred. Structurally, both paralogues appear functional, and transcription is demonstrated for both copies. In the lamiid group, the d copy has lost introns 18-23. The well supported phylogenetic relationships implied by the RPB2 gene phylogeny are largely congruent with well supported phylogenetic hypotheses based on other sequence data. However, Ilex, usually assigned to the campanuliid clade, is instead supported as being a member of the lamiid clade, both from sequence data and the presence of an I copy as well as the loss of introns 18-23 in the d copy. Escallonia, supported as a member of the campanuliid clade both by RPB2-d-sequences and previously published DNA sequence data, has all the introns 18-23 in its d copy, as do all other members studied from the campanuliid group. We used the Markov Chain Monte Carlo (MCMC) approach of the MrBayes program to implement Maximum Likelihood bootstrapping. Under the same model of evolution, bootstrapping frequencies are significantly lower than the Bayesian posterior probabilities inferred from the MCMC chain.

    PMID: 15223030 [PubMed - indexed for MEDLINE]

  • 111. Peacock, Christopher S
    et al.
    Seeger, Kathy
    Harris, David
    Murphy, Lee
    Ruiz, Jeronimo C
    Quail, Michael A
    Peters, Nick
    Adlem, Ellen
    Tivey, Adrian
    Aslett, Martin
    Kerhornou, Arnaud
    Ivens, Alasdair
    Fraser, Audrey
    Rajandream, Marie-Adele
    Carver, Tim
    Norbertczak, Halina
    Chillingworth, Tracey
    Hance, Zahra
    Jagels, Kay
    Moule, Sharon
    Ormond, Doug
    Rutter, Simon
    Squares, Rob
    Whitehead, Sally
    Rabbinowitsch, Ester
    Arrowsmith, Claire
    White, Brian
    Thurston, Scott
    Bringaud, Frédéric
    Baldauf, Sandra L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Faulconbridge, Adam
    Jeffares, Daniel
    Depledge, Daniel P
    Oyola, Samuel O
    Hilley, James D
    Brito, Loislene O
    Tosi, Luiz R O
    Barrell, Barclay
    Cruz, Angela K
    Mottram, Jeremy C
    Smith, Deborah F
    Berriman, Matthew
    Comparative genomic analysis of three Leishmania species that cause diverse human disease.2007In: Nature Genetics, ISSN 1061-4036, E-ISSN 1546-1718, Vol. 39, no 7, p. 839-847Article in journal (Refereed)
    Abstract [en]

    Leishmania parasites cause a broad spectrum of clinical disease. Here we report the sequencing of the genomes of two species of Leishmania: Leishmania infantum and Leishmania braziliensis. The comparison of these sequences with the published genome of Leishmania major reveals marked conservation of synteny and identifies only 200 genes with a differential distribution between the three species. L. braziliensis, contrary to Leishmania species examined so far, possesses components of a putative RNA-mediated interference pathway, telomere-associated transposable elements and spliced leader–associated SLACS retrotransposons. We show that pseudogene formation and gene loss are the principal forces shaping the different genomes. Genes that are differentially distributed between the species encode proteins implicated in host-pathogen interactions and parasite survival in the macrophage.

  • 112.
    Popp, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Disentangling the Reticulate History of Polyploids in Silene (Caryophyllaceae)2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    DNA sequences from the rps16 intron and the psbE-petL spacer from the chloroplast genome, the ribosomal nuclear ITS region, and introns from the low copy nuclear genes RPA2, RPB2, RPD2a and RPD2b, are in different combinations used to infer phylogenetic relationships in Sileneae (Caryophyllaceae). Used in concert, the biparentally inherited nuclear regions are useful to distinguish between paralogy due to allopolyploidy and single gene duplications, respectively, because the latter are not expected to give rise to repeated phylogenetic patterns in potentially unlinked sequence regions. In addition, the sequences resolve previously poorly known relationships in the tribe Sileneae. Several independent losses and incomplete concerted evolution are inferred between the two RPD2 paralogues in a subgroup of Silene.

    An allopolyploid origin is suggested for the tetraploid S. aegaea, with the maternal ancestor from the diploid S. pentelica lineage, and the paternal contributor from the diploid S. sedoides lineage.

    Silene involucrata originated as an allotetraploid with the diploid lineage of Arctic S. uralensis as cytoplasmic donor and the diploid Siberian/Northeast Asian S. ajanensis lineage as pollen donor. A subsequent allopolyploidization with the S. ajanensis lineage as pollen donor and the tetraploid S. involucrata lineage as cytoplasmic donor resulted in the hexaploid lineage of S. sorensenis sensu lato.

    A monophyletic origin of the North American polyploids is rejected. One lineage consists of tetraploid S. menziesii and its diploid allies. A separate lineage leads to a clade consisting of both diploid and polyploid Arctic, European and Asian taxa in addition to the majority of the North American polyploids. The tetraploid S. californica and the hexaploid S. hookeri are derived from separate allopolyploidization events between these two lineages.

    List of papers
    1. Inferring the history of the polyploid Silene aegaea (Caryophyllaceae) using plastid and homoeologous nuclear DNA sequences
    Open this publication in new window or tab >>Inferring the history of the polyploid Silene aegaea (Caryophyllaceae) using plastid and homoeologous nuclear DNA sequences
    2001 In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, Vol. 20, no 3, p. 474-481Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91241 (URN)
    Available from: 2004-01-13 Created: 2004-01-13Bibliographically approved
    2. Evolution of a RNA polymerase gene family in Silene (Caryophyllaceae) - incomplete concerted evolution and topological congruence among paralogues
    Open this publication in new window or tab >>Evolution of a RNA polymerase gene family in Silene (Caryophyllaceae) - incomplete concerted evolution and topological congruence among paralogues
    2004 (English)In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 53, no 6, p. 914-932Article in journal (Refereed) Published
    Abstract [sv]

    Four low-copy nuclear DNA intron regions from the second largest subunits of the RNA polymerase gene family (RPA2, RPB2, RPD2a, and RPD2b), the internal transcribed spacers (ITSs) from the nuclear ribosomal regions, and the rps16 intron from the chloroplast were sequenced and used in a phylogenetic analysis of 29 species from the tribe Sileneae (Caryophyllaceae). We used a low stringency nested polymerase chain reaction (PCR) approach to overcome the difficulties of constructing specific primers for amplification of the low copy nuclear DNA regions. Maximum parsimony analyses resulted in largely congruent phylogenetic trees for all regions. We tested overall model congruence in a likelihood context using the software PLATO and found that ITSs, RPA2, and RPB2 deviated from the maximum likelihood model for the combined data. The topology parameter was then isolated and topological congruence assessed by nonparametric bootstrapping. No strong topological incongruence was found. The analysis of the combined data sets resolves previously poorly known major relationships within Sileneae. Two paralogues of RPD2 were found, and several independent losses and incomplete concerted evolution were inferred. The among-site rate variation was significantly lower in the RNA polymerase introns than in the rps16 intron and ITSs, a property that is attractive in phylogenetic analyses.

    Keywords
    DNA-Directed RNA Polymerases/*genetics, Evolution; Molecular, Introns, Phylogeny, Polymerase Chain Reaction, Research Support; Non-U.S. Gov't, Silene/*genetics
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-91242 (URN)10.1080/10635150490888840 (DOI)15764560 (PubMedID)
    Available from: 2004-01-13 Created: 2004-01-13 Last updated: 2017-12-14Bibliographically approved
    3. Origin and evolution of a circumpolar polyploid species complex in Silene (Caryophyllaceae)
    Open this publication in new window or tab >>Origin and evolution of a circumpolar polyploid species complex in Silene (Caryophyllaceae)
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-91243 (URN)
    Available from: 2004-01-13 Created: 2004-01-13 Last updated: 2010-01-13Bibliographically approved
    4. Origin and evolution of North American Polyploid Silene (Caryophyllaceae)
    Open this publication in new window or tab >>Origin and evolution of North American Polyploid Silene (Caryophyllaceae)
    2007 (English)In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 94, no 3, p. 330-349Article in journal (Refereed) Published
    Abstract [en]

    Nuclear DNA sequences from introns of the low-copy nuclear gene family encoding the second largest subunit of RNA polymerases and the ribosomal internal transcribed spacer (ITS) regions, combined with the psbE-petL spacer and the rps16 intron from the chloroplast genome were used to infer origins and phylogenetic relationships of North American polyploid Silene species and their closest relatives. Although the vast majority of North American Silene species are polyploid, which contrasts to the diploid condition dominating in other parts of the world, the phylogenetic analyses rejected a single origin of the North American polyploids. One lineage consists of tetraploid Silene menziesii and its diploid allies. A second lineage, Physolychnis s.l., consists of Arctic, European, Asian, and South American taxa in addition to the majority of the North American polyploids. The hexaploid S. hookeri is derived from an allopolyploidization between these two lineages. The tetraploid S. nivea does not belong to any of these lineages, but is closely related to the European diploid S. baccifera. The poor resolution within Physolychnis s.l. may be attributed to rapid radiation, recombination among homoeologues, homoplasy, or any combination of these factors. No extant diploid donors could be identified in Physolychnis s.l.

    Keywords
    Caryophyllaceae, cpDNA, low-copy nuclear DNA, molecular phylogeny, North America, rapid radiation, RNA polymerase, Silene
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-91244 (URN)10.3732/ajb.94.3.330 (DOI)000245097500005 ()
    Available from: 2004-01-13 Created: 2004-01-13 Last updated: 2017-12-14Bibliographically approved
  • 113.
    Popp, Magnus
    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.
    Erixon, Per
    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.
    Eggens, Frida
    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.
    Origin and evolution of a circumpolar polyploid species complex in Silene (Caryophyllaceae).2005In: Systematic Botany, Vol. 30, p. 302-311Article in journal (Refereed)
  • 114.
    Popp, Magnus
    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.
    Origin and evolution of North American Polyploid Silene (Caryophyllaceae)2007In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 94, no 3, p. 330-349Article in journal (Refereed)
    Abstract [en]

    Nuclear DNA sequences from introns of the low-copy nuclear gene family encoding the second largest subunit of RNA polymerases and the ribosomal internal transcribed spacer (ITS) regions, combined with the psbE-petL spacer and the rps16 intron from the chloroplast genome were used to infer origins and phylogenetic relationships of North American polyploid Silene species and their closest relatives. Although the vast majority of North American Silene species are polyploid, which contrasts to the diploid condition dominating in other parts of the world, the phylogenetic analyses rejected a single origin of the North American polyploids. One lineage consists of tetraploid Silene menziesii and its diploid allies. A second lineage, Physolychnis s.l., consists of Arctic, European, Asian, and South American taxa in addition to the majority of the North American polyploids. The hexaploid S. hookeri is derived from an allopolyploidization between these two lineages. The tetraploid S. nivea does not belong to any of these lineages, but is closely related to the European diploid S. baccifera. The poor resolution within Physolychnis s.l. may be attributed to rapid radiation, recombination among homoeologues, homoplasy, or any combination of these factors. No extant diploid donors could be identified in Physolychnis s.l.

  • 115.
    Popp, Magnus
    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.
    The significance of reticulate evolution in the phylogenetic history of Sileneae (Caryophyllaceae).2004In: Plant evolution in Mediterranean Climate Zones.: IXth IOPB Meeting, Valencia,, 2004, p. 65-Conference paper (Other scientific)
  • 116.
    Rautenberg, Anja
    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. Systematisk botanik.
    Filatov, Dmitry
    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. Systematisk botanik.
    Phylogenetic origins of dioecy in Silene2005In: Abstracts IBC XVII, 2005Conference paper (Other scientific)
    Abstract [en]

    The aim of this project is to provide a phylogenetic/taxonomic framework for the evolution of dioecy within Silene (Caryophyllaceae). There are several dioecious taxa within the genus, traditionally classified in the sections Elisanthe and Otites. To understand how dioecy has evolved, these dioecious taxa need to be compared with their closest relatives. Available data suggest that the dioecious taxa within Elisanthe do not form a monophyletic group with the hermaphrodites in the section. Instead they seem more related to section Conoimorpha. This study is based on data from several Silene genes: (i) a gene sex-linked in the dioecious Elisanthe species (SlXY1) and a homologous autosomal gene in hermaphroditic taxa, (ii) intron sequences from the genes encoding the second largest subunits in the RNA polymerase gene family (RPA2, RPB2, RPD2) and (iii) chloroplast DNA. Remarkably, preliminary data suggest recombination between phylogenetically distant SIXY1 lineages.

  • 117.
    Rautenberg, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Filatov, Dmitry
    Department of Plant Sciences, University of Oxford, UK.
    Svennblad, Bodil
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Mathematical Statistics.
    Heidari, Nahid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Institutionen för växt- och miljövetenskaper, Göteborgs universitet.
    Conflicting phylogenetic signals in the SlX1/Y1 gene in Silene2008In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 8, no 1, p. 299-Article in journal (Refereed)
    Abstract [en]

    Background: Increasing evidence from DNA sequence data has revealed that phylogenies based on different genes may drastically differ from each other. This may be due to either inter- or intralineage processes, or to methodological or stochastic errors. Here we investigate a spectacular case where two parts of the same gene (SlX1/Y1) show conflicting phylogenies within Silene (Caryophyllaceae). SlX1 and SlY1 are sex-linked genes on the sex chromosomes of dioecious members of Silene sect. Elisanthe.

    Results: We sequenced the homologues of the SlX1/Y1 genes in several Sileneae species. We demonstrate that different parts of the SlX1/Y1 region give different phylogenetic signals. The major discrepancy is that Silene vulgaris and S. sect. Conoimorpha (S. conica and relatives) exchange positions. To determine whether gene duplication followed by recombination (an intralineage process) may explain the phylogenetic conflict in the Silene SlX1/Y1 gene, we use a novel probabilistic, multiple primer-pair PCR approach. We did not find any evidence supporting gene duplication/loss as explanation to the phylogenetic conflict.

    Conclusion: The phylogenetic conflict in the Silene SlX1/Y1 gene cannot be explained by paralogy or artefacts, such as in vitro recombination during PCR. The support for the conflict is strong enough to exclude methodological or stochastic errors as likely sources. Instead, the phylogenetic incongruence may have been caused by recombination of two divergent alleles following ancient interspecific hybridization or incomplete lineage sorting. These events probably took place several million years ago. This example clearly demonstrates that different parts of the genome may have different evolutionary histories and stresses the importance of using multiple genes in reconstruction of taxonomic relationships.

  • 118.
    Rautenberg, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Hathaway, Louise
    Oxelman, Bengt
    Prentice, Honor C.
    Phylogenetic relationships of Silene section Elisanthe (Caryophyllaceae) as inferred from chloroplast and nuclear DNA sequencesManuscript (Other academic)
  • 119.
    Rautenberg, Anja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Hathaway, Louise
    Prentice, Honor C.
    Oxelman, Bengt
    Phylogenetic relationships and optimal genealogical species delimitations of Silene section Melandrium (Caryophyllaceae)Manuscript (Other academic)
  • 120.
    Rautenberg, Anja
    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. Systematisk botanik.
    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. Systematisk botanik.
    Recombination between distinct lineages in Silene?2007In: Abstracts - XI Congress European Society for Evolutionary Biology, 2007Conference paper (Other scientific)
    Abstract [en]

    One of the challenges of evolutionary biologists is to reconstruct phylogenies, which are essential in order to understand the mechanisms of evolution. In systematic research, often only very small portions of the total genome are analyzed and assumed to reflect the species phylogeny. In principle, however, the resulting phylogenies do not reflect the history of the species, but rather the history of the individual DNA regions themselves. Sometimes the phylogenies show incongruences when based on different genomes, different genes, different copies of a gene, or different parts of a gene. These conflicts can either reflect complex phylogenetic patterns, or simply highlight errors and problems in lab procedures and/or phylogenetic methods. An example of a plant taxon with cases of conflicting gene phylogenies is Sileneae DC. (Caryophyllaceae). Silene section Elisanthe contains dioecious taxa with a X/Y chromosome system similar to that in humans. In order to understand the evolution of dioecy in Silene section Elisanthe, we compare the dioeciuos taxa with their closest relatives, using several molecular markers. We also test the utility of the potentially useful low-copy nuclear gene SlX1/SlY1, and its homologues in hermaphroditic taxa. We discovered that Elisanthe change places in the phylogenetic trees based on different parts of the SlX1/SlY1 alignment. We show that this may indicate that recombination between phylogenetically distant SlX1/SlY1 lineages has taken place.

  • 121.
    Razafimandimbison, Sylvain G
    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.
    Kellogg, Elisabeth A
    Bremer, Birgitta
    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.
    Recent origin and phylogenetic utility of divergent ITS putative pseudogenes: A case study from Naucleeae (Rubiaceae)2004In: Systematic Biology, Vol. 53, no 2, p. 177-192Article in journal (Refereed)
  • 122.
    Razafimandimbison, Sylvain G
    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.
    Moog, Joachim
    Lantz, Henrik
    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.
    Maschwitz, Ulrich
    Bremer, Birgitta
    Re-assessment of monophyly, evolution of myrmecophytism, and rapid radiation in Neonauclea s.s. (Rubiaceae)2005In: Molecular Phylogenetics and Evolution, Vol. 34, p. 334-354Article in journal (Refereed)
  • 123. Razafimandimbison, Sylvain
    et al.
    Lantz, Henrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Bremer, Birgitta
    New combinations and names in Peponidium and Pyrostria (Rubiaceae, Vanguerieae)2007In: Novon, ISSN 1055-3177, E-ISSN 1945-6174, Vol. 17, no 4, p. 516-521Article in journal (Refereed)
    Abstract [en]

    The newly circumscribed dioeeious group (sensu Razafimandimbison et al.) of tribe Vanguerieae in the subfamily Ixoroideae (Rubiaceae) comprises over 200 species classified in four morphologically distinct genera: Cyclophyllum Hooker f., Peponidium (Baillon) Arenes, Pyrostria Commerson ex jussieu, and one new genus affined to species of Canthium subg. Bullockia Bridson. Here, we present a total of 3 7 new combinations, 20 of which are in Peponidium: P. alleizettei (Dubard & Dop) Razafimandimbison, Lantz & B. Bremer, P. andringitrense (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. ankaranense (Arenes ex Cavaco) Razafimandimbison, Lantz & B. Bremer, A anoveanum (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. arenesianum (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. blepharodon (Arenes ex Cavaco) Razafimandimbison, Lantz & B. Bremer, P. boinense (Arenes ex Cavaco) Razafimandimbison, Lantz & B. Bremer, P. bosseri (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. buxifolium (Baker) Razafimandimbison, Lantz & B. Bremer (lectotypified here), P. cystiporon (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. decaryi (Homolle ex Cavaco) Razafimandimbison, Lantz & B. Bremer, P. humbertianum (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. latiflorum (Homolle ex Cavaco) Razafimandimbison, Lantz & B. Bremer, P. mandrarense (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. marojejyense (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. sahafaryense (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. subevenium (K. Schumann) Razafimandimbison, Lantz & B. Bremer, P. tamatavense (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. venulosum (Boivin ex Baillon) Razafimandimbison, Lantz & B. Bremer, and P. viguieri (Homolle ex Cavaco) Razafimandimbison, Lantz & B. Bremer. The other 17 new combinations are in Pyrostria: P. ambongensis (Homolle ex Arenes) Razafimandimbison, Lantz & B. Bremer, P. ampijoroensis (Arenes) Razafimandimbison, Lantz & B. Bremer, P. ankaranensis (Cavaco) Razafirnandimbison, Lantz & B. Bremer, P. antsalovensis (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. asosa (Arenes) Razafiniandimbison, Lantz & B. Bremer, P. capuronii (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. ixorifolia (Homolle ex Arenes) Razafimandimbison, Lantz & B. Bremer, P. longiflora (Cavaco) Razafiniandimbison, Lantz & B. Bremer, P. neriifolia (Homolle ex Arenes) Razafimandimbison, Lantz & B. Bremer, P. oleifolia (Homolle ex Arenes) Razafimandimbison, Lantz & B. Bremer, P. perrieri (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. revolula (Balfour f.) Razafimandimbison, Lantz & B. Bremer, P. richardiae (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. sambavensis (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. suarezensis (Cavaco) Razafimandimbison, Lantz & B. Bremer, P. tulearensis (Cavaco) Razafimandimbison, Lantz & B. Bremer, and P. verdcourtii (Cavaco) Razafimandimbison, Lantz & B. Bremer. Finally, three new names, Peponidium sakalavense Razafimandimbison, Lantz & B. Bremer, Pyrostria antsirananensis Razafimandimbison, Lantz & B. Bremer, and Pyrostria louvelii Razafimandimbison, Lantz & B. Bremer, are published here.

  • 124.
    Reese Næsborg, Rikke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Disentangling Lecania2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on phylogenetic, taxonomic, ecological, and conservation aspects of the crustose lichen genus Lecania (Ramalinaceae, lichenized Ascomycota). Lecania has previously been defined on basis of relatively few morphological characters, and the genus had never been treated in molecular phylogenies.

    The molecular phylogeny of the genus is inferred from DNA sequences. Twenty-five species traditionally placed in Lecania are included in the study along with 21 species from closely related genera. Lecania is a polyphyletic genus. A well-supported monophyletic group containing 16 Lecania species, including the type species L. fuscella is discovered, i.e. Lecania s. str. Nine species formerly included in Lecania do not belong in the genus. A new species, L. belgica, is described.

    The relationships of a group of morphologically similar Lecania species, i.e. the L. cyrtella group are investigated using morphological and molecular methods. Haplotype network and phylogenetic analyses indicate that the included species, as conceived in the morphological examinations, all are monophyletic. Two new species, L. leprosa and L. madida, are described, L. proteiformis is resurrected from synonymy, and the known range of L. prasinoides is greatly expanded.

    The type species Lecania fuscella has become endangered in many countries. Twelve localities in Sweden where the species had been found historically are investigated, but L. fuscella is only recovered in one locality. The species composition in these 12 localities, 58 old and 5 new collections with L. fuscella is determined and analyzed. The vegetation community differs between the old and the new collections, and between the locality where the species is recovered and those where it is not. Lecania fuscella has not been able to adapt to environmental changes and now only appears in a specific type of vegetation community. The phylogenetic diversity of the species is calculated, but does not reflect the species’ evolutionary potential.

    List of papers
    1. Molecular phylogeny of the genus Lecania (Ramalinaceae, lichenized Ascomycota)
    Open this publication in new window or tab >>Molecular phylogeny of the genus Lecania (Ramalinaceae, lichenized Ascomycota)
    2007 (English)In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 111, no 5, p. 581-591Article in journal (Refereed) Published
    Abstract [en]

    The molecular phylogeny of the lichen genus Lecaniawas investigated using nucleotide sequences from the mt-SSU rRNA, the ITS region of the nu-rDNA, and the RNA polymerase II second largest subunit. Forty-six species representing Lecania and other genera likely to influence the phylogeny were included in the study. Phylogenetic reconstructions were carried out using Bayesian inference, ML, and MP approaches. Lecania, as traditionally circumscribed, is not a monophyletic genus. However, a monophyletic group containing a large number of Lecania species, including the type species L. fuscella, was discovered in the analysis, and recognition of Lecania sensu stricto is suggested. L. baeomma, L. glauca, L. gerlachei, L. brialmontii, L. racovitzae, L. hyalina (alias Biatora globulosa), L. chlorotiza, L. naegelii, and L. furfuracea do not belong in Lecania s. str., although the latter two are closely related to Lecania s. str. Representatives of the genus Bilimbia form a well-supported group, as does the ‘Thamnolecania’ group containing the Antarctic ‘Lecania’ species, L. gerlachei, L. brialmontii, and L. racovitzae. An alternative to recognizing these two genera would be a wider circumscription of Bilimbia to include the ‘Thamnolecania’ group as well as affiliated taxa.

    Keywords
    ITS region, Lecanorales, Lichens, MCMC, RNA polymerase II second largest subunit, SSU mt-rRNA gene
    National Category
    Biological Systematics
    Research subject
    Biology with specialization in Systematics
    Identifiers
    urn:nbn:se:uu:diva-96136 (URN)10.1016/j.mycres.2007.03.001 (DOI)000247865900005 ()17512709 (PubMedID)
    Available from: 2007-09-05 Created: 2007-09-05 Last updated: 2018-03-29
    2. Lecania belgica van den Boom & Reese Næsborg, a new saxicolous species from Western Europe
    Open this publication in new window or tab >>Lecania belgica van den Boom & Reese Næsborg, a new saxicolous species from Western Europe
    2007 (English)In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 39, no 6, p. 499-503Article in journal (Refereed) Published
    Abstract [en]

    A new species, Lecania belgica, is described and illustrated. It is a saxicolous lichen known only from the type locality in Belgium. It is characterized by apothecia with pruinose, irregularly undulating discs, relatively short ascospores, and by having 12-16 spores in the asci. It was found on mortar together with Diplotomma alboatrum.

    Keywords
    Belgium, ecology, saxicolous, species nova, taxonomy
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96137 (URN)10.1017/S0024282907007244 (DOI)000252672500001 ()
    Available from: 2007-09-05 Created: 2007-09-05 Last updated: 2017-12-14Bibliographically approved
    3. Taxonomic revision of the Lecania cyrtella group (Ramalinaceae, lichenized Ascomycota) based on molecular and morphological evidence
    Open this publication in new window or tab >>Taxonomic revision of the Lecania cyrtella group (Ramalinaceae, lichenized Ascomycota) based on molecular and morphological evidence
    2008 (English)In: Mycologia, ISSN 0027-5514, E-ISSN 1557-2536, Vol. 100, no 3, p. 397-416Article in journal (Refereed) Published
    Abstract [en]

    This investigation elucidates relationships within the Lecania Crytella group (Ramalinaceae lichenized Ascomycota) by employing morphological: anatomical and molecular methods. The morphological studies included eleven species of Lecania, L. cyrtella, L. cyrtellina, L. dubitans, L. erysibe, L. hutchinsiae, L. Leprosa, L. madida, L. prasinoides, L. sambrucina, L. sordida and L. sylvestris, and a key to the Species Plus species descriptions are provided. Lecania madida, a new species from the Pacific Northwest of North America, L. leprosa, a new species from eastern Europe, and L. sordida, a new species from Europe, are described here. The known range of L. prasinoides is greatly extended to include the Baltic countries, Nordic countries and western Canada. Lectotypes are designated for L. cyrtella and L. sambucina. Molecular relationships within the group were examined with haplotype network estimations and phylogenetic reconstructions. Part of the IGS region as well as the complete ITS region were sequenced and analyzed. Both the haplotype network and the phylogenetic analyses indicate that the included species, as conceived in the morphological examinations, all are monophyletic.

    Keywords
    haplotype network analysis, key to species, lichens, maximum parsimony; new species, species descriptions, statistical parsimony
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96138 (URN)10.3852/07-080R (DOI)000258494800006 ()
    Available from: 2007-09-05 Created: 2007-09-05 Last updated: 2017-12-14Bibliographically approved
    4. The phylogenetic diversity of Lecania fuscella does not reflect its evolutionary potential
    Open this publication in new window or tab >>The phylogenetic diversity of Lecania fuscella does not reflect its evolutionary potential
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-96139 (URN)
    Available from: 2007-09-05 Created: 2007-09-05 Last updated: 2010-01-14Bibliographically approved
  • 125.
    Reese Næsborg, Rikke
    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. Systematisk botanik.
    Lecania - Phylogeny, Generic Delimitation, Ecology, and A Revision Of The Swedish Species2004In: Book Of Abstracts Of The 5th IAL Symposium: Lichens In Focus, 2004Conference paper (Refereed)
  • 126.
    Reese Næsborg, Rikke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Taxonomic revision of the Lecania cyrtella group (Ramalinaceae, lichenized Ascomycota) based on molecular and morphological evidence2008In: Mycologia, ISSN 0027-5514, E-ISSN 1557-2536, Vol. 100, no 3, p. 397-416Article in journal (Refereed)
    Abstract [en]

    This investigation elucidates relationships within the Lecania Crytella group (Ramalinaceae lichenized Ascomycota) by employing morphological: anatomical and molecular methods. The morphological studies included eleven species of Lecania, L. cyrtella, L. cyrtellina, L. dubitans, L. erysibe, L. hutchinsiae, L. Leprosa, L. madida, L. prasinoides, L. sambrucina, L. sordida and L. sylvestris, and a key to the Species Plus species descriptions are provided. Lecania madida, a new species from the Pacific Northwest of North America, L. leprosa, a new species from eastern Europe, and L. sordida, a new species from Europe, are described here. The known range of L. prasinoides is greatly extended to include the Baltic countries, Nordic countries and western Canada. Lectotypes are designated for L. cyrtella and L. sambucina. Molecular relationships within the group were examined with haplotype network estimations and phylogenetic reconstructions. Part of the IGS region as well as the complete ITS region were sequenced and analyzed. Both the haplotype network and the phylogenetic analyses indicate that the included species, as conceived in the morphological examinations, all are monophyletic.

  • 127.
    Reese Næsborg, Rikke
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    The phylogenetic diversity of Lecania fuscella does not reflect its evolutionary potentialManuscript (Other (popular science, discussion, etc.))
  • 128.
    Reese Næsborg, Rikke
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Ekman, Stefan
    Uppsala University, Music and Museums, Museum of Evolution.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Molecular phylogeny of the genus Lecania (Ramalinaceae, lichenized Ascomycota)2007In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 111, no 5, p. 581-591Article in journal (Refereed)
    Abstract [en]

    The molecular phylogeny of the lichen genus Lecaniawas investigated using nucleotide sequences from the mt-SSU rRNA, the ITS region of the nu-rDNA, and the RNA polymerase II second largest subunit. Forty-six species representing Lecania and other genera likely to influence the phylogeny were included in the study. Phylogenetic reconstructions were carried out using Bayesian inference, ML, and MP approaches. Lecania, as traditionally circumscribed, is not a monophyletic genus. However, a monophyletic group containing a large number of Lecania species, including the type species L. fuscella, was discovered in the analysis, and recognition of Lecania sensu stricto is suggested. L. baeomma, L. glauca, L. gerlachei, L. brialmontii, L. racovitzae, L. hyalina (alias Biatora globulosa), L. chlorotiza, L. naegelii, and L. furfuracea do not belong in Lecania s. str., although the latter two are closely related to Lecania s. str. Representatives of the genus Bilimbia form a well-supported group, as does the ‘Thamnolecania’ group containing the Antarctic ‘Lecania’ species, L. gerlachei, L. brialmontii, and L. racovitzae. An alternative to recognizing these two genera would be a wider circumscription of Bilimbia to include the ‘Thamnolecania’ group as well as affiliated taxa.

  • 129.
    Reese Næsborg, Rikke
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    van den Boom, Pieter P. G.
    Lecania belgica van den Boom & Reese Næsborg, a new saxicolous species from Western Europe2007In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 39, no 6, p. 499-503Article in journal (Refereed)
    Abstract [en]

    A new species, Lecania belgica, is described and illustrated. It is a saxicolous lichen known only from the type locality in Belgium. It is characterized by apothecia with pruinose, irregularly undulating discs, relatively short ascospores, and by having 12-16 spores in the asci. It was found on mortar together with Diplotomma alboatrum.

  • 130. Sanderson, Michael J.
    et al.
    Thorne, Jeffrey I.
    Wikström, Niklas
    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. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk Botanik.
    Bremer, Kåre
    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. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk Botanik.
    Molecular evidence on plant divergence times2004In: American Journal of Botany: The plant tree of life, Vol. 91, no 10, p. 1656-1665Article in journal (Refereed)
    Abstract [en]

    Estimation of divergence times from sequence data has become increasingly feasible in recent years. Conflicts between fossil evidence and molecular dates have sparked the development of new methods for inferring divergence times, further encouraging these efforts. In this paper, available methods for estimating divergence times are reviewed, especially those geared toward handling the widespread variation in rates of molecular evolution observed among lineages. The assumptions, strengths, and weaknesses of local clock, Bayesian, and rate smoothing methods are described. The rapidly growing literature applying these methods to key divergence times in plant evolutionary history is also reviewed. These include the crown group ages of green plants, land plants, seed plants, angiosperms, and major subclades of angiosperms. Finally, attempts to infer divergence times are described in the context of two very different temporal settings: recent adaptive radiations and much more ancient biogeographic patterns.

  • 131. Sarrión, F.
    et al.
    Burgaz, A.
    Tibell, L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Calicium chlorosporum new to Europe2007In: Botanica complutensis, ISSN 0214-4565, no 31, p. 23-25Article in journal (Refereed)
    Abstract [en]

    Calicium chlorosporum has been found for the first time in Europe. It was growing on wood of Abies pinsapo in southern Spain. Thedescription of the taxa and related species as well as a world distributional map is provided.

  • 132.
    Savic, Sanja
    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. Systematisk botanik.
    Systematics, phylogeny and conservation status of Polyblastia in Sweden2004In: IAL5 Book of abstracts: Lichens in Focus, 2004Conference paper (Refereed)
  • 133.
    Savic, Sanja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk Botanik.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk Botanik.
    Checklist of the lichens of Serbia2006In: Mycologia Balcanica, ISSN 1312-3300, Vol. 3, no 2-3, p. 187-215Article in journal (Refereed)
    Abstract [en]

    A list of lichenized fungi of Serbia is presented. It summarizes records from 1859, when the first lichens from Serbia were published, until now. It also offers a first attempt to present a complete bibliography of Serbian lichens including all past records. Synonyms relevant for the Serbian records are also included, mainly for the species level.

  • 134.
    Savic, Sanja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematic Botany.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematic Botany.
    Andreev, Mikahail
    New and interesting lichenized and lichenicolous fungi from Serbia2006In: Mycologia Balcanica, ISSN 1312-3300, Vol. 3, no 2-3, p. 99-106Article in journal (Refereed)
    Abstract [en]

    A list of lichens from Serbia is presented, comprising species not earlier known from Serbia and species that have been recorded once or a few times only. It also includes a few lichenicolous fungi. The list is based on investigations of material in the lichen collection of the Belgrade Natural History Museum, and material collected by the authors. In all 70 species of lichens and eight lichenicolous fungi are reported from Serbia for the first time. The lichen genera Brodoa, Cornicularia, Hypocenomyce, Lobothallia, Pycnora, Pyrenocollema, Rhizoplaca, Rinodinella, Schaereria, Solenopsora, and Trapelia, and the lichenicolous genera Abrothallus, Carbonea, Cercidospora, Lichenodiplis, Muellerella, Scutula, and Vouxiella are new to Serbia. For 17 lichen species (previously recorded without any locality indication), first localities from Serbia are given. Additional localities are given for 77 species, for which only a few localities have been published.

  • 135.
    Savić, Sanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Phylogeny and Taxonomy of Polyblastia and allied taxa (Verrucariaceae)2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Polyblastia A. Massal. is a genus of lichenized fungi belonging to Verrucariaceae (Ascomycota). Traditional classification heavily rested on a few cardinal characters, primarily ascoma structure and spore morphology, but the delimitation of Polyblastia was problematic. Using DNA sequences from nucLSU, and RPB1 the position of the ‘Polyblastia group’, as a strongly supported clade within Verrucariaceae, was confirmed. A three marker phylogeny (including nucITS) based on a wide taxon sampling reveals strongly supported clades within the ‘Polyblastia group’. Thus Polyblastia s.str. is recognized. The phylogeny of the strongly supported Thelidium clade is not completely resolved. In a different clade, Verrucaria rupestris, the type of Verrucaria, is a sister to the Henrica melaspora/H. theleodes clade. Trimmatothele perquisita, the type of Trimmatothele, forms a strongly supported group with a Verrucaria species. The genus Sporodictyon, until recently included in Polyblastia, is resurrected.

    Species delimitation in Sporodictyon is investigated, and the morphological variation within and between the monophyletic groups is evaluated in an effort to reconcile morphological and molecular data. A taxonomic revision of Sporodictyon, occurring in Northern Europe and the adjacent Arctic is provided, and two new species are described. A comprehensive material is investigated, a key to the species is provided.

    A generic revision of the family Verrucariaceae, based on recent molecular phylogenetic analyses and previous morphological studies, is offered. Three new genera (Hydropunctaria, Parabagliettoa and Wahlenbergiella) are proposed. Several other monophyletic groups are identified for which the taxon sampling is insufficient for proposing taxonomic changes. The nomenclature of the genera in the family is revised, including the study of type materials and several lectotypifications are suggested.

    The new genus Atla (Verrucariaceae) is described, and three new species to science, A. alpina, A. palicei and A. praetermissa, are included. An identification key to the species and a revision of the genus is supplied.

    List of papers
    1. Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera
    Open this publication in new window or tab >>Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera
    2008 (English)In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 112, no Part 11, p. 1307-1318Article in journal (Refereed) Published
    Abstract [en]

    Phylogenetic relationships of the lichen genus Polyblastia and closely related taxa in the family Verrucariaceae (Verrucariales, Chaetothyriomycetidae) were studied. A total of 130 sets of sequences (nuLSU rDNA, nuITS rDNA and RPB1 region A-D), including 129 newly generated sequences, were analysed. Phylogenetic relationships were inferred using a Bayesian approach based on two datasets. A first analysis of a larger, two-locus dataset (nuLSU and RPB1) for 128 members of the Verrucariaceae, confirmed the polyphyly of Polyblastia, Thelidium, Staurothele, and Verrucaria, as currently construed. The second analysis focused on 56 Polyblastia and allied taxa, but using an additional locus (nuITS rDNA) and two closely related outgroup taxa. The latter analysis revealed strongly supported groups, such as Polyblastia s. str., the Thelidium group (a mixture of Polyblastia, Thelidium, Staurothele and Verrucaria species). The genus Sporodictyon, which is here accepted, also accommodates Sporodictyon terrestre comb. nov. Morphological features traditionally used for characterizing Polyblastia, Thelidium, Staurothele and Verrucaria, such as spore septation and colour, occurrence of hymenial photobiont, involucrellum structure, and substrate preference, were found to be only partially consistent within the strongly supported clades, and thus are not always reliable features for characterizing natural groups.

    Keywords
    Cardinal characters, RPB1, Sporodictyon, Staurothele, Thelidium, Trimmatothele, Verrucaria
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96490 (URN)10.1016/j.mycres.2008.05.002 (DOI)000261368000004 ()
    Available from: 2007-11-22 Created: 2007-11-22 Last updated: 2018-03-29
    2. Taxonomy and species delimitation in Sporodictyon (Verrucariaceae) in Northern Europe and the adjacent Arctic – reconciling molecular and morphological data
    Open this publication in new window or tab >>Taxonomy and species delimitation in Sporodictyon (Verrucariaceae) in Northern Europe and the adjacent Arctic – reconciling molecular and morphological data
    2009 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 58, no 2, p. 585-605Article in journal (Refereed) Published
    Abstract [en]

    Morphological variation in Sporodictyon is scrutinized in an effort to   reconcile it with monophyletic groups based oil molecular evidence.   Molecular data (nucITS, nucLSU, RPBI) are investigated by Bayesian and parsimony phylogenetic analyses, statistical parsiniony, and split   decomposition. Morphological variation within and between the   monophyletic groups is evaluated. Four monophyletic groups strongly  Supported by Molecular data correspond to morphologically well-characterized species. Sporodictyon schaererianum and S. terrestre   are morphologically variable, especially with respect to thallus   structure. Two distinct subclades are found in both species, but they   could, however, not be distinguished morphologically and may be   regarded as cryptic species. A combination of ascoma size, spore   pigmentation, spore size and thallus structure characterizes the   species recognized, whereas thallus thickness, involucrellum thickness   and excipulum pigmentation are found to be quite plastic. A taxonomic revision of Sporodictyon Northern Europe and the adjacent Arctic is   provided, recognizing five species. Two new species, S. arcticum and S.   minutum, are described. The name Polyblastia theleodes has been  misapplied for S. schaereriamum. Several taxonomic synonyms are   proposed, particularly for S. terrestre, and lectotypes for several species names are designated.

    Keywords
    haplotype networks, MCMC, phylogeny, species recognition, split decomposition analysis, revision
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96491 (URN)000266525800022 ()
    Available from: 2007-11-22 Created: 2007-11-22 Last updated: 2018-03-29
    3. The main genera of Verrucariaceae (Ascomycota) as supported by recent morphological and molecular studies.
    Open this publication in new window or tab >>The main genera of Verrucariaceae (Ascomycota) as supported by recent morphological and molecular studies.
    Show others...
    (English)In: TaxonArticle in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-96492 (URN)
    Available from: 2007-11-22 Created: 2007-11-22 Last updated: 2018-03-29Bibliographically approved
    4. Atla, a new genus in the Verrucariaceae (Verrucariales)
    Open this publication in new window or tab >>Atla, a new genus in the Verrucariaceae (Verrucariales)
    2008 (English)In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 40, no Part 4, p. 269-282Article in journal (Refereed) Published
    Abstract [en]

    The new genus Atla forms a well-supported clade in a molecular phylogeny based on the ITS1-5.8S-ITS2 and LSU regions of the nuclear ribosomal DNA. The genus has a crustose thallus, a hamathecium at maturity without hyphal elements except for pseudoparaphyses remaining at the ostiolum, and large, muriform spores. Atla wheldonii was previously referred to Polyblastia. Three new species, A. alpina (the type of the new genus), A. palicei and A. praetermissa, are included in the genus and described here as new to science. They were found on calcareous rocks and soil in Northern Scandinavia, A. alpina also occurs in Central Europe, and A. wheldonii likewise in Central Europe, the Pyrenees and in the British Isles. An identification key to the species and a revision of the genus are also provided.

    Keywords
    ascomycetes, lichens, molecular phylogeny, morphology, revision
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-96493 (URN)10.1017/S0024282908007512 (DOI)000258047000001 ()
    Available from: 2007-11-22 Created: 2007-11-22 Last updated: 2018-03-29
  • 136.
    Savić, Sanja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Atla, a new genus in the Verrucariaceae (Verrucariales)2008In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 40, no Part 4, p. 269-282Article in journal (Refereed)
    Abstract [en]

    The new genus Atla forms a well-supported clade in a molecular phylogeny based on the ITS1-5.8S-ITS2 and LSU regions of the nuclear ribosomal DNA. The genus has a crustose thallus, a hamathecium at maturity without hyphal elements except for pseudoparaphyses remaining at the ostiolum, and large, muriform spores. Atla wheldonii was previously referred to Polyblastia. Three new species, A. alpina (the type of the new genus), A. palicei and A. praetermissa, are included in the genus and described here as new to science. They were found on calcareous rocks and soil in Northern Scandinavia, A. alpina also occurs in Central Europe, and A. wheldonii likewise in Central Europe, the Pyrenees and in the British Isles. An identification key to the species and a revision of the genus are also provided.

  • 137.
    Savić, Sanja
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Gueidan, Cécile
    Lutzoni, François
    Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera2008In: Mycological Research, ISSN 0953-7562, E-ISSN 1469-8102, Vol. 112, no Part 11, p. 1307-1318Article in journal (Refereed)
    Abstract [en]

    Phylogenetic relationships of the lichen genus Polyblastia and closely related taxa in the family Verrucariaceae (Verrucariales, Chaetothyriomycetidae) were studied. A total of 130 sets of sequences (nuLSU rDNA, nuITS rDNA and RPB1 region A-D)