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  • 1.
    Ament-Velásquez, S. Lorena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Stockholm University.
    Vogan, Aaron A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Granger-Farbos, Alexandra
    Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, France.
    Bastiaans, Eric
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Laboratory of Genetics, Wageningen University & Research, Droeven-daalsesteeg 1, Wageningen, The Netherlands.
    Martinossi-Allibert, Ivain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Norwegian University of Science and Technology.
    Saupe, Sven J.
    Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Université de Bordeaux, France.
    de Groot, Suzette
    Laboratory of Genetics, Wageningen University & Research, Droeven-daalsesteeg 1, Wageningen, The Netherlands.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Debets, Alfons J. M.
    Laboratory of Genetics, Wageningen University & Research, Droeven-daalsesteeg 1, Wageningen, The Netherlands.
    Clavé, Corinne
    Institut de Biochimie et de Génétique Cellulaire, UMR 5095 CNRS, Uni-versité de Bordeaux, France.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Allorecognition genes drive reproductive isolation in Podospora anserina2022In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 6, no 7, p. 910-923Article in journal (Refereed)
    Abstract [en]

    Allorecognition, the capacity to discriminate self from conspecific non-self, is a ubiquitous organismal feature typically governed by genes evolving under balancing selection. Here, we show that in the fungus Podospora anserina, allorecognition loci controlling vegetative incompatibility (het genes), define two reproductively isolated groups through pleiotropic effects on sexual compatibility. These two groups emerge from the antagonistic interactions of the unlinked loci het-r (encoding a NOD-like receptor) and het-v (encoding a methyltransferase and an MLKL/HeLo domain protein). Using a combination of genetic and ecological data, supported by simulations, we provide a concrete and molecularly defined example whereby the origin and coexistence of reproductively isolated groups in sympatry is driven by pleiotropic genes under balancing selection.

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  • 2. An, Junghwa
    et al.
    Bechet, Arnaud
    Berggren, Åsa
    Brown, Sarah K.
    Bruford, Michael W.
    Cai, Qingui
    Cassel-Lundhagen, Anna
    Cezilly, Frank
    Chen, Song-Lin
    Cheng, Wei
    Choi, Sung-Kyoung
    Ding, X.Y.
    Fan, Yong
    Feldheim, Kevin A.
    Feng, Z.Y.
    Friesen, Vicki L.
    Gaillard, Maria
    Galaraza, Juan A.
    Gallo, Leonardo
    Ganeshaiah, K. N.
    Geraci, Julia
    Gibbons, John G.
    Grant, William S.
    Grauvogel, Zac
    Gustafsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Guyon, Jeffrey R.
    Han, L.
    Heath, Daniel D.
    Hemmilä, Sofia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Hogan, Derek
    Hou, B. W.
    Jakse, Jernej
    Javornik, Branka
    Kanuch, Peter
    Kim, Kyung-Kil
    Kim, Kyung-Seok
    Kim, Sang-Gyu
    Kim, Sang-In
    Kim, Woo-Jin
    Kim, Yi-Kyung
    Klich, Maren A.
    Kreiser, Brian R.
    Kwan, Ye-Seul
    Lam, Athena W.
    Lasater, Kelly
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Lee, Hang
    Lee, Yun-Sun
    Li, D. L.
    Li, Shao-Jing
    Li, W. Y.
    Liao, Xiaolin
    Liber, Zlatko
    Lin, Lin
    Liu, Shaoying
    Luo, Xin-Hui
    Ma, Y. H.
    Ma, Yajun
    Marchelli, Paula
    Min, Mi-Sook
    Moccia, Maria Domenica
    Mohana, Kumara P.
    Moore, Marcelle
    Morris-Pocock, James A.
    Park, Han-Chan
    Pfunder, Monika
    Ivan, Radosavljevic
    Ravikanth, G.
    Roderick, George K.
    Rokas, Antonis
    Sacks, Benjamin N.
    Saski, Christopher A.
    Satovic, Zlatko
    Schoville, Sean D.
    Sebastiani, Federico
    Sha, Zhen-Xia
    Shin, Eun-Ha
    Soliani, Carolina
    Sreejayan, N.
    Sun, Zhengxin
    Tao, Yong
    Taylor, Scott A.
    Templin, William D.
    Shaanker, R. Uma
    Vasudeva, R.
    Vendramin, Giovanni G.
    Walter, Ryan P.
    Wang, Gui-Zhong
    Wang, Ke-Jian
    Wang, Y. Q.
    Wattier, Rémi A.
    Wei, Fuwen
    Widmer, Alex
    Woltmann, Stefan
    Won, Yong-Jin
    Wu, Jing
    Xie, M. L.
    Xu, Genbo
    Xu, Xiao-Jun
    Ye, Hai-Hui
    Zhan, Xiangjiang
    Zhang, F.
    Zhong, J.
    Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2009-30 November 20092010In: Molecular Ecology Resources, ISSN 1755-098X, Vol. 10, no 2, p. 404-408Article in journal (Refereed)
    Abstract [en]

    This article documents the addition of 411 microsatellite marker loci and 15 pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Acanthopagrus schlegeli, Anopheles lesteri, Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus oryzae, Aspergillus terreus, Branchiostoma japonicum, Branchiostoma belcheri, Colias behrii, Coryphopterus personatus, Cynogolssus semilaevis, Cynoglossus semilaevis, Dendrobium officinale, Dendrobium officinale, Dysoxylum malabaricum, Metrioptera roeselii, Myrmeciza exsul, Ochotona thibetana, Neosartorya fischeri, Nothofagus pumilio, Onychodactylus fischeri, Phoenicopterus roseus, Salvia officinalis L., Scylla paramamosain, Silene latifo, Sula sula, and Vulpes vulpes. These loci were cross-tested on the following species: Aspergillus giganteus, Colias pelidne, Colias interior, Colias meadii, Colias eurytheme, Coryphopterus lipernes, Coryphopterus glaucofrenum, Coryphopterus eidolon, Gnatholepis thompsoni, Elacatinus evelynae, Dendrobium loddigesii Dendrobium devonianum, Dysoxylum binectariferum, Nothofagus antarctica, Nothofagus dombeyii, Nothofagus nervosa, Nothofagus obliqua, Sula nebouxii, and Sula variegata. This article also documents the addition of 39 sequencing primer pairs and 15 allele specific primers or probes for Paralithodes camtschaticus.

  • 3.
    Bartoszek, Krzysztof
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. CNRS Univ Montpellier IRD EPHE, UMR ISEM 5554, Montpellier, France..
    Kaj, Ingemar
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Using the Ornstein-Uhlenbeck process to model the evolution of interacting populations2017In: Journal of Theoretical Biology, ISSN 0022-5193, E-ISSN 1095-8541, Vol. 429, p. 35-45Article in journal (Refereed)
    Abstract [en]

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

  • 4.
    Benavides, Raquel
    et al.
    CSIC, Museo Nacl Ciencias Nat, Dept Biogeog & Global Change, LINCGlobal, C Serrano 115 Dpdo, Madrid 28006, Spain..
    Carvalho, Barbara
    CSIC, Museo Nacl Ciencias Nat, Dept Biogeog & Global Change, LINCGlobal, C Serrano 115 Dpdo, Madrid 28006, Spain..
    Bastias, Cristina C.
    CSIC, Museo Nacl Ciencias Nat, Dept Biogeog & Global Change, LINCGlobal, C Serrano 115 Dpdo, Madrid 28006, Spain.;Univ Montpellier, Univ Paul Valery, UMR CEFE 5175, CNRS,EPHE,IRD, Montpellier, France..
    Lopez-Quiroga, David
    CSIC, Museo Nacl Ciencias Nat, Dept Biogeog & Global Change, LINCGlobal, C Serrano 115 Dpdo, Madrid 28006, Spain..
    Mas, Antonio
    CSIC, Museo Nacl Ciencias Nat, Dept Biogeog & Global Change, LINCGlobal, C Serrano 115 Dpdo, Madrid 28006, Spain..
    Cavers, Stephen
    UK Ctr Ecol & Hydrol, Penicuik, Midlothian, Scotland..
    Gray, Alan
    UK Ctr Ecol & Hydrol, Penicuik, Midlothian, Scotland..
    Albet, Audrey
    INRAE, UEFP, Cestas, France..
    Alia, Ricardo
    INIA CIFOR, Inst Nacl Invest & Tecnol Agr & Alimentaria, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    Ambrosio, Olivier
    INRAE, URFM, Avignon, France..
    Aravanopoulos, Filippos
    Aristotle Univ Thessaloniki, Sch Forestry & Nat Environm, Lab Forest Genet & Tree Breeding, Thessaloniki, Greece..
    Aunon, Francisco
    INIA CIFOR, Inst Nacl Invest & Tecnol Agr & Alimentaria, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    Avanzi, Camilla
    Natl Res Council CNR, Inst Biosci & BioResources, Sesto Fiorentino, Italy..
    Avramidou, Evangelia V.
    Aristotle Univ Thessaloniki, Sch Forestry & Nat Environm, Lab Forest Genet & Tree Breeding, Thessaloniki, Greece..
    Bagnoli, Francesca
    Natl Res Council CNR, Inst Biosci & BioResources, Sesto Fiorentino, Italy..
    Ballesteros, Eduardo
    INIA CIFOR, Inst Nacl Invest & Tecnol Agr & Alimentaria, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    Barbas, Evangelos
    Aristotle Univ Thessaloniki, Sch Forestry & Nat Environm, Lab Forest Genet & Tree Breeding, Thessaloniki, Greece..
    Bastien, Catherine
    INRAE, BioForA, ONF, Orleans, France..
    Bernier, Frederic
    INRAE, UEFP, Cestas, France..
    Bignalet, Henry
    INRAE, UEFP, Cestas, France..
    Bouic, Damien
    INRAE, UEFP, Cestas, France..
    Brunetto, William
    INRAE, URFM, Avignon, France..
    Buchovska, Jurata
    Vytautas Magnus Univ, Akademija, Lithuania..
    Cabanillas-Saldana, Ana M.
    Gobierno Aragon, Dept Agr Ganaderia & Medio Ambiente, Zaragoza, Spain..
    Cheval, Nicolas
    INRAE, UEFP, Cestas, France..
    Climent, Jose M.
    INIA CIFOR, Inst Nacl Invest & Tecnol Agr & Alimentaria, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    Correard, Marianne
    INRAE, UEFM, Avignon, France..
    Cremer, Eva
    Bavarian Off Forest Seeding & Planting ASP, Teisendorf, Germany..
    Danusevicius, Darius
    Vytautas Magnus Univ, Akademija, Lithuania..
    Dauphin, Benjamin
    Swiss Fed Res Inst WSL, Birmensdorf, Switzerland..
    Del Cano, Fernando
    INIA CIFOR, Inst Nacl Invest & Tecnol Agr & Alimentaria, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    Denou, Jean-Luc
    INRAE, UEFP, Cestas, France..
    Dokhelar, Bernard
    INRAE, UEFP, Cestas, France..
    Dourthe, Remi
    INRAE, UEFP, Cestas, France..
    Farsakoglou, Anna-Maria
    Aristotle Univ Thessaloniki, Sch Forestry & Nat Environm, Lab Forest Genet & Tree Breeding, Thessaloniki, Greece..
    Fera, Andreas
    Austrian Res Ctr Forests BFW, Dept Forest Growth & Silviculture, Vienna, Austria..
    Fonti, Patrick
    Swiss Fed Res Inst WSL, Birmensdorf, Switzerland..
    Ganopoulos, Ioannis
    Aristotle Univ Thessaloniki, Sch Forestry & Nat Environm, Lab Forest Genet & Tree Breeding, Thessaloniki, Greece.;Hellen Agr Org DEMETER Ex NAGREF, Inst Plant Breeding & Genet Resources, Thermi, Greece..
    Garcia del Barrio, Jose M.
    INIA CIFOR, Inst Nacl Invest & Tecnol Agr & Alimentaria, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    Gilg, Olivier
    INRAE, UEFM, Avignon, France..
    Gonzalez-Martinez, Santiago C.
    Univ Bordeaux, INRAE, BIOGECO, Cestas, France..
    Graf, Rene
    Swiss Fed Res Inst WSL, Birmensdorf, Switzerland..
    Grivet, Delphine
    INIA CIFOR, Inst Nacl Invest & Tecnol Agr & Alimentaria, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    Gugerli, Felix
    Swiss Fed Res Inst WSL, Birmensdorf, Switzerland..
    Hartleitner, Christoph
    LIECO, Kalwang, Austria..
    Heer, Katrin
    Philipps Univ Marburg, Dept Biol, Marburg, Germany..
    Hollenbach, Enja
    Philipps Univ Marburg, Dept Biol, Marburg, Germany..
    Hurel, Agathe
    Univ Bordeaux, INRAE, BIOGECO, Cestas, France..
    Issehuth, Bernard
    INRAE, UEFP, Cestas, France..
    Jean, Florence
    INRAE, URFM, Avignon, France..
    Jorge, Veronique
    INRAE, BioForA, ONF, Orleans, France..
    Jouineau, Arnaud
    INRAE, URFM, Avignon, France..
    Kappner, Jan-Philipp
    Philipps Univ Marburg, Dept Biol, Marburg, Germany..
    Karkkainen, Katri
    Univ Oulu, Nat Resources Inst Finland, Oulu, Finland..
    Kesalahti, Robert
    Univ Oulu, Oulu, Finland..
    Knutzen, Florian
    Bavarian Off Forest Seeding & Planting ASP, Teisendorf, Germany..
    Kujala, Sonja T.
    Univ Oulu, Nat Resources Inst Finland, Oulu, Finland..
    Kumpula, Timo
    Univ Oulu, Oulu, Finland..
    Labriola, Mariaceleste
    Natl Res Council CNR, Inst Biosci & BioResources, Sesto Fiorentino, Italy..
    Lalanne, Celine
    Univ Bordeaux, INRAE, BIOGECO, Cestas, France..
    Lambertz, Johannes
    Philipps Univ Marburg, Dept Biol, Marburg, Germany..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Le Provost, Gregoire
    Univ Bordeaux, INRAE, BIOGECO, Cestas, France..
    Liesebach, Mirko
    Thunen Inst Forest Genet, Grosshansdorf, Germany..
    Malliarou, Ermioni
    Aristotle Univ Thessaloniki, Sch Forestry & Nat Environm, Lab Forest Genet & Tree Breeding, Thessaloniki, Greece..
    Marchon, Jeremy
    Swiss Fed Res Inst WSL, Birmensdorf, Switzerland..
    Mariotte, Nicolas
    INRAE, URFM, Avignon, France..
    Martinez-Sancho, Elisabet
    Swiss Fed Res Inst WSL, Birmensdorf, Switzerland..
    Matesanz, Silvia
    Univ Rey Juan Carlos, Area Biodiversidad & Conservac, Mostoles, Spain..
    Meischner, Helge
    Philipps Univ Marburg, Dept Biol, Marburg, Germany..
    Michotey, Celia
    INRAE, URGI, Route St Cyr, Versailles, France..
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Morganti, Sandro
    Swiss Fed Res Inst WSL, Birmensdorf, Switzerland..
    Myking, Tor
    Norwegian Inst Bioecon Res NIBIO, Div Forestry & Forest Resources, As, Norway..
    Nilsen, Anne E.
    Norwegian Inst Bioecon Res NIBIO, Div Forestry & Forest Resources, As, Norway..
    Notivol, Eduardo
    Ctr Invest & Tecnol Agroalimentaria Aragon, Unidad Recursos Forestales CITA, Zaragoza, Spain..
    Opgenoorth, Lars
    Swiss Fed Res Inst WSL, Birmensdorf, Switzerland.;Philipps Univ Marburg, Dept Biol, Marburg, Germany..
    ostreng, Geir
    Norwegian Inst Bioecon Res NIBIO, Div Forestry & Forest Resources, As, Norway..
    Pakull, Birte
    Thunen Inst Forest Genet, Grosshansdorf, Germany..
    Piotti, Andrea
    Natl Res Council CNR, Inst Biosci & BioResources, Sesto Fiorentino, Italy..
    Plomion, Christophe
    Univ Bordeaux, INRAE, BIOGECO, Cestas, France..
    Poinot, Nicolas
    INRAE, UEFP, Cestas, France..
    Pringarbe, Mehdi
    INRAE, UEFM, Avignon, France..
    Puzos, Luc
    INRAE, UEFP, Cestas, France..
    Pyhajarvi, Tanja
    Univ Oulu, Oulu, Finland..
    Raffin, Annie
    INRAE, UEFP, Cestas, France..
    Ramirez-Valiente, Jose A.
    INIA CIFOR, Inst Nacl Invest & Tecnol Agr & Alimentaria, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    Rellstab, Christian
    Swiss Fed Res Inst WSL, Birmensdorf, Switzerland..
    Richter, Sebastian
    Philipps Univ Marburg, Dept Biol, Marburg, Germany..
    Robledo-Arnuncio, Juan J.
    INIA CIFOR, Inst Nacl Invest & Tecnol Agr & Alimentaria, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    San Segundo, Sergio
    INIA CIFOR, Inst Nacl Invest & Tecnol Agr & Alimentaria, Forest Res Ctr, Dept Forest Ecol & Genet, Madrid, Spain..
    Savolainen, Outi
    Univ Oulu, Nat Resources Inst Finland, Oulu, Finland..
    Schneck, Volker
    Thunen Inst Forest Genet, Waldsieversdorf, Germany..
    Schueler, Silvio
    Austrian Res Ctr Forests BFW, Dept Forest Growth & Silviculture, Vienna, Austria..
    Scotti, Ivan
    INRAE, URFM, Avignon, France..
    Semerikov, Vladimir
    RAS, Ural Branch, Inst Plant & Anim Ecol, Ekaterinburg, Russia..
    Henrik Sonstebo, Jorn
    Norwegian Inst Bioecon Res NIBIO, Div Forestry & Forest Resources, As, Norway..
    Spanu, Ilaria
    Natl Res Council CNR, Inst Biosci & BioResources, Sesto Fiorentino, Italy..
    Thevenet, Jean
    INRAE, UEFM, Avignon, France..
    Tollefsrud, Mari Mette
    Norwegian Inst Bioecon Res NIBIO, Div Forestry & Forest Resources, As, Norway..
    Turion, Norbert
    INRAE, UEFM, Avignon, France..
    Vendramin, Giovanni Giuseppe
    Natl Res Council CNR, Inst Biosci & BioResources, Sesto Fiorentino, Italy..
    Villar, Marc
    INRAE, BioForA, ONF, Orleans, France..
    Westin, Johan
    Skogforsk, Uppsala, Sweden..
    Fady, Bruno
    INRAE, URFM, Avignon, France..
    Valladares, Fernando
    CSIC, Museo Nacl Ciencias Nat, Dept Biogeog & Global Change, LINCGlobal, C Serrano 115 Dpdo, Madrid 28006, Spain.;Univ Rey Juan Carlos, Area Biodiversidad & Conservac, Mostoles, Spain..
    The GenTree Leaf Collection: Inter- and intraspecific leaf variation in seven forest tree species in Europe2021In: Global Ecology and Biogeography, ISSN 1466-822X, E-ISSN 1466-8238, Vol. 30, no 3, p. 590-597Article in journal (Refereed)
    Abstract [en]

    Motivation Trait variation within species can reveal plastic and/or genetic responses to environmental gradients, and may indicate where local adaptation has occurred. Here, we present a dataset of rangewide variation in leaf traits from seven of the most ecologically and economically important tree species in Europe. Sample collection and trait assessment are embedded in the GenTree project (EU-Horizon 2020), which aims at characterizing the genetic and phenotypic variability of forest tree species to optimize the management and sustainable use of forest genetic resources. Our dataset captures substantial intra- and interspecific leaf phenotypic variability, and provides valuable information for studying the relationship between ecosystem functioning and trait variability of individuals, and the response and resilience of species to environmental changes. Main types of variable contained We chose morphological and chemical characters linked to trade-offs between acquisition and conservation of resources and water use, namely specific leaf area, leaf size, carbon and nitrogen content and their ratio, and the isotopic signature of stable isotope C-13 and N-15 in leaves. Spatial location and grain We surveyed between 18 and 22 populations per species, 141 in total, across Europe. Time period Leaf sampling took place between 2016 and 2017. Major taxa and level of measurement We sampled at least 25 individuals in each population, 3,569 trees in total, and measured traits in 35,755 leaves from seven European tree species, i.e. the conifers Picea abies, Pinus pinaster and Pinus sylvestris, and the broadleaves Betula pendula, Fagus sylvatica, Populus nigra and Quercus petraea. Software format The data files are in ASCII text, tab delimited, not compressed.

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

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

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  • 6.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ravikanth, Gudasalamani
    Ashoka Trust Res Ecol & Environm, Bangalore 560064, Karnataka, India.;Univ Agr Sci, Sch Ecol & Conservat, Bangalore 560065, Karnataka, India..
    Ismail, Sascha A.
    Swiss Fed Inst Technol, Dept Environm Syst Sci, Ecosyst Management, Univ Str 16, CH-8092 Zurich, Switzerland..
    Patel, Mohana Kumara
    Univ Agr Sci, Sch Ecol & Conservat, Bangalore 560065, Karnataka, India..
    Spanu, Ilaria
    CNR, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Vasudeva, Ramesh
    Univ Agr Sci, Dept Forest Biol, Coll Forestry, Sirsi 581401, Karnataka, India..
    Shaanker, Ramanan Uma
    Ashoka Trust Res Ecol & Environm, Bangalore 560064, Karnataka, India.;Univ Agr Sci, Sch Ecol & Conservat, Bangalore 560065, Karnataka, India.;Univ Agr Sci, Dept Crop Physiol, Bangalore 560065, Karnataka, India..
    Vendramin, Giovanni Giuseppe
    CNR, Inst Biosci & Bioresources, Via Madonna del Piano 10, I-50019 Florence, Italy..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Tsukuba, Sugadaira Montane Res Ctr, 1278-294 Sugadairakogen, Ueda, Nagano 3862204, Japan..
    Fine- and local- scale genetic structure of Dysoxylum malabaricum, a late-successional canopy tree species in disturbed forest patches in the Western Ghats, India2017In: Conservation Genetics, ISSN 1566-0621, E-ISSN 1572-9737, Vol. 18, no 1, p. 1-15Article in journal (Refereed)
    Abstract [en]

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

  • 7.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Yang, J-C
    Taiwan Forestry Research Institute.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Origin and demographic history of the endemic Taiwan spruce (Picea morrisonicola)2013In: Ecology and Evolution, E-ISSN 2045-7758, Vol. 3, no 10, p. 3320-3333Article in journal (Refereed)
    Abstract [en]

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

  • 8.
    Bodare, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ravikanth, G
    Ashoka Trust for Research in Ecology and the Environment.
    Uma Shaanker, R
    Ashoka Trust for Research in Ecology and the Environment.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genetic structure and demographic history of the endangered tree species, Dysoxylum  malabaricum (Meliaceae) in Western Ghats, India: Implications for conservation in a  biodiversity hotspot2013In: Ecology and Evolution, E-ISSN 2045-7758, Vol. 3, no 10, p. 3233-3248Article in journal (Other academic)
    Abstract [en]

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

  • 9.
    Brousseau, Louise
    et al.
    INRA, Domaine St Paul, URFM Ecol Forets Mediterraneennes UR629, Site Agroparc CS,Site Agroparc CS 40509, F-84914 Avignon 9, France.;Natl Res Council IBBR CNR, Div Florence, Inst Biosci & BioResources, Via Madonna Piano 10, I-50019 Sesto Fiorentino, FI, France..
    Postolache, Dragos
    Natl Res Council IBBR CNR, Div Florence, Inst Biosci & BioResources, Via Madonna Piano 10, I-50019 Sesto Fiorentino, FI, France.;Scuola Super Sant Anna, Piazza Martiri Liberta 33, I-56127 Pisa, Italy.;Natl Inst Forest Res & Dev INCDS, Res Stn Simeria, Str Biscaria 1, Simeria 335900, Romania..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Drouzas, Andreas D.
    Aristotle Univ Thessaloniki, Sch Biol, GR-54124 Thessaloniki, Greece..
    Källman, Thomas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Leonarduzzi, Cristina
    Natl Res Council IBBR CNR, Div Florence, Inst Biosci & BioResources, Via Madonna Piano 10, I-50019 Sesto Fiorentino, FI, France.;Natl 3 Res Council Corso Calatafimi, Div Palermo, Inst Biosci & BioResources, Natl Res Council IBBR CNR, I-90129 Palermo, PA, Italy..
    Liepelt, Sascha
    Univ Marburg, Fac Biol, Conservat Biol, Karl von Frisch Str, D-35032 Marburg, Germany..
    Piotti, Andrea
    Natl Res Council IBBR CNR, Div Florence, Inst Biosci & BioResources, Via Madonna Piano 10, I-50019 Sesto Fiorentino, FI, France..
    Popescu, Flaviu
    Natl Inst Forest Res & Dev INCDS, Res Stn Simeria, Str Biscaria 1, Simeria 335900, Romania..
    Roschanski, Anna M.
    Univ Marburg, Fac Biol, Conservat Biol, Karl von Frisch Str, D-35032 Marburg, Germany.;Leibniz Inst Plant Genet & Crop Plant Res IPK, Genebank Collect North, Inselstr 9, D-23999 Malchow Poel, Germany..
    Zhelev, Peter
    Univ Forestry, 10 Kl Ohridsky Blvd, Sofia 1797, Bulgaria..
    Fady, Bruno
    INRA, Domaine St Paul, URFM Ecol Forets Mediterraneennes UR629, Site Agroparc CS,Site Agroparc CS 40509, F-84914 Avignon 9, France..
    Vendramin, Giovanni Giuseppe
    Natl Res Council IBBR CNR, Div Florence, Inst Biosci & BioResources, Via Madonna Piano 10, I-50019 Sesto Fiorentino, FI, France..
    Local Adaptation in European Firs Assessed through Extensive Sampling across Altitudinal Gradients in Southern Europe2016In: PLOS ONE, E-ISSN 1932-6203, Vol. 11, no 7, article id e0158216Article in journal (Refereed)
    Abstract [en]

    Background Local adaptation is a key driver of phenotypic and genetic divergence at loci responsible for adaptive traits variations in forest tree populations. Its experimental assessment requires rigorous sampling strategies such as those involving population pairs replicated across broad spatial scales. Methods A hierarchical Bayesian model of selection (HBM) that explicitly considers both the replication of the environmental contrast and the hierarchical genetic structure among replicated study sites is introduced. Its power was assessed through simulations and compared to classical 'within-site' approaches (FDIST, BAYESCAN) and a simplified, within-site, version of the model introduced here (SBM). Results HBM demonstrates that hierarchical approaches are very powerful to detect replicated patterns of adaptive divergence with low false-discovery (FDR) and false-non-discovery (FNR) rates compared to the analysis of different sites separately through within-site approaches. The hypothesis of local adaptation to altitude was further addressed by analyzing replicated Abies alba population pairs (low and high elevations) across the species' southern distribution range, where the effects of climatic selection are expected to be the strongest. For comparison, a single population pair from the closely related species A. cephalonica was also analyzed. The hierarchical model did not detect any pattern of adaptive divergence to altitude replicated in the different study sites. Instead, idiosyncratic patterns of local adaptation among sites were detected by within-site approaches. Conclusion Hierarchical approaches may miss idiosyncratic patterns of adaptation among sites, and we strongly recommend the use of both hierarchical (multi-site) and classical (within-site) approaches when addressing the question of adaptation across broad spatial scales.

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  • 10.
    Chen, Jun
    et al.
    Zhejiang Univ, Coll Life Sci, Hangzhou, Zhejiang, Peoples R China..
    Bataillon, Thomas
    Aarhus Univ, Bioinformat Res Ctr, Aarhus, Denmark..
    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, Unite Mixte Rech UMR 6553, Rennes, France.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Hunting for Beneficial Mutations: Conditioning on SIFT Scores When Estimating the Distribution of Fitness Effect of New Mutations2022In: Genome Biology and Evolution, ISSN 1759-6653, E-ISSN 1759-6653, Vol. 14, no 1Article in journal (Refereed)
    Abstract [en]

    The distribution of fitness effects (DFE) of new mutations is a key parameter of molecular evolution. The DFE can in principle be estimated by comparing the site frequency spectra (SFS) of putatively neutral and functional polymorphisms. Unfortunately, the DFE is intrinsically hard to estimate, especially for beneficial mutations because these tend to be exceedingly rare. There is therefore a strong incentive to find out whether conditioning on properties of mutations that are independent of the SFS could provide additional information. In the present study, we developed a new measure based on SIFT scores. SIFT scores are assigned to nucleotide sites based on their level of conservation across a multispecies alignment: the more conserved a site, the more likely mutations occurring at this site are deleterious, and the lower the SIFT score. If one knows the ancestral state at a given site, one can assign a value to new mutations occurring at the site based on the change of SIFT score associated with the mutation. We called this new measure delta. We show that properties of the DFE as well as the flux of beneficial mutations across classes covary with delta and, hence, that SIFT scores are informative when estimating the fitness effect of new mutations. In particular, conditioning on SIFT scores can help to characterize beneficial mutations.

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  • 11.
    Chen, Jun
    et al.
    Zhejiang Univ, Coll Life Sci, Hangzhou 310058, Zhejiang, Peoples R China..
    Bataillon, Thomas
    Aarhus Univ, Bioinformat Res Ctr, CF Mollers Alle 8, DK-8000 Aarhus C, Denmark..
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Rennes, Ctr Natl Rech Sci CNRS, ECOBIO Ecosyst Biodiversite Evolut, Unite Mixte Rech UMR 6553, F-35000 Rennes, France..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    What does the distribution of fitness effects of new mutations reflect?: Insights from plants2022In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 233, no 4, p. 1613-1619Article, review/survey (Refereed)
    Abstract [en]

    The distribution of fitness effects (DFE) of new mutations plays a central role in molecular evolution. It is therefore crucial to be able to estimate it accurately from genomic data and to understand the factors that shape it. After a rapid overview of available methods to characterize the fitness effects of mutations, we review what is known on the factors affecting them in plants. Available data indicate that life history traits (e.g. mating system and longevity) have a major effect on the DFE. By contrast, the impact of demography within species appears to be more limited. These results remain to be confirmed, and methods to estimate the joint evolution of demography, life history traits, and the DFE need to be developed.

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  • 12.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Zhejiang Univ, Coll Life Sci, Hangzhou 310058, Zhejiang, Peoples R China.
    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 Biodivers Evolut, Unite Mixte Rech UMR 6553, F-35000 Rennes, France..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    From Drift to Draft: How Much Do Beneficial Mutations Actually Contribute to Predictions of Ohta's Slightly Deleterious Model of Molecular Evolution?2020In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 214, no 4, p. 1005-1018Article in journal (Refereed)
    Abstract [en]

    Since its inception in 1973, the slightly deleterious model of molecular evolution, also known as the nearly neutral theory of molecular evolution, remains a central model to explain the main patterns of DNA polymorphism in natural populations. This is not to say that the quantitative fit to data are perfect. A recent study used polymorphism data from Drosophila melanogaster to test whether, as predicted by the nearly neutral theory, the proportion of effectively neutral mutations depends on the effective population size (N-e). It showed that a nearly neutral model simply scaling with N-e variation across the genome could not alone explain the data, but that consideration of linked positive selection improves the fit between observations and predictions. In the present article, we extended the work in two main directions. First, we confirmed the observed pattern on a set of 59 species, including high-quality genomic data from 11 animal and plant species with different mating systems and effective population sizes, hence a priori different levels of linked selection. Second, for the 11 species with high-quality genomic data we also estimated the full distribution of fitness effects (DFE) of mutations, and not solely the DFE of deleterious mutations. Both N-e and beneficial mutations contributed to the relationship between the proportion of effectively neutral mutations and local N-e across the genome. In conclusion, the predictions of the slightly deleterious model of molecular evolution hold well for species with small N-e, but for species with large N-e, the fit is improved by incorporating linked positive selection to the model.

  • 13.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Montpellier, CNRS, IRD, Inst Sci Evolut,EPHE,UMR 5554, Montpellier, France..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Genetic Diversity and the Efficacy of Purifying Selection across Plant and Animal Species2017In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 34, no 6, p. 1417-1428Article in journal (Refereed)
    Abstract [en]

    A central question in evolutionary biology is why some species have more genetic diversity than others and a no less important question is why selection efficacy varies among species. Although these questions have started to be tackled in animals, they have not been addressed to the same extent in plants. Here, we estimated nucleotide diversity at synonymous, pi(S), and nonsynonymous sites, pi(N), and a measure of the efficacy of selection, the ratio pi(N)/pi(S), in 34 animal and 28 plant species using full genome data. We then evaluated the relationship of nucleotide diversity and selection efficacy with effective population size, the distribution of fitness effect and life history traits. In animals, our data confirm that longevity and propagule size are the variables that best explain the variation in pi(S) among species. In plants longevity also plays a major role as well as mating system. As predicted by the nearly neutral theory of molecular evolution, the log of pi(N)/pi(S) decreased linearly with the log of pi(S) but the slope was weaker in plants than in animals. This appears to be due to a higher mutation rate in long lived plants, and the difference disappears when pi(S) is rescaled by the mutation rate. Differences in the distribution of fitness effect of new mutations also contributed to variation in pi(N)/pi(S) among species.

  • 14.
    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.

  • 15.
    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 Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ma, Xiao-Fei
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Chinese Acad Sci, Key Lab Stress Physiol & Ecol Cold & Arid Reg, Lanzhou, Peoples R China..
    Zaina, Giusi
    Univ Udine, Dept Agr Food Environm & Anim Sci, I-33100 Udine, Italy..
    Morgante, Michele
    Univ Udine, Dept Agr Food Environm & Anim Sci, I-33100 Udine, Italy..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Identifying Genetic Signatures of Natural Selection Using Pooled Population Sequencing in Picea abies2016In: G3: Genes, Genomes, Genetics, E-ISSN 2160-1836, Vol. 6, no 7, p. 1979-1989Article in journal (Refereed)
    Abstract [en]

    The joint inference of selection and past demography remain a costly and demanding task. We used next generation sequencing of two pools of 48 Norway spruce mother trees, one corresponding to the Fennoscandian domain, and the other to the Alpine domain, to assess nucleotide polymorphism at 88 nuclear genes. These genes are candidate genes for phenological traits, and most belong to the photoperiod pathway. Estimates of population genetic summary statistics from the pooled data are similar to previous estimates, suggesting that pooled sequencing is reliable. The nonsynonymous SNPs tended to have both lower frequency differences and lower F-ST values between the two domains than silent ones. These results suggest the presence of purifying selection. The divergence between the two domains based on synonymous changes was around 5 million yr, a time similar to a recent phylogenetic estimate of 6 million yr, but much larger than earlier estimates based on isozymes. Two approaches, one of them novel and that considers both F-ST and difference in allele frequencies between the two domains, were used to identify SNPs potentially under diversifying selection. SNPs from around 20 genes were detected, including genes previously identified as main target for selection, such as PaPRR3 and PaGI.

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  • 16.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Li, Lili
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Jansson, Gunnar
    Forestry Res Inst Sweden Skogforsk, Uppsala, Sweden.
    Berlin, Mats
    Forestry Res Inst Sweden Skogforsk, Uppsala, Sweden.
    Karlsson, Bo
    Forestry Res Inst Sweden Skogforsk, Ekebo, Sweden.
    Aleksic, Jelena
    Univ Belgrade, Inst Mol Genet & Genet Engn, Belgrade, Serbia.
    Vendramin, Giovanni G.
    CNR, Natl Res Council IBBR, Div Florence, Inst Biosci & BioResources, Sesto Fiorentino, Italy.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genomic data provide new insights on the demographic history and the extent of recent material transfers in Norway spruce2019In: Evolutionary Applications, E-ISSN 1752-4571, Vol. 12, no 8, p. 1539-1551Article in journal (Refereed)
    Abstract [en]

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

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  • 17.
    Chen, Jun
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tsuda, Yoshiaki
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stocks, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kallman, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Xu, Nannan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Karkkainen, Katri
    Huotari, Tea
    Semerikov, Vladimir L.
    Vendramin, Giovanni G.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Clinal Variation at Phenology-Related Genes in Spruce: Parallel Evolution in FTL2 and Gigantea?2014In: Genetics, ISSN 0016-6731, E-ISSN 1943-2631, Vol. 197, no 3, p. 1025-1038Article in journal (Refereed)
    Abstract [en]

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

  • 18.
    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, 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.

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  • 19.
    Chen, Zeyuan
    et al.
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China.
    Ai, Fandi
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China.
    Zhang, Junlin
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China.
    Ma, Xinzhi
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China.
    Yang, Wenlu
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China.
    Wang, Weiwei
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China.
    Su, Yutao
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China.
    Wang, Mingcheng
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China.
    Yang, Yongzhi
    Lanzhou Univ, State Key Lab Grassland Agroecosyst, Inst Innovat Ecol, Lanzhou 730000, Peoples R China; Lanzhou Univ, Coll Life Sci, Lanzhou 730000, Peoples R China.
    Mao, Kangshan
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China.
    Wang, Qingfeng
    Chinese Acad Sci, Key Lab Aquat Bot & Watershed Ecol, Wuhan 430074, Hubei, Peoples R China.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Liu, Jianquan
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China; Lanzhou Univ, State Key Lab Grassland Agroecosyst, Inst Innovat Ecol, Lanzhou 730000, Peoples R China; Lanzhou Univ, Coll Life Sci, Lanzhou 730000, Peoples R China.
    Ma, Tao
    Sichuan Univ, State Key Lab Hydraul & Mt River Engn, Coll Life Sci, Minist Educ, Key Lab Bioresource & Ecoenvironm, Chengdu 610065, Peoples R China.
    Survival in the Tropics despite isolation, inbreeding and asexual reproduction: insights from the genome of the world's southernmost poplar (Populus ilicifolia)2020In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 103, no 1, p. 430-442Article in journal (Refereed)
    Abstract [en]

    Species are becoming extinct at unprecedented rates as a consequence of human activity. Hence it is important to understand the evolutionary dynamics of species with already small population sizes. Populus ilicifolia is a vulnerable poplar species that is isolated from other poplar species and is uniquely adapted to the Tropics. It has a very limited size, reproduces partly clonally and is therefore an excellent case study for conservation genomics. We present here the first annotated draft genome of P. ilicifolia, characterize genome-wide patterns of polymorphisms and compare those to other poplar species with larger natural ranges. P. ilicifolia experienced a more prolonged and severe decline of effective population size (Ne) and signs of genetic erosion than any other poplar species with which it was compared. At present, the species has the lowest genome-wide genetic diversity, the highest abundance of long runs of homozygosity, high inbreeding levels as well as a high overall accumulation of deleterious variants. However, more effective purging of severely deleterious variants and adaptation to the Tropics may have contributed to its survival. Hence, in spite of its limited genetic variation, it is certainly worth pursuing the conservation efforts of this unique species.

  • 20.
    Chen, Zhi-Qiang
    et al.
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90183 Umeå, Sweden..
    Zan, Yanjun
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90183 Umeå, Sweden..
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Zhou, Linghua
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90183 Umeå, Sweden..
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Zhejiang Univ, Coll Life Sci, Hangzhou 310058, Zhejiang, Peoples R China..
    Li, Lili
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Cui, BinBin
    Baoding Univ, Coll Biochem & Environm Engn, Baoding 071000, Hebei, Peoples R China..
    Niu, Shihui
    Beijing Forestry Univ, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Beijing, Peoples R China..
    Westin, Johan
    Skogforsk, Box 3, SE-91821 Savar, Sweden.;Swedish Univ Agr Sci, Unit Field Based Forest Res, SE-90183 Umeå, Sweden..
    Karlsson, Bo
    Skogforsk, Ekebo 2250, SE-26890 Svalov, Sweden..
    Garcia-Gil, Maria Rosario
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90183 Umeå, Sweden..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wu, Harry X.
    Swedish Univ Agr Sci, Umeå Plant Sci Ctr, Dept Forest Genet & Plant Physiol, SE-90183 Umeå, Sweden.;Beijing Forestry Univ, Beijing Adv Innovat Ctr Tree Breeding Mol Design, Beijing, Peoples R China.;CSIRO Natl Collect Res Australia, Black Mt Lab, Canberra, ACT 2601, Australia..
    Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis2021In: Genome Biology, ISSN 1465-6906, E-ISSN 1474-760X, Vol. 22, no 1, article id 179Article in journal (Refereed)
    Abstract [en]

    Background: Genome-wide association studies (GWAS) identify loci underlying the variation of complex traits. One of the main limitations of GWAS is the availability of reliable phenotypic data, particularly for long-lived tree species. Although an extensive amount of phenotypic data already exists in breeding programs, accounting for its high heterogeneity is a great challenge. We combine spatial and factor-analytics analyses to standardize the heterogeneous data from 120 field experiments of 483,424 progenies of Norway spruce to implement the largest reported GWAS for trees using 134 605 SNPs from exome sequencing of 5056 parental trees.

    Results: We identify 55 novel quantitative trait loci (QTLs) that are associated with phenotypic variation. The largest number of QTLs is associated with the budburst stage, followed by diameter at breast height, wood quality, and frost damage. Two QTLs with the largest effect have a pleiotropic effect for budburst stage, frost damage, and diameter and are associated with MAP3K genes. Genotype data called from exome capture, recently developed SNP array and gene expression data indirectly support this discovery.

    Conclusion: Several important QTLs associated with growth and frost damage have been verified in several southern and northern progeny plantations, indicating that these loci can be used in QTL-assisted genomic selection. Our study also demonstrates that existing heterogeneous phenotypic data from breeding programs, collected over several decades, is an important source for GWAS and that such integration into GWAS should be a major area of inquiry in the future.

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  • 21.
    Corcoran, Padraic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England.
    Anderson, Jennifer L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Jacobson, David J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Sun, Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ni, Peixiang
    BGI HongKong, Hong Kong, Hong Kong, Peoples R China.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma.2016In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 26, no 4, p. 486-498Article in journal (Refereed)
    Abstract [en]

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

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  • 22.
    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.

  • 23.
    Cornille, Amandine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Salcedo, A.
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M6R 1M3, Canada..
    Kryvokhyzha, Dmytro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wright, S. I.
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M6R 1M3, Canada..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa-pastoris)2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 2, p. 616-629Article in journal (Refereed)
    Abstract [en]

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

  • 24.
    Cornille, Amandine
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Paris Saclay, INRAE, AgroParisTech, GQE Le Moulon,CNRS, F-91190 Gif Sur Yvette, France..
    Tiret, Mathieu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Salcedo, Adriana
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada..
    Huang, Huirun R.
    Chinese Acad Sci, Key Lab Plant Resources Conservat & Sustainable U, South China Bot Garden, Guangzhou 510650, Peoples R China.;Chinese Acad Sci, Ctr Conservat Biol, Core Bot Gardens, Guangzhou 510650, Peoples R China..
    Orsucci, Marion
    Swedish Univ Agr Sci, Dept Plant Biol, S-75007 Uppsala, Sweden..
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kryvokhyzha, Dmytro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Ge, Xue-Jun
    Chinese Acad Sci, Key Lab Plant Resources Conservat & Sustainable U, South China Bot Garden, Guangzhou 510650, Peoples R China.;Chinese Acad Sci, Ctr Conservat Biol, Core Bot Gardens, Guangzhou 510650, Peoples R China..
    Stinchcombe, John R.
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada..
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Rennes 1, UMR CNRS ECOBIO 6553, F-35042 Rennes, France..
    Wright, Stephen, I
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The relative role of plasticity and demographic history in Capsella bursa-pastoris: a common garden experiment in Asia and Europe2022In: AoB Plants, E-ISSN 2041-2851, Vol. 14, no 3, article id plac011Article in journal (Refereed)
    Abstract [en]

    The respective role of demography, plasticity and adaptation in the colonization success of plant species remains an intense topic of investigation in evolutionary ecology and genomics. A screening of phenotypic traits of hundreds of genotypes in large-scale common garden experiments in Eastern Asia and Europe shows that both demography and a high phenotypic plasticity underlie the success of the tetraploid and self-fertilizing species, Capsella bursa-pastoris, the shepherd's purse, at different stages of expansion. This study provides insight into the causes of the ecological success of a plant species during range expansion. The colonization success of a species depends on the interplay between its phenotypic plasticity, adaptive potential and demographic history. Assessing their relative contributions during the different phases of a species range expansion is challenging, and requires large-scale experiments. Here, we investigated the relative contributions of plasticity, performance and demographic history to the worldwide expansion of the shepherd's purse, Capsella bursa-pastoris. We installed two large common gardens of the shepherd's purse, a young, self-fertilizing, allopolyploid weed with a worldwide distribution. One common garden was located in Europe, the other in Asia. We used accessions from three distinct genetic clusters (Middle East, Europe and Asia) that reflect the demographic history of the species. Several life-history traits were measured. To explain the phenotypic variation between and within genetic clusters, we analysed the effects of (i) the genetic clusters, (ii) the phenotypic plasticity and its association to fitness and (iii) the distance in terms of bioclimatic variables between the sampling site of an accession and the common garden, i.e. the environmental distance. Our experiment showed that (i) the performance of C. bursa-pastoris is closely related to its high phenotypic plasticity; (ii) within a common garden, genetic cluster was a main determinant of phenotypic differences; and (iii) at the scale of the experiment, the effect of environmental distance to the common garden could not be distinguished from that of genetic clusters. Phenotypic plasticity and demographic history both play important role at different stages of range expansion. The success of the worldwide expansion of C. bursa-pastoris was undoubtedly influenced by its strong phenotypic plasticity.

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  • 25. Das, S
    et al.
    Lagercrantz, Ulf
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär Funktionsgenomik.
    Lascoux, Martin
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär Funktionsgenomik.
    Black mustard2006In: Genome mapping and molecular breeding in plants: Oilseeds, Springer, , 2006Chapter in book (Refereed)
  • 26. Douglas, Gavin M.
    et al.
    Gos, Gesseca
    Steige, Kim A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Salcedo, Adriana
    Holm, Karl
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Josephs, Emily B.
    Arunkumar, Ramesh
    Agren, J. Arvid
    Hazzouri, Khaled M.
    Wang, Wei
    Platts, Adrian E.
    Williamson, Robert J.
    Neuffer, Barbara
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Slotte, Tanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wright, Stephen I.
    Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris2015In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 112, no 9, p. 2806-2811Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 28.
    Duan, Tianlin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sicard, Adrien
    Glémin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. UMR CNRS 6553 ECOBIO, Campus Beaulieu, bât 14a, p.118, CS 74205, 35042 Rennes, France.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Expression pattern of resynthesized allotetraploid Capsella is determined by hybridization, not whole genome duplication2023In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 237, no 1, p. 339-353Article in journal (Refereed)
    Abstract [en]
    • Polyploidization, the process leading to the increase in chromosome sets, is a major evolutionary transition in plants. Whole-genome duplication (WGD) within the same species gives rise to autopolyploids, whereas allopolyploids result from a compound process with two distinct components: WGD and interspecific hybridization.
    • To dissect the instant effects of WGD and hybridization on gene expression and phenotype, we created a series of synthetic hybrid and polyploid Capsella plants, including diploid hybrids, autotetraploids of both parental species, and two kinds of resynthesized allotetraploids with different orders of WGD and hybridization.
    • Hybridization played a major role in shaping the relative expression pattern of the neo-allopolyploids, whereas WGD had almost no immediate effect on relative gene expression pattern but, nonetheless, still affected phenotypes. No transposable element-mediated genomic shock scenario was observed in either neo-hybrids or neo-polyploids. Finally, WGD and hybridization interacted and the distorting effects of WGD were less strong in hybrids. Whole-genome duplication may even improve hybrid fertility.
    • In summary, while the initial relative gene expression pattern in neo-allotetraploids was almost entirely determined by hybridization, WGD only had trivial effects on relative expression patterns, both processes interacted and had a strong impact on physical attributes and meiotic behaviors.
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  • 29. Dymshakova, O. S.
    et al.
    Semerikov, V. L.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    AFLP analysis to estimate the genetic contribution of parents to progeny from hybridization between Saxifraga sibirica L. and S. cernua L.2012In: Russian journal of ecology, ISSN 1067-4136, E-ISSN 1608-3334, Vol. 43, no 5, p. 347-351Article in journal (Refereed)
    Abstract [en]

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

  • 30.
    Fady, Bruno
    et al.
    URFM, INRAE, Ecol Mediterranean Forests, Avignon, France..
    Aravanopoulos, Filippos
    Aristotle Univ Thessaloniki, Thessaloniki, Greece..
    Benavides, Raquel
    CSIC, Madrid, Spain..
    Gonzalez-Martinez, Santiago
    INRAE, BIOGECO, Bordeaux, France..
    Grivet, Delphine
    INIA Madrid, Madrid, Spain..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lindner, Marcus
    EFI, Bonn, Germany..
    Rellstab, Christian
    Swiss Fed Res Inst WSL, Birmensdorf, Switzerland..
    Valladares, Fernando
    CSIC, Madrid, Spain..
    Vinceti, Barbara
    Biovers Int, Rome, Italy..
    Genetics to the rescue: managing forests sustainably in a changing world2020In: Tree Genetics & Genomes, ISSN 1614-2942, E-ISSN 1614-2950, Vol. 16, no 6, article id 80Article in journal (Refereed)
    Abstract [en]

    There is growing concern that the implementation of political agreements on climate change and biodiversity will not be enough to protect forests in the short run and up to the end of the 21st century. As mitigation efforts are lagging behind self-imposed, reasonable targets, genetic diversity will have a large and significant part to play in the process of adapting forests to climate change. Genetic diversity, the raw material of evolution, can be used for adaptation by natural selection and artificial breeding, in naturally regenerated and plantation forests alike. The 2-day scientific conference: "#rescueforests: Genetics to the rescue - Managing forests sustainably in a changing world," addressed the genetic diversity of forests. More specifically, the conference was about natural as well as assisted adaptive processes, their spatial scale, from fine grain to landscape and ecoregions, and how much of the genome it involves. It also dealt with phenotypes and how much of their variation is determined by underlying genetic diversity. And finally, and perhaps most importantly, the conference emphasized the importance of conservation and sustainable use of this genetic diversity as a nature-based solution to adapt under the fast pace of climate change. The conference demonstrated how improved knowledge on genomic diversity and evolutionary mechanisms can help to rescue forests, either naturally or by means of management.

  • 31.
    Fogelqvist, Johan
    et al.
    Swedish Univ Agr Sci, Uppsala BioCtr, Linnean Ctr Plant Biol, Dept Plant Biol, SE-75007 Uppsala, Sweden..
    Verkhozina, Alla V.
    Siberian Inst Plant Physiol & Biochem, Irkutsk 664033, Russia..
    Katyshev, Alexander I.
    Siberian Inst Plant Physiol & Biochem, Irkutsk 664033, Russia..
    Pucholt, Pascal
    Swedish Univ Agr Sci, Uppsala BioCtr, Linnean Ctr Plant Biol, Dept Plant Biol, SE-75007 Uppsala, Sweden..
    Dixelius, Christina
    Swedish Univ Agr Sci, Uppsala BioCtr, Linnean Ctr Plant Biol, Dept Plant Biol, SE-75007 Uppsala, Sweden..
    Ronnberg-Wastljung, Ann Christin
    Swedish Univ Agr Sci, Uppsala BioCtr, Linnean Ctr Plant Biol, Dept Plant Biol, SE-75007 Uppsala, Sweden..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Berlin, Sofia
    Swedish Univ Agr Sci, Uppsala BioCtr, Linnean Ctr Plant Biol, Dept Plant Biol, SE-75007 Uppsala, Sweden..
    Genetic and morphological evidence for introgression between three species of willows2015In: BMC Evolutionary Biology, E-ISSN 1471-2148, Vol. 15, article id 193Article in journal (Refereed)
    Abstract [en]

    Background: Hybridization and introgression are said to occur relatively frequently in plants, and in particular among different species of willows. However, data on the actual frequency of natural hybridization and introgression is rare. Here, we report the first fine-scale genetic analysis of a contact zone shared between the three basket willow species, Salix dasyclados, S. schwerinii and S. viminalis in the vicinity of the Lake Baikal in Southern Siberia. Individuals were sampled in fourteen populations and classified as pure species or hybrids based on a set of morphological characters. They were then genotyped at 384 nuclear SNP and four chloroplast SSR loci. The STRUCTURE and NewHybrids softwares were used to estimate the frequency and direction of hybridization using genotypic data at the nuclear SNP loci. Results: As many as 19 % of the genotyped individuals were classified as introgressed individuals and these were mainly encountered in the centre of the contact zone. All introgressed individuals were backcrosses to S. viminalis or S. schwerinii and no F1 or F2 hybrids were found. The rest of the genotyped individuals were classified as pure species and formed two clusters, one with S. schwerinii individuals and the other with S. viminalis and S. dasyclados individuals. The two clusters were significantly genetically differentiated, with F-ST = 0.333 (0.282-0.382, p < 0.001). In contrast, for the chloroplast haplotypes, no genetic differentiation was observed as they were completely shared between the species. Based on morphological classification only 5 % of the individuals were classified as introgressed individuals, which was much less than what was detected using genotypic data. Conclusions: We have discovered a new willow hybrid zone with relatively high frequency of introgressed individuals. The low frequency of F1 hybrids indicates that ongoing hybridization is limited, which could be because of the presence of reproductive barriers or simply because the conditions are not favorable for hybridization. We further conclude that in order to get a complete picture of the species composition of a hybrid zone it is necessary to use a combination of morphological characters and genetic data from both nuclear and chloroplast markers.

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  • 32.
    Fu, Ruirui
    et al.
    Zhejiang Univ, Coll Life Sci, Hangzhou, Peoples R China.
    Zhu, Yuxiang
    Zhejiang Univ, Coll Life Sci, Hangzhou, Peoples R China.
    Liu, Ying
    Zhejiang Univ, Coll Life Sci, Hangzhou, Peoples R China.
    Feng, Yu
    Zhejiang Univ, Coll Life Sci, Hangzhou, Peoples R China.;Chinese Acad Sci, Chengdu Inst Biol, CAS Key Lab Mt Ecol Restorat & Bioresource Utiliz, Chengdu, Peoples R China.;Chinese Acad Sci, Chengdu Inst Biol, Ecol Restorat & Biodivers Conservat Key Lab Sichu, Chengdu, Peoples R China.
    Lu, Rui-Sen
    Zhejiang Univ, Coll Life Sci, Hangzhou, Peoples R China.;Jiangsu Prov & Chinese Acad Sci, Inst Bot, Nanjing, Peoples R China.
    Li, Yao
    Nanjing Forestry Univ, Coll Biol & Environm, Key Lab, State Forestry & Grassland Adm Subtrop Forest Bio, Nanjing, Peoples R China.
    Li, Pan
    Zhejiang Univ, Coll Life Sci, Hangzhou, Peoples R China.
    Kremer, Antoine
    Univ Bordeaux, UMR BIOGECO, INRAE, Cestas, France.
    Lascoux, Martin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics.
    Chen, Jun
    Zhejiang Univ, Coll Life Sci, Hangzhou, Peoples R China.
    Genome-wide analyses of introgression between two sympatric Asian oak species2022In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 6, no 7, p. 924-+Article in journal (Refereed)
    Abstract [en]

    Introgression can be an important source of new alleles for adaption under rapidly changing environments, perhaps even more important than standing variation. Though introgression has been extensively studied in many plants and animals, key questions on the underlying mechanisms of introgression still remain unanswered. In particular, we are yet to determine the genomic distribution of introgressed regions along the genome; whether the extent and patterns of introgression are influenced by ecological factors; and when and how introgression contributes to adaptation. Here, we generated high-quality genomic resources for two sympatric widespread Asian oak species, Quercus acutissima and Q. variabilis, sampled in multiple forests to study introgression between them. We show that introgressed regions are broadly distributed across the genome. Introgression was affected by genetic divergence between pairs of populations and by the similarity of the environments in which they live-populations occupying similar ecological sites tended to share the same introgressed regions. Introgressed genomic footprints of adaptation were preferentially located in regions with suppressed recombination rate. Introgression probably confers adaptation in these oak populations by introducing allelic variation in cis-regulatory elements, in particular through transposable element insertions, thereby altering the regulation of genes related to stress. Our results provide new avenues of research for uncovering mechanisms of adaptation due to hybridization in sympatric species. Introgression is an important source of genetic variation. Analysing genomes of two sympatric widespread Asian oak species, the authors find introgression across the genome and signatures of adaptive introgression in regions with suppressed recombination rate.

  • 33. Gerber, Sophie
    et al.
    Chadoeuf, Joel
    Gugerli, Felix
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Buiteveld, Joukje
    Cottrell, Joan
    Dounavi, Aikaterini
    Fineschi, Silvia
    Forrest, Laura L.
    Fogelqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Goicoechea, Pablo G.
    Jensen, Jan Svejgaard
    Salvini, Daniela
    Vendramin, Giovanni G.
    Kremer, Antoine
    High Rates of Gene Flow by Pollen and Seed in Oak Populations across Europe2014In: PLOS ONE, E-ISSN 1932-6203, Vol. 9, no 1, p. e85130-Article in journal (Refereed)
    Abstract [en]

    Gene flow is a key factor in the evolution of species, influencing effective population size, hybridisation and local adaptation. We analysed local gene flow in eight stands of white oak (mostly Quercus petraea and Q. robur, but also Q. pubescens and Q. faginea) distributed across Europe. Adult trees within a given area in each stand were exhaustively sampled (range [239, 754], mean 423), mapped, and acorns were collected ([17,147], 51) from several mother trees ([3,47], 23). Seedlings ([65,387], 178) were harvested and geo-referenced in six of the eight stands. Genetic information was obtained from screening distinct molecular markers spread across the genome, genotyping each tree, acorn or seedling. All samples were thus genotyped at 5-8 nuclear microsatellite loci. Fathers/parents were assigned to acorns and seedlings using likelihood methods. Mating success of male and female parents, pollen and seed dispersal curves, and also hybridisation rates were estimated in each stand and compared on a continental scale. On average, the percentage of the wind-borne pollen from outside the stand was 60%, with large variation among stands (21-88%). Mean seed immigration into the stand was 40%, a high value for oaks that are generally considered to have limited seed dispersal. However, this estimate varied greatly among stands (20-66%). Gene flow was mostly intraspecific, with large variation, as some trees and stands showed particularly high rates of hybridisation. Our results show that mating success was unevenly distributed among trees. The high levels of gene flow suggest that geographically remote oak stands are unlikely to be genetically isolated, questioning the static definition of gene reserves and seed stands.

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  • 34. González-Martínez, SC
    et al.
    Dillon, S
    Garnier-Géré, P
    Krutovsky, KV
    Alía, R
    Burgarella, C
    Eckert, A
    García-Gil, MR
    Grivet, D
    Heuetz, M
    Jaramillo-Correa, JP
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Neale, DB
    Savolainen, O
    Tsumura, Y
    Vendramin, GG
    Patterns of Nucleotide Diversity and Association Mapping2011In: Genetics, Genomics and Breeding of Conifers / [ed] Christophe Plomion, Jersey: Science Publishers Inc., 2011, p. 239-275Chapter in book (Refereed)
  • 35.
    Hantemirova, E. V.
    et al.
    Russian Acad Sci, Inst Plant & Anim Ecol, Ural Branch, 8 Marta Str,202, Ekaterinburg 620144, Russia..
    Heinze, B.
    Austrian Fed Res Ctr Forests, Dept Forest Genet, Seckendorff Gudent Weg 8, A-1130 Vienna, Austria..
    Knyazeva, S. G.
    Russian Acad Sci, Forest Inst, Siberian Branch, Krasnojarsk Akademgorodo 660036, Russia..
    Musaev, A. M.
    Russian Acad Sci, Dagestan Sci Ctr, Mt Bot Garden, 45 M Gadgiev St, Makhachkala 367000, Republic Of Dag, Russia..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Semerikov, V. L.
    Russian Acad Sci, Inst Plant & Anim Ecol, Ural Branch, 8 Marta Str,202, Ekaterinburg 620144, Russia..
    A new Eurasian phylogeographical paradigm?: Limited contribution of southern populations to the recolonization of high latitude populations in Juniperus communis L.(Cupressaceae)2017In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 44, no 2, p. 271-282Article in journal (Refereed)
    Abstract [en]

    AimThe aims of this population genetics study of the common juniper across Eurasia were to (1) assess the contribution of southern mountain ranges to the post-glacial recolonization of high latitudes and (2) test whether recent expansion or high gene flow could explain the low genetic differentiation in Northern Eurasia. LocationNorthern Eurasia and mountain regions of Central Europe and Asia. MethodsSix hundred and twenty-two individuals were sampled in 42 populations. Two chloroplast DNA (cpDNA) fragments were investigated (trnT-trnL and 16S-trnA). Analyses of the distribution of haplotypes across the continent included a suite of phylogeographical and phylogenetic tests. Putative geographical distribution in the past was reconstructed using environmental niche modelling. ResultsEighty-four haplotypes clustered into four main clades (GL1-GL4). The largest clade, GL3, corresponds to populations from the Alps, northern Europe, Western Caucasus and Siberia. These populations were moderately differentiated (28%) compared to the total range (76%) and Fu's F-s statistic was negative, indicating a population expansion. Some haplotypes within GL3 form subclades with a restricted geographical distribution, suggesting a local origin of the mutation and limited dispersal. In line with these findings, modelling of ecological niches found no significant reduction in the expected range during the LGM. Remarkably, populations from the eastern part of North Caucasus, the Himalayas, Tien Shan and south Siberia were distinctly different from populations in the rest of the range. Main conclusionsAs in Siberian larch species, the pattern of genetic diversity at cpDNA across the natural range of J. communis suggests that colonization of northern Europe and Siberia started from a limited area and predated the last glaciation. It is likely that juniper survived the subsequent glacial epoch at high latitudes in cryptic refugia serving as secondary centres of recolonization. Southern mountain refugia contribution to the recolonization of high latitudes was, at best, limited.

  • 36.
    Hemmilä, Sofia
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Mohana Kumara, P.
    Ravikanth, G.
    Gustafsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Functional Genomics.
    Sreejayan, N.
    Vasudeva, R.
    Ganeshaiah, K. N.
    Uma Shaanker, R.
    Lascoux, Martin
    Development of polymorphic microsatellite loci in the endangered tree species Dysoxylum malabaricum2010Manuscript (preprint) (Other academic)
    Abstract [en]

    Dysoxylum malabaricum Bedd. (Meliaceae) is an economically important tree species occurring in the Western Ghats, a mega-diversity hotspot in southern India. In this paper, we report the development of fifteen microsatellite markers for D. malabaricum. The microsatellite primers development of fifteen microsatellite markers for D. malabaricum. The microsatellite primers screened had 2-9 alleles per locus and the observed and expected heterozygosity ranged from 0.07 to 1.00 and 0.07 to 0.9 respectively. Seven microsatellites cross amplified in the related species Dysoxylum binectariferum and showed good polymorphism. These are the first microsatellites described for D. malabaricum and they will be used to study population structure and genetic diversity.

  • 37.
    Huang, Hui-Run
    et al.
    Chinese Acad Sci, South China Bot Garden, Key Lab Plant Resources Conservat & Sustainable U, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Guangzhou 510650, Guangdong, Peoples R China.
    Liu, Jia-Jia
    Chinese Acad Sci, South China Bot Garden, Key Lab Plant Resources Conservat & Sustainable U, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Guangzhou 510650, Guangdong, Peoples R China.
    Xu, Yong
    Chinese Acad Sci, South China Bot Garden, Key Lab Plant Resources Conservat & Sustainable U, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Guangzhou 510650, Guangdong, Peoples R China.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ge, Xue-Jun
    Chinese Acad Sci, South China Bot Garden, Key Lab Plant Resources Conservat & Sustainable U, Guangzhou 510650, Guangdong, Peoples R China;Chinese Acad Sci, Guangdong Prov Key Lab Appl Bot, South China Bot Garden, Guangzhou 510650, Guangdong, Peoples R China.
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON M5S 3B2, Canada.
    Homeologue-specific expression divergence in the recently formed tetraploid Capsella bursa-pastoris (Brassicaceae)2018In: New Phytologist, ISSN 0028-646X, E-ISSN 1469-8137, Vol. 220, no 2, p. 624-635Article in journal (Refereed)
    Abstract [en]

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

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

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

  • 39.
    James, Jennifer
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Swedish Collegium for Advanced Study (SCAS).
    Kastally, Chedly
    Univ Helsinki, Dept Forest Sci, Helsinki, Finland.;Univ Helsinki, Viikki Plant Sci Ctr, Helsinki, Finland..
    Budde, Katharina B.
    Georg August Univ Goettingen, Dept Forest Genet & Forest Tree Breeding, Gottingen, Germany.;Univ Goettingen, Ctr Biodivers & Sustainable Land Use CBL, Gottingen, Germany..
    Gonzalez-Martinez, Santiago C.
    Univ Bordeaux, Natl Res Inst Agr Food & Environm INRAE, BIOGECO, Cestas, France..
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Pyhajarvi, Tanja
    Univ Helsinki, Dept Forest Sci, Helsinki, Finland.;Univ Helsinki, Viikki Plant Sci Ctr, Helsinki, Finland..
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Between but Not Within-Species Variation in the Distribution of Fitness Effects2023In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 40, no 11, article id msad228Article in journal (Refereed)
    Abstract [en]

    New mutations provide the raw material for evolution and adaptation. The distribution of fitness effects (DFE) describes the spectrum of effects of new mutations that can occur along a genome, and is, therefore, of vital interest in evolutionary biology. Recent work has uncovered striking similarities in the DFE between closely related species, prompting us to ask whether there is variation in the DFE among populations of the same species, or among species with different degrees of divergence, that is whether there is variation in the DFE at different levels of evolution. Using exome capture data from six tree species sampled across Europe we characterized the DFE for multiple species, and for each species, multiple populations, and investigated the factors potentially influencing the DFE, such as demography, population divergence, and genetic background. We find statistical support for the presence of variation in the DFE at the species level, even among relatively closely related species. However, we find very little difference at the population level, suggesting that differences in the DFE are primarily driven by deep features of species biology, and those evolutionarily recent events, such as demographic changes and local adaptation, have little impact.

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  • 40. Jarvinen, Pia
    et al.
    Palme, Anna
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Morales, Luis Orlando
    Lenanpää, Mika
    Kenainen, Marku
    Sopanen, Tuomas
    Lascoux, Martin
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Phylogenetics relationships of Betula species (Betulaceae) based on nuclear ADH and chloroplast MatK sequences2004In: American Journal of Botany, Vol. 91, p. 1834-1845Article in journal (Refereed)
  • 41.
    Kaj, I
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Mathematics. Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics.
    Krone, SM
    Lascoux, M
    Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Coalescent theory for seed bank models2001In: Journal of Applied Probability, ISSN 0021-9002, Vol. 38, no 2, p. 285-300Article in journal (Refereed)
    Abstract [en]

    We study the genealogical structure of samples from a population for which any given generation is made up of direct descendants from several previous generations. These occur in nature when there are seed banks or egg banks allowing an individual to leav

  • 42.
    Kaj, I
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Mathematics and Computer Science, Department of Mathematics. Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Matematisk statistik.
    Lascoux, M
    Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Probability of identity by descent in metapopulations1999In: Genetics, Vol. 152, no 3, p. 1217-1228Article in journal (Refereed)
    Abstract [en]

    Equilibrium probabilities of identity by descent (IBD), for pairs of genes within individuals, for genes between individuals within subpopulations, and for genes between subpopulations are calculated in metapopulation models with fixed or varying colony sizes. A continuous-time analog to the Moran model was used in either case. For fixed-colony size both propagule and migrant pool models were considered. The varying population size model is based on a birth-death-immigration (BDI) process, to which migration between colonies is added. Wright's F statistics are calculated and compared to previous results. Adding between-island migration to the BDI model can have an important effect on the equilibrium probabilities of IBD and on Wright's index.

  • 43.
    Kaj, Ingemar
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Analysis and Probability Theory.
    Glémin, Sylvain
    CNRS, Université Rennes 1, ECOBIO (écosystèmes, biodiversité, évolution) – UMR 6553, Avenue du général Leclerc, 35042, Rennes, France.
    Tahir, Daniah
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Analysis of diversity-dependent species evolution using concepts in population genetics2021In: Journal of Mathematical Biology, ISSN 0303-6812, E-ISSN 1432-1416, Vol. 82, no 4, article id 22Article in journal (Refereed)
    Abstract [en]

    In this work, we consider a two-type species model with trait-dependent speciation, extinction and transition rates under an evolutionary time scale. The scaling approach and the diffusion approximation techniques which are widely used in mathematical population genetics provide modeling tools and conceptual background to assist in the study of species dynamics, and help exploring the analogy between trait-dependent species diversification and the evolution of allele frequencies in the population genetics setting. The analytical framework specified is then applied to models incorporating diversity-dependence, in order to infer effective results from processes in which the net diversification of species depends on the total number of species. In particular, the long term fate of a rare trait may be analyzed under a partly symmetric scenario, using a time-change transform technique.

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  • 44.
    Kruskopf-Österberg, M
    et al.
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. Evolutionär funktionsgenomik.
    Shavorskaya, O
    Lascoux, M
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Lagercrantz, U
    Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics. Uppsala University, Teknisk-naturvetenskapliga vetenskapsområdet, Faculty of Science and Technology, Department of Evolution, Genomics and Systematics, Evolutionary Functional Genomics. evolutionär funktionsgenomik.
    Naturally occurring indel variation in the B. nigra COL1 gene is associated with variation in flowering time.2002In: Genetics, Vol. 161, p. 299-306Article in journal (Refereed)
  • 45.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Holm, Karl
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Cornille, Amandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Univ Montpellier, CNRS IRD EPHE, ISEM UMR 5554, Inst Sci Evolut, Pl Eugene Bataillon, F-34075 Montpellier, France..
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolut, 25 Willcocks St, Toronto, ON M5S 3B2, Canada..
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae)2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 5, p. 1106-1121Article in journal (Refereed)
    Abstract [en]

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

  • 46.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Milesi, Pascal
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Duan, Tianlin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Orsucci, Marion
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolutionary Biol, Toronto, ON, Canada.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Rennes, CNRS, ECOBIO Ecosyst Biodivers Evolut UMR 6553, Rennes, France.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Towards the new normal: Transcriptomic convergence and genomic legacy of the two subgenomes of an allopolyploid weed (Capsella bursa-pastoris)2019In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 5, article id e1008131Article in journal (Refereed)
    Abstract [en]

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

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  • 47.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Salcedo, Adriana
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Eriksson, Mimmi C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Duan, Tianlin
    Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tawari, Nilesh
    ASTAR, Genome Inst Singapore, Computat & Syst Biol Grp, Singapore, Singapore.
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Guerrina, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Kreiner, Julia M.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Kent, Tyler V.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Stinchcombe, John R.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ Rennes 1, CNRS, UMR 6553, ECOBIO,Ecosyst,Biodivers,Evolut, F-35000 Rennes, France.
    Wright, Stephen I.
    Univ Toronto, Dept Ecol & Evolut, Toronto, ON, Canada.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)2019In: PLOS Genetics, ISSN 1553-7390, E-ISSN 1553-7404, Vol. 15, no 2, article id e1007949Article in journal (Refereed)
    Abstract [en]

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

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  • 48.
    Kryvokhyzha, Dmytro
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Salcedo, Adriana
    Eriksson, Mimmi C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Duan, Tianlin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Tawari, Nilesh
    Chen, Jun
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Guerrina, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Kreiner, Julia M.
    Kent, Tyler V.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Stinchcombe, John R.
    Glemin, Sylvain
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Wright, Stephen I.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Parental legacy, demography, and introgression influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae)2017Manuscript (preprint) (Other academic)
    Abstract [en]

    Allopolyploidy is generally perceived as a major source of evolutionary novelties and as an instantaneous way to create isolation barriers. However, we do not have a clear understanding of how two subgenomes evolve and interact once they have fused in an allopolyploid species and how isolated they are from their relatives. Here, we address these questions by analyzing genomic and transcriptomic data of allotetraploid Capsella bursa-pastoris in three differentiated populations, Asia, Europe and the Middle East. We phased the two subgenomes, one descended from the outcrossing and highly diverse Capsella grandiflora (Cg) and the other one from the selfing and genetically depauperate Capsella orientalis (Co). For each subgenome, we assessed its relationship with the diploid relatives, temporal change of effective population size Ne, signatures of positive and negative selection, and gene expression patterns. Introgression between C. bursa-pastoris and its diploid relatives was widespread and the two subgenomes were impacted differentially depending on geographic region. In all three regions, Ne of the two subgenomes decreased gradually and the Co subgenome accumulated more deleterious changes than Cg. Selective sweeps were more common on the Cg subgenome in Europe and the Middle East, and on the Co subgenome in Asia. In contrast, differences in expression were limited with the Cg subgenome slightly more expressed than Co in Europe and the Middle-East. In summary, after more than 100,000 generations of co-existence, the two subgenomes of C. bursa-pastoris still retained a strong signature of parental legacy and were differentially affected by introgression and selection.

  • 49.
    Källman, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    De Mita, Stéphane
    INRA Nancy, 54280 Champenoux, France.
    Larsson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Gyllenstrand, Niclas
    Dept. of Plant Biology and Forest Genetics, Swedish Agricultural University, Uppsala, Sweden.
    Heuertz, Myriam
    Forest Research Centre INIA-CIFOR, 28040, Madrid, Spain.
    Parducci, Laura
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Suyama, Yoshihisa
    Graduate School of Agricultural Science, Tohoku University, Japan.
    Lagercrantz, Ulf
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Patterns of nucleotide diversity at photoperiod related genes in the conifer Norway spruce [Picea abies (L.) (Karst)]2014In: PLOS ONE, E-ISSN 1932-6203, Vol. 9, no 5, p. e95306-Article in journal (Refereed)
    Abstract [en]

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

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  • 50.
    Lafon-Placette, Clement
    et al.
    Swedish Univ Agr Sci, Dept Plant Biol, Uppsala, Sweden;Linnean Ctr Plant Biol, Uppsala, Sweden;Charles Univ Prague, Dept Bot, Prague, Czech Republic.
    Hatorangan, Marcelinus R.
    Swedish Univ Agr Sci, Dept Plant Biol, Uppsala, Sweden;Linnean Ctr Plant Biol, Uppsala, Sweden.
    Steige, Kim A.
    Stockholm Univ, Dept Ecol Environm & Plant Sci, Sci Life Lab, Stockholm, Sweden;Univ Cologne, Inst Bot, Bioctr, Cologne, Germany.
    Cornille, Amandine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution.
    Slotte, Tanja
    Stockholm Univ, Dept Ecol Environm & Plant Sci, Sci Life Lab, Stockholm, Sweden.
    Kohler, Claudia
    Swedish Univ Agr Sci, Dept Plant Biol, Uppsala, Sweden;Linnean Ctr Plant Biol, Uppsala, Sweden.
    Paternally expressed imprinted genes associate with hybridization barriers in Capsella2018In: NATURE PLANTS, ISSN 2055-026X, Vol. 4, no 6, p. 352-357Article in journal (Refereed)
    Abstract [en]

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

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