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  • 251.
    Carter, Mauricio J.
    et al.
    Univ Chile, Ctr Nacl Medio Ambiente, Ave Larrain 9975, Santiago, Chile.;Univ Andres Bello, Dept Ecol, Fac Ecol & Recursos Nat, Santiago, Chile..
    Lind, Martin I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Dennis, Stuart R.
    Eawag, Dept Aquat Ecol, Uberlandstr 133, CH-8600 Dubendorf, Switzerland..
    Hentley, William
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England..
    Beckerman, Andrew P.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England..
    Evolution of a predator-induced, nonlinear reaction norm2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1861, article id 20170859Article in journal (Refereed)
    Abstract [en]

    Inducible, anti-predator traits are a classic example of phenotypic plasticity. Their evolutionary dynamics depend on their genetic basis, the historical pattern of predation risk that populations have experienced and current selection gradients. When populations experience predators with contrasting hunting strategies and size preferences, theory suggests contrasting micro-evolutionary responses to selection. Daphnia pulex is an ideal species to explore the microevolutionary response of anti-predator traits because they face heterogeneous predation regimes, sometimes experiencing only invertebrate midge predators and other times experiencing vertebrate fish and invertebrate midge predators. We explored plausible patterns of adaptive evolution of a predator-induced morphological reaction norm. We combined estimates of selection gradients that characterize the various habitats that D. pulex experiences with detail on the quantitative genetic architecture of inducible morphological defences. Our data reveal a fine scale description of daphnid defensive reaction norms, and a strong covariance between the sensitivity to cues and the maximum response to cues. By analysing the response of the reaction norm to plausible, predator-specific selection gradients, we show how in the context of this covariance, micro-evolution may be more uniform than predicted from size-selective predation theory. Our results show how covariance between the sensitivity to cues and the maximum response to cues for morphological defence can shape the evolutionary trajectory of predator-induced defences in D. pulex.

  • 252.
    Carter, Mauricio J.
    et al.
    Universidad de Chile, Centro Nacional del Medio Ambiente; Universidad Andres Bello, Facultad de Ecología y Recursos Naturales, Departamento de Ecología.
    Lind, Martin I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Dennis, Stuart R.
    Eawag, Department of Aquatic Ecology.
    Hentley, William
    University of Sheffield, Department of Animal and Plant Sciences.
    Beckerman, Andrew P.
    University of Sheffield, Department of Animal and Plant Sciences.
    Evolution of a predator-induced, nonlinear reaction norm2017In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 284, no 1861, article id 20170859Article in journal (Refereed)
    Abstract [en]

    Inducible, anti-predator traits are a classic example of phenotypic plasticity. Their evolutionary dynamics depend on their genetic basis, the historical pattern of predation risk that populations have experienced and current selection gradients. When populations experience predators with contrasting hunting strategies and size preferences, theory suggests contrasting micro-evolutionary responses to selection. Daphnia pulex is an ideal species to explore the microevolutionary response of anti-predator traits because they face heterogeneous predation regimes, sometimes experiencing only invertebrate midge predators and other times experiencing vertebrate fish and invertebrate midge predators. We explored plausible patterns of adaptive evolution of a predator-induced morphological reaction norm. We combined estimates of selection gradients that characterize the various habitats that D. pulex experiences with detail on the quantitative genetic architecture of inducible morphological defences. Our data reveal a fine scale description of daphnid defensive reaction norms, and a strong covariance between the sensitivity to cues and the maximum response to cues. By analysing the response of the reaction norm to plausible, predator-specific selection gradients, we show how in the context of this covariance, micro-evolution may be more uniform than predicted from size-selective predation theory. Our results show how covariance between the sensitivity to cues and the maximum response to cues for morphological defence can shape the evolutionary trajectory of predator-induced defences in D. pulex.

  • 253.
    Caruso, Christina M.
    et al.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada.
    Eisen, Katherine E.
    Univ Guelph, Dept Integrat Biol, Guelph, ON, Canada; Cornell Univ, Dept Ecol & Evolutionary Biol, Ithaca, NY, USA.
    Martin, Ryan A.
    Case Western Reserve Univ, Dept Biol, Cleveland, OH, USA.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    A meta-analysis of the agents of selection on floral traits2019In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 73, no 1, p. 4-14Article in journal (Refereed)
    Abstract [en]

    Floral traits are hypothesized to evolve primarily in response to selection by pollinators. However, selection can also be mediated by other environmental factors. To understand the relative importance of pollinator-mediated selection and its variation among trait and pollinator types, we analyzed directional selection gradients on floral traits from experiments that manipulated the environment to identify agents of selection. Pollinator-mediated selection was stronger than selection by other biotic factors (e.g., herbivores), but similar in strength to selection by abiotic factors (e.g., soil water), providing partial support for the hypothesis that floral traits evolve primarily in response to pollinators. Pollinator-mediated selection was stronger on pollination efficiency traits than on other trait types, as expected if efficiency traits affect fitness via interactions with pollinators, but other trait types also affect fitness via other environmental factors. In addition to varying among trait types, pollinator-mediated selection varied among pollinator taxa: selection was stronger when bees, long-tongued flies, or birds were the primary visitors than when the primary visitors were Lepidoptera or multiple animal taxa. Finally, reducing pollinator access to flowers had a relatively small effect on selection on floral traits, suggesting that anthropogenic declines in pollinator populations would initially have modest effects on floral evolution.

  • 254.
    Caruso, Christina M.
    et al.
    Univ Guelph, Dept Integrat Biol..
    Martin, Ryan A.
    Case Western Reserve Univ, Dept Biol..
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Morrissey, Michael B.
    Univ St Andrews, Sch Biol..
    Wade, Michael J.
    Indiana Univ, Dept Biol..
    Augustine, Kate E.
    Univ N Carolina, Dept Biol..
    Carlson, Stephanie M.
    Univ Calif Berkeley, Dept Environm Sci Policy & Management..
    MacColl, Andrew D. C.
    Univ Nottingham, Sch Life Sci..
    Siepielski, Adam M.
    Univ Arkansas, Dept Biol Sci..
    Kingsolver, Joel G.
    Univ N Carolina, Dept Biol..
    What Are the Environmental Determinants of Phenotypic Selection?: A Meta-analysis of Experimental Studies2017In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 190, no 3, p. 363-376Article in journal (Refereed)
    Abstract [en]

    Although many selection estimates have been published, the environmental factors that cause selection to vary in space and time have rarely been identified. One way to identify these factors is by experimentally manipulating the environment and measuring selection in each treatment. We compiled and analyzed selection estimates from experimental studies. First, we tested whether the effect of manipulating the environment on selection gradients depends on taxon, trait type, or fitness component. We found that the effect of manipulating the environment was larger when selection was measured on life-history traits or via survival. Second, we tested two predictions about the environmental factors that cause variation in selection. We found support for the prediction that variation in selection is more likely to be caused by environmental factors that have a large effect on mean fitness but not for the prediction that variation is more likely to be caused by biotic factors. Third, we compared selection gradients from experimental and observational studies. We found that selection varied more among treatments in experimental studies than among spatial and temporal replicates in observational studies, suggesting that experimental studies can detect relationships between environmental factors and selection that would not be apparent in observational studies.

  • 255.
    Cauchard, Laure
    et al.
    Univ Montreal, Dept Sci Biol, Montreal, PQ, Canada.
    Angers, Bernard
    Univ Montreal, Dept Sci Biol, Montreal, PQ, Canada.
    Boogert, Neeltje J.
    Univ Exeter, Ctr Ecol & Conservat, Penryn, England.
    Lenarth, Melissa
    Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland.
    Bize, Pierre
    Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland;Univ Aberdeen, Inst Biol & Environm Sci, Aberdeen, Scotland.
    Doligez, Blandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Lyon 1, Dept Biometry & Evolutionary Biol, CNRS, Villeurbanne, France.
    An Experimental Test of a Causal Link between Problem-Solving Performance and Reproductive Success in Wild Great Tits2017In: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 5, article id 107Article in journal (Refereed)
    Abstract [en]

    Recent studies have uncovered relationships between measures of various cognitive performances and proxies of fitness such as reproductive success in non-human animals. However, to better understand the evolution of cognition in the wild, we still have to determine the causality of these relationships and the underlying mechanisms. The cognitive ability of an individual may directly influence its ability to raise many and/or high quality young through for example its provisioning ability. Conversely, large and/or high quality broods may lead to high parental motivation to solve problems related to their care. To answer this question, we manipulated reproductive success through brood size and measured subsequent problem-solving performance in wild great tit parents. Our results show that brood size manipulation did not affect the probability to solve the task. Moreover, solver pairs fledged more young than non-solver pairs independently of brood size treatment in one of the two experimental years and they showed higher nestling provisioning rate in both years. Overall, it shows that problem-solving performance was not driven by motivation and suggest that problem-solvers may achieve higher fledging success through higher provisioning rates. Our study constitutes a first key step toward a mechanistic understanding of the consequences of innovation ability for individual fitness in the wild.

  • 256.
    Cenci, Ugo
    et al.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.
    Sibbald, Shannon J.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.
    Curtis, Bruce A.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.
    Kamikawa, Ryoma
    Kyoto Univ, Grad Sch Human & Environm Studies, Kyoto, Kyoto 6068501, Japan.
    Eme, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada.
    Moog, Daniel
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada;Philipps Univ Marburg, Cell Biol Lab, Karl von Frisch Str 8, D-35043 Marburg, Germany.
    Henrissat, Bernard
    Univ Aix Marseille, CNRS, AFMB, 163 Ave Luminy, F-13288 Marseille, France;INRA, USC AFMB 1408, F-13288 Marseille, France;King Abdulaziz Univ, Dept Biol Sci, Jeddah 21589, Saudi Arabia.
    Marechal, Eric
    Univ Grenoble Alpes, Lab Physiol Cellulaire & Vegetale, CNRS, CEA,INRA,Inst Biosci & Biotechnol Grenoble,CEA Gr, 17 Rue Martyrs, F-38000 Grenoble, France.
    Chabi, Malika
    Univ Lille 1, UMR 8576, Unite Glycobiol Struct & Fonct, F-59650 Villeneuve Dascq, France.
    Djemiel, Christophe
    Univ Lille 1, UMR 8576, Unite Glycobiol Struct & Fonct, F-59650 Villeneuve Dascq, France.
    Roger, Andrew J.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada;Canadian Inst Adv Res, Program Integrated Microbial Biodivers, Toronto, ON, Canada.
    Kim, Eunsoo
    Amer Museum Nat Hist, Div Invertebrate Zool, Cent Pk West & 79 St, New York, NY 10024 USA;Amer Museum Nat Hist, Sackler Inst Comparat Genom, Cent Pk West & 79 St, New York, NY 10024 USA.
    Archibald, John M.
    Dalhousie Univ, Dept Biochem & Mol Biol, Halifax, NS B3H 4R2, Canada;Dalhousie Univ, Ctr Comparat Genom & Evolutionary Bioinformat, Halifax, NS, Canada;Canadian Inst Adv Res, Program Integrated Microbial Biodivers, Toronto, ON, Canada.
    Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids2018In: BMC Biology, ISSN 1741-7007, E-ISSN 1741-7007, Vol. 16, article id 137Article in journal (Refereed)
    Abstract [en]

    Background: The evolution of photosynthesis has been a major driver in eukaryotic diversification. Eukaryotes have acquired plastids (chloroplasts) either directly via the engulfment and integration of a photosynthetic cyanobacterium (primary endosymbiosis) or indirectly by engulfing a photosynthetic eukaryote (secondary or tertiary endosymbiosis). The timing and frequency of secondary endosymbiosis during eukaryotic evolution is currently unclear but may be resolved in part by studying cryptomonads, a group of single-celled eukaryotes comprised of both photosynthetic and non-photosynthetic species. While cryptomonads such as Guillardia theta harbor a red algal-derived plastid of secondary endosymbiotic origin, members of the sister group Goniomonadea lack plastids. Here, we present the genome of Goniomonas avonlea-the first for any goniomonad-to address whether Goniomonadea are ancestrally non-photosynthetic or whether they lost a plastid secondarily. Results: We sequenced the nuclear and mitochondrial genomes of Goniomonas avonlea and carried out a comparative analysis of Go. avonlea, Gu. theta, and other cryptomonads. The Go. avonlea genome assembly is similar to 92 Mbp in size, with 33,470 predicted protein-coding genes. Interestingly, some metabolic pathways (e.g., fatty acid biosynthesis) predicted to occur in the plastid and periplastidal compartment of Gu. theta appear to operate in the cytoplasm of Go. avonlea, suggesting that metabolic redundancies were generated during the course of secondary plastid integration. Other cytosolic pathways found in Go. avonlea are not found in Gu. theta, suggesting secondary loss in Gu. theta and other plastid-bearing cryptomonads. Phylogenetic analyses revealed no evidence for algal endosymbiont-derived genes in the Go. avonlea genome. Phylogenomic analyses point to a specific relationship between Cryptista (to which cryptomonads belong) and Archaeplastida. Conclusion: We found no convincing genomic or phylogenomic evidence that Go. avonlea evolved from a secondary red algal plastid-bearing ancestor, consistent with goniomonads being ancestrally non-photosynthetic eukaryotes. The Go. avonlea genome sheds light on the physiology of heterotrophic cryptomonads and serves as an important reference point for studying the metabolic "rewiring" that took place during secondary plastid integration in the ancestor of modern-day Cryptophyceae.

  • 257. Chapman, T
    et al.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Bangham, J
    Rowe, L
    Response to Eberhard and Cordero, and Cordoba-Aguilar and Contreras-Garduno: sexual conflict and female choice2003In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 18, no 9, p. 440-441Article in journal (Refereed)
  • 258. Chapman, T
    et al.
    Arnqvist, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Bangham, J
    Rowe, L
    Sexual conflict2003In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 18, no 1, p. 41-47, article id PII S0169-5347(02)00004-6Article in journal (Refereed)
  • 259.
    Chapron, Guillaume
    et al.
    Swedish University of Agricultural Sciences, Department of Ecology, Grimsö Wildlife Research Station, Riddarhyttan, Sweden.
    Epstein, Yaffa
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Law, Department of Law.
    Trouwborst, Arie
    Tilburg University, Department of European and International Law, Tilburg, The Netherlands.
    Vicente López-Bao, José
    Oviedo University, Research Unit of Biodiversity (UO/CSIC/PA), Mieres, Spain.
    Bolster Legal Boundaries to Stay within Planetary Boundaries2017In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 1, no 3, article id UNSP 0086Article in journal (Refereed)
    Abstract [en]

    The mounting threats posed to the global environment by harmful human activities cannot be averted without effective legislation controlling those activities. However, the environmental laws designed for this purpose are themselves under global attack. Because it is binding and enforceable, legislation is a unique and essential instrument in the overall effort to keep humanity’s impacts on the planet from transgressing critical thresholds. For instance, biodiversity laws do so by designating and protecting natural areas and controlling the exploitation of wildlife populations. Yet, due to short-term economic and other interests, such laws face constant pressures aimed at weakening their regulating impact on human activities. 

    This new study reveals and illustrates the staggering number and diversity of tactics used to weaken biodiversity legislation across the globe. This ‘taxonomy of tactics’ encompasses dozens of categories, ranging from the creative re-definition of terms to the ‘fast-tracking’ of environmentally harmful projects, and from limiting concerned citizens’ access to court, to the silent or even express refusal of appointed authorities to enforce biodiversity laws.

    Whereas the predicament of the planet’s wild fauna and flora would have been even worse without the legal protection they have received so far, the onslaught against biodiversity laws has prevented these from fully performing their assigned function. The global acceleration of wildlife population declines bears witness to this. To stem the tide, strategic approaches are needed to anticipate and counter attacks on biodiversity legislation; to make the most of existing laws, including in court if need be; and to develop new or improved laws where necessary.

  • 260.
    Chapurlat, Elodie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Evolutionary Ecology of Floral Traits in Fragrant Orchids2018Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Why are flowers so diverse? Much of floral evolution is thought to be driven by pollinator-mediated selection. However, the connection between macroevolutionary patterns of floral diversity and microevolutionary processes remains poorly understood. In this thesis, I have used the fragrant orchids Gymnadenia conopsea s.s. and Gymnadenia densiflora to investigate the role of pollinators as agents of selection on floral traits and to test whether they cause spatial variation in selection. I addressed the following questions (1) Is there divergent selection on flowering phenology and floral traits between these two closely related species? (2) What is the contribution of pollinators relative to other selective agents to selection on phenology, visual display, floral scent and spur length? (3) Do diurnal and nocturnal pollinators mediate different selection patterns? (4) Does spatial variation in pollinator communities cause spatial variation in selection?

    A phenotypic selection study in G. conopsea s.s. and G. densiflora indicated that divergent selection on flowering time contributes to the maintenance of phenological differentiation between the two species. Hand-pollination experiments combined with selection analysis showed that while pollinators were the main selective agent on spur length, their contribution to selection on phenology, visual display and floral scent was more variable and sometimes opposed by non-pollinator mediated selection. Selection analyses combined with a selective exclusion experiment showed that diurnal and nocturnal pollinators exerted different selection patterns on floral traits. Hand-pollination experiments also demonstrated that variation in pollinator-mediated selection largely explained spatial variation in net selection on phenology, visual display and spur length among four populations. A study of floral scent emission of G. conopsea s.s. in the field coupled with a growth-chamber experiment revealed genetically-based variation in floral scent consistent with a scenario where spatial variation in relative importance of nocturnal and diurnal pollinators has resulted in the evolution of different scent emission rhythms.

    Taken together, the results support the hypothesis that pollinators cause spatial variation in selection on floral traits. They also highlight the importance of experimentally identifying sources of selection to reveal conflicting and reinforcing selection by multiple agents and thus advance our understanding of the evolutionary ecology of floral traits.

    List of papers
    1. Divergent selection on flowering phenology but not on floral morphology between two closely related orchids
    Open this publication in new window or tab >>Divergent selection on flowering phenology but not on floral morphology between two closely related orchids
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-358245 (URN)
    Available from: 2018-08-26 Created: 2018-08-26 Last updated: 2018-08-26
    2. Spatial variation in pollinator-mediated selection on phenology, floral display and spur length in the orchid Gymnadenia conopsea
    Open this publication in new window or tab >>Spatial variation in pollinator-mediated selection on phenology, floral display and spur length in the orchid Gymnadenia conopsea
    2015 (English)In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 208, no 4, p. 1264-1275Article in journal (Refereed) Published
    Abstract [en]

    Spatial variation in plant-pollinator interactions may cause variation in pollinator-mediated selection on floral traits, but to establish this link conclusively experimental studies are needed. We quantified pollinator-mediated selection on flowering phenology and morphology in four populations of the fragrant orchid Gymnadenia conopsea, and compared selection mediated by diurnal and nocturnal pollinators in two of the populations. Variation in pollinator-mediated selection explained most of the among-population variation in the strength of directional and correlational selection. Pollinators mediated correlational selection on pairs of display traits, and on one display trait and spur length, a trait affecting pollination efficiency. Only nocturnal pollinators selected for longer spurs, and mediated stronger selection on the number of flowers compared with diurnal pollinators in one population. The two types of pollinators caused correlational selection on different pairs of traits and selected for different combinations of spur length and number of flowers. The results demonstrate that spatial variation in interactions with pollinators may result in differences in directional and correlational selection on floral traits in a plant with a semi-generalized pollination system, and suggest that differences in the relative importance of diurnal and nocturnal pollinators can cause variation in selection.

    National Category
    Ecology
    Identifiers
    urn:nbn:se:uu:diva-275786 (URN)10.1111/nph.13555 (DOI)000365393000025 ()
    Funder
    Swedish Research CouncilSwedish Research Council Formas
    Available from: 2016-02-06 Created: 2016-02-06 Last updated: 2018-08-26Bibliographically approved
    3. Diel pattern of floral scent emission matches the relative importance of diurnal and nocturnal pollinators in populations of Gymnadenia conopsea
    Open this publication in new window or tab >>Diel pattern of floral scent emission matches the relative importance of diurnal and nocturnal pollinators in populations of Gymnadenia conopsea
    Show others...
    2018 (English)In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 121, p. 711-721Article in journal (Refereed) Published
    Abstract [en]

    Background and Aims

    Floral scent is considered an integral component of pollination syndromes, and its composition and timing of emission are thus expected to match the main pollinator type and time of activity. While floral scent differences among plant species with different pollination systems can be striking, studies on intraspecific variation are sparse, which limits our understanding of the role of pollinators in driving scent divergence.

    Methods

    Here, we used dynamic headspace sampling to quantify floral scent emission and composition during the day and at night in the natural habitat of six Scandinavian populations of the fragrant orchid Gymnadenia conopsea. We tested whether diel scent emission and composition match pollinator type by comparing four populations in southern Sweden, where nocturnal pollinators are more important for plant reproductive success than are diurnal pollinators, with two populations in central Norway, where the opposite is true. To determine to what extent scent patterns quantified in the field reflected plasticity, we also measured scent emission in a common growth chamber environment.

    Key Results

    Both scent composition and emission rates differed markedly between day and night, but only the latter varied significantly among populations. The increase in scent emission rate at night was considerably stronger in the Swedish populations compared with the Norwegian populations. These patterns persisted when plants were transferred to a common environment, suggesting a genetic underpinning of the scent variation.

    Conclusions

    The results are consistent with a scenario where spatial variation in relative importance of nocturnal and diurnal pollinators has resulted in selection for different scent emission rhythms. Our study highlights the importance of adding a characterization of diel variation of scent emission rates to comparative studies of floral scent, which so far have often focused on scent composition only.

    Keywords
    diel variation, diurnal and nocturnal pollination, floral evolution, floral scent, geographic variation, Gymnadenia conopsea (fragrant orchid), plasticity, population differentiation, scent emission rate, scent rhythm, semi-generalkized pollination, spatial variation
    National Category
    Evolutionary Biology Ecology
    Identifiers
    urn:nbn:se:uu:diva-358243 (URN)10.1093/aob/mcx203 (DOI)000427884200015 ()29360931 (PubMedID)
    Funder
    Swedish Research Council FormasSwedish Research Council
    Available from: 2018-08-26 Created: 2018-08-26 Last updated: 2019-06-28Bibliographically approved
    4. Conflicting selection on floral scent in the fragrant orchid Gymnadenia conopsea s.s.
    Open this publication in new window or tab >>Conflicting selection on floral scent in the fragrant orchid Gymnadenia conopsea s.s.
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Ecology Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-358247 (URN)
    Available from: 2018-08-26 Created: 2018-08-26 Last updated: 2018-08-26
  • 261.
    Chapurlat, Elodie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Anderson, Joseph
    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.
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Lund University.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conflicting selection on floral scent in the fragrant orchid Gymnadenia conopsea s.s.Manuscript (preprint) (Other academic)
  • 262.
    Chapurlat, Elodie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Anderson, Joseph
    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.
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Diel pattern of floral scent emission matches the relative importance of diurnal and nocturnal pollinators in populations of Gymnadenia conopsea2018In: Annals of Botany, ISSN 0305-7364, E-ISSN 1095-8290, Vol. 121, p. 711-721Article in journal (Refereed)
    Abstract [en]

    Background and Aims

    Floral scent is considered an integral component of pollination syndromes, and its composition and timing of emission are thus expected to match the main pollinator type and time of activity. While floral scent differences among plant species with different pollination systems can be striking, studies on intraspecific variation are sparse, which limits our understanding of the role of pollinators in driving scent divergence.

    Methods

    Here, we used dynamic headspace sampling to quantify floral scent emission and composition during the day and at night in the natural habitat of six Scandinavian populations of the fragrant orchid Gymnadenia conopsea. We tested whether diel scent emission and composition match pollinator type by comparing four populations in southern Sweden, where nocturnal pollinators are more important for plant reproductive success than are diurnal pollinators, with two populations in central Norway, where the opposite is true. To determine to what extent scent patterns quantified in the field reflected plasticity, we also measured scent emission in a common growth chamber environment.

    Key Results

    Both scent composition and emission rates differed markedly between day and night, but only the latter varied significantly among populations. The increase in scent emission rate at night was considerably stronger in the Swedish populations compared with the Norwegian populations. These patterns persisted when plants were transferred to a common environment, suggesting a genetic underpinning of the scent variation.

    Conclusions

    The results are consistent with a scenario where spatial variation in relative importance of nocturnal and diurnal pollinators has resulted in selection for different scent emission rhythms. Our study highlights the importance of adding a characterization of diel variation of scent emission rates to comparative studies of floral scent, which so far have often focused on scent composition only.

  • 263.
    Chapurlat, Elodie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Le Roncé, Iris
    Ecole Normale Supérieure de Lyon.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Divergent selection on flowering phenology but not on floral morphology between two closely related orchidsManuscript (preprint) (Other academic)
  • 264.
    Chapurlat, Elodie
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ågren, Jon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Anderson, Joseph
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Friberg, Magne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Lund Univ, Dept Biol, SE-22362 Lund, Sweden.
    Sletvold, Nina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conflicting selection on floral scent emission in the orchid Gymnadenia conopsea2019In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 222, no 4, p. 2009-2022Article in journal (Refereed)
    Abstract [en]

    Floral scent is a crucial trait for pollinator attraction. Yet only a handful of studies have estimated selection on scent in natural populations and no study has quantified the relative importance of pollinators and other agents of selection. In the fragrant orchid Gymnadenia conopsea, we used electroantennographic data to identify floral scent compounds detected by local pollinators and quantified pollinator-mediated selection on emission rates of 10 target compounds as well as on flowering start, visual display and spur length. Nocturnal pollinators contributed more to reproductive success than diurnal pollinators, but there was significant pollinator-mediated selection on both diurnal and nocturnal scent emission. Pollinators selected for increased emission of two compounds and reduced emission of two other compounds, none of which were major constituents of the total bouquet. In three cases, pollinator-mediated selection was opposed by nonpollinator-mediated selection, leading to weaker or no detectable net selection. Our study demonstrates that minor scent compounds can be targets of selection, that pollinators do not necessarily favour stronger scent signalling, and that some scent compounds are subject to conflicting selection from pollinators and other agents of selection. Hence, including floral scent traits into selection analysis is important for understanding the mechanisms behind floral evolution.

  • 265.
    Cheeke, Tanya E.
    et al.
    Swedish Univ Agr Sci, Uppsala Bioctr, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden.;Indiana Univ, Dept Biol, 1001 E Third St, Bloomington, IN 47405 USA..
    Phillips, Richard P.
    Indiana Univ, Dept Biol, 1001 E Third St, Bloomington, IN 47405 USA..
    Brzostek, Edward R.
    West Virginia Univ, Dept Biol, 53 Campus Dr, Morgantown, WV 26506 USA..
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Bever, James D.
    Indiana Univ, Dept Biol, 1001 E Third St, Bloomington, IN 47405 USA.;Univ Kansas, Dept Ecol & Evolutionary Biol, 2041 Haworth Hall,1200 Sunnyside Ave, Lawrence, KS 66045 USA..
    Fransson, Petra
    Swedish Univ Agr Sci, Uppsala Bioctr, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden..
    Dominant mycorrhizal association of trees alters carbon and nutrient cycling by selecting for microbial groups with distinct enzyme function2017In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 214, no 1, p. 432-442Article in journal (Refereed)
    Abstract [en]

    While it is well established that plants associating with arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi cycle carbon (C) and nutrients in distinct ways, we have a limited understanding of whether varying abundance of ECM and AM plants in a stand can provide integrative proxies for key biogeochemical processes. We explored linkages between the relative abundance of AM and ECM trees and microbial functioning in three hardwood forests in southern Indiana, USA. Across each site's 'mycorrhizal gradient', we measured fungal biomass, fungal : bacterial (F : B) ratios, extracellular enzyme activities, soil carbon : nitrogen ratio, and soil pH over a growing season. We show that the percentage of AM or ECM trees in a plot promotes microbial communities that both reflect and determine the C to nutrient balance in soil. Soils dominated by ECM trees had higher F : B ratios and more standing fungal biomass than AM stands. Enzyme stoichiometry in ECM soils shifted to higher investment in extracellular enzymes needed for nitrogen and phosphorus acquisition than in C-acquisition enzymes, relative to AM soils. Our results suggest that knowledge of mycorrhizal dominance at the stand or landscape scale may provide a unifying framework for linking plant and microbial community dynamics, and predicting their effects on ecological function.

  • 266.
    Chen, Dong Lei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tafforeau, Paul
    Estonian Marine Institute, University of Tartu.
    Märss, Tiiu
    Estonian Marine Institute, University of Tartu.
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Development of cyclic shedding teeth from semi-shedding teeth: the inner dental arcade of the stem osteichthyan Lophosteus 2017In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 4, no 5, article id 161084Article in journal (Refereed)
    Abstract [en]

    The numerous cushion-shaped tooth-bearing plates attributed to the stem-group osteichthyan Lophosteus superbus, which are argued here to represent the ancient form of inner dental arcade, display a unique and presumably primitive way of tooth shedding by basal hard tissue resorption. They carry regularly spaced, recumbent, gently recurved teeth arranged in transverse tooth files that diverge towards the lingual margin of the cushion. Three-dimensional (3D) reconstruction from propagation phase contrast synchrotron microtomography (PPC-SRμCT) reveals remnants of the first-generation teeth embedded in the basal plate that have never been discerned in any taxa. These teeth were shed by semi-basal resorption with the periphery of their bases retained as dentine rings. The rings are highly overlapped, which evidences tooth shedding prior to adding the next first-generation tooth. Later teeth at the same sites underwent cyclical replacing and shedding through basal resorption, producing stacks of buried resorption surfaces separated by bone of attachment. The number and spatial arrangement of resorption surfaces elucidates that basal resorption of replacement teeth had taken place at the older tooth sites before the addition of the youngest first-generation teeth at the lingual margin. Thus the replacement tooth buds cannot have been generated by a single permanent dental lamina, but must have arisen either from successional dental laminae associated with the predecessor teeth, or directly from the dental epithelium of these teeth. The virtual histological dissection of these Late Silurian microfossils broadens our understanding of the development of the gnathostome dental systems and the acquisition of the osteichthyan-type of tooth replacement. 

  • 267.
    Chen, Donglei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Squamation in Andreolepis from the late Silurian of Sweden2010Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    The origin of osteichthyans (bony fishes and tetrapods) dates back to the Late Silurian, but theearly evolution of osteichthyans is poorly understood. Andreolepis is one of the oldest knownosteichthyans, but exclusively documented by detached and fragmented dermal microremains.Nevertheless, Andreolepis has unequivocally been attributed to the osteichthyan stem group.A variety of isolated scales of Andreolepis from Gotland, Sweden provides a large dataset,which would potentially improve our understanding of the acquisition of the osteichthyanbody plan. In the present study, various forms of Andreolepis scales were classified into tenmorphotypes by landmark-based geometric morphometrics. Based on comparative anatomyand functional morphology, each morphotype was assigned to a specific area of the body anda squamation model of Andreolepis was established. In this model, scales are allocated toanterior-mid lateral flank scales, posterior lateral flank scales, caudal peduncle scales, pectoralpeduncle scales, dorsal flank scales, dorsal fulcral scales, caudal fulcral scales, ventral flankscales, medioventral scales and cranial scales.

  • 268.
    Chen, Donglei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The Origin of Tooth Replacement: Three-dimensional Synchrotron Histology Visualizes the Dental Development of Silurian Stem Osteichthyans2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Mechanisms of tooth replacement distribute incongruently among extant gnathostomes (jawed vertebrates): a permanent tooth-generating dental lamina exists in chondrichthyans (cartilaginous fish) and tetrapods but not teleosts, whereas tooth shedding by basal hard tissue resorption occurs in tetrapods and teleosts but not chondrichthyans. Theories about the evolution of tooth development have been biased towards the chondrichthyan conveyor-belt replacement, since there has been no fossil evidence for the origin of osteichthyan (bony fish and tetrapods) tooth replacement until now. 3D virtual dissections with submicron-scale resolution, based on propagation phase contrast synchrotron microtomography (PPC-SRµCT), reveal the growth history of the dentitions of Andreolepis and Lophosteus, 423-Myr-old Silurian stem osteichthyans close to the common ancestor of tetrapods and teleosts. Their marginal jawbones and “tooth cushions” (possible homologues of coronoids) shed teeth by in situ cyclic basal resorption, the earliest examples of osteichthyan-style tooth replacement. The replacement cycles were site-autonomic, and occurred in broad irregular multi-row tooth fields, including at sites separated from the margin of the bone by intervening teeth, showing that the production of replacement teeth did not occur in a single deep dental lamina, but in pockets associated with each tooth, as in many teleosts. It suggests that the functionally and anatomically similar laminae of chondrichthyans and tetrapods are convergent. The marginal jaw bones of both genera carry an initial non-shedding dentition arranged in alternate transverse files, labial to the shedding tooth field, overgrown by later dermal ornament and probably not belonging to the oral domain, but bearing in vivo biting damage showing that they functioned as teeth. The most lingual of these odontodes have been resorbed apically and are overlain by shedding teeth. The first-generation teeth on the tooth cushions display basal resorption in Andreolepis, but semi-basal resorption in Lophosteus. The latter leaves a basal dentine ring from each tooth, implying only odontoclasts are involved in the semi-basal resorption, which is probably the first step towards evolving a site-specific resorption. The polarized displacement of each generation of resorption surfaces reflects the fact that the cyclic replacement, as well as the sequential addition of tooth sites, is closely related to bone growth. Resorption surfaces and growth arrest surfaces also record the life history and the replacement rate. These data provide unique insights into the origin of osteichthyan tooth replacement.

    List of papers
    1. The stem osteichthyan Andreolepis and the origin of tooth replacement
    Open this publication in new window or tab >>The stem osteichthyan Andreolepis and the origin of tooth replacement
    Show others...
    2016 (English)In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 539, no 7628, p. 237-+Article in journal (Refereed) Published
    Abstract [en]

    The teeth of gnathostomes (jawed vertebrates) show rigidly patterned, unidirectional replacement that may or may not be associated with a shedding mechanism. These mechanisms, which are critical for the maintenance of the dentition, are incongruently distributed among extant gnathostomes. Although a permanent tooth-generating dental lamina is present in all chondrichthyans, many tetrapods and some teleosts, it is absent in the non-teleost actinopterygians. Tooth-shedding by basal hard tissue resorption occurs in most osteichthyans (including tetrapods) but not in chondrichthyans. Here we report a three-dimensional virtual dissection of the dentition of a 424-million-year-old stem osteichthyan, Andreolepis hedei, using propagation phase-contrast synchrotron microtomography, with a reconstruction of its growth history. Andreolepis, close to the common ancestor of all extant osteichthyans, shed its teeth by basal resorption but probably lacked a permanent dental lamina. This is the earliest documented instance of resorptive tooth shedding and may represent the primitive osteichthyan mode of tooth replacement.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-310754 (URN)10.1038/nature19812 (DOI)000387318500034 ()27750278 (PubMedID)
    Funder
    EU, European Research Council, 233111Knut and Alice Wallenberg Foundation
    Available from: 2016-12-20 Created: 2016-12-19 Last updated: 2017-11-29Bibliographically approved
    2. Development of cyclic shedding teeth from semi-shedding teeth: the inner dental arcade of the stem osteichthyan Lophosteus 
    Open this publication in new window or tab >>Development of cyclic shedding teeth from semi-shedding teeth: the inner dental arcade of the stem osteichthyan Lophosteus 
    Show others...
    2017 (English)In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 4, no 5, article id 161084Article in journal (Refereed) Published
    Abstract [en]

    The numerous cushion-shaped tooth-bearing plates attributed to the stem-group osteichthyan Lophosteus superbus, which are argued here to represent the ancient form of inner dental arcade, display a unique and presumably primitive way of tooth shedding by basal hard tissue resorption. They carry regularly spaced, recumbent, gently recurved teeth arranged in transverse tooth files that diverge towards the lingual margin of the cushion. Three-dimensional (3D) reconstruction from propagation phase contrast synchrotron microtomography (PPC-SRμCT) reveals remnants of the first-generation teeth embedded in the basal plate that have never been discerned in any taxa. These teeth were shed by semi-basal resorption with the periphery of their bases retained as dentine rings. The rings are highly overlapped, which evidences tooth shedding prior to adding the next first-generation tooth. Later teeth at the same sites underwent cyclical replacing and shedding through basal resorption, producing stacks of buried resorption surfaces separated by bone of attachment. The number and spatial arrangement of resorption surfaces elucidates that basal resorption of replacement teeth had taken place at the older tooth sites before the addition of the youngest first-generation teeth at the lingual margin. Thus the replacement tooth buds cannot have been generated by a single permanent dental lamina, but must have arisen either from successional dental laminae associated with the predecessor teeth, or directly from the dental epithelium of these teeth. The virtual histological dissection of these Late Silurian microfossils broadens our understanding of the development of the gnathostome dental systems and the acquisition of the osteichthyan-type of tooth replacement. 

    Place, publisher, year, edition, pages
    ROYAL SOC, 2017
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-315882 (URN)10.1098/rsos.161084 (DOI)000402541800020 ()28573003 (PubMedID)
    Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2017-08-02Bibliographically approved
    3. Microstructures of the most primitive form of inner dental arcade and life history of the Silurian stem osteichthyan Andreolepis.
    Open this publication in new window or tab >>Microstructures of the most primitive form of inner dental arcade and life history of the Silurian stem osteichthyan Andreolepis.
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-315883 (URN)
    Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2017-02-22
    4. The marginal dentition of Lophosteus superbus Pander 1856, a Late Silurian stem osteichthyan from Estonia.
    Open this publication in new window or tab >>The marginal dentition of Lophosteus superbus Pander 1856, a Late Silurian stem osteichthyan from Estonia.
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-315884 (URN)
    Available from: 2017-02-22 Created: 2017-02-22 Last updated: 2017-02-22
  • 269.
    Chen, Donglei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    The marginal dentition of Lophosteus superbus Pander 1856, a Late Silurian stem osteichthyan from Estonia.Manuscript (preprint) (Other academic)
  • 270.
    Chen, Donglei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Tafforeau, Paul
    European Synchrotron Radiation Facility.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Microstructures of the most primitive form of inner dental arcade and life history of the Silurian stem osteichthyan Andreolepis.Manuscript (preprint) (Other academic)
  • 271.
    Chen, Donglei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Sanchez, Sophie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. European Synchrotron Radiat Facil, 6 Rue Jules Horowitz, F-38043 Grenoble, France..
    Tafforeau, Paul
    European Synchrotron Radiat Facil, 6 Rue Jules Horowitz, F-38043 Grenoble, France..
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The stem osteichthyan Andreolepis and the origin of tooth replacement2016In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 539, no 7628, p. 237-+Article in journal (Refereed)
    Abstract [en]

    The teeth of gnathostomes (jawed vertebrates) show rigidly patterned, unidirectional replacement that may or may not be associated with a shedding mechanism. These mechanisms, which are critical for the maintenance of the dentition, are incongruently distributed among extant gnathostomes. Although a permanent tooth-generating dental lamina is present in all chondrichthyans, many tetrapods and some teleosts, it is absent in the non-teleost actinopterygians. Tooth-shedding by basal hard tissue resorption occurs in most osteichthyans (including tetrapods) but not in chondrichthyans. Here we report a three-dimensional virtual dissection of the dentition of a 424-million-year-old stem osteichthyan, Andreolepis hedei, using propagation phase-contrast synchrotron microtomography, with a reconstruction of its growth history. Andreolepis, close to the common ancestor of all extant osteichthyans, shed its teeth by basal resorption but probably lacked a permanent dental lamina. This is the earliest documented instance of resorptive tooth shedding and may represent the primitive osteichthyan mode of tooth replacement.

  • 272.
    Chen, Donglei
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Janvier, Philippe
    Département Histoire de la Terre, Muséum National d'Histoire Naturelle,.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Blom, Henning
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Scale morphology and squamation of the Late Silurian osteichthyan Andreolepis from Gotland, Sweden2012In: Historical Biology, ISSN 0891-2963, E-ISSN 1029-2381, Vol. 24, no 4, p. 411-423Article in journal (Refereed)
    Abstract [en]

    The origin of osteichthyans (bony fishes and tetrapods) dates back to the Late Silurian, but the early evolution of the group is poorly understood. Andreolepis is one of the oldest known osteichthyans, but exclusively documented by detached and fragmentary dermal microremains. A large data-set of Andreolepis scales from the Silurian of Gotland has been used to explore the scale morphology on different parts of the body. Landmark-based geometric morphometrics together with comparative anatomy and functional morphology has allowed 10 morphotypes to be identified and incorporated into a squamation model, in which scales are allocated to anterior-mid lateral flank scales, posterior lateral flank scales, caudal peduncle scales, pectoral peduncle scales, dorsal flank scales, dorsal fulcral scales, caudal fulcral scales, ventral flank scales, medioventral scales and cranial scales. The scale morphology and squamation pattern ofAndreolepis may be primitive for the Osteichthyes and thus informative about the acquisition of the osteichthyan body plan.

  • 273.
    Chen, Hwei -Yen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Spagopoulou, Foteini
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Maklakov, Alexei A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Evolution of male age-specific reproduction under differential risks and causes of death: males pay the cost of high female fitness2016In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 29, no 4, p. 848-856Article in journal (Refereed)
    Abstract [en]

    Classic theories of ageing evolution predict that increased extrinsic mortality due to an environmental hazard selects for increased early reproduction, rapid ageing and short intrinsic lifespan. Conversely, emerging theory maintains that when ageing increases susceptibility to an environmental hazard, increased mortality due to this hazard can select against ageing in physiological condition and prolong intrinsic lifespan. However, evolution of slow ageing under high-condition-dependent mortality is expected to result from reallocation of resources to different traits and such reallocation may be hampered by sex-specific trade-offs. Because same life-history trait values often have different fitness consequences in males and females, sexually antagonistic selection can preserve genetic variance for lifespan and ageing. We previously showed that increased condition-dependent mortality caused by heat shock leads to evolution of long-life, decelerated late-life mortality in both sexes and increased female fecundity in the nematode, Caenorhabditis remanei. Here, we used these cryopreserved lines to show that males evolving under heat shock suffered from reduced early-life and net reproduction, while mortality rate had no effect. Our results suggest that heat-shock resistance and associated long-life trade-off with male, but not female, reproduction and therefore sexually antagonistic selection contributes to maintenance of genetic variation for lifespan and fitness in this population.

  • 274.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Conifer Evolution, from Demography and Local Adaptation to Evolutionary Rates: Examples from the Picea genus2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Evolutionary process can be inferred at three different levels: the species level, the population level and the molecular level. In this thesis, I applied approaches at these three levels and aimed to get a comprehensive picture of conifer evolution, from speciation and demography to geographic variation and local adaptation, and then to the molecular evolution of proteins and small regulatory RNAs.

    Spruce species have been observed to possess a large number of trans-species shared polymorphisms. Using an “Isolation with migration” model, we found that the large effective population size of spruce retained these shared polymorphisms, inheriting them from the common ancestor. Post-divergence gene flow only existed between Picea abies and P. glauca, and between P. wilsonii and P. schrenkiana. The combination of Tajima’s D and Fay & Wu’s H at most of loci suggested an ancient and severe bottleneck for most species except P. breweriana.

    Furthermore, I investigated the effect of local selection in two parallel clines, which is one of the major forces that can cause divergence or even speciation. The timing of bud set and growth cessation was found correlated with latitude in populations of P. abies and P. obovata. Using allele frequency spectrum analyses we identified three genes under local selection in both species including two circadian-clock genes GI and PRR7, and one photoperiodic gene FTL2. This indicated that parallel evolution could occur through groups of genes within related pathways. Clinal variation at expression level provided stronger evidence of selection in FTL2, which has previously been associated with bud set in P. abies.

    Finally we focused on the molecular evolution of mRNA and small regulatory RNAs in P. abies. With the help of Next-Generation sequencing, we have achieved in spruce the first de novel assembly of the needle transcriptome and a preliminary characterization of sRNA populations. Along with features common in plants, spruce also exhibited novelties in many aspects including lower substitution rate and protein evolutionary rate, dominance of 21-nt sRNA, and a large proportion of TIR-NBS-LRR genes as sRNA sources and targets.

    List of papers
    1. New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict
    Open this publication in new window or tab >>New insights on the speciation history and nucleotide diversity of three boreal spruce species and a Tertiary relict
    2010 (English)In: Heredity, ISSN 0018-067X, E-ISSN 1365-2540, Vol. 104, no 1, p. 3-14Article in journal (Refereed) Published
    Abstract [en]

    In all, 10 nuclear loci were re-sequenced in four spruce species. Three of the species are boreal species with very large natural ranges: Picea mariana and P. glauca are North American, and P. abies, is Eurasian. The fourth species, P. breweriana, is a Tertiary relict from Northern California, with a very small natural range. Although the boreal species population sizes have fluctuated through the Ice Ages, P. breweriana is believed to have had a rather stable population size through the Quaternary. Indeed, the average Tajima’s D was close to zero in this species and negative in the three boreal ones. Reflecting differences in current population sizes, nucleotide diversity was an order of magnitude lower in P. breweriana than in the boreal species. This is in contrast to the similar and high levels of heterozygosity observed in previous studies at allozyme loci across species. As the species have very different histories and effective population sizes, selection at allozyme loci rather than demography appears to be a better explanation for this discrepancy. Parameters of Isolation-with-Migration (IM) models were also estimated for pairs of species. Shared polymorphisms were extensive and fixed polymorphisms few. Divergence times were much shorter than those previously reported. There was also evidence of historical gene flow between P. abies and P. glauca. The latter was more closely related to P. abies than to its sympatric relative P. mariana. This last result suggests that North American and Eurasian species might have been geographically much closer in the recent past than they are today.

    Keywords
    picea; nucleotide diversity; divergence time; migration; speciation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-119939 (URN)10.1038/hdy.2009.88 (DOI)000272794600002 ()
    Available from: 2010-03-03 Created: 2010-03-03 Last updated: 2017-12-12Bibliographically approved
    2. Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    Open this publication in new window or tab >>Demographic histories of four spruce (Picea) species of the Qinghai-Tibetan Plateau and neighboring areas inferred from multiple nuclear loci
    Show others...
    2010 (English)In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 27, no 5, p. 1001-1014Article in journal (Refereed) Published
    Abstract [en]

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

    Keywords
    Picea, Qinghai Tibetan Plateau, effective population size, divergence time, introgression, speciation
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-121399 (URN)10.1093/molbev/msp301 (DOI)000276994800004 ()20031927 (PubMedID)
    Available from: 2010-03-23 Created: 2010-03-23 Last updated: 2017-12-12Bibliographically approved
    3. Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)
    Open this publication in new window or tab >>Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)
    Show others...
    2012 (English)In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 191, no 3, p. 865-881Article in journal (Refereed) Published
    Abstract [en]

    Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (F(ST) = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to F(ST). The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.

    Keywords
    clinal variation, photoperiodic pathway, Norway spruce, FT genes
    National Category
    Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-177467 (URN)10.1534/genetics.112.140749 (DOI)000308999900015 ()22542968 (PubMedID)
    Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2017-12-07Bibliographically approved
    4. Clinal variation in allele frequency at photoperiodic genes in Siberian spruce: an example of convergent evolution?
    Open this publication in new window or tab >>Clinal variation in allele frequency at photoperiodic genes in Siberian spruce: an example of convergent evolution?
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology Genetics
    Research subject
    Biology with specialization in Evolutionary Functional Genomics; Biology with specialization in Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-177474 (URN)
    Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2013-01-22
    5. Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms compared to angiosperms
    Open this publication in new window or tab >>Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms compared to angiosperms
    Show others...
    2012 (English)In: BMC Genomics, ISSN 1471-2164, E-ISSN 1471-2164, Vol. 13, p. 589-Article in journal (Other academic) Published
    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.

    National Category
    Evolutionary Biology Genetics
    Identifiers
    urn:nbn:se:uu:diva-177479 (URN)10.1186/1471-2164-13-589 (DOI)000314646900001 ()
    Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2017-12-07Bibliographically approved
    6. Major difference in short RNA populations among plants - the results of interaction with pathogen?
    Open this publication in new window or tab >>Major difference in short RNA populations among plants - the results of interaction with pathogen?
    (English)Manuscript (preprint) (Other academic)
    Abstract [en]

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

    National Category
    Evolutionary Biology Genetics
    Research subject
    Biology with specialization in Evolutionary Functional Genomics
    Identifiers
    urn:nbn:se:uu:diva-177475 (URN)
    Available from: 2012-07-13 Created: 2012-07-13 Last updated: 2013-06-27
  • 275.
    Chen, Jun
    et al.
    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.
    Ma, Xiaofei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Zaina, Giusi
    Morgante, Michele
    Bousquet, Jean
    Eckert, Andrew
    Wegrzyn, Jill
    Neale, David
    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.
    Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea abies)2012In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 191, no 3, p. 865-881Article in journal (Refereed)
    Abstract [en]

    Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (F(ST) = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to F(ST). The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.

  • 276.
    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)
  • 277.
    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)
  • 278.
    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.

  • 279. Chen, Yu-Chia
    et al.
    Harrison, Peter W.
    Kotrschal, Alexander
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Kolm, Niclas
    Mank, Judith E.
    Panula, Pertti
    Expression change in Angiopoietin-1 underlies change in relative brain size in fish2015In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 282, no 1810, article id 20150872Article in journal (Refereed)
    Abstract [en]

    Brain size varies substantially across the animal kingdom and is often associated with cognitive ability; however, the genetic architecture underpinning natural variation in these key traits is virtually unknown. In order to identify the genetic architecture and loci underlying variation in brain size, we analysed both coding sequence and expression for all the loci expressed in the telencephalon in replicate populations of guppies (Poecilia reticulata) artificially selected for large and small relative brain size. A single gene, Angiopoietin-1 (Ang-1), a regulator of angiogenesis and suspected driver of neural development, was differentially expressed between large-and small-brain populations. Zebra fish (Danio rerio) morphants showed that mild knock down of Ang-1 produces a small-brained phenotype that could be rescued with Ang-1 mRNA. Translation inhibition of Ang-1 resulted in smaller brains in larvae and increased expression of Notch-1, which regulates differentiation of neural stem cells. In situ analysis of newborn large-and small-brained guppies revealed matching expression patterns of Ang-1 and Notch-1 to those observed in zebrafish larvae. Taken together, our results suggest that the genetic architecture affecting brain size in our population may be surprisingly simple, and Ang-1 may be a potentially important locus in the evolution of vertebrate brain size and cognitive ability.

  • 280.
    Cheng, George
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Uncovering the genetic organisation of Claroideoglomus candidum2019Independent thesis Advanced level (degree of Master (Two Years)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    Arbuscular mycorrhizal (AM) fungi are hypothesized to have been key players in facilitating thetransition from aquatic to terrestrial plants and continue to benefit plants through their symbioticassociation after 450 million years. These fungi form mycelia that can contain hundreds of nucleiwithin one aseptate cytoplasm, which leads to the ongoing debate on whether thesemultinucleated fungi are homokaryotic or heterokaryotic. Not only is there evidence to supportthe hypothesis of the nuclei as genetically identical, but also the other hypothesis of divergentnuclei within a single strain. There has been no evidence of sexual reproduction, howeverspecialized genomic regions specific to meiosis and a putative mating-type (MAT) locus haverecently been identified and may help answer the ongoing debate between homokaryosis andheterokaryosis.

    In this study I applied de novo genome assembly and annotation of 24 individual nuclei from asingle spore of Claroideoglomus candidum. The full length of the de novo genome assembly was87.6 Mb with 17,542 genes. Estimated polymorphism between the nuclei was very low. Iidentified the MAT locus in C. candidum, using a previously sequenced MAT locus fromanother congeneric species. Only one of the MAT locus alleles was found in the examined spore.The evidence points towards homokaryosis as the genetic organization of Claroideoglomuscandidum.

  • 281. Childs, Liam H
    et al.
    Witucka-Wall, Hanna
    Günther, Torsten
    Sulpice, Ronan
    Korff, Maria V
    Stitt, Mark
    Walther, Dirk
    Schmid, Karl J
    Altmann, Thomas
    Single feature polymorphism (SFP)-based selective sweep identification and association mapping of growth-related metabolic traits in Arabidopsis thaliana.2010In: BMC genomics, ISSN 1471-2164, Vol. 11, p. 188-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Natural accessions of Arabidopsis thaliana are characterized by a high level of phenotypic variation that can be used to investigate the extent and mode of selection on the primary metabolic traits. A collection of 54 A. thaliana natural accession-derived lines were subjected to deep genotyping through Single Feature Polymorphism (SFP) detection via genomic DNA hybridization to Arabidopsis Tiling 1.0 Arrays for the detection of selective sweeps, and identification of associations between sweep regions and growth-related metabolic traits.

    RESULTS: A total of 1,072,557 high-quality SFPs were detected and indications for 3,943 deletions and 1,007 duplications were obtained. A significantly lower than expected SFP frequency was observed in protein-, rRNA-, and tRNA-coding regions and in non-repetitive intergenic regions, while pseudogenes, transposons, and non-coding RNA genes are enriched with SFPs. Gene families involved in plant defence or in signalling were identified as highly polymorphic, while several other families including transcription factors are depleted of SFPs. 198 significant associations between metabolic genes and 9 metabolic and growth-related phenotypic traits were detected with annotation hinting at the nature of the relationship. Five significant selective sweep regions were also detected of which one associated significantly with a metabolic trait.

    CONCLUSIONS: We generated a high density polymorphism map for 54 A. thaliana accessions that highlights the variability of resistance genes across geographic ranges and used it to identify selective sweeps and associations between metabolic genes and metabolic phenotypes. Several associations show a clear biological relationship, while many remain requiring further investigation.

  • 282.
    Choo, Brian
    et al.
    Chinese Acad Sci, Key Lab Vertebrate Evolut & Human Origins, Inst Vertebrate Paleontol & Paleoanthropol, Beijing, Peoples R China.;Flinders Univ S Australia, Sch Biol Sci, Adelaide, SA, Australia..
    Zhu, Min
    Chinese Acad Sci, Key Lab Vertebrate Evolut & Human Origins, Inst Vertebrate Paleontol & Paleoanthropol, Beijing, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing, Peoples R China..
    Qu, Qinming
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Univ Ottawa, Ctr Adv Res Environm Genom, Ottawa, ON, Canada..
    Yu, Xiaobo
    Chinese Acad Sci, Key Lab Vertebrate Evolut & Human Origins, Inst Vertebrate Paleontol & Paleoanthropol, Beijing, Peoples R China.;Kean Univ, Dept Biol Sci, Union, NJ USA..
    Jia, Liantao
    Chinese Acad Sci, Key Lab Vertebrate Evolut & Human Origins, Inst Vertebrate Paleontol & Paleoanthropol, Beijing, Peoples R China..
    Zhao, Wenjin
    Chinese Acad Sci, Key Lab Vertebrate Evolut & Human Origins, Inst Vertebrate Paleontol & Paleoanthropol, Beijing, Peoples R China.;Univ Chinese Acad Sci, Coll Earth Sci, Beijing, Peoples R China..
    A new osteichthyan from the late Silurian of Yunnan, China2017In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 12, no 3, article id e0170929Article in journal (Refereed)
    Abstract [en]

    Our understanding of early gnathostome evolution has been hampered by a generally scant fossil record beyond the Devonian. Recent discoveries from the late Silurian Xiaoxiang Fauna of Yunnan, China, have yielded significant new information, including the earliest articulated osteichthyan fossils from the Ludlow-aged Kuanti Formation. Here we describe the partial postcranium of a new primitive bony fish from the Kuanti Formation that represents the second known taxon of pre-Devonian osteichthyan revealing articulated remains. The new form, Sparalepis tingi gen. et sp. nov., displays similarities with Guiyu and Psarolepis, including a spine-bearing pectoral girdle and a placoderm-like dermal pelvic girdle, a structure only recently identified in early osteichthyans. The squamation with particularly thick rhombic scales shares an overall morphological similarity to that of Psarolepis. However, the anterior flank scales of Sparalepis possess an unusual interlocking system of ventral bulges embraced by dorsal concavities on the outer surfaces. A phylogenetic analysis resolves Sparalepis within a previously recovered cluster of stem-sarcopterygians including Guiyu, Psarolepis and Achoania. The high diversity of osteichthyans from the Ludlow of Yunnan strongly contrasts with other Silurian vertebrate assemblages, suggesting that the South China block may have been an early center of diversification for early gnathostomes, well before the advent of the Devonian "Age of Fishes".

  • 283.
    Chylenski, Maciej
    et al.
    Adam Mickiewicz Univ, Fac Hist, Inst Archaeol, Umultowska 89D, PL-61614 Poznan, Poland..
    Juras, Anna
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland..
    Ehler, Edvard
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland.;Charles Univ Prague, Fac Educ, Dept Biol & Environm Studies, Magdaleny Rettigove 4, Prague 11639, Czech Republic..
    Malmström, Helena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Piontek, Janusz
    Adam Mickiewicz Univ, Fac Biol, Inst Anthropol, Dept Human Evolutionary Biol, Umultowska 89, PL-61614 Poznan, Poland..
    Jakobsson, Mattias
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Marciniak, Arkadiusz
    Adam Mickiewicz Univ, Fac Hist, Inst Archaeol, Umultowska 89D, PL-61614 Poznan, Poland..
    Dabert, Miroslawa
    Adam Mickiewicz Univ, Fac Biol, Mol Biol Techn Lab, Umultowska 89, PL-61614 Poznan, Poland..
    Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5th millennium BC2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 80Article in journal (Refereed)
    Abstract [en]

    Background: Recent aDNA studies are progressively focusing on various Neolithic and Hunter-Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities. Results: Here we address this issue by presenting 5 complete mitochondrial genomes of various late Danubian individuals from modern-day Poland and combining it with available published data. Our data show that Late Danubian cultures are maternally closely related to Funnel Beaker groups instead of culturally similar LBK. Conclusions: We assume that it is an effect of the presence of individuals belonging to U5 haplogroup both in Late Danubians and the TRB. The U5 haplogroup is thought to be a typical for HGs of Europe and therefore we argue that it is an additional evidence of genetic exchange between farming and HG groups taking place at least as far back as in middle Neolithic, in the Late Danubian communities.

  • 284.
    Cibois, Alice
    et al.
    Nat Hist Museum Geneva, CP 6434, CH-1211 Geneva 6, Switzerland.
    Gelang, Magnus
    Goteborgs Nat Hist Museum, Gothenburg, Sweden.
    Alström, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Chinese Acad Sci, Inst Zool, Key Lab Zool Systemat & Evolut, Beijing, Peoples R China;Swedish Univ Agr Sci, Swedish Species Informat Ctr, Uppsala, Sweden.
    Pasquet, Eric
    Sorbonne Univ, Museum Natl Hist Nat, Inst Systemat, UMR7205,Evolut,Biodiversite,CNRS,MNHN,UPMC,EPHE, Paris, France;Sorbonne Univ, Museum Natl Hist Nat, UMS MNHN, CNRS 2700,OMSI, Paris, France.
    Fjeldsa, Jon
    Nat Hist Museum Denmark, Ctr Macroecol Evolut & Climate, Zool Museum, Copenhagen, Denmark.
    Ericson, Per G. P.
    Swedish Museum Nat Hist, Dept Vertebrate Zool, Mol Systemat Lab, Stockholm, Sweden.
    Olsson, Urban
    Univ Gothenburg, Dept Zool, Gothenburg, Sweden.
    Comprehensive phylogeny of the laughingthrushes and allies (Aves, Leiothrichidae) and a proposal for a revised taxonomy2018In: Zoologica Scripta, ISSN 0300-3256, E-ISSN 1463-6409, Vol. 47, no 4, p. 428-440Article in journal (Refereed)
    Abstract [en]

    DNA phylogenies have gradually shed light on the phylogenetic relationships of the large babbler group. We focus in this study on the family Leiothrichidae (laughingthrushes and song babblers), which represents the largest clade of babblers in terms of species diversity. Our phylogeny includes all genera and 82% of the recognized species, using mitochondrial and nuclear loci. The sister group to Leiothrichidae is composed of the Pellorneidae (jungle babblers) plus the genus Alcippe. Within Leiothrichidae, four strongly supported primary clades (A-D) are recovered. Clade A includes Grammatoptila, Laniellus and Cutia. Clade B includes a large group of laughingthrushes, all of them classified in Trochalopteron. In Clade C, the two laughingthrushes endemic to southern India, T.fairbanki and T.cachinnans, which have recently been proposed to be placed in the newly erected genus Montecincla, form a sister clade to the group comprising the song babblers (Lioptila, Leiothrix, Heterophasia, Minla, Liocichla, Actinodura, Chrysominla, Siva, and Sibia). Clade D includes the African babblers (Turdoides, Phyllanthus, Kupeornis), Asian relatives (Argya, Acanthoptila, Chatarrhaea) and all remaining laughingthrushes (Garrulax). The time estimates suggest that the early diversification of the Leiothrichidae occurred in the mid-Miocene, a period that corresponds to the diversification of many passerine groups in Asia. A revised taxonomic classification of the family is proposed in the light of these results.

  • 285.
    Cirulis, Aivars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Separating the sexes: sexual conflict and how to resolve it2016Independent thesis Advanced level (degree of Master (One Year)), 30 credits / 45 HE creditsStudent thesis
    Abstract [en]

    During the evolution of sex, different sexual conflicts arise. Sexual conflicts reduce fitness of the opposite sex. That is why several mechanisms have evolved to resolve them, which leads to rapid and unpredictable co-evolution of male and female traits involved in reproduction. This rapid co-evolution of male and female reproductive traits driven by sexual conflict can further lead to reproductive isolation resulting in speciation.

                I used the hermaphroditic fungus Neurospora crassa, which has two mating types, as a model organism. Mating types are proxy to sex, because both are needed for sexual reproduction, but they are not limited to either sex role. However by using male pheromone knock-out lines, I created an evolutionary setup, where either mating type is forced to adapt to its restricted sex role. After 21 sexual generations of adaptive co-evolution, I tested if mating types had adapted to the assigned sex by measuring fitness (production of sexual spores called ascospores). I used three evolutionary setups (lines): Δccg4 lines, where mat A is female and mat a is adapted to the male role, Δmfa1 lines, where conversely mat A is adapted to the male role and mat a is female, and wild-type lines used as controls, where both mating types have maintained and adapted to both sex roles. And discovered one Δccg4 line, which indeed adapted to the newly assigned sex roles. At generation 15 and 21 I obtained mixed results for the presence of sexual conflict by correlating male and female fitness in hermaphroditic partner mat a in this line, however I found a sexual conflict also in the asexual growth, where male role is associated with increased, but female role with decreased mycelium growth rate. This work will further allow to study genomic mechanisms underlying this adaptation.

  • 286.
    Clarac, Francois
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Sorbonne Univ, CNRS, MNHN, CR2P,UMR 7207,Ctr Rech Paleobiodiversite & Paleoe, Paris, France.
    Quilhac, A.
    Sorbonne Univ, CNRS, MNHN, CR2P,UMR 7207,Ctr Rech Paleobiodiversite & Paleoe, Paris, France.
    The crocodylian skull and osteoderms: A functional exaptation to ectothermy?2019In: Zoology (Jena), ISSN 0944-2006, E-ISSN 1873-2720, Vol. 132, p. 31-40Article in journal (Refereed)
    Abstract [en]

    The crocodylians are ectothermic semi-aquatic vertebrates which are assessed to have evolved from endothermic terrestrial forms during the Mesozoic. Such a physiological transition should have involved modifications in their cardio-vascular system allowing to increase the heat transfers with the surrounding environment by growing a peripheral vascularization which would be mainly located in the dermal skeleton: the dermatocranium and the osteoderms. In order to assess the implication of these anatomical regions in thermal exchanges, we have recorded the temperature above a set of representative skin areas in order to draw comparisons between the skull, the osteoderms, and the rest of the body parts which present either none or residual dermal ossification. We computed the data after the specimens were successively laid in different stereotyped environmental conditions which involved significant variations in the environmental temperature. Our results show that the osteoderms collect the external heat during the basking periods as they become significantly warmer than the surrounding skin; they further release the heat into the core of the organism as they turn out to be colder than the surrounding skin after a significant cooling period. In disregard of the environmental temperature variations, the skull table (which encloses the braincase) remains warmer than the rest of the cranial regions and shows less temperature variations than the osteoderms; a result which has lead us to think that the braincase temperature is monitored and controlled by a thermoregulatory system. Therefore, as hypothesized by previous authors regarding the ectothermic diapsids, we assume that the crocodylian skull possesses shunting blood pathways which tend to maintain both the braincase and the main sensory organs at the nearest to the optimal physiological temperature depending on the external temperature variations. Concerning the skin vascularization, the study of an albino Alligator mississippiensis specimen permitted to observe the repartition of the superficial blood vessels by transparency through the skin. We thus testify that the skin which covers either the skull or the osteoderms is more vascularized than the skin which does not present any subjacent dermal ossification. We consequently deduce that the significant contrast in the thermal behavior between the dermal skeleton and the rest of the body is indeed correlated with a difference in the relative degree of skin vascularization. This last assessment confirms that the development of the dermal skeleton should have played a functional role in the crocodylian transition from endothermy to ectothermy through the set-up of a peripheral vessel network.

  • 287. Clarholm, Marianne
    et al.
    Skyllberg, Ulf
    Rosling, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Organic acid induced release of nutrients from metal-stabilized soil organic matter - The unbutton model2015In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 84, p. 168-176Article, review/survey (Refereed)
    Abstract [en]

    Processes of soil organic matter (SOM) stabilization and the reverse, destabilization of SOM resulting in subsequent release and mobilization of nutrients from SOM, remain largely unresolved. The perception of SOM as supramolecular aggregates built of low molecular mass biomolecules is currently emerging. Polyvalent metal cations contribute to SOM tertiary structure by bridging functional groups of such molecules (Simpson et al., 2002). The strong bond to metals protects high quality organic material from being immediately accessed and decomposed. Here we propose a three-step process by which low molecular mass organic acids (LMMOAs) and hydrolytic enzymes act in series to destabilize SOM supramolecules to release organic nitrogen (N) and phosphorus (P) for local hyphal and root uptake. Complexation of the stabilizing metals by fungal-released LMMOA gives fungal-root consortia direct access to organic substrates of good quality. Because of their small sizes and carboxyl group configuration, citric and oxalic acids are the most effective LMMOAs forming stable complexes with the main SOM bridging metals Ca and Al in SOM. Citrate, forming particularly strong complexes with the trivalent cations Al and Fe, is dominant in soil solutions of low-productive highly acidic boreal forest soils where mycorrhizal associations with roots are formed predominantly by fungi with hydrophobic hyphal surfaces. In these systems mycelia participate in the formation of N-containing SOM with a significant contribution from strong Al bridges. In less acidic soils of temperate forests, including calcareous influenced soils, SOM is stabilized predominantly by Ca bridges. In such systems mycorrhizal fungi with more hydrophilic surfaces dominate, and oxalic acid, forming strong bidentate complexes with Ca, is the most common LMMOA exuded. A plant-fungus driven biotic mechanism at the supramolecular aggregate level (10(3)-10(5) Da) resolves micro-spatial priming of SOM, where the destabilization step is prerequisite for subsequent release of nutrients. (C) 2015 Elsevier Ltd. All rights reserved.

  • 288.
    Clement, Alice
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology. Flinders Univ S Australia, Coll Sci & Engn, Adelaide, SA, Australia;Museum Victoria, Dept Sci, Melbourne, Vic, Australia.
    King, Benedict
    Flinders Univ S Australia, Coll Sci & Engn, Adelaide, SA, Australia;Nat Biodivers Ctr, Leiden, Netherlands.
    Giles, Sam
    Univ Oxford, Dept Earth Sci, Oxford, England.
    Choo, Brian
    Flinders Univ S Australia, Coll Sci & Engn, Adelaide, SA, Australia.
    Ahlberg, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Young, Gavin C.
    Australian Natl Univ, Res Sch Phys & Engn, Dept Appl Math, Canberra, ACT, Australia;Australian Museum, Res Inst, Sydney, NSW, Australia.
    Long, John A.
    Flinders Univ S Australia, Coll Sci & Engn, Adelaide, SA, Australia;Museum Victoria, Dept Sci, Melbourne, Vic, Australia.
    Neurocranial anatomy of an enigmatic Early Devonian fish sheds light on early osteichthyan evolution2018In: eLIFE, E-ISSN 2050-084X, Vol. 7, article id e34349Article in journal (Refereed)
    Abstract [en]

    The skull of 'Ligulalepis' from the Early Devonian of Australia (AM-F101607) has significantly expanded our knowledge of early osteichthyan anatomy, but its phylogenetic position has remained uncertain. We herein describe a second skull of 'Ligulalepis' and present micro-CT data on both specimens to reveal novel anatomical features, including cranial endocasts. Several features previously considered to link 'Ligulalepis' with actinopterygians are now considered generalized osteichthyan characters or of uncertain polarity. The presence of a lateral cranial canal is shown to be variable in its development between specimens. Other notable new features include the presence of a pineal foramen, the some detail of skull roof sutures, the shape of the nasal capsules, a placoderm-like hypophysial vein, and a chondrichthyan-like labyrinth system. New phylogenetic analyses place 'Ligulalepis' as a stem osteichthyan, specifically as the sister taxon to 'psarolepids' plus crown osteichthyans. The precise position of 'psarolepids' differs between parsimony and Bayesian analyses.

  • 289.
    Clement, Alice M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Nysjö, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Strand, Robin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Brain – Endocast relationship in the Australian lungfish, Neoceratodus forsteri, elucidated from tomographic data (Sarcopterygii: Dipnoi)2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 10, article id e0141277Article in journal (Refereed)
    Abstract [en]

    Although the brains of the three extant lungfish genera have been previously described, the spatial relationship between the brain and the neurocranium has never before been fully described nor quantified. Through the application of virtual microtomography (mu CT) and 3D rendering software, we describe aspects of the gross anatomy of the brain and labyrinth region in the Australian lungfish, Neoceratodus forsteri and compare this to previous accounts. Unexpected characters in this specimen include short olfactory peduncles connecting the olfactory bulbs to the telencephalon, and an oblong telencephalon. Furthermore, we illustrate the endocast (the mould of the internal space of the neurocranial cavity) of Neoceratodus, also describing and quantifying the brain-endocast relationship in a lungfish for the first time. Overall, the brain of the Australian lungfish closely matches the size and shape of the endocast cavity housing it, filling more than four fifths of the total volume. The forebrain and labyrinth regions of the brain correspond very well to the endocast morphology, while the midbrain and hindbrain do not fit so closely. Our results cast light on the gross neural and endocast anatomy in lungfishes, and are likely to have particular significance for palaeoneurologists studying fossil taxa.

  • 290.
    Clement, Alice M.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    Strand, Robin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Nysjö, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Long, John A.
    Ahlberg, Per E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Evolution and Developmental Biology.
    A new method for reconstructing brain morphology: Applying the brain-neurocranial spatial relationship in an extant lungfish to a fossil endocast2016In: Royal Society Open Science, E-ISSN 2054-5703, Vol. 3, no 7, article id 160307Article in journal (Refereed)
  • 291.
    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.

  • 292.
    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'.

  • 293.
    Connallon, Tim
    et al.
    Monash Univ, Sch Biol Sci, Clayton, Vic 3800, Australia;Monash Univ, Ctr Geometr Biol, Clayton, Vic 3800, Australia.
    Olito, Colin
    Monash Univ, Sch Biol Sci, Clayton, Vic 3800, Australia;Monash Univ, Ctr Geometr Biol, Clayton, Vic 3800, Australia;Lund Univ, Sect Evolutionary Ecol, Dept Biol, S-22362 Lund, Sweden.
    Dutoit, Ludovic
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Univ Otago, Dept Zool, Dunedin 9054, New Zealand.
    Papoli, Homa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Ruzicka, Filip
    UCL, Res Dept Genet Evolut & Environm, London WC1E 6BT, England.
    Yong, Lengxob
    Univ Exeter, Ctr Ecol & Conservat, Penryn TR10 9FE, England.
    Local adaptation and the evolution of inversions on sex chromosomes and autosomes2018In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 373, no 1757, article id 20170423Article in journal (Refereed)
    Abstract [en]

    Spatially varying selection with gene flow can favour the evolution of inversions that bind locally adapted alleles together, facilitate local adaptation and ultimately drive genomic divergence between species. Several studies have shown that the rates of spread and establishment of new inversions capturing locally adaptive alleles depend on a suite of evolutionary factors, including the strength of selection for local adaptation, rates of gene flow and recombination, and the deleterious mutation load carried by inversions. Because the balance of these factors is expected to differ between X (or Z) chromosomes and autosomes, opportunities for inversion evolution are likely to systematically differ between these genomic regions, though such scenarios have not been formally modelled. Here, we consider the evolutionary dynamics of X-linked and autosomal inversions in populations evolving at a balance between migration and local selection. We identify three factors that lead to asymmetric rates of X-linked and autosome inversion establishment: (1) sex-biased migration, (2) dominance of locally adapted alleles and (3) chromosome-specific deleterious mutation loads. This theory predicts an elevated rate of fixation, and depressed opportunities for polymorphism, for X-linked inversions. Our survey of data on the genomic distribution of polymorphic and fixed inversions supports both theoretical predictions. This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.

  • 294.
    Corcoran, Pádraic
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Neurospora tetrasperma from Natural Populations: Toward the Population Genomics of a Model Fungus2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The study of DNA sequence variation is a powerful approach to study genome evolution, and to reconstruct evolutionary histories of species. In this thesis, I have studied genetic variation in the fungus Neurospora tetrasperma and other closely related Neurospora species. I have focused on N. tetrasperma in my research because it has large regions of suppressed recombination on its mating-type chromosomes, had undergone a recent change in reproductive mode and is composed of multiple reproductively isolated lineages. Using DNA sequence data from a large sample set representing multiple species of Neurospora I estimated that N. tetrasperma evolved ~1 million years ago and that it is composed of at least 10 lineages. My analysis of the type of asexual spores produced using newly described N. tetrasperma populations in Britain revealed that lineages differ considerably in life history characteristics that may have consequences for their evolution. A comparative genomic analysis using three genomes of N. tetrasperma and the genome of N. crassa revealed that the mat a chromosomes in the lineages examine have been introgressed from other Neurospora species and that this introgression has reduced levels of molecular degeneration on the mating-type chromosomes. Finally, I generated a population genomic dataset composed of 92 N. tetrasperma genomes and two genomes of other Neurospora species. Analysis of these genomes revealed that all strains of N. tetrasperma have large regions of suppressed recombination on their mating-type chromosomes ranging from 69-84% of the chromosome and that the extent of divergence between mating-type chromosomes within lineages varies greatly (from 1.3 to 3.2%). I concluded that the source of this great divergence mating-type chromosome is large-scale introgression from other Neurospora species, and that these introgressed tracts have become fixed within N. tetrasperma lineages. I also discovered that genes within non-recombining introgressed regions of the mating-type chromosome have severely reduced levels of genetic variation as compared to the autosomes, and exhibit signatures of reduced molecular degeneration. My analysis of variation in coding regions revealed that positive selection on the introgressed regions has resulted in the removal of deleterious mutations and is responsible for the reductions in molecular degeneration observed.

    List of papers
    1. Large-Scale Introgression Shapes the Evolution of the Mating-Type Chromosomes of the Filamentous Ascomycete Neurospora tetrasperma
    Open this publication in new window or tab >>Large-Scale Introgression Shapes the Evolution of the Mating-Type Chromosomes of the Filamentous Ascomycete Neurospora tetrasperma
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    2012 (English)In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 8, no 7, p. e1002820-Article in journal (Refereed) Published
    Abstract [en]

    The significance of introgression as an evolutionary force shaping natural populations is well established, especially in animal and plant systems. However, the abundance and size of introgression tracts, and to what degree interspecific gene flow is the result of adaptive processes, are largely unknown. In this study, we present medium coverage genomic data from species of the filamentous ascomycete Neurospora, and we use comparative genomics to investigate the introgression landscape at the genomic level in this model genus. We revealed one large introgression tract in each of the three investigated phylogenetic lineages of Neurospora tetrasperma (sizes of 5.6 Mbp, 5.2 Mbp, and 4.1 Mbp, respectively). The tract is located on the chromosome containing the locus conferring sexual identity, the mating-type (mat) chromosome. The region of introgression is confined to the region of suppressed recombination and is found on one of the two mat chromosomes (mat a). We used Bayesian concordance analyses to exclude incomplete lineage sorting as the cause for the observed pattern, and multilocus genealogies from additional species of Neurospora show that the introgression likely originates from two closely related, freely recombining, heterothallic species (N. hispaniola and N. crassa/N. perkinsii). Finally, we investigated patterns of molecular evolution of the mat chromosome in Neurospora, and we show that introgression is correlated with reduced level of molecular degeneration, consistent with a shorter time of recombination suppression. The chromosome specific (mat) and allele specific (mat a) introgression reported herein comprise the largest introgression tracts reported to date from natural populations. Furthermore, our data contradicts theoretical predictions that introgression should be less likely on sex-determining chromosomes. Taken together, the data presented herein advance our general understanding of introgression as a force shaping eukaryotic genomes.

    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-181143 (URN)10.1371/journal.pgen.1002820 (DOI)000306840400034 ()
    Available from: 2012-09-18 Created: 2012-09-17 Last updated: 2017-12-07Bibliographically approved
    2. Quantifying functional heterothallism in the pseudohomothallic ascomycete Neurospora tetrasperma
    Open this publication in new window or tab >>Quantifying functional heterothallism in the pseudohomothallic ascomycete Neurospora tetrasperma
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    2012 (English)In: Fungal Biology, ISSN 1878-6146, E-ISSN 1878-6162, Vol. 116, no 9, p. 962-975Article in journal (Refereed) Published
    Abstract [en]

    Neurospora tetrasperma is a pseudohomothallic filamentous ascomycete that has evolved from heterothallic ancestors. Throughout its life cycle, it is predominantly heterokaryotic for mating type, and thereby self-fertile. However, studies of N. tetrasperma have revealed the occasional production of self-sterile asexual and sexual spores of a single-mating type, indicating that it can be functionally heterothallic. Here, we report the extensive sampling and isolation of natural, heterokaryotic, strains of N. tetrasperma from the United Kingdom (UK): 99 strains were collected from Surrey, England, and four from Edinburgh, Scotland. We verified by phylogenetic analyses that these strains belong to N. tetrasperma. We isolated cultures from single germinated asexual spores (conidia) from 17 of these newly sampled UK strains from Surrey, and 16 previously sampled strains of N. tetrasperma from New Zealand (NZ). Our results show that the N. tetrasperrna strains from the UK population produced a significantly greater proportion of self-sterile, homokaryotic conidia than the NZ population: the proportion of homokaryotic conidia was 42.6 % (133/312 spores) and 15.3 % (59/386) from the UK and the NZ populations, respectively. Although homokaryons recovered from several strains show a bias for one of the mating types, the total ratio of mat A to mat a mating type in homokaryons (UK: 72/61, NZ 28/31) did not deviate significantly from the expected 1:1 ratio for either of these populations. These results indicate that different populations exhibit differences in their life cycle characteristics, and that a higher degree of outcrossing might be expected from the UK population. This study points to the importance of studying multiple strains and populations when investigating life history traits of an organism with a complex life cycle, as previously undetected differences between populations may be revealed.

    Keywords
    Conidia, Heterothallism, Neurospora tetrasperma, Outcrossing, Populations, Pseudohomothallism
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-185648 (URN)10.1016/j.funbio.2012.06.006 (DOI)000310038800003 ()
    Available from: 2012-11-27 Created: 2012-11-27 Last updated: 2017-12-07Bibliographically approved
    3. A global multilocus analysis of the model fungus Neurospora reveals a single recent origin of a novel genetic system
    Open this publication in new window or tab >>A global multilocus analysis of the model fungus Neurospora reveals a single recent origin of a novel genetic system
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    2014 (English)In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 78, p. 136-147Article in journal (Refereed) Published
    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.

    Keywords
    Mating Systems, Population Structure, Phylogenetics, Neurospora
    National Category
    Evolutionary Biology
    Research subject
    Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-208792 (URN)10.1016/j.ympev.2014.05.007 (DOI)000342480400012 ()
    Available from: 2013-10-07 Created: 2013-10-07 Last updated: 2017-12-06Bibliographically approved
    4. Adaptive introgression slows down molecular degeneration of the mating-type chromosome in Neurospora tetrasperma
    Open this publication in new window or tab >>Adaptive introgression slows down molecular degeneration of the mating-type chromosome in Neurospora tetrasperma
    Show others...
    (English)Manuscript (preprint) (Other academic)
    Keywords
    Neurospora, introgression, recombination, genomes
    National Category
    Evolutionary Biology Genetics
    Research subject
    Evolutionary Genetics
    Identifiers
    urn:nbn:se:uu:diva-208794 (URN)
    Available from: 2013-10-07 Created: 2013-10-07 Last updated: 2014-01-23
  • 295.
    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)
  • 296.
    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.

  • 297.
    Cortazar-Chinarro, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Immunogenetic variation along the latitudinal gradient in Scandinavian anuran species: Evolutionary processes, demography and infection2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The evolutionary and demographic processes affecting how genetic variation is partitioned and distributed over large geographical scales is of fundamental importance for our understanding of how organisms may adapt to their environments. Northern peripheral populations generally have lower genetic variation and individuals in these populations may therefore face difficulties adapting to their local environment. At northern latitudes lack of genetic variation could be detrimental in face of newly emerging diseases as a result of anthropogenic actions and warmer climate in these areas. In this thesis, I explore genetic variation and the contemporary evolutionary processes affecting genes involved in the adaptive immune defense (Major Histocompatibility Complex; MHC) and the innate immune defense (AMP; Antimicrobial Peptides) over a large geographical gradient in anuran species (paper I, II and IV). I study signatures of historical selection on the MHC class II exon 2 and AMP (Temporin, Brevinin and Palustrin) sequences in the Signal Peptide and the Acidic Propiece domains (paper II and III). Finally, I investigate potential associations between specific MHC class II exon 2 alleles and a chytrid fungus infection (Bd) in common toads (Bufo bufo) (paper IV). The results reveal that genetic variation of MHC class II exon 2 decreases towards northern latitudes in R. arvalis and B. bufo and have been shaped by complex evolutionary processes (drift, selection, migration) affected by different demographic scenarios. On the other hand, AMP nucleotide variation is divergent among geographical areas, but there is no clear geographical pattern along the same gradient, suggesting diversifying selection as the main force shaping genetic variation. Finally, I found an effect of two specific MHC class II exon 2 alleles on survival in juvenile B. bufo when infected with Bd. In summary, my thesis unravels the complex patterns shaping genetic diversity at large scales. My results may guide conservation practices aiming to prevent amphibian mass mortality events on-going all over the world.

    List of papers
    1. Drift, selection, or migration?: Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian
    Open this publication in new window or tab >>Drift, selection, or migration?: Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian
    Show others...
    2017 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 189Article in journal (Refereed) Published
    Abstract [en]

    Background: Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. Results: Using outlier analyses, we identified the MHC II exon 2 (corresponding to the beta-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. Conclusion: Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.

    Keywords
    Genetic drift, Natural selection, Major histocompatibility complex, Microsatellites, Outlier tests, Rana arvalis
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-332660 (URN)10.1186/s12862-017-1022-z (DOI)000407567900003 ()
    Funder
    Swedish Research Council Formas, 146,400,178Swedish Research Council, 621-2013-4503
    Available from: 2017-10-31 Created: 2017-10-31 Last updated: 2019-04-20Bibliographically approved
    2. Contrasting patterns of AMP nucleotide and peptide variation along a latitudinal gradient in two frog species
    Open this publication in new window or tab >>Contrasting patterns of AMP nucleotide and peptide variation along a latitudinal gradient in two frog species
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-382091 (URN)
    Available from: 2019-04-20 Created: 2019-04-20 Last updated: 2019-04-20
    3. Signatures of historical selection on MHC reveal different selection patterns in the moor frog (Rana arvalis)
    Open this publication in new window or tab >>Signatures of historical selection on MHC reveal different selection patterns in the moor frog (Rana arvalis)
    2018 (English)In: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 70, no 7, p. 477-484Article in journal (Refereed) Published
    Abstract [en]

    MHC genes are key components in disease resistance and an excellent system for studying selection acting on genetic variation in natural populations. Current patterns of variation in MHC genes are likely to be influenced by past and ongoing selection as well as demographic fluctuations in population size such as those imposed by post-glacial recolonization processes. Here, we investigated signatures of historical selection and demography on an MHC class II gene in 12 moor frog populations along a 1700-km latitudinal gradient. Sequences were obtained from 207 individuals and consecutively assigned into two different clusters (northern and southern clusters, respectively) in concordance with a previously described dual post-glacial colonization route. Selection analyses comparing the relative rates of non-synonymous to synonymous substitutions (dN/dS) suggested evidence of different selection patterns in the northern and the southern clusters, with divergent selection prevailing in the south but uniform positive selection predominating in the north. Also, models of codon evolution revealed considerable differences in the strength of selection: The southern cluster appeared to be under strong selection while the northern cluster showed moderate signs of selection. Our results indicate that the MHC alleles in the north diverged from southern MHC alleles as a result of differential selection patterns.

    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-341392 (URN)10.1007/s00251-017-1051-1 (DOI)000435594000006 ()29387920 (PubMedID)
    Funder
    Swedish Research Council Formas, 215-2014-594Swedish Research Council, 621-2013-4503
    Available from: 2018-02-07 Created: 2018-02-07 Last updated: 2019-04-20Bibliographically approved
    4. Latitudinal MHC variation and haplotype associated differential survival in response to experimental infection of two strains of Bd-GPL in common toads
    Open this publication in new window or tab >>Latitudinal MHC variation and haplotype associated differential survival in response to experimental infection of two strains of Bd-GPL in common toads
    Show others...
    (English)Manuscript (preprint) (Other academic)
    National Category
    Evolutionary Biology
    Identifiers
    urn:nbn:se:uu:diva-382090 (URN)10.1101/597559 (DOI)
    Available from: 2019-04-20 Created: 2019-04-20 Last updated: 2019-04-20
  • 298.
    Cortazar-Chinarro, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Lattenkamp, Ella Z.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Max Planck Inst Psycholinguist, Dept Neurogenet Vocal Commun, Box 310, NL-6500 Nijmegen, Netherlands..
    Meyer-Lucht, Yvonne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Luquet, Emilien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Univ Claude Bernard Lyon I, CNRS, UMR 5023, LEHNA, 3-6 Rue Raphael Dubois,Batiments Darwin C & Forel, F-69622 Villeurbanne 43, France..
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Drift, selection, or migration?: Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian2017In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 17, article id 189Article in journal (Refereed)
    Abstract [en]

    Background: Past events like fluctuations in population size and post-glacial colonization processes may influence the relative importance of genetic drift, migration and selection when determining the present day patterns of genetic variation. We disentangle how drift, selection and migration shape neutral and adaptive genetic variation in 12 moor frog populations along a 1700 km latitudinal gradient. We studied genetic differentiation and variation at a MHC exon II locus and a set of 18 microsatellites. Results: Using outlier analyses, we identified the MHC II exon 2 (corresponding to the beta-2 domain) locus and one microsatellite locus (RCO8640) to be subject to diversifying selection, while five microsatellite loci showed signals of stabilizing selection among populations. STRUCTURE and DAPC analyses on the neutral microsatellites assigned populations to a northern and a southern cluster, reflecting two different post-glacial colonization routes found in previous studies. Genetic variation overall was lower in the northern cluster. The signature of selection on MHC exon II was weaker in the northern cluster, possibly as a consequence of smaller and more fragmented populations. Conclusion: Our results show that historical demographic processes combined with selection and drift have led to a complex pattern of differentiation along the gradient where some loci are more divergent among populations than predicted from drift expectations due to diversifying selection, while other loci are more uniform among populations due to stabilizing selection. Importantly, both overall and MHC genetic variation are lower at northern latitudes. Due to lower evolutionary potential, the low genetic variation in northern populations may increase the risk of extinction when confronted with emerging pathogens and climate change.

  • 299.
    Cortazar-Chinarro, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University.
    Meurling, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Schroyens, Laurens
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Ritcher-Boix, Alex
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Latitudinal MHC variation and haplotype associated differential survival in response to experimental infection of two strains of Bd-GPL in common toadsManuscript (preprint) (Other academic)
  • 300.
    Cortazar-Chinarro, Maria
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology. Uppsala University.
    Meyer-Lucht, Yvonne
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Laurila, Anssi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Höglund, Jacob
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal ecology.
    Signatures of historical selection on MHC reveal different selection patterns in the moor frog (Rana arvalis)2018In: Immunogenetics, ISSN 0093-7711, E-ISSN 1432-1211, Vol. 70, no 7, p. 477-484Article in journal (Refereed)
    Abstract [en]

    MHC genes are key components in disease resistance and an excellent system for studying selection acting on genetic variation in natural populations. Current patterns of variation in MHC genes are likely to be influenced by past and ongoing selection as well as demographic fluctuations in population size such as those imposed by post-glacial recolonization processes. Here, we investigated signatures of historical selection and demography on an MHC class II gene in 12 moor frog populations along a 1700-km latitudinal gradient. Sequences were obtained from 207 individuals and consecutively assigned into two different clusters (northern and southern clusters, respectively) in concordance with a previously described dual post-glacial colonization route. Selection analyses comparing the relative rates of non-synonymous to synonymous substitutions (dN/dS) suggested evidence of different selection patterns in the northern and the southern clusters, with divergent selection prevailing in the south but uniform positive selection predominating in the north. Also, models of codon evolution revealed considerable differences in the strength of selection: The southern cluster appeared to be under strong selection while the northern cluster showed moderate signs of selection. Our results indicate that the MHC alleles in the north diverged from southern MHC alleles as a result of differential selection patterns.

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