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  • 1.
    Bremer, Birgitta
    et al.
    Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum. Stockholm University, Faculty of Science, Department of Botany.
    Eriksson, Torsten
    Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum. Stockholm University, Faculty of Science, Department of Botany.
    Timetree of Rubiaceae - Phylogeny and dating the family, subfamilies and tribes2009In: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 170, no 6, p. 766-793Article in journal (Refereed)
    Abstract [en]

    Rubiaceae are one of the largest families of plants, with ;13,000 species. In this study, we have estimated the phylogeny for 534Rubiaceae taxa from329 generawith up to five different chloroplast regions by Bayesian analysis. It resulted in a highly resolved tree with many strongly supported nodes. There is strong support for the three subfamilies (Cinchonoideae, Ixoroideae, Rubioideae) and most of the 44 included tribes. A scaled-down data set of 173 Rubiaceae taxawas usedwith a Bayesian approach to estimate divergence times for clades classified as tribes and subfamilies. Four fossils were used as minimum age priors, one inside each subfamily and one for Rubiaceae as a whole (Faramea-type pollen, Scyphiphora pollen, Cephalanthus pusillus fruits, and Paleorubiaceophyllum eocenicum leaves). The estimated lineage (stem) divergence time for Rubiaceae is 90.4Ma. The estimated lineage divergence times for the subfamilies are 84.4 (86.6)Ma for Rubioideae, 73.1Ma for Ixoroideae, and 73.1Ma for Cinchonoideae.The estimated lineage divergence times for the tribes vary between 86.6 and 14.2Ma. Classification, relationships, geographical distribution, and age estimates are presented and discussed for all tribes.

  • 2.
    Gehrke, Berit
    et al.
    University of Zurich, Institute for Systematic Botany.
    Bräuchler, Christian
    Department Biologie I, Systematische Botanik, LMU Munich.
    Romoleroux, Katia
    Herbario QCA, Pontificia Universidad Católica del Ecuador.
    Lundberg, Magnus
    Stockholm University, Faculty of Science, Department of Botany.
    Heubl, G
    Department Biologie I, Systematische Botanik, LMU Munich.
    Eriksson, Torsten
    Stockholm University, Faculty of Science, Department of Botany. Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Molecular phylogenetics of Alchemilla, Aphanes and Lachemilla (Rosaceae) inferred from plastid and nuclear intron and spacer DNA sequences, with comments on generic classification2008In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 47, p. 1030-1044Article in journal (Refereed)
    Abstract [en]

    Alchemilla (the lady’s mantles) is a well known but inconspicuous group in the Rosaceae, notable for its ornamental leaves and pharmaceutical properties. The systematics of Alchemilla has remained poorly understood, most likely due to confusion resulting from apomixis, polyploidisation and hybridisation, which are frequently observed in the group, and which have led to the description of a large number of (micro-) species. A molecular phylogeny of the genus, including all sections of Alchemilla and Lachemilla as well as five representatives of Aphanes, based on the analysis of the chloroplast trnL–trnF and the nuclear ITS regions is presented here. Gene phylogenies reconstructed from the nuclear and chloroplast sequence data were largely congruent. Limited conflict between the data partitions was observed with respect to a small number of taxa. This is likely to be the result of hybridisation/introgression or incomplete lineage sorting. Four distinct clades were resolved, corresponding to major geographical division and life forms: Eurasian Alchemilla, annual Aphanes, South American Lachemilla and African Alchemilla. We argue for a wider circumscription of the genus Alchemilla, including Lachemilla and Aphanes, based on the morphology and the phylogenetic relationships between the different clades.

  • 3.
    Kainulainen, Kent
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Persson, Claes
    University of Gothenburg, Department of Systematic Botany.
    Eriksson, Torsten
    Swedish Museum of Natural History, Entomology Department.
    Bremer, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Molecular systematics and morphological character evolution of the Condamineeae (Rubiaceae)2010In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 97, no 12, p. 1961-1981Article in journal (Refereed)
    Abstract [en]

    • Premise of the study: The Condamineeae have in previous molecular studies been shown to be part of an early-divergent cladewithin the subfamily Ixoroideae, together with the tribes Calycophylleae, and Hippotideae, and genera of the former Cinchoneae and Rondeletieae. Generic relationships within this clade have, however, remained largely unresolved

    .• Methods: In this study, the systematics of the Condamineeae was further examined by phylogenetic reconstruction of six cpDNA regions and one nrDNA region using parsimony and Bayesian Markov chain Monte Carlo inference. Morphological character evolution within the tribe was assessed by ancestral state reconstruction using likelihood optimization of characters onto Bayesian trees.

    • Key results: Calycophylleae appears polyphyletic. “Hippotideae” is monophyletic but nested within the Condamineeae. The phylogenetic hypotheses presented support a resurrection of the genera Holtonia, Schizocalyx, and Semaphyllanthe. Furthermore, Bathysa is found to be polyphyletic, Tresanthera is found nested within Rustia, and the taxonomically disputed genus Dialypetalanthus is here shown to be sister to a BothriosporaWittmackanthus clade. Morphological ancestral state reconstructions indicate that protogyny have evolved at least two times within the tribe and that indehiscent fruits, loculicidal fruit dehiscence, and intrapetiolar stipules have evolved independently several times. The occurrence of calycophylls (leaf-like calyx lobes), poricidal anthers, and winged seeds also appear homoplastic within the tribe.

    • Conclusions : A diagnosis and delimitation of the tribe Condamineeae is presented, with taxonomic proposals to synonymize Tresanthera and to transfer several species of Bathysa as well as Phitopis to a resurrected Schizocalyx.

  • 4.
    Lundberg, Magnus
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Töpel, Mats
    Gothenburg University, Department of Environmental Sciences.
    Eriksen, Bente
    Gothenburg University, Department of Environmental Sciences.
    Nylander, Johan
    Stockholm University, Faculty of Science, Department of Botany.
    Eriksson, Torsten
    Stockholm University, Faculty of Science, Department of Botany. Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification2009In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 51, no 2, p. 269-280Article in journal (Refereed)
    Abstract [en]

    Potential events of allopolyploidy may be indicated by incongruences between separate phylogenies based on plastid and nuclear gene sequences. We sequenced two plastid regions and two nuclear ribosomal regions for 34 ingroup taxa in Fragariinae (Rosaceae), and six outgroup taxa. We found five well supported incongruences that might indicate allopolyploidy events. The incongruences involved Aphanes arvensis, Potentilla miyabei, Potentilla cuneata, Fragaria vesca/moschata, and the Drymocallis clade. We evaluated the strength of conflict and conclude that allopolyploidy may be hypothesised in the four first cases. Phylogenies were estimated using Bayesian inference and analyses were evaluated using convergence diagnostics. Taxonomic implications are discussed for genera such as Alchemilla, Sibbaldianthe, Chamaerhodos, Drymocallis and Fragaria, and for the monospecific Sibbaldiopsis and Potaninia that are nested inside other genera. Two orphan Potentilla species, P. miyabei and P. cuneata are placed in Fragariinae. However, due to unresolved topological incongruences they are not reclassified in any genus.

  • 5. Potter, Daniel
    et al.
    Eriksson, Torsten
    Stockholm University, Faculty of Science, Department of Botany. Bergianska stiftelsen.
    Evans, Rodger C
    Oh, S
    Smedmark, Jenny
    Stockholm University, Faculty of Science, Department of Botany. Bergianska stiftelsen.
    Morgan, David R
    Kerr, Malin
    Robertson, Kenneth R
    Arsenault, Matthew
    Dickinson, Timothy A
    Campbell, Christopher S
    Phylogeny and classification of Rosaceae2007In: Plant Systematics and Evolution, Vol. 266, p. 5-43Article in journal (Refereed)
  • 6. Rutschmann, Frank
    et al.
    Eriksson, Torsten
    Stockholm University, Faculty of Science, Department of Botany. Bergianska stiftelsen.
    Abu Salim, Kamariah
    Conti, Elena
    Assessing calibration uncertainty in molecular dating: The assignment of fossils to alternative calibration points2007In: Systematic Biology, ISSN 1063-5157, Vol. 56, no 4, p. 591-608Article in journal (Refereed)
  • 7. Wartiainen, Ingvild
    et al.
    Eriksson, Torsten
    Stockholm University, Faculty of Science, Bergianska botaniska trädgården (tills m Kungl. Vet. Ak.). Department of Botany. Bergianska stiftelsen.
    Zheng, Weiwen
    Rasmussen, Ulla
    Department of Botany. Växtfysiologi.
    Variation in the active diazotrophic community in rice paddy - nifH PCR-DGGE analysis of rhizosphere and bulk soil2008In: Applied Soil Ecology, Vol. 39, p. 65-75Article in journal (Refereed)
    Abstract [en]

    Biological nitrogen fixation (BNF) is an important source of nitrogen input in many natural ecosystems. The rice production today depends on large amounts of chemical nitrogen fertilizer, which is an environmental hazard in rice producing areas. Better exploitation of BNF is one way to reduce the use of chemical nitrogen fertilizer in the future. In this study the active diazotrophic community was investigated in nitrogen fertilized and un-fertilized rice field soils in Fujian Province, southeast China by PCR-DGGE of nifH mRNA, and the potential community by PCR-DGGE of the nifH gene. A total of 45 sequences representing 33 different sequence types were recovered from the DGGE gels. The retrieved cDNA sequences representing the active population of diazotrophs both in fertilized and un-fertilized soils dispersed throughout the nifH clades (alpha-, beta- and gamma Proteobacteria, Firmicutes and Archaea). Thirteen of the sequence types were most closely related to Azoarcus endophytes indicating widespread associations between heterotrophic nitrogen fixing bacteria and rice (Oryza sativa). The majority of the 13 sequence types were identified from the cDNA samples, showing that the Azoarcus might be an important active nitrogen fixing diazotroph in the paddy field. None of the sequence types were closely related to cyanobacteria, nevertheless previous studies from the same area had documented the presence of cyanobacteira in rice fields. The lack of identified cyanobacteria might be due to template discrimination in the PCR reactions, or low abundance of cyanobacteria compared to heterotrophic nitrogen fixing bacteria.

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