uu.seUppsala University Publications
Change search
Refine search result
2345678 201 - 250 of 537
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf
Rows per page
  • 5
  • 10
  • 20
  • 50
  • 100
  • 250
Sort
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
  • Standard (Relevance)
  • Author A-Ö
  • Author Ö-A
  • Title A-Ö
  • Title Ö-A
  • Publication type A-Ö
  • Publication type Ö-A
  • Issued (Oldest first)
  • Issued (Newest first)
  • Created (Oldest first)
  • Created (Newest first)
  • Last updated (Oldest first)
  • Last updated (Newest first)
  • Disputation date (earliest first)
  • Disputation date (latest first)
Select
The maximal number of hits you can export is 250. When you want to export more records please use the Create feeds function.
  • 201.
    Huang, Hui-Run
    et al.
    Chinese Acad Sci, South China Bot Garden, Key Lab Plant Resources Conservat & Sustainable U, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Guangzhou 510650, Guangdong, Peoples R China.
    Liu, Jia-Jia
    Chinese Acad Sci, South China Bot Garden, Key Lab Plant Resources Conservat & Sustainable U, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Guangzhou 510650, Guangdong, Peoples R China.
    Xu, Yong
    Chinese Acad Sci, South China Bot Garden, Key Lab Plant Resources Conservat & Sustainable U, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Guangzhou 510650, Guangdong, Peoples R China.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ge, Xue-Jun
    Chinese Acad Sci, South China Bot Garden, Key Lab Plant Resources Conservat & Sustainable U, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Guangzhou 510650, Guangdong, Peoples R China.
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada.
    Homeologue-specific expression divergence in the recently formed tetraploid Capsella bursa-pastoris (Brassicaceae)2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 220, no 2, p. 624-635Article in journal (Refereed)
    Abstract [en]

    Following allopolyploid formation, extensive genome evolution occurs, with the eventual loss of many homeologous gene copies. Although this process of diploidization has occurred many times independently, the evolutionary forces determining the probability and rate of gene loss remain poorly understood. Here, we conduct genome and transcriptome sequencing in a broad sample of Chinese accessions of Capsella bursa-pastoris, a recently formed allotetraploid. Our whole genome data reveal three groups of these accessions: an Eastern group from low-altitude regions, a Western group from high-altitude regions, and a much more differentiated Northwestern group. Population differentiation in total expression was limited among closely related populations; by contrast, the relative expression of the two homeologous copies closely mirrors the genome-wide SNP divergence. Consistent with this, we observe a negative correlation between expression changes in the two homeologues. However, genes showing population genomic evidence for adaptive evolution do not show an enrichment for expression divergence between homeologues, providing no clear evidence for adaptive shifts in relative gene expression. Overall, these patterns suggest that neutral drift may contribute to the population differentiation in the expression of the homeologues, and drive eventual gene loss over longer periods of time.

  • 202. Huang, Hui-Run
    et al.
    Yan, Peng-Cheng
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ge, Xue-Jun
    Flowering time and transcriptome variation in Capsella bursa-pastoris (Brassicaceae)2012In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 194, no 3, p. 676-689Article, review/survey (Refereed)
    Abstract [en]

    Flowering is a major developmental transition and its timing in relation to environmental conditions is of crucial importance to plant fitness. Understanding the genetic basis of flowering time variation is important to determining how plants adapt locally. Here, we investigated flowering time variation of Capsella bursa-pastoris collected from different latitudes in China. We also used a digital gene expression ( DGE) system to generate partial gene expression profiles for 12 selected samples. We found that flowering time was highly variable and most strongly correlated with day length and winter temperature. Significant differences in gene expression between early-and late-flowering samples were detected for 72 candidate genes for flowering time. Genes related to circadian rhythms were significantly overrepresented among the differentially expressed genes. Our data suggest that circadian rhythms and circadian clock genes play an important role in the evolution of flowering time, and C. bursa-pastoris plants exhibit expression differences for candidate genes likely to affect flowering time across the broad range of environments they face in China.

  • 203. Huttunen, Piritta
    et al.
    Karkkainen, Katri
    Loe, Geir
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Rautio, Pasi
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Leaf trichome production and responses to defoliation and drought in Arabidopsis lyrata (Brassicaceae)2010In: Annales Botanici Fennici, ISSN 0003-3847, E-ISSN 1797-2442, Vol. 47, no 3, p. 199-207Article in journal (Refereed)
    Abstract [en]

    Leaf trichomes can protect plants against herbivory and drought, but can be costly to produce. Theory suggests that selection for reduced costs of resistance may result in the evolution of inducible defences. We quantified variation in tolerance to drought and defoliation, and tested the hypotheses that (a) tolerance is associated with cost, (b) leaf trichome production increases tolerance to drought, and (c) trichome production is increased in response to defoliation and drought stress in Arabidopsis lyrata (Brassicaceae). Eight maternal half-sib families were exposed to two watering regimes and four defoliation treatments in a factorial design. Tolerance to drought varied among families and was inversely related to leaf size, but was not related to trichome density. Family mean performance in the low-watering treatment tended to correlate negatively with that in the control treatment. Trichome production was not induced by defoliation or drought stress. The results suggest that there is genetic variation in tolerance to drought in the study population, that tolerance to drought is associated with a cost, and that trichome production does not increase tolerance to drought in A. lyrata.

  • 204. Hytteborn, H.
    et al.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Skoglund, J.
    Viable seeds in sediments in Lake Hjälmaren1991In: Aquatic Botany, Vol. 40, p. 289-293Article in journal (Refereed)
  • 205.
    Hytteborn, Håkan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Svensson, Brita M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kempe, Kerstin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Press, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Century-long tree population dynamics in a deciduous forest stand in central Sweden2017In: Journal of Vegetation Science, ISSN 1100-9233, E-ISSN 1654-1103, Vol. 28, no 5, p. 1057-1069Article in journal (Refereed)
    Abstract [en]

    Question: We quantify tree dynamics over a century of free development in a small broadleaved forest dominated by Fraxinus excelsior and Ulmus glabra. What are the internal and external factors driving the changes, and how predictable are they? What were the time scale and effects of the spread of Dutch elm disease (DED)? Location: Vårdsätra, eastern central Sweden.

    Methods: The survival, growth and recruitment of all trees (≥ 12 cm in girth) were monitored in 1912, 1967, 1988 and 2013 (more often for a part of the forest). Woody species in the field and shrub layers were surveyed in permanent plots in 1976 and 2012. We used transition matrix models to project changes in population sizes and species composition within the century and for 2050.

    Results: The results indicate that the forest was in a successional development during the first period. The species composition had stabilised by 1967, except for an expansion of Acer platanoides and the drastic effect of DED that struck the forest around 2000. It took only a decade to kill virtually all large elms in the forest, leading to strong decrease in stem density and basal area. The evidence for effects of DED is still weak, but there has been an increase in saplings, notably of Fraxinus, Prunus padus, Ulmus, and of shoots of Corylus avellana. Several species that are abundant in the vicinity and as seeds fail to establish (Picea abies, Betula spp., Quercus robur, Populus tremula). Projections for 2050 based on the third period (1988-2013) are probably unrealistic since also Fraxinus may disappear because of the recent arrival of the ash dieback.

    Conclusions: Slow dynamics in forests that could follow from climate change will locally probably be overruled by unforeseen catastrophes, such as invasions by forest pathogens. These initiate changes with long lag phases difficult to quantify. Still, a dense deciduous forest can resist invasion of colonist species and of regionally dominant conifers; the reason being unfavourable conditions for establishment rather than dispersal limitation

  • 206.
    Hytteborn, Håkan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Verwijst, Theo
    Small-scale disturbance and stand structure dynamics in an old-growth Picea abies forest over 54 yr in central Sweden2014In: Journal of Vegetation Science, ISSN 1100-9233, E-ISSN 1654-1103, Vol. 25, no 1, p. 100-112Article in journal (Refereed)
    Abstract [en]

    QuestionsCan assumptions of the existence of spatially distinct patches (delineated structurally homogeneous parts of the forest, being either areas consisting of canopy trees or areas without canopy trees but in an early or later regenerative phase) and of directional development over time of the vegetation in such patches, as implied by current theory of storm gap dynamics, be verified by remapping previous study sites? LocationNatural, unmanaged boreo-nemoral spruce-dominated forest in eastern central Sweden. MethodsBy re-mapping three plots, ca, 50yr after the first inventory, we studied the structure and dynamics of gaps (patches without canopy tree cover) and major tree populations. The old and new maps allowed us to compare two independent assessments of the forest dynamics: one based on tree population changes and one on changes in gap area over time. ResultsThe current population structure could partly be described through the earlier-encountered structures of the different tree populations and consecutive processes of recruitment and mortality. However, the re-mapping exercise showed that spatially delineated patches did not develop directionally over time, nor was their development spatially discrete. ConclusionsPatch dynamics proceeds in such a way that the fate of a single patch may depend on the development of neighbouring patches. As gaps may partly close or merge into larger gaps, and as gap disappearance rate is a function of actual gap size, performance of an initially delimited patch is largely determined by developments in neighbouring patches and cannot be predicted from its momentary patch characteristics. Consequently, we propose an open matrix model' to describe the changes in a boreo-nemoral spruce forest, rather than a storm gap dynamics' model.

  • 207.
    Hytteborn, Håkan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Verwijst, Theo
    The importance of gaps and dwarf trees in the regeneration of Swedish spruce forests: The origin and content of Sernander's (1936) gap dynamics theory2011In: Scandinavian Journal of Forest Research, ISSN 0282-7581, E-ISSN 1651-1891, Vol. 26, no S10, p. 3-16Article in journal (Refereed)
    Abstract [en]

    This article is a review of a classic paper (1936) by the late Professor Rutger Sernander. This work by Sernander includes the very first formulations of a general theory about forest dynamics driven by storm fellings in fire refugia. Sernander discussed forest dynamics on three different scales: at the landscape, stand and individual tree scale. This article discusses all the important variables and the different stages in forest dynamics brought up by Sernander, such as different susceptibility to storm damage of stands growing on different soil types, the importance of different wind directions and speed, and differences between tree species with regard to susceptibility to wind. It also discusses differences in gap sizes and forms, decomposition degrees of fallen trees, different regeneration modes in connection with gap creation, the effects of wind disturbance on the field-layer vegetation and other stand characteristics, as observed by Sernander.

  • 208.
    Höglund, Solveig
    et al.
    Department of Ecology, Swedish University of Agricultural Sciences.
    Rönnberg-Wästljung, Ann Christin
    Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Larsson, Stig
    Department of Ecology, Swedish University of Agricultural Sciences.
    A rare major plant QTL determines non-responsiveness to a gall-forming insect in willow2012In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 8, no 5, p. 1051-1060Article in journal (Refereed)
    Abstract [en]

    Growth and defence are plant traits that determine attack success by sessile herbivorous insects. Models of plant resistance suggest induced resistance to be an especially important mechanism in growth-dominated plant species. Little is known, however, about the effects of absence of induced responses as an alternative resistance mechanism. Large genetically based intraspecific variation in resistance (neonate larval mortality) occurs in Salix viminalis against the gall midge Dasineura marginemtorquens. In certain resistant genotypes, larval mortality is associated with formation of necrotic lesions and biochemical changes commonly found in hypersensitive response (HR). More detailed studies, however, have shown that resistance can occur without HR symptoms. By means of a quantitative trait locus (QTL) analysis, this study tested whether (1) resistance is caused by the HR or (2) by the failure of the midge to initiate a gall (non-responsiveness). One QTL explained 68 and 18 % of the variation in resistance in the experimental population during 2 years of investigation. Co-location of QTLs for resistance and HR was found in only one of the years, i.e. when HR was suppressed. The data suggest that the mechanism of resistance involves non-responsiveness, implying that the insect starves to death due to lack of resources. Such symptomless defence may be more important than previously thought because it is difficult to observe in nature.

  • 209.
    Höök, Lars
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Leal, Luis
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Talla, Venkat
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Backström, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly2019In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 11, no 9, p. 2633-2652Article in journal (Refereed)
    Abstract [en]

    In species with genetic sex determination, dosage compensation can evolve to equal expression levels of sex-linked and autosomal genes. Current knowledge about dosage compensation has mainly been derived frommale-heterogametic (XX/XY) model organisms, whereas less is understood about the process in female-heterogametic systems (ZZ/ZW). In moths and butterflies, downregulation of Z-linked expression in males (ZZ) to match the expression level in females (ZW) is often observed. However, little is known about the underlying regulatory mechanisms, or if dosage compensation patterns vary across ontogenetic stages. In this study, we assessed dynamics of Z-linked and autosomal expression levels across developmental stages in the wood white (Leptidea sinapis). We found that although expression of Z-linked genes in general was reduced compared with autosomal genes, dosage compensation was actually complete for some categories of genes, in particular sex-biased genes, but equalization in females was constrained to a narrower gene set. We also observed a noticeable convergence in Z-linked expression between males and females after correcting for sex-biased genes. Sex-biased expression increased successively across developmental stages, and male-biased genes were enriched on the Z-chromosome. Finally, all five core genes associated with the ribonucleoprotein dosage compensation complex male-specific lethal were detected in adult females, in correspondence with a reduction in the expression difference between autosomes and the single Z-chromosome. We show that tuning of gene dosage is multilayered in Lepidoptera and argue that expression balance across chromosomal classes may predominantly be driven by enrichment of male-biased genes on the Z-chromosome and cooption of available dosage regulators.

  • 210. Iwaizumi, Masakazu G.
    et al.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ohtani, Masato
    Tsumura, Yoshihiko
    Takahashi, Makoto
    Recent distribution changes affect geographic clines in genetic diversity and structure of Pinus densiflora natural populations in Japan2013In: Forest Ecology and Management, ISSN 0378-1127, E-ISSN 1872-7042, Vol. 304, p. 407-416Article in journal (Refereed)
    Abstract [en]

    Geographic patterns of genetic diversity of widespread tree species with a disturbance-dependent distribution can be influenced by not only past climate change but also disturbance by human activities. This is especially true for species that are dominant mainly in semi-mountainous areas and near human habitation, and also available for forestry. Pinus densiflora is both an economically and ecologically important conifer in semi-mountainous forest landscapes of Japan, and information on its genetic variation is essential for designing programs to manage its natural genetic resources and breeding zones. The geographic pattern of genetic diversity and structure of 62 P. densiflora populations (a total of 1883 trees) across their natural distribution in Japan was examined using eight nuclear microsatellite markers. We found that the allelic richness was somewhat, but significantly, lower in both northern and eastern marginal populations. Analysis of recent bottlenecks detected a significant heterozygosity excess more frequently in the northern and eastern populations. The overall value of the standardized measure of population differentiation was moderate (G'(ST) = 0.122) and similar both to other widespread Japanese tree species and to continental Pinus species. STRUCTURE software analysis revealed a gradual dine in the genetic structure, with three main clusters corresponding to the western, central and northeastern populations; the northeastern cluster showed the highest F value. These results indicated strong genetic drift in the past through rapid population expansion of P. densiflora in northeastern Japan, related to progress in agriculture suggested by anthropological and paleoecological studies. Results obtained on this neutral genetic variation in the nuclear genome should provide fundamental information for designing conservation units and breeding zones and in light of evaluation of its adaptive genetic variation in future studies.

  • 211. Jagerbrand, Annika K.
    et al.
    Alatalo, Juha M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Effects of human trampling on abundance and diversity of vascular plants, bryophytes and lichens in alpine heath vegetation, Northern Sweden2015In: SpringerPlus, E-ISSN 2193-1801, Vol. 4, article id 95Article in journal (Refereed)
    Abstract [en]

    This study investigated the effects of human trampling on cover, diversity and species richness in an alpine heath ecosystem in northern Sweden. We tested the hypothesis that proximity to trails decreases plant cover, diversity and species richness of the canopy and the understory. We found a significant decrease in plant cover with proximity to the trail for the understory, but not for the canopy level, and significant decreases in the abundance of deciduous shrubs in the canopy layer and lichens in the understory. Proximity also had a significant negative impact on species richness of lichens. However, there were no significant changes in species richness, diversity or evenness of distribution in the canopy or understory with proximity to the trail. While not significant, liverworts, acrocarpous and pleurocarpous bryophytes tended to have contrasting abundance patterns with differing proximity to the trail, indicating that trampling may cause shifts in dominance hierarchies of different groups of bryophytes. Due to the decrease in understory cover, the abundance of litter, rock and soil increased with proximity to the trail. These results demonstrate that low-frequency human trampling in alpine heaths over long periods can have major negative impacts on lichen abundance and species richness. To our knowledge, this is the first study to demonstrate that trampling can decrease species richness of lichens. It emphasises the importance of including species-level data on non-vascular plants when conducting studies in alpine or tundra ecosystems, since they often make up the majority of species and play a significant role in ecosystem functioning and response in many of these extreme environments.

  • 212. Jagerbrand, Annika K.
    et al.
    Alatalo, Juha M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kudo, Gaku
    Variation in responses to temperature treatments ex situ of the moss Pleurozium schreberi (Willd. ex Brid.) Mitt. originating from eight altitude sites in Hokkaido, Japan2014In: Journal of Bryology, ISSN 0373-6687, E-ISSN 1743-2820, Vol. 36, no 3, p. 209-216Article in journal (Refereed)
    Abstract [en]

    Thermal acclimatisations are important for the survival and growth of individuals and populations but seldom studied for different populations of bryophytes. The aims of this study were to (I) investigate if responses to temperature treatments were independent of the site sampled or if the intra- and inter-population variation in responses were larger than the responses to the temperature treatments (control, press, and pulse), and to (II) examine if experimental responses varied, depending on the sampled sites. We collected samples of the circumpolar bryophyte species, Pleurozium schreberi (Willd. ex Brid.) Mitt., originating from eight altitude sites on Mt. Oakan in Hokkaido, Japan, and exposed them to three different temperature treatments ex situ for four weeks. Thermal acclimatisation was estimated by measuring responses in growth length increase, biomass increase, number of branches, and the maximum quantum yield of PS II (Fv/Fm). We found that responses to temperature treatments were dependent on the site sampled, and that differences were most pronounced in the length increase. Results also shows that the responses to experimental treatments may differ between sites. Our results therefore raise important concerns regarding the general validity of both ex situ and in situ experiments when performed on a single or a limited number of sites.

  • 213.
    Jakobsson, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Padron, Benigno
    Does the invasive Lupinus polyphyllus increase pollinator visitation to a native herb through effects on pollinator population sizes?2014In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 174, no 1, p. 217-226Article in journal (Refereed)
    Abstract [en]

    Invasive plants may compete with native species for abiotic factors as light, space and nutrients, and have also been shown to affect native pollination interactions. Studies have mainly focused on how invasive plants affect pollinator behaviour, i.e. attraction of pollinators to or away from native flowers. However, when an invasive plant provides resources utilized by native pollinators this could increase pollinator population sizes and thereby pollination success in natives. Effects mediated through changes in pollinator population sizes have been largely ignored in previous studies, and the dominance of negative interactions suggested by meta-analyses may therefore be biased. We investigated the impact of the invasive Lupinus polyphyllus on pollination in the native Lotus corniculatus using a study design comparing invaded and uninvaded sites before and after the flowering period of the invasive. We monitored wild bee abundance in transects, and visit rate and seed production of potted Lotus plants. Bumblebee abundance increased 3.9 times in invaded sites during the study period, whereas it was unaltered in uninvaded sites. Total visit rate per Lotus plant increased 2.1 times in invaded sites and decreased 4.4 times in uninvaded sites. No corresponding change in seed production of Lotus was found. The increase in visit rate to Lotus was driven by an increase in solitary bee visitation, whereas mainly bumblebees were observed to visit the invasive Lupinus. The mechanism by which the invasive increases pollinator visit rates to Lotus could be increased availability of other flower resources for solitary bees when bumblebees forage on Lupinus.

  • 214.
    Jakobsson, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Padrón, Benigno
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Distance-dependent effects of invasive Lupinus polyphyllus on pollination and reproductive success of two native herbs2015In: Basic and Applied Ecology, ISSN 1439-1791, E-ISSN 1618-0089, Vol. 16, no 2, p. 120-127Article in journal (Refereed)
    Abstract [en]

    A comprehensive understanding of the effects of invasive plants on native species requires identification of both the mechanisms of interaction and the spatial scale over which they act. Indirect interactions involving mobile organisms such as pollinators are likely to be scale-dependent, yet most studies examining effects of invasive species on pollination of native plants have considered effects across a single distance between interacting species. We examined the effects of the invasive herb Lupinus polyphyllus on pollination of two native herbs using multiple distances between the invasive and the natives. We recorded pollinator visitation and seed production in the native herbs Lotus corniculatus and Lychnis viscaria at 0, 5 m or 200 m away from L. polyphyllus. To reduce the influence of confounding factors, we used experimentally established populations of the invasive and potted individuals of the natives. In the immediate vicinity to L. polyphyllus, visitation to L. corniculatus was higher than 200 m away, and seed production per flower was higher than 5 m and 200 m away. In L. viscaria, bumblebee visitation was higher adjacent to L. polyphyllus than 5 m and 200 m away, but total pollinator visitation and reproductive success did not vary with distance. The results indicate that L. polyphyllus facilitates pollination of the native plants, and that this occurs at a very local spatial scale as effects dropped off already at a distance of 5 m. Presence of L. polyphyllus could benefit both pollinators and pollination of native herbs, and these positive effects should be considered along with likely negative effects due to resource competition. Moreover, the results illustrate the necessity to consider scale-dependent effects when assessing the impact of invasive flowering plants on native pollination interactions.

  • 215.
    Jakobsson, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Distance to semi-natural grassland influences seed production of insect-pollinated herbs2014In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 175, no 1, p. 199-208Article in journal (Refereed)
    Abstract [en]

    Marginal grassland fragments, such as road verges and field margins, may act as important supplemental habitats for grassland plants in the modern agricultural landscape. However, abundance of pollinators in such fragments has been found to decline with distance to larger natural and semi-natural habitats, and this could have corresponding effects on plant pollination. In this study, we performed a field experiment on road verges with three insect-pollinated grassland herbs to examine the relationship between distance to semi-natural grassland and plant reproductive success in two landscapes with contrasting farming intensities. In Lychnis viscaria and Lotus corniculatus, seed production tended to decrease with increasing distance to semi-natural grassland, but only in the landscape with high farming intensity. Seed production in Armeria maritima spp. maritima decreased with distance in both landscapes. Although many studies have investigated effects of natural habitat on crop pollination, little is known about the impact on pollination in native plants. The results from this study indicate that management of semi-natural grasslands improves not only biodiversity within the actual grassland but also pollination of native plants in the surrounding agricultural landscape.

  • 216.
    Jander, K. Charlotte
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Yale Univ, Dept Ecol & Evolutionary Biol, New Haven, CT USA. Smithsonian Trop Res Inst, Panama City, Panama..
    Indirect mutualism: ants protect fig seeds and pollen dispersers from parasites2015In: Ecological Entomology, ISSN 0307-6946, E-ISSN 1365-2311, Vol. 40, no 5, p. 500-510Article in journal (Refereed)
    Abstract [en]

    1. Mutualisms are ubiquitous and ecologically important, but may be particularly vulnerable to exploitation by species outside of the mutualism owing to a combination of an attractive reward and potentially limited defence options. For some mutualisms, ants can offer dynamic and relatively selective protection against herbivores and parasites. 2. The mutualism between fig trees and their pollinating wasps, a keystone mutualism in tropical forests, is particularly well suited for ant protection because pollinators are protected inside hollow inflorescences but parasites are exposed on the outside. 3. In the present study, it was shown that the presence of ants provides a fitness benefit for both the pollinators and the hosting fig tree. The presence of ants (i) reduced abortions of developing figs, (ii) reduced herbivory of figs, and (iii) reduced parasitic wasp loads, resulting in more pollinators and more seeds in ant-protected figs. Even when taking costs such as ant predation on emerging pollinators into account, the total fitness increase of hosting ants was threefold for the tree and fivefold for the pollinators. 4. It was further shown that the seemingly most vulnerable parasitic wasps, of the genus Idarnes, have a specific behaviour that allows them to evade ant attack while continuing to oviposit. 5. Ants were present on 79% of surveyed Panamanian fig trees. Together with previous studies from the Old World, the results found here imply that ants are both powerful and common protectors of the fig mutualism worldwide.

  • 217.
    Jandér, Charlotte
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Herre, Edward Allen
    Simms, Ellen L.
    Precision of host sanctions in the fig tree-fig wasp mutualism: consequences for uncooperative symbionts2012In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 15, no 12, p. 1362-1369Article in journal (Refereed)
    Abstract [en]

    Host sanctions that reduce the relative fitness of uncooperative symbionts provide a mechanism that can limit cheating and thus stabilise mutualisms over evolutionary timescales. Sanctions have been demonstrated empirically in several mutualisms. However, if multiple individual symbionts interact with each host, the precision with which individual cheating symbionts are targeted by host sanctions is critical to their short- and long-term effectiveness. No previous empirical study has directly addressed this issue. Here, we report the precision of host sanctions in the mutualism between fig trees and their pollinating wasps. Using field experiments and molecular parentage analyses, we show that sanctions in Ficus nymphaeifolia act at the level of entire figs (syconia), not at the level of the individual flowers within. Such fig-level sanctions allow uncooperative wasps, which do not bring pollen, to avoid sanctions in figs to which other wasps bring pollen. We discuss the relevance of sanction precision to other mutualisms.

  • 218. Johnson, Matthew G.
    et al.
    Granath, Gustaf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tahvanainen, Teemu
    Pouliot, Remy
    Stenoien, Hans K.
    Rochefort, Line
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Shaw, A. Jonathan
    Evolution of niche preference in Sphagnum peat mosses2015In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 69, no 1, p. 90-103Article in journal (Refereed)
    Abstract [en]

    Peat mosses (Sphagnum) are ecosystem engineersspecies in boreal peatlands simultaneously create and inhabit narrow habitat preferences along two microhabitat gradients: an ionic gradient and a hydrological hummock-hollow gradient. In this article, we demonstrate the connections between microhabitat preference and phylogeny in Sphagnum. Using a dataset of 39 species of Sphagnum, with an 18-locus DNA alignment and an ecological dataset encompassing three large published studies, we tested for phylogenetic signal and within-genus changes in evolutionary rate of eight niche descriptors and two multivariate niche gradients. We find little to no evidence for phylogenetic signal in most component descriptors of the ionic gradient, but interspecific variation along the hummock-hollow gradient shows considerable phylogenetic signal. We find support for a change in the rate of niche evolution within the genusthe hummock-forming subgenus Acutifolia has evolved along the multivariate hummock-hollow gradient faster than the hollow-inhabiting subgenus Cuspidata. Because peat mosses themselves create some of the ecological gradients constituting their own habitats, the classic microtopography of Sphagnum-dominated peatlands is maintained by evolutionary constraints and the biological properties of related Sphagnum species. The patterns of phylogenetic signal observed here will instruct future study on the role of functional traits in peatland growth and reconstruction.

  • 219.
    Junker, Robert R.
    et al.
    Salzburg Univ, Dept Ecol & Evolut, Hellbrunnerstr 34, A-5020 Salzburg, Austria.
    Kuppler, Jonas
    Salzburg Univ, Dept Ecol & Evolut, Hellbrunnerstr 34, A-5020 Salzburg, Austria.
    Amo, Luisa
    Netherlands Inst Ecol NIOO KNAW, Dept Anim Ecol, NL-6700 EH Wageningen, Netherlands;CSIC, Museo Nacl Ciencias Nat, Dept Evolutionary Ecol, E-28006 Madrid, Spain.
    Blande, James D.
    Univ Eastern Finland, Dept Environm & Biol Sci, Kuopio 70211, Finland.
    Borges, Renee M.
    Indian Inst Sci, Ctr Ecol Sci, Bangalore 560012, Karnataka, India.
    van Dam, Nicole M.
    Halle Jena Leipzig Friedrich Schiller Univ Jena, German Ctr Integrat Biodivers Res iDiv, Deutsch Pl 5e, D-04103 Leipzig, Germany.
    Dicke, Marcel
    Wageningen Univ, Entomol Lab, POB 16, NL-6700 AA Wageningen, Netherlands.
    Dötterl, Stefan
    Salzburg Univ, Dept Ecol & Evolut, Hellbrunnerstr 34, A-5020 Salzburg, Austria.
    Ehlers, Bodil K.
    Aarhus Univ, Dept Biosci, Vejlsovej 25, DK-8600 Silkeborg, Denmark.
    Etl, Florian
    Salzburg Univ, Dept Ecol & Evolut, Hellbrunnerstr 34, A-5020 Salzburg, Austria;Univ Vienna, Dept Bot & Biodivers Res, A-1030 Vienna, Austria.
    Gershenzon, Jonathan
    Max Planck Inst Chem Ecol, Dept Biochem, D-07745 Jena, Germany.
    Glinwood, Robert
    Swedish Univ Agr Sci, Dept Crop Prod Ecol, Box 7043, S-75007 Uppsala, Sweden.
    Gols, Rieta
    Wageningen Univ, Entomol Lab, POB 16, NL-6700 AA Wageningen, Netherlands.
    Groot, Astrid T.
    Univ Amsterdam, IBED, NL-1090 GE Amsterdam, Netherlands;Max Planck Inst Chem Ecol, Dept Entomol, D-07745 Jena, Germany.
    Heil, Martin
    CINVESTAV Irapuato, Dept Ingn Genet, Irapuato 36821, Mexico.
    Hoffmeister, Mathias
    Salzburg Univ, Dept Ecol & Evolut, Hellbrunnerstr 34, A-5020 Salzburg, Austria.
    Holopainen, Jarmo K.
    Univ Eastern Finland, Dept Environm & Biol Sci, Kuopio 70211, Finland.
    Jarau, Stefan
    Ulm Univ, Inst Neurobiol, Helmholtzstr 10-1, D-89081 Ulm, Germany.
    John, Lena
    Ulm Univ, Inst Neurobiol, Helmholtzstr 10-1, D-89081 Ulm, Germany.
    Kessler, Andre
    Cornell Univ, Dept Ecol & Evolutionary Biol, Ithaca, NY 14853 USA.
    Knudsen, Jette T.
    Lund Univ, Deptartment Biol, SE-22362 Lund, Sweden;Nattaro Labs AB, S-22381 Lund, Sweden.
    Kost, Christian
    Max Planck Inst Chem Ecol, Res Grp Expt Ecol & Evolut, D-07745 Jena, Germany;Univ Osnabruck, Sch Biol Chem, Dept Ecol, D-49074 Osnabruck, Germany.
    Larue-Kontic, Anne-Amelie C.
    Salzburg Univ, Dept Ecol & Evolut, Hellbrunnerstr 34, A-5020 Salzburg, Austria.
    Leonhardt, Sara Diana
    Wurzburg Univ, Dept Anim Ecol & Trop Biol, D-97074 Wurzburg, Germany.
    Lucas-Barbosa, Dani
    Wageningen Univ, Entomol Lab, POB 16, NL-6700 AA Wageningen, Netherlands.
    Majetic, Cassie J.
    St Marys Coll, Dept Biol, Notre Dame, IN 46556 USA.
    Menzel, Florian
    Johannes Gutenberg Univ Mainz, Inst Zool, D-55128 Mainz, Germany.
    Parachnowitsch, Amy L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Pasquet, Remy S.
    IRD, Dept ECOBIO, 44 Bd Dunkerque, F-13572 Marseille 02, France.
    Poelman, Erik H.
    Wageningen Univ, Entomol Lab, POB 16, NL-6700 AA Wageningen, Netherlands.
    Raguso, Robert A.
    Cornell Univ, Dept Neurobiol & Behav, Ithaca, NY 14853 USA.
    Ruther, Joachim
    Univ Regensburg, Inst Zool, Univ Str 31, D-93053 Regensburg, Germany.
    Schiestl, Florian P.
    Univ Zurich, Dept Systemat & Evolutionary Bot, Zollikerstr 107, CH-8008 Zurich, Switzerland.
    Schmitt, Thomas
    Wurzburg Univ, Dept Anim Ecol & Trop Biol, D-97074 Wurzburg, Germany.
    Tholl, Dorothea
    Virginia Tech, Dept Biol Sci, Blacksburg, VA 24061 USA.
    Unsicker, Sybille B.
    Max Planck Inst Chem Ecol, Dept Biochem, D-07745 Jena, Germany.
    Verhulst, Niels
    Wageningen Univ, Entomol Lab, POB 16, NL-6700 AA Wageningen, Netherlands.
    Visser, Marcel E.
    Netherlands Inst Ecol NIOO KNAW, Dept Anim Ecol, NL-6700 EH Wageningen, Netherlands.
    Weldegergis, Berhane T.
    Wageningen Univ, Entomol Lab, POB 16, NL-6700 AA Wageningen, Netherlands.
    Köllner, Tobias G.
    Max Planck Inst Chem Ecol, Dept Biochem, D-07745 Jena, Germany.
    Covariation and phenotypic integration in chemical communication displays: biosynthetic constraints and eco-evolutionary implications2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 220, no 3, p. 739-749Article in journal (Refereed)
    Abstract [en]

    Chemical communication is ubiquitous. The identification of conserved structural elements in visual and acoustic communication is well established, but comparable information on chemical communication displays (CCDs) is lacking. We assessed the phenotypic integration of CCDs in a meta-analysis to characterize patterns of covariation in CCDs and identified functional or biosynthetically constrained modules. Poorly integrated plant CCDs (i.e. low covariation between scent compounds) support the notion that plants often utilize one or few key compounds to repel antagonists or to attract pollinators and enemies of herbivores. Animal CCDs (mostly insect pheromones) were usually more integrated than those of plants (i.e. stronger covariation), suggesting that animals communicate via fixed proportions among compounds. Both plant and animal CCDs were composed of modules, which are groups of strongly covarying compounds. Biosynthetic similarity of compounds revealed biosynthetic constraints in the covariation patterns of plant CCDs. We provide a novel perspective on chemical communication and a basis for future investigations on structural properties of CCDs. This will facilitate identifying modules and biosynthetic constraints that may affect the outcome of selection and thus provide a predictive framework for evolutionary trajectories of CCDs in plants and animals.

  • 220. Junker, Robert R.
    et al.
    Parachnowitsch, Amy L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Working Towards a Holistic View on Flower Traits-How Floral Scents Mediate Plant-Animal Interactions in Concert with Other Floral Characters2015In: Journal of the Indian Institute of Science, ISSN 0970-4140, Vol. 95, no 1, p. 43-67Article in journal (Refereed)
    Abstract [en]

    Flowers are complex structures, synchronously displaying both olfactory and visual signals/cues in the context of a particular floral morphology, that also vary in resource quantity and quality. Despite or possibly because of this complexity, many studies focus on a single or few traits rather than studying floral phenotypes in a more integrated fashion. However, each of these distinct trait classes (signals/cues, morphology and resources) mediates interactions with floral visitors, demanding a more holistic view of flowers. In our review, we integrate floral scents into the broader context of the whole-flower phenotype. We discuss the functions of scent bouquets, colouration, morphology and rewards in flower visitor interactions from an ecological and evolutionary perspective in isolation and taken together. Studies demonstrate that floral scent bouquets can act additively or synergistically with other modalities, and that their effects on flower visitors are context-dependent. We also present field study results showing that reward levels modulate dose-dependent responses to volatiles by honeybees. To motivate studies examining complex floral phenotypes, we outline statistical approaches suited to deal with the complex multivariate datasets generated by these studies. We conclude with a discussion on why flowers display multimodal traits and suggest future research efforts. Our aim is to foster a fresh view on integrated floral phenotypes and stimulate studies exploring the combined effects of olfactory, visual, morphological and nutritional traits on flower animal interactions.

  • 221.
    Kaarlejärvi, Elina
    et al.
    Department of Ecology and Environmental Sciences, Umeå University.
    Baxter, Robert
    School of Biological and Biomedical Sciences, University of Durham.
    Hofgaard, Annika
    Norwegian Institute for Nature Research,Trondheim.
    Hytteborn, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Khitun, Olga
    Department of Biological and Environmental Sciences, University of Gothenburg.
    Molau, Ulf
    Department of Biological and Environmental Sciences, University of Gothenburg.
    Sjögersten, Sofie
    School of Biosciences, University of Nottingham.
    Wookey, Philip
    Department of Geography, University of Sheffield.
    Olofsson, Johan
    Department of Ecology and Environmental Sciences, Umeå University.
    Effects of warming on shrub abundance and chemistry drive ecosystem-level changes in a forest-tundra ecotone2012In: Ecosystems (New York. Print), ISSN 1432-9840, E-ISSN 1435-0629, Vol. 15, no 8, p. 1219-1233Article in journal (Refereed)
    Abstract [en]

    Tundra vegetation is responding rapidly to on-going climate warming. The changes in plant abundance and chemistry might have cascading effects on tundra food webs, but an integrated understanding of how the responses vary between habitats and across environmental gradients is lacking. We assessed responses in plant abundance and plant chemistry to warmer climate, both at species and community levels, in two different habitats. We used a long-term and multisite warming (OTC) experiment in the Scandinavian forest–tundra ecotone to investigate (i) changes in plant community composition and (ii) responses in foliar nitrogen, phosphorus, and carbon-based secondary compound concentrations in two dominant evergreen dwarf-shrubs (Empetrum hermaphroditum and Vaccinium vitis-idaea) and two deciduous shrubs (Vaccinium myrtillus and Betula nana). We found that initial plant community composition, and the functional traits of these plants, will determine the responsiveness of the community composition, and thus community traits, to experimental warming. Although changes in plant chemistry within species were minor, alterations in plant community composition drive changes in community-level nutrient concentrations. In view of projected climate change, our results suggest that plant abundance will increase in the future, but nutrient concentrations in the tundra field layer vegetation will decrease. These effects are large enough to have knock-on consequences for major ecosystem processes like herbivory and nutrient cycling. The reduced food quality could lead to weaker trophic cascades and weaker top down control of plant community biomass and composition in the future. However, the opposite effects in forest indicate that these changes might be obscured by advancing treeline forests.

  • 222.
    Kaj, Ingemar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tahir, Daniah
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Analysis of diversity-dependent species evolution using concepts in population geneticsManuscript (preprint) (Other academic)
    Abstract [en]

    In this work, we consider a two-type species model with trait dependent speciation, extinction and transition rates under an evolutionary time scale. The scaling approach and the diffusion approximation techniques which are widely used in mathematical population genetics provide background and tools to assist in the study of species dynamics, and help explore the analogy between trait dependent species diversication and the evolution of allele frequencies in the population genetics setting. The analytical framework specied is then applied to models incorporating diversity-dependence, in order to infer effective results from processes in which the net growth of species depends on their current population sizes.

  • 223. Kapfer, Jutta
    et al.
    Grytnes, John-Arvid
    Gunnarsson, Urban
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Birks, H. John B.
    Fine-scale changes in vegetation composition in a boreal mire over 50 years2011In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 99, no 5, p. 1179-1189Article in journal (Refereed)
    Abstract [en]

    1. In the face of a rapidly changing environment, long-term studies provide important insights into patterns of vegetation and processes of change, but long-term studies are rare for many ecosystems. 2. We studied recent vegetation changes at a fine scale in a Sphagnum-dominated bog in south Sweden by resurveying part of the bog 54 years after the original phytosociological survey. We used an indirect approach to identify changes in vegetation composition in relation to environment because of a lack of permanent sampling units. By applying a weighted averaging technique, we calculated relative changes in species optimum values for different environmental gradients as represented by indicator values for light, temperature, pH, moisture and nutrients. 3. Species composition of the mire vegetation has changed significantly over the past five decades, as indicated by significant changes in species frequencies and species optima for the gradients examined. Species with lower indicator values for moisture and light and higher indicator values for nutrients have become more frequent on the mire. In particular, species of trees and dwarf shrubs increased in frequency, whereas typical mire species decreased (e. g. Trichophorum cespitosum (L.) Hartm.) or disappeared from the study site (e. g. Scheuchzeria palustris L.). 4. Synthesis. Composition of the mire vegetation is found to be dynamic at different temporal and spatial scales. Increased air temperature and nutrient availability in south Sweden over the past few decades may have augmented productivity (e. g. tree growth), resulting in drier and shadier conditions for several species. This study successfully demonstrated the applicability of an indirect approach for detecting long-term vegetation change at a fine scale. This approach is an effective way of using historic and modern phytosociological data sets to detect vegetation and environmental change through time.

  • 224.
    Karlgren, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genetic Control of Annual Growth Rhythm in the Conifer Norway Spruce (Picea Abies L. Karst)2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Norway spruce (Picea abies L. Karst) is a conifer belonging to the group gymnosperms and is an ecologically and economically important species in several parts of Europe. It is crucial for trees like Norway spruce to adapt timing of events such as bud set and growth cessation to the local environment in order to maximize the growth period while avoiding frost damage.

    This thesis aims at widening the knowledge about genetic control of annual growth rhythm in Norway spruce and particularly the control of bud set. Using spruce transformants ectopically expressing PaFT/TFL1-LIKE 2 (PaFTL2) the prior hypothesis that PaFTL2 induces bud set is confirmed. This is further supported by spatial and temporal expression patterns in seedlings and adult trees. It is further shown that gymnosperms possess at least two FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like genes with TFL1-like function, suggesting the ancestor of FT and TFL1 to be more TFL1-like. PaFTL1 appears to have complementary expression patterns to that of PaFTL2 both spatially and temporally indicating they may act together to control growth in Norway spruce.

    Since bud set is controlled by photoperiod and circadian clock genes are implicated in this process, putative clock homologs were studied to gain insight into the circadian clock in gymnosperms. Several clock homologs were identified and their expression showed a diurnal pattern but the expression was rapidly damped in constant conditions. Transgenic Arabidopsis expressing putative core clock genes from spruce indicate that at least three genes, PaCCA1, PaGI and PaZTL, appear to have a conserved function between angiosperms and gymnosperms. Taken together these results suggest that gymnosperms have a similar core clock structure as angiosperms even though fundamental differences might exist since the cycling of the clock genes were rapidly damped in free-running conditions.

    The studies presented in this thesis support substantial conservation of pathway components controlling photoperiodic responses in angiosperms and gymnosperms and identify PaFTL2 as a component of growth rhythm control. However, important changes in these processes are also evident. The results provide a solid basis for future research on molecular mechanisms controlling an adaptive trait in an important non-model organism.

    List of papers
    1. Evolution of the PEBP Gene Family in Plants: Functional Diversification in Seed Plant Evolution
    Open this publication in new window or tab >>Evolution of the PEBP Gene Family in Plants: Functional Diversification in Seed Plant Evolution
    Show others...
    2011 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 156, no 4, p. 1967-1977Article in journal (Refereed) Published
    Abstract [en]

    The phosphatidyl ethanolamine-binding protein (PEBP) gene family is present in all eukaryote kingdoms, with three subfamilies identified in angiosperms (FLOWERING LOCUS T [FT], MOTHER OF FT AND TFL1 [MFT], and TERMINAL FLOWER1 [TFL1] like). In angiosperms, PEBP genes have been shown to function both as promoters and suppressors of flowering and to control plant architecture. In this study, we focus on previously uncharacterized PEBP genes from gymnosperms. Extensive database searches suggest that gymnosperms possess only two types of PEBP genes, MFT-like and a group that occupies an intermediate phylogenetic position between the FT-like and TFL1-like (FT/TFL1-like). Overexpression of Picea abies PEBP genes in Arabidopsis (Arabidopsis thaliana) suggests that the FT/TFL1-like genes (PaFTL1 and PaFTL2) code for proteins with a TFL1-like function. However, PaFTL1 and PaFTL2 also show highly divergent expression patterns. While the expression of PaFTL2 is correlated with annual growth rhythm and mainly confined to needles and vegetative and reproductive buds, the expression of PaFTL1 is largely restricted to microsporophylls of male cones. The P. abies MFT-like genes (PaMFT1 and PaMFT2) show a predominant expression during embryo development, a pattern that is also found for many MFT-like genes from angiosperms. P. abies PEBP gene expression is primarily detected in tissues undergoing physiological changes related to growth arrest and dormancy. A first duplication event resulting in two families of plant PEBP genes (MFT-like and FT/TFL1-like) seems to coincide with the evolution of seed plants, in which independent control of bud and seed dormancy was required, and the second duplication resulting in the FT-like and TFL1-like clades probably coincided with the evolution of angiosperms.

    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-157251 (URN)10.1104/pp.111.176206 (DOI)000293568800025 ()
    Available from: 2011-08-25 Created: 2011-08-22 Last updated: 2017-12-08Bibliographically approved
    2. FLOWERING LOCUS T/TERMINAL FLOWER1-Like Genes Affect Growth Rhythm and Bud Set in Norway Spruce
    Open this publication in new window or tab >>FLOWERING LOCUS T/TERMINAL FLOWER1-Like Genes Affect Growth Rhythm and Bud Set in Norway Spruce
    2013 (English)In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 163, no 2, p. 792-803Article in journal (Refereed) Published
    Abstract [en]

    The timing of bud set, as one determinant of the annual growth rhythm, is critical for local adaptation of the conifer Norway spruce (Picea abies). Previous gene expression and population genetic studies have suggested a role for P. abies FLOWERING LOCUS T/TERMINAL FLOWER1-Like2 (PaFTL2) in the control of growth cessation and bud set in Norway spruce as well as in local adaptation resulting in clinal variation for timing of bud set. Using transgenic plants with PaFTL2 driven by an inducible promoter, we found that PaFTL2 indeed induces bud set and most probably also growth cessation. PaFTL2 shows high expression around the procambium and vascular tissue and in the crown region in buds of both seedlings and older trees. Furthermore, PaFTL2 expression is induced in vegetative shoots and all bud types in late summer, when growth cessation occurs. This supports the notion that PaFTL2 is involved in growth cessation. A close paralog to PaFTL2, PaFTL1, is strongly expressed in meristems during the summer, possibly to repress meristem activity and the formation of needle primordia during this period. The temporal and spatial expression of PaFTL1 and PaFTL2 largely complement each other, which suggests that they act in concert to control perennial growth in Norway spruce.

    Keywords
    bud set, Picea abies, transformants, FT/TFL1-like genes, growth cessation
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-192123 (URN)10.1104/pp.113.224139 (DOI)000325554100031 ()
    Available from: 2013-01-16 Created: 2013-01-16 Last updated: 2017-12-06Bibliographically approved
    3. No time for spruce: rapid dampening of circadian rhythms in Picea abies (L. Karst)
    Open this publication in new window or tab >>No time for spruce: rapid dampening of circadian rhythms in Picea abies (L. Karst)
    Show others...
    2014 (English)In: Plant and Cell Physiology, ISSN 0032-0781, E-ISSN 1471-9053, Vol. 55, no 3, p. 535-550Article in journal (Refereed) Published
    Keywords
    Picea abies, circadian clock, diurnal cycling, phylogeny, gene expression, delayed fluorescence
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-192178 (URN)10.1093/pcp/pct199 (DOI)000333096200007 ()
    Available from: 2013-01-16 Created: 2013-01-16 Last updated: 2017-12-06Bibliographically approved
    4. Conserved function of core clock proteins in the gymnosperm Norway spruce (Picea abies L. Karst)
    Open this publication in new window or tab >>Conserved function of core clock proteins in the gymnosperm Norway spruce (Picea abies L. Karst)
    2013 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 3, p. e60110-Article in journal (Refereed) Published
    Abstract [en]

    From studies of the circadian clock in the plant model species Arabidopsis (Arabidopsis thaliana), a number of important properties and components have emerged. These include the genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), GIGANTEA (GI), ZEITLUPE (ZTL) and TIMING OF CAB EXPRESSION 1 (TOC1 also known as PSEUDO-RESPONSE REGULATOR 1 (PRR1)) that via gene expression feedback loops participate in the circadian clock. Here, we present results from ectopic expression of four Norway spruce (Picea abies) putative homologs (PaCCA1, PaGI, PaZTL and PaPRR1) in Arabidopsis, their flowering time, circadian period length, red light response phenotypes and their effect on endogenous clock genes were assessed. For PaCCA1-ox and PaZTL-ox the results were consistent with Arabidopsis lines overexpressing the corresponding Arabidopsis genes. For PaGI consistent results were obtained when expressed in the gi2 mutant, while PaGI and PaPRR1 expressed in wild type did not display the expected phenotypes. These results suggest that protein function of PaCCA1, PaGI and PaZTL are at least partlyconserved compared to Arabidopsis homologs, however further studies are needed to reveal the protein function of PaPRR1. Our data suggest that components of thethree-loop network typical of the circadian clock in angiosperms were present beforethe split of gymnosperms and angiosperms.

    Keywords
    circadian clock, Picea abies (Norway spruce), transformants, gymnosperm, ZEITLUPE (ZTL), GIGANTEA (GI), TIMING OF CAB1 (TOC1 or PRR1), CIRCADIAN CLOCK ASSOCIATED 1 (CCA1)
    National Category
    Biochemistry and Molecular Biology
    Identifiers
    urn:nbn:se:uu:diva-192151 (URN)10.1371/journal.pone.0060110 (DOI)000317262200084 ()
    Available from: 2013-01-16 Created: 2013-01-16 Last updated: 2017-12-06Bibliographically approved
  • 225.
    Karlgren, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Växtbiologi och skogsgenetik, Plant Biology and Forest Genetics.
    Clapham, David
    Växtbiologi och skogsgenetik, Plant Biology and Forest Genetics.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    FLOWERING LOCUS T/TERMINAL FLOWER1-Like Genes Affect Growth Rhythm and Bud Set in Norway Spruce2013In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 163, no 2, p. 792-803Article in journal (Refereed)
    Abstract [en]

    The timing of bud set, as one determinant of the annual growth rhythm, is critical for local adaptation of the conifer Norway spruce (Picea abies). Previous gene expression and population genetic studies have suggested a role for P. abies FLOWERING LOCUS T/TERMINAL FLOWER1-Like2 (PaFTL2) in the control of growth cessation and bud set in Norway spruce as well as in local adaptation resulting in clinal variation for timing of bud set. Using transgenic plants with PaFTL2 driven by an inducible promoter, we found that PaFTL2 indeed induces bud set and most probably also growth cessation. PaFTL2 shows high expression around the procambium and vascular tissue and in the crown region in buds of both seedlings and older trees. Furthermore, PaFTL2 expression is induced in vegetative shoots and all bud types in late summer, when growth cessation occurs. This supports the notion that PaFTL2 is involved in growth cessation. A close paralog to PaFTL2, PaFTL1, is strongly expressed in meristems during the summer, possibly to repress meristem activity and the formation of needle primordia during this period. The temporal and spatial expression of PaFTL1 and PaFTL2 largely complement each other, which suggests that they act in concert to control perennial growth in Norway spruce.

  • 226.
    Karlgren, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Växtbiologi och skogsgenetik, Plant Biology and Forest Genetics.
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conserved function of core clock proteins in the gymnosperm Norway spruce (Picea abies L. Karst)2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 3, p. e60110-Article in journal (Refereed)
    Abstract [en]

    From studies of the circadian clock in the plant model species Arabidopsis (Arabidopsis thaliana), a number of important properties and components have emerged. These include the genes CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), GIGANTEA (GI), ZEITLUPE (ZTL) and TIMING OF CAB EXPRESSION 1 (TOC1 also known as PSEUDO-RESPONSE REGULATOR 1 (PRR1)) that via gene expression feedback loops participate in the circadian clock. Here, we present results from ectopic expression of four Norway spruce (Picea abies) putative homologs (PaCCA1, PaGI, PaZTL and PaPRR1) in Arabidopsis, their flowering time, circadian period length, red light response phenotypes and their effect on endogenous clock genes were assessed. For PaCCA1-ox and PaZTL-ox the results were consistent with Arabidopsis lines overexpressing the corresponding Arabidopsis genes. For PaGI consistent results were obtained when expressed in the gi2 mutant, while PaGI and PaPRR1 expressed in wild type did not display the expected phenotypes. These results suggest that protein function of PaCCA1, PaGI and PaZTL are at least partlyconserved compared to Arabidopsis homologs, however further studies are needed to reveal the protein function of PaPRR1. Our data suggest that components of thethree-loop network typical of the circadian clock in angiosperms were present beforethe split of gymnosperms and angiosperms.

  • 227.
    Karlgren, Anna
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sundström, Jens F.
    Moore, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Evolution of the PEBP Gene Family in Plants: Functional Diversification in Seed Plant Evolution2011In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 156, no 4, p. 1967-1977Article in journal (Refereed)
    Abstract [en]

    The phosphatidyl ethanolamine-binding protein (PEBP) gene family is present in all eukaryote kingdoms, with three subfamilies identified in angiosperms (FLOWERING LOCUS T [FT], MOTHER OF FT AND TFL1 [MFT], and TERMINAL FLOWER1 [TFL1] like). In angiosperms, PEBP genes have been shown to function both as promoters and suppressors of flowering and to control plant architecture. In this study, we focus on previously uncharacterized PEBP genes from gymnosperms. Extensive database searches suggest that gymnosperms possess only two types of PEBP genes, MFT-like and a group that occupies an intermediate phylogenetic position between the FT-like and TFL1-like (FT/TFL1-like). Overexpression of Picea abies PEBP genes in Arabidopsis (Arabidopsis thaliana) suggests that the FT/TFL1-like genes (PaFTL1 and PaFTL2) code for proteins with a TFL1-like function. However, PaFTL1 and PaFTL2 also show highly divergent expression patterns. While the expression of PaFTL2 is correlated with annual growth rhythm and mainly confined to needles and vegetative and reproductive buds, the expression of PaFTL1 is largely restricted to microsporophylls of male cones. The P. abies MFT-like genes (PaMFT1 and PaMFT2) show a predominant expression during embryo development, a pattern that is also found for many MFT-like genes from angiosperms. P. abies PEBP gene expression is primarily detected in tissues undergoing physiological changes related to growth arrest and dormancy. A first duplication event resulting in two families of plant PEBP genes (MFT-like and FT/TFL1-like) seems to coincide with the evolution of seed plants, in which independent control of bud and seed dormancy was required, and the second duplication resulting in the FT-like and TFL1-like clades probably coincided with the evolution of angiosperms.

  • 228.
    Karrenberg, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Speciation genetics: Limits and promises2010In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 59, no 5, p. 1404-1412Article in journal (Refereed)
    Abstract [en]

    Many central questions on speciation genetics such as the nature of genetic changes involved and the role of selection in speciation have been under prolonged and intense debate. The development of massively parallel sequencing and increased cooperation among ecological, population and molecular geneticists, offer the promise to find answers to these questions. However, there currently is evidence for the involvement of many different factors and processes in speciation, with their relative importance unresolved. Processes implicated in speciation include not only geographic isolation and structural change through small-effect mutations, but also regulatory mutations, copy number variation and chromosomal rearrangements, as well as scenarios of divergence-with-gene-flow and evolution through genetic conflict. In this review, I summarize current views and persistent limitations in speciation genetics, explore two promising research approaches in this field and end with an overview on current and expected progress in plant speciation genetics.

  • 229.
    Karrenberg, Sophie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Liu, Xiaodong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Hallander, Emelie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Swedish Board Agr, Jönkoping, Sweden.
    Favre, Adrien
    Goethe Univ, Inst Ecol Evolut & Div, Dept Div & Evolut Higher Plants, Frankfurt, Germany; Senckenberg Res Inst, Frankfurt, Germany; Nat Hist Museum, Frankfurt, Germany.
    Herforth-Rahme, Joelle
    Swiss Fed Inst Technol, Inst Integrat Biol, Zurich, Switzerland; Res Inst Organ Agr FiBL, Dept Soil Sci, Frick, Switzerland.
    Widmer, Alex
    Swiss Fed Inst Technol, Inst Integrat Biol, Zurich, Switzerland.
    Ecological divergence plays an important role in strong but complex reproductive isolation in campions (Silene)2019In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 73, no 2, p. 245-261Article in journal (Refereed)
    Abstract [en]

    New species arise through the evolution of reproductive barriers between formerly interbreeding lineages. Yet, comprehensive assessments of potential reproductive barriers, which are needed to make inferences on processes driving speciation, are only available for a limited number of systems. In this study, we estimated individual and cumulative strengths of seven prezygotic and six postzygotic reproductive barriers between the recently diverged taxa Silene dioica (L.) Clairv. and S. latifolia Poiret using both published and new data. A combination of multiple partial reproductive barriers resulted in near-complete reproductive isolation between S. dioica and S. latifolia, consistent with earlier estimates of gene flow between the taxa. Extrinsic barriers associated with adaptive ecological divergence were most important, while intrinsic postzygotic barriers had moderate individual strength but contributed only little to total reproductive isolation. These findings are in line with ecological divergence as driver of speciation. We further found extensive variation in extrinsic reproductive isolation, ranging from sites with very strong selection against migrants and hybrids to intermediate sites where substantial hybridization is possible. This situation may allow for, or even promote, heterogeneous genetic divergence.

  • 230.
    Karrenberg, Sophie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Liu, Xiaodong
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Hallander, Emelie
    Favre, Adrien
    Herforth-Rahmé, Joelle
    Widmer, Alex
    Ecological divergence plays an important role in strong but complex reproductive isolation in campions (Silene).Manuscript (preprint) (Other academic)
  • 231. Kato, Shuri
    et al.
    Matsumoto, Asako
    Yoshimura, Kensuke
    Katsuki, Toshio
    Iwamoto, Kojiro
    Kawahara, Takayuki
    Mukai, Yuzuru
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ishio, Shogo
    Nakamura, Kentaro
    Moriwaki, Kazuo
    Shiroishi, Toshihiko
    Gojobori, Takashi
    Yoshimaru, Hiroshi
    Origins of Japanese flowering cherry (Prunus subgenus Cerasus) cultivars revealed using nuclear SSR markers2014In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 10, no 3, p. 477-487Article in journal (Refereed)
    Abstract [en]

    Japanese flowering cherry (Prunus subgenus Cerasus) cultivars, which are characterized by beautiful flowers, have been developed through hybridization among wild Prunus taxa. The long history of cultivation has caused significant confusion over the origins of these cultivars. We conducted molecular analysis using nuclear simple sequence repeat (SSR) polymorphisms to trace cultivar origins. Bayesian clustering based on the STRUCTURE analysis using SSR genotypes revealed that many cultivars originated from hybridization between two or more wild species. This suggests that morphological variations among flowering cherry cultivars probably arose through a complex sequence of hybridizations. Our findings generally supported estimates of the origins of cultivars based on morphological study, although there were some exceptions.

  • 232. Kato, Shuri
    et al.
    Matsumoto, Asako
    Yoshimura, Kensuke
    Katsuki, Toshio
    Iwamoto, Kojiro
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ishio, Shogo
    Nakamura, Kentaro
    Moriwaki, Kazuo
    Shiroishi, Toshihiko
    Gojobori, Takashi
    Yoshimaru, Hiroshi
    Clone identification in Japanese flowering cherry (Prunus subgenus Cerasus) cultivars using nuclear SSR markers2012In: Breeding Science, ISSN 1344-7610, E-ISSN 1347-3735, Vol. 62, no 3, p. 248-255Article in journal (Refereed)
    Abstract [en]

    Numerous cultivars of Japanese flowering cherry (Prunus subgenus Cerasus) are recognized, but in many cases they are difficult to distinguish morphologically. Therefore, we evaluated the clonal status of 215 designated cultivars using 17 SSR markers. More than half the cultivars were morphologically distinct and had unique genotypes. However, 22 cultivars were found to consist of multiple clones, which probably originate from the chance seedlings, suggesting that their unique characteristics have not been maintained through propagation by grafting alone. We also identified 23 groups consisting of two or more cultivars with identical genotypes. Most members of these groups were putatively synonymously related and morphologically identical. However, some of them were probably derived from bud sport mutants and had distinct morphologies. SSR marker analysis provided useful insights into the clonal status of the examined Japanese flowering cherry cultivars and proved to be a useful tool for cultivar characterization.

  • 233.
    Kemi, Ulla
    et al.
    Department of Biology, University of Oulu.
    Niittyvuopio, Anne
    Department of Biology, University of Oulu.
    Tiovainen, Tuomas
    Department of Biology, University of Oulu.
    Pasanen, Anu
    Department of Biology, University of Oulu.
    Quilot-Turion, Bénédicte
    Department of Biology, University of Oulu.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Savolainen, Outi
    Department of Biology, University of Oulu.
    Kuittinen, Helmi
    Department of Biology, University of Oulu.
    Role of vernalization and of duplicated Flowering Locus C in the perennial Arabidopsis lyrata2013In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 197, no 1, p. 323-335Article in journal (Refereed)
    Abstract [en]

    FLOWERING LOCUS C (FLC) is one of the main genes influencing the vernalization requirement and natural flowering time variation in the annual Arabidopsis thaliana. Here we studied the effects of vernalization on flowering and its genetic basis in the perennial Arabidopsis lyrata. Two tandemly duplicated FLC genes (FLC1 and FLC2) were compared with respect to expression and DNA sequence. The effect of vernalization on flowering and on the expression of FLC1 was studied in three European populations. The genetic basis of the FLC1 expression difference between two of the populations was further studied by expression quantitative trait locus (eQTL) mapping and sequence analysis. FLC1 was shown to have a likely role in the vernalization requirement for flowering in A. lyrata. Vernalization decreased its expression and the northern study populations showed higher FLC1 expression than the southern one. eQTL mapping between two of the populations revealed one eQTL affecting FLC1 expression in the genomic region containing the FLC genes. Most FLC1 sequence differences between the study populations were found in the promoter region and in the first intron. Variation in the FLC1 sequence may cause differences in FLC1 expression between late- and early-flowering A. lyrata populations.

  • 234. Kitamura, Keiko
    et al.
    Matsui, Tetsuya
    Kobayashi, Makoto
    Saitou, Hitoshi
    Namikawa, Kanji
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Decline in gene diversity and strong genetic drift in the northward-expanding marginal populations of Fagus crenata2015In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 11, no 3, article id 36Article in journal (Refereed)
    Abstract [en]

    The species distribution of Fagus crenata, or Japanese beech, in the Japanese archipelago shifted northward during phytogeographical changes that occurred during the Pleistocene and Holocene epochs. Presently, the continuous natural distribution of beech reaches north to the Kuromatsunai-Depression of Hokkaido Island, Japan. In addition, dozens of marginal patches and isolated individuals north of the continuous distribution have been observed. F. crenata grows remarkably well among these small-scattered northern marginal populations, which must have originated from seeds dispersed beyond the northern limit of the continuous beech forest. It is conceivable that the distribution of F. crenata is still in the process of expanding northward. We investigated the genetic structure of 33 beech populations to evaluate the population gene diversity at the leading northern edge of the range expansion. We analyzed 12 nuclear microsatellite loci in each of the 1,693 individuals. Genetic diversity parameters such as expected heterozygosity and allelic richness were clearly lower in the northernmost populations. We found genetic differentiation in the northernmost distribution range (F-ST=0.045, G(ST)'=0.242). STRU CTURE analysis revealed that the southwestern continuous populations consisted of homogeneous ancestral clusters. However, northeastern marginal populations consisted of mixtures of highly differentiated clusters with higher levels of genetic drift than found in the continuous populations.

  • 235.
    Kivela, Sami M.
    et al.
    Stockholm Univ, Dept Zool, Svante Arrhenius Vag 18b, SE-10691 Stockholm, Sweden.;Univ Tartu, Inst Ecol & Earth Sci, Dept Zool, Vanemuise 46, EE-51014 Tartu, Estonia..
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wiklund, Christer
    Stockholm Univ, Dept Zool, Svante Arrhenius Vag 18b, SE-10691 Stockholm, Sweden..
    Gotthard, Karl
    Stockholm Univ, Dept Zool, Svante Arrhenius Vag 18b, SE-10691 Stockholm, Sweden..
    Adaptive developmental plasticity in a butterfly: mechanisms for size and time at pupation differ between diapause and direct development2017In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 122, no 1, p. 46-57Article in journal (Refereed)
    Abstract [en]

    Diapause (overwintering) and direct development are alternative developmental pathways in temperate insects. Diapause necessitates physiological preparations for dormancy, while direct development is associated with strong time constraints, resulting in selection for fast development under the direct development pathway. Physiological and behavioural preparations for pupation contribute to development time, so divergent selection in them is expected between the alternative developmental pathways. Critical mass for pupation induction is a central physiological parameter for the pupation process. Here, we compare the critical masses and the characteristics of the wandering stage - wandering taking place after the cessation of growth and before pupation - between diapausing and directly developing larvae in the butterfly Pieris napi. Critical mass estimation succeeded only for diapausing individuals, among which it was lower in females than in males, indicating an inter-pathway difference in the physiology of critical mass. Directly developing individuals wandered for a shorter time and distance and lost less mass before pupation than diapausing individuals. These physiological and behavioural differences represent adaptive phenotypic plasticity and contribute to fast development under direct development. Thus, the observed developmental plasticity in physiology offers a mechanistic explanation for adaptive life-history variation between alternative developmental pathways and sexual dimorphism.

  • 236.
    Kivela, Sami M.
    et al.
    Stockholm Univ, Dept Zool, SE-10691 Stockholm, Sweden..
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wiklund, Christer
    Stockholm Univ, Dept Zool, SE-10691 Stockholm, Sweden..
    Leimar, Olof
    Stockholm Univ, Dept Zool, SE-10691 Stockholm, Sweden..
    Gotthard, Karl
    Stockholm Univ, Dept Zool, SE-10691 Stockholm, Sweden..
    Towards a mechanistic understanding of insect life history evolution: oxygen-dependent induction of moulting explains moulting sizes2016In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 117, no 3, p. 586-600Article in journal (Refereed)
    Abstract [en]

    Moults characterise insect growth trajectories, typically following a consistent pattern known as Dyar's rule; proportional size increments remain constant across inter-instar moults. Empirical work suggests that oxygen limitation triggers moulting. The insect respiratory system, and its oxygen supply capacity, grows primarily at moults. It is hypothesized that the oxygen demand increases with increasing body mass, eventually meeting the oxygen supply capacity at an instar-specific critical mass where moulting is triggered. Deriving from this hypothesis, we develop a novel mathematical model for moulting and growth in insect larvae. Our mechanistic model has great success in predicting moulting sizes in four butterfly species, indirectly supporting a size-dependent mechanism underlying moulting. The results demonstrate that an oxygen-dependent induction of moulting mechanism would be sufficient to explain moulting sizes in the study species. Model predictions deviated slightly from Dyar's rule, the deviations being typically negligible within the present data range. The developmental decisions (e.g. moulting) made by growing larvae significantly affect age and size at maturity, which has important life history implications. The successful modelling of moulting presented here provides a novel framework for the development of realistic insect growth models, which are required for a better understanding of life history evolution.

  • 237.
    Klimkowska, Agata
    et al.
    Univ Warsaw, Inst Bot, Biol & Chem Res Ctr, Dept Plant Ecol & Environm Conservat, Warsaw, Poland;Ecorecover Ecosyst Restorat Advice, Dieren, Netherlands.
    Goldstein, Klara
    Univ Warsaw, Inst Bot, Biol & Chem Res Ctr, Dept Plant Ecol & Environm Conservat, Warsaw, Poland.
    Wyszomirski, Tomasz
    Univ Warsaw, Inst Bot, Biol & Chem Res Ctr, Dept Plant Ecol & Environm Conservat, Warsaw, Poland.
    Kozub, Lukasz
    Univ Warsaw, Inst Bot, Biol & Chem Res Ctr, Dept Plant Ecol & Environm Conservat, Warsaw, Poland.
    Wilk, Mateusz
    Univ Warsaw, Inst Bot, Biol & Chem Res Ctr, Dept Plant Ecol & Environm Conservat, Warsaw, Poland.
    Aggenbach, Camiel
    Univ Antwerp, Dept Biol, Ecosyst Management Res Grp, Antwerp, Belgium.
    Bakker, Jan P.
    Univ Groningen, Community & Conservat Ecol Grp, Groningen, Netherlands.
    Belting, Heinrich
    Niedersachs Landesbetrieb Wasserwirtschaft Kusten, Staatl Vogelschutzwarte Naturschutzstn Dummer, Ochsenmoor, Germany.
    Beltman, Boudewijn
    Univ Utrecht, Environm Biol, Utrecht, Netherlands.
    Blüml, Volker
    BMS Umweltplanung, Osnabruck, Germany;Univ Bremen, Bremen, Germany.
    De Vries, Yzaak
    Univ Groningen, Community & Conservat Ecol Grp, Groningen, Netherlands.
    Geiger-Udod, Beate
    Regierung von Oberbayern, Nat 2000 Team, Munich, Germany.
    Grootjans, Ab P.
    Univ Groningen, Community & Conservat Ecol Grp, Groningen, Netherlands;Univ Groningen, Ctr Energy & Environm Sci, Groningen, Netherlands.
    Hedberg, Petter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Hedberg Ekologkonsult AB, Lidingo, Sweden.
    Jager, Henk J.
    It Fryske Gea Frysian Landscape, Olterterp, Netherlands.
    Kerkhof, Dick
    Zuid Hollands Landschap, Delft, Netherlands.
    Kollmann, Johannes
    Tech Univ Munich, Dept Ecol & Ecosyst Management, Freising Weihenstephan, Germany.
    Pawlikowski, Pawel
    Univ Warsaw, Inst Bot, Biol & Chem Res Ctr, Dept Plant Ecol & Environm Conservat, Warsaw, Poland.
    Pleyl, Elisabeth
    Zentrum Umwelt & Kultur Benediktbeuern ZUK, Benediktbeuern, Germany.
    Reinink, Warner
    Zuid Hollands Landschap, Delft, Netherlands.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Schrautzer, Joachim
    Univ Kiel, Inst Ecosyst Res, Kiel, Germany.
    Sliva, Jan
    Tech Univ Munich, Dept Ecol & Ecosyst Management, Freising Weihenstephan, Germany.
    Stanko, Robert
    Klub Przyrodnikow, Swiebodzin, Poland.
    Sundberg, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Timmermann, Tiemo
    Ernst Moritz Arndt Univ Greifswald, Inst Bot & Landscape Ecol, Landscape Ecol & Ecosyst Dynam, Greifswald, Germany.
    Wolejko, Leslaw
    West Pomeranian Univ Technol, Inst Bot & Nat Conservat, Dept Bot, Szczecin, Poland.
    van der Burg, Rob F.
    KNNV, Heeze & Florist Werkgrp, Cooperatie Bosgrp Zuid Nederland, Eindhoven, Netherlands.
    van der Hoek, Dick
    Wageningen Univ, Nat Conservat & Plant Ecol Grp, Wageningen, Netherlands.
    van Diggelen, Jose M. H.
    B WARE BV Res Ctr, Nijmegen, Netherlands.
    van Heerden, Adrie
    Prov Zuid Holland, The Hague, Netherlands.
    van Tweel, Loekie
    Landschap Overijssel, Dalfsen, Netherlands.
    Vegelin, Kees
    BNL Vegelin, Murchin, Germany.
    Kotowski, Wiktor
    Univ Warsaw, Inst Bot, Biol & Chem Res Ctr, Dept Plant Ecol & Environm Conservat, Warsaw, Poland.
    Are we restoring functional fens?: The outcomes of restoration projects in fens re-analysed with plant functional traits2019In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 14, no 4, article id e0215645Article in journal (Refereed)
    Abstract [en]

    In peatland restoration we often lack an information whether re-established ecosystems are functionally similar to non-degraded ones. We re-analysed the long-term outcomes of restoration on vegetation and plant functional traits in 38 European fens restored by rewetting (18 sites) and topsoil removal (20 sites). We used traits related to nutrient acquisition strategies, competitiveness, seed traits, and used single- and multi-trait metrics. A separate set of vegetation records from near-natural fens with diverse plant communities was used to generate reference values to aid the comparisons. We found that both restoration methods enhanced the similarity of species composition to non-degraded systems but trait analysis revealed differences between the two approaches. Traits linked to nutrient acquisition strategies indicated that topsoil removal was more effective than rewetting. After topsoil removal competitive species in plant communities had decreased, while stress-tolerant species had increased. A substantial reduction in nutrient availability ruled out the effect of initial disturbance. An ability to survive and grow in anoxic conditions was enhanced after restoration, but the reference values were not achieved. Rewetting was more effective than topsoil removal in restricting variation in traits values permitted in re-developing vegetation. We found no indication of a shift towards reference in seed traits, which suggested that dispersal constraint and colonization deficit can be a widespread phenomena. Two functional diversity indices: functional richness and functional dispersion showed response to restoration and shifted values towards reference mires and away from the degraded systems. We concluded that targeting only one type of environmental stressor does not lead to a recovery of fens, as it provides insufficient level of stress to restore a functional ecosystem. In general, restoration efforts do not ensure the re-establishment and long-term persistence of fens. Restoration efforts result in recovery of fen ecosystems, confirmed with our functional trait analysis, although more rigid actions are needed for restoring fully functional mires, by achieving high and constant levels of anoxia and nutrient stresses.

  • 238.
    Kokko, Hanna
    et al.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, CH-8057 Zurich, Switzerland..
    Chaturvedi, Anurag
    Univ Leuven, Lab Aquat Ecol Evolut & Conservat, B-3000 Leuven, Belgium..
    Croll, Daniel
    Swiss Fed Inst Technol, Inst Integrat Biol, Plant Pathol, CH-8092 Zurich, Switzerland..
    Fischer, Martin C.
    Swiss Fed Inst Technol, Inst Integrat Biol, Plant Ecol Genet, CH-8092 Zurich, Switzerland..
    Guillaume, Frederic
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, CH-8057 Zurich, Switzerland..
    Karrenberg, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kerr, Ben
    Univ Washington, Dept Biol, Seattle, WA 98195 USA..
    Rolshausen, Gregor
    Senckenberg Biodivers & Climate Res Ctr BIK F, D-60325 Frankfurt, Germany..
    Stapley, Jessica
    Swiss Fed Inst Technol, Ctr Adaptat Changing Environm, CH-8095 Zurich, Switzerland..
    Can Evolution Supply What Ecology Demands?2017In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 32, no 3, p. 187-197Article, review/survey (Refereed)
    Abstract [en]

    A simplistic view of the adaptive process pictures a hillside along which a population can climb: when ecological 'demands' change, evolution 'supplies' the variation needed for the population to climb to a new peak. Evolutionary ecologists point out that this simplistic view can be incomplete because the fitness landscape changes dynamically as the population evolves. Geneticists meanwhile have identified complexities relating to the nature of genetic varia-tion and its architecture, and the importance of epigenetic variation is under debate. In this review, we highlight how complexity in both ecological 'demands' and the evolutionary 'supply' influences organisms' ability to climb fitness landscapes that themselves change dynamically as evolution proceeds, and encourage new synthetic effort across research disciplines towards eco-logically realistic studies of adaptation.

  • 239.
    Kolseth, Anna-Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Evolutionary Processes and Spatial Genetic Variation in Euphrasia stricta on the Baltic Island of Gotland2008Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The identification of processes governing genetic structure at different spatial scales remains a major challenge in evolutionary biology and is of considerable applied interest in conservation biology. In Euphrasia stricta five varieties have been identified (brevipila, gotlandica, stricta, suecica and tenuis) based on differences in habitat, phenology and morphology. In this thesis, I examined genetic variation at AFLP and microsatellite marker loci in relation to variation in habitat and morphology within and among varieties of E. stricta on the island Gotland in the Baltic Sea. The results are discussed in relation to evolutionary processes acting within this species complex.

    In a study conducted at the regional scale, the two early-flowering varieties suecica and tenuis each formed a genetically distinct group, while the three late-flowering varieties brevipila, gotlandica and stricta formed a third group. The results suggest that suecica and tenuis have ancient origins since they are genetically different both from the brevipila/gotlandica/stricta group and from each other despite their similar habitat preferences. This pattern was obtained using both marker systems. Discrepancies between AFLP and microsatellites were found in patterns of isolation by distance and in estimates of expected heterozygosity, He.

    Focusing on the mixed genetic group brevipila/gotlandica/stricta and the causes behind their clustering together despite differences in morphology and habitat preferences, I performed a study at a smaller geographic scale. Studying a population of E. stricta I found that, although gene flow within the population was strong, it had not prevented the formation of genetic groups associated with micro-habitat properties.

    An important result for conservation of the rare variety suecica is its distinct genetic separation from variety tenuis. If the aim of conservation is to preserve the uniqueness of suecica, the two varieties should be treated as separated entities.

    List of papers
    1. Genetic structure in Euphrasia stricta on the Baltic Ilsand of Gotland, Sweden
    Open this publication in new window or tab >>Genetic structure in Euphrasia stricta on the Baltic Ilsand of Gotland, Sweden
    2005 In: Ecography, ISSN 0906-7590, Vol. 28, p. 443-452Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-96854 (URN)
    Available from: 2008-03-14 Created: 2008-03-14Bibliographically approved
    2. Regional Genetic Structure in the Tetraploid Hemiparasite Euphrasia stricta Inferred from Microsatellites
    Open this publication in new window or tab >>Regional Genetic Structure in the Tetraploid Hemiparasite Euphrasia stricta Inferred from Microsatellites
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-96855 (URN)
    Available from: 2008-03-14 Created: 2008-03-14 Last updated: 2010-01-13Bibliographically approved
    3. Habitat Associations of Fine-scale Genetic Structure in an Euphrasia stricta Population
    Open this publication in new window or tab >>Habitat Associations of Fine-scale Genetic Structure in an Euphrasia stricta Population
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-96856 (URN)
    Available from: 2008-03-14 Created: 2008-03-14 Last updated: 2010-01-13Bibliographically approved
    4. Genetic Structure in two Meadow Varieties of Euphrasia stricta on the Baltic Island of Gotland (Sweden) and Implications for Conservation
    Open this publication in new window or tab >>Genetic Structure in two Meadow Varieties of Euphrasia stricta on the Baltic Island of Gotland (Sweden) and Implications for Conservation
    2005 In: Folia Geobotanica, ISSN 1211-9520, Vol. 40, p. 163-176Article in journal (Refereed) Published
    Identifiers
    urn:nbn:se:uu:diva-96857 (URN)
    Available from: 2008-03-14 Created: 2008-03-14Bibliographically approved
  • 240.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Cornille, Amandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Montpellier, CNRS IRD EPHE, ISEM UMR 5554, Inst Sci Evolut, Pl Eugene Bataillon, F-34075 Montpellier, France..
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolut, 25 Willcocks St, Toronto, ON M5S 3B2, Canada..
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 5, p. 1106-1121Article in journal (Refereed)
    Abstract [en]

    Population structure is a potential problem when testing for adaptive phenotypic differences among populations. The observed phenotypic differences among populations can simply be due to genetic drift, and if the genetic distance between them is not considered, the differentiation may be falsely interpreted as adaptive. Conversely, adaptive and demographic processes might have been tightly associated and correcting for the population structure may lead to false negatives. Here, we evaluated this problem in the cosmopolitan weed Capsella bursa-pastoris. We used RNA-Seq to analyse gene expression differences among 24 accessions, which belonged to a much larger group that had been previously characterized for flowering time and circadian rhythm and were genotyped using genotyping-by-sequencing (GBS) technique. We found that clustering of accessions for gene expression retrieved the same three clusters that were obtained with GBS data previously, namely Europe, the Middle East and Asia. Moreover, the three groups were also differentiated for both flowering time and circadian rhythm variation. Correction for population genetic structure when analysing differential gene expression analysis removed all differences among the three groups. This may suggest that most differences are neutral and simply reflect population history. However, geographical variation in flowering time and circadian rhythm indicated that the distribution of adaptive traits might be confounded by population structure. To bypass this confounding effect, we compared gene expression differentiation between flowering ecotypes within the genetic groups. Among the differentially expressed genes, FLOWERING LOCUS C was the strongest candidate for local adaptation in regulation of flowering time.

  • 241.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Duan, Tianlin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Orsucci, Marion
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON, Canada.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Rennes, CNRS, ECOBIO Ecosyst Biodivers Evolut UMR 6553, Rennes, France.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)2019In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 5, article id e1008131Article in journal (Refereed)
    Abstract [en]

    Allopolyploidy has played a major role in plant evolution but its impact on genome diversity and expression patterns remains to be understood. Some studies found important genomic and transcriptomic changes in allopolyploids, whereas others detected a strong parental legacy and more subtle changes. The allotetraploid C. bursa-pastoris originated around 100,000 years ago and one could expect the genetic polymorphism of the two subgenomes to follow similar trajectories and their transcriptomes to start functioning together. To test this hypothesis, we sequenced the genomes and the transcriptomes (three tissues) of allotetraploid C. bursa-pastoris and its parental species, the outcrossing C. grandiflora and the self-fertilizing C. orientalis. Comparison of the divergence in expression between subgenomes, on the one hand, and divergence in expression between the parental species, on the other hand, indicated a strong parental legacy with a majority of genes exhibiting a conserved pattern and cis-regulation. However, a large proportion of the genes that were differentially expressed between the two subgenomes, were also under trans-regulation reflecting the establishment of a new regulatory pattern. Parental dominance varied among tissues: expression in flowers was closer to that of C. orientalis and expression in root and leaf to that of C. grandiflora. Since deleterious mutations accumulated preferentially on the C. orientalis subgenome, the bias in expression towards C. orientalis observed in flowers indicates that expression changes could be adaptive and related to the selfing syndrome, while biases in the roots and leaves towards the C. grandiflora subgenome may be reflective of the differential genetic load.

  • 242.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Salcedo, Adriana
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Eriksson, Mimmi C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Duan, Tianlin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tawari, Nilesh
    ASTAR, Genome Inst Singapore, Computat & Syst Biol Grp, Singapore, Singapore.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Guerrina, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kreiner, Julia M.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Kent, Tyler V.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Stinchcombe, John R.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Rennes 1, CNRS, UMR 6553, ECOBIO,Ecosyst,Biodivers,Evolut, F-35000 Rennes, France.
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)2019In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 2, article id e1007949Article in journal (Refereed)
    Abstract [en]

    Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species nor how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe, and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cbp(Cg)) and the other one from the selfing and genetically depauperate Capsella orientalis (Cbp(Co)). For each subgenome, we assessed its relationship with the diploid relatives, temporal changes of effective population size (N-e), signatures of positive and negative selection, and gene expression patterns. In all three regions, N-e of the two subgenomes decreased gradually over time and the Cbp(Co) subgenome accumulated more deleterious changes than Cbp(Cg). There were signs of widespread admixture between C. bursa-pastoris and its diploid relatives. The two subgenomes were impacted differentially depending on geographic region suggesting either strong interploidy gene flow or multiple origins of C. bursa-pastoris. Selective sweeps were more common on the Cbp(Cg) subgenome in Europe and the Middle East, and on the Cbp(Co) subgenome in Asia. In contrast, differences in expression were limited with the Cbp(Cg) subgenome slightly more expressed than Cbp(Co) in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy but their evolutionary trajectory strongly varied across geographic regions. Author summary Allopolyploid species have two or more sets of chromosomes that originate from hybridization of different species. It remains largely unknown how the two genomes evolve in the same organism and how strongly their evolutionary trajectory depends on the initial differences between the two parental species and the specific demographic history of the newly formed allopolyploid species. To address these questions, we analyzed the genomic and gene expression variation of the shepherd's purse, a recent allopolyploid species, in three regions of its natural range. After approximate to 100,000 generations of co-existence within the same species, the two subgenomes had still retained part of the initial difference between the two parental species in the number of deleterious mutations reflecting a history of mating system differences. This difference, as well as differences in patterns of positive selection and levels of gene expression, also strongly depended on the specific histories of the three regions considered. Most strikingly, and unexpectedly, the allopolyploid species showed signs of hybridization with different diploid relatives or multiple origins in different parts of its range. Regardless if it was hybridization or multiple origins, this profoundly altered the relationship between the two subgenomes in different regions. Hence, our study illustrates how both the genomic structure and ecological arena interact to determine the evolutionary trajectories of allopolyploid species.

  • 243.
    Källman, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species2013In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 162, no 2, p. 741-754Article in journal (Refereed)
    Abstract [en]

    Small RNAs (sRNAs), including microRNA (miRNA) and short-interfering RNA (siRNA), are important in the regulation of diverse biological processes. Comparative studies of sRNAs from plants have mainly focused on miRNA, even though they constitute a mere fraction of the total sRNA diversity. In this study, we report results from an in-depth analysis of the sRNA population from the conifer spruce (Picea abies) and compared the results with those of a range of plant species. The vast majority of sRNA sequences in spruce can be assigned to 21-nucleotide-long siRNA sequences, of which a large fraction originate from the degradation of transcribed sequences related to nucleotide-binding site-leucine-rich repeat-type resistance genes. Over 90% of all genes predicted to contain either a Toll/interleukin-1 receptor or nucleotide-binding site domain showed evidence of siRNA degradation. The data further suggest that this phased degradation of resistance-related genes is initiated from miRNA-guided cleavage, often by an abundant 22-nucleotide miRNA. Comparative analysis over a range of plant species revealed a huge variation in the abundance of this phenomenon. The process seemed to be virtually absent in several species, including Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), and nonvascular plants, while particularly high frequencies were observed in spruce, grape (Vitis vinifera), and poplar (Populus trichocarpa). This divergent pattern might reflect a mechanism to limit runaway transcription of these genes in species with rapidly expanding nucleotide-binding site-leucine-rich repeat gene families. Alternatively, it might reflect variation in a counter-counter defense mechanism between plant species.

  • 244.
    Källman, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Department of Plant Biology and Forest Genetics, Swedish University of Agriculture Science.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Major difference in short RNA populations among plants - the results of interaction with pathogen?Manuscript (preprint) (Other academic)
    Abstract [en]

    Small RNA (sRNA) including miRNA and siRNA are important in the regulation of diverse biological processes. Comparative studies of sRNA from plants have mainly focused on miRNA even though this group in most cases is just a mere fraction of the total sRNA diversity. In the present study we report results from an in-depth analysis of the sRNA population from the conifer Picea abies and compared the results to those of a range of species from the plant kingdom. The vast majority of sRNA in P. abies was 21 nucleotides long siRNA, of which a large fraction originate from degradation of transcribed sequences related to TIR-NBS-LRR (Toll/Interleukin-1-Nucleotide Binding Site-Leucine Rich Repeats) type resistance genes. Over 90% of all genes predicted to contain either a TIR or an NBS domain showed evidence of siRNA degradation. Data further suggests that those phased siRNA are initiated from miRNA guided cleavage, often by an abundant 22 nt miRNA. Comparative analysis over a range of divergent plant species revealed a large variation between species in the abundance of this phenomenon. The process seemed to be virtually absent in several species, including Arabidopsis thaliana, Oryza sativa and non-vascular plants, while particularly high frequencies were observed in Vitis vinifera and Populus thrichocarpa. This divergent pattern between species might reflect a mechanism to limit runaway transcription of these genes in species with rapidly expanding NBS-LRR gene families. Alternatively it might reflect variation in a counter-counter defence mechanism partly affected by differences in life history traits, e.g. perennial versus annual life cycles. A major difference between annuals and perennials, affecting the evolution of resistance, is that perennials will with almost certainty encounter many different pathogens before reproduction, and that the long generation times confers problems in matching the evolutionary rates of the pathogens.

  • 245.
    Källman, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    De Mita, Stéphane
    INRA Nancy, 54280 Champenoux, France.
    Larsson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Dept. of Plant Biology and Forest Genetics, Swedish Agricultural University, Uppsala, Sweden.
    Heuertz, Myriam
    Forest Research Centre INIA-CIFOR, 28040, Madrid, Spain.
    Parducci, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Suyama, Yoshihisa
    Graduate School of Agricultural Science, Tohoku University, Japan.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Patterns of nucleotide diversity at photoperiod related genes in the conifer Norway spruce [Picea abies (L.) (Karst)]2014In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 5, p. e95306-Article in journal (Refereed)
    Abstract [en]

    The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce

  • 246.
    Laenen, Benjamin
    et al.
    Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    Tedder, Andrew
    Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    Nowak, Michael D.
    Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    Toräng, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wunder, Jörg
    Max Planck Inst Plant Breeding Res, D-50829 Cologne, Germany..
    Wötzel, Stefan
    Max Planck Inst Plant Breeding Res, D-50829 Cologne, Germany..
    Steige, Kim A.
    Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden.;Univ Cologne, Inst Bot, Biozentrum, D-50674 Cologne, Germany..
    Kourmpetis, Yiannis
    Wageningen Univ & Res Ctr, Biometris, NL-6700 AC Wageningen, Netherlands.;Nestle Inst Hlth Sci, CH-1015 Lausanne, Switzerland..
    Odong, Thomas
    Wageningen Univ & Res Ctr, Biometris, NL-6700 AC Wageningen, Netherlands..
    Drouzas, Andreas D.
    Aristotle Univ Thessaloniki, Sch Biol, Thessaloniki 54124, Greece..
    Bink, Marco C. A. M.
    Wageningen Univ & Res Ctr, Biometris, NL-6700 AC Wageningen, Netherlands.;Hendrix Genet Res Technol & Serv, NL-5830 AC Boxmeer, Netherlands..
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Coupland, George
    Max Planck Inst Plant Breeding Res, D-50829 Cologne, Germany..
    Slotte, Tanja
    Stockholm Univ, Sci Life Lab, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina2018In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 115, no 4, p. 816-821Article in journal (Refereed)
    Abstract [en]

    Plant mating systems have profound effects on levels and structuring of genetic variation and can affect the impact of natural selection. Although theory predicts that intermediate outcrossing rates may allow plants to prevent accumulation of deleterious alleles, few studies have empirically tested this prediction using genomic data. Here, we study the effect of mating system on purifying selection by conducting population-genomic analyses on whole-genome resequencing data from 38 European individuals of the arctic-alpine crucifer Arabis alpina. We find that outcrossing and mixed-mating populations maintain genetic diversity at similar levels, whereas highly self-fertilizing Scandinavian A. alpina show a strong reduction in genetic diversity, most likely as a result of a postglacial colonization bottleneck. We further find evidence for accumulation of genetic load in highly self-fertilizing populations, whereas the genome-wide impact of purifying selection does not differ greatly between mixed-mating and outcrossing populations. Our results demonstrate that intermediate levels of outcrossing may allow efficient selection against harmful alleles, whereas demographic effects can be important for relaxed purifying selection in highly selfing populations. Thus, mating system and demography shape the impact of purifying selection on genomic variation in A. alpina. These results are important for an improved understanding of the evolutionary consequences of mating system variation and the maintenance of mixed-mating strategies.

  • 247.
    Lafon-Placette, Clement
    et al.
    Swedish Univ Agr Sci, Dept Plant Biol, Uppsala, Sweden;Linnean Ctr Plant Biol, Uppsala, Sweden;Charles Univ Prague, Dept Bot, Prague, Czech Republic.
    Hatorangan, Marcelinus R.
    Swedish Univ Agr Sci, Dept Plant Biol, Uppsala, Sweden;Linnean Ctr Plant Biol, Uppsala, Sweden.
    Steige, Kim A.
    Stockholm Univ, Dept Ecol Environm & Plant Sci, Sci Life Lab, Stockholm, Sweden;Univ Cologne, Inst Bot, Bioctr, Cologne, Germany.
    Cornille, Amandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Slotte, Tanja
    Stockholm Univ, Dept Ecol Environm & Plant Sci, Sci Life Lab, Stockholm, Sweden.
    Kohler, Claudia
    Swedish Univ Agr Sci, Dept Plant Biol, Uppsala, Sweden;Linnean Ctr Plant Biol, Uppsala, Sweden.
    Paternally expressed imprinted genes associate with hybridization barriers in Capsella2018In: NATURE PLANTS, ISSN 2055-026X, Vol. 4, no 6, p. 352-357Article in journal (Refereed)
    Abstract [en]

    Hybrid seed lethality is a widespread type of reproductive barrier among angiosperm taxa(1,2) that contributes to species divergence by preventing gene flow between natural populations(3,4). Besides its ecological importance, it is an important obstacle to plant breeding strategies(5). Hybrid seed lethality is mostly due to a failure of the nourishing endosperm tissue, resulting in embryo arrest(3,6,7). The cause of this failure is a parental dosage imbalance in the endosperm that can be a consequence of either differences in parental ploidy levels or differences in the 'effective ploidy', also known as the endosperm balance number (EBN)(8,9). Hybrid seed defects exhibit a parent-of-origin pattern(3,6,7), suggesting that differences in number or expression strength of parent-of-origin-specific imprinted genes underpin, as the primary or the secondary cause, the molecular basis of the EBN7,10. Here, we have tested this concept in the genus Capsella and show that the effective ploidy of three Capsella species correlates with the number and expression level of paternally expressed genes (PEGs). Importantly, the number of PEGs and the effective ploidy decrease with the selfing history of a species: the obligate outbreeder Capsella grandiflora had the highest effective ploidy, followed by the recent selfer Capsella rubella and the ancient selfer Capsella orientalis. PEGs were associated with the presence of transposable elements and their silencing mark, DNA methylation in CHH context (where H denotes any base except C). This suggests that transposable elements have driven the imprintome divergence between Capsella species. Together, we propose that variation in transposable element insertions, the resulting differences in PEG number and divergence in their expression level form one component of the effective ploidy variation between species of different breeding system histories, and, as a consequence, allow the establishment of endosperm-based hybridization barriers.

  • 248. Laing, C. G.
    et al.
    Granath, G.
    Belyea, L. R.
    Allton, K. E.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tradeoffs and scaling of functional traits in Sphagnum as drivers of carbon cycling in peatlands2014In: Oikos, ISSN 0030-1299, E-ISSN 1600-0706, Vol. 123, no 7, p. 817-828Article in journal (Refereed)
    Abstract [en]

    Growth and decomposition of Sphagnum controls turnover of a large global store of soil organic carbon. We investigated variation in morphological and physiological traits of Sphagnum shoots, and related this variation to canopy variables relevant to peatland carbon cycling. We sampled Sphagnum along a bog plateau-swamp forest gradient and measured a suite of shoot traits and canopy variables. Major axes of variation were identified using principal component analysis and correlated with canopy variables such as growth, biomass and decomposition. We also examined scaling of shoot traits with one another and with canopy variables. Two distinct tradeoffs in shoot traits emerged. From dry to wet habitats, individual metabolic rates and capitulum size increased while numerical density decreased, leading to faster growth and elongation on an individual basis. From treed to open habitats, photosynthetic efficiency decreased and photosynthetic biomass increased, driving faster growth on an area basis and slower litter mass loss. The tradeoffs identified have important implications for peatlands undergoing climate-related changes in water and light availability. Sphagnum trait comparisons, combined with scaling analyses, offer a promising approach to understanding and predicting the effects of environmental change on peatland carbon cycling.

  • 249.
    Laing, Chris
    et al.
    School of Geography, Queen Mary University of London .
    Granath, Gustaf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Allton, Kathryn E
    School of Geography, Queen Mary University of London.
    Belyea, Lisa
    School of Geography, Queen Mary University of London.
    Functional traits in Sphagnum, allometry, and their impacts on carbon cycling in peatlandsManuscript (preprint) (Other academic)
  • 250.
    Larsson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Population Genetics and Genome Organization of Norway Spruce2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Understanding the underlying genetic causes of adaptation to local conditions is one of the main goals of population genetics. A strong latitudinal cline in the phenotypic trait of bud set is observed in present day populations of Norway spruce (Picea abies (L.) Karst). The first step towards determining how this strong selection on adaptive traits translates at the loci underlying the trait was to use multilocus sequence data to gain information on the fundamental population genetic properties of Norway spruce. We determined that the level of LD was low and genetic diversity was in the low range. Coalescent simulations revealed a demographic scenario of a fairly old and severe bottleneck as consistent with the observed data. To examine the role of selection at genes putatively involved in the control of bud set we, again, used a multilocus data set to test for deviations from neutrality and demographic scenarios inferred from background loci. Different candidate genes were identified by using different approaches, highlighting the difficulty in predicting how local adaptation will manifest itself on different time scales and in rangewide samples. When examining properties important in the design of association studies, the inevitable next step in identifying genes involved in local adaptation, we found that previous estimates of a low level of LD were highly influenced by the joint analysis of several loci over a large distribution range and that estimates of LD was in fact heterogeneous across loci and increased within populations. In addition, we found that within species tests for deviations from neutral expectations were highly sensitive to sample size. Additional genomic sequence characterization in Norway spruce is necessary to provide more comprehensive sets of markers for association studies, also including gene promoters and non-genic regions of the genome. In the final paper we show that the HMPR method is effective in constructing libraries enriched for the single copy fraction of the genome when applied to the large and dominantly repetitive genome of Norway spruce.

    In summary, the studies presented in this thesis together constitute a foundation for future studies on adaptive evolution in Norway spruce.

    List of papers
    1. Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]
    Open this publication in new window or tab >>Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce [Picea abies (L.) Karst]
    Show others...
    2006 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 174, no 4, p. 2095-2105Article in journal (Refereed) Published
    Abstract [en]

    DNA polymorphism at 22 loci was studied in an average of 47 Norway spruce [Picea abies (L.) Karst.] haplotypes sampled in seven populations representative of the natural range. The overall nucleotide variation was limited, being lower than that observed in most plant species so far studied. Linkage disequilibrium was also restricted and did not extend beyond a few hundred base pairs. All populations, with the exception of the Romanian population, could be divided into two main domains, a Baltico-Nordic and an Alpine one. Mean Tajima's D and Fay and Wu's H across loci were both negative, indicating the presence of an excess of both rare and high-frequency-derived variants compared to the expected frequency spectrum in a standard neutral model. Multilocus neutrality tests based on D and H led to the rejection of the standard neutral model and exponential growth in the whole population as well as in the two main domains. On the other hand, in all three cases the data are compatible with a severe bottleneck occurring some hundreds of thousands of years ago. Hence, demographic departures from equilibrium expectations and population structure will have to be accounted for when detecting selection at candidate genes and in association mapping studies, respectively.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-24392 (URN)10.1534/genetics.106.065102 (DOI)000243284500033 ()17057229 (PubMedID)
    Available from: 2007-02-12 Created: 2007-02-12 Last updated: 2017-12-07Bibliographically approved
    2. Patterns of nucleotide diversity at photoperiod related genes in the conifer Norway spruce [Picea abies (L.) (Karst)]
    Open this publication in new window or tab >>Patterns of nucleotide diversity at photoperiod related genes in the conifer Norway spruce [Picea abies (L.) (Karst)]
    Show others...
    2014 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 9, no 5, p. e95306-Article in journal (Refereed) Published
    Abstract [en]

    The ability of plants to track seasonal changes is largely dependent on genes assigned to the photoperiod pathway, and variation in those genes is thereby important for adaptation to local day length conditions. Extensive physiological data in several temperate conifer species suggest that populations are adapted to local light conditions, but data on the genes underlying this adaptation are more limited. Here we present nucleotide diversity data from 19 genes putatively involved in photoperiodic response in Norway spruce (Picea abies). Based on similarity to model plants the genes were grouped into three categories according to their presumed position in the photoperiod pathway: photoreceptors, circadian clock genes, and downstream targets. An HKA (Hudson, Kreitman and Aquade) test showed a significant excess of diversity at photoreceptor genes, but no departure from neutrality at circadian genes and downstream targets. Departures from neutrality were also tested with Tajima's D and Fay and Wu's H statistics under three demographic scenarios: the standard neutral model, a population expansion model, and a more complex population split model. Only one gene, the circadian clock gene PaPRR3 with a highly positive Tajima's D value, deviates significantly from all tested demographic scenarios. As the PaPRR3 gene harbours multiple non-synonymous variants it appears as an excellent candidate gene for control of photoperiod response in Norway spruce

    National Category
    Natural Sciences Genetics Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-180367 (URN)10.1371/journal.pone.0095306 (DOI)000338213300010 ()
    Available from: 2012-09-05 Created: 2012-09-05 Last updated: 2017-12-07Bibliographically approved
    3. Distribution of long-range Linkage Disequilibrium and Tajima's D in Scandinavian populations of Norway spruce (Picea abies)
    Open this publication in new window or tab >>Distribution of long-range Linkage Disequilibrium and Tajima's D in Scandinavian populations of Norway spruce (Picea abies)
    (English)Manuscript (preprint) (Other academic)
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-180369 (URN)
    Available from: 2012-09-05 Created: 2012-09-05 Last updated: 2013-01-23
    4. The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)
    Open this publication in new window or tab >>The HypoMethylated Partial Restriction (HMPR) method reduces the repetitive content of genomic libraries in Norway spruce (Picea abies)
    Show others...
    2013 (English)In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 9, no 2, p. 601-612Article in journal (Refereed) Published
    Abstract [en]

    To evaluate the usefulness of Reduced Representation Libraries (RRL) in species with large and highly repetitive genomes such as conifers, we employed Hypomethylated Partial Restriction (HMPR) on the genome of Norway spruce (Picea abies). The HMPR method preferentially removes the commonly hypermethylated, repetitive fraction of the genome. Hence, RRLs should be enriched for the hypomethylated gene space. For comparison, a standard shotgun library was constructed and samples of the respective libraries were obtained through Sanger sequencing. We obtained a 9-fold gene enrichment, a value which is slightly higher than for other plant species. The amount of repetitive DNA was reduced by 45 % in the RRLs, demonstrating the ability to efficiently remove hypermethylated DNA. Annotating sequences in an uncharacterized genome remains challenging and a large number of sequences could not be classified as either repetitive DNA or as belonging to the gene space. Upon further investigation, we found that some of these uncharacterized fragments were expressed, and in most cases the expression was spatially differentiated, indicating that they might have a function. Full-length transcripts of a subset of expressed fragments also revealed that these could be long non-coding RNAs. In conclusion, our study shows that the HMPR method is effective in constructing libraries enriched for the genic fraction of the genome, while simultaneously reducing the repetitive fraction, in P. abies and may prove a valuable tool for the discovery, validation, and assessment of genetic markers in population studies and breeding efforts when combined with next-generation sequencing technology.

    Keywords
    HMPR libraries, Reduced representation, Picea
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-180368 (URN)10.1007/s11295-012-0582-8 (DOI)000316366200023 ()
    Available from: 2012-09-05 Created: 2012-09-05 Last updated: 2017-12-07Bibliographically approved
2345678 201 - 250 of 537
CiteExportLink to result list
Permanent link
Cite
Citation style
  • apa
  • ieee
  • modern-language-association
  • vancouver
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf