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  • 1. Ahlandsberg, Staffan
    Metabolic engineering of starch synthesis in barley2001Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Starch is an important industrial raw material both for food and non-food purposes. In plants, starch is deposited in the leaf and in the storage tissues such as seed endosperm, roots or tubers. Starch is a glucose polymer, and its synthesis involves four groups of enzymes, ADP-glucose-pyrophosphorylase (AGPase), starch synthases (SS), starch branching enzymes (SBE), and starch debranching enzymes (DBE). In barley, four isoforms of SBE have been identified and the temporal and spatial expression of their genes (sbe) has been studied in our lab.

    The long-term objective of our research is to produce novel starches in planta for industrial applications. This requires the transformation of barley in order to produce transgenic plants with altered activity for one or more sbe genes. Using a plant-optimized version of Green Fluorescent Protein (GFP) as the only marker we produced a transgenic Nordic elite cultivar of barley in 1999. The usefulness of GFP as a marker has also been applied in various transient experiments and for this reason a set of monocotyledonous expression vectors has been developed. Using these vectors, the spatial expression pattern of the sbeII genes has been investigated.

    The sbeIIa and sbeIIb genes are differentially transcribed during barley seed development. The sbeIIb gene is expressed exclusively in the endosperm while the sbeIIa gene is expressed also in embryonic and vegetative tissues. The tissue specific regulation of the sbeII genes was hown to be executed via a repressor protein acting on a cis element located in the second intron of the sbeIIb gene. We also suggest that the repression is controlled by the local sugar concentration in the barley seed endosperm.

  • 2. Amer, Ranya
    et al.
    Diez, Beatriz
    Stockholm University, Faculty of Science, Department of Botany.
    El-Shehawy, Rehab
    Stockholm University, Faculty of Science, Department of Botany.
    Diversity of hepatotoxic cyanobacteria in the Nile Delta, Egypt2009In: Journal of Environmental Monitoring, ISSN 1464-0325, E-ISSN 1464-0333, Vol. 11, no 1, p. 126-133Article in journal (Refereed)
    Abstract [en]

    Optimized denaturing gradient gel electrophoresis (DGGE) fingerprinting and real-time PCR were performed to identify and quantify the potential hepatotoxic microcystin-and nodularin-producing cyanobacteria present in freshwater samples collected during different seasons at three different sites from the Nile River Delta. The combined use of molecular gene markers (targeting the aminotransferase domain of the hepatotoxin synthetase modules and the 16S rRNA gene) and light microscopy demonstrated the dominance of different freshwater Microcystis phylotypes, including the potential hepatotoxin producers M. wesenbergii and M. aeruginosa, several Synechococcus and Cyanobium phylotypes, as well as the presence of Nodularia spumigena and Cylindrospermopsis raciborskii in the samples ""collected during summer 2006 and winter 2007''. Certain seasonal changes (summer and winter) in Microcystis microdiversity were detected. Real-time PCR revealed no difference in the quantities of potential hepatotoxin-producing cyanobacterial communities between summer and winter, but did show differences between the three sampling sites investigated. The expression of the aminotransferase domain analyzed by DGGE fingerprinting demonstrated that all Microcystis phylotypes present in the samples might have been active at the time of the sampling. Statistical analysis showed a significant effect of TP, and not TN, on the relative abundance of the potentially hepatotoxic cyanobacterial community.

  • 3.
    Anderhag, Per
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Hepler, P. K.
    Lazzaro, M. D.
    Microtubules and microfilaments are both responsible for pollen tube elongation in the coniferPicea abies (Norway spruce)2000In: Protoplasma, ISSN 0033-183X, E-ISSN 1615-6102, Vol. 214, no 3, p. 141-157Article in journal (Refereed)
    Abstract [en]

    InPicea abies (Norway spruce), microtubules and actin microfllaments both form a dense matrix throughout the tube mainly parallel to the direction of elongation. In these conifer pollen tubes the organization of this matrix is different from that in angiosperms. This study tests our hypothesis that differences in cytoskeletal organization are responsible for differences in tube growth and physiology. Pollen grains were germinated in media containing cytoskeletal disrupters and analyzed for germination, tube length, tube branching, and tip swelling. Disruption of microtubules significantly inhibits tube elongation and induces tube branching and tip swelling. Tip swelling is probably caused by disruption of the microtubules in the tip that are perpendicular to the direction of elongation. Confocal microscopy indicates that colchicine and propyzamide cause fragmentation of microtubules throughout the tube. Oryzalin and amiprophosmethyl cause a complete loss of microtubules from the tip back toward the tube midpoint but leave microtubules intact from the midpoint back to the grain. Disruption of microfilaments by cytochalasins B and D and inhibition of myosin by N-ethylmaleimide or 2,3-butanedione monoxime stops tube growth and inhibits germination. Microfilament disruption induces short branches in tubes, probably originating from defective microfilament organization behind the tip. In addition, confocal microscopy coupled with microinjection of fluorescein-labeled phalloidin into actively growing pollen tubes indicates that microfllament bundles extend into the plastid-free zone at the tip but are specifically excluded from the growing tip. We conclude that microtubules and microfilaments coordinate to drive tip extension in conifer pollen tubes in a model that differs from angiosperms.

  • 4.
    Andersson, Petter
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Hambäck, Peter A.
    Stockholm University, Faculty of Science, Department of Botany.
    What shapes local density?: The importance of migration rates and local growth for density-patch size relationships in two Cionus weevils2012In: Ecological Entomology, ISSN 0307-6946, E-ISSN 1365-2311, Vol. 37, no 1, p. 90-98Article in journal (Refereed)
    Abstract [en]

    1. The relative effect of migration and local growth on the spatio-temporal density-distribution of two co-existing herbivorous weevils, Cionus scrophulariae L. and C. tuberculosus Scop., in 32 host plant Scrophularia nodosa L. patches of varying sizes was investigated. 2. Predictions of the temporal development of the slope in the density-patch size relationships were derived from a basic population model with scale-dependent migration rates. The model indicated that the slopes in the density-patch size relationships during the early season should be reflected by the net scaling of immigration and emigration rates, whereas the slopes during the later season should increase as a result of local growth. 3. Emigration rates of the weevils were estimated in a field experiment, were the weevils coexisted in space and time. These results were then combined with a previous estimate of immigration rates in order to determine the net scaling of migration rates. 4. The emigration rate differed between species, caused by different movement rates in small patches, which could explain differences in the general slope of the density-patch size relationships of the weevils in the natural figwort patches throughout the summer. The slopes in the relationships in the early season were largely predicted by the net scaling of migration rates. The slope also increased in the later season for C. tuberculosus, whereas the slope decreased for C. scrophulariae. 5. It was concluded that the understanding of both inter- and intra-specific variations in density-patch size relationships of insect herbivores can be improved using population models incorporating scale-dependent migration and local growth.

  • 5.
    Andersson, Sylvia
    Stockholm University, Faculty of Science.
    The influence of salinity and antifouling agents on Baltic Sea Fucus vesiculosus with emphasis on reproduction1996Doctoral thesis, comprehensive summary (Other academic)
  • 6. Andriamihajarivo, Tefy H.
    et al.
    Razafimandimbison, Sylvain G.
    Stockholm University, Faculty of Science, Department of Botany.
    Karehed, Jesper
    Phyllopentas flava (Rubiaceae), a New Morphologically Heterodistylous and Functionally Dioecious Species from Madagascar2011In: Systematic Botany, ISSN 0363-6445, E-ISSN 1548-2324, Vol. 36, no 4, p. 1024-1027Article in journal (Refereed)
    Abstract [en]

    A new species of the Afro-Malagasy genus Phyllopentas Karehed & B. Bremer, Phyllopentas flava Razafim., T. Andriam. et Karehed, is described and illustrated. This plant is restricted to the Itremo region in southeastern Madagascar and is distinct morphologically from the other species of the genus by its pubescent, narrowly ovate to narrowly elliptic leaves, grey-whitish and thickly hairy midribs and secondary veins on the lower surfaces of leaves, and functionally dioecious and heterodistylous flowers. Summaries of distribution, phenology, habitat, and ecology are given and a conservation assessment is also provided.

  • 7. Appelhans, M. S.
    et al.
    Smets, E.
    Razafimandimbison, Sylvain G.
    Stockholm University, Faculty of Science, Department of Botany.
    Haevermans, T.
    van Marle, E. J.
    Couloux, A.
    Rabarison, H.
    Randrianarivelojosia, M.
    Kessler, P. J. A.
    Phylogeny, evolutionary trends and classification of the Spathelia-Ptaeroxylon clade: morphological and molecular insights2011In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 107, no 8, p. 1259-1277Article in journal (Refereed)
    Abstract [en]

    Background and Aims The Spathelia-Ptaeroxylon clade is a group of morphologically diverse plants that have been classified together as a result of molecular phylogenetic studies. The clade is currently included in Rutaceae and recognized at a subfamilial level (Spathelioideae) despite the fact that most of its genera have traditionally been associated with other families and that there are no obvious morphological synapomorphies for the clade. The aim of the present study is to construct phylogenetic trees for the Spathelia-Ptaeroxylon clade and to investigate anatomical characters in order to decide whether it should be kept in Rutaceae or recognized at the familial level. Anatomical characters were plotted on a cladogram to help explain character evolution within the group. Moreover, phylogenetic relationships and generic limits within the clade are also addressed. Methods A species-level phylogenetic analysis of the Spathelia-Ptaeroxylon clade based on five plastid DNA regions (rbcL, atpB, trnL-trnF, rps16 and psbA-trnH) was conducted using Bayesian, maximum parsimony and maximum likelihood methods. Leaf and seed anatomical characters of all genera were (re) investigated by light and scanning electron microscopy. Key Results With the exception of Spathelia, all genera of the Spathelila-Ptaeroxylon clade are monophyletic. The typical leaf and seed anatomical characters of Rutaceae were found. Further, the presence of oil cells in the leaves provides a possible synapomorphy for the clade. Conclusions The Spathelia-Ptaeroxylon clade is well placed in Rutaceae and it is reasonable to unite the genera into one subfamily (Spathelioideae). We propose a new tribal classification of Spathelioideae. A narrow circumscription of Spathelia is established to make the genus monophyletic, and Sohnreyia is resurrected to accommodate the South American species of Spathelia. The most recent common ancestor of Spathelioideae probably had leaves with secretory cavities and oil cells, haplostemonous flowers with appendaged staminal filaments, and a tracheidal tegmen.

  • 8.
    Asplund-Samuelsson, Johannes
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Bergman, Birgitta
    Stockholm University, Faculty of Science, Department of Botany.
    Larsson, John
    Stockholm University, Faculty of Science, Department of Botany.
    Prokaryotic Caspase Homologs: Phylogenetic Patterns and Functional Characteristics Reveal Considerable Diversity2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 11, p. e49888-Article in journal (Refereed)
    Abstract [en]

    Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18%) were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota). Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse subgroups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.

  • 9.
    Auffret, Alistair G.
    Stockholm University, Faculty of Science, Department of Physical Geography and Quaternary Geology.
    Can seed dispersal by human activity play a useful role for the conservation of European grasslands?2011In: Applied Vegetation Science, ISSN 1402-2001, E-ISSN 1654-109X, Vol. 14, no 3, p. 291-303Article in journal (Refereed)
    Abstract [en]

    Objective: To review the recent research into human-mediated dispersal (HMD) in the European rural landscape, and explore the potential positive aspect of HMD for grassland conservation, in contrast to it's common association with the spread of invasive species. Methods: A literature search was undertaken to identify HMD vectors in the rural landscape for discussion regarding dispersal potential past and present, implications for management, and the identification of future research needs. Results: Grazing animals are important propagule dispersers, but the reduced movement of livestock through the landscape has also meant a reduction in seeds dispersed in this way. Other, non-standard human-mediated dispersal vectors such as clothing and motor vehicles can also transport seeds of many species, and HMD vectors often transport seeds with a variety of dispersal specialisations. Recommendations: There should be a greater movement of grazing animals throughout the landscape, either within larger grazing areas or between existing grasslands. Where this is not possible, other, more directed dispersal of propagules from species-rich communities to target sites should be considered. The potential of non-standard HMD vectors to make a positive contribution to biodiversity should be considered, but more research into all types of HMD vectors is important if we are to fully understand their role in the dispersal of plant species in fragmented landscapes.

  • 10.
    Bauer, Karolina
    Stockholm University, Faculty of Science, Department of Botany.
    Diazotrophy and diversity of benthic cyanobacteria in tropical coastal zones2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Discoveries in recent years have disclosed the importance of marine cyano-bacteria in the context of primary production and global nitrogen cycling. It is hypothesized here that microbial mats in tropical coastal habitats harbour a rich diversity of previously uncharacterized cyanobacteria and that benthic marine nitrogen fixation in coastal zones is substantial.

    A polyphasic approach was used to investigate cyanobacterial diversity in three tropical benthic marine habitats of different characters; an intertidal sand flat and a mangrove forest floor in the Indian Ocean, and a beach rock in the Pacific Ocean. In addition, nitrogenase activity was measured over diel cycles at all sites. The results revealed high cyanobacterial diversity, both morphologically and genetically. Substantial nitrogenase activity was observed, with highest rates at daytime where heterocystous species were present. However, the three habitats were dominated by non-heterocystous and unicellular genera such as Microcoleus, Lyngbya, Cyanothece and a large group of thin filamentous species, identified as members of the Pseudanabaenaceae family. In these consortia nocturnal nitrogenase activities were highest and nifH sequencing also revealed presence of non-cyanobacterial potential diazotrophs. A conclusive phylogenetic analysis of partial nifH sequences from the three sites and sequences from geographi-cally distant microbial mats revealed new clusters of benthic potentially ni-trogen-fixing cyanobacteria. Further, the non-heterocystous cyanobacterium Lyngbya majuscula was subjected to a physiological characterization to gain insights into regulatory aspects of its nitrogen fixation. The data demon-strated that nitrogenase activity is restricted to darkness, which called upon a re-evaluation of its diazotrophic behaviour.

  • 11.
    Bengtson, Annika
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Systematics and biogeography of the South African Metalasia clade (Asteraceae-Gnaphalieae)2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The Metalasia clade (Asteraceae–Gnaphalieae) consisting of the genera Metalasia, Atrichantha, Calotesta, Dolichothrix, Hydroidea, Lachnospermum, Phaenocoma, and Planea is endemic to South Africa with a main distribution within the Cape Floristic Region (CFR), a region known for its remarkable botanical diversity.

    The monophyly of the Metalasia clade, the relationships of its genera, and the circumscription of these as well as their position within the tribe Gnaphalieae is investigated using molecular data. The study confirms the Metalasia clade to be a monophyletic group, untangling the relationships between the included genera.

    Five new Metalasia species have been described since the latest revision of the genus, three of which are described in the present work. An updated key to all 57 species of the genus is also provided.

    A phylogenetic study of the genus Metalasia, including all 57 species, based on a combination of morphological and molecular data shows that Metalasia consists of two sister clades, Clade A and Clade B, morphologically separated by the papillose cypselas of Clade A. Metalasia is, however, not supported as monophyletic, and Lachnospermum is placed together with the Metalasia species of Clade B. Further, the monotypic Planea, originally described as Metalasia schlechteri, is placed well within Clade B.

    A biogeographical study reveals Metalasia to have evolved in the CFR around 6.9 Ma. Ancestral area estimations present a possible scenario for the radiation of Metalasia and show a difference between Clade A and B, correlated to the different rainfall regimes of southern Africa. The results show that Clade B began to diversify around 6.4 Ma in the winter rainfall area, whereas the diversification of the Clade A crown group, which is estimated to only 3.3 Ma, was initiated in the all-year rainfall area.

  • 12.
    Bengtson, Annika
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Anderberg, A. A.
    Karis, Per Ola
    Stockholm University, Faculty of Science, Department of Botany.
    Three new species of metalasia (asteraceae gnaphalieae) from the western cape and an updated key to the genus2013In: South African Journal of Botany, ISSN 0254-6299, E-ISSN 1727-9321, Vol. 84, p. 72-82Article in journal (Refereed)
    Abstract [en]

    Three new species of Metalasia from the Western Cape of South Africa are described; Metalasia tristis A.Bengtson & P.O.Karis, a small shrublet from the Groot Winterhoek Mountains, and Metalasia formosa A.Bengtson & P.O.Karis and Metalasia eburnea A.Bengtson & P.O.Karis both found in the Langeberg Mountains. The morphology and relationships of the three new species are discussed, and an updated key to the genus is provided.

  • 13.
    Bengtson, Annika
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Anderberg, Arne A.
    Karis, Per Ola
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Phylogeny and evolution of the South African genus Metalasia (Asteraceae-Gnaphalieae) inferred from molecular and morphological data2014In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 174, no 2, p. 173-198Article in journal (Refereed)
    Abstract [en]

    Metalasia is a genus in tribe Gnaphalieae (Asteraceae), endemic to South Africa and with its main distribution in the Cape Floristic Region. The genus comprises 57 species and, with a number of closely related genera, it constitutes the Metalasia clade'. A species-level phylogenetic analysis is presented, based on DNA sequences from two nuclear (internal and external transcribed spacer: ITS, ETS) and two plastid (psbA-trnH, trnL-trnF) regions together with morphological data. Analyses combining molecular and morphological data attempt not only to resolve species interrelationships, but also to detect patterns in character evolution. Phylogenetic analyses corroborate our earlier study and demonstrate that Metalasia is formed of two equally sized, well-supported sister groups, one of which is characterized by papillose cypselas. The results differ greatly from earlier hypotheses based on morphology alone, as few morphological characters support the phylogenetic patterns obtained. The two clades of Metalasia do, however, appear to differ in distribution, corresponding to the different rainfall regimes of South Africa. Analyses show a few taxa to be problematic; one example is the widely distributed M.densa which appears to be an intricate species complex.

  • 14.
    Bengtson, Annika
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Anderberg, Arne A.
    Karis, Per Ola
    Stockholm University, Faculty of Science, Department of Botany.
    PHYLOGENY AND GENERIC DELIMITATION OF THE METALASIA CLADE (ASTERACEAE-GNAPHALIEAE)2011In: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 172, no 8, p. 1067-1075Article in journal (Refereed)
    Abstract [en]

    The Metalasia clade, which consists of the genus Metalasia and a number of much smaller satellite genera, is a South African group in the tribe Gnaphalieae (Asteraceae). This study scrutinizes the phylogenetic relationships of the Metalasia clade by means of chloroplast (trnL-trnF, psbA-trnH) and nuclear (external transcribed spacer, internal transcribed spacer) sequence data. The Metalasia clade is confirmed to be a monophyletic group, and the phylogenetic positions of the included genera are determined. The genus Metalasia may be monophyletic if the monotypic Planea is included, but the node has very poor support and further studies are needed. The Metalasia species fall into two well-supported groups, distinguishing the members of Karis's Metalasia densa group from the others. Lachnospermum is shown to be monophyletic and is placed as a possible sister group to Metalasia. Phaenocoma is placed as sister to the branch consisting of Metalasia and Lachnospermum. Calotesta, Hydroidea, and Atrichantha form a clade, with the monotypic Dolichothrix as their sister group.

  • 15.
    Bergqvist, Claes
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Arsenic accumulation in plants for food and phytoremediation: Influence by external factors2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Arsenic (As) appears in the environment as various As species, which may vary in plant uptake and toxicity. Moreover, As exposure may vary between habitat due to availability and speciation, both of which are influenced by redox potential. To decrease As uptake, addition of silicate may be a tool.

    The aim of the study was to investigate how the external factors As availability, plant habitats, silicon and oxygen level, influenced the accumulation and speciation of As in plants for food and phytoremediation in a temperate region. The external factors were chosen due to their previously showed influence on As in plants.

    The risks with dietary As was investigated by plant As accumulation and speciation in carrot, lettuce and spinach grown in alum shale and glassworks soils, and by the influence of silicon on As accumulation in lettuce in hydroponics. Suitable plants for As phytoremediation was investigated by analysing plants from various habitats, and by the O2 influence on phytofiltration.

    The results showed that vegetables accumulated more As in soils with higher As extractability, and the As extractability in the rhizosphere was higher than in bulk soil. Also, the As concentration in lettuce was higher in hydroponics than in soil, but silicon reduced the accumulation of As in lettuce in hydroponics. Also, the more toxic inorganic As were the main As species detected in vegetables, compared with the less toxic organic As. For phytoremediation, the results showed a low As accumulation in emergent and terrestrial plants. Submerged plants had had a higher shoot As concentration. In general, the habitat had a major influence on the As accumulation in plants. The results also showed that the As accumulation properties in Elodea canadensis was reduced at higher O2.

    In conclusion, consumption of vegetables cultivated in As polluted soils can result in an elevated intake of inorganic As, and E. canadensis is a promising candidate for As phytofiltration in a temperate region.

  • 16.
    Bergqvist, Claes
    Stockholm University, Faculty of Science, Department of Botany.
    Arsenic accumulation in various plant types2011Licentiate thesis, comprehensive summary (Other academic)
  • 17.
    Bergqvist, Claes
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Greger, Maria
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Arsenic accumulation and speciation in plants from different habitats2012In: Applied Geochemistry, ISSN 0883-2927, E-ISSN 1872-9134, Vol. 27, no 3, p. 615-622Article in journal (Refereed)
    Abstract [en]

    Understanding As accumulation in plants is necessary in order to alleviate problems with As in the environment and to improve sustainable As phytotechnologies. To find suitable candidates for phytoremediation purposes and to investigate specific accumulation patterns due to growth habitat and plant groups, As accumulation in 124 plant species collected from different habitats and speciation in 6 of these plant species, was determined. The data show that submerged plants have a higher accumulation than emergent and terrestrial plants. The As concentration in terrestrial and emergent plants were correlated with the [As](soil), while the accumulation factor correlated negatively with [As](soil). Gymnosperms had a high [As](shoot):[As](root) ratio. The inorganic As species, arsenate and arsenite were found in plants from all habitats and methylarsonic acid (MMA) in all but one plant species. Arsenate predominated in submerged plants. The results suggest that the habitat and the [As](soil) have a strong influence on the As accumulation in plants and that submerged plants and/or gymnosperms might be suitable for phytoremediation of As.

  • 18.
    Bergqvist, Claes
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Greger, Maria
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Oxygen influences on arsenic behaviour in sediment-water-plant system of Elodea canadensisManuscript (preprint) (Other academic)
    Abstract [en]

    Phytofiltration can be used to remove arsenic (As) from water using the submerged macrophyte Elodea canadensis. To understand the effects of aeration on this system, we investigated the influence of different O2 levels on the As concentration and speciation in sediment, water and E. canadensis,and the efficiency of phytofiltration of As by this plant. The water in pots with As, E. canadensis and/or sediment were aerated with N2, air or left unmodified to create low, high and medium O2 levels, respectively. Analyses of As concentration and species were performed with HPLC-AAS. The results showed that the As accumulation properties by E. canadensis decreased at high O2. Medium O2 had the lowest As release from sediment to water and among the highest plant As accumulation. Arsenate predominated in the sediment-water-plant system, but arsenite increased with decreasing O2. To create conditions favouring the binding of As in sediment and accumulation from water by E. canadensis, the O2 concentration should be medium.

  • 19.
    Bergqvist, Claes
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Herbert, Roger
    Department of Earth Sciences, Uppsala University.
    Persson, Ingmar
    Department of Inorganic and Physical Chemistry, Swedish University of Agricultural Sciences.
    Greger, Maria
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Accumulation and speciation of arsenic in vegetables cultivated in soils with various As availabilityManuscript (preprint) (Other academic)
    Abstract [en]

    The toxicity of arsenic (As) in the environment is controlled by its concentration, availability and speciation. The aims of the study were to evaluate the accumulation and speciation of As in three vegetables (carrot, lettuce, spinach) cultivated in both contaminated and natural soils with various As concentrations and to estimate the concomitant health risks associated with the consumption of the vegetables. Arsenic concentration and speciation in plant tissues and soils was analysed by HPLC, AAS and X-ray absorption near-edge structure (XANES) spectroscopy. To estimate the plants influence in the rhizosphere, organic acids in lettuce root exudates were analysed by ion chromatography. The results showed that the As accumulation was higher in plants cultivated in soil with higher As extractability. Arsenate predominated in the soils, rhizosphere and root exudates of lettuce. Succinic acid was the major organic acid in lettuce root exudates. Arsenite was the predominating As species in the shoots of healthy looking plants. In plants showing signs of phytotoxicity, arsenate was predominating. Ingestion of the tested vegetables may result in an intake of elevated levels of As.

  • 20. Berry, Alison M.
    et al.
    Mendoza-Herrera, Alberto
    Guo, Ying-Yi
    Hayashi, Jennifer
    Persson, Tomas
    Stockholm University, Faculty of Science, Department of Botany.
    Barabote, Ravi
    Demchenko, Kirill
    Zhang, Shuxiao
    Pawlowski, Katharina
    Stockholm University, Faculty of Science, Department of Botany.
    New perspectives on nodule nitrogen assimilation in actinorhizal symbioses2011In: Functional Plant Biology, ISSN 1445-4408, E-ISSN 1445-4416, Vol. 38, no 8-9, p. 645-652Article, review/survey (Refereed)
    Abstract [en]

    Nitrogen-fixing root nodules are plant organs specialised for symbiotic transfer of nitrogen and carbon between microsymbiont and host. The organisation of nitrogen assimilation, storage and transport processes is partitioned at the subcellular and tissue levels, in distinctive patterns depending on the symbiotic partners. In this review, recent advances in understanding of actinorhizal nodule nitrogen assimilation are presented. New findings indicate that Frankia within nodules of Datisca glomerata (Presl.) Baill. carries out both primary nitrogen assimilation and biosynthesis of arginine, rather than exporting ammonium. Arginine is a typical storage form of nitrogen in plant tissues, but is a novel nitrogen carrier molecule in root nodule symbioses. Thus Frankia within D. glomerata nodules exhibits considerable metabolic independence. Furthermore, nitrogen reassimilation is likely to take place in the host in the uninfected nodule cortical cells of this root nodule symbiosis, before amino acid export to host sink tissues via the xylem. The role of an augmented pericycle in carbon and nitrogen exchange in root nodules deserves further attention in actinorhizal symbiosis, and further highlights the importance of a comprehensive, structure-function approach to understanding function in root nodules. Moreover, the multiple patterns of compartmentalisation in relation to nitrogen flux within root nodules demonstrate the diversity of possible functional interactions between host and microsymbiont that have evolved in the nitrogen-fixing clade.

  • 21.
    Bertell, Gertrud
    Stockholm University, Faculty of Science, Department of Botany.
    Interaction between auxin, cytokinin and ethylene in the regulation of root growth in Pisum sativum L.1992Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The effects of exogenous auxins (indole-3-acetic acid (IAA), indole-3-butyric acid (IBA) and 2,4-dichlorophenoxyacetic acid (2,4-D)), cytokinins (benzylaminopurine (BAP) and zeatin) and ethylene, applied as the precursor 1 -aminocyclopropane- 1-carboxylic acid (ACC), on the root growth of pea (Pisumsativum L.) seedlings were investigated. Ethylene production was determined in the excised root tips of intact seedlings that had been growing in the test solutions for specified time periods. Treatment of roots with auxins, cytokinins or ACC inhibited root elongation and caused swelling (increased diameter) of the part of the roots formed in the presence of the regulator. Both auxins and cytokinins are known to stimulate ethylene production in plant materials. Over the last 20 years there have been many proponents of the hypothesis that the inhibition of root elongation caused by auxin is mediated by an auxin-induced increasein ethylene production in the roots. In an investigation with IAA at concentrations causing partial inhibition, three lines of evidence indicated that the hypothesis was not valid for intact roots: (1) IAA caused only a small, transient increase in ethylene production, but the inhibition of root growth was longlasting; (2) ethylene produced from added ACC only caused a similar degree of inhibition in cases where its production was increased several times and lasted throughout the growth period; (3) inhibitors of ethylene biosynthesis (cobalt ions) and action (silver ions) counteracted the effects of added ACC but notof IAA. In addition, ethylene and auxins interacted synergistically in inducing elongation and swelling of the roots. The cytokinin BAP caused a more prolonged increase in ethylene production than the auxins, and the effects of this regulator on elongation and swelling could be reversed, especially by cobalt ions.Ethylene produced from ACC decreased the endogenous level of IAA, whereas BAP increased the IAA amount per root tip. The degree to which BAP inhibited elongation depended on the concentration of calcium in the growth medium.

  • 22. Bisang, Irene
    et al.
    Ehrlén, Johan
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Persson, Christin
    Hedenas, Lars
    Family affiliation, sex ratio and sporophyte frequency in unisexual mosses2014In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 174, no 2, p. 163-172Article in journal (Refereed)
    Abstract [en]

    Patterns of sex expression and sex ratios are key features of the life histories of organisms. Bryophytes are the only haploid-dominant land plants. In contrast with seed plants, more than half of bryophyte species are dioecious, with rare sexual expression and sporophyte formation and a commonly female-biased sex ratio. We asked whether variation in sex expression, sex ratio and sporophyte frequency in ten dioecious pleurocarpous wetland mosses of two different families was best explained by assuming that character states evolved: (1) in ancestors within the respective families or (2) at the species level as a response to recent habitat conditions. Lasso regression shrinkage identified relationships between family membership and sex ratio and sporophyte frequency, whereas environmental conditions were not correlated with any investigated reproductive trait. Sex ratio and sporophyte frequency were correlated with each other. Our results suggest that ancestry is more important than the current environment in explaining reproductive patterns at and above the species level in the studied wetland mosses, and that mechanisms controlling sex ratio and sporophyte frequency are phylogenetically conserved. Obviously, ancestry should be considered in the study of reproductive character state variation in plants.(c) 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174, 163-172.

  • 23. Blackmore, Stephen
    et al.
    Wortley, Alexandra H.
    Skvarla, John J.
    Gabarayeva, Nina I.
    Rowley, John R.
    Stockholm University, Faculty of Science, Department of Botany.
    Developmental origins of structural diversity in pollen walls of Compositae2010In: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110, Vol. 284, no 02-jan, p. 17-32Article in journal (Refereed)
    Abstract [en]

    Compositae exhibit some of the most complex and diverse pollen grains in flowering plants. This paper reviews the evolutionary and developmental origins of this diversity in pollen structure using recent models based on the behaviour of colloids and formation of micelles in the differentiating microspore glycocalyx and primexine. The developmental model is consistent with observations of structures recovered by pollen wall dissolution. Pollen wall diversity in Compositae is inferred to result from small changes in the glycocalyx, for example ionic concentration, which trigger the self-assembly of highly diverse structures. Whilst the fine details of exine substructure are, therefore, not under direct genetic control, it is likely that genes establish differences in the glycocalyx which define the conditions for self-assembly. Because the processes described here for Compositae can account for some of the most complex exine structures known, it is likely that they also operate in pollen walls with much simpler organisation.

  • 24.
    Bolinder, Kristina
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Pollen and pollination in Ephedra (Gnetales)2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Ephedra (Gnetales) is a gymnosperm genus with a long evolutionary history; the first dispersed pollen grains with affinity to the group are known already from the Permian. This thesis focuses on the evolutionary history of the group and different aspects of its pollination mechanisms. Despite the limited number of extant species of the genus (50-60), and a low morphological and genetic divergence among species, there is variation in pollination syndrome in the genus. The prevailing state in Ephedra, and most gymnosperms, is wind pollination. It is therefore surprising that one species, E. foeminea, is insect-pollinated. Together with co-workers I documented the pollination syndromes of E. foeminea and a sympatric species, E. distachya, based on long term field experiments in north-eastern Greece and aerodynamic investigations and calculations. Placing the results into an evolutionary framework reveals that the insect-pollinated species E. foeminea is sister to the remaining (mostly wind-pollinated) genus, and indicates that insect pollination is the ancestral state in the Gnetales. During the course of evolution of the group there has been a shift to wind pollination, which may have played a crucial role for the diversification of the crown group in the Paleogene. Pollination biology is often correlated with the morphology of the pollen such that pollen grains of anemophilous plants are small with a smooth surface, whereas pollen grains of entomophilous plants are larger with an ornamented surface and a covering of pollenkitt. The pollen morphology of Ephedra can be broadly divided into two types: an ancestral type with an unbranched pseudosulcus between each pair of plicae, and a derived type with a branched pseudosulcus between each pair of plicae. Further, the pollen morphology and ultrastructure of the pollen wall in Ephedra are to some degree correlated with the pollination syndrome and capability of long distance dispersal. Pollen of E. foeminea has a denser ultrastructure, as a result a higher settling velocity and is therefore capable of flying shorter distances than does pollen of the anemophilous E. distachya, and other investigated anemophilous species that show a more spacious ultrastructure of the pollen grain. These results can be useful in the reconstruction of the pollination mechanism of extinct taxa of the Ephedra-lineage in the future.

  • 25.
    Bolinder, Kristina
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Pollination in Ephedra (Gnetales)2014Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Pollination, i.e., the transport of male gametophytes to female gametophytes, can occur with biotic or abiotic vectors and is necessary for fertilization and completion of the lifecycle in all seed plants. Insect pollination and the co-evolution between angiosperms and insects have during the last century been discussed as one possible solution to Darwin’s abominable mystery and an important explanation for the relatively abrupt turn-over from a vegetation dominated by gymnosperms to a vegetation dominated by angiosperms in the Cretaceous. Insect pollination is, however, a much older phenomenon that can be traced back to the Devonian, but is it an ancestral trait that has been lost in many seed plant groups, or has it originated multiple times in parallel? These questions have to be addressed in a phylogenetic framework comprising extant and extinct seed plant groups. The Gnetales are constantly in focus in studies of seed plant phylogeny, probably because they have repeatedly been suggested, and refuted, to be the closest living relatives of angiosperms. The order consists of three genera, Gnetum, Welwitschia and Ephedra, of which the former two have long been known to be insect pollinated. Pollination biology in Ephedra has, however, been poorly studied and understood. In this thesis pollination mechanisms in Ephedra (Gnetales) are investigated by field experiments and observations (Paper I) and aerodynamic simulations and studies of pollen morphology (Paper II). The results show that there are multiple pollination mechanisms within this otherwise morphologically and ecologically uniform genus. Further, in contrast to what has often been assumed, insect pollination is shown to be ancestral in the Gnetales and not a derived feature that has evolved within the group. Using this new information on pollination biology in the Gnetales and data from the literature, I explore evolution of pollen morphology and pollination mode in seed plants.

  • 26.
    Bolmgren, Kjell
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Oxelman, Bengt
    Generic limits in Rhamnus s.l. L. (Rhamnaceae) inferred from nuclear and chloroplast DNA sequence phylogenies.2004In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 53, no 2, p. 383-390Article in journal (Refereed)
    Abstract [en]

    This study tested the monophyly of the previously proposed genera Alaternus, Frangula, Oreoherzogia, and Rhamnus s.str., and the phylogenetic relations suggested by Grubov (1949), within the Rhamnus s.l. clade.Based on a global sample of 22 species, we derived phylogenetic hypotheses using parsimony analysis of variation in trnL-F (chloroplast) and ITS (nuclear) DNA regions. Both Alaternus, Frangula, and Oreoherzogia gained strong support, and our results further support recognition of Frangula as a monophyletic genus. The resolution between Alaternus, Oreoherzogia, and the rest of Rhamnus s.str. was less clear, and the mainly Mediterranean Oreoherzogia was strongly grouped with the American R. crocea. Therefore, we consider it as unjustified to split the rest of Rhamnus into smaller genera. Regarding Grubov's phylogenetic hypothesis, our study could only support the dichotomy between Frangula and the rest of Rhamnus.

  • 27.
    Borg, Agneta Julia
    Stockholm University, Faculty of Science, Department of Botany.
    Evolutionary relationships in Thunbergioideae and other early branching lineages of Acanthaceae2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Acanthaceae as circumscribed today consists of the three subfamilies Acanthoideae (Acanthaceae sensu stricto), Thunbergioideae and Nelsoniodieae, plus the genus Avicennia. Due to the morphological dissimilarities of Thunbergioideae and Nelsonioideae, the delimitation of the family has been controversial. The mangrove genus Avicennia was only recently associated with Acanthaceae for the first time, based on molecular evidence, but without morphological support. In this thesis, phylogenetic analyses of nuclear and chloroplast DNA sequences were used to test the monophyly and exact positions of Thunbergioideae and Nelsonioideae, and to infer detailed phylogenetic relationships within these subfamilies and among major lineages of Acanthaceae. Floral structure and development were comparatively studied in Avicennia and other Acanthaceae using scanning electron microscopy and stereo microscopy. Phylogenetic analyses strongly support monophyly of Thunbergioideae and Nelsonioideae, and place the latter clade with strong support as sister to all other plants treated as Acanthaceae. Thunbergioideae and Avicennia are moderately supported as sister taxa, and together they are sister to Acanthoideae. The general morphology of Avicennia can be easily accommodated in the Acanthaceae, and three synapomorphies support the suggested sister group relationship of Avicennia and Thunbergioideae: (1) collateral ovule arrangement, (2) vertical orientation of ovule curvature, and (3) an exposed nucellus that is contiguous with the ovary wall. Within Thunbergioideae and Nelsonioideae, support values for major lineages are generally high. With some exceptions, the constituent genera are supported as monophyletic. Evolutionary relationships among and within genera are discussed in a morphological and biogeographical context.

  • 28.
    Borg, Agneta Julia
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Schoenenberger, Juerg
    Comparative floral development and structure of the black mangrove genus Avicennia L. and related taxa in the Acanthaceae2011In: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 172, no 3, p. 330-344Article in journal (Refereed)
    Abstract [en]

    Phylogenetic relationships of Avicennia have been difficult to trace because of the presence of convergent characters related to the mangrove environment. Recent molecular data suggest a close relationship to Thunbergioideae, a subfamily within Acanthaceae (Lamiales), but morphological support for the new findings has been equivocal. Floral structure and development are comparatively studied here in three species of Avicennia, with special attention given to the ovary and the ovules, which are also studied in Thunbergioideae. The suggested sister group relationship of Avicennia and Thunbergioideae is supported by three synapomorphies: (1) collateral ovule arrangement, (2) vertical orientation of ovule curvature, and (3) an exposed nucellus that is contiguous with the ovary wall, at least during early stages of ovule development. We interpret the latter character as a neotenic feature that is retained in the anthetic ovules of Avicennia. We confirm that the apparently tetramerous flowers of Avicennia have a basically pentamerous floral ground plan. Additional floral characters shared between Avicennia and Thunbergioideae include left contort corolla aestivation, thickened filament bases with glandular hairs, presence of pollen sac placentoids, and various aspects of fruit morphology and embryology. However, these features are either symplesiomorphic or are not known well enough to allow for unequivocal conclusion on character evolution in Acanthaceae.

  • 29.
    Bremer, Kåre
    et al.
    Stockholm University.
    Barreda, V. D.
    Palazzesi, L.
    Katinas, L.
    Crisci, J. V.
    Telleria, M. C.
    Passala, M. G.
    Bechis, F.
    Corsolini, R.
    An extinct Eocene taxon of the daisy family (Asteraceae): evolutionary, ecological and biogeographical implications2012In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 109, no 1, p. 127-134Article in journal (Refereed)
    Abstract [en]

    Background and Aims: Morphological, molecular and biogeographical information bearing on early evolution of the sunflower alliance of families suggests that the clade containing the extant daisy family (Asteraceae) differentiated in South America during the Eocene, although palaeontological studies on this continent failed to reveal conclusive support for this hypothesis. Here we describe in detail Raiguenrayun cura gen. & sp. nov., an exceptionally well preserved capitulescence of Asteraceae recovered from Eocene deposits of northwestern Patagonia, Argentina.

    Methods: The fossil was collected from the 47.5 million-year-old Huitrera Formation at the Estancia Don Hipolito locality, Rio Negro Province, Argentina.

    Key Results: The arrangement of the capitula in a cymose capitulescence, the many-flowered capitula with multiseriate-imbricate involucral bracts and the pappus-like structures indicate a close morphological relationship with Asteraceae. Raiguenrayun cura and the associated pollen Mutisiapollis telleriae do not match exactly any living member of the family, and clearly represent extinct taxa. They share a mosaic of morphological features today recognized in taxa phylogenetically close to the root of Asteraceae, such as Stifftieae, Wunderlichioideae and Gochnatieae (Mutisioideae sensu lato) and Dicomeae and Oldenburgieae (Carduoideae), today endemic to or mainly distributed in South America and Africa, respectively.

    Conclusions: This is the first fossil genus of Asteraceae based on an outstandingly preserved capitulescence that might represent the ancestor of Mutisioideae-Carduoideae. It might have evolved in southern South America some time during the early Palaeogene and subsequently entered Africa, before the biogeographical isolation of these continents became much more pronounced. The new fossil represents the first reliable point for calibration, favouring an earlier date to the split between Barnadesioideae and the rest of Asteraceae than previously thought, which can be traced back at least 47.5 million years. This is the oldest well dated member of Asteraceae and perhaps the earliest indirect evidence for bird pollination in the family.

  • 30.
    Buapet, Pimchanok
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Beyond carbon-limitation: A re-evaluation of the ecological role of photorespiration and direct oxygen photoreduction in seagrasses2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Seagrasses living in shallow coastal waters are regularly subjected to changes in environmental conditions including the two essential factors for photosynthesis: dissolved inorganic carbon (DIC) and irradiance. This thesis focuses on the photosynthetic responses of seagrasses to carbon limitation induced by community metabolism and/or high light intensities. Field sampling conducted in seagrass-dominated embayments along the Swedish west coast revealed that high pH and low levels of DIC caused by community photosynthesis are common in shallow coastal waters. These effects were found on a scale of a whole bay and were affected by the composition of the vegetation. Such carbon limitation and at the same time an increase in O2 concentration negatively affected photosynthesis of the seagrass species Zostera marina L. and Ruppia maritima L. by compromising carbon assimilation as well as enhancing photorespiration.  In contrast to the results from the two seagrasses, it was found that gross photosynthetic rates did not increase under low O2 concentrations in the green alga Ulva intestinalis L., suggesting that its efficient carbon acquisition mechanisms are able to suppress photorespiration. The role of photorespiration in seagrass photosynthesis was further investigated in Z. marina. It was found that under conditions of carbon limitation, photorespiration provides the major alternative sink for electrons, sustaining substantial electron transport via photosystem II while the Mehler reaction has a smaller contribution as an alternative electron sink. Photorespiration was however not a significant component of the photoprotective mechanisms in Z. marina under high irradiance. Here the down-regulation of electron transport via non-photochemical quenching appeared to be the more efficient mechanism for dissipating excess energy. Overall, this study highlights the role of O2 in seagrass photosynthesis which appears to be of greater importance than previously envisaged, particularly in the productive waters where carbon availability is occasionally limited. 

  • 31.
    Buapet, Pimchanok
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences. Prince Songkla University, Thailand.
    Rasmusson, Lina M.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Gullström, Martin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Björk, Mats
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Photorespiration and carbon limitation determine productivity in temperate seagrasses2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 12, article id e83804Article in journal (Refereed)
    Abstract [en]

    The gross primary productivity of two seagrasses, Zostera marina and Ruppia maritima, and one green macroalga, Ulva intestinalis, was assessed in laboratory and field experiments to determine whether the photorespiratory pathway operates at a substantial level in these macrophytes and to what extent it is enhanced by naturally occurring shifts in dissolved inorganic carbon (DIC) and O2 in dense vegetation. To achieve these conditions in laboratory experiments, seawater was incubated with U. intestinalis in light to obtain a range of higher pH and O2 levels and lower DIC levels. Gross photosynthetic O2 evolution was then measured in this pretreated seawater (pH, 7.8–9.8; high to low DIC:O2 ratio) at both natural and low O2concentrations (adjusted by N2 bubbling). The presence of photorespiration was indicated by a lower gross O2 evolution rate under natural O2 conditions than when O2 was reduced. In all three macrophytes, gross photosynthetic rates were negatively affected by higher pH and lower DIC. However, while both seagrasses exhibited significant photorespiratory activity at increasing pH values, the macroalga U. intestinalis exhibited no such activity. Rates of seagrass photosynthesis were then assessed in seawater collected from the natural habitats (i.e., shallow bays characterized by high macrophyte cover and by low DIC and high pH during daytime) and compared with open baymouth water conditions (where seawater DIC is in equilibrium with air, normal DIC, and pH). The gross photosynthetic rates of both seagrasses were significantly higher when incubated in the baymouth water, indicating that these grasses can be significantly carbon limited in shallow bays. Photorespiration was also detected in both seagrasses under shallow bay water conditions. Our findings indicate that natural carbon limitations caused by high community photosynthesis can enhance photorespiration and cause a significant decline in seagrass primary production in shallow waters.

  • 32. Bucas, M.
    et al.
    Bergström, U.
    Downie, A-L
    Sundblad, G.
    Gullström, Martin
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    von Numers, M.
    Siaulys, A.
    Lindegarth, M.
    Empirical modelling of benthic species distribution, abundance, and diversity in the Baltic Sea: evaluating the scope for predictive mapping using different modelling approaches2013In: ICES Journal of Marine Science, ISSN 1054-3139, E-ISSN 1095-9289, Vol. 70, no 6, p. 1233-1243Article in journal (Refereed)
    Abstract [en]

    The predictive performance of distribution models of common benthic species in the Baltic Sea was compared using four non-linear methods: generalized additive models (GAMs), multivariate adaptive regression splines, random forest (RF), and maximum entropy modelling (MAXENT). The effects of data traits were also tested. In total, 292 occurrence models and 204 quantitative (abundance and diversity) models were assessed. The main conclusions are that (i) the spatial distribution, abundance, and diversity of benthic species in the Baltic Sea can be successfully predicted using several non-linear predictive modelling techniques; (ii) RF was the most accurate method for both models, closely followed by GAM and MAXENT; (iii) correlation coefficients of predictive performance among the modelling techniques were relatively low, suggesting that the performance of methods is related to specific responses; (iv) the differences in predictive performance among the modelling methods could only partly be explained by data traits; (v) the response prevalence was the most important explanatory variable for predictive accuracy of GAM and MAXENT on occurrence data; (vi) RF on the occurrence data was the only method sensitive to sampling density; (vii) a higher predictive accuracy of abundance models could be achieved by reducing variance in the response data and increasing the sample size.

  • 33. Buckley, Thomas R.
    et al.
    Attanayake, Dilini
    Nylander, Johan A. A.
    Stockholm University, Faculty of Science, Department of Botany.
    Bradler, Sven
    The phylogenetic placement and biogeographical origins of the New Zealand stick insects (Phasmatodea)2010In: Systematic Entomology, ISSN 0307-6970, E-ISSN 1365-3113, Vol. 35, no 2, p. 207-225Article, review/survey (Refereed)
    Abstract [en]

    The Lanceocercata are a clade of stick insects (Phasmatodea) that have undergone an impressive evolutionary radiation in Australia, New Caledonia, the Mascarene Islands and areas of the Pacific. Previous research showed that this clade also contained at least two of the nine New Zealand stick insect genera. We have constructed a phylogeny of the Lanceocercata using 2277 bp of mitochondrial and nuclear DNA sequence data to determine whether all nine New Zealand genera are indeed Lanceocercata and whether the New Zealand fauna is monophyletic. DNA sequence data were obtained from mitochondrial cytochrome oxidase subunits I and II and the nuclear large subunit ribosomal RNA and histone subunit 3. These data were subjected to Bayesian phylogenetic inference under a partitioned model and maximum parsimony. The resulting trees show that all the New Zealand genera are nested within a large New Caledonian radiation. The New Zealand genera do not form a monophyletic group, with the genus Spinotectarchus Salmon forming an independent lineage from the remaining eight genera. We analysed Lanceocercata apomorphies to confirm the molecular placement of the New Zealand genera and to identify characters that confirm the polyphyly of the fauna. Molecular dating analyses under a relaxed clock coupled with a Bayesian extension to dispersal-vicariance analysis was used to reconstruct the biogeographical history for the Lanceocercata. These analyses show that Lanceocercata and their sister group, the Stephanacridini, probably diverged from their South American relatives, the Cladomorphinae, as a result of the separation of Australia, Antarctica and South America. The radiation of the New Caledonian and New Zealand clade began 41.06 million years ago (mya, 29.05-55.40 mya), which corresponds to a period of uplift in New Caledonia. The main New Zealand lineage and Spinotectarchus split from their New Caledonian sister groups 33.72 (23.9-45.62 mya) and 29.9 mya (19.79-41.16 mya) and began to radiate during the late Oligocene and early Miocene, probably in response to a reduction in land area and subsequent uplift in the late Oligocene and early Miocene. We discuss briefly shared host plant patterns between New Zealand and New Caledonia. Because Acrophylla sensu Brock & Hasenpusch is polyphyletic, we have removed Vetilia Stal from synonymy with Acrophylla Gray.

  • 34. Buerki, Sven
    et al.
    Forest, Felix
    Alvarez, Nadir
    Nylander, Johan A. A.
    Stockholm University, Faculty of Science, Department of Botany.
    Arrigo, Nils
    Sanmartin, Isabel
    An evaluation of new parsimony-based versus parametric inference methods in biogeography: a case study using the globally distributed plant family Sapindaceae2011In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 38, no 3, p. 531-550Article in journal (Refereed)
    Abstract [en]

    Aim Recently developed parametric methods in historical biogeography allow researchers to integrate temporal and palaeogeographical information into the reconstruction of biogeographical scenarios, thus overcoming a known bias of parsimony-based approaches. Here, we compare a parametric method, dispersal-extinction-cladogenesis (DEC), against a parsimony-based method, dispersal-vicariance analysis (DIVA), which does not incorporate branch lengths but accounts for phylogenetic uncertainty through a Bayesian empirical approach (Bayes-DIVA). We analyse the benefits and limitations of each method using the cosmopolitan plant family Sapindaceae as a case study. Location World-wide. Methods Phylogenetic relationships were estimated by Bayesian inference on a large dataset representing generic diversity within Sapindaceae. Lineage divergence times were estimated by penalized likelihood over a sample of trees from the posterior distribution of the phylogeny to account for dating uncertainty in biogeographical reconstructions. We compared biogeographical scenarios between Bayes-DIVA and two different DEC models: one with no geological constraints and another that employed a stratified palaeogeographical model in which dispersal rates were scaled according to area connectivity across four time slices, reflecting the changing continental configuration over the last 110 million years. Results Despite differences in the underlying biogeographical model, Bayes-DIVA and DEC inferred similar biogeographical scenarios. The main differences were: (1) in the timing of dispersal events - which in Bayes-DIVA sometimes conflicts with palaeogeographical information, and (2) in the lower frequency of terminal dispersal events inferred by DEC. Uncertainty in divergence time estimations influenced both the inference of ancestral ranges and the decisiveness with which an area can be assigned to a node. Main conclusions By considering lineage divergence times, the DEC method gives more accurate reconstructions that are in agreement with palaeogeographical evidence. In contrast, Bayes-DIVA showed the highest decisiveness in unequivocally reconstructing ancestral ranges, probably reflecting its ability to integrate phylogenetic uncertainty. Care should be taken in defining the palaeogeographical model in DEC because of the possibility of overestimating the frequency of extinction events, or of inferring ancestral ranges that are outside the extant species ranges, owing to dispersal constraints enforced by the model. The wide-spanning spatial and temporal model proposed here could prove useful for testing large-scale biogeographical patterns in plants.

  • 35.
    Carr, Herman
    Stockholm University, Faculty of Science, Department of Botany.
    Energy balance during active carbon uptake and at excess irradiance in three marine macrophytes2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The marine environment is an important habitat where many processes occur that affect life conditions on earth. Macrophytes and planktonic oxygen evolvers are an essential component for almost all marine life forms and have developed in an environment that differs largely from the terrestrial habitats. For instance in regards to available ionic forms of inorganic carbon and moving water masses which affects incoming light. It is therefore relevant to examine the physiology of algae and marine plants to identify their unique features and differences to terrestrial plants that once orginated from algae. By using chlorophyll fluorescence measurements alone or combined with measurements of oxygen evolution and protein analysis photosynthetic strategies to withstand excess energy have been evaluated under a variety of experimental conditions. Furthermore metabolic pathways involved in energy transfer from photosynthesis to the site of active carbon uptake have been examined. The following was found:

    * The ratio between photosynthetic gross oxygen evolution and estimated electron transport rate varies in Ulva spp depending on previous history of light and dark exposures. To obtain P/I curves with ratios close to the theoretical 1:4 value, measurements should be performed on separate pieces of tissue at each irradiance level.

    * Under carbon deficient conditions, the estimated ETR is larger than the gross oxygen evolution, which may be due to the so called “water-water” cycle and absorption changes in PSII which are not corrected for in the calculation of ETR.

    * Upon exposure to high irradiances (1500 µmol photons m-2s-1) the PSII core protein D1 is broken down with a concomittant reduction in ETR in Ulva spp. With the decrease in electron transport between PSII and PSI the acidification of the lumen decreases and the ability to dissipate excess energy as heat. At prolonged irradiance, an acclimation occurs with a lesser or no breakdown of D1 indicating an additional photo-protective strategy other than heat dissipation.

    * Laminaria saccharina is dependent on mitochondrial respiration for active utilization of bicarbonate. By extruding protons outside the plasmalemma an acidification takes place that favors the conversion of bicarbonate into carbon dioxide that then can diffuse in to the cell. These proton pumps are driven by ATP supplied to a large degree from mitochondria, likely through the reductant NADPH produced photochemically.

    * The marine angiosperm Zostera marina is dependent on mitochondrial respiration for utilization of bicarbonate in a manner similar to that in Laminaria saccharina . However, the water-water cycle may supply additional ATP to the proton pumps in Zostera marina. Both species exhibit a lag-phase at the onset of illumination after a dark incubation period and at least part of this lag-phase is due to a lag in an activation of mitochondrial supported bicarbonate utilization. It is clear that the marine environment holds complex plant and algae species and much is still to discover about the oxygen evolvers that grow beneath the water surface.

  • 36.
    Carr, Herman
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Axelsson, Lennart
    Photosynthetic utilization of bicarbonate in Zostera marina is reduced by inhibitors of mitochondrial ATPase and electron transport2008In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 147, no 2, p. 879-885Article in journal (Refereed)
    Abstract [en]

    When Zostera marina was irradiated after a period of darkness, initiation of photosynthetic O-2 evolution occurred in two phases. During a lag phase, lasting 4 to 5 min, photosynthesis was supported by a diffusive entry of CO2. Photosynthesis then rapidly increased to its full rate. Tris buffer, at a concentration of 50 mM, completely inhibited this increase without affecting CO2-supported photosynthesis during the lag phase. These results verify that the increase in photosynthesis after the lag phase depended on an activation of bicarbonate (HCO3-) utilization through acid zones generated by proton pumps located to the outer cell membrane. In similar experiments, 6.25 mu M of the mitochondrial ATPase blocker oligomycin inhibited photosynthetic HCO3- utilization by more than 60%. Antimycin A, a selective blocker of mitochondrial electron transport, caused a similar inhibition of HCO3- utilization. Measurements at elevated CO2 concentrations verified that neither oligomycin nor antimycin interfered with linear photosynthetic electron transport or with CO2 fixation. Thus, a major part of the ATP used for the generation of acid zones involved in HCO3- utilization in Z. marina was derived from mitochondrial respiration.

  • 37.
    Chang, Christine Chi-Chen
    Stockholm University, Faculty of Science, Department of Botany.
    Mechanisms and genes controlling the signalling network for biotic and abiotic stress defences in Arabidopsis thaliana (L.) Heyhn: Functional cross-talk between photo-produced reactive oxygen species, photosynthesis and plant disease defence responses2005Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Excess excitation energy, mechanical injury and defence against pathogens, each trigger rapid production of reactive oxygen species (ROS) in Arabidopsis thaliana leaves. ROS, such as hydrogen peroxide (H2O2), are required for the induction of systemic acquired acclimation and may lead to redox changes in photosynthetic electron transport (PET). On one hand, enhanced ROS production during stress can destroy cells, and on the other, ROS can also act as signals for the activation of stress responsive and defensive pathways.

    In this work, physiological and molecular analyses of Arabidopsis mutants and transgenic lines were applied to investigate the signalling network controlling biotic and abiotic stress responses. A key enzyme of the antioxidant network is encoded by ASCORBATE PEROXIDASE 2 (APX2). Wounded leaves showed low induction of APX2 expression and when exposed to excess light, APX2 expression was increased synergistically. Signalling pathways dependent upon jasmonic acid, chitosan and abscisic acid were not involved in the wound-induced expression of APX2, but PET was required, and APX2 induction was preceded by a depressed rate of CO2 fixation.

    Analysis of lsd1 (LESION SIMULATING DISEASE 1) strongly suggests that light acclimatory processes and pathogen defences are genetically and functionally linked. It is important to know that LSD1 type of mutants have mainly been studied with regard to pathogenesis. From this work, it reveals that association of LSD1 with hypersensitive response may only be supplementary.

    GLUTATHIONE PEROXIDASES (GPXs) are another major family of ROS scavenging enzymes. Analysis of the Arabidopsis genome database revealed a new open-reading frame, thus increasing the total number of AtGPX gene family to eight (AtGPX1-AtGPX8). Arabidopsis thaliana transgenic lines with reduced expression of both putative chloroplastic isoforms (AtGPX1 and AtGPX7) and AtGPX7 knock-out mutant (ko-GPX7) were more sensitive to photo-oxidative stress but had a reduced bacterial growth rate when inoculated with virulent strains Pseudomonas syringae pv. tomato DC3000 and P.s.t. maculicola strain ES4326, indicating increased resistance to pathogenesis. This, to our knowledge, is the first functional and genetic analysis of chloroplastic GPXs in plants, and confirms that light and chloroplastic ROS metabolism is important for basal resistance against virulent pathogens.

    The above results confirm that light sensing, light acclimatory processes and photo-produced ROS also govern pathogen defence pathways. This has a great ecological relevance for Darwinian fitness of plants growing in the natural environment, where simultaneous pathogen attack and fluctuations in light, temperature and other environmental factors make rapid acclimation a constant necessity. Molecular, biochemical and physiological analysis of pathogen responses in mutants impaired in light sensing, EEE-dissipatory mechanisms, and similar analysis of light acclimatory processes in mutants impaired in pathogen defences may prove to be seminal.

  • 38.
    Chang, Christine
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Slesak, Ireneusz
    Jorda, Lucia
    Sotnikov, Alexey
    Stockholm University, Faculty of Science, Department of Botany.
    Melzer, Michael
    Miszalski, Zbigniew
    Mullineaux, Philip M.
    Parker, Jane E.
    Karpinska, Barbara
    Karpinski, Stanislaw
    Arabidopsis Chloroplastic Glutathione Peroxidases Play a Role in Cross Talk between Photooxidative Stress and Immune Responses2009In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 150, no 2, p. 670-683Article in journal (Refereed)
    Abstract [en]

    Glutathione peroxidases (GPXs; EC 1.11.1.9) are key enzymes of the antioxidant network in plants and animals. In order to investigate the role of antioxidant systems in plant chloroplasts, we generated Arabidopsis (Arabidopsis thaliana) transgenic lines that are depleted specifically in chloroplastic (cp) forms of GPX1 and GPX7. We show that reduced cpGPX expression, either in transgenic lines with lower total cpGPX expression (GPX1 and GPX7) or in a gpx7 insertion mutant, leads to compromised photooxidative stress tolerance but increased basal resistance to virulent bacteria. Depletion of both GPX1 and GPX7 expression also caused alterations in leaf cell and chloroplast morphology. Leaf tissues were characterized by shorter and more rounded palisade cells, irregular spongy mesophyll cells, and larger intercellular air spaces compared with the wild type. Chloroplasts had larger and more abundant starch grains than in wild-type and gpx7 mutant plants. Constitutively reduced cpGPX expression also led to higher foliar ascorbic acid, glutathione, and salicylic acid levels in plants exposed to higher light intensities. Our results suggest partially overlapping functions of GPX1 and GPX7. The data further point to specific changes in the chloroplast ascorbate-glutathione cycle due to reduced cpGPX expression, initiating reactive oxygen species and salicylic acid pathways that affect leaf development, light acclimation, basal defense, and cell death programs. Thus, cpGPXs regulate cellular photooxidative tolerance and immune responses.

  • 39.
    Chen, Hao-Jie
    Stockholm University, Faculty of Science.
    The role of cytokinins in vegetative bud development in Norway spruce, Picea abies1996Doctoral thesis, comprehensive summary (Other academic)
  • 40. Cherian, Sam
    et al.
    Weyens, Niele
    Lindberg, Sylvia
    Stockholm University, Faculty of Science, Department of Botany.
    Vangronsveld, Jaco
    Phytoremediation of Trace element Contaminated Environments and the Potential of Endophytic Bacteria for Improving this Process2012In: Critical reviews in environmental science and technology, ISSN 1064-3389, E-ISSN 1547-6537, Vol. 42, no 21, p. 2215-2260Article, review/survey (Refereed)
    Abstract [en]

    Trace elements (heavy metals and metalloids) are among the most widespread contaminants that pose serious threat to all living organisms. Plant and microbial-assisted remediation holds great promise for in situ remediation of trace element contaminated environments. An extended knowledge of plant processes generally involved in the uptake, translocation, storage and detoxification of contaminants, and plant-microbe interactions were essential in developing improved technologies for environmental clean up. Currently, with the initiation of transgenic technologies, great strides have been made in trace element phytoremediation research. In this review, we provide an overview of the current knowledge of how plants cope with trace elements and discuss the development of transgenic plants with improved trace element remediation capabilities. In addition, this review also addresses the recent progress made towards understanding the plant-microbe interactions, especially of endophytic bacteria (natural and genetically engineered), and their contribution in improving the efficiency and versatility of trace element phytoremediation. 

  • 41. Cornelissen, Johannes H. C.
    et al.
    van Bodegom, Peter M.
    Aerts, Rien
    Callaghan, Terry V.
    van Logtestijn, Richard S. P.
    Alatalo, Juha
    Chapin, F. Stuart
    Gerdol, Renato
    Gudmundsson, Jon
    Gwynn-Jones, Dylan
    Hartley, Anne E.
    Hik, David S.
    Hofgaard, Annika
    Jonsdottir, Ingibjorg S.
    Karlsson, Staffan
    Klein, Julia A.
    Laundre, Jim
    Magnusson, Borgthor
    Michelsen, Anders
    Molau, Ulf
    Onipchenko, Vladimir G.
    Quested, Helen M.
    Stockholm University, Faculty of Science, Department of Botany.
    Sandvik, Sylvi M.
    Schmidt, Inger K.
    Shaver, Gus R.
    Solheim, Bjorn
    Soudzilovskaia, Nadejda A.
    Stenstrom, Anna
    Tolvanen, Anne
    Totland, Orjan
    Wada, Naoya
    Welker, Jeffrey M.
    Zhao, Xinquan
    Global negative vegetation feedback to climate warming responses of leaf litter decomposition rates in cold biomes2007In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 10, no 7, p. 619-627Article in journal (Refereed)
    Abstract [en]

    Whether climate change will turn cold biomes from large long-term carbon sinks into sources is hotly debated because of the great potential for ecosystem-mediated feedbacks to global climate. Critical are the direction, magnitude and generality of climate responses of plant litter decomposition. Here, we present the first quantitative analysis of the major climate-change-related drivers of litter decomposition rates in cold northern biomes worldwide. Leaf litters collected from the predominant species in 33 global change manipulation experiments in circum-arctic-alpine ecosystems were incubated simultaneously in two contrasting arctic life zones. We demonstrate that longer-term, large-scale changes to leaf litter decomposition will be driven primarily by both direct warming effects and concomitant shifts in plant growth form composition, with a much smaller role for changes in litter quality within species. Specifically, the ongoing warming-induced expansion of shrubs with recalcitrant leaf litter across cold biomes would constitute a negative feedback to global warming. Depending on the strength of other (previously reported) positive feedbacks of shrub expansion on soil carbon turnover, this may partly counteract direct warming enhancement of litter decomposition.

  • 42. Cornwell, William K.
    et al.
    Cornelissen, Johannes H. C.
    Amatangelo, Kathryn
    Dorrepaal, Ellen
    Eviner, Valerie T.
    Godoy, Oscar
    Hobbie, Sarah E.
    Hoorens, Bart
    Kurokawa, Hiroko
    Perez-Harguindeguy, Natalia
    Quested, Helen M.
    Stockholm University, Faculty of Science, Department of Botany.
    Santiago, Louis S.
    Wardle, David A.
    Wright, Ian J.
    Aerts, Rien
    Allison, Steven D.
    van Bodegom, Peter
    Brovkin, Victor
    Chatain, Alex
    Callaghan, Terry V.
    Diaz, Sandra
    Garnier, Eric
    Gurvich, Diego E.
    Kazakou, Elena
    Klein, Julia A.
    Read, Jenny
    Reich, Peter B.
    Soudzilovskaia, Nadejda A.
    Victoria Vaieretti, M.
    Westoby, Mark
    Plant species traits are the predominant control on litter decomposition rates within biomes worldwide2008In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 11, no 10, p. 1065-1071Article in journal (Refereed)
    Abstract [en]

    Worldwide decomposition rates depend both on climate and the legacy of plant functional traits as litter quality. To quantify the degree to which functional differentiation among species affects their litter decomposition rates, we brought together leaf trait and litter mass loss data for 818 species from 66 decomposition experiments on six continents. We show that: (i) the magnitude of species-driven differences is much larger than previously thought and greater than climate-driven variation; (ii) the decomposability of a species' litter is consistently correlated with that species' ecological strategy within different ecosystems globally, representing a new connection between whole plant carbon strategy and biogeochemical cycling. This connection between plant strategies and decomposability is crucial for both understanding vegetation-soil feedbacks, and for improving forecasts of the global carbon cycle.

  • 43.
    Cousins, Sara
    Stockholm University, Faculty of Science, Department of Physical Geography and Quaternary Geology.
    Extinction debt in fragmented grasslands: paid or not?2009In: Journal of Vegetation Science, ISSN 1100-9233, E-ISSN 1654-1103, Vol. 20, no 1, p. 3-7Article in journal (Refereed)
    Abstract [en]

    Fragmentation of grasslands and forests is considered amajor threat to biodiversity. In the case of plants, theeffect of fragmentation or landscape context is still unclearand published results are divergent. One explanation forthis divergence is the slow response of long-lived plants,creating an extinction debt. However, this has not beenempirically confirmed. In this study, data were compiledfrom broad-scale studies of grasslands from throughoutthe world that relate plant diversity to fragmentationeffects. Only seven studies from northern Europe, out ofa total 61, gave any information on actual habitat fragmentationin time and space. In landscapes with 410%grassland remaining, present-day species richness wasrelated to past landscape or habitat pattern. In landscapeswith o10% grassland remaining, in contrast, plant speciesrichness was more related to contemporary landscapeor habitat pattern. Studies from landscapes with 410%grassland remaining supported the concept of an extinctiondebt, while studies from more fragmented landscapesdid not provide any evidence of an extinction debt. Inorder to make generalisations about historical legacies onspecies diversity in grasslands it is important to consider arange of highly transformed landscapes, and not onlylandscapes with a high amount of grassland remaining.

  • 44.
    Cousins, Sara A. O.
    Stockholm University, Faculty of Science, Department of Physical Geography and Quaternary Geology.
    Moving towards the edge: matrix matters!2013In: Journal of Vegetation Science, ISSN 1100-9233, E-ISSN 1654-1103, Vol. 24, no 1, p. 7-8Article in journal (Refereed)
    Abstract [en]

    In this issue of the Journal of Vegetation Science, Chabrerie et al. use plant inventories and geographical data to investigate effects on species richness and turnover caused by management intensity in the surrounding matrix in new and old forest fragments. Although forest edge age was important, more intensive management of the matrix clearly sharpened the edgeinterior gradient.

  • 45.
    Dahlgren, Johan P.
    Stockholm University, Faculty of Science, Department of Botany.
    Alternative regression methods are not considered in Murtaugh (2009) or by ecologists in general2010In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 13, no 5, p. E7-E9Article in journal (Refereed)
    Abstract [en]

    Murtaugh (2009) recently illustrated that all subsets variable selection is very similar to stepwise regression. This, however, does not necessarily mean both methods are useful. On the contrary, the same problems with overfitting should apply. Ecologists should, if model building is indeed necessary, consider more reliable regression methods now available

  • 46.
    Dahlgren, Johan P.
    et al.
    Stockholm University, Faculty of Science, Department of Botany.
    Garcia, Maria B.
    Ehrlén, Johan
    Stockholm University, Faculty of Science, Department of Botany.
    Nonlinear relationships between vital rates and state variables in demographic models2011In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 92, no 5, p. 1181-1187Article in journal (Refereed)
    Abstract [en]

    To accurately estimate population dynamics and viability, structured population models account for among-individual differences in demographic parameters that are related to individual state. In the widely used matrix models, such differences are incorporated in terms of discrete state categories, whereas integral projection models (IPMs) use continuous state variables to avoid artificial classes. In IPMs, and sometimes also in matrix models, parameterization is based on regressions that do not always model nonlinear relationships between demographic parameters and state variables. We stress the importance of testing for nonlinearity and propose using restricted cubic splines in order to allow for a wide variety of relationships in regressions and demographic models. For the plant Borderea pyrenaica, we found that vital rate relationships with size and age were nonlinear and that the parameterization method had large effects on predicted population growth rates, lambda (linear IPM, 0.95; nonlinear IPMs, 1.00; matrix model, 0.96). Our results suggest that restricted cubic spline models are more reliable than linear or polynomial models. Because even weak nonlinearity in relationships between vital rates and state variables can have large effects on model predictions, we suggest that restricted cubic regression splines should be considered for parameterizing models of population dynamics whenever linearity cannot be assumed.

  • 47. Dahlgren, Jonas
    et al.
    Oksanen, Lauri
    Oksanen, Tarja
    Olofsson, Johan
    Hambäck, Peter A.
    Stockholm University, Faculty of Science, Department of Botany.
    Lindgren, Åsa
    Stockholm University, Faculty of Science, Department of Botany.
    Plant defences to no avail?: Responses of plants of varying edibility to food web manipulations in a low arctic scrubland2009In: Evolutionary Ecology Research, ISSN 1522-0613, E-ISSN 1937-3791, Vol. 11, no 8, p. 1189-1203Article in journal (Refereed)
    Abstract [en]

    Background: According to the Green World Hypothesis of Hairston, Smith, and Slobodkin, all plants are edible for some herbivores. Hence, the copious abundance of plant biomass, typical for terrestrial ecosystems, depends on the collective regulatory action of predators on the herbivore guild. According to the counterarguments of Polis and Strong, the defensive traits of terrestrial plants attenuate terrestrial trophic cascades to species-specific trickles, so elimination of predators might lead to increased abundance of inedible plants but will not influence community-level plant biomass. Question: Does the elimination of predators from a low arctic scrubland, with high-quality forage plants and poorly edible evergreen ericoids, lead to a reduction of community-level plant biomass or to an increased abundance of well-defended evergreen ericoids? Methods: In 1991, we introduced grey-sided voles (Myodes rufocanus) to islands, initially harbouring dense scrubland vegetation, and established permanent plots there. In 2000, we transplanted vegetation blocks from a large three-trophic-level island with voles and predators, to two-trophic-level islands with introduced voles but without resident predators, and also to vole-free one-trophic-level islands, and back to the three-trophic-level island. Vole densities were monitored by semi-annual live trapping. Vegetation was monitored by the point-frequency method. Results: In the absence of predators, vole densities increased 3.7-fold and the community-level plant biomass was decimated. The least palatable plant group, evergreen ericoids, suffered especially heavily, whereas palatable herbaceous plants increased in abundance. However, all three functional plant groups responded positively to the elimination of grey-sided voles. Conclusions: Our results corroborate the Green World Hypothesis, indicating that in the absence of predators, plant defences do not prevent runaway consumption of the vegetation. The fate of plants in predator-free systems with browsing vertebrates depends primarily on the accessibility of each plant during the limiting season. Evergreen ericoids then form the most sensitive functional group.

  • 48. Davis, Aaron
    et al.
    Razafimandimbison, Sylvain G.
    Stockholm University, Faculty of Science, Department of Botany. Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Andriambololonera, Sylvie
    Nomenclatural changes in the genus Bremeria (Rubiaceae)2011In: Blumea - Journal of plant taxonomy and plant geography, ISSN 0006-5196, E-ISSN 2212-1676, Vol. 56, no 1, p. 4-5Article in journal (Refereed)
    Abstract [en]

    Five new combinations are made in the genus Bremeria: B. arachnocarpa, B. eriantha, B. scabrella, B. landia var. holosericea, and B. landia var. stadmanii. Bremeria gerrardii is conspecific with Gaertnera phanerophlebia, and thus excluded from Bremeria. Lectotypes are designated for Mussaenda erectiloba var. scabrella, M. stadmanii, and M. trichophlebia.

  • 49. De Block, Petra
    et al.
    Razafimandimbison, Sylvain G.
    Stockholm University, Faculty of Science, Department of Botany. Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Janssens, Steven
    Ochoterena, Helga
    Robbrecht, Elmar
    Bremer, Birgitta
    Stockholm University, Faculty of Science, Department of Botany. Stockholm University, Faculty of Science, The Bergius Botanical Garden Museum.
    Molecular phylogenetics and generic assessment in the tribe Pavetteae (Rubiaceae)2015In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 64, no 1, p. 79-95Article in journal (Refereed)
    Abstract [en]

    This is the first phylogenetic study focused on the Pavetteae, one of the most species-rich and morphologically diverse tribes within the coffee family (Rubiaceae). Fifteen of the 17 currently recognized genera, represented by 85 taxa, were sequenced for rps16, trnT-F and ITS and analysed using Bayesian inference and maximum likelihood methods. The monophyly of the Pavetteae is confirmed. Four major lineages are identified, but their phylogenetic relationships are not fully resolved. The continental African genera Rutidea, Nichallea and Tennantia, the Madagascan genera Homollea and Robbrechtia, and the paleotropical genus Pavetta are monophyletic. Other genera are paraphyletic in their current circumscriptions and the following changes are made: Homolliella is placed in synonymy with Paracephaelis, and Coleactina and Dictyandra with Leptactina, resulting in four new combinations. The large paleotropical genus Tarenna is shown not to be monophyletic. In the future, the name Tarenna should not be used for continental African species. Most of these could be transferred to the hitherto monospecific genus Cladoceras, but other species might constitute altogether new genera. The relationship between the monophyletic Asian-Pacific and Madagascan Tarenna species remains unclear. The phylogeny of the Madagascan genera of the Pavetteae is largely unresolved and the largest Madagascar-centred genus Coptosperma was not recovered as monophyletic. The low resolution for the Madagascan taxa can be considered as an indication of rapid radiation. Further molecular and morphological studies are necessary to clarify the phylogeny of the Pavetteae, especially regarding the African Tarenna species and the Madagascan genera of the tribe.

  • 50. De Frenne, Pieter
    et al.
    Baeten, Lander
    Graae, Bente J.
    Brunet, Jorg
    Wulf, Monika
    Orczewska, Anna
    Kolb, Annette
    Jansen, Ivy
    Jamoneau, Aurelien
    Jacquemyn, Hans
    Hermy, Martin
    Diekmann, Martin
    De Schrijver, An
    De Sanctis, Michele
    Decocq, Guillaume
    Cousins, Sara A. O.
    Stockholm University, Faculty of Science, Department of Physical Geography and Quaternary Geology.
    Verheyen, Kris
    Interregional variation in the floristic recovery of post-agricultural forests2011In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 99, no 2, p. 600-609Article in journal (Refereed)
    Abstract [en]

    1. Worldwide, the floristic composition of temperate forests bears the imprint of past land use for decades to centuries as forests regrow on agricultural land. Many species, however, display significant interregional variation in their ability to (re)colonize post-agricultural forests. This variation in colonization across regions and the underlying factors remain largely unexplored. 2. We compiled data on 90 species and 812 species x study combinations from 18 studies across Europe that determined species' distribution patterns in ancient (i.e. continuously forested since the first available land use maps) and post-agricultural forests. The recovery rate (RR) of species in each landscape was quantified as the log-response ratio of the percentage occurrence in post-agricultural over ancient forest and related to the species-specific life-history traits and local (soil characteristics and light availability) and regional factors (landscape properties as habitat availability, time available for colonization, and climate). 3. For the herb species, we demonstrate a strong (interactive) effect of species' life-history traits and forest habitat availability on the RR of post-agricultural forest. In graminoids, however, none of the investigated variables were significantly related to the RR. 4. The better colonizing species that mainly belonged to the short-lived herbs group showed the largest interregional variability. Their recovery significantly increased with the amount of forest habitat within the landscape, whereas, surprisingly, the time available for colonization, climate, soil characteristics and light availability had no effect. 5. Synthesis. By analysing 18 independent studies across Europe, we clearly showed for the first time on a continental scale that the recovery of short-lived forest herbs increased with the forest habitat availability in the landscape. Small perennial forest herbs, however, were generally unsuccessful in colonizing post-agricultural forest even in relatively densely forested landscapes. Hence, our results stress the need to avoid ancient forest clearance to preserve the typical woodland flora.

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