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  • 101.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Li, Lili
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jansson, Gunnar
    Forestry Res Inst Sweden Skogforsk, Uppsala, Sweden.
    Berlin, Mats
    Forestry Res Inst Sweden Skogforsk, Uppsala, Sweden.
    Karlsson, Bo
    Forestry Res Inst Sweden Skogforsk, Ekebo, Sweden.
    Aleksic, Jelena
    Univ Belgrade, Inst Mol Genet & Genet Engn, Belgrade, Serbia.
    Vendramin, Giovanni G.
    CNR, Natl Res Council IBBR, Div Florence, Inst Biosci & BioResources, Sesto Fiorentino, Italy.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce2019In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 12, no 8, p. 1539-1551Article in journal (Refereed)
    Abstract [en]

    Primeval forests are today exceedingly rare in Europe, and transfer of forest reproductive material for afforestation and improvement has been very common, especially over the last two centuries. This can be a serious impediment when inferring past population movements in response to past climate changes such as the last glacial maximum (LGM), some 18,000 years ago. In the present study, we genotyped 1,672 individuals from three Picea species (P. abies, P. obovata, and P. omorika) at 400K SNPs using exome capture to infer the past demographic history of Norway spruce (P. abies) and estimate the amount of recent introduction used to establish the Norway spruce breeding program in southern Sweden. Most of these trees belong to P. abies and originate from the base populations of the Swedish breeding program. Others originate from populations across the natural ranges of the three species. Of the 1,499 individuals stemming from the breeding program, a large proportion corresponds to recent introductions from mainland Europe. The split of P. omorika occurred 23 million years ago (mya), while the divergence between P. obovata and P. abies began 17.6 mya. Demographic inferences retrieved the same main clusters within P. abies than previous studies, that is, a vast northern domain ranging from Norway to central Russia, where the species is progressively replaced by Siberian spruce (P. obovata) and two smaller domains, an Alpine domain and a Carpathian one, but also revealed further subdivision and gene flow among clusters. The three main domains divergence was ancient (15 mya), and all three went through a bottleneck corresponding to the LGM. Approximately 17% of P. abies Nordic domain migrated from P. obovata ~103K years ago, when both species had much larger effective population sizes. Our analysis of genomewide polymorphism data thus revealed the complex demographic history of Picea genus in Western Europe and highlighted the importance of material transfer in Swedish breeding program.

  • 102.
    Chen, Jun
    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.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kallman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Xu, Nannan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Karkkainen, Katri
    Huotari, Tea
    Semerikov, Vladimir L.
    Vendramin, Giovanni G.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Clinal Variation at Phenology-Related Genes in Spruce: Parallel Evolution in FTL2 and Gigantea?2014In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 197, no 3, p. 1025-1038Article in journal (Refereed)
    Abstract [en]

    Parallel clines in different species, or in different geographical regions of the same species, are an important source of information on the genetic basis of local adaptation. We recently detected latitudinal clines in SNPs frequencies and gene expression of candidate genes for growth cessation in Scandinavian populations of Norway spruce (Picea abies). Here we test whether the same clines are also present in Siberian spruce (P. obovata), a close relative of Norway spruce with a different Quaternary history. We sequenced nine candidate genes and 27 control loci and genotyped 14 SSR loci in six populations of P. obovata located along the Yenisei river from latitude 56 N to latitude 67 N. In contrast to Scandinavian Norway spruce that both departs from the standard neutral model (SNM) and shows a clear population structure, Siberian spruce populations along the Yenisei do not depart from the SNM and are genetically unstructured. Nonetheless, as in Norway spruce, growth cessation is significantly clinal. Polymorphisms in photoperiodic (FTL2) and circadian clock (Gigantea, GI, PRR3) genes also show significant clinal variation and/or evidence of local selection. In GI, one of the variants is the same as in Norway spruce. Finally, a strong cline in gene expression is observed for FTL2, but not for GI. These results, together with recent physiological studies, confirm the key role played by FTL2 and circadian clock genes in the control of growth cessation in spruce species and suggest the presence of parallel adaptation in these two species.

  • 103.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tsuda, Yoshiaki
    CNR, Plant Genetics Institute, Sesto Fiorentino, Firenze, Italy.
    Stocks, Michael
    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.
    Semerikov, Vladimir
    Institute of Plant and Animal Ecology, Ural Division of the Russian Academy of Sciences.
    Vendramin, Giovanni
    CNR, Plant Genetics Institute, Sesto Fiorentino, Firenze, Italy.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Clinal variation in allele frequency at photoperiodic genes in Siberian spruce: an example of convergent evolution?Manuscript (preprint) (Other academic)
  • 104.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tsuda, Yoshiaki
    CNR, Plant Genetics Institute, Sesto Fiorentino, Firenze, Italy.
    Stocks, Michael
    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.
    Xu, Nannan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Semerikov, Vladimir
    Institute of Plant and Animal Ecology, Ural Division of the Russian Academy of Sciences.
    Vendramin, Giovanni
    CNR, Plant Genetics Institute, Sesto Fiorentino, Firenze, Italy.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Clinal variation in allele frequency and gene expression at photoperiodic and circadian genes in Siberian spruce: an example of parallel evolution?Manuscript (preprint) (Other academic)
  • 105.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Uebbing, Severin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gyllenstrand, Niclas
    Department of Plant Biology and Forest Genetics, Swedish University of Agriculture Science.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    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.
    Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms compared to angiosperms2012In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 13, p. 589-Article in journal (Other academic)
    Abstract [en]

    Background: A detailed knowledge about which genes are expressed in which tissues and at which developmental stage is important for understanding both the function of genes and their evolution. For the vast majority of species, transcriptomes are still largely uncharacterized and even in those where substantial information is available it is often in the form of partially sequenced transcriptomes. With the development of next generation sequencing, a single experiment can now give both a snap-shot of the transcribed part of a species genome and simultaneously estimate levels of gene expression.

    Results: mRNA from actively growing needles of Norway spruce (Picea abies) was sequenced using next generation sequencing technology. In total, close to 70 million fragments with a length of 76 bp were sequenced resulting in 5 Gbp of raw data. A de novo assembly of these reads were, together with publicly available expressed sequence tag (EST) data from Norway spruce, used to create a reference transcriptome. Of the 38,419 PUTs (putative unique transcripts) longer than 150 bp in this reference assembly, 59% show similarity to ESTs from other spruce species and of the remaining PUTs, 3,704 show similarity to protein sequences from other plant species, leaving 4,167 PUTs with limited similarity to currently available plant proteins. By predicting coding frames and comparing not only the Norway spruce PUTs, but also PUTs from the close relatives Picea glauca and Picea sitchensis to both Pinus taeda and Taxus mairei, we obtained estimates of synonymous and non-synonymous divergence among conifer species. In addition, we detected close to 15,000 SNPs of high quality and estimated gene expression difference between samples collected during dark and light conditions.

    Conclusions: Our study yielded a large number of single nucleotide polymorphisms as well as estimates of gene expression on transcriptome scale. In agreement with a recent study we find that the synonymous substitution rate per year (0.6 × 10-09 and 1.1 × 10-09) is an order of magnitude smaller than values reported for angiosperm herbs, but if one takes generation time in to account, most of this difference disappear. The estimates of the non-synonymous over the synonymous divergence (dN/dS ratio) reported here is in general much lower than 1 and only a few genes showed a ratio larger than 1.

  • 106.
    Cherif, E.
    et al.
    Ctr IRD, UMR DIADE, IRD CIRAD Palm Grp F2F, 911 Ave Agropolis, F-34394 Montpellier, France.;Univ Tunis El Manar, Fac Sci Tunis, Lab Genet Mol Immunol & Biotechnol, El Manar, Tunisia..
    Zehdi-Azouzi, S.
    Univ Tunis El Manar, Fac Sci Tunis, Lab Genet Mol Immunol & Biotechnol, El Manar, Tunisia..
    Crabos, A.
    Ctr IRD, UMR DIADE, IRD CIRAD Palm Grp F2F, 911 Ave Agropolis, F-34394 Montpellier, France..
    Castillo, K.
    Ctr IRD, UMR DIADE, IRD CIRAD Palm Grp F2F, 911 Ave Agropolis, F-34394 Montpellier, France..
    Chabrillange, N.
    Ctr IRD, UMR DIADE, IRD CIRAD Palm Grp F2F, 911 Ave Agropolis, F-34394 Montpellier, France..
    Pintaud, J. -C
    Salhi-Hannachi, A.
    Univ Tunis El Manar, Fac Sci Tunis, Lab Genet Mol Immunol & Biotechnol, El Manar, Tunisia..
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Unite Mixte Rech 5554 Univ Montpellier CNRS IRD E, Inst Sci Evolut Montpellier, Montpellier, France..
    Aberlenc-Bertossi, F.
    Ctr IRD, UMR DIADE, IRD CIRAD Palm Grp F2F, 911 Ave Agropolis, F-34394 Montpellier, France..
    Evolution of sex chromosomes prior to speciation in the dioecious Phoenix species2016In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 29, no 8, p. 1513-1522Article in journal (Refereed)
    Abstract [en]

    Understanding the driving forces and molecular processes underlying dioecy and sex chromosome evolution, leading from hermaphroditism to the occurrence of male and female individuals, is of considerable interest in fundamental and applied research. The genus Phoenix, belonging to the Arecaceae family, consists uniquely of dioecious species. Phylogenetic data suggest that the genus Phoenix has diverged from a hermaphroditic ancestor which is also shared with its closest relatives. We have investigated the cessation of recombination in the sex-determination region within the genus Phoenix as a whole by extending the analysis of P.dactylifera SSR sex-related loci to eight other species within the genus. Phylogenetic analysis of a date palm sex-linked PdMYB1 gene in these species has revealed that sex-linked alleles have not clustered in a species-dependent way but rather in X and Y-allele clusters. Our data show that sex chromosomes evolved from a common autosomal origin before the diversification of the extant dioecious species.

  • 107.
    Clement, Yves
    et al.
    Montpellier SupAgro, UMR AGAP, Montpellier, France.;Univ Montpellier, CNRS IRD EPHE, UMR ISEM 5554, Montpellier, France.;PSL Res Univ, Ecole Normale Super, CNRS, IBENS,INSERM, Paris, France..
    Sarah, Gautier
    INRA, UMR AGAP, Montpellier, France.;SouthGreen Platform, Montpellier, France..
    Holtz, Yan
    Montpellier SupAgro, UMR AGAP, Montpellier, France..
    Homa, Felix
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. SouthGreen Platform, Montpellier, France..
    Pointet, Stephanie
    SouthGreen Platform, Montpellier, France.;CIRAD, UMR AGAP, Montpellier, France.;ALCEDIAG CNRS Sys2Diag FRE3690, Biol Complex Syst Modelling & Engn Diag, Montpellier, France..
    Contreras, Sandy
    SouthGreen Platform, Montpellier, France.;GenoScreen, Lille, France..
    Nabholz, Benoit
    Univ Montpellier, CNRS IRD EPHE, UMR ISEM 5554, Montpellier, France..
    Sabot, Francois
    SouthGreen Platform, Montpellier, France.;IRD, UMR DIADE, Montpellier, France..
    Saune, Laure
    INRA, CBGP UMR1062, Montferrier Sur Lez, France..
    Ardisson, Morgane
    INRA, UMR AGAP, Montpellier, France..
    Bacilieri, Roberto
    INRA, UMR AGAP, Montpellier, France..
    Besnard, Guillaume
    Univ Toulouse III, CNRS ENSFEA IRD, UMR EDB 5174, Toulouse, France..
    Berger, Angelique
    CIRAD, UMR AGAP, Montpellier, France..
    Cardi, Celine
    CIRAD, UMR AGAP, Montpellier, France..
    De Bellis, Fabien
    CIRAD, UMR AGAP, Montpellier, France..
    Fouet, Olivier
    CIRAD, UMR AGAP, Montpellier, France..
    Jourda, Cyril
    CIRAD, UMR AGAP, Montpellier, France.;CIRAD, UMR PVBMT, St Pierre, Reunion, France..
    Khadari, Bouchaib
    INRA, UMR AGAP, Montpellier, France..
    Lanaud, Claire
    CIRAD, UMR AGAP, Montpellier, France..
    Leroy, Thierry
    CIRAD, UMR AGAP, Montpellier, France..
    Pot, David
    Sauvage, Christopher
    INRA, GAFL UR1052, Montfavet, France..
    Scarcelli, Nora
    IRD, UMR DIADE, Montpellier, France..
    Tregear, James
    IRD, UMR DIADE, Montpellier, France..
    Vigouroux, Yves
    IRD, UMR DIADE, Montpellier, France..
    Yahiaoui, Nabila
    CIRAD, UMR AGAP, Montpellier, France..
    Ruiz, Manuel
    SouthGreen Platform, Montpellier, France.;CIRAD, UMR AGAP, Montpellier, France..
    Santoni, Sylvain
    INRA, UMR AGAP, Montpellier, France..
    Labouisse, Jean-Pierre
    CIRAD, UMR AGAP, Montpellier, France..
    Pham, Jean-Louis
    IRD, UMR DIADE, Montpellier, France..
    David, Jacques
    Montpellier SupAgro, UMR AGAP, Montpellier, France..
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Montpellier.
    Evolutionary forces affecting synonymous variations in plant genomes2017In: PLoS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 13, no 5, article id e1006799Article in journal (Refereed)
    Abstract [en]

    Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.

  • 108.
    Clergeot, Pierre-Henri
    et al.
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, SE-75007 Uppsala, Sweden.
    Rode, Nicolas O.
    Univ Montpellier, Montpellier SupAgro, IRD, CBGP,INRA,Ctr Cooperat Int Rech Agron Dev CIRAD, F-34988 Montpellier, France.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Rennes, CNRS, ECOBIO Ecosyst Biodiversite Evolut UMR 6553, F-35000 Rennes, France.
    Durling, Mikael Brandstrom
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, SE-75007 Uppsala, Sweden.
    Ihrmark, Katarina
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, SE-75007 Uppsala, Sweden.
    Olson, Ake
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, SE-75007 Uppsala, Sweden.
    Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum2019In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 211, no 3, p. 963-976Article in journal (Refereed)
    Abstract [en]

    Many eukaryote species, including taxa such as fungi or algae, have a lifecycle with substantial haploid and diploid phases. A recent theoretical model predicts that such haploid-diploid lifecycles are stable over long evolutionary time scales when segregating deleterious mutations have stronger effects in homozygous diploids than in haploids and when they are partially recessive in heterozygous diploids. The model predicts that effective dominance-a measure that accounts for these two effects-should be close to 0.5 in these species. It also predicts that diploids should have higher fitness than haploids on average. However, an appropriate statistical framework to conjointly investigate these predictions is currently lacking. In this study, we derive a new quantitative genetic model to test these predictions using fitness data of two haploid parents and their diploid offspring, and genome-wide genetic distance between haploid parents. We apply this model to the root-rot basidiomycete fungus Heterobasidion parviporum-a species where the heterokaryotic (equivalent to the diploid) phase is longer than the homokaryotic (haploid) phase. We measured two fitness-related traits (mycelium growth rate and the ability to degrade wood) in both homokaryons and heterokaryons, and we used whole-genome sequencing to estimate nuclear genetic distance between parents. Possibly due to a lack of power, we did not find that deleterious mutations were recessive or more deleterious when expressed during the heterokaryotic phase. Using this model to compare effective dominance among haploid-diploid species where the relative importance of the two phases varies should help better understand the evolution of haploid-diploid life cycles.

  • 109.
    Colautti, Robert I.
    et al.
    Queens Univ, Dept Biol, 116 Barrie St, Kingston, ON K7L 3N6, Canada..
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Anderson, Jill T.
    Univ Georgia, Dept Genet, 120 Green St, Athens, GA 30602 USA.;Univ Georgia, Odum Sch Ecol, 120 Green St, Athens, GA 30602 USA..
    Phenological shifts of native and invasive species under climate change: insights from the Boechera - Lythrum model2017In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 372, no 1712, article id 20160032Article, review/survey (Refereed)
    Abstract [en]

    Warmer and drier climates have shifted phenologies of many species. However, the magnitude and direction of phenological shifts vary widely among taxa, and it is often unclear when shifts are adaptive or how they affect long-term viability. Here, we model evolution of flowering phenology based on our long-term research of two species exhibiting opposite shifts in floral phenology: Lythrum salicaria, which is invasive in North America, and the sparse Rocky Mountain native Boechera stricta. Genetic constraints are similar in both species, but differences in the timing of environmental conditions that favour growth lead to opposite phenological shifts under climate change. As temperatures increase, selection is predicted to favour earlier flowering in native B. stricta while reducing population viability, even if populations adapt rapidly to changing environmental conditions. By contrast, warming is predicted to favour delayed flowering in both native and introduced L. salicaria populations while increasing long-term viability. Relaxed selection from natural enemies in invasive L. salicaria is predicted to have little effect on flowering time but a large effect on reproductive fitness. Our approach highlights the importance of understanding ecological and genetic constraints to predict the ecological consequences of evolutionary responses to climate change on contemporary timescales. This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'.

  • 110.
    Corcoran, Padraic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England.
    Anderson, Jennifer L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Jacobson, David J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Sun, Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ni, Peixiang
    BGI HongKong, Hong Kong, Hong Kong, Peoples R China.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma.2016In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 26, no 4, p. 486-498Article in journal (Refereed)
    Abstract [en]

    Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora tetrasperma, it has been proposed that this molecular degeneration is counteracted by the introgression of nondegenerated DNA from closely related species. In this study, we used comparative and population genomic analyses of 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma, and its three closest relatives, to investigate the factors shaping the evolutionary history of the genomes. We found that suppressed recombination extends across at least 6 Mbp (similar to 63%) of the mating-type (mat) chromosome in N. tetrasperma and is associated with decreased genetic diversity, which is likely the result primarily of selection at linked sites. Furthermore, analyses of molecular evolution revealed an increased mutational load in this region, relative to recombining regions. However, comparative genomic and phylogenetic analyses indicate that the mat chromosomes are temporarily regenerated via introgression from sister species; six of eight lineages show introgression into one of their mat chromosomes, with multiple Neurospora species acting as donors. The introgressed tracts have been fixed within lineages, suggesting that they confer an adaptive advantage in natural populations, and our analyses support the presence of selective sweeps in at least one lineage. Thus, these data strongly support the previously hypothesized role of introgression as a mechanism for the maintenance of mating-type determining chromosomal regions.

  • 111.
    Corcoran, Pádraic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Chen, Fen
    BGI, Hong Kong.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ni, Peixang
    BGI, Hong Kong.
    Johanesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Adaptive introgression slows down molecular degeneration of the mating-type chromosome in Neurospora tetraspermaManuscript (preprint) (Other academic)
  • 112.
    Corcoran, Pádraic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dettman, Jeremy
    University of Ottawa.
    Sun, Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Luque, Eva
    Universidad de Sevilla.
    Corrochano, Luis
    Universidad de Sevilla.
    Taylor, John
    University of California Berkeley.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A global multilocus analysis of the model fungus Neurospora reveals a single recent origin of a novel genetic system2014In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 78, p. 136-147Article in journal (Refereed)
    Abstract [en]

    The large diversity of mating systems observed in the fungal kingdom underlines the importance of mating system change in fungal evolution. The selfing species Neurospora tetrasperma has evolved a novel method of achieving self-fertility by a mating system referred to as pseudohomothallism. However, little is known about the origin of N. tetrasperma and its relationship to the self-sterile, heterothallic, Neurospora species. In this study, we used a combination of phylogenetic and population genetic analyses to reconstruct the evolutionary history of N. tetrasperma and its heterothallic relatives. We sequenced 9 unlinked nuclear loci from 106 strains of N. tetrasperma sampled from across the globe, and a sample of 28 heterothallic strains of Neurospora. Our analyses provide strong support for monophyly of N. tetrasperma, but reject the monophyly of N. crassa. We estimate that N. tetrasperma is of a recent origin and that it diverged from the heterothallic species ~1 million years ago. We also extend previous findings on the diversification within the N. tetrasperma clade, with 10 lineages identified. Taken together, these findings indicate that N. tetrasperma is younger than has been previously reported and that a rapid diversification of lineages has occurred within the N. tetrasperma clade.

  • 113.
    Cornille, Amandine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Feurtey, Alice
    Gelin, Uriel
    Ropars, Jeanne
    Misvanderbrugge, Kristine
    Gladieux, Pierre
    Giraud, Tatiana
    Anthropogenic and natural drivers of gene flow in a temperate wild fruit tree: a basis for conservation and breeding programs in apples2015In: Evolutionary Applications, ISSN 1752-4571, E-ISSN 1752-4571, Vol. 8, no 4, p. 373-384Article in journal (Refereed)
    Abstract [en]

    Gene flow is an essential component of population adaptation and species evolution. Understanding of the natural and anthropogenic factors affecting gene flow is also critical for the development of appropriate management, breeding, and conservation programs. Here, we explored the natural and anthropogenic factors impacting crop-to-wild and within wild gene flow in apples in Europe using an unprecedented dense sampling of 1889 wild apple (Malus sylvestris) from European forests and 339 apple cultivars (Malus domestica). We made use of genetic, environmental, and ecological data (microsatellite markers, apple production across landscapes and records of apple flower visitors, respectively). We provide the first evidence that both human activities, through apple production, and human disturbance, through modifications of apple flower visitor diversity, have had a significant impact on crop-to-wild interspecific introgression rates. Our analysis also revealed the impact of previous natural climate change on historical gene flow in the nonintrogressed wild apple M.sylvestris, by identifying five distinct genetic groups in Europe and a north-south gradient of genetic diversity. These findings identify human activities and climate as key drivers of gene flow in a wild temperate fruit tree and provide a practical basis for conservation, agroforestry, and breeding programs for apples in Europe.

  • 114.
    Cornille, Amandine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Salcedo, A.
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M6R 1M3, Canada..
    Kryvokhyzha, Dmytro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wright, S. I.
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M6R 1M3, Canada..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 2, p. 616-629Article in journal (Refereed)
    Abstract [en]

    Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa-pastoris) is one of the most common weed species in the world. It is highly self-fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C.bursa-pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C.bursa-pastoris accessions spread across Europe, the Middle East and Asia, using genotyping-by-sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C.bursa-pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human-mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C.bursa-pastoris and highlight ABC and genotyping-by-sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.

  • 115.
    Cortes, Andres J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Monserrate, Fredy A.
    Ramirez-Villegas, Julian
    Madrinan, Santiago
    Blair, Matthew W.
    Drought Tolerance in Wild Plant Populations: The Case of Common Beans (Phaseolus vulgaris L.)2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 5, p. e62898-Article in journal (Refereed)
    Abstract [en]

    Reliable estimations of drought tolerance in wild plant populations have proved to be challenging and more accessible alternatives are desirable. With that in mind, an ecological diversity study was conducted based on the geographical origin of 104 wild common bean accessions to estimate drought tolerance in their natural habitats. Our wild population sample covered a range of mesic to very dry habitats from Mexico to Argentina. Two potential evapotranspiration models that considered the effects of temperature and radiation were coupled with the precipitation regimes of the last fifty years for each collection site based on geographical information system analysis. We found that wild accessions were distributed among different precipitation regimes following a latitudinal gradient and that habitat ecological diversity of the collection sites was associated with natural sub-populations. We also detected a broader geographic distribution of wild beans across ecologies compared to cultivated common beans in a reference collection of 297 cultivars. Habitat drought stress index based on the Thornthwaite potential evapotranspiration model was equivalent to the Hamon estimator. Both ecological drought stress indexes would be useful together with population structure for the genealogical analysis of gene families in common bean, for genome-wide genetic-environmental associations, and for postulating the evolutionary history and diversification processes that have occurred for the species. Finally, we propose that wild common bean should be taken into account to exploit variation for drought tolerance in cultivated common bean which is generally considered susceptible as a crop to drought stress.

  • 116.
    Cortes, Andres J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    This, Dominique
    Chavarro, Carolina
    Madrinan, Santiago
    Blair, Matthew W.
    Nucleotide diversity patterns at the drought-related DREB2 encoding genes in wild and cultivated common bean (Phaseolus vulgaris L.)2012In: Theoretical and Applied Genetics, ISSN 0040-5752, E-ISSN 1432-2242, Vol. 125, no 5, p. 1069-1085Article in journal (Refereed)
    Abstract [en]

    Common beans are an important food legume faced with a series of abiotic stresses the most severe of which is drought. The crop is interesting as a model for the analysis of gene phylogenies due to its domestication process, race structure, and origins in a group of wild common beans found along the South American Andes and the region of Mesoamerica. Meanwhile, the DREB2 transcription factors have been implicated in controlling non-ABA dependent responses to drought stress. With this in mind our objective was to study in depth the genetic diversity for two DREB2 genes as possible candidates for association with drought tolerance through a gene phylogenetic analysis. In this genetic diversity assessment, we analyzed nucleotide diversity at the two candidate genes Dreb2A and Dreb2B, in partial core collections of 104 wild and 297 cultivated common beans with a total of 401 common bean genotypes from world-wide germplasm analyzed. Our wild population sample covered a range of semi-mesic to very dry habitats, while our cultivated samples presented a wide spectrum of low to high drought tolerance. Both genes showed very different patterns of nucleotide variation. Dreb2B exhibited very low nucleotide diversity relative to neutral reference loci previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, Dreb2A exhibited higher levels of nucleotide diversity, which is indicative of adaptive selection and population expansion. These patterns were more distinct in wild compared to cultivated common beans. These approximations suggested the importance of Dreb2 genes in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits. We discuss the utility of allele mining in the DREB gene family for the discovery of new drought tolerance traits from wild common bean.

  • 117.
    Cortes, Andres J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Waeber, S.
    Lexer, C.
    Sedlacek, J.
    Wheeler, J. A.
    van Kleunen, M.
    Bossdorf, O.
    Hoch, G.
    Rixen, C.
    Wipf, S.
    Karrenberg, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Small-scale patterns in snowmelt timing affect gene flow and the distribution of genetic diversity in the alpine dwarf shrub Salix herbacea2014In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 113, no 3, p. 233-239Article in journal (Refereed)
    Abstract [en]

    Current threats to biodiversity, such as climate change, are thought to alter the within-species genetic diversity among microhabitats in highly heterogeneous alpine environments. Assessing the spatial organization and dynamics of genetic diversity within species can help to predict the responses of organisms to environmental change. In this study, we evaluated whether small-scale heterogeneity in snowmelt timing restricts gene flow between microhabitats in the common long-lived dwarf shrub Salix herbacea L. We surveyed 273 genets across 12 early-and late-snowmelt sites (that is, ridges and snowbeds) in the Swiss Alps for phenological variation over 2 years and for genetic variation using seven SSR markers. Phenological differentiation triggered by differences in snowmelt timing did not correlate with genetic differentiation between microhabitats. On the contrary, extensive gene flow appeared to occur between microhabitats and slightly less extensively among adjacent mountains. However, ridges exhibited significantly lower levels of genetic diversity than snowbeds, and patterns of effective population size (Ne) and migration (Nem) between microhabitats were strongly asymmetric, with ridges acting as sources and snowbeds as sinks. As no recent genetic bottlenecks were detected in the studied sites, this asymmetry is likely to reflect current metapopulation dynamics of the species dominated by gene flow via seeds rather than ancient re-colonization after the last glacial period. Overall, our results suggest that seed dispersal prevents snowmelt-driven genetic isolation, and snowbeds act as sinks of genetic diversity. We discuss the consequences of such small-scale variation in gene flow and diversity levels for population responses to climate change.

  • 118.
    Cortés, Andres J,
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    On the origin of the Common Bean (Phaseolus vulgaris L.)2013In: American Journal of Plant Sciences, ISSN 2158-2742, E-ISSN 2158-2750, Vol. 4, no 10, p. 1998-2000Article in journal (Refereed)
    Abstract [en]

    Phylogeographic methods provide the tools to accurately access the geographic origin and diversification of crop species. In the present commentary, I urge the common bean community to face those methods and a tree-thinking mentality with regards to the long standing debate of the origin of common bean. Such efforts will ultimately bring back interest into wild bean studies and reinforce the uniqueness of this species as a system to study diversification, domestication and adaptive processes across the two most diverse hotspots in the world.

  • 119.
    Cortés, Andrés
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genome-wide patterns of microhabitat-driven divergence in the alpine dwarf shrub Salix herbacea L.Manuscript (preprint) (Other academic)
  • 120.
    Cortés, Andrés
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Maintenance of female-bias in a polygenic sex determination system is consistent with genomic conflictManuscript (preprint) (Other academic)
  • 121.
    Cortés, Andrés J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    On The Big Challenges of a Small Shrub: Ecological Genetics of Salix herbacea L2015Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The response of plants to climate change is among the main questions in ecology and evolution. Faced with changing conditions, populations may respond by adapting, going extinct or migrating. Fine-scale environmental variation offers a unique mosaic to explore these alternatives. In this thesis, I used ecological surveys, field experiments and molecular methods to study the range of possible responses at a very local scale in the alpine dwarf willow Salix herbacea L. Since gene flow may impact the potential for adaptation and migration, I first explored whether phenological divergence driven by snowmelt patterns impacts gene flow. I found that sites with late snowmelt work as sinks of the genetic diversity, as compared to sites with early snowmelt. I also used a combined approach that looked at the selection, heritability and genomic architecture of ecologically-relevant traits, as well as genomic divergence across the snowmelt mosaic. In this way, I was able to understand which genomic regions may relate to phenological, growth and fitness traits, and which regions in the genome harbor genetic variation associated with late- and early- snowmelt sites. I found that most of the genomic divergence driven by snowmelt is novel and is localized in few regions. Also, Salix herbacea has a strong female bias. Sex bias may matter for adaptation to climate change because different sexes of many dioecious species differ in several functions that may fluctuate with changing conditions. I found that the bias is uniform across environments and is already present at seeds and seedlings. A polygenic sex determination system together with transmission distortion may be maintaining the bias. Overall, fast-evolving microhabitat-driven genomic divergence and, at the same time, genetically-based trait variation at a larger scale may play a role for the ability of S. herbacea to persist in diverse and variable conditions.

    List of papers
    1. Small-scale patterns in snowmelt timing affect gene flow and the distribution of genetic diversity in the alpine dwarf shrub Salix herbacea
    Open this publication in new window or tab >>Small-scale patterns in snowmelt timing affect gene flow and the distribution of genetic diversity in the alpine dwarf shrub Salix herbacea
    Show others...
    2014 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 113, no 3, p. 233-239Article in journal (Refereed) Published
    Abstract [en]

    Current threats to biodiversity, such as climate change, are thought to alter the within-species genetic diversity among microhabitats in highly heterogeneous alpine environments. Assessing the spatial organization and dynamics of genetic diversity within species can help to predict the responses of organisms to environmental change. In this study, we evaluated whether small-scale heterogeneity in snowmelt timing restricts gene flow between microhabitats in the common long-lived dwarf shrub Salix herbacea L. We surveyed 273 genets across 12 early-and late-snowmelt sites (that is, ridges and snowbeds) in the Swiss Alps for phenological variation over 2 years and for genetic variation using seven SSR markers. Phenological differentiation triggered by differences in snowmelt timing did not correlate with genetic differentiation between microhabitats. On the contrary, extensive gene flow appeared to occur between microhabitats and slightly less extensively among adjacent mountains. However, ridges exhibited significantly lower levels of genetic diversity than snowbeds, and patterns of effective population size (Ne) and migration (Nem) between microhabitats were strongly asymmetric, with ridges acting as sources and snowbeds as sinks. As no recent genetic bottlenecks were detected in the studied sites, this asymmetry is likely to reflect current metapopulation dynamics of the species dominated by gene flow via seeds rather than ancient re-colonization after the last glacial period. Overall, our results suggest that seed dispersal prevents snowmelt-driven genetic isolation, and snowbeds act as sinks of genetic diversity. We discuss the consequences of such small-scale variation in gene flow and diversity levels for population responses to climate change.

    National Category
    Genetics Ecology
    Identifiers
    urn:nbn:se:uu:diva-232992 (URN)10.1038/hdy.2014.19 (DOI)000341087900006 ()
    Available from: 2014-10-13 Created: 2014-09-29 Last updated: 2019-03-11Bibliographically approved
    2. Evolutionary potential in the Alpine: trait heritabilities and performance variation of the dwarf willow Salix herbacea from different elevations and microhabitats
    Open this publication in new window or tab >>Evolutionary potential in the Alpine: trait heritabilities and performance variation of the dwarf willow Salix herbacea from different elevations and microhabitats
    Show others...
    2016 (English)In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 6, no 12, p. 3940-3952Article in journal (Refereed) Published
    Abstract [en]

    Alpine ecosystems are seriously threatened by climate change. One of the key mechanisms by which plants can adapt to changing environmental conditions is through evolutionary change. However, we still know little about the evolutionary potential in wild populations of long-lived alpine plants. Here, we investigated heritabilities of phenological traits, leaf size, and performance traits in natural populations of the long-lived alpine dwarf shrub Salix herbacea using relatedness estimates inferred from SSR (Simple Sequence Repeat) markers. Salix herbacea occurs in early-and late-snowmelt microhabitats (ridges and snowbeds), and we assessed how performance consequences of phenological traits and leaf size differ between these microhabitats in order to infer potential for evolutionary responses. Salix herbacea showed low, but significant, heritabilities of leaf size, clonal and sexual reproduction, and moderate heritabilities of phenological traits. In both microhabitats, we found that larger leaves, longer intervals between snowmelt and leaf expansion, and longer GDD (growing-degree days) until leaf expansion resulted in a stronger increase in the number of stems (clonal reproduction). In snowbeds, clonal reproduction increased with a shorter GDD until flowering, while the opposite was found on ridges. Furthermore, the proportion of flowering stems increased with GDD until flowering in both microhabitats. Our results suggest that the presence of significant heritable variation in morphology and phenology might help S. herbacea to adapt to changing environmental conditions. However, it remains to be seen if the rate of such an evolutionary response can keep pace with the rapid rate of climate change.

    Keywords
    Adaptive evolution; alpine ecosystem; animal model; long-lived plants; snowmelt microhabitats; SSR markers
    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-262237 (URN)10.1002/ece3.2171 (DOI)000379342900008 ()
    Available from: 2015-09-10 Created: 2015-09-10 Last updated: 2019-03-11Bibliographically approved
    3. Genome-wide patterns of microhabitat-driven divergence in the alpine dwarf shrub Salix herbacea L.
    Open this publication in new window or tab >>Genome-wide patterns of microhabitat-driven divergence in the alpine dwarf shrub Salix herbacea L.
    (English)Manuscript (preprint) (Other academic)
    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-262229 (URN)
    Available from: 2015-09-10 Created: 2015-09-10 Last updated: 2015-11-23
    4. Maintenance of female-bias in a polygenic sex determination system is consistent with genomic conflict
    Open this publication in new window or tab >>Maintenance of female-bias in a polygenic sex determination system is consistent with genomic conflict
    (English)Manuscript (preprint) (Other academic)
    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-262230 (URN)
    Available from: 2015-09-10 Created: 2015-09-10 Last updated: 2015-11-23
  • 122.
    Cortés, Andrés J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Carolina Chavarro, M.
    Madrinan, Santiago
    This, Dominique
    Blair, Matthew W.
    Molecular ecology and selection in the drought-related Asr gene polymorphisms in wild and cultivated common bean (Phaseolus vulgaris L.)2012In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 13, p. 58-Article in journal (Refereed)
    Abstract [en]

    Background: The abscisic acid (ABA) pathway plays an important role in the plants' reaction to drought stress and ABA-stress response (Asr) genes are important in controlling this process. In this sense, we accessed nucleotide diversity at two candidate genes for drought tolerance (Asr1 and Asr2), involved in an ABA signaling pathway, in the reference collection of cultivated common bean (Phaseolus vulgaris L.) and a core collection of wild common bean accessions. Results: Our wild population samples covered a range of mesic (semi-arid) to very dry (desert) habitats, while our cultivated samples presented a wide spectrum of drought tolerance. Both genes showed very different patterns of nucleotide variation. Asr1 exhibited very low nucleotide diversity relative to the neutral reference loci that were previously surveyed in these populations. This suggests that strong purifying selection has been acting on this gene. In contrast, Asr2 exhibited higher levels of nucleotide diversity, which is indicative of adaptive selection. These patterns were more notable in wild beans than in cultivated common beans indicting that natural selection has played a role over long time periods compared to farmer selection since domestication. Conclusions: Together these results suggested the importance of Asr1 in the context of drought tolerance, and constitute the first steps towards an association study between genetic polymorphism of this gene family and variation in drought tolerance traits. Furthermore, one of our major successes was to find that wild common bean is a reservoir of genetic variation and selection signatures at Asr genes, which may be useful for breeding drought tolerance in cultivated common bean.

  • 123. Cozzolino, Salvatore
    et al.
    Fineschi, Silvia
    Litto, Maria
    Scopece, Giovanni
    Trunschke, Judith
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Schiestl, Florian P.
    Herbivory increases fruit set in Silene latifolia: a consequence of induced pollinator-attracting floral volatiles?2015In: Journal of Chemical Ecology, ISSN 0098-0331, E-ISSN 1573-1561, Vol. 41, no 7, p. 622-630Article in journal (Refereed)
    Abstract [en]

    Although the effect of herbivory on plant reproduction has been investigated in some detail, little is known about how herbivores affect floral signalling. Here, we investigated the effect of foliar herbivory by the African Cotton Leafworm (Spodoptera littoralis) on floral signalling and fruit set in the White Campion (Silene latifolia). We found no effects of herbivory on floral traits involved in visual signalling (flower number, corolla diameter, calyx length, petal length) or in amount of nectar produced. However, Spodoptera-infested plants emitted higher amounts of the two floral volatiles, (Z)-3-hexenyl acetate and β-ocimene, than control plants. Open pollinated, infested plants also were found to produce more fruits than control plants, but only with nocturnal pollinators. Experimental addition of the two induced floral volatiles to non-infested Silene flowers also led to the production of more fruits with nocturnal pollination. This suggests that higher fruit production in herbivore-infested plants was caused by increased nocturnal pollinator attraction, mediated by the induced floral emission of these two volatiles. Our results show that the effects of herbivory on plant reproductive success are not necessarily detrimental, as plants can compensate herbivory with increased investment in pollinator attraction.

  • 124.
    Dahlgren, Johan P.
    et al.
    Univ Southern Denmark, Max Planck Odense Ctr Biodemog Aging, Dept Biol, Campusvej 55, DK-5230 Odense M, Denmark..
    Bengtsson, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ehrlen, Johan
    Stockholm Univ, Dept Ecol Environm & Plant Sci, SE-10691 Stockholm, Sweden..
    The demography of climate-driven and density-regulated population dynamics in a perennial plant2016In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 97, no 4, p. 899-907Article in journal (Refereed)
    Abstract [en]

    Identifying the internal and external drivers of population dynamics is a key objective in ecology, currently accentuated by the need to forecast the effects of climate change on species distributions and abundances. The interplay between environmental and density effects is one particularly important aspect of such forecasts. We examined the simultaneous impact of climate and intraspecific density on vital rates of the dwarf shrub Fumana procumbens over 20 yr, using generalized additive mixed models. We then analyzed effects on population dynamics using integral projection models. The population projection models accurately captured observed fluctuations in population size. Our analyses suggested the population was intrinsically regulated but with annual fluctuations in response to variation in weather. Simulations showed that implicitly assuming variation in demographic rates to be driven solely by the environment can overestimate extinction risks if there is density dependence. We conclude that density regulation can dampen effects of climate change on Fumana population size, and discuss the need to quantify density dependence in predictions of population responses to environmental changes.

  • 125.
    Dahlgren, Johan Petter
    et al.
    Univ Southern Denmark, Max Planck Odense Ctr Biodemog Aging, DK-5230 Odense, Denmark.;Univ Southern Denmark, Dept Biol, DK-5230 Odense, Denmark..
    Colchero, Fernando
    Univ Southern Denmark, Max Planck Odense Ctr Biodemog Aging, DK-5230 Odense, Denmark.;Univ Southern Denmark, Dept Math & Comp Sci, DK-5230 Odense, Denmark..
    Jones, Owen R.
    Univ Southern Denmark, Max Planck Odense Ctr Biodemog Aging, DK-5230 Odense, Denmark.;Univ Southern Denmark, Dept Biol, DK-5230 Odense, Denmark..
    Oien, Dag-Inge
    Norwegian Univ Sci & Technol, NTNU Univ Museum, Dept Nat Hist, N-7491 Trondheim, Norway..
    Moen, Asbjorn
    Norwegian Univ Sci & Technol, NTNU Univ Museum, Dept Nat Hist, N-7491 Trondheim, Norway..
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Actuarial senescence in a long-lived orchid challenges our current understanding of ageing2016In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 283, no 1842, article id 20161217Article in journal (Refereed)
    Abstract [en]

    The dominant evolutionary theory of actuarial senescence-an increase in death rate with advancing age-is based on the concept of a germ cell line that is separated from the somatic cells early in life. However, such a separation is not clear in all organisms. This has been suggested to explain the paucity of evidence for actuarial senescence in plants. We used a 32 year study of Dactylorhiza lapponica that replaces its organs each growing season, to test whether individuals of this tuberous orchid senesce. We performed a Bayesian survival trajectory analysis accounting for reproductive investment, for individuals under two types of land use, in two climatic regions. The mortality trajectory was best approximated by a Weibull model, showing clear actuarial senescence. Rates of senescence in this model declined with advancing age, but were slightly higher in mown plots and in the more benign climatic region. At older ages, senescence was evident only when accounting for a positive effect of reproductive investment on mortality. Our results demonstrate actuarial senescence as well as a survival-reproduction trade-off in plants, and indicate that environmental context may influence senescence rates. This knowledge is crucial for understanding the evolution of demographic senescence and for models of plant population dynamics.

  • 126. Dahlström, A.
    et al.
    Borgegård, S.-O.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kärlväxtfloran på nedlagda ängar och åkrar vid torp i Kilsbergen efter 50 och 90 års igenväxning1998In: Svensk Botanisk Tidskrift, Vol. 91, p. 211-226Article in journal (Refereed)
  • 127.
    Dengler, Juergen
    et al.
    Zurich Univ Appl Sci ZHAW, Inst Nat Resource Sci IUNR, Vegetat Ecol Grp, Gruentalstr 14, CH-8820 Wadenswil, Switzerland.;Univ Bayreuth, Bayreuth Ctr Ecol & Environm Res BayCEER, Plant Ecol, Univ Str 30, D-95447 Bayreuth, Germany.;German Ctr Integrat Biodivers Res iDiv, Deutsch Pl 5e, D-04103 Leipzig, Germany..
    Wagner, Viktoria
    Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2R3, Canada..
    Dembicz, Iwona
    Univ Warsaw, Fac Biol, Dept Plant Ecol & Environm Conservat, Ul Zwirki & Wigury 101, PL-02089 Warsaw, Poland..
    Garcia-Mijangos, Itziar
    Univ Basque Country, UPV EHU, Dept Plant Biol & Ecol, POB 644, Bilbao 48080, Spain..
    Naqinezhad, Alireza
    Univ Mazandaran, Fac Basic Sci, Dept Biol, POB 47416-95447, Babol Sar, Mazandaran, Iran..
    Boch, Steffen
    Swiss Fed Res Inst WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Chiarucci, Alessandro
    Univ Bologna, Dept Biol Geol & Environm Sci, Via Irnerio 42, I-40126 Bologna, Italy..
    Conradi, Timo
    Univ Bayreuth, Bayreuth Ctr Ecol & Environm Res BayCEER, Plant Ecol, Univ Str 30, D-95447 Bayreuth, Germany.;Aarhus Univ, Dept Biosci, Ecoinformat & Biodivers, DK-8000 Aarhus, Denmark..
    Filibeck, Goffredo
    Univ Tuscia, Dept Agr & Forestry Sci DAFNE, I-01100 Viterbo, Italy..
    Guarino, Riccardo
    Univ Palermo, Dept STEBICEF, Bot Unit, Via Archiarafi 38, I-90123 Palermo, Italy..
    Janisova, Monika
    Slovak Acad Sci, Plant Sci & Biodivers Ctr, Inst Bot, Dumbierska 1, Banska Bystrica 97411, Slovakia..
    Steinbauer, Manuel J.
    Friedrich Alexander Univ Erlangen Nurnberg FAU, Dept Geog & Geosci, GeoZentrum Nordbayern, Loewenichstr 28, D-91054 Erlangen, Germany..
    Acic, Svetlana
    Univ Belgrade, Fac Agr, Dept Bot, Nemanjina 6, Belgrade 11080, Serbia..
    Acosta, Alicia T. R.
    Univ Roma Tre, Dipartimento Sci, Viale Marconi 446, I-00146 Rome, Italy..
    Akasaka, Munemitsu
    Tokyo Univ Agr & Technol, Inst Agr, Fuchu, Tokyo 1838509, Japan..
    Allers, Marc-Andre
    Albert Einstein Str 11a, D-14473 Potsdam, Germany..
    Apostolova, Iva
    Bulgarian Acad Sci, Inst Biodivers & Ecosyst Res, 23 Acad Georgi Bonchev Str, BU-1113 Sofia, Bulgaria..
    Axmanova, Irena
    Masaryk Univ, Dept Bot & Zool, Kotlarska 2, CS-61137 Brno, Czech Republic..
    Bakan, Branko
    Univ Maribor, Fac Nat Sci & Math, Biol Dept, Koroska Cesta 160, SLO-2000 Maribor, Slovenia..
    Baranova, Alina
    Univ Hamburg, CEN Ctr Earth Syst Res & Sustainabil, Bundesstr 55, D-20146 Hamburg, Germany..
    Bardy-Durchhalter, Manfred
    Austrian Acad Sci, Inst Interdisciplinary Mt Res, GLORIA Coordinat, Silbergasse 30-3, A-1190 Vienna, Austria..
    Bartha, Sandor
    MTA Ctr Ecol Res, Inst Ecol & Bot, Alkotmany U 2, H-2163 Vacratot, Hungary..
    Baumann, Esther
    Univ Bayreuth, Biogeog, Univ Str 30, D-95447 Bayreuth, Germany..
    Becker, Thomas
    Univ Trier, Geobot Reg & Environm Sci, Behringstr 21, D-54296 Trier, Germany..
    Becker, Ute
    Johannes Gutenberg Univ Mainz, Gnune Schule Bot Garten, Anselm Franz von Bentzel Weg 9b, D-55128 Mainz, Germany..
    Belonovskaya, Elena
    Russian Acad Sci, Inst Geog, Staromonetny Per 29, Moscow 119017, Russia..
    Bengtsson, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Benito Alonso, Jose Luis
    C Mariano Rguez De Ledesma 4-3 A, Jaca 22700, Spain..
    Berastegi, Asun
    Gest Ambiental Navarra SA, Biodivers Team, Padre Adoain 219, Pamplona 31015, Spain..
    Bergamini, Ariel
    Swiss Fed Res Inst WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Bonini, Ilaria
    Univ Siena, Life Sci, PA Mattioli 4, I-53100 Siena, Italy..
    Bruun, Hans Henrik
    Univ Copenhagen, Dept Biol, Sect Ecol & Evolut, Univ Pk 15, DK-2100 Copenhagen, Denmark..
    Budzhak, Vasyl
    Chernivtsi Natl Univ, Bot & Nat Protect Dept, Fedkovich St 11, UA-58022 Chernovtsy, Ukraine..
    Bueno, Alvaro
    Univ Oviedo, Inst Recursos Nat & Ordenac Terr INDUROT, Campus Mieres Edificio Invest, Mieres 33600, Spain..
    Antonio Campos, Juan
    Univ Basque Country, UPV EHU, Dept Plant Biol & Ecol, POB 644, Bilbao 48080, Spain..
    Cancellieri, Laura
    Univ Tuscia, Dept Agr & Forestry Sci DAFNE, I-01100 Viterbo, Italy..
    Carboni, Marta
    Univ Grenoble Alpes, Lab Ecol Alpine, UMR CNRS 5553, BP 53, F-38041 Grenoble 9, France..
    Chocarro, Cristina
    Univ Lleida, Crop & Forest Sci, Rovira Roure 177, Lleida 25110, Spain..
    Conti, Luisa
    Univ Roma Tre, Dipartimento Sci, Viale Marconi 446, I-00146 Rome, Italy..
    Czarniecka-Wiera, Marta
    Univ Wroclaw, Bot Garden, Sienkiewicza 23, PL-50335 Wroclaw, Poland..
    De Frenne, Pieter
    Univ Ghent, Forest & Nat Lab, Geraardsbergsesteenweg 267, B-9090 Gontrode, Belgium..
    Deak, Balazs
    Univ Debrecen, Dept Ecol, Egyet Ter 1, H-4032 Debrecen, Hungary..
    Didukh, Yakiv P.
    MG Kholodny Inst Bot NAS Ukraine, Geobot & Ecol Dept, Tereschenkivska Str 2, UA-1601 Kiev, Ukraine..
    Diekmann, Martin
    Univ Bremen, Vegetat Okol & Nat Schutzbiol, FB 2,Leobener Str 5, D-28359 Bremen, Germany..
    Dolnik, Christian
    Univ Kiel, Ecol Ctr Kid, Olshausenstr 40, D-24098 Kiel, Germany..
    Dupre, Cecilia
    Univ Bremen, Vegetat Okol & Nat Schutzbiol, FB 2,Leobener Str 5, D-28359 Bremen, Germany..
    Ecker, Klaus
    Swiss Fed Res Inst WSL, Zurcherstr 111, CH-8903 Birmensdorf, Switzerland..
    Ermakov, Nikolai
    Russian Acad Sci, Cent Siberian Bot Garden, Zolotodolinskaya 101, Novosibirsk 630090, Russia..
    Erschbamer, Brigitta
    Univ Innsbruck, Dept Bot, Sternwartestr 15, A-6020 Innsbruck, Austria..
    Escudero, Adrian
    Univ Rey Juan Carlos, Dept Biol Geol Phys & Inorgan Chem, Tulipan S-N, Mostoles 28933, Spain..
    Etayo, Javier
    Navarro Villoslada 16-3 Dcha, Pamplona 31003, Spain..
    Fajmonova, Zuzana
    Czech Acad Sci, Inst Bot, Dept Vegetat Ecol, Lidicka 25-27, Brno 60200, Czech Republic..
    Felde, Vivian A.
    Univ Bergen, Dept Biol, Postbox 7803, N-5020 Bergen, Norway..
    Fernandez Calzado, Maria Rosa
    Univ Granada, Fac Pharm, Dept Bot, Campus Cartuja S-N, E-18071 Granada, Spain..
    Finckh, Manfred
    Univ Hamburg, Bioctr Klein Flottbek, Biodivers Evolut & Ecol Plants BEE, Ohnhorststr 18, D-22609 Hamburg, Germany.;Univ Hamburg, Bot Garden, Ohnhorststr 18, D-22609 Hamburg, Germany..
    Fotiadis, Georgios
    TEI Technol Educ Inst Sterea Ellada, Dept Forestry & Nat Environm Management, Dimokratias 3, Karpenisi 36100, Greece..
    Fracchiolla, Mariano
    Univ Bari, Dept Agr & Environm Sci, Via Orabona 4, I-70126 Bari, Italy..
    Ganeva, Anna
    Bulgarian Acad Sci, Inst Biodivers & Ecosyst Res, 23 Acad Georgi Bonchev Str, BU-1113 Sofia, Bulgaria..
    Garcia-Magro, Daniel
    Univ Basque Country, UPV EHU, Dept Plant Biol & Ecol, POB 644, Bilbao 48080, Spain..
    Gavilan, Rosario G.
    Univ Complutense Madrid, Fac Farm, Dept Biol Vegetal 2, E-28040 Madrid, Spain..
    Germany, Markus
    Univ Kiel, Inst Ecosyst Res, Olshausenstr 75, D-24118 Kiel, Germany..
    Giladi, Itamar
    Ben Gurion Univ Negev, Swiss Inst Dryland Environm & Energy Res, Jacob Blaustein Inst Desert Res, Mitrani Dept Desert Ecol, Sede Boger Campus, IL-84990 Midreshet Ben Gurion, Israel..
    Gillet, Francois
    Univ Franche Comte, UMR Chronoenvironm, 16 Route Gray, F-25030 Besancon, France..
    Giusso del Galdo, Gian Pietro
    Univ Catania, Dept Biol Geol & Environm Sci BiGeA, Via A Longo 19, I-95125 Catania, Italy..
    Gonzalez, Jose M.
    Univ Rey Juan Carlos, Dept Biol Geol Phys & Inorgan Chem, Tulipan S-N, Mostoles 28933, Spain..
    Grytnes, John-Arvid
    Univ Bergen, Dept Biol, Postbox 7803, N-5020 Bergen, Norway..
    Hajek, Michal
    Masaryk Univ, Dept Bot & Zool, Kotlarska 2, CS-61137 Brno, Czech Republic..
    Hajkova, Petra
    Masaryk Univ, Dept Bot & Zool, Kotlarska 2, CS-61137 Brno, Czech Republic..
    Helm, Aveliina
    Univ Tartu, Inst Ecol & Earth Sci, Lai 40, EE-51005 Tartu, Estonia..
    Herrera, Mercedes
    Univ Basque Country, UPV EHU, Dept Plant Biol & Ecol, POB 644, Bilbao 48080, Spain..
    Hettenbergerova, Eva
    Masaryk Univ, Dept Bot & Zool, Kotlarska 2, CS-61137 Brno, Czech Republic..
    Hobohm, Carsten
    Univ Flensburg, Interdisciplinary Inst Environm Social & Human Sc, Campus 1, D-24943 Flensburg, Germany..
    Huellbusch, Elisabeth M.
    Univ Bayreuth, Bayreuth Ctr Ecol & Environm Res BayCEER, Plant Ecol, Univ Str 30, D-95447 Bayreuth, Germany..
    Ingerpuu, Nele
    Univ Tartu, Inst Ecol & Earth Sci, Lai 40, EE-51005 Tartu, Estonia..
    Jandt, Ute
    Martin Luther Univ Halle Wittenberg, Inst Biol, Geobot & Bot Garden, Kirchtor 1, D-6108 Halle, Saale, Germany..
    Jeltsch, Florian
    Univ Potsdam, Plant Ecol & Nat Conservat, Muhlenberg 3, D-14476 Potsdam, Germany..
    Jensen, Kai
    Univ Hamburg, Bioctr Klein Flottbek, Appl Plant Ecol, Ohnhorststr 18, D-22609 Hamburg, Germany..
    Jentsch, Anke
    Univ Bayreuth, Bayreuth Ctr Ecol & Environm Res BayCEER, Disturbance Ecol, Univ Str 30, D-95447 Bayreuth, Germany..
    Jeschke, Michael
    Friesenstr 47, D-82223 Eichenau, Germany..
    Jimenez-Alfaro, Borja
    Oviedo Univ, Res Unit Biodivers CSIC UO PA, Campus Mieres, Mieres 33600, Spain..
    Kacki, Zygmunt
    Univ Wroclaw, Bot Garden, Sienkiewicza 23, PL-50335 Wroclaw, Poland..
    Kakinuma, Kaoru
    Columbia Univ, NASA, Goddard Inst Space Studies, 2880 Broadway, New York, NY 10025 USA..
    Kapfer, Jutta
    Norwegian Inst Bioecon Res, Dept Landscape Monitoring, Div Geog & Stat, Holtveien 66, N-9269 Tromso, Norway..
    Kavgaci, Ali
    Southwest Anatolia Forest Res Inst, POB 264, TR-07002 Antalya, Turkey..
    Kelemen, Andras
    Univ Debrecen, Dept Ecol, Egyet Ter 1, H-4032 Debrecen, Hungary..
    Kiehl, Kathrin
    Univ Appl Sci Osnabruck, Fac Agr Sci & Landscape Architecture, Vegetat Ecol & Bot, Oldenburger Landstr 24, D-49090 Osnabruck, Germany..
    Koyama, Asuka
    Univ Tokyo, Inst Sustainable Agroecosyst Serv, 1-1-1 Midori Cho, Tokyo 1880002, Japan..
    Koyanagi, Tomoyo F.
    Tokyo Gakugei Univ, Field Studies Inst Environm Educ, 4-1-1 Koganei, Tokyo 1848501, Japan..
    Kozub, Lukasz
    Univ Warsaw, Fac Biol, Dept Plant Ecol & Environm Conservat, Ul Zwirki & Wigury 101, PL-02089 Warsaw, Poland..
    Kuzemko, Anna
    MG Kholodny Inst Bot NAS Ukraine, Geobot & Ecol Dept, Tereschenkivska Str 2, UA-1601 Kiev, Ukraine..
    Kyrkjeeide, Magni Olsen
    Norwegian Inst Nat Res, N-7485 Trondheim, Norway..
    Landi, Sara
    Univ Sassari, Dept Sci Nat & Terr, Via Piandanna, I-07100 Sassari, Italy..
    Langer, Nancy
    Schwarzesee 27, D-16227 Eberswalde, Germany..
    Lastrucci, Lorenzo
    Univ Bari, Dept Agr & Environm Sci, Via Orabona 4, I-70126 Bari, Italy..
    Lazzaro, Lorenzo
    Univ Bari, Dept Agr & Environm Sci, Via Orabona 4, I-70126 Bari, Italy..
    Lelli, Chiara
    Univ Bologna, Dept Biol Geol & Environm Sci, Via Irnerio 42, I-40126 Bologna, Italy..
    Leps, Jan
    Univ South Bohemia, Fac Sci, Dept Bot, Branisovska 31, Ceske Budejovice 37005, Czech Republic..
    Loebel, Swantje
    Inst Geoecol, Landscape Ecol & Environm Syst Anal, Langer Kamp 19c, D-38106 Braunschweig, Germany..
    Luzuriaga, Arantzazu L.
    Univ Rey Juan Carlos, Dept Biol Geol Phys & Inorgan Chem, Tulipan S-N, Mostoles 28933, Spain..
    Maccherini, Simona
    Univ Siena, Life Sci, PA Mattioli 4, I-53100 Siena, Italy..
    Magnes, Martin
    Karl Franzens Univ Graz, Inst Plant Sci, Holteigasse 6, A-8010 Graz, Austria..
    Malicki, Marek
    Univ Wroclaw, Dept Bot, Ul Kanonia 6-8, PL-50328 Wroclaw, Poland..
    Marceno, Corrado
    Univ Basque Country, UPV EHU, Dept Plant Biol & Ecol, POB 644, Bilbao 48080, Spain..
    Mardari, Constantin
    Alexandru Ioan Cuza Univ, Anastasie Fatu Bot Garden, Dumbrava Rosie 7-9, Iasi 700487, Romania..
    Mauchamp, Leslie
    Univ Franche Comte, UMR Chronoenvironm, 16 Route Gray, F-25030 Besancon, France..
    May, Felix
    German Ctr Integrat Biodivers Res iDiv, Biodivers Synth Res Grp, Deutsch Pl 5e, D-04103 Leipzig, Germany..
    Michelsen, Ottar
    Norwegian Univ Sci & Technol, NTNU Sustainabil, N-7491 Trondheim, Norway..
    Mesa, Joaquin Molero
    Univ Granada, Fac Pharm, Dept Bot, Campus Cartuja S-N, E-18071 Granada, Spain..
    Molnar, Zsolt
    MTA Ctr Ecol Res, Inst Ecol & Bot, Alkotmany U 2, H-2163 Vacratot, Hungary..
    Moysiyenko, Ivan Y.
    Kherson State Univ, Dept Bot, Ul Univ Ska 27, UA-73000 Kherson, Ukraine..
    Nakaga, Yuko K.
    Kobe Univ, Grad Sch Human Dev & Environm, 3-11 Tsrurukabuto, Kobe, Hyogo 6578501, Japan..
    Natcheva, Rayna
    Bulgarian Acad Sci, Inst Biodivers & Ecosyst Res, 23 Acad Georgi Bonchev Str, BU-1113 Sofia, Bulgaria..
    Noroozi, Jalil
    Univ Vienna, Dept Bot & Biodivers Res, Rennweg 14, A-1030 Vienna, Austria..
    Pakeman, Robin J.
    James Hutton Inst, Ecol Sci, Craigiebuckler AB15 8QH, Aberdeen, Scotland..
    Palpurina, Salza
    Masaryk Univ, Dept Bot & Zool, Kotlarska 2, CS-61137 Brno, Czech Republic..
    Partel, Meelis
    Univ Tartu, Inst Ecol & Earth Sci, Lai 40, EE-51005 Tartu, Estonia..
    Paetsch, Ricarda
    Georg August Univ Gottingen, Vegetat & Phytodivers Anal, Untere Karspule 2, D-37073 Gottingen, Germany..
    Pauli, Harald
    Austrian Acad Sci, Inst Interdisciplinary Mt Res, GLORIA Coordinat, Silbergasse 30-3, A-1190 Vienna, Austria..
    Pedashenko, Hristo
    Bulgarian Acad Sci, Inst Biodivers & Ecosyst Res, 23 Acad Georgi Bonchev Str, BU-1113 Sofia, Bulgaria..
    Peet, Robert K.
    Univ N Carolina, Dept Biol, Chapel Hill, NC 27599 USA..
    Pielech, Remigiusz
    Agr Univ Krakow, Fac Forestry, Dept Forest Biodivers, Al 29 Listopada 46, PL-31425 Krakow, Poland..
    Pipenbaher, Natasa
    Univ Maribor, Fac Nat Sci & Math, Biol Dept, Koroska Cesta 160, SLO-2000 Maribor, Slovenia..
    Pirini, Chrisoula
    Aristotle Univ Thessaloniki, Sch Biol, Dept Bot, Thessaloniki 54124, Greece..
    Pleskova, Zuzana
    Masaryk Univ, Dept Bot & Zool, Kotlarska 2, CS-61137 Brno, Czech Republic..
    Polyakova, Mariya A.
    Russian Acad Sci, Cent Siberian Bot Garden, Zolotodolinskaya 101, Novosibirsk 630090, Russia..
    Prentice, Honor C.
    Lund Univ, Dept Biol, Ecol Bldg, S-22362 Lund, Sweden..
    Reinecke, Jennifer
    Senckenberg Museum Nat Hist Gorlitz, Bot Dept, Museum 1, D-2826 Gorlitz, Germany..
    Reitalu, Triin
    Tallinn Univ Technol, Inst Geol, Ehitajate Tee 5, EE-19086 Tallinn, Estonia..
    Pilar Rodriguez-Rojo, Maria
    Univ Castilla La Mancha, Inst Environm Sci, Ave Carlos 3 S-N, Toledo 45071, Spain..
    Rolecek, Jan
    Masaryk Univ, Dept Bot & Zool, Kotlarska 2, CS-61137 Brno, Czech Republic.;Czech Acad Sci, Inst Bot, Dept Vegetat Ecol, Lidicka 25-27, Brno 60200, Czech Republic..
    Ronkin, Vladimir
    Khark Natl Univ, Dept Zool & Ecol, 4 Svobody Sq, UA-61022 Kharkov, Ukraine..
    Rosati, Leonardo
    Univ Basilicata, Sch Agr Forest Food & Environm Sci, Via Ateneo Lucano 10, I-85100 Potenza, Italy..
    Rosén, Ejvind
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ruprecht, Eszter
    Babes Bolyai Univ, Hungarian Dept Biol & Ecol, Republ Str 42, Cluj Napoca 400015, Romania..
    Rusina, Solvita
    Univ Latvia, Fac Geog & Earth Sci, 1 Jelgavas St, LV-1004 Riga, Latvia..
    Sabovljevic, Marko
    Univ Belgrade, Fac Biol, Inst Bot & Bot Garden Jevremovac, Takovska 43, Belgrade 11000, Serbia..
    Maria Sanchez, Ana
    Univ Rey Juan Carlos, Dept Biol Geol Phys & Inorgan Chem, Tulipan S-N, Mostoles 28933, Spain..
    Savchenko, Galina
    Khark Natl Univ, Dept Zool & Ecol, 4 Svobody Sq, UA-61022 Kharkov, Ukraine..
    Schuhmacher, Oliver
    NABU Hamburg, Stadtbad 45, D-29451 Dannenberg, Germany..
    Skornik, Sonja
    Univ Maribor, Fac Nat Sci & Math, Biol Dept, Koroska Cesta 160, SLO-2000 Maribor, Slovenia..
    Sperandii, Marta Gaia
    Univ Roma Tre, Dipartimento Sci, Viale Marconi 446, I-00146 Rome, Italy..
    Staniaszek-Kik, Monika
    Univ Lodz, Dept Geobot & Plant Ecol, Banacha 12-16, PL-90237 Lodz, Poland..
    Stevanovic-Dajic, Zora
    Univ Belgrade, Fac Agr, Dept Bot, Nemanjina 6, Belgrade 11080, Serbia..
    Stock, Marin
    Schleswig Holstein Agcy Coastal Def, Natl Pk & Marine Conservat, Natl Pk Author, Schlossgarten 1, D-25832 Tonning, Germany..
    Suchrow, Sigrid
    Univ Hamburg, Bioctr Klein Flottbek, Appl Plant Ecol, Ohnhorststr 18, D-22609 Hamburg, Germany..
    Sutcliffe, Laura M. E.
    Georg August Univ Gottingen, Plant Ecol & Ecosyst Res, Untere Karspule 2, D-37073 Gottingen, Germany..
    Swacha, Grzegorz
    Univ Wroclaw, Bot Garden, Sienkiewicza 23, PL-50335 Wroclaw, Poland..
    Sykes, Martin
    Lund Univ, Dept Phys Geog & Ecosyst Sci, Solvegatan 12, S-22362 Lund, Sweden..
    Szabo, Anna
    Romanian Ornithol Soc, Gh Dima St 49, Cluj Napoca 400342, Romania..
    Talebi, Amir
    Univ Tehran, Coll Sci, Sch Biol, Tehran 141556455, Iran.;Univ Tehran, Coll Sci, Ctr Excellence Phylogeny Living Organisms, Tehran 141556455, Iran..
    Tanase, Catalin
    Alexandru Ioan Cuza Univ, Fac Biol, Carol I 20A, Iasi 700505, Romania..
    Terzi, Massimo
    Italian Natl Council Res CNR, Inst Biosci & Bioresources IBBR, Via Amendola 165-A, I-70126 Bari, Italy..
    Tolgyesi, Csaba
    Univ Szeged, Dept Ecol, Kozep Fasor 52, H-6726 Szeged, Hungary..
    Torca, Marta
    Univ Basque Country, UPV EHU, Dept Plant Biol & Ecol, POB 644, Bilbao 48080, Spain..
    Torok, Peter
    MTA DE Lendulet Funct & Restorat Ecol Res Grp, Egyet Ter 1, H-4032 Debrecen, Hungary..
    Tothmeresz, Bela
    MTA DE Lendulet Funct & Restorat Ecol Res Grp, Egyet Ter 1, H-4032 Debrecen, Hungary..
    Tsarevskaya, Nadezda
    Russian Acad Sci, Inst Geog, Staromonetny Per 29, Moscow 119017, Russia..
    Tsiripidis, Ioannis
    Aristotle Univ Thessaloniki, Sch Biol, Dept Bot, Thessaloniki 54124, Greece..
    Tzonev, Rossen
    Sofia Univ St Kliment Ohridski, Dept Ecol & Environm Protect, 8 Dragan Tzankov Blvd, Sofia 1164, Bulgaria..
    Ushimaru, Atushi
    Kobe Univ, Grad Sch Human Dev & Environm, 3-11 Tsrurukabuto, Kobe, Hyogo 6578501, Japan..
    Valko, Orsolya
    Univ Debrecen, Dept Ecol, Egyet Ter 1, H-4032 Debrecen, Hungary..
    van der Maarel, Eddy
    Univ Groningen, Ctr Ecol & Evolutionary Studies, Linnaeusborg Nijenborgh 7 Bldg U, NL-9747 AG Groningen, Netherlands..
    Vanneste, Thomas
    Univ Ghent, Forest & Nat Lab, Geraardsbergsesteenweg 267, B-9090 Gontrode, Belgium..
    Vashenyak, Iuliia
    Khmelnytskyi Inst Interreg Acad Personnel Managem, Prospect Myru Str 101A, UA-29015 Khmelnytskyi, Ukraine..
    Vassilev, Kiril
    Bulgarian Acad Sci, Inst Biodivers & Ecosyst Res, 23 Acad Georgi Bonchev Str, BU-1113 Sofia, Bulgaria..
    Viciani, Daniele
    Univ Bari, Dept Agr & Environm Sci, Via Orabona 4, I-70126 Bari, Italy..
    Villar, Luis
    Inst Pirena Ecol, Consejo Super Invest Cient, Jaca 22700, Spain..
    Virtanen, Risto
    Univ Oulu, Ecol & Genet, POB 3000, Oulu 90014, Finland..
    Kosic, Ivana Vitasovic
    Univ Zagreb, Dept Agr Bot, Fac Agr, Svetosimunska Cesta 25, Zagreb 10000, Croatia..
    Wang, Yun
    Senckenberg Museum Nat Hist Gorlitz, Bot Dept, Museum 1, D-2826 Gorlitz, Germany..
    Weiser, Frank
    Univ Bayreuth, Biogeog, Univ Str 30, D-95447 Bayreuth, Germany..
    Went, Julia
    Univ Bayreuth, Bayreuth Ctr Ecol & Environm Res BayCEER, Plant Ecol, Univ Str 30, D-95447 Bayreuth, Germany..
    Wesche, Karsten
    German Ctr Integrat Biodivers Res iDiv, Deutsch Pl 5e, D-04103 Leipzig, Germany.;Senckenberg Museum Nat Hist Gorlitz, Bot Dept, Museum 1, D-2826 Gorlitz, Germany..
    White, Hannah
    Univ Coll Dublin, Sch Biol & Environm Sci, Earth Inst, Dublin 4, Ireland..
    Winkler, Manuela
    Austrian Acad Sci, Inst Interdisciplinary Mt Res, GLORIA Coordinat, Silbergasse 30-3, A-1190 Vienna, Austria..
    Zaniewski, Piotr T.
    Warsaw Univ Life Sci SGGW, Fac Forestry, Dept Forest Bot, Nowoursynowska 159, PL-02776 Warsaw, Poland..
    Zhang, Hui
    Chinese Acad Sci, Key Lab Vegetat Restorat & Management Degraded Ec, South China Bot Garden, Xingke Rd 723, Guangzhou 510650, Guangdong, Peoples R China..
    Ziv, Yaron
    Ben Gurion Univ Negev, Dept Life Sci, IL-84105 Negev, Israel..
    Znamenskiy, Sergey
    Karelian Res Ctr RAS, Inst Biol, Pushkinskaya 11, Petrozavodsk 185910, Russia..
    Biurrun, Idoia
    Univ Basque Country, UPV EHU, Dept Plant Biol & Ecol, POB 644, Bilbao 48080, Spain..
    GrassPlot - a database of multi-scale plant diversity in Palaearctic grasslands2018In: Phytocoenologia, ISSN 0340-269X, Vol. 48, no 3, p. 331-347Article in journal (Refereed)
    Abstract [en]

    GrassPlot is a collaborative vegetation-plot database organised by the Eurasian Dry Grassland Group (EDGG) and listed in the Global Index of Vegetation-Plot Databases (GIVD ID EU-00-003). GrassPlot collects plot records (releves) from grasslands and other open habitats of the Palaearctic biogeographic realm. It focuses on precisely delimited plots of eight standard grain sizes (0.0001; 0.001;... 1,000 m(2)) and on nested-plot series with at least four different grain sizes. The usage of GrassPlot is regulated through Bylaws that intend to balance the interests of data contributors and data users. The current version (v. 1.00) contains data for approximately 170,000 plots of different sizes and 2,800 nested-plot series. The key components are richness data and metadata. However, most included datasets also encompass compositional data. About 14,000 plots have near-complete records of terricolous bryophytes and lichens in addition to vascular plants. At present, GrassPlot contains data from 36 countries throughout the Palaearctic, spread across elevational gradients and major grassland types. GrassPlot with its multi-scale and multi-taxon focus complements the larger international vegetationplot databases, such as the European Vegetation Archive (EVA) and the global database " sPlot". Its main aim is to facilitate studies on the scale-and taxon-dependency of biodiversity patterns and drivers along macroecological gradients. GrassPlot is a dynamic database and will expand through new data collection coordinated by the elected Governing Board. We invite researchers with suitable data to join GrassPlot. Researchers with project ideas addressable with GrassPlot data are welcome to submit proposals to the Governing Board.

  • 128. Dinca, V.
    et al.
    Wiklund, C.
    Lukhtanov, V. A.
    Kodandaramaiah, U.
    Noren, K.
    Dapporto, L.
    Wahlberg, N.
    Vila, R.
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex2013In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 26, no 10, p. 2095-2106Article in journal (Refereed)
    Abstract [en]

    Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence.

  • 129.
    Dinca, Vlad
    et al.
    Univ Guelph, Biodivers Inst Ontario, Guelph, ON N1G 2W1, Canada..
    Backstrom, Niclas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Dapporto, Leonardo
    Oxford Brookes Univ, Dept Biol & Med Sci, Oxford OX3 0BP, England..
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Garcia-Barros, Enrique
    Univ Autonoma Madrid, Dept Biol, Madrid 28049, Spain..
    Hebert, Paul D. N.
    Univ Guelph, Biodivers Inst Ontario, Guelph, ON N1G 2W1, Canada..
    Hernandez-Roldan, Juan
    Univ Autonoma Madrid, Dept Biol, Madrid 28049, Spain..
    Hornett, Emily
    Univ Cambridge, Dept Zool, Cambridge CB2 3EJ, England..
    Lukhtanov, Vladimir
    Russian Acad Sci, Inst Zool, Dept Karyosystemat, St Petersburg 199034, Russia..
    Marec, Frantisek
    Univ South Bohemia, Fac Sci, Ceske Budejovice 37005, Czech Republic..
    DNA barcodes highlight unique research models in European butterflies2015In: Genome, ISSN 0831-2796, E-ISSN 1480-3321, Vol. 58, no 5, p. 212-212Article in journal (Other academic)
  • 130. Dittmar, Emily L.
    et al.
    Oakley, Christopher G.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Schemske, Douglas W.
    Flowering time QTL in natural populations of Arabidopsis thaliana and implications for their adaptive value2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 17, p. 4291-4303Article in journal (Refereed)
    Abstract [en]

    The genetic basis of phenotypic traits is of great interest to evolutionary biologists, but their contribution to adaptation in nature is often unknown. To determine the genetic architecture of flowering time in ecologically relevant conditions, we used a recombinant inbred line population created from two locally adapted populations of Arabidopsis thaliana from Sweden and Italy. Using these RILs, we identified flowering time QTL in growth chambers that mimicked the natural temperature and photoperiod variation across the growing season in each native environment. We also compared the genomic locations of flowering time QTL to those of fitness (total fruit number) QTL from a previous three-year field study. Ten total flowering time QTL were found, and in all cases, the Italy genotype caused early flowering regardless of the conditions. Two QTL were consistent across chamber environments, and these had the largest effects on flowering time. Five of the fitness QTL colocalized with flowering time QTL found in the Italy conditions, and in each case, the local genotype was favoured. In contrast, just two flowering time QTL found in the Sweden conditions colocalized with fitness QTL and in only one case was the local genotype favoured. This implies that flowering time may be more important for adaptation in Italy than Sweden. Two candidate genes (FLC and VIN3) underlying the major flowering time QTL found in the current study are implicated in local adaptation.

  • 131. Doak, Daniel F.
    et al.
    Boor, Gina K. Himes
    Bakker, Victoria J.
    Morris, William F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Louthan, Allison
    Morrison, Scott A.
    Stanley, Amanda
    Crowder, Larry B.
    Recommendations for Improving Recovery Criteria under the US Endangered Species Act2015In: BioScience, ISSN 0006-3568, E-ISSN 1525-3244, Vol. 65, no 2, p. 189-199Article in journal (Refereed)
    Abstract [en]

    Recovery criteria, the thresholds mandated by the Endangered Species Act that define when species may be considered for downlisting or removal from the endangered species list, are a key component of conservation planning in the United States. We recommend improvements in the definition and scientific justification of recovery criteria, addressing both data-rich and data-poor situations. We emphasize the distinction between recovery actions and recovery criteria and recommend the use of quantitative population analyses to measure the impacts of threats and to explicitly tie recovery criteria to population status. To this end, we provide a brief tutorial on the legal and practical requirements and constraints of recovery criteria development. We conclude by contrasting our recommendations with other alternatives and by describing ways in which academic scientists can contribute productively to the planning process and to endangered species recovery.

  • 132. Douglas, Gavin M.
    et al.
    Gos, Gesseca
    Steige, Kim A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Salcedo, Adriana
    Holm, Karl
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Josephs, Emily B.
    Arunkumar, Ramesh
    Agren, J. Arvid
    Hazzouri, Khaled M.
    Wang, Wei
    Platts, Adrian E.
    Williamson, Robert J.
    Neuffer, Barbara
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Slotte, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wright, Stephen I.
    Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 9, p. 2806-2811Article in journal (Refereed)
    Abstract [en]

    Whole-genome duplication (WGD) events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection, and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole-genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole-genome data provide strong support for recent hybrid origins of the tetraploid species within the past 100,000-300,000 y from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide due to the combined effects of demography, selfing, and genome redundancy from WGD. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that non-functionalization can receive a "head start" through a legacy of deleterious variants and differential expression originating in parental diploid populations.

  • 133. Du, Fang K.
    et al.
    Peng, Xiao Li
    Liu, Jian Quan
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Hu, Feng Sheng
    Petit, Remy J.
    Direction and extent of organelle DNA introgression between two spruce species in the Qinghai-Tibetan Plateau2011In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 192, no 4, p. 1024-1033Article in journal (Refereed)
    Abstract [en]

    A recent model has shown that, during range expansion of one species in a territory already occupied by a related species, introgression should take place preferentially from the resident species towards the invading species and genome components experiencing low rates of gene flow should introgress more readily than those experiencing high rates of gene flow. Here, we use molecular markers from two organelle genomes with contrasted rates of gene flow to test these predictions by examining genetic exchanges between two morphologically distinct spruce Picea species growing in the Qinghai-Tibetan Plateau. The haplotypes from both mitochondrial (mt) DNA and chloroplast (cp) DNA cluster into two distinct lineages that differentiate allopatric populations of the two species. By contrast, in sympatry, the species share the same haplotypes, suggesting interspecific genetic exchanges. As predicted by the neutral model, all sympatric populations of the expanding species had received their maternally inherited mtDNA from the resident species, whereas for paternally inherited cpDNA introgression is more limited and not strictly unidirectional. Our results underscore cryptic introgressions of organelle DNAs in plants and the importance of considering rates of gene flow and range shifts to predict direction and extent of interspecific genetic exchanges.

  • 134. Dun, Xiaoling
    et al.
    Shen, Wenhao
    Hu, Kaining
    Zhou, Zhengfu
    Xia, Shengqian
    Wen, Jing
    Yi, Bin
    Shen, Jinxiong
    Ma, Chaozhi
    Tu, Jinxing
    Fu, Tingdong
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Neofunctionalization of Duplicated Tic40 Genes Caused a Gain-of-Function Variation Related to Male Fertility in Brassica oleracea Lineages2014In: Plant Physiology, ISSN 0032-0889, E-ISSN 1532-2548, Vol. 166, no 3, p. 1403-1419Article in journal (Refereed)
    Abstract [en]

    Gene duplication followed by functional divergence in the event of polyploidization is a major contributor to evolutionary novelties. The Brassica genus evolved from a common ancestor after whole-genome triplication. Here, we studied the evolutionary and functional features of Brassica spp. homologs to Tic40 (for translocon at the inner membrane of chloroplasts with 40 kDa). Four Tic40 loci were identified in allotetraploid Brassica napus and two loci in each of three basic diploid Brassica spp. Although these Tic40 homologs share high sequence identities and similar expression patterns, they exhibit altered functional features. Complementation assays conducted on Arabidopsis thaliana tic40 and the B. napus male-sterile line 7365A suggested that all Brassica spp. Tic40 homologs retain an ancestral function similar to that of AtTic40, whereas BolC9.Tic40 in Brassica oleracea and its ortholog in B. napus, BnaC9.Tic40, in addition, evolved a novel function that can rescue the fertility of 7365A. A homologous chromosomal rearrangement placed bnac9.tic40 originating from the A genome (BraA10.Tic40) as an allele of BnaC9.Tic40 in the C genome, resulting in phenotypic variation for male sterility in the B. napus near-isogenic two-type line 7365AB. Assessment of the complementation activity of chimeric B. napus Tic40 domain-swapping constructs in 7365A suggested that amino acid replacements in the carboxyl terminus of BnaC9.Tic40 cause this functional divergence. The distribution of these amino acid replacements in 59 diverse Brassica spp. accessions demonstrated that the neofunctionalization of Tic40 is restricted to B. oleracea and its derivatives and thus occurred after the divergence of the Brassica spp. A, B, and C genomes.

  • 135. Dymshakova, O. S.
    et al.
    Semerikov, V. L.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    AFLP analysis to estimate the genetic contribution of parents to progeny from hybridization between Saxifraga sibirica L. and S. cernua L.2012In: Russian journal of ecology, ISSN 1067-4136, E-ISSN 1608-3334, Vol. 43, no 5, p. 347-351Article in journal (Refereed)
    Abstract [en]

    It is shown that the method of amplified fragment length polymorphism (AFLP) can be used to estimate the contribution of parent plants to the genome of the progeny from artificial crosses between Saxifraga cernua and S. sibirica. According to Nei's (1972) genetic distances between plant groups, F-1 plants are intermediate between the parent species but closer to S. cernua, probably because its genome size is twice that of S. sibirica. Conversely, B-1 plants proved to be closer to S. sibirica, because the hybrid progeny were crossed back to this species.

  • 136.
    Edelfeldt, Stina
    et al.
    Univ Southern Denmark, Dept Biol, Campusvej 55, DK-5230 Odense M, Denmark;Univ Southern Denmark, Interdisciplinary Ctr Populat Dynam, Campusvej 55, DK-5230 Odense M, Denmark.
    Bengtsson, Karin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Dahlgren, Johan P.
    Univ Southern Denmark, Dept Biol, Campusvej 55, DK-5230 Odense M, Denmark;Univ Southern Denmark, Interdisciplinary Ctr Populat Dynam, Campusvej 55, DK-5230 Odense M, Denmark.
    Demographic senescence and effects on population dynamics of a perennial plant2019In: Ecology, ISSN 0012-9658, E-ISSN 1939-9170, Vol. 100, no 8, article id e02742Article in journal (Refereed)
    Abstract [en]

    Demographic rates in plants are usually assumed to be more stage or size dependent than age dependent, and aging is therefore not considered in demographic models. However, little is known about the effect of age on demographic rates, as there still are few studies based on long-term individual-based plant population data that consider both individual age and size. In addition, little is known about how aging of individuals may affect population dynamics. We present analyses of demographic data for three populations of Fumana procumbens collected 1985-2013, on individuals with known year of germination. We modeled age- and size-dependence of the vital rates of survival, growth, fruiting probability, and fruit number using thin plate spline regressions, and constructed an age x size integral projection model (IPM) to project population-level effects of aging. We found strong correlations between age and vital rates in solely age-based vital rate models, where vital rates initially increased with age, after which they stabilized and, in some cases, eventually declined. In survival models with both age and size, the effects of age were statistically significant, whereas size effects were insignificant at two of the sites. For other vital rates, most of the effect of age could be explained by size alone. In addition, including the age effects on survival in the IPM led to lower population growth rates compared to predictions of a size-only IPM. These results illustrate that demographic senescence does occur in perennial plants, which has only been demonstrated clearly in a few recent detailed studies. Moreover, we show that population projections may be overly optimistic if they do not consider plant age. We conclude that the possibility of demographic senescence should be considered in demographic population models, such as those used in viability analyses of threatened species.

  • 137. Ehrlen, Johan
    et al.
    Morris, William F.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Predicting changes in the distribution and abundance of species under environmental change2015In: Ecology Letters, ISSN 1461-023X, E-ISSN 1461-0248, Vol. 18, no 3, p. 303-314Article, review/survey (Refereed)
    Abstract [en]

    Environmental changes are expected to alter both the distribution and the abundance of organisms. A disproportionate amount of past work has focused on distribution only, either documenting historical range shifts or predicting future occurrence patterns. However, simultaneous predictions of abundance and distribution across landscapes would be far more useful. To critically assess which approaches represent advances towards the goal of joint predictions of abundance and distribution, we review recent work on changing distributions and on effects of environmental drivers on single populations. Several methods have been used to predict changing distributions. Some of these can be easily modified to also predict abundance, but others cannot. In parallel, demographers have developed a much better understanding of how changing abiotic and biotic drivers will influence growth rate and abundance in single populations. However, this demographic work has rarely taken a landscape perspective and has largely ignored the effects of intraspecific density. We advocate a synthetic approach in which population models accounting for both density dependence and effects of environmental drivers are used to make integrated predictions of equilibrium abundance and distribution across entire landscapes. Such predictions would constitute an important step forward in assessing the ecological consequences of environmental changes.

  • 138. Eidesen, Pernille Bronken
    et al.
    Mueller, Eike
    Lettner, Christian
    Alsos, Inger Greve
    Bender, Morgan
    Kristiansen, Martin
    Peeters, Bart
    Postma, Froukje
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Verweij, Koen Frans
    Tetraploids do not form cushions: association of ploidy level, growth form and ecology in the High Arctic Saxifraga oppositifolia L. s. lat. (Saxifragaceae) in Svalbard2013In: Polar Research, ISSN 0800-0395, E-ISSN 1751-8369, Vol. 32, p. UNSP 20071-Article in journal (Refereed)
    Abstract [en]

    Saxifraga oppositifolia L. is a common circumpolar plant species that displays considerable morphological and genetic variation throughout its range. It is mainly diploid, but tetraploids are reported from several regions. The growth form varies from prostate to cushion-shaped, and the plant thrives in wet snow beds as well as on dry ridges. This variation has triggered the curiosity of many researchers, but as yet, no one has explained the observed morphological variation using ecological and/or genetic factors. However, the ploidy level has rarely been taken into account. This is the first study that demonstrates a significant correlation between ploidy level, ecology and growth form in S. oppositifolia. We successfully analysed 193 individuals of S. oppositifolia from 15 locations in Svalbard to investigate possible relationships among growth forms (prostrate, intermediate and cushion), ecological factors (vegetation and soil characteristics) and ploidy level. Results from flow cytometry reported 106 diploids, eight triploids and 79 tetraploids. Tetraploids almost exclusively showed prostrate growth, while the diploids displayed all three growth forms, evidence that growth form is at least partly genetically determined. Our analyses of environmental and vegetation data in relation to ploidy level indicated overlapping niches, but the tetraploids showed a narrower niche, and one shifted towards more benign habitats characterized by higher pH, higher soil temperatures and higher cover of vascular plants. The latter may suggest that tetraploids are slightly better competitors, but less hardy. Thus, autopolyploidy in S. oppositifolia has expanded the ecological amplitude of this species complex.

  • 139. Ekbohm, G.
    et al.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    On estimating the species-area relationship: commenting Loehle1990In: Oikos, Vol. 57, p. 145-146Article in journal (Refereed)
  • 140. Eklund, D. Magnus
    et al.
    Ishizaki, Kimitsune
    Flores-Sandoval, Eduardo
    Kikuchi, Saya
    Takebayashi, Yumiko
    Tsukamoto, Shigeyuki
    Hirakawa, Yuki
    Nonomura, Maiko
    Kato, Hirotaka
    Kouno, Masaru
    Bhalerao, Rishikesh P.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kasahara, Hiroyuki
    Kohchi, Takayuki
    Bowman, John L.
    Auxin Produced by the Indole-3-Pyruvic Acid Pathway Regulates Development and Gemmae Dormancy in the Liverwort Marchantia polymorph2015In: The Plant Cell, ISSN 1040-4651, E-ISSN 1532-298X, Vol. 27, no 6, p. 1650-1669Article in journal (Refereed)
    Abstract [en]

    The plant hormone auxin (indole-3-acetic acid [IAA]) has previously been suggested to regulate diverse forms of dormancy in both seed plants and liverworts. Here, we use loss-and gain-of-function alleles for auxin synthesis-and signaling-related genes, as well as pharmacological approaches, to study how auxin regulates development and dormancy in the gametophyte generation of the liverwort Marchantia polymorpha. We found that M. polymorpha possess the smallest known toolkit for the indole-3-pyruvic acid (IPyA) pathway in any land plant and that this auxin synthesis pathway mainly is active in meristematic regions of the thallus. Previously a Trp-independent auxin synthesis pathway has been suggested to produce a majority of IAA in bryophytes. Our results indicate that the Trp-dependent IPyA pathway produces IAA that is essential for proper development of the gametophyte thallus of M. polymorpha. Furthermore, we show that dormancy of gemmae is positively regulated by auxin synthesized by the IPyA pathway in the apex of the thallus. Our results indicate that auxin synthesis, transport, and signaling, in addition to its role in growth and development, have a critical role in regulation of gemmae dormancy in M. polymorpha.

  • 141.
    Eklund, D. Magnus
    et al.
    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.
    Kanei, Masakazu
    Tokyo Univ Agr, Dept Biosci, Tokyo 1568502, Japan.
    Flores-Sandoval, Eduardo
    Monash Univ, Sch Biol Sci, Melbourne, Vic 3800, Australia.
    Ishizaki, Kimitsune
    Kobe Univ, Grad Sch Sci, Kobe, Hyogo 6578501, Japan.
    Nishihama, Ryuichi
    Kyoto Univ, Grad Sch Biostudies, Kyoto 6068502, Japan.
    Kohchi, Takayuki
    Kyoto Univ, Grad Sch Biostudies, Kyoto 6068502, Japan.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Bhalerao, Rishikesh P.
    Swedish Univ Agr Sci, Dept Forest Genet & Plant Physiol, Umea Plant Sci Ctr, S-90183 Umea, Sweden.
    Sakata, Yoichi
    Tokyo Univ Agr, Dept Biosci, Tokyo 1568502, Japan.
    Bowman, John L.
    Monash Univ, Sch Biol Sci, Melbourne, Vic 3800, Australia.
    An Evolutionarily Conserved Abscisic Acid Signaling Pathway Regulates Dormancy in the Liverwort Marchantia polymorpha2018In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 28, no 22, p. 3691-3699.e3Article in journal (Refereed)
    Abstract [en]

    Dormancy is a key process allowing land plants to adapt to changing conditions in the terrestrial habitat, allowing the cessation of growth in response to environmental or physiological cues, entrance into a temporary quiescent state, and subsequent reactivation of growth in more favorable environmental conditions [1-3]. Dormancy may be induced seasonally, sporadically (e.g., in response to drought), or developmentally (e.g., seeds and apical dominance). Asexual propagules, known as gemmae, derived via clonal reproduction in bryophytes, are often dormant until displaced from the parent plant. In the liverwort Marchantia polymorpha, gemmae are produced within specialized receptacles, gemma cups, located on the dorsal side of the vegetative thallus [4]. Mature gemmae are detached from the parent plant but may remain in the cup, with gemma growth suppressed as long as the gemmae remain in the gemma cup and the parental plant is alive [5]. Following dispersal of gemmae from gemma cups by rain, the gemmae germinate in the presence of light and moisture, producing clonal offspring [6]. In land plants, the plant hormone abscisic acid (ABA) regulates many aspects of dormancy and water balance [7]. Here, we demonstrate that ABA plays a central role in the control of gemma dormancy as transgenic M. polymorpha gemmae with reduced sensitivity to ABA fail to establish and/or maintain dormancy. Thus, the common ancestor of land plants used the ABA signaling module to regulate germination of progeny in response to environmental cues, with both gemmae and seeds being derived structures co-opting an ancestral response system.

  • 142.
    Ekroos, Johan
    et al.
    Lund Univ, Ctr Environm & Climate Res, Lund, Sweden..
    Jakobsson, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wideen, Joel
    Lund Univ, Ctr Environm & Climate Res, Lund, Sweden..
    Herbertsson, Lina
    Lund Univ, Ctr Environm & Climate Res, Lund, Sweden..
    Rundlof, Maj
    Lund Univ, Dept Biol, Lund, Sweden..
    Smith, Henrik G.
    Lund Univ, Ctr Environm & Climate Res, Lund, Sweden.;Lund Univ, Dept Biol, Lund, Sweden..
    Effects of landscape composition and configuration on pollination in a native herb: a field experiment2015In: Oecologia, ISSN 0029-8549, E-ISSN 1432-1939, Vol. 179, no 2, p. 509-518Article in journal (Refereed)
    Abstract [en]

    Bumble bee abundance in agricultural landscapes is known to decrease with increasing distance from seminatural grasslands, but whether the pollination of bumble-bee-pollinated wild plants shows a similar pattern is less well known. In addition, the relative effects of landscape composition (landscape heterogeneity) and landscape configuration (distance from seminatural grassland) on wild plant pollination, and the interaction between these landscape effects, have not been studied using landscape-level replication. We performed a field experiment to disentangle these landscape effects on the pollination of a native herb, the sticky catchfly (Lychnis viscaria), while accounting for the proportion of oilseed rape across landscapes and the local abundance of bee forage flowers. We measured pollen limitation (the degree to which seed set is pollen-limited), seed set, and seed set stability using potted plants placed in landscapes that differed in heterogeneity (composition) and distance from seminatural grassland (configuration). Pollen limitation and seed set in individual plants did not respond to landscape composition, landscape configuration, or proportion of oilseed rape. Instead, seed set increased with increasing local bee forage flower cover. However, we found within-plant variability in pollen limitation and seed set to increase with increasing distance from seminatural pasture. Our results suggest that average within-plant levels of pollen limitation and seed set respond less swiftly than the within-plant variability in pollen limitation and seed set to changes in landscape configuration. Although landscape effects on pollination were less important than predicted, we conclude that landscape configuration and local habitat characteristics play larger roles than landscape composition in the pollination of L. viscaria.

  • 143.
    Ellis, Thomas James
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. IST Austria, Klosterneuburg, Austria.
    Field, David Luke
    Univ Vienna, Dept Bot & Biodivers Res, Vienna, Austria;IST Austria, Klosterneuburg, Austria.
    Barton, Nicholas H.
    IST Austria, Klosterneuburg, Austria.
    Efficient inference of paternity and sibship inference given known maternity via hierarchical clustering2018In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 18, no 5, p. 988-999Article in journal (Refereed)
    Abstract [en]

    Pedigree and sibship reconstruction are important methods in quantifying relationships and fitness of individuals in natural populations. Current methods employ a Markov chain-based algorithm to explore plausible possible pedigrees iteratively. This provides accurate results, but is time-consuming. Here, we develop a method to infer sibship and paternity relationships from half-sibling arrays of known maternity using hierarchical clustering. Given 50 or more unlinked SNP markers and empirically derived error rates, the method performs as well as the widely used package Colony, but is faster by two orders of magnitude. Using simulations, we show that the method performs well across contrasting mating scenarios, even when samples are large. We then apply the method to open-pollinated arrays of the snapdragon Antirrhinum majus and find evidence for a high degree of multiple mating. Although we focus on diploid SNP data, the method does not depend on marker type and as such has broad applications in nonmodel systems.

  • 144.
    Ellis, Tom J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. IST Austria, Campus 1, A-3400 Klosterneuburg, Austria..
    Field, David L.
    IST Austria, Campus 1, A-3400 Klosterneuburg, Austria..
    Repeated gains in yellow and anthocyanin pigmentation in flower colour transitions in the Antirrhineae2016In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 117, no 7, p. 1133-1140Article in journal (Refereed)
    Abstract [en]

    Background and aims Angiosperms display remarkable diversity in flower colour, implying that transitions between pigmentation phenotypes must have been common. Despite progress in understanding transitions between anthocyanin (blue, purple, pink or red) and unpigmented (white) flowers, little is known about the evolutionary patterns of flower-colour transitions in lineages with both yellow and anthocyanin-pigmented flowers. This study investigates the relative rates of evolutionary transitions between different combinations of yellow- and anthocyanin-pigmentation phenotypes in the tribe Antirrhineae. Methods We surveyed taxonomic literature for data on anthocyanin and yellow floral pigmentation for 369 species across the tribe. We then reconstructed the phylogeny of 169 taxa and used phylogenetic comparative methods to estimate transition rates among pigmentation phenotypes across the phylogeny. Key Results In contrast to previous studies we found a bias towards transitions involving a gain in pigmentation, although transitions to phenotypes with both anthocyanin and yellow taxa are nevertheless extremely rare. Despite the dominance of yellow and anthocyanin-pigmented taxa, transitions between these phenotypes are constrained to move through a white intermediate stage, whereas transitions to double-pigmentation are very rare. The most abundant transitions are between anthocyanin-pigmented and unpigmented flowers, and similarly the most abundant polymorphic taxa were those with anthocyanin-pigmented and unpigmented flowers. Conclusions Our findings show that pigment evolution is limited by the presence of other floral pigments. This interaction between anthocyanin and yellow pigments constrains the breadth of potential floral diversity observed in nature. In particular, they suggest that selection has repeatedly acted to promote the spread of single-pigmented phenotypes across the Antirrhineae phylogeny. Furthermore, the correlation between transition rates and polymorphism suggests that the forces causing and maintaining variance in the short term reflect evolutionary processes on longer time scales.

  • 145.
    Elumeeva, Tatiana G.
    et al.
    Lomonosov Moscow State Univ, Fac Biol, Dept Geobot, Moscow, Russia.
    Onipchenko, Vladimir G.
    Lomonosov Moscow State Univ, Fac Biol, Dept Geobot, Moscow, Russia.
    Cornelissen, Johannes H. C.
    Vrije Univ Amsterdam, Fac Earth & Life Sci, Dept Ecol Sci, Syst Ecol, Amsterdam, Netherlands.
    Semenova, Galina V.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Perevedentseva, Lidia G.
    Perm State Univ, Dept Bot & Plant Genet, Fac Biol, Perm, Russia.
    Freschet, Gregoire T.
    Univ Paul Valery Montpellier, EPHE, Univ Montpellier, CNRS,UMR 5175,Ctr Ecol Fonct & Evolut, Montpellier, France.
    van Logtestijn, Richard S. P.
    Vrije Univ Amsterdam, Fac Earth & Life Sci, Dept Ecol Sci, Syst Ecol, Amsterdam, Netherlands.
    Soudzilovskaia, Nadejda A.
    Leiden Univ, CML, Inst Environm Sci, Environm Biol Dept, Leiden, Netherlands.
    Is intensity of plant root mycorrhizal colonization a good proxy for plant growth rate, dominance and decomposition in nutrient poor conditions?2018In: Journal of Vegetation Science, ISSN 1100-9233, E-ISSN 1654-1103, Vol. 29, no 4, p. 715-725Article in journal (Refereed)
    Abstract [en]

    QuestionsMycorrhizae may be a key element of plant nutritional strategies and of carbon and nutrient cycling. Recent research suggests that in natural conditions, intensity of mycorrhizal colonization should be considered an important plant feature. How are inter-specific variations in mycorrhizal colonization rate, plant relative growth rate (RGR) and leaf litter decomposability related? Is (arbuscular) mycorrhizal colonization linked to the dominance of plant species in nutrient-stressed ecosystems? LocationTeberda State Biosphere Reserve, northwest Caucasus, Russia. MethodsWe measured plant RGR under mycorrhizal limitation and under natural nutrition conditions, together with leaf litter decomposability and field intensity of mycorrhizal colonization across a wide range of plant species, typical for alpine communities of European mountains. We applied regression analysis to test whether the intensity of mycorrhizal colonization is a good predictor of RGR and decomposition rate, and tested how these traits predict plant dominance in communities. ResultsForb species with a high level of field mycorrhizal colonization had lower RGR under nutritional and mycorrhizal limitation, while grasses were unaffected. Litter decomposition rate was not related to the intensity of mycorrhizal colonization. Dominant species mostly had a higher level of mycorrhizal colonization and lower RGR without mycorrhizal colonization than subordinate species, implying that they were more dependent on mycorrhizal symbionts. There were no differences in litter decomposability. ConclusionsIn alpine herbaceous plant communities dominated by arbuscular mycorrhizae, nutrient dynamics are to a large extent controlled by mycorrhizal symbiosis. Intensity of mycorrhizal colonization is a negative predictor for whole plant RGR. Our study highlights the importance of mycorrhizal colonization as a key trait underpinning the role of plant species in carbon and nutrient dynamics in nutrient-limited herbaceous plant communities.

  • 146.
    Emsens, Willem-Jan
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Univ Antwerp, Dept Biol, Ecosyst Management Res Grp, Univ Pl 1C, B-2610 Antwerp, Belgium.
    Aggenbach, Camiel J. S.
    Univ Antwerp, Dept Biol, Ecosyst Management Res Grp, Univ Pl 1C, B-2610 Antwerp, Belgium;KWR Watercycle Res Inst, POB 1072, NL-3430 BB Nieuwegein, Netherlands.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Smolders, Alfons J. P.
    Radboud Univ Nijmegen, Inst Wetland & Water Res, Dept Aquat Ecol & Environm Biol, Heyendaalseweg 135-1, NL-6525 ED Nijmegen, Netherlands;B WARE Res Ctr, Toernootveld 1, NL-6525 ED Nijmegen, Netherlands.
    van Diggelen, Rudy
    Univ Antwerp, Dept Biol, Ecosyst Management Res Grp, Univ Pl 1C, B-2610 Antwerp, Belgium.
    Competition for light as a bottleneck for endangered fen species: An introduction experiment2018In: Biological Conservation, ISSN 0006-3207, E-ISSN 1873-2917, Vol. 220, p. 76-83Article in journal (Refereed)
    Abstract [en]

    Many endangered plant species remain absent in rewetted, previously drained fens. We performed a 3-year introduction experiment with endangered fen species (9 Carex- and 6 bryophyte species) in 4 hydrologically restored fens to investigate which factors hamper establishment and survival. Carex species were introduced as adults and seedlings, mosses as gametophytes. Introductions were done on (initially) bare soil, which allowed us to exclude excessive competition for light during the first year. First year survival of the transplants was high in all fens (mean survival = 96%), indicating that there were no direct abiotic constraints on establishment. However, survival analysis revealed that a decrease in relative light intensity (RLI) at the soil surface during consecutive years (indicating an increase in biotic competition for light) drove high mortality rates in most species. As a result, overall final survival was lowest in the two most productive (low light) fens (mean survival = 38%), while most transplants persisted in the two less productive (high light) fens (mean survival = 79%). Taller and faster-growing Carex species were able to outgrow light limitation near the soil surface, and thus had a higher overall survivability than smaller and slower-growing species. Light limitation also drove the loss of 5 out of 6 bryophyte species. We conclude that both dispersal limitation and asymmetric competition for light may explain the lack and loss of small and endangered plant species in rewetted fens. A minimum empirical threshold of c. 30% relative light intensity near the soil surface is required for successful introduction.

  • 147. Falahati-Anbaran, Mohsen
    et al.
    Lundemo, Sverre
    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.
    Stenoien, Hans K.
    Genetic consequences of seed banks in the perennial herb Arabidopsis lyrata subsp. petraea (Brassicaceae)2011In: American Journal of Botany, ISSN 0002-9122, E-ISSN 1537-2197, Vol. 98, no 9, p. 1475-1485Article in journal (Refereed)
    Abstract [en]

    Premise of the Study: Seed banks may increase the effective population size (N(e)) of plants as a result of elevated coalescence times for alleles residing in the populations. This has been empirically demonstrated in populations of the annual Arabidopsis thaliana, whereas comparable data for perennial species are currently lacking. We studied the contribution of seed banks to effective sizes of natural populations of the self-incompatible, perennial Arabidopsis lyrata subsp. petraea, a close relative of A. thaliana. Methods: Fourteen populations of A. lyrata collected throughout the Norwegian distribution range were analyzed using micro-satellite markers. Key Results: The genetic composition of seed-bank and aboveground cohorts was found to be highly similar, with little genetic differentiation between cohorts in most populations. However, the proportion of private alleles was higher in aboveground than in seed-bank cohorts. The presence of seed banks significantly increased total N(e), but the contribution from seed banks to overall N(e) were lower than the contribution from aboveground cohorts in most populations. Estimated historical N(e) values, reflecting the effective sizes of populations throughout the history of the species, were considerably higher than estimates of contemporary N(e), reflecting number of reproducing individuals within the past few generations. Conclusions: The results show that the seed bank contributes to total N(e) in the perennial herb A. lyrata. However, the contribution is similar to or lower than that of the above-ground fraction of the population and markedly weaker than that previously documented in the annual A. thaliana.

  • 148. Falkengren-Grerup, U.
    et al.
    Ericson, L.
    Gunnarsson, U.
    Nordin, A.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wallén, B.
    Does nitrogen deposition change the flora?2000In: Effects of nitrogen deposition on forest ecosystems, Stockholm: Naturvårdsverket , 2000Chapter in book (Refereed)
  • 149. Falkengren-Grerup, U.
    et al.
    Ericson, L.
    Gunnarsson, U.
    Nordin, A.
    Rydin, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wallén, B.
    Förändras floran av kvävenedfallet?2000In: Effekter av kvävenedfall på skogsekosystem, Stockholm: Naturvårdsverket , 2000Chapter in book (Refereed)
  • 150. Favre, Adrien
    et al.
    Karrenberg, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stress tolerance in closely related species and their first-generation hybrids: a case study of Silene2011In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 99, no 6, p. 1415-1423Article in journal (Refereed)
    Abstract [en]

    1. Hybridization is common in natural plant populations. Trait expression and ecological performance of hybrids determine the consequences of hybridization such as the degree and direction of gene flow or the generation of phenotypic novelty.

    2. We investigated responses to shade and drought stress in crosses within the naturally hybridizing campions Silene dioica and S. latifolia and reciprocal crosses between them. We collected data on fitness proxies and on leaf and root traits in a 2-year greenhouse experiment.

    3. Responses to drought stress did not differ between cross types. Shade stress, in contrast, led to a reduced flowering incidence in S. dioica but not in S. latifolia. Rapid flowering under stress conditions in S. latifolia could be an adaptation to disturbance in its habitat, whereas a delay of reproduction might be adaptive in the more predictable environment of S. dioica.

    4. Hybrids exhibited intermediate, parental-like and transgressive trait expression. Both hybrid cross types were similar to S. latifolia in terms of biomass production possibly because of dominance of S. latifolia alleles or heterosis. Hybrids further had a strongly reduced flowering incidence under shade stress as did S. dioica, suggesting dominance of S. dioica alleles for flower induction. Under shade stress, both hybrid cross types produced much larger leaves than either of the two species suggesting that epigenetic interactions are disturbed. Reciprocal hybrids did not differ in fitness; however, maternal effects were observed for root cross-sectional area and mass per male flower, possibly supporting asymmetric gene flow in natural populations.

    5.Synthesis. Silene latifolia and S. dioica responded to stress with differences in life history rather than in growth. Our results further suggest that different modes of gene action are responsible for the specific combination of intermediate, parental-like and transgressive traits observed in first-generation hybrids that may limit their performance and thus gene flow between the species.

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