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  • 1. Aarrestad, P. A.
    et al.
    Hytteborn, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Masunga, G.
    Skarpe, C.
    Vegetation: Between Soils and Herbivores2014In: Elephants and Savanna Woodland Ecosystems: A Study from Chobe National Park, Botswana / [ed] Christina Skarpe, Johan T. du Toit and Stein R. Moe, Wiley-Blackwell, 2014, 61-88 p.Chapter in book (Refereed)
    Abstract [en]

    The vegetation of the study area in Chobe National Park is influenced by a range of factors, including inundation by the Chobe River, soil moisture and fertility, and the impacts of different-size grazers and browsers. This chapter focuses on how the structure and species composition of the present vegetation in northern Chobe National Park is related to recent herbivory by elephants, as agents shaping the vegetation, and by mesoherbivores acting as controllers or responders, along with abiotic controllers such as soil type and distance to the river. In the study, a two-way indicator species analysis classified the vegetation data into four more or less distinct plant community groups (i) Baikiaea plurijuga-Combretum apiculatum woodland, (ii) Combretum mossambicense-Friesodielsia obovata wooded shrubland, (iii) Capparis tomentosa-Flueggea virosa shrubland and (iv) Cynodon dactylon-Heliotropium ovalifolium floodplain, named after the TWINSPAN indicator or preferential species with high cover, and the relative amount of shrubs and trees.

  • 2. Aarrestad, P. A.
    et al.
    Masunga, G. S.
    Hytteborn, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Pitlagano, M. L.
    Marokane, W.
    Skarpe, C.
    Influence of soil, tree cover and large herbivores on field layer vegetation along a savanna landscape gradient in northern Botswana2011In: Journal of Arid Environments, ISSN 0140-1963, E-ISSN 1095-922X, Vol. 75, no 3, 290-297 p.Article in journal (Refereed)
    Abstract [en]

    The response of the field layer vegetation to co-varying resource availability (soil nutrients, light) and resource loss (herbivory pressure) was investigated along a landscape gradient highly influenced by elephants and smaller ungulates at the Chobe River front in Botswana. TWINSPAN classification was used to identify plant communities. Detrended Correspondence Analysis (DCA) and Canonical Correspondence Analysis (CCA) were used to explore the vegetation-environment relationships. Four plant communities were described: Panicum maximum woodland, Tribulus terrestris woodland/shrubland, Chloris virgata shrubland and Cynodon dactylon floodplain. Plant height, species richness and diversity decreased with increasing resource availability and resource loss. The species composition was mainly explained by differences in soil resources, followed by variables related to light availability (woody cover) and herbivory, and by interactions between these variables. The vegetation structure and species richness, on the other hand, followed the general theories of vegetation responses to herbivory more closely than resource related theories. The results suggest a strong interaction between resource availability and herbivory in their influence on the composition, species richness and structure of the plant communities.

  • 3.
    Akiyama, Reiko
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Life History and Tolerance and Resistance against Herbivores in Natural Populations of Arabidopsis thaliana2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    In this thesis, I combined observational studies with field and greenhouse experiments to examine selection on life history traits and variation in tolerance and resistance against herbivores in natural populations of the annual herb Arabidopsis thaliana in its native range. I investigated (1) phenotypic selection on flowering time and plant size, (2) the effects of timing of germination on plant fitness, (3) the effect of leaf damage on seed production, and (4) correlations between resistance against a specialist and a generalist insect herbivore.

    In all three study populations, flowering time was negatively related to plant fitness, but in only one of the populations, significant selection on flowering time was detected when controlling for size prior to the flowering season. The results show that correlations between flowering time and plant fecundity may be confounded by variation in plant size prior to the reproductive season.

    A field experiment detected conflicting selection on germination time: Early germination was associated with low seedling survival, but also with large leaf rosette before winter and high survival and fecundity among established plants. The results suggest that low survival among early germinating seeds is the main force opposing the evolution of earlier germination, and that the optimal timing of germination should vary in space and time as a function of the relative strength of selection acting during different life-history stages.

    Experimental leaf damage demonstrated that tolerance to damage was lowest among vegetative plants early in the season, and highest among flowering plants later in the season. Given similar damage levels, leaf herbivores feeding on plants before flowering should thus exert stronger selection on defence traits than those feeding on plants during flowering.

    Resistance against larval feeding by the specialist Plutella xylostella was negatively correlated with resistance against larval feeding by the generalist Mamestra brassicae and with resistance against oviposition by P. xylostella when variation in resistance was examined within and among two Swedish and two Italian A. thaliana populations. The results suggest that negative correlations between resistance against different herbivores and different life-history stages of herbivores may contribute to the maintenance of genetic variation in resistance.

    List of papers
    1. Selection on flowering time in three natural populations of Arabidopsis thaliana
    Open this publication in new window or tab >>Selection on flowering time in three natural populations of Arabidopsis thaliana
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology Evolutionary Biology Botany
    Research subject
    Biology with specialization in Ecological Botany
    Identifiers
    urn:nbn:se:uu:diva-159506 (URN)
    Funder
    Swedish Research Council
    Available from: 2011-10-06 Created: 2011-10-03 Last updated: 2011-11-10
    2. Conflicting selection on the timing of germination in a natural population of Arabidopsis thaliana
    Open this publication in new window or tab >>Conflicting selection on the timing of germination in a natural population of Arabidopsis thaliana
    2014 (English)In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 27, no 1, 193-199 p.Article in journal (Refereed) Published
    Abstract [en]

    The timing of germination is a key life-history trait that may strongly influence plant fitness and that sets the stage for selection on traits expressed later in the life cycle. In seasonal environments, the period favourable for germination and the total length of the growing season are limited. The optimal timing of germination may therefore be governed by conflicting selection through survival and fecundity. We conducted a field experiment to examine the effects of timing of germination on survival, fecundity and overall fitness in a natural population of the annual herb Arabidopsis thaliana in north-central Sweden. Seedlings were transplanted at three different times in late summer and in autumn covering the period of seed germination in the study population. Early germination was associated with low seedling survival, but also with high survival and fecundity among established plants. The advantages of germinating early more than balanced the disadvantage and selection favoured early germination. The results suggest that low survival among early germinating seeds is the main force opposing the evolution of earlier germination and that the optimal timing of germination should vary in space and time as a function of the direction and strength of selection acting during different life-history stages.

    National Category
    Ecology Evolutionary Biology Botany
    Research subject
    Biology with specialization in Ecological Botany
    Identifiers
    urn:nbn:se:uu:diva-159664 (URN)10.1111/jeb.12293 (DOI)000329254500018 ()
    Funder
    Swedish Research Council
    Available from: 2011-10-06 Created: 2011-10-06 Last updated: 2017-12-08Bibliographically approved
    3. Magnitude and timing of leaf damage affect seed production in a natural population of Arabidopsis thaliana (Brassicaceae)
    Open this publication in new window or tab >>Magnitude and timing of leaf damage affect seed production in a natural population of Arabidopsis thaliana (Brassicaceae)
    2012 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 1, e30015- p.Article in journal (Refereed) Published
    Abstract [en]

    Background: The effect of herbivory on plant fitness varies widely. Understanding the causes of this variation is of considerable interest because of its implications for plant population dynamics and trait evolution. We experimentally defoliated the annual herb Arabidopsis thaliana in a natural population in Sweden to test the hypotheses that (a) plant fitness decreases with increasing damage, (b) tolerance to defoliation is lower before flowering than during flowering, and (c) defoliation before flowering reduces number of seeds more strongly than defoliation during flowering, but the opposite is true for effects on seed size.

    Methodology/Principal Findings: In a first experiment, between 0 and 75% of the leaf area was removed in May from plants that flowered or were about to start flowering. In a second experiment, 0, 25%, or 50% of the leaf area was removed from plants on one of two occasions, in mid April when plants were either in the vegetative rosette or bolting stage, or in mid May when plants were flowering. In the first experiment, seed production was negatively related to leaf area removed, and at the highest damage level, also mean seed size was reduced. In the second experiment, removal of 50% of the leaf area reduced seed production by 60% among plants defoliated early in the season at the vegetative rosettes, and by 22% among plants defoliated early in the season at the bolting stage, but did not reduce seed output of plants defoliated one month later. No seasonal shift in the effect of defoliation on seed size was detected.

    Conclusions/Significance: The results show that leaf damage may reduce the fitness of A. thaliana, and suggest that in this population leaf herbivores feeding on plants before flowering should exert stronger selection on defence traits than those feeding on plants during flowering, given similar damage levels.

    National Category
    Ecology Evolutionary Biology Botany
    Research subject
    Biology with specialization in Ecological Botany
    Identifiers
    urn:nbn:se:uu:diva-159665 (URN)10.1371/journal.pone.0030015 (DOI)000301457200028 ()
    Funder
    Swedish Research Council
    Available from: 2011-10-06 Created: 2011-10-06 Last updated: 2017-12-08Bibliographically approved
    4. Genetic variation in leaf morphology and resistance against specialist and generalist insect herbivores in natural populations of Arabidopsis thaliana
    Open this publication in new window or tab >>Genetic variation in leaf morphology and resistance against specialist and generalist insect herbivores in natural populations of Arabidopsis thaliana
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology Evolutionary Biology Botany
    Research subject
    Biology with specialization in Ecological Botany
    Identifiers
    urn:nbn:se:uu:diva-159685 (URN)
    Funder
    Swedish Research Council
    Available from: 2011-10-06 Created: 2011-10-06 Last updated: 2011-11-10
  • 4.
    Akiyama, Reiko
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Noack, Sibylle
    Department of Zoology, Stockholm University.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genetic variation in leaf morphology and resistance against specialist and generalist insect herbivores in natural populations of Arabidopsis thalianaManuscript (preprint) (Other academic)
  • 5.
    Akiyama, Reiko
    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.
    Conflicting selection on the timing of germination in a natural population of Arabidopsis thaliana2014In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 27, no 1, 193-199 p.Article in journal (Refereed)
    Abstract [en]

    The timing of germination is a key life-history trait that may strongly influence plant fitness and that sets the stage for selection on traits expressed later in the life cycle. In seasonal environments, the period favourable for germination and the total length of the growing season are limited. The optimal timing of germination may therefore be governed by conflicting selection through survival and fecundity. We conducted a field experiment to examine the effects of timing of germination on survival, fecundity and overall fitness in a natural population of the annual herb Arabidopsis thaliana in north-central Sweden. Seedlings were transplanted at three different times in late summer and in autumn covering the period of seed germination in the study population. Early germination was associated with low seedling survival, but also with high survival and fecundity among established plants. The advantages of germinating early more than balanced the disadvantage and selection favoured early germination. The results suggest that low survival among early germinating seeds is the main force opposing the evolution of earlier germination and that the optimal timing of germination should vary in space and time as a function of the direction and strength of selection acting during different life-history stages.

  • 6.
    Akiyama, Reiko
    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.
    Magnitude and timing of leaf damage affect seed production in a natural population of Arabidopsis thaliana (Brassicaceae)2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 1, e30015- p.Article in journal (Refereed)
    Abstract [en]

    Background: The effect of herbivory on plant fitness varies widely. Understanding the causes of this variation is of considerable interest because of its implications for plant population dynamics and trait evolution. We experimentally defoliated the annual herb Arabidopsis thaliana in a natural population in Sweden to test the hypotheses that (a) plant fitness decreases with increasing damage, (b) tolerance to defoliation is lower before flowering than during flowering, and (c) defoliation before flowering reduces number of seeds more strongly than defoliation during flowering, but the opposite is true for effects on seed size.

    Methodology/Principal Findings: In a first experiment, between 0 and 75% of the leaf area was removed in May from plants that flowered or were about to start flowering. In a second experiment, 0, 25%, or 50% of the leaf area was removed from plants on one of two occasions, in mid April when plants were either in the vegetative rosette or bolting stage, or in mid May when plants were flowering. In the first experiment, seed production was negatively related to leaf area removed, and at the highest damage level, also mean seed size was reduced. In the second experiment, removal of 50% of the leaf area reduced seed production by 60% among plants defoliated early in the season at the vegetative rosettes, and by 22% among plants defoliated early in the season at the bolting stage, but did not reduce seed output of plants defoliated one month later. No seasonal shift in the effect of defoliation on seed size was detected.

    Conclusions/Significance: The results show that leaf damage may reduce the fitness of A. thaliana, and suggest that in this population leaf herbivores feeding on plants before flowering should exert stronger selection on defence traits than those feeding on plants during flowering, given similar damage levels.

  • 7.
    Akiyama, Reiko
    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.
    Selection on flowering time in three natural populations of Arabidopsis thalianaManuscript (preprint) (Other academic)
  • 8.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jaegerbrand, Annika K.
    Molau, Ulf
    Climate change and climatic events: community-, functional- and species-level responses of bryophytes and lichens to constant, stepwise, and pulse experimental warming in an alpine tundra2014In: Alpine Botany, ISSN 1664-2201, E-ISSN 1664-221X, Vol. 124, no 2, 81-91 p.Article in journal (Refereed)
    Abstract [en]

    We experimentally imposed three different kinds of warming scenarios over 3 years on an alpine meadow community to identify the differential effects of climate warming and extreme climatic events on the abundance and biomass of bryophytes and lichens. Treatments consisted of (a) a constant level of warming with open top chambers (an average temperature increase of 1.87 A degrees C), (b) a yearly stepwise increase of warming (average temperature increases of 1.0; 1.87 and 3.54 A degrees C, consecutively), and (c) a pulse warming, i.e., a single first year pulse event of warming (average temperature increase of 3.54 A degrees C only during the first year). To our knowledge, this is the first climate change study that attempts to distinguish between the effects of constant, stepwise and pulse warming on bryophyte and lichen communities. We hypothesised that pulse warming would have a significant short-term effect compared to the other warming treatments, and that stepwise warming would have a significant mid-term effect compared to the other warming treatments. Acrocarpous bryophytes as a group increased in abundance and biomass to the short-term effect of pulse warming. We found no significant effects of mid-term (third-year) stepwise warming. However, one pleurocarpous bryophyte species, Tomentypnum nitens, generally increased in abundance during the warm year 1997 but decreased in control plots and in response to the stepwise warming treatment. Three years of experimental warming (all treatments as a group) did have a significant impact at the community level, yet changes in abundance did not translate into significant changes in the dominance hierarchies at the functional level (for acrocarpous bryophytes, pleurocarpous bryophytes, Sphagnum or lichens), or in significant changes in other bryophyte or lichen species. The results suggest that bryophytes and lichens, both at the functional group and species level, to a large extent are resistant to the different climate change warming simulations that were applied.

  • 9.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jagerbrand, Annika K.
    VTI, Swedish Natl Rd & Transport Res Inst, S-10215 Stockholm, Sweden..
    Molau, Ulf
    Univ Gothenburg, Dept Biol & Environm Sci, SE-40530 Gothenburg, Sweden..
    Testing reliability of short-term responses to predict longer-term responses of bryophytes and lichens to environmental change2015In: Ecological Indicators, ISSN 1470-160X, E-ISSN 1872-7034, Vol. 58, 77-85 p.Article in journal (Refereed)
    Abstract [en]

    Environmental changes are predicted to have severe and rapid impacts on polar and alpine regions. At high latitudes/altitudes, cryptogams such as bryophytes and lichens are of great importance in terms of biomass, carbon/nutrient cycling, cover and ecosystem functioning. This seven-year factorial experiment examined the effects of fertilizing and experimental warming on bryophyte and lichen abundance in an alpine meadow and a heath community in subarctic Sweden. The aim was to determine whether shortterm responses (five years) are good predictors of longer-term responses (seven years). Fertilizing and warming had significant negative effects on total and relative abundance of bryophytes and lichens, with the largest and most rapid decline caused by fertilizing and combined fertilizing and warming. Bryophytes decreased most in the alpine meadow community, which was bryophyte-dominated, and lichens decreased most in the heath community, which was lichen-dominated. This was surprising, as the most diverse group in each community was expected to be most resistant to perturbation. Warming alone had a delayed negative impact. Of the 16 species included in statistical analyses, seven were significantly negatively affected. Overall, the impacts of simulated warming on bryophytes and lichens as a whole and on individual species differed in time and magnitude between treatments and plant communities (meadow and heath). This will likely cause changes in the dominance structures over time. These results underscore the importance of longer-term studies to improve the quality of data used in climate change models, as models based on short-term data are poor predictors of long-term responses of bryophytes and lichens.

  • 10.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Little, Chelsea J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Simulated global change: contrasting short and medium term growth and reproductive responses of a common alpine/Arctic cushion plant to experimental warming and nutrient enhancement2014In: SpringerPlus, E-ISSN 2193-1801, Vol. 3, 157Article in journal (Refereed)
    Abstract [en]

    Cushion plants are important components of alpine and Arctic plant communities around the world. They fulfill important roles as facilitators, nurse plants and foundation species across trophic levels for vascular plants, arthropods and soil microorganisms, the importance of these functions increasing with the relative severity of the environment. Here we report results from one of the few experimental studies simulating global change impacts on cushion plants; a factorial experiment with warming and nutrient enhancement that was applied to an alpine population of the common nurse plant, Silene acaulis, in sub-arctic Sweden. Experimental perturbations had significant short-term impacts on both stem elongation and leaf length. S. acaulis responded quickly by increasing stem elongation and (to a lesser extent) leaf length in the warming, nutrient, and the combined warming and nutrient enhancements. Cover and biomass also initially increased in response to the perturbations. However, after the initial positive short-term responses, S. acaulis cover declined in the manipulations, with the nutrient and combined warming and nutrient treatments having largest negative impact. No clear patterns were found for fruit production. Our results show that S. acaulis living in harsh environments has potential to react quickly when experiencing years with favorable conditions, and is more responsive to nutrient enhancement than to warming in terms of vegetative growth. While these conditions have an initial positive impact, populations experiencing longer-term increased nutrient levels will likely be negatively affected.

  • 11.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Little, Chelsea J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jagerbrand, Annika K.
    Molau, Ulf
    Dominance hierarchies, diversity and species richness of vascular plants in an alpine meadow: contrasting short and medium term responses to simulated global change2014In: PeerJ, ISSN 2167-8359, E-ISSN 2167-8359, Vol. 2, e406- p.Article in journal (Refereed)
    Abstract [en]

    We studied the impact of simulated global change on a high alpine meadow plant community. Specifically, we examined whether short-term (5 years) responses are good predictors for medium-term (7 years) changes in the system by applying a factorial warming and nutrient manipulation to 20 plots in Latnjajaure, subarctic Sweden. Seven years of experimental warming and nutrient enhancement caused dramatic shifts in dominance hierarchies in response to the nutrient and the combined warming and nutrient enhancement treatments. Dominance hierarchies in the meadow moved from a community being dominated by cushion plants, deciduous, and evergreen shrubs to a community being dominated by grasses, sedges, and forbs. Short-termresponses were shown to be inconsistent in their ability to predict medium-term responses for most functional groups, however, grasses showed a consistent and very substantial increase in response to nutrient addition over the seven years. The non-linear responses over time point out the importance of longer-term studies with repeated measurements to be able to better predict future changes. Forecasted changes to temperature and nutrient availability have implications for trophic interactions, and may ultimately influence the access to and palatability of the forage for grazers. Depending on what anthropogenic change will be most pronounced in the future (increase in nutrient deposits, warming, or a combination of them both), different shifts in community dominance hierarchies may occur. Generally, this study supports the productivity-diversity relationship found across arctic habitats, with community diversity peaking in mid-productivity systems and degrading as nutrient availability increases further. This is likely due the increasing competition in plant-plant interactions and the shifting dominance structure with grasses taking over the experimental plots, suggesting that global change could have high costs to biodiversity in the Arctic.

  • 12.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Little, Chelsea J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jagerbrand, Annika K.
    Molau, Ulf
    Vascular plant abundance and diversity in an alpine heath under observed and simulated global change2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, 10197Article in journal (Refereed)
    Abstract [en]

    Global change is predicted to cause shifts in species distributions and biodiversity in arctic tundra. We applied factorial warming and nutrient manipulation to a nutrient and species poor alpine/arctic heath community for seven years. Vascular plant abundance in control plots increased by 31%. There were also notable changes in cover in the nutrient and combined nutrient and warming treatments, with deciduous and evergreen shrubs declining, grasses overgrowing these plots. Sedge abundance initially increased significantly with nutrient amendment and then declined, going below initial values in the combined nutrient and warming treatment. Nutrient addition resulted in a change in dominance hierarchy from deciduous shrubs to grasses. We found significant declines in vascular plant diversity and evenness in the warming treatment and a decline in diversity in the combined warming and nutrient addition treatment, while nutrient addition caused a decline in species richness. The results give some experimental support that species poor plant communities with low diversity may be more vulnerable to loss of species diversity than communities with higher initial diversity. The projected increase in nutrient deposition and warming may therefore have negative impacts on ecosystem processes, functioning and services due to loss of species diversity in an already impoverished environment.

  • 13.
    Alatalo, Juha M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ostapenko, Oksana V.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The Swedish system: The image cracking when taking a closer look2014In: Geoforum, ISSN 0016-7185, E-ISSN 1872-9398, Vol. 53, 82-83 p.Article, review/survey (Refereed)
    Abstract [en]

    Sweden has a high international profile regarding social issues and projects an image as one of the best countries in the world in terms of social indicators. Here we argue for a revised view as the reality is that Swedish system is very segregated, particularly in terms of (1) relative lack of women in positions of high influence, (2) it is the worst country in the EU28 regarding long-term unemployment for people born outside the country, and (3) it has a education system that after a number of reforms is involved in a "race towards the bottom" to profit from students. At the same time Sweden undervalues foreign academic qualifications and getting work largely depends on "who you know", not "what you know".

  • 14. Alberts, Susan C.
    et al.
    Altmann, Jeanne
    Brockman, Diane K.
    Cords, Marina
    Fedigan, Linda M.
    Pusey, Anne
    Stoinski, Tara S.
    Strier, Karen B.
    Morris, William F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bronikowski, Anne M.
    Reproductive aging patterns in primates reveal that humans are distinct2013In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 110, no 33, 13440-13445 p.Article in journal (Refereed)
    Abstract [en]

    Women rarely give birth after similar to 45 y of age, and they experience the cessation of reproductive cycles, menopause, at similar to 50 y of age after a fertility decline lasting almost two decades. Such reproductive senescence in mid-lifespan is an evolutionary puzzle of enduring interest because it should be inherently disadvantageous. Furthermore, comparative data on reproductive senescence from other primates, or indeed other mammals, remains relatively rare. Here we carried out a unique detailed comparative study of reproductive senescence in seven species of nonhuman primates in natural populations, using long-term, individual-based data, and compared them to a population of humans experiencing natural fertility and mortality. In four of seven primate species we found that reproductive senescence occurred before death only in a small minority of individuals. In three primate species we found evidence of reproductive senescence that accelerated throughout adulthood; however, its initial rate was much lower than mortality, so that relatively few individuals experienced reproductive senescence before death. In contrast, the human population showed the predicted and well-known pattern in which reproductive senescence occurred before death for many women and its rate accelerated throughout adulthood. These results provide strong support for the hypothesis that reproductive senescence in midlife, although apparent in natural-fertility, natural-mortality populations of humans, is generally absent in other primates living in such populations.

  • 15. Armbruster, W. Scott
    et al.
    Hansen, Thomas F.
    Pélabon, Christophe
    Pérez-Barrales, Rocio
    Maad, Johanne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The adaptive accuracy of flowers: measurement and microevolutionary patterns2009In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 103, no 9, 1529-1545 p.Article in journal (Refereed)
  • 16.
    Asplund, Linnea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Evolution.
    Hagenblad, Jenny
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Leino, Matti W.
    Re-evaluating the history of the wheat domestication gene NAM-B1 using historical plant material2010In: Journal of Archaeological Science, ISSN 0305-4403, E-ISSN 1095-9238, Vol. 37, no 9, 2303-2307 p.Article in journal (Refereed)
    Abstract [en]

    The development of agriculture is closely associated with the domestication of wheat, one of the earliest crop species. During domestication key genes underlying traits important to Neolithic agriculture were targeted by selection. One gene believed to be such a domestication gene is NAM-B1, affecting both nutritional quality and yield but with opposite effects. A null mutation, first arisen in emmer wheat, decreases the nutritional quality but delays maturity and increases grain size; previously the ancestral allele was believed lost during the domestication of durum and bread wheat by indirect selection for larger grain. By genotyping 63 historical seed samples originating from the 1862 International Exhibition in London, we found that the ancestral allele was present in two spelt wheat and two bread wheat cultivars widely cultivated at the time. This suggests that fixation of the mutated allele of NAM-B1 in bread wheat, if at all, occurred during modern crop improvement rather than during domestication. We also discuss the value of using archaeological and historical plant material to further the understanding of the development of agriculture.

  • 17.
    Asplund, Linnea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Leino, Matti W.
    Hagenblad, Jenny
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Allelic Variation at the Rht8 Locus in a 19th Century Wheat Collection2012In: Scientific World Journal, ISSN 1537-744X, E-ISSN 1537-744X, 385610- p.Article in journal (Refereed)
    Abstract [en]

    Wheat breeding during the 20th century has put large efforts into reducing straw length and increasing harvest index. In the 1920s an allele of Rht8 with dwarfing effects, found in the Japanese cultivar "Akakomugi," was bred into European cultivars and subsequently spread over the world. Rht8 has not been cloned, but the microsatellite marker WMS261 has been shown to be closely linked to it and is commonly used for genotyping Rht8. The "Akakomugi" allele is strongly associated with WMS261-192bp. Numerous screens of wheat cultivars with different geographical origin have been performed to study the spread and influence of the WMS261-192bp during 20th century plant breeding. However, the allelic diversity of WMS261 in wheat cultivars before modern plant breeding and introduction of the Japanese dwarfing genes is largely unknown. Here, we report a study of WMS261 allelic diversity in a historical wheat collection from 1865 representing worldwide major wheats at the time. The majority carried the previously reported 164 bp or 174 bp allele, but with little geographical correlation. In a few lines, a rare 182 bp fragment was found. Although straw length was recognized as an important character already in the 19th century, Rht8 probably played a minor role for height variation. The use of WMS261 and other functional markers for analyses of historical specimens and characterization of historic crop traits is discussed.

  • 18. Avia, Komlan
    et al.
    Karkkainen, Katri
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Savolainen, Outi
    Association of FLOWERING LOCUS T/TERMINAL FLOWER 1-like gene FTL2 expression with growth rhythm in Scots pine (Pinus sylvestris)2014In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 204, no 1, 159-170 p.Article in journal (Refereed)
    Abstract [en]

    Understanding the genetic basis of the timing of bud set, an important trait in conifers, is relevant for adaptation and forestry practice. In common garden experiments, both Scots pine (Pinus sylvestris) and Norway spruce (Picea abies) show a latitudinal cline in the trait. We compared the regulation of their bud set biology by examining the expression of PsFTL2, a Pinus sylvestris homolog to PaFTL2, a FLOWERING LOCUS T/TERMINAL FLOWER 1 (FT/TFL1)-like gene, the expression levels of which have been found previously to be associated with the timing of bud set in Norway spruce. In a common garden study, we analyzed the relationship of bud phenology under natural and artificial photoperiods and the expression of PsFTL2 in a set of Scots pine populations from different latitudes. The expression of PsFTL2 increased in the needles preceding bud set and decreased during bud burst. In the northernmost population, even short night periods were efficient to trigger this expression, which also increased earlier under all photoperiodic regimes compared with the southern populations. Despite the different biology, with few limitations, the two conifers that diverged 140 million yr ago probably share an association of FTL2 with bud set, pointing to a common mechanism for the timing of growth cessation in conifers.

  • 19.
    Backéus, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Dynamik och evolution på de östafrikanska bergen2017In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 111, no 5, 228-239 p.Article in journal (Refereed)
    Abstract [en]

    A brief overview of the conspicuous alpine flora and vegetation of the East African mountains is presented. 

  • 20.
    Backéus, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ett etnobotaniskt livsverk2015In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 109, no 6, 346-347 p.Article in journal (Refereed)
    Abstract [sv]

    Vagn J. Brøndegaard skrev mer än 1600 artiklar om allt som hade med relationen mellan växter och människor att göra. Många av dessa har nu ställts samman i två vackra volymer.

  • 21.
    Backéus, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gunnar Björkman och hans expedition till Lule lappmark 1924: Gunnar Björkman’s expedition to Swedish Lapland in 19242013In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 107, no 6, 354-358 p.Article in journal (Other academic)
    Abstract [en]

    Drawings by Torsten Höjer from Gunnar Björkman's botanical expedition to Swedish Lapland in 1924 are presented with some biographical notes on Björkman. The paleontologist  Birger Bohlin also participated.

  • 22.
    Backéus, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Mossflora över Sankta Helena2013In: Myrinia, ISSN 1102-4194, Vol. 23, 84-87 p.Article in journal (Other academic)
    Abstract [en]

    A new bryophyte flora of St. Helena in the South Atlantic is presented. Of the known 110 species, 26 are (as presently known) endemic.

  • 23.
    Backéus, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Swedish Biodiversity Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sankta Helena: en hotad endemisk flora. 1. Den ursprungliga floran och vegetationen och den historiska utvecklingen2014In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 108, no 3-4, 206-218 p.Article in journal (Other academic)
    Abstract [en]

    An overview of the endemic flora and the original vegetation of Saint Helena is given.

  • 24.
    Backéus, Ingvar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Swedish Biodiversity Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sankta Helena: en hotad endemisk flora. 2. situationen i dag2014In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 108, no 5, 232-244 p.Article in journal (Refereed)
    Abstract [en]

    The present-day situation for the endemic flora of Saint Helena is described.

  • 25.
    Backéus, Ingvar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Swedish Biodiversity Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Emanuelsson, Urban
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Swedish Biodiversity Centre.
    Karakin, Vladimir (Contributor)
    Russian Academy of Sciences, Far East Division, Vladivostok.
    von Bothmer, Roland (Contributor)
    Swedish University of Agriculture, Alnarp.
    The rural landscapes of Northeast Asia.2016Book (Other academic)
  • 26.
    Bai, Yang
    et al.
    Shanghai Acad Environm Sci, Inst Appl Ecol, Shanghai 200233, Peoples R China..
    Jiang, Bo
    Changjiang Water Resources Protect Inst, Wuhan 430051, Peoples R China..
    Wang, Min
    Shanghai Acad Environm Sci, Inst Appl Ecol, Shanghai 200233, Peoples R China..
    Li, Hui
    Yunnan Univ, Sch Urban Construct & Management, Kunming 650091, Peoples R China..
    Alatalo, Juha M.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Qatar Univ, Coll Arts & Sci, Dept Biol & Environm Sci, POB 2713, Doha, Qatar..
    Huang, Shenfa
    Shanghai Acad Environm Sci, Inst Appl Ecol, Shanghai 200233, Peoples R China..
    New ecological redline policy (ERP) to secure ecosystem services in China2016In: Land use policy, ISSN 0264-8377, E-ISSN 1873-5754, Vol. 55, 348-351 p.Article in journal (Refereed)
    Abstract [en]

    China is facing huge environmental problems, with its current rapid rate of urbanization and industrialization causing biodiversity loss, ecosystem degradation, and land resources degradation on a major scale. To overcome management conflicts and secure ecosystem services, China has proposed a new 'ecological redline policy' (ERP) using ecosystem services as a way to meet its targets. By giving environmental policy redline status, China is demonstrating strong commitment in its efforts to tackle environmental degradation and secure ecosystem services for the future. This is already having impact, as the Chinese Ministry of Environmental Protection and the National Development and Reform Commission are prepared to work together to implement the new environmental policy.

  • 27. Bakker, Jan P.
    et al.
    Hoffmann, Frank
    Ozinga, Wim A.
    Rosén, Eje
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Shading results in depletion of the soil seed bank2014In: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 32, no 5, 674-679 p.Article in journal (Refereed)
    Abstract [en]

    To what extent is the decline of characteristic dry alvar species related to the decline in the soil seed bank during scrub encroachment? We recorded the number of flower stems in the vegetation in relation to light attenuation along an encroachment series progressing from open alvar through small gaps inside dense scrub of Juniperus communis (cover of 60%) to intact dense scrub (cover of 100%) on the island of oland, Sweden. This measurement of potential reproduction (number of flower stems) was then compared to the number of species in the soil seed bank at each site along the alvar encroachment series. Scrub encroachment results in light attenuation between and under the shrubs. The total number of flower stems averaged over all species was similar between gaps and open alvar, but that of alvar species was significantly lower in the gaps, indicating that light attenuation could reduce their seed set. Shading in gaps is related to depletion of the soil seed bank and loss of alvar species, particularly those that do not form a persistent soil seed bank.

  • 28. Bakker, Jan P.
    et al.
    Rosén, Eje
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ozinga, Wim A.
    Bretfeld, Mario
    Feldt, Tobias
    Stahl, Julia
    Long-term effects of scrub clearance and litter removal on the re-establishment of dry alvar grassland species2012In: Annales Botanici Fennici, ISSN 0003-3847, E-ISSN 1797-2442, Vol. 49, no 1-2, 21-30 p.Article in journal (Refereed)
    Abstract [en]

    Many characteristic dry alvar grassland species disappear after cessation of livestock grazing as a result of encroachment by Juniperus communis. We studied the re-establishment of these species after scrub clearance with and without the removal of the layer of litter and mosses in long-term (14 years) permanent plots. Most of the species belonging to the community species pool of dry alvar grassland species before clearance were found in permanent plots between 2 and 14 years after the clearance. A large part originated from vegetative spread of already occurring species in the established vegetation in the surroundings. Only a small part of the long-term persistent soil seed bank resulted in the re-establishment of alvar species. There was no significant difference in the traits soil seed bank, seed weight and long-distance dispersal by wind, dung or fur of animals of established and non-established species. Removal of litter and mosses positively affected the re-establishment of alvar species.

  • 29.
    Bartoszek, Krzysztof
    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. CNRS Univ Montpellier IRD EPHE, UMR ISEM 5554, Montpellier, France..
    Kaj, Ingemar
    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.
    Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations2017In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 429, 35-45 p.Article in journal (Refereed)
    Abstract [en]

    The Ornstein-Uhlenbeck (OU) process plays a major role in the analysis of the evolution of phenotypic traits along phylogenies. The standard OU process includes random perturbations and stabilizing selection and assumes that species evolve independently. However, evolving species may interact through various ecological process and also exchange genes especially in plants. This is particularly true if we want to study phenotypic evolution among diverging populations within species. In this work we present a straightforward statistical approach with analytical solutions that allows for the inclusion of adaptation and migration in a common phylogenetic framework, which can also be useful for studying local adaptation among populations within the same species. We furthermore present a detailed simulation study that clearly indicates the adverse effects of ignoring migration. Similarity between species due to migration could be misinterpreted as very strong convergent evolution without proper correction for these additional dependencies. Finally, we show that our model can be interpreted in terms of ecological interactions between species, providing a general framework for the evolution of traits between "interacting" species or populations.

  • 30. Bella, Eleni
    et al.
    Liepelt, Sascha
    Parducci, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Drouzas, Andreas D.
    Genetic insights into the hybrid origin of Abies borisii-regis Mattf.2015In: Plant Systematics and Evolution, ISSN 0378-2697, E-ISSN 1615-6110, Vol. 301, no 2, 749-759 p.Article in journal (Refereed)
    Abstract [en]

    Abies × borisii-regis Mattf. (King Boris fir) is a taxon endemic to the southern Balkan Peninsula, described as a hybrid between the widespread A. alba Mill. (Silver fir) and the Greek endemic A. cephalonica Loud (Greek fir). Even though A. × borisii-regis has attracted much research attention in the past, its origin, geographical distribution and taxonomic status are not fully elucidated and molecular evidence for hybridization is missing. To shed more light on this issue, we analyzed representative populations from these three Abies taxa using paternally inherited (chloroplast) and maternally inherited (mitochondrial) DNA markers. Both Silver and Greek fir could be clearly distinguished using mitochondrial markers, while we observed a mixture of maternal lineages in theA. × borisii-regis populations. In contrast, using chloroplast markers, we could not identify species-specific haplotypes, but a neighbor-joining analysis of population genetic distances revealed two separate clusters for the Silver fir and the Greek fir, while the A. × borisii-regis populations were placed in intermediate positions. Our results are in agreement with the hypothesis that the A. ×borisii-regis populations investigated are a result of hybridization between A. cephalonica and A. alba.

  • 31.
    Bengtsson, Fia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Granath, Gustaf
    Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Photosynthesis, growth, and decay traits in Sphagnum – a multispecies comparison2016In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 6, no 10, 3325-3341 p.Article in journal (Refereed)
    Abstract [en]

    Peat mosses (Sphagnum) largely govern carbon sequestration in Northern Hemisphere peatlands. We investigated functional traits related to growth and decomposition in Sphagnum species. We tested the importance of environment and phylogeny in driving species traits and investigated trade-offs among them. We selected 15 globally important Sphagnum species, representing four sections (subgenera) and a range of peatland habitats. We measured rates of photosynthesis and decomposition in standard laboratory conditions as measures of innate growth and decay potential, and related this to realized growth, production, and decomposition in their natural habitats. In general, we found support for a trade-off between measures of growth and decomposition. However, the relationships are not strong, with r ranging between 0.24 and 0.45 for different measures of growth versus decomposition. Using photosynthetic rate to predict decomposition in standard conditions yielded R2 = 0.20. Habitat and section (phylogeny) affected the traits and the trade-offs. In a wet year, species from sections Cuspidata and Sphagnum had the highest production, but in a dry year, differences among species, sections, and habitats evened out. Cuspidata species in general produced easily decomposable litter, but their decay in the field was hampered, probably due to near-surface anoxia in their wet habitats. In a principal components analysis, PCA, photosynthetic capacity, production, and laboratory decomposition acted in the same direction. The species were imperfectly clustered according to vegetation type and phylogeny, so that some species clustered with others in the same section, whereas others clustered more clearly with others from similar vegetation types. Our study includes a wider range of species and habitats than previous trait analyses in Sphagnum and shows that while the previously described growth–decay trade-off exists, it is far from perfect. We therefore suggest that our species-specific trait measures offer opportunities for improvements of peatland ecosystem models. Innate qualities measured in laboratory conditions translate differently to field responses. Most dramatically, fast-growing species could only realize their potential in a wet year. The same species decompose fast in laboratory, but their decomposition was more retarded in the field than that of other species. These relationships are crucial for understanding the long-term dynamics of peatland communities.

  • 32. Bengtsson, J.
    et al.
    Fagerström, T.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Competition and coexistence in plant communities1994In: Trends in Ecology & Evolution, Vol. 9, 246-250 p.Article in journal (Refereed)
  • 33. Berlin, S.
    et al.
    Trybush, S. O.
    Fogelqvist, J.
    Gyllenstrand, N.
    Hallingbaeck, H. R.
    Ahman, I.
    Nordh, N-E
    Shield, I.
    Powers, S. J.
    Weih, M.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Roennberg-Waestljung, A-C
    Karp, A.
    Hanley, S. J.
    Genetic diversity, population structure and phenotypic variation in European Salix viminalis L. (Salicaceae)2014In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 10, no 6, 1595-1610 p.Article in journal (Refereed)
    Abstract [en]

    To investigate the potential of association genetics for willow breeding, Salix viminalis germplasm was assembled from UK and Swedish collections (comprising accessions from several European countries) and new samples collected from nature. A subset of the germplasm was planted at two sites (UK and Sweden), genotyped using 38 SSR markers and assessed for phenological and biomass traits. Population structure, genetic differentiation (F-ST) and quantitative trait differentiation (Q(ST)) were investigated. The extent and patterns of trait adaptation were assessed by comparing F-ST and Q(ST) parameters. Of the 505 genotyped diploid accessions, 27 % were not unique. Genetic diversity was high: 471 alleles was amplified; the mean number of alleles per locus was 13.46, mean observed heterozygosity was 0.55 and mean expected heterozygosity was 0.62. Bayesian clustering identified four subpopulations which generally corresponded to Western Russia, Western Europe, Eastern Europe and Sweden. All pairwise F-ST values were highly significant (p<0.001) with the greatest genetic differentiation detected between the Western Russian and the Western European subpopulations (F-ST = 0.12), and the smallest between the Swedish and Eastern European populations (F-ST = 0.04). The Swedish population also had the highest number of identical accessions, supporting the view that S. viminalis was introduced into this country and has been heavily influenced by humans. Q(ST) values were high for growth cessation and leaf senescence, and to some extent stem diameter, but low for bud burst time and shoot number. Overall negative clines between longitudinal coordinates and leaf senescence, bud burst and stem diameter were also found.

  • 34.
    Berlin, Sofia
    et al.
    Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences.
    Fogelqvist, Johan
    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.
    Rönnberg-Wästljung, Ann Christin
    Department of Plant Biology and Forest Genetics, Uppsala BioCenter, Swedish University of Agricultural Sciences.
    Polymorphism and divergence of two willow species, Salix viminalis L. and Salix schwerinii E. Wolf2011In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 1, no 5, 387-400 p.Article in journal (Refereed)
    Abstract [en]

    We investigated species divergence, present and past gene flow, levels of nucleotide polymorphism, and linkage disequilibrium in two willows from the plant genus Salix. Salix belongs together with Populus to the Salicaceae family; however, most population genetic studies of Salicaceae have been performed in Populus, the model genus in forest biology. Here we present a study on two closely related willow species Salix viminalis and S. schwerinii, in which we have resequenced 33 and 32 nuclear gene segments representing parts of 18 nuclear loci in 24 individuals for each species. We used coalescent simulations and estimated the split time to around 600,000 years ago and found that there is currently limited gene flow between the species. Mean intronic nucleotide diversity across gene segments was slightly higher in S. schwerinii (πi = 0.00849) than in S. viminalis (πi = 0.00655). Compared with other angiosperm trees, the two willows harbor intermediate levels of silent polymorphisms. The decay of linkage disequilibrium was slower in S. viminalis compared with S. schwerinii, and we speculate that this is due to different demographic histories as S. viminalis has been partly domesticated in Europe.

  • 35. Blair, M. W.
    et al.
    Soler, A.
    Cortés, Andrés J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Diversification and Population Structure in Common Beans (Phaseolus vulgaris L.)2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 11, e49488- p.Article in journal (Refereed)
    Abstract [en]

    Wild accessions of crops and landraces are valuable genetic resources for plant breeding and for conserving alleles and gene combinations in planta. The primary genepool of cultivated common beans includes wild accessions of Phaseolus vulgaris. These are of the same species as the domesticates and therefore are easily crossable with cultivated accessions. Molecular marker assessment of wild beans and landraces is important for the proper utilization and conservation of these important genetic resources. The goal of this research was to evaluate a collection of wild beans with fluorescent microsatellite or simple sequence repeat markers and to determine the population structure in combination with cultivated beans of all known races. Marker diversity in terms of average number of alleles per marker was high (13) for the combination of 36 markers and 104 wild genotypes that was similar to the average of 14 alleles per marker found for the 606 cultivated genotypes. Diversity in wild beans appears to be somewhat higher than in cultivated beans on a per genotype basis. Five populations or genepools were identified in structure analysis of the wild beans corresponding to segments of the geographical range, including Mesoamerican (Mexican), Guatemalan, Colombian, Ecuadorian-northern Peruvian and Andean (Argentina, Bolivia and Southern Peru). The combined analysis of wild and cultivated accessions showed that the first and last of these genepools were related to the cultivated genepools of the same names and the penultimate was found to be distinct but not ancestral to the others. The Guatemalan genepool was very novel and perhaps related to cultivars of race Guatemala, while the Colombian population was also distinct. Results suggest geographic isolation, founder effects or natural selection could have created the different semi-discrete populations of wild beans and that multiple domestications and introgression were involved in creating the diversity of cultivated beans.

  • 36.
    Blair, Matthew W.
    et al.
    Department of Plant Breeding and Genetics, Cornell University.
    Cortés, Andres J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Penmetsa, R.Varma
    University of California, Davis.
    Farmer, Andrew
    National Center for Genomic Research, Albuquerque.
    Carrasquilla-Garcia, Noelia
    University of California, Davis.
    Cook, Doug R.
    University of California, Davis.
    A high-throughput SNP marker system for parental polymorphism screening, and diversity analysis in common bean (Phaseolus vulgaris L.)2013In: Theoretical and Applied Genetics, ISSN 0040-5752, E-ISSN 1432-2242, Vol. 126, no 2, 535-548 p.Article in journal (Refereed)
    Abstract [en]

    Single nucleotide polymorphism (SNP) detection has become a marker system of choice, because of the high abundance of source polymorphisms and the ease with which allele calls are automated. Various technologies exist for the evaluation of SNP loci and previously we validated two medium throughput technologies. In this study, our goal was to utilize a 768 feature, Illumina GoldenGate assay for common bean (Phaseolus vulgaris L.) developed from conserved legume gene sequences and to use the new technology for (1) the evaluation of parental polymorphisms in a mini-core set of common bean accessions and (2) the analysis of genetic diversity in the crop. A total of 736 SNPs were scored on 236 diverse common bean genotypes with the GoldenGate array. Missing data and heterozygosity levels were low and 94 % of the SNPs were scorable. With the evaluation of the parental polymorphism genotypes, we estimated the utility of the SNP markers in mapping for inter-genepool and intra-genepool populations, the latter being of lower polymorphism than the former. When we performed the diversity analysis with the diverse genotypes, we found Illumina GoldenGate SNPs to provide equivalent evaluations as previous gene-based SNP markers, but less fine-distinctions than with previous microsatellite marker analysis. We did find, however, that the gene-based SNPs in the GoldenGate array had some utility in race structure analysis despite the low polymorphism. Furthermore the SNPs detected high heterozygosity in wild accessions which was probably a reflection of ascertainment bias. The Illumina SNPs were shown to be effective in distinguishing between the genepools, and therefore were most useful in saturation of inter-genepool genetic maps. The implications of these results for breeding in common bean are discussed as well as the advantages and disadvantages of the GoldenGate system for SNP detection.

  • 37. Blair, Matthew W.
    et al.
    Cortés, Andrés J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    This, Dominique
    Identification of an ERECTA gene and drought adaptation associations in wild and cultivated common bean2016In: Plant Science, ISSN 0168-9452, E-ISSN 1873-2259, Vol. 242, 250-259 p.Article in journal (Refereed)
    Abstract [en]

    In this research, we cloned and accessed nucleotide diversity in the common beanERECTA gene which has been implicated in drought tolerance and stomatal patterning.The homologous gene segment was isolated with degenerate primer and was found to be located on Chromosome 1. The gene had at least one paralog on Chromosome 9 and duplicate copies in soybean for each homolog. ERECTA-like genes were also discovered but the function of these was of less interest due to low similarity with the ERECTA gene from Arabidopsis. The diversity of the 5’ end of the large Chr. 1 PvERECTA gene was evaluated in a collection of 145 wild and cultivated common beans that were also characterized by geographic source and drought tolerance, respectively. Our wild population sampled a range of wet to dry habitats, while our cultivated samples were representative of landrace diversity and the patterns of nucleotide variation differed between groups. The 5’ region exhibited lower levels of diversity in the cultivated collection, which was indicative of population bottlenecks associated with the domestication process, compared to the wild collection where diversity was associated with ecological differences. We discuss associations of nucleotide diversity at PvERECTA with drought tolerance prediction for the genotypes.

  • 38. Blake, S.
    et al.
    Wikelski, M.
    Cabrera, F.
    Guezou, A.
    Silva, M.
    Sadeghayobi, Elham
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Yackulic, C. B.
    Jaramillo, P.
    Seed dispersal by Galápagos tortoises2012In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 39, no 11, 1961-1972 p.Article in journal (Refereed)
    Abstract [en]

    Aim Large-bodied vertebrates often have a dramatic role in ecosystem function through herbivory, trampling, seed dispersal and nutrient cycling. The iconic Galápagos tortoises (Chelonoidis nigra) are the largest extant terrestrial ectotherms, yet their ecology is poorly known. Large body size should confer a generalist diet, benign digestive processes and long-distance ranging ability, rendering giant tortoises adept seed dispersers. We sought to determine the extent of seed dispersal by Galápagos tortoises and their impact on seed germination for selected species, and to assess potential impacts of tortoise dispersal on the vegetation dynamics of the Galápagos. Location Galápagos, Ecuador. Methods To determine the number of seeds dispersed we identified and counted intact seeds from 120 fresh dung piles in both agricultural and national park land. To estimate the distance over which tortoises move seeds we used estimated digesta retention times from captive tortoises as a proxy for retention times of wild tortoises and tortoise movement data obtained from GPS telemetry. We conducted germination trials for five plant species to determine whether tortoise processing influenced germination success. Results In our dung sample, we found intact seeds from >45 plant species, of which 11 were from introduced species. Tortoises defecated, on average, 464 (SE 95) seeds and 2.8 (SE 0.2) species per dung pile. Seed numbers were dominated by introduced species, particularly in agricultural land. Tortoises frequently moved seeds over long distances; during mean digesta retention times (12days) tortoises moved an average of 394m (SE 34) and a maximum of 4355m over the longest recorded retention time (28days). We did not find evidence that tortoise ingestion or the presence of dung influenced seed germination success. Main conclusions Galápagos tortoises are prodigious seed dispersers, regularly moving large quantities of seeds over long distances. This may confer important advantages to tortoise-dispersed species, including transport of seeds away from the parent plants into sites favourable for germination. More extensive research is needed to quantify germination success, recruitment to adulthood and demography of plants under natural conditions, with and without tortoise dispersal, to determine the seed dispersal effectiveness of Galápagos tortoises.

  • 39.
    Boberg, Elin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Alexandersson, Ronny
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jonsson, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Maad, Johanne
    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.
    Nilsson, Anders L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Pollinator shifts and the evolution of spur length in the moth-pollinated orchid Platanthera bifolia2014In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 113, no 2, 267-275 p.Article in journal (Refereed)
    Abstract [en]

    Plantpollinator interactions are thought to have shaped much of floral evolution. Yet the relative importance of pollinator shifts and coevolutionary interactions for among-population variation in floral traits in animal-pollinated species is poorly known. This study examined the adaptive significance of spur length in the moth-pollinated orchid Platanthera bifolia. Geographical variation in the length of the floral spur of P. bifolia was documented in relation to variation in the pollinator fauna across Scandinavia, and a reciprocal translocation experiment was conducted in south-east Sweden between a long-spurred woodland population and a short-spurred grassland population. Spur length and pollinator fauna varied among regions and habitats, and spur length was positively correlated with the proboscis length of local pollinators. In the reciprocal translocation experiment, long-spurred woodland plants had higher pollination success than short-spurred grassland plants at the woodland site, while no significant difference was observed at the grassland site. The results are consistent with the hypothesis that optimal floral phenotype varies with the morphology of the local pollinators, and that the evolution of spur length in P. bifolia has been largely driven by pollinator shifts.

  • 40.
    Bodare, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conservation Genetics and Speciation in Asian Forest Trees2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Tropical forests are important because they are the home of millions of species at the same time as they perform ecosystem services and provide food, cash income and raw materials for the people living there. The present thesis elucidates questions relevant to the conservation of selected forest trees as it adds to the knowledge in the phylogeny, population structure, genetic diversity and adaptation in these species.

    We investigated the genetic diversity and speciation of four spruce species around the Qinghai-Tibetan Plateau (QTP), Western China, and one from Taiwan. Nucleotide diversity was low in P. schrenkiana and the Taiwanese P. morrisonicola but higher in P. likiangensis, P. purpurea and P. wilsonii. This can be explained by the population bottlenecks that were detected in the two former species by coalescent-based analysis. The phylogenetic relationships between the five species were difficult to interpret, possibly because other Asian spruce species might have been involved. However, all species are distinct except P. purpurea, which likely has a hybrid origin. 

    The rate of bud set and expression of the FTL2 gene in response to photoperiod in the southernmost growing spruce species, P. morrisonicola, was studied. We found that in this species, although growing near the equator, bud set appears to be induced mainly by a shortening of photoperiod, similarly to its more northerly growing spruce relatives. In addition, seedlings originating from mother trees growing at higher elevations showed a trend towards earlier bud set than seedlings originating from mother trees at lower altitudes.

    We also studied the population structure and genetic diversity in the endemic white cedar (Dysoxylum malabaricum) in the Western Ghats, India. Overall, no increase in inbreeding that could be related to human activities could be detected. Populations appear to have maintained genetic diversity and gene flow in spite of forest fragmentation over the distribution range. However, there is a severe lack of juveniles and young adults in several populations that needs to be further addressed. Finally, we recommend conservation units based on population structure.

    List of papers
    1. Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    Open this publication in new window or tab >>Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    Show others...
    2010 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 27, no 5, 1001-1014 p.Article in journal (Refereed) Published
    Abstract [en]

    Nucleotide variation at 12 to 16 nuclear loci was studied in three spruce species from the Qinghai-Tibetan Plateau (QTP), Picea likiangensis, P. wilsonii and P. purpurea, and one species from the Tian Shan mountain range, P. schrenkiana. Silent nucleotide diversity was limited in P. schrenkiana and high in the three species from the QTP, with values higher than in boreal spruce species, despite their much more restricted distributions compared to that of the boreal species. In contrast to European boreal species that have experienced severe bottlenecks in the past, coalescent-based analysis suggests that DNA polymorphism in the species from the QTP and adjacent areas is compatible with the standard neutral model (P. likiangensis, P. wilsonii, P. schrenkiana) or with population growth (P. purpurea). In order to test if P. purpurea is a diploid hybrid of P. likiangensis and P. wilsonii, we used a combination of approaches, including model based inference of population structure, Isolation-with-Migration models and recent theoretical results on the effect of introgression on the geographic distribution of diversity. In contrast to the three other species, each of which was predominantly assigned to a single cluster in the Structure analysis, P. purpurea individuals were scattered over the three main clusters and not, as we had expected, confined to the P. likiangensis and P. wilsonii clusters. Furthermore the contribution of P. schrenkiana was by far the largest one. In agreement with this, the divergence between P. purpurea and P. schrenkiana was lower than the divergence of either P. likiangensis or P. wilsonii from P. schrenkiana. These results, together with previous ones showing that P. purpurea and P. wilsonii share the same haplotypes at both chloroplast and mitochondrial markers, suggest that P. purpurea has a complex origin, possibly involving additional species.

    Keyword
    Picea, Qinghai Tibetan Plateau, effective population size, divergence time, introgression, speciation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121399 (URN)10.1093/molbev/msp301 (DOI)000276994800004 ()20031927 (PubMedID)
    Available from: 2010-03-23 Created: 2010-03-23 Last updated: 2017-12-12Bibliographically approved
    2. Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)
    Open this publication in new window or tab >>Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)
    2013 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, 3320-3333 p.Article in journal (Refereed) Published
    Abstract [en]

    Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long-term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3–0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false-positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4–8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.

    National Category
    Natural Sciences Evolutionary Biology
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-198100 (URN)10.1002/ece3.698 (DOI)000324932600011 ()
    Note

    De två (2) första författarna delar förstaförfattarskapet.

    Available from: 2013-04-09 Created: 2013-04-09 Last updated: 2017-12-06Bibliographically approved
    3. Photoperiodic control of bud set and FTL2 expression in a tropical spruce species  (Picea morrisonicola)
    Open this publication in new window or tab >>Photoperiodic control of bud set and FTL2 expression in a tropical spruce species  (Picea morrisonicola)
    (English)Manuscript (preprint) (Other academic)
    National Category
    Natural Sciences
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-198107 (URN)
    Available from: 2013-04-09 Created: 2013-04-09 Last updated: 2013-08-30
    4. Genetic structure and demographic history of the endangered tree species, Dysoxylum  malabaricum (Meliaceae) in Western Ghats, India: Implications for conservation in a  biodiversity hotspot
    Open this publication in new window or tab >>Genetic structure and demographic history of the endangered tree species, Dysoxylum  malabaricum (Meliaceae) in Western Ghats, India: Implications for conservation in a  biodiversity hotspot
    Show others...
    2013 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, 3233-3248 p.Article in journal (Other academic) Published
    Abstract [en]

    The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylummalabaricum (white cedar) is an economically important tree species, endemic to theWestern Ghats, India, one of the world's eight most important biodiversity hotspots. As D.malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-widegenetic structure of twelve D.malabaricum populations was evaluated to assess the impact ofhuman activities on genetic diversity and infer the species' evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (F-IS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred beforethe last glacial maximum. Finally we discussed the implications of these results, in particularthe presence of a clear pattern of historical genetic subdivision, on conservation policies.

    National Category
    Natural Sciences
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-198109 (URN)10.1002/ece3.669 (DOI)000324932600004 ()
    Note

    De två (2) första författarna delar förstaförfattarskapet.

    Available from: 2013-04-09 Created: 2013-04-09 Last updated: 2017-12-06Bibliographically approved
    5. Landscape and fine-scale genetic structure of white cedar (Dysoxylum malabaricum) in disturbed forest patches of the Western Ghats, India
    Open this publication in new window or tab >>Landscape and fine-scale genetic structure of white cedar (Dysoxylum malabaricum) in disturbed forest patches of the Western Ghats, India
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keyword
    Conservation genetics, Dysoxylum malabaricum, fragmentation, land use, spatial genetic structure, Western Ghats
    National Category
    Natural Sciences
    Research subject
    Biology with specialization in Population Biology
    Identifiers
    urn:nbn:se:uu:diva-198700 (URN)
    Funder
    Sida - Swedish International Development Cooperation Agency
    Available from: 2013-04-23 Created: 2013-04-23 Last updated: 2013-08-30
  • 41.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Källman, Thomas
    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.
    Photoperiodic control of bud set and FTL2 expression in a tropical spruce species  (Picea morrisonicola)Manuscript (preprint) (Other academic)
  • 42.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ravikanth, G
    Ashoka Trust for Research in Ecology and the Environment.
    Sascha A, Ismail
    Department of Environmental Systems Science, ETH Zürich.
    Kumara Patel, Mohana
    University of Agricultural Sciences, Bangalore .
    Spanu, Ilaria
    Plant Genetics Institute National Research Council.
    Vasudeva, R
    Dharwad College of Forestry, Campus Karnataka .
    Uma Shaanker, R
    Ashoka Trust for Research in Ecology and the Environment.
    Vendramin, Giovanni Giuseppe
    5Plant Genetics Institute National Research Council.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Landscape and fine-scale genetic structure of white cedar (Dysoxylum malabaricum) in disturbed forest patches of the Western Ghats, IndiaManuscript (preprint) (Other academic)
  • 43.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ravikanth, Gudasalamani
    Ashoka Trust Res Ecol & Environm, Bangalore 560064, Karnataka, India.;Univ Agr Sci, Sch Ecol & Conservat, Bangalore 560065, Karnataka, India..
    Ismail, Sascha A.
    Swiss Fed Inst Technol, Dept Environm Syst Sci, Ecosyst Management, Univ Str 16, CH-8092 Zurich, Switzerland..
    Patel, Mohana Kumara
    Univ Agr Sci, Sch Ecol & Conservat, Bangalore 560065, Karnataka, India..
    Spanu, Ilaria
    CNR, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Vasudeva, Ramesh
    Univ Agr Sci, Dept Forest Biol, Coll Forestry, Sirsi 581401, Karnataka, India..
    Shaanker, Ramanan Uma
    Ashoka Trust Res Ecol & Environm, Bangalore 560064, Karnataka, India.;Univ Agr Sci, Sch Ecol & Conservat, Bangalore 560065, Karnataka, India.;Univ Agr Sci, Dept Crop Physiol, Bangalore 560065, Karnataka, India..
    Vendramin, Giovanni Giuseppe
    CNR, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Tsukuba, Sugadaira Montane Res Ctr, 1278-294 Sugadairakogen, Ueda, Nagano 3862204, Japan..
    Fine- and local- scale genetic structure of Dysoxylum malabaricum, a late-successional canopy tree species in disturbed forest patches in the Western Ghats, India2017In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 18, no 1, 1-15 p.Article in journal (Refereed)
    Abstract [en]

    Dysoxylum malabaricum (white cedar) is an economically important tree species, endemic to the Western Ghats, India, which is the world's most densely populated biodiversity hotspot. In this study, we used variation at ten nuclear simple sequence repeat loci to investigate genetic diversity and fine scale spatial genetic structure (FSGS) in seedlings and adults of D. malabaricum from four forest patches in the northern part of the Western Ghats. When genetic variation was compared between seedlings and adults across locations, significant differences were detected in allelic richness, observed heterozygosity, fixation index (F (IS)), and relatedness (P < 0.05). Reduced genetic diversity and increased relatedness at the seedling stage might be due to fragmentation and disturbance. There was no FSGS at the adult stage and FSGS was limited to shorter distance classes at the seedling stage. However, there was clear spatial genetic structure at the landscape level (< 50 km), regardless of age class, due to limited gene flow between forest patches. A comparison of the distributions of size classes in the four locations with published data from a more southern area, showed that large trees (diameter at breast height, DBH, > 130 cm) are present in the southern sacred forests but not in the northern forest reserves. This pattern is likely due to stronger harvesting pressure in the north compared to the south, because in the north there are no cultural taboos regulating the extraction of natural resources. The implications for forest conservation in this biodiversity hotspot are discussed.

  • 44.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Yang, J-C
    Taiwan Forestry Research Institute.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)2013In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, 3320-3333 p.Article in journal (Refereed)
    Abstract [en]

    Taiwan spruce (Picea morrisonicola) is a vulnerable conifer species endemic to the island of Taiwan. A warming climate and competition from subtropical tree species has limited the range of Taiwan spruce to the higher altitudes of the island. Using seeds sampled from an area in the central mountain range of Taiwan, 15 nuclear loci were sequenced in order to measure genetic variation and to assess the long-term genetic stability of the species. Genetic diversity is low and comparable to other spruce species with limited ranges such as Picea breweriana, Picea chihuahuana, and Picea schrenkiana. Importantly, analysis using approximate Bayesian computation (ABC) provides evidence for a drastic decline in the effective population size approximately 0.3–0.5 million years ago (mya). We used simulations to show that this is unlikely to be a false-positive result due to the limited sample used here. To investigate the phylogenetic origin of Taiwan spruce, additional sequencing was performed in the Chinese spruce Picea wilsonii and combined with previously published data for three other mainland China species, Picea purpurea, Picea likiangensis, and P. schrenkiana. Analysis of population structure revealed that P. morrisonicola clusters most closely with P. wilsonii, and coalescent analyses using the program MIMAR dated the split to 4–8 mya, coincidental to the formation of Taiwan. Considering the population decrease that occurred after the split, however, led to a much more recent origin.

  • 45.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ravikanth, G
    Ashoka Trust for Research in Ecology and the Environment.
    Uma Shaanker, R
    Ashoka Trust for Research in Ecology and the Environment.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genetic structure and demographic history of the endangered tree species, Dysoxylum  malabaricum (Meliaceae) in Western Ghats, India: Implications for conservation in a  biodiversity hotspot2013In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 3, no 10, 3233-3248 p.Article in journal (Other academic)
    Abstract [en]

    The impact of fragmentation by human activities on genetic diversity of forest trees is an important concern in forest conservation, especially in tropical forests. Dysoxylummalabaricum (white cedar) is an economically important tree species, endemic to theWestern Ghats, India, one of the world's eight most important biodiversity hotspots. As D.malabaricum is under pressure of disturbance and fragmentation together with overharvesting, conservation efforts are required in this species. In this study, range-widegenetic structure of twelve D.malabaricum populations was evaluated to assess the impact ofhuman activities on genetic diversity and infer the species' evolutionary history, using both nuclear and chloroplast (cp) DNA simple sequence repeats (SSR). As genetic diversity and population structure did not differ among seedling, juvenile and adult age classes, reproductive success among the old-growth trees and long distance seed dispersal by hornbills were suggested to contribute to maintain genetic diversity. The fixation index (F-IS) was significantly correlated with latitude, with a higher level of inbreeding in the northern populations, possibly reflecting a more severe ecosystem disturbance in those populations. Both nuclear and cpSSRs revealed northern and southern genetic groups with some discordance of their distributions; however, they did not correlate with any of the two geographic gaps known as genetic barriers to animals. Approximate Bayesian computation-based inference from nuclear SSRs suggested that population divergence occurred beforethe last glacial maximum. Finally we discussed the implications of these results, in particularthe presence of a clear pattern of historical genetic subdivision, on conservation policies.

  • 46. Borgegård, S.-O.
    et al.
    Morander, R.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Vegetationen på skär bildade vid Hjälmarsänkningen i hundraårigt perspektiv1987In: Årsbok 1987, Hembygdsföreningen Arboga Minne , 1987Chapter in book (Refereed)
  • 47. Borgegård, S.-O.
    et al.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Biomass, root penetration and heavy metal uptake in birch in a soil cover over copper tailings1989In: Journal of Applied Ecology, Vol. 26, 585-595 p.Article in journal (Refereed)
  • 48. Borgegård, S.-O.
    et al.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Utilization of waste products and inorganic fertilizer in the restoration of iron-mine tailings1989In: Journal of Applied Ecology, Vol. 26, 1083-1088 p.Article in journal (Refereed)
  • 49. Bowman, John L
    et al.
    Kohchi, Takayuki
    Yamato, Katsuyuki T
    Jenkins, Jerry
    Shu, Shengqiang
    Ishizaki, Kimitsune
    Yamaoka, Shohei
    Nishihama, Ryuichi
    Nakamura, Yasukazu
    Berger, Frédéric
    Adam, Catherine
    Aki, Shiori Sugamata
    Althoff, Felix
    Araki, Takashi
    Arteaga-Vazquez, Mario A
    Balasubrmanian, Sureshkumar
    Barry, Kerrie
    Bauer, Diane
    Boehm, Christian R
    Briginshaw, Liam
    Caballero-Perez, Juan
    Catarino, Bruno
    Chen, Feng
    Chiyoda, Shota
    Chovatia, Mansi
    Davies, Kevin M
    Delmans, Mihails
    Demura, Taku
    Dierschke, Tom
    Dolan, Liam
    Dorantes-Acosta, Ana E
    Eklund, D. Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Monash Univ, Sch Biol Sci, Melbourne, Vic 3800, Australia.
    Florent, Stevie N
    Flores-Sandoval, Eduardo
    Fujiyama, Asao
    Fukuzawa, Hideya
    Galik, Bence
    Grimanelli, Daniel
    Grimwood, Jane
    Grossniklaus, Ueli
    Hamada, Takahiro
    Haseloff, Jim
    Hetherington, Alexander J
    Higo, Asuka
    Hirakawa, Yuki
    Hundley, Hope N
    Ikeda, Yoko
    Inoue, Keisuke
    Inoue, Shin-Ichiro
    Ishida, Sakiko
    Jia, Qidong
    Kakita, Mitsuru
    Kanazawa, Takehiko
    Kawai, Yosuke
    Kawashima, Tomokazu
    Kennedy, Megan
    Kinose, Keita
    Kinoshita, Toshinori
    Kohara, Yuji
    Koide, Eri
    Komatsu, Kenji
    Kopischke, Sarah
    Kubo, Minoru
    Kyozuka, Junko
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lin, Shih-Shun
    Lindquist, Erika
    Lipzen, Anna M
    Lu, Chia-Wei
    De Luna, Efraín
    Martienssen, Robert A
    Minamino, Naoki
    Mizutani, Masaharu
    Mizutani, Miya
    Mochizuki, Nobuyoshi
    Monte, Isabel
    Mosher, Rebecca
    Nagasaki, Hideki
    Nakagami, Hirofumi
    Naramoto, Satoshi
    Nishitani, Kazuhiko
    Ohtani, Misato
    Okamoto, Takashi
    Okumura, Masaki
    Phillips, Jeremy
    Pollak, Bernardo
    Reinders, Anke
    Rövekamp, Moritz
    Sano, Ryosuke
    Sawa, Shinichiro
    Schmid, Marc W
    Shirakawa, Makoto
    Solano, Roberto
    Spunde, Alexander
    Suetsugu, Noriyuki
    Sugano, Sumio
    Sugiyama, Akifumi
    Sun, Rui
    Suzuki, Yutaka
    Takenaka, Mizuki
    Takezawa, Daisuke
    Tomogane, Hirokazu
    Tsuzuki, Masayuki
    Ueda, Takashi
    Umeda, Masaaki
    Ward, John M
    Watanabe, Yuichiro
    Yazaki, Kazufumi
    Yokoyama, Ryusuke
    Yoshitake, Yoshihiro
    Yotsui, Izumi
    Zachgo, Sabine
    Schmutz, Jeremy
    Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome2017In: Cell, ISSN 0092-8674, E-ISSN 1097-4172, Vol. 171, no 2, 287-304.15 p.Article in journal (Refereed)
    Abstract [en]

    The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant. PAPERCLIP.

  • 50.
    Breed, Martin F.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ottewell, K. M.
    Gardner, M. G.
    Marklund, Maria H. K.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Dormontt, E. E.
    Lowe, A. J.
    Mating patterns and pollinator mobility are critical traits in forest fragmentation genetics2015In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 115, no 2, 108-114 p.Article in journal (Refereed)
    Abstract [en]

    Most woody plants are animal-pollinated, but the global problem of habitat fragmentation is changing the pollination dynamics. Consequently, the genetic diversity and fitness of the progeny of animal-pollinated woody plants sired in fragmented landscapes tend to decline due to shifts in plant-mating patterns (for example, reduced outcrossing rate, pollen diversity). However, the magnitude of this mating-pattern shift should theoretically be a function of pollinator mobility. We first test this hypothesis by exploring the mating patterns of three ecologically divergent eucalypts sampled across a habitat fragmentation gradient in southern Australia. We demonstrate increased selfing and decreased pollen diversity with increased fragmentation for two small-insect-pollinated eucalypts, but no such relationship for the mobile-bird-pollinated eucalypt. In a meta-analysis, we then show that fragmentation generally does increase selfing rates and decrease pollen diversity, and that more mobile pollinators tended to dampen these mating-pattern shifts. Together, our findings support the premise that variation in pollinator form contributes to the diversity of mating-pattern responses to habitat fragmentation.

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