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  • 1. 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)
  • 2. 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)
  • 3.
    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.

  • 4. 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)
  • 5. 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.

  • 6.
    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.

  • 7.
    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.

  • 8.
    Frajman, Bozo
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Jogan, Nec
    Oxelman, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Heliosperma insulare Trinajstic' (Caryophyllaceae, Sileneae), a neglected species from the island Mljet (Croatia).2004In: Book of Abstracts.: Croatian Botanical Society, Zagreb, 2004, p. 110-111Conference paper (Other scientific)
  • 9.
    Frajman, Bozo
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Phylogeny of Heliosperma based on chloroplast and nuclear DNA sequences.2004In: Plant evolution in Mediterranean Climate Zones.: IXth IOPB Meeting, Valencia, 2004, p. 66-Conference paper (Other scientific)
  • 10.
    Frajman, Božo
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Reticulate phylogenetics and phytogeographical structure of Heliosperma (Sileneae, Caryophyllaceae) inferred from chloroplast and nuclear DNA sequences2007In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 43, no 1, p. 140-155Article in journal (Refereed)
    Abstract [en]

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

  • 11. Grundt, Hanne Hegre
    et al.
    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.
    Brochmann, Christian
    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.
    Polyploid origins in a circumpolar complex in Draba (Brassicaceae) inferred from cloned nuclear DNA sequences and fingerprints.2004In: Mol Phylogenet Evol, ISSN 1055-7903, Vol. 32, no 3, p. 695-710Article in journal (Refereed)
  • 12. Huber, Katharina T.
    et al.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Lott, Martin
    Moulton, Vincent
    Reconstructing the evolutionary history of polyploids from multilabeled trees2006In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 23, no 9, p. 1784-1791Article in journal (Refereed)
    Abstract [en]

    In recent studies, phylogenetic networks have been derived from so-called multilabeled trees in order to understand the origins of certain polyploids. Although the trees used in these studies were constructed using sophisticated techniques in phylogenetic analysis, the presented networks were inferred using ad hoc arguments that cannot be easily extended to larger, more complicated examples. In this paper, we present a general method for constructing such networks, which takes as input a multilabeled phylogenetic tree and outputs a phylogenetic network with certain desirable properties. To illustrate the applicability of our method, we discuss its use in reconstructing the evolutionary history of plant allopolyploids. We conclude with a discussion concerning possible future directions. The network construction method has been implemented and is freely available for use from http://www.uea.ac.uk/similar to a043878/padre.html.

  • 13.
    Kool, Anneleen
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Systematisk botanik.
    Oxelman, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Systematisk botanik.
    Thulin, Mats
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Systematisk botanik.
    Phylogeny of Withania (Solanaceae)2005In: abstracts XVII International Botanical Congress: Vienna, Austria, Europe 17-23 July 2005, 2005Conference paper (Other scientific)
    Abstract [en]

    Withania is a genus of about 11 species, six endemic in the Horn of Africa region, three in the Canary Islands, North Africa and Spain, one in southern Asia, and one widespread in the Old World tropics and subtropics. A phylogeny was inferred on the basis of DNA sequence data from three plastid regions: the trnL intron, trnL-F intergenic spacer, and the rps16 intron, as well as the nuclear ribosomal internal transcribed spacer (ITS). We found strong evidence for monophyly of Withania. The enigmatic Mellissia begonifolia, endemic to St Helena, probably is Withania’s nearest sistergroup and as sister of Withania and Mellissia we found some evidence for a clade consisting of Athenaea and Aureliana. All species of Withania except for W. aristata and W. frutescens form a clade that have W. aristata and/or W. frutescens as sister group. W. coagulans groups together with W. riebeckii in the chloroplast phylogeny but does not so on the basis of the ITS data. It may be of allopolyploid origin. Otherwise the phylogeny of the Horn of Africa taxa remains poorly resolved.

  • 14.
    Oxelman, Bengt
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Kornhall, Per
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Norman, Eliane
    Buddlejaceae2004In: The families and genera of flowering plants, Springer-Verlag, Berlin , 2004, p. 39-44Chapter in book (Refereed)
  • 15.
    Oxelman, Bengt
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk Botanik.
    Kornhall, Per
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Olmstead, Richard G.
    Bremer, Birgitta
    Further disintegration of Scrophulariaceae2005In: TAXON, Vol. 54, p. 411-425Article in journal (Refereed)
  • 16.
    Oxelman, Bengt
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Popp, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lazkov, Georgy
    Frajman, Bozo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Erixon, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Långström, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Rautenberg, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Heidari, Nahid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Treelike and reticulate phylogeny of Sileneae and its implications on taxonomy2005In: XVII International Botanical Congress: abstracts : Vienna, Austria, Europe, Austria Center Vienna 17-23 July 2005 : 100 Years after the II IBC in Vienna 1905, 2005, p. 11-11Conference paper (Other academic)
  • 17.
    Oxelman, Bengt
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Yoshikawa, Nori
    McConaughy, Betty L
    Luo, Jie
    Denton, Amy L
    Hall, Benjamin D
    RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids.2004In: Molecular Phylogenetics and Evolution, Vol. 32, no 2, p. 462-479Article in journal (Refereed)
    Abstract [en]

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

    PMID: 15223030 [PubMed - indexed for MEDLINE]

  • 18.
    Popp, Magnus
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Erixon, Per
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Eggens, Frida
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Origin and evolution of a circumpolar polyploid species complex in Silene (Caryophyllaceae).2005In: Systematic Botany, Vol. 30, p. 302-311Article in journal (Refereed)
  • 19.
    Popp, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Origin and evolution of North American Polyploid Silene (Caryophyllaceae)2007In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 94, no 3, p. 330-349Article in journal (Refereed)
    Abstract [en]

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

  • 20.
    Popp, Magnus
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Oxelman, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    The significance of reticulate evolution in the phylogenetic history of Sileneae (Caryophyllaceae).2004In: Plant evolution in Mediterranean Climate Zones.: IXth IOPB Meeting, Valencia,, 2004, p. 65-Conference paper (Other scientific)
  • 21.
    Rautenberg, Anja
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk botanik.
    Filatov, Dmitry
    Oxelman, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk botanik.
    Phylogenetic origins of dioecy in Silene2005In: Abstracts IBC XVII, 2005Conference paper (Other scientific)
    Abstract [en]

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

  • 22.
    Rautenberg, Anja
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk botanik.
    Oxelman, Bengt
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Systematic Botany. Systematisk botanik.
    Recombination between distinct lineages in Silene?2007In: Abstracts - XI Congress European Society for Evolutionary Biology, 2007Conference paper (Other scientific)
    Abstract [en]

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

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