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  • 1.
    Aagaard, Sunniva MD
    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.
    Såstad, Sigurd M
    Greilhuber, J
    Moen, A
    A secondary hybrid zone between diploid Dactylorhiza incarnata ssp cruenta and allotetraploid D-lapponica (Orchidaceae)2005In: Heredity, Vol. 94, p. 488-496Article in journal (Refereed)
  • 2. Aguirre-Hudson, B.
    et al.
    Kokubun, T.
    Spooner, B.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Taxonomy of Calicium victorianum (F. Wilson) Tibell (Caliciaceae, Lecanorales), a lichenized ascomycete new to Europe2007In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 39, no 5, p. 401-407Article in journal (Refereed)
    Abstract [en]

    The morphological features and chemical compounds found in the first European collection of Calicium victorianum are compared with type material from Australia of C. piperatum F. Wilson. The phylogenetic relationships of the species are discussed by comparing its nuclear rDNA ITS 1-5.8S-ITS2 with that of other species of Calicium.

  • 3. Albach, Dirk
    et al.
    Meudt, Heidi
    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.
    Piecing together the "new" Plantaginaceae.2005In: American Journal of Botany, Vol. 92, p. 297-315Article in journal (Refereed)
  • 4.
    Anderson, Cajsa Lisa
    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.
    Bremer, Kåre
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Friis, Else Marie
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Dating phylogenetically basal eudicots using rbcL sequences and multiple fossil reference points2005In: American Journal of Botany, Vol. 92, p. 1737-1748Article in journal (Refereed)
    Abstract [en]

    A molecular dating of the phylogenetically basal eudicots (Ranunculales, Proteales, Sabiales, Buxales and Trochodendrales sensu

    Angiosperm Phylogeny Group II) has been performed using several fossils as minimum age constraints. All rbcL sequences available

    in GenBank were sampled for the taxa in focus. Dating was performed using penalized likelihood, and results were compared with

    nonparametric rate smoothing. Fourteen eudicot fossils, all with a Cretaceous record, were included in this study for age constraints.

    Nine of these are assigned to basal eudicots and the remaining five taxa represent core eudicots. Our study shows that the choice of

    methods and fossil constraints has a great impact on the age estimates, and that removing one single fossil change the results in the

    magnitude of tens of million years. The use of several fossil constraints increase the probability of approaching the true ages. Our

    results suggest a rapid diversification during the late Early Cretaceous, with all the lineages of basal eudicots emerging during the

    latest part of the Early Cretaceous. The age of Ranunculales was estimated to 120 my, Proteales to 119 my, Sabiales to 118 my,

    Buxales to 117 my, and Trochodendrales to 116 my.

  • 5.
    Anderson, Cajsa Lisa
    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.
    Bremer, Kåre
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Friis, Else Marie
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Divergence times of phylogenetically basal eudicots2005In: XVII International Botanical Congress: Vienna, Austria, Europe 17-23 July 2005, 2005, p. 728-Conference paper (Refereed)
    Abstract [en]

    A molecular dating of the phylogenetically basal eudicots (Ranunculales, Proteales, Sabiales, Buxales and Trochodendrales sensu APGII) has been performed using several fossils as minimum age constraints. We have sampled all rbcL sequences available in GenBank for the taxa in focus. Dating was done using Penalized Likelihood, and compared with NonParametric Rate Smoothing. We show that choice of method and fossil constraints has a great impact on the age estimates, and that it is important to use several fossil constraints to yield good age estimates. We discuss the 14 fossils we have chosen to include in this study and present a critical review of other fossils potentially useful in dating studies within the basal eudicots. Our results suggest a rapid diversification during the Early-mid Cretaceous, with all the lineages of basal eudicots emerging during the latest part of the Early Cretaceous. The age of Ranunculales was estimated to 120 myr, Proteales to 119 myr, Sabiales to 118 myr, Buxales to 117 myr and Trochodendrales to 116 myr.

  • 6.
    Andreasen, Katarina
    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.
    Implications of molecular systematic analyses on the conservation of rare and threatened taxa: Contrasting examples from Malvaceae2005In: Conservation Genetics, Vol. 6, p. 399-412Article in journal (Refereed)
  • 7.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk botanik.
    Implications of molecular systematic analyses on the conservation of rare and threatened taxa: contrasting examples from Malvaceae2005In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 6, no 3, p. 399-412Article in journal (Refereed)
    Abstract [en]

    Systematic research provides essential evidence for setting conservation priorities for rare and endangered taxa. Phylogenetic analyses can identify cryptic, genetically distinct lineages as well as actively interbreeding, and hence, non-distinctive lineages earlier perceived as separate taxa. A major aim of this study was to identify genetically distinct, rare lineages within two Malvaceae sister-genera, Sidalcea and Eremalche. The focus was two taxon-pairs each consisting of one rare and one more common taxon. The results demonstrate that even within two closely related genera, with a large number of rare taxa, molecular phylogenetic analyses can reveal contrasting degrees of evolutionary divergence and thus contrasting conservation implications for threatened taxa. Contrary to expectations, the substitution rate in the nuclear ribosomal transcribed spacers for annualEremalche did not correspond to the faster evolutionary rate of annuals – compared to perennials – detected earlier within Sidalcea. Branch lengths in the (annual) Eremalche clade were shorter than those of annual members of Sidalcea. The phylogenetic analyses showed that the rare and endangered S. keckii and E. kernensis each are most closely related to a common species that has been regarded as insufficiently distinct to warrant separate taxonomic status. An additional aim of the study was to test the utility of the Phylogenetic Diversity (PD) measure to formalize the procedure of prioritizing conservation efforts. The measure demonstrated S. keckii (but not E. kernensis) to be genetically distinct from its closest relative and a good candidate for conservation. The PD measure was earlier used for assessing conservation priorities for areas, but proved useful to more objectively suggest conservation priorities among threatened taxa. Because this measure is calculated directly from the data, it retains more character information and gives a better representation of genetic diversity than other measures relying on tree topologies.

  • 8.
    Articus, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Neuropogon and the phylogeny of Usnea s. lat. (Parmeliaceae, Ascomycetes)In: TAXONArticle in journal (Refereed)
  • 9.
    Articus, Kristina
    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.
    Neuropogon and the phylogeny of Usnea s.l. (Parmeliaceae, Lichenized Ascomycetes)2004In: TAXON, Vol. 53, no 4, p. 925-934Article in journal (Refereed)
  • 10.
    Articus, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Phylogenetic Studies in Usnea (Parmeliaceae) and Allied Genera2004Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis deals with the phylogeny of the lichen genus Usnea (Parmeliaceae, Ascomycetes). The relationships and the morphological variation among Usnea species has been studied, as well as the relationship of Usnea to allied genera.

    Two species, U. florida and U. subfloridana, which earlier were regarded to form two separate species have been synonymized. In an analysis based on sequence data these two taxa formed a monophyletic group of intermixed specimens. Usnea florida and U. subfloridana have earlier been regarded to form a species pair, but the species pairs concept cannot be applied in this case.

    The morphological characters traditionally used for species recognition of a number of European Usnea species have been analyzed regarding their reliability. The evolution and distribution of the morphological characters was studied in relation to a phylogeny based on sequence data. Most characters proved to be homoplastic in relation to the phylogeny. Few characters were consistent in a clade, and the same character could be inconsistent in another clade. Therefore a combination of several characters is recommended for species recognition.

    The relationship of Neuropogon to Usnea was investigated based on sequence data. Neuropogon showed to be closely related to Usnea subg. Usnea. The subgenera Eumitria and Dolichousnea formed the sister group to the clade comprising subg. Usnea and Neuropogon. Usnea is paraphyletic in this investigation. Eumitria is treated as a genus and the subgenus Dolichousnea is elevated to generic rank.

    The position of Usnea, Neuropogon, Eumitria, and Dolichousnea in the family Parmeliaceae was investigated based on a phylogeny obtained by sequence data. Protousnea probably forms the sister group to the clade of Usnea, Neuropogon, Eumitria, and Dolichousnea. Several monophyletic groups in the family Parmeliaceae were identified.

    List of papers
    1. Ribosomal DNA and β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species
    Open this publication in new window or tab >>Ribosomal DNA and β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species
    Show others...
    2002 (English)In: Mycological Research, no 4, p. 412-418Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-91304 (URN)
    Available from: 2004-02-04 Created: 2004-02-04 Last updated: 2009-04-02Bibliographically approved
    2. Morphology and sequence data - conflict and concordance in a phylogeny of some European Usnea species
    Open this publication in new window or tab >>Morphology and sequence data - conflict and concordance in a phylogeny of some European Usnea species
    (English)In: Botanical Journal of the Linnean SocietyArticle in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-91305 (URN)
    Available from: 2004-02-04 Created: 2004-02-04 Last updated: 2018-03-29Bibliographically approved
    3. Neuropogon and the phylogeny of Usnea s. lat. (Parmeliaceae, Ascomycetes)
    Open this publication in new window or tab >>Neuropogon and the phylogeny of Usnea s. lat. (Parmeliaceae, Ascomycetes)
    (English)In: TAXONArticle in journal (Refereed) Submitted
    Identifiers
    urn:nbn:se:uu:diva-91306 (URN)
    Available from: 2004-02-04 Created: 2004-02-04 Last updated: 2009-04-02Bibliographically approved
    4. The monophyletic groups in the Parmeliaceae
    Open this publication in new window or tab >>The monophyletic groups in the Parmeliaceae
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-91307 (URN)
    Available from: 2004-02-04 Created: 2004-02-04 Last updated: 2010-01-14Bibliographically approved
  • 11.
    Articus, Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Mattsson, Jan-Eric
    Tibell, Leif
    Grube, Martin
    Wedin, Mats
    Ribosomal DNA and β-tubulin data do not support the separation of the lichens Usnea florida and U. subfloridana as distinct species2002In: Mycological Research, no 4, p. 412-418Article in journal (Refereed)
  • 12.
    Articus, Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Mattsson, Jan-Eric
    Wedin, Mats
    Tibell, Leif
    Morphology and sequence data - conflict and concordance in a phylogeny of some European Usnea speciesIn: Botanical Journal of the Linnean SocietyArticle in journal (Refereed)
  • 13.
    Backlund, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Nilsson, Siwert
    Naturhistoriska Riksmuséet.
    Pollen morphology and the systematic position of Triplostegia (Dipsacales)1997In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 46, no 1, p. 21-31Article in journal (Refereed)
    Abstract [en]

    Triplostegia comprises two species of perennial herbs from southeast Asia, T. glandulifera and T. grandiflora. The systematic position of the genus has been debated ever since it was described, and it has been placed in either Dipsacaceae or Valerianaceae, or in a family of its own Triplo-stegiaceae. Pollen of Triplostegia, investigated by light microscopy and scanning electron micro-scopy, is similar to that of both Dipsacaceae and Valerianaceae. Presence of numerous branched and bent columellae as well as an aperturem argins tructurer esemblingt he halo found in Valeria-naceae indicates a closer relationship to the Valerianaceae. A sister-group relationship between Triplostegia and the Valerianaceae is furthermore supported by other studies of molecular and morphological data. In order to maximize information content in the framework of mandatory classificational ranks, Triplostegia is best included in the family Valerianaceae, as the sole mem-ber of a subfamily Triplostegioideae.

  • 14.
    Backlund, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Phylogenetic Studies in the Gentianales – Approaches at Different Taxonomic Levels2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis deals with phylogenetic relationships at different taxonomic levels. All the plants studied are or have been included in the order Gentianales, which comprises about 17 200 species. The phylogenies are based on parsimony analyses of nucleotide sequence data (DNA) from different regions in the chloroplast genome, but morphological characteristics have also been studied.

    Analyses of sequence data from the genes rbcL and ndhF provide the interfamilial structure of the order Gentianales, shown to comprise the families Apocynaceae (incl. Asclepiadaceae), Gelsemiaceae, Gentianaceae, Loganiaceae, and Rubiaceae. Exclusion of certain genera from the Loganiaceae is confirmed and their phylogenetic positions are clarified. Some of these genera remain within the Gentianales, while others belong to other orders. Exclusion of the tribe Buddlejeae from the Loganiaceae is confirmed, and a monophyletic group formed by Buddleja, Emorya, Gomphostigma, and Nicodemia is recognized and placed in the Lamiales. The Loganiaceae s.str. forms, after these exclusions, a strongly supported monophyletic group comprising 13 genera.

    The tribe Paederieae in the family Rubiaceae is analysed using sequence data from the regions rbcL gene, rps16 intron, and the regions trnT-F, and is shown to be paraphyletic. These results lead to a new circumscription of Paederieae comprising the genera Leptodermis, Paederia, Serissa, and Spermadictyon. The tribe Putorieae is reestablished with the single genus Plocama, including 34 species. Aitchisonia, Choulettia, Crocyllis, Gaillonia, Jaubertia, Pseudogaillonia, Pterogaillonia, and Putoria are reduced to synonyms of Plocama based on the molecular analyses and morphological studies.

    The Mediterranean species of the re-circumscribed Plocama, previously segregated as the genus Putoria, are revised. Two species, Plocama calabrica and P. brevifolia, are recognized, their synonymics are established, and seven lectotypes are selected.

    List of papers
    1. Relationships of the Buddlejaceae s.l. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF andrbcL sequence data
    Open this publication in new window or tab >>Relationships of the Buddlejaceae s.l. investigated using parsimony jackknife and branch support analysis of chloroplast ndhF andrbcL sequence data
    1999 (English)In: Systematic Botany, Vol. 24, no 2, p. 164-182Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93714 (URN)
    Available from: 2005-11-10 Created: 2005-11-10 Last updated: 2009-04-02Bibliographically approved
    2. Phylogenetic relationships within the order Gentianales based on ndhF and rbcL sequences, with particular reference to the Loganiaceae
    Open this publication in new window or tab >>Phylogenetic relationships within the order Gentianales based on ndhF and rbcL sequences, with particular reference to the Loganiaceae
    2000 (English)In: American Journal of Botany, Vol. 87, no 7, p. 1029-1043Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-93715 (URN)
    Available from: 2005-11-10 Created: 2005-11-10 Last updated: 2009-04-02Bibliographically approved
    3. Paraphyly of Paederieae, recognition of Putorieae and expansion of Plocama (Rubiaceae-Rubioideae)
    Open this publication in new window or tab >>Paraphyly of Paederieae, recognition of Putorieae and expansion of Plocama (Rubiaceae-Rubioideae)
    2007 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 2, p. 315-328Article in journal (Refereed) Published
    Abstract [en]

    Phylogenetic analyses of taxa that have been included in the tribe Paederieae are performed on the basis of a molecular dataset of plastid DNA sequences (the rbcL gene, rps16 intron, and the regions trnT-F). The paraphyly of Paederieae as currently circumscribed is confirmed. A clade comprising Paederia, Spermadictyon, Leptodermis, and Serissa is retrieved and the circumscription of Paederieae is proposed to be restricted to this clade. Paederia is sister to a clade with Spermadictyon, Leptodermis, and Serissa. Paederia is subdivided into an Asian and an African clade, and within the African clade seven species endemic to Madagascar are sister to P. pospischilii in north-eastern Africa. The position of Kelloggia as sister to Rubieae is confirmed and a position of Saprosma in the Spermacoceae alliance is supported. The genera Putoria, Gaillonia (with segregates), Plocama, and Aitchisonia form a clade that is sister to Theligoneae/Kelloggia/Rubieae. The name Putorieae is resurrected for the members of this clade. A synopsis of Putorieae is provided, where all species are placed in an expanded Plocama with 34 species. Thirty-one new combinations in Plocama are proposed. Plocama pendula on the Canary Islands is strongly supported as sister to a clade with P. crocyllis (former Crocyllis) in southern Africa and P. yemenensis and P. tinctoria (former Gaillonia) in southern Arabia/Horn of Africa.

    Keywords
    Gaillonia, molecular phylogenetics, Paederieae, Plocama, Putorieae, rbcL, rps16, Rubiaceae, trnT-F
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-93716 (URN)000247420000006 ()
    Available from: 2005-11-10 Created: 2005-11-10 Last updated: 2017-12-14Bibliographically approved
    4. Revision of the Mediterranean species of Plocama (Rubiaceae)
    Open this publication in new window or tab >>Revision of the Mediterranean species of Plocama (Rubiaceae)
    2007 (English)In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 2, p. 516-520Article in journal (Refereed) Published
    Abstract [en]

    The Mediterranean species of Plocama (incl. Putoria) are revised and two species, the widespread P. calabrica, comb. nov., and P. brevifolia, comb. nov., in Morocco and Algeria, are recognized. The variation and circumscription of the species are discussed and distribution maps are provided. Several names are reduced to synonymy and seven lectotypes are designated.

    Keywords
    distribution maps; Mediterranean region; Plocama; Putoria; Putorieae; Rubiaceae; taxonomy; typification
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-93717 (URN)000247420000022 ()
    Available from: 2005-11-10 Created: 2005-11-10 Last updated: 2017-12-14Bibliographically approved
  • 15.
    Backlund, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Bremer, Birgitta
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Paraphyly of Paederieae, recognition of Putorieae and expansion of Plocama (Rubiaceae-Rubioideae)2007In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 2, p. 315-328Article in journal (Refereed)
    Abstract [en]

    Phylogenetic analyses of taxa that have been included in the tribe Paederieae are performed on the basis of a molecular dataset of plastid DNA sequences (the rbcL gene, rps16 intron, and the regions trnT-F). The paraphyly of Paederieae as currently circumscribed is confirmed. A clade comprising Paederia, Spermadictyon, Leptodermis, and Serissa is retrieved and the circumscription of Paederieae is proposed to be restricted to this clade. Paederia is sister to a clade with Spermadictyon, Leptodermis, and Serissa. Paederia is subdivided into an Asian and an African clade, and within the African clade seven species endemic to Madagascar are sister to P. pospischilii in north-eastern Africa. The position of Kelloggia as sister to Rubieae is confirmed and a position of Saprosma in the Spermacoceae alliance is supported. The genera Putoria, Gaillonia (with segregates), Plocama, and Aitchisonia form a clade that is sister to Theligoneae/Kelloggia/Rubieae. The name Putorieae is resurrected for the members of this clade. A synopsis of Putorieae is provided, where all species are placed in an expanded Plocama with 34 species. Thirty-one new combinations in Plocama are proposed. Plocama pendula on the Canary Islands is strongly supported as sister to a clade with P. crocyllis (former Crocyllis) in southern Africa and P. yemenensis and P. tinctoria (former Gaillonia) in southern Arabia/Horn of Africa.

  • 16.
    Backlund, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Bremer, Birgitta
    Phylogenetic relationships within the order Gentianales based on ndhF and rbcL sequences, with particular reference to the Loganiaceae2000In: American Journal of Botany, Vol. 87, no 7, p. 1029-1043Article in journal (Refereed)
  • 17.
    Backlund, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Revision of the Mediterranean species of Plocama (Rubiaceae)2007In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 2, p. 516-520Article in journal (Refereed)
    Abstract [en]

    The Mediterranean species of Plocama (incl. Putoria) are revised and two species, the widespread P. calabrica, comb. nov., and P. brevifolia, comb. nov., in Morocco and Algeria, are recognized. The variation and circumscription of the species are discussed and distribution maps are provided. Several names are reduced to synonymy and seven lectotypes are designated.

  • 18.
    Beier, Björn Axel
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Zoology. Systematisk botanik.
    Nylander, Johan
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Zoology. Systematisk zoologi.
    Chase, Mark W
    Thulin, Mats
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Zoology. Systematisk botanik.
    Phylogenetic relationships and biogeography of the desert plant genus Fagonia (Zygophyllaceae), inferred by parsimony and Bayesian model averaging2004In: Molecular Phylogenetics and Evolution, Vol. 33, no 1, p. 91-108Article in journal (Refereed)
  • 19.
    Beier, Björn-Axel
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    A revision of the desert shrub Fagonia (Zygophyllaceae)2005In: Systematics and Biodiversity, Vol. 3, p. 221-263Article in journal (Refereed)
  • 20.
    Beier, Björn-Axel
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Avdelningen för systematisk botanik.
    Thulin, Mats
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Avdelningen för systematisk botanik.
    Proposal to conserve the name Tetraena against Petrusia (Zygophyllaceae)2004In: Taxon, Vol. 53, p. 1078-1079Article in journal (Refereed)
  • 21.
    Björk, Lars
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Tunon, Håkan
    Framtidens växter2005In: Människan och floran: Etnobiologi i Sverige 2, Wahlstöm och Widstrand, Stockholm , 2005, p. 471-482Chapter in book (Other (popular scientific, debate etc.))
  • 22. Bolmgren, Kjell
    et al.
    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.
    Generic limits in Rhamnus L. s.l. (Rhamnaceae) inferred from nuclear and chloroplast DNA sequence phylogenies2004In: TAXON, ISSN 0040-0262, Vol. 53, no 2, p. 383-390Article in journal (Refereed)
  • 23.
    Bremer, Kåre
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Bremer, Birgitta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Introduction to phylogeny and systematics of flowering plants2003 (ed. Ny utg.)Book (Other academic)
  • 24.
    Bremer, Kåre
    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.
    Fries, Else-Marie
    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.
    Molecular phylogenetic dating of asterid flowering plants shows early Cretaceous diversification2004In: Systematic Biology, Vol. 53, no 3, p. 496-505Article in journal (Refereed)
  • 25. Britton, Tom
    et al.
    Anderson, Cajsa Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Jaquet, David
    Lundqvist, Samuel
    Bremer, Kåre
    Estimating divergence times in large phylogenetic trees2007In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 5, p. 741-752Article in journal (Refereed)
    Abstract [en]

    A new method, PATHd8, for estimating ultrametric trees from trees with edge (branch) lengths proportional to the number of substitutions is proposed. The method allows for an arbitrary number of reference nodes for time calibration, each defined either as absolute age, minimum age, or maximum age, and the tree need not be fully resolved. The method is based on estimating node ages by mean path lengths from the node to the leaves but correcting for deviations from a molecular clock suggested by reference nodes. As opposed to most existing methods allowing substitution rate variation, the new method smoothes substitution rates locally, rather than simultaneously over the whole tree, thus allowing for analysis of very large trees. The performance of PATHd8 is compared with other frequently used methods for estimating divergence times. In analyses of three separate data sets, PATHd8 gives similar divergence times to other methods, the largest difference being between crown group ages, where unconstrained nodes get younger ages when analyzed with PATHd8. Overall, chronograms obtained from other methods appear smoother, whereas PATHd8 preserves more of the heterogeneity seen in the original edge lengths. Divergence times are most evenly spread over the chronograms obtained from the Bayesian implementation and the clock-based Langley-Fitch method, and these two methods produce very similar ages for most nodes. Evaluations of PATHd8 using simulated data suggest that PATHd8 is slightly less precise compared with penalized likelihood, but it gives more sensible answers for extreme data sets. A clear advantage with PATHd8 is that it is more or less instantaneous even with trees having several thousand leaves, whereas other programs often run into problems when analyzing trees with hundreds of leaves. PATHd8 is implemented in freely available software.

  • 26.
    Britton, Tom
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Svennblad, Bodil
    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.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Bayesian support is larger than bootstrap support in phylogenetic inference: a mathematical argument.2007In: Mathematical Medicine and Biology, ISSN 1477-8599, E-ISSN 1477-8602, Vol. 24, no 4, p. 401-411Article in journal (Refereed)
    Abstract [en]

    In phylogenetic inference, the support of an estimated phylogenetic tree topology and its interior branches is usually measured either with non-parametric bootstrap support (BS) values or with Bayesian posterior probabilities (BPPs). Extensive empirical evidence indicates that BPP values are systematically larger than BS when measured on the same data set, but there are no theoretical results supporting such a systematic difference. In the present note, we give a heuristic mathematical argument supporting the empirically observed phenomenon. The argument uses properties of the marginal and profile likelihoods of the normal distribution. The heuristic arguments are supported in a simulation study evaluating different steps in the argument.

  • 27. Brysting, A. K.
    et al.
    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.
    Scheen, A.-C.
    Brochmann, Christian
    Tracking the origin and evolution of a group of high polyploid Cerastium species - (Caryophyllaceae) using non-coding regions of the RNA polymerase genes.2005Conference paper (Other scientific)
  • 28. Brysting, Anne K.
    et al.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Huber, Katharina T.
    Moulton, Vincent
    Brochmann, Christian
    Untangling complex histories of genome mergings in high polyploids2007In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 56, no 3, p. 467-476Article in journal (Refereed)
    Abstract [en]

    Polyploidy, the duplication of entire genomes, plays a major role in plant evolution. In allopolyploids, genome duplication is associated with hybridization between two or more divergent genomes. Successive hybridization and polyploidization events can build up species complexes of allopolyploids with complicated network-like histories, and the evolutionary history of many plant groups cannot be adequately represented by phylogenetic trees because of such reticulate events. The history of complex genome mergings within a high-polyploid species complex in the genus Cerastium (Caryophyllaceae) is here untangled by the use of a network algorithm and noncoding sequences of a low-copy number gene. The resulting network illustrates how hybridization and polyploidization have acted as key evolutionary processes in creating a plant group where high-level allopolyploids clearly outnumber extant parental genomes.

  • 29. Cafferty, Steve
    et al.
    Oxelman, Bengt
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Proposal to reject the name Silene polyphylla L. 1753 (Caryophyllaceae)2001In: Taxon, ISSN 0040-0262, Vol. 50, no 3, p. 923-924Article in journal (Refereed)
  • 30.
    Constantinescu, O.
    et al.
    Uppsala University, Museums etc., Museum of Evolution. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Mel'nik, V.A.
    Verkley, G.J.M.
    Two parasitic fungi on a new host, Syringa (Oleaceae)2006In: Mycotaxon, Vol. 94, p. 175-179Article in journal (Refereed)
    Abstract [en]

    Thedgonia ligustrina, the agent of Ligustrum leaf-spot, and Gloeosporidiella turgida, known as a parasite of Fraxinus, are reported for the first time on Syringa spp. Both fungi were found in Sweden, the first in a tree nursery in the south, and the second on plants cultivated in Uppsala. Brief descriptions and illustration are provided and the distribution of T. ligustrina is reviewed.

  • 31.
    Constantinescu, Ovidiu
    et al.
    Uppsala University, Museums etc., Museum of Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Thines, Marco
    Dimorphism of sporangia in Albuginaceae (Chromista, Peronosporomycetes)2006In: Sydowia, ISSN 0082-0598, Vol. 58, no 2, p. 178-190Article in journal (Refereed)
    Abstract [en]

    By using light- and scanning electron microscopy, the dimorphism of sporangia in Albuginales is demonstrated in 220 specimens of Albugo, Pustula and Wilsoniana, parasitic on plants belonging to 13 families. The presence of two kinds of sporangia is due to the sporangiogenesis and considered to be present in all representatives of the Albuginales. Primary and secondary sporangia are the term recommended to be used for these dissemination organs.

  • 32. Crespo, Ana
    et al.
    Lumbsch, H. Thorsten
    Mattsson, Jan-Eric
    Blanco, Oscar
    Divakar, Pradeep K.
    Articus, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Wiklund, Elisabeth
    Bawingan, Paulina A.
    Wedin, Mats
    Testing morphology-based hypotheses of phylogenetic relationships in Parmeliaceae (Ascomycota) using three ribosomal markers and the nuclear RPB1 gene2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 44, no 2, p. 812-824Article in journal (Refereed)
    Abstract [en]

    Parmeliaceae is the largest family of lichen-forming fungi with more than 2000 species and includes taxa with different growth forms. Morphology was widely employed to distinguish groups within this large, cosmopolitan family. In this study we test these morphology-based groupings using DNA sequence data from three nuclear and one mitochondrial marker from 1.20 taxa that include 59 genera and represent the morphological and chemical diversity in this lineage. Parmeliaceae is strongly supported as monophyletic and six well-supported main clades can be distinguished within the family. The relationships among them remain unresolved. The clades largely agree with the morphology-based groupings and only the placement of four of the genera studied is rejected by molecular data, while four other genera belong to clades previously unrecognised. The classification of these previously misplaced genera, however, has already been questioned by some authors based on morphological evidence. These results support morphological characters as important for the identification of monophyletic clades within Parmeliaceae.

  • 33. Daniel, Thomas F.
    et al.
    McDade, Lucinda A.
    Manktelow, Mariette
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Kiel, Carrie A.
    The "Tetramerium Lineage" (Acanthaceae : Acanthoideae : Justicieae): Delimitation and intra-lineage relationships based on cp and nrITS sequence data2008In: Systematic Botany, ISSN 0363-6445, E-ISSN 1548-2324, Vol. 33, no 2, p. 416-436Article in journal (Refereed)
    Abstract [en]

    We used DNA sequence data from five genic regions (nrITS; chloroplast trnL-F, trnT-L, rps16, trnS-G) to study phylogenetic relationships of the Tetramerium lineage (Acanthaceae: Justicieae). From a sample of 70 species (representing 25 genera) previously affiliated with the Tetramerium lineage, 68 are included therein. Our analyses excluded Papuasian Calycacanthus and Neotropical Streblacanthus monospermus from the Tetramerium lineage; however, two species described in Justicia (J. gonzalezii and J. medranoi) and a Malagasy species of uncertain generic affinities are nested within the lineage. A monophyletic Tetramerium lineage consists of 23 currently recognized genera with at least 168 species, more than 70% of which occur in the New World. Old World Chlamydocardia and Clinacanthus are serially sister to all other members of the lineage. Other Old World taxa consist of: Ecbolium clade (all sampled species of Ecbolium plus Malagasy Populina richardii), Megalochlamys clade (Megalochlamys, Trichaulax and the unidentified Malagasy species), and two isolated taxa (Angkalanthus and Chorisochora). All analyses strongly support monophyly of the New World Tetramerium lineage. The basal clades of New World plants, all with nototribic flowers, are: 1) the taxonomically heterogeneous but palynologically consistent Mirandea clade, and 2) the Pachystachys clade + the South American Anisacanthus clade. The second is sister to all other NW plants, referred to here as the core Tetramerium lineage. We recognize five clades within the core Tetramerium lineage related as follows: (Henrya clade (Carlowrightia parviflora clade (North American Anisacanthus clade (core Carlowrightia clade + Tetramerium)))). Macromorphological synapomorphies are unknown for the Tetramerium lineage and for many of its constituent clades. However, we propose sternotribic flowers as synapomorphic for the core Tetramerium lineage, and flowers with the lower-central lobe of the corolla modified into a keel as a synapomorphy for a lineage consisting of Tetramerium and the core Carlowrightia clade. Palynological characters provide putative synapomorphies for some clades (e.g. Ecbolium clade, Mirandea clade) and autapomorphies for several species (e.g. Mexacanthus mcvaughii, Trichalux mwasumbii). An Old World origin is postulated for the Tetramerium lineage, and we posit a single dispersal event to America and subsequent extensive radiation there, especially in arid zones of Mexico and adjacent regions. Taxonomic implications of our results are extensive. Notably, many traditionally recognized genera (e.g. Anisacanthus, Carlowrightia, Mirandea) are not monophyletic and emphasis on floral form often has been phylogenetically misleading; for example, floral adaptations to pollination by hummingbirds have evolved at least eight times in the New World Tetramerium lineage.

  • 34.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Hagemann, Ulrich
    Bate, Jenny
    Meyboom, Ronald H. B.
    Allergic reactions to medicines derived from Pelargonium species2007In: Drug Safety, ISSN 0114-5916, E-ISSN 1179-1942, Vol. 30, no 8, p. 677-680Article in journal (Refereed)
    Abstract [en]

    Pelargonium (Pelargonium sidoides DC and P. reniforme Curtis) is reported to have immune modulating properties and antibacterial activity, and Pelargonium extracts have been used for the treatment of respiratory tract and gastrointestinal infections. Introduced in the early 1980s in Germany, Umckaloabo® (ISO Arzneimittel), an ethanolic extract of the roots of P. sidoides and P. reniforme, was the first Pelargonium-derived product to be commonly used in a country in the EU. According to the Umckaloabo® product information, this extract has no known adverse effects. However, there is a theoretical risk of interactions with anticoagulants such as warfarin, and antiplatelet drugs, such as aspirin (acetylsalicylic acid). To date, the Uppsala Monitoring Centre has, through the WHO international pharmacovigilance programme, received 34 case reports of allergic reactions suspected to be associated with the use of Pelargonium extract, all originating from Germany. In a number of these reports, the description and timing of the event was indicative of an acute Coombs and Gell Type I hypersensitivity reaction; two of these patients needed treatment for circulatory failure. So far, the experience of such reactions is limited to Germany. Since Pelargonium-containing herbal products have recently been approved in a number of other countries, the possibility of the occurrence of allergic reactions has become of more general interest and further information regarding these products is needed.

  • 35.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kool, Anneleen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Björk, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Ethnobotanical research and teaching: A Case in Bulgaria2006In: Program of the Society for Economic Botany 47th Annual Meeting, 2006Conference paper (Other (popular science, discussion, etc.))
    Abstract [en]

    Introduction

    Bulgarian people in rural areas have a tradition of using herbal medicine as household remedies,

    due partly to the scarcity of pharmaceuticals during the Soviet era. As part of a fieldwork exercise

    in the ethnobotany course taught at Uppsala University students carried out ethnobotanical

    research in different areas in Bulgaria to study and describe these traditions.

    Objectives

    To study: Plants used to treat fevers and cold; plants used to treat wounds and for pain-relief;

    plants grown in home gardens; plants used for magical purposes; and awareness of endangerment

    of medicinally used plants.

    Methods

    Our group of 16 students was divided in groups of two-three students. Each group had written a

    project proposal focusing on one of the study objectives, and carried out this research with the help

    of a Bulgarian translator, who was knowledgeable about the local flora. Three field sites had been

    selected to spread the students throughout the country and to prevent informant fatigue. Interviews

    were semi-structured and if necessary, walks were made with the informants to point out plants and

    collect herbarium vouchers.

    Results

    The students as a whole managed to collect an enormous amount of data in a very short time, and

    some groups carried out as many as 18 interviews during the 8-day field period. Results were

    analyzed per group and presented during a one-day seminar at Ruse University, Bulgaria.

    Conclusion

    Bulgarian villagers, mainly ederly people, rely to a great extent on the use of medicinal plants to

    treat common and non-threatening chronic diseases. These plants are often grown in home

    gardens, and less so collected in the wild. Knowledge is often based on books, and less so on

    maternal or paternal transmission. The people living in Roussenski Lom national park experience

    that most medicinally used wild plants have stayed equal or increased in abundance over the last

    decennium. Carrying out ethnobotanical field research can be effective and efficiently done as part

    of a course training ethnobotany students.

  • 36.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Kool, Anneleen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Broberg, Anders
    Department of Chemistry, Swedish University of Agricultural Sciences.
    Mziray, William R
    National Herbarium of Tanzania, Tropical Pesticide Research Institute.
    Hedberg, Inga
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Levenfors, Jolanta J
    Agrivir AB, Uppsala.
    Anti-fungal and anti-bacterial activity of some herbal remedies from Tanzania2005In: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 96, no 3, p. 461-469Article in journal (Refereed)
    Abstract [en]

    Plants are not only important to the millions of people to whom traditional medicine serves as the only opportunity for health care and to those who use plants for various purposes in their daily lives, but also as a source of new pharmaceuticals. During interviews with the Pare people from Northeastern Tanzania, 29 plants that are used for medicinal purposes as well as 41 plants used for non-medicinal purposes were reported. Six medicinally used plants were selected for bioactivity analysis. Extracts of Coccinia adoensis, Cineraria grandiflora, Pavonia urens, Marattia fraxinea, Clutia abyssinica var. usambarica, and Vangueria infausta were made using ethyl acetate, methanol, cold water and boiling water. The antimicrobial activity was tested on Candida albicans, Aspergillus fumigatus, Fusarium culmorum, Staphylococcus aureus, Pseudomonas syringae, and Erwinia amylovora. All plants showed activity against several test organisms.

  • 37.
    de Boer, Hugo J.
    et al.
    Avd f systematisk botanik. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Thulin, Mats
    Avd f systematisk botanik. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Lectotypification of Callicocca ipecacuanha Brot. and neotypification of Cephaelis acuminata H.Karst., with reference to the drug ipecac2005In: Taxon, ISSN 0040-0262, Vol. 54, no 4, p. 1080-1082Article in journal (Refereed)
  • 38.
    de Boer, Hugo
    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.
    Wieringa, Jan
    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. systematisk botanik.
    Lectotypification of Callicocca ipecacuanha Brot. and neotypification of Cephaelis acuminata H.Karst., with reference to the drug Ipecac2005In: abstracts XVII International Botanical Congress: Vienna, Austria, Europe 17-23 July 2005, 2005Conference paper (Other (popular scientific, debate etc.))
    Abstract [en]

    The main pharmacopoeias cite the roots of Cephaelis ipecacuanha (syn. Callicocca ipecacuanha Brot.) together with the roots of Cephaelis acuminata H.Karst. are the sources of the crude drug ipecac (European Pharmacopoeia, 2002, 2004; United States Pharmacopeia, 2004; British Pharmacopoeia, 2003; Japanese Pharmacopoeia, 2001). Ipecac is an important emetic and expectorant used in case of poisoning, mainly in children. However, C. acuminata does not occur in botanical literature, except in connection with the original description, and this falls entirely within the variation of the widespread and variable Cephaelis ipecacuanha. Callicocca ipecacuanha was described from Brazil, but no type specimen has been found and the name is here lectotypified with an illustration from the protologue. For Cephaelis acuminata, described from Colombia, no original material is extant, and a recent specimen from Colombia is here selected to serve as neotype.

  • 39. Denk, Thomas
    et al.
    Oh, Il-Chan
    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 Schisandraceae based on morphological data: evidence from modern plants and the fossil record2005In: Plant Systematics and Evolution, Vol. 256, p. 113-145Article in journal (Refereed)
  • 40.
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Proposal to conserve the name Silene linearis Decne. against Silene linearis Sweet (Caryophyllaceae)Manuscript (Other (popular science, discussion, etc.))
  • 41.
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Systematics in Sileneae (Caryophyllaceae) – Taxonomy and Phylogenetic patterns2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The focus for the first part of the thesis is on the systematics of species belonging to Silene subgenus Silene. Phylogenetic relationships are inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ITS, intron of the RPB2 gene) genomes. Silene section Rigidulae is shown to be non-monophyletic in its previous circumscription, but instead consisting of six separate clades, each correlated to the geographical distribution of the included species. The taxonomic consequences for each clade are discussed. One of the clades is recognized as a new section and described as Silene sect. Arenosae sect. nov. The morphological descriptions of the species are formalized using a novel implementation of the Prometheus Description Model. Two proposals are included in the thesis, one to reject the name Silene polyphylla L., which is a senior synonym to S. portensis L. Silene linearis Decne. is proposed for conservation against the rarely used S. linearis Sweet.

    Silene antirrhina, a weedy American annual, is strongly supported as sister to the Hawaiian endemic species of Silene, suggesting an American origin for these. Two of the endemics have evolved woodiness after introduction to Hawaii.

    In the second part of the thesis we use four nuclear DNA regions, (introns from RPA2, RPB2, RPD2a, RPD2b), and the chloroplast psbE-petG spacer. A framework is developed to evaluate different phylogenetic explanations for conflicting gene trees, where divergence times are used to discriminate among inter- and intralineage processes. The incongruences observed regarding the relationships among the three major lineages of Heliosperma are best explained by homoploid hybridization. The pattern regarding the origin of Heliosperma itself is more complicated and is likely to include several reticulate events. Two lineages have probably been involved in the origin of Heliosperma, one leading to Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.

    List of papers
    1. A re-evaluation of Silene sect. Rigidulae (Caryophyllaceae) based on multiple gene phylogenies
    Open this publication in new window or tab >>A re-evaluation of Silene sect. Rigidulae (Caryophyllaceae) based on multiple gene phylogenies
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95247 (URN)
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2010-01-14Bibliographically approved
    2. Proposal to reject the name Silene polyphylla L. 1753 (Caryophyllaceae)
    Open this publication in new window or tab >>Proposal to reject the name Silene polyphylla L. 1753 (Caryophyllaceae)
    2001 (English)In: Taxon, ISSN 0040-0262, Vol. 50, no 3, p. 923-924Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-95248 (URN)
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2009-04-02Bibliographically approved
    3. A taxonomic revision of Silene sect. Arenosae sect. nov. (Caryophyllaceae)
    Open this publication in new window or tab >>A taxonomic revision of Silene sect. Arenosae sect. nov. (Caryophyllaceae)
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95249 (URN)
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2010-01-14Bibliographically approved
    4. Proposal to conserve the name Silene linearis Decne. against Silene linearis Sweet (Caryophyllaceae)
    Open this publication in new window or tab >>Proposal to conserve the name Silene linearis Decne. against Silene linearis Sweet (Caryophyllaceae)
    (English)Manuscript (Other (popular science, discussion, etc.))
    Identifiers
    urn:nbn:se:uu:diva-95250 (URN)
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2010-01-14Bibliographically approved
    5. The Origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae)
    Open this publication in new window or tab >>The Origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae)
    Show others...
    2007 (English)In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 94, no 2, p. 210-218Article in journal (Refereed) Published
    Abstract [en]

    The Hawaiian endemic Silene are a small group of woody or semiwoody representatives from a large, predominantly herbaceous, species-rich genus. We here investigated the origin and number of introductions of the endemic Hawaiian Silene based on phylogenetic relationships inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ribosomal internal transcribed sequences, ITS, and intron 23 of the RPB2 gene) genomes. Silene antirrhina, a widespread weedy American annual, is strongly supported as sister to a monophyletic group consisting of the Hawaiian Silene, indicating a single colonization event. There are no obvious morphological similarities between S. antirrhina and any of the species of Hawaiian Silene. Our results suggest an American origin for the Hawaiian endemics because that would require only a single trans-ocean dispersal. Two of the Hawaiian endemics (S. struthioloides and S. hawaiiensis) that form a subclade in the analyses have evolved woodiness after introduction to the Hawaiian Islands. Our results contribute to other recent results based on molecular phylogenetics that emphasize the American continent as a source area for the Hawaiian flora and support a striking morphological radiation and evolution of woodiness from a single introduction to the archipelago.

    Keywords
    Caryophyllaceae, Hawaiian Silene, ITS, phylogeny, RPB2, rps16, Silene antirrhina, woodiness
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-95251 (URN)10.3732/ajb.94.2.210 (DOI)000244241800008 ()
    Available from: 2006-11-28 Created: 2006-11-28 Last updated: 2017-12-14Bibliographically approved
    6. 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
  • 42.
    Eggens, Frida
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    A re-evaluation of Silene sect. Rigidulae (Caryophyllaceae) based on multiple gene phylogeniesManuscript (Other (popular science, discussion, etc.))
  • 43.
    Eggens, Frida
    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.
    Popp, Magnus
    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.
    Nepokreoff, Molly
    Wagner, Warren L.
    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.
    The Origin of the Hawaiian endemic Silene species2005In: Abstracts - XVII International Botanical Congress: Vienna, Austria, 2005Conference paper (Other scientific)
    Abstract [en]

    Geographically, one could expect an Asian origin for species from the Hawaiian Islands. Despite this, a number of Hawaiian taxa have been shown to have their closest relatives on the North American continent. The seven species of Silene endemic to Hawaii were placed in a section with two Japanese Silene in the latest global revision of the genus. They were thought to be the result of two colonizations, one for the shrubby species and one for the remaining herbaceous ones. Our results, based on DNA sequences from the plastid genome, ITS, and the nuclear low copy number gene RPB2 of five of the seven species (representing both of the putative colonizations) instead strongly indicate a close relationship between the endemic Hawaiian species and the North American species S. antirrhina, which is sister to a monophyletic group of the Hawaiian Silene, indicating a single colonization event. S. antirrhina is a diploid North American species that is not related to other native North American Silene, of which the majority are polyploid and belong to other clades. There is no obvious morphological support for the relationship between the Hawaiian Silene and S. antirrhina.

  • 44.
    Eggens, Frida
    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.
    Nepokroeff, Molly
    Wagner, Warren L.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    The Origin and number of introductions of the Hawaiian endemic Silene species (Caryophyllaceae)2007In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 94, no 2, p. 210-218Article in journal (Refereed)
    Abstract [en]

    The Hawaiian endemic Silene are a small group of woody or semiwoody representatives from a large, predominantly herbaceous, species-rich genus. We here investigated the origin and number of introductions of the endemic Hawaiian Silene based on phylogenetic relationships inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ribosomal internal transcribed sequences, ITS, and intron 23 of the RPB2 gene) genomes. Silene antirrhina, a widespread weedy American annual, is strongly supported as sister to a monophyletic group consisting of the Hawaiian Silene, indicating a single colonization event. There are no obvious morphological similarities between S. antirrhina and any of the species of Hawaiian Silene. Our results suggest an American origin for the Hawaiian endemics because that would require only a single trans-ocean dispersal. Two of the Hawaiian endemics (S. struthioloides and S. hawaiiensis) that form a subclade in the analyses have evolved woodiness after introduction to the Hawaiian Islands. Our results contribute to other recent results based on molecular phylogenetics that emphasize the American continent as a source area for the Hawaiian flora and support a striking morphological radiation and evolution of woodiness from a single introduction to the archipelago.

  • 45.
    Eggens, Frida
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Thollesson, Mikael
    Oxelman, Bengt
    A taxonomic revision of Silene sect. Arenosae sect. nov. (Caryophyllaceae)Manuscript (Other (popular science, discussion, etc.))
  • 46.
    Ekenäs, Catarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Baldwin, Bruce G.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    A molecular phylogenetic study of Arnica (Asteraceae): Low chloroplast DNA variation and problematic subgeneric classification2007In: Systematic Botany, ISSN 0363-6445, E-ISSN 1548-2324, Vol. 32, no 4, p. 917-928Article in journal (Refereed)
    Abstract [en]

    DNA sequences from five chloroplast DNA regions (the rpl16 and rps16 introns and the psbA-trnH, ycf4-cemA, and trnT-L spacers), and the nuclear ribosomal internal and external transcribed spacer (ITS and ETS) regions, were analyzed using maximum parsimony and Bayesian methods to explore the putatively complicated history of the mainly North American genus Arnica. The chloroplast regions were found to contain minimal variation in Arnica. Of 3710 nucleotides, only 119 were variable and 45 informative. However, combined with the ribosomal DNA data, the analysis yielded a number of well-supported clades. Strong support for the monophyly of Arnica was found in both the separate and combined analyses but none of the five currently recognized subgenera was resolved as monophyletic in any of the analyses. Arnica (Whitneya) dealbata and A. mallotopus (Mallotopus japonicus), two species that were previously placed outside Arnica, were confidently confirmed as members of the genus. The analyses revealed that A. nevadensis (subg. Austromontana) is most closely related to A. dealbata and that A. mallotopus forms a strongly supported clade with A. unalaschcensis (subg. Andropurpurea). Earlier biogeographical hypotheses that suggested an arctic origin and southward spread of the genus are not supported by our analyses. Hybridization, homoplasy, and rapid evolution are possible explanations for conflicts between the chloroplast and nuclear ribosomal data sets and for low support of the deeper nodes.

  • 47. Ericson, Per G. P.
    et al.
    Anderson, Cajsa Lisa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Britton, Tom
    Elzanowski, Andrzej
    Johansson, Ulf S.
    Källersjö, Mari
    Ohlson, Jan I.
    Parsons, Thomas J.
    Zuccon, Dario
    Mayr, Gerald
    Diversification of Neoaves through time: Integration of molecular sequence data and fossils2006In: Biology Letters, ISSN 1744-9561, E-ISSN 1744-957X, Vol. 2, no 4, p. 543-547Article in journal (Refereed)
    Abstract [en]

    Patterns of diversification and timing of evolution within Neoaves, which includes almost 95% of all bird species, are virtually unknown. On the other hand, molecular data consistently indicate a Cretaceous origin of many neoavian lineages and the fossil record seems to support an Early Tertiary diversification. Here, we present the first well-resolved molecular phylogeny for Neoaves, together with divergence time estimates calibrated with a large number of stratigraphically and phylogenetically well-documented fossils. Our study defines several well-supported clades within Neoaves. The calibration results suggest that Neoaves, after an initial split from Galloanseres in Mid-Cretaceous, diversified around or soon after the K/T boundary. Our results thus do not contradict palaeontological data and show that there is no solid molecular evidence for an extensive pre-Tertiary radiation of Neoaves.

  • 48.
    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
  • 49.
    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)
  • 50.
    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.

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