Liste Rouge Des Plantes Vasculaires Du Canton De Genève Une Institution Ville De Genève

Total Page:16

File Type:pdf, Size:1020Kb

Liste Rouge Des Plantes Vasculaires Du Canton De Genève Une Institution Ville De Genève F. Mombrial Liste Rouge M. Chevalier E. Favre des plantes vasculaires A. Lacroix du canton de Genève E. Sandoz F. Sandoz S. Tribot VAUD 1 Lac Léman Versoix HAUTE CHAÎNE DU JURA PAYS DE GEX 2 Data sources: SRTM data V4/CIAT – SITG 2019 DREAL Auvergne Rhône-Alpes Data sources: SRTM data V4/CIAT Hermance 5 Allondon 4 10 11 3 12 Foron 6 VOIRONS CHABLAIS Seymaz 9 Rhône Rhône Arve Drize Arve Aire 7 8 1 Enclave de Céligny Laire 2 Secteur de la Versoix 3 Aéroport et secteur industriel 4 Rive droite du Lac 5 Rive gauche du Lac 6 Mandement VUACHE 7 Champagne GENEVOIS 8 Plaine de l’Aire 9 Centre urbain et périurbain 10 Plaine de la Seymaz SALÈVE 11 Bois de Jussy 0 5 10km 12 Marais de Sionnet VALLÉE DE L’ARVE Liste Rouge des plantes vasculaires du canton de Genève www.cjb-geneve.ch Une institution Ville de Genève Directeur Pierre-André Loizeau Rédacteur Florian Mombrial Graphisme Matthieu Berthod Photographies Pages 20 – 21 Association pour la Sauvegarde du Léman (8) OCAN (2, 6, 11) La Libellule (10) Mombrial F. (1, 3, 4, 5, 7, 9, 12, 13) Cartographies © SITG, SIPV, CJBG ISBN 978-2-8277-0139-1 Publication Hors-Série n°20 ©CONSERVATOIRE ET JARDIN BOTANIQUES DE LA VILLE DE GENÈVE Liste Rouge des plantes vasculaires du canton de Genève Florian Mombrial Matthieu Chevalier Emmanuelle Favre Alison Lacroix Emilie Sandoz Frédéric Sandoz Sandra Tribot Avec la collaboration de Catherine Lambelet Pascal Martin Raoul Palese Sophie Vallée Nicolas Wyler En hommage à notre cher ami Lionel SAGER, botaniste et humaniste. Remerciements Ce projet de révision de la Liste Rouge des plantes vasculaires du canton de Genève a débuté en 2016. Un tel travail ne peut se faire sans la mise à jour des données de terrain. Nombreuses sont les personnes qui y ont contribué et nous tenons ici à leur faire part de notre intense reconnaissance. Les auteurs remercient: • les experts locaux qui ont répondu favo- rablement et avec enthousiasme à notre appel pour collaborer à l’évaluation des statuts de menace. Il s’agit de Laurent Burgisser, Patrick Charlier, Alain Demierre, Simon Lézat, Helder Santiago, Christian Schneider et Michel Vauthey; • l’ensemble des collaborateurs d’Info Flora et plus particulièrement Christophe Bornand et Lionel Sager () pour leurs conseils avisés sur les aspects méthodologiques; • la Société Botanique de Genève pour son étroite collaboration dans la mise à jour des données de terrain des plantes communes du canton de Genève. Ce travail n’aurait pu voir le jour sans le sou- tien de l’Office Fédéral de l’Environnement (OFEV), l’Office Cantonal de l’Agriculture et de la Nature (OCAN) et des Conservatoire et Jardin botaniques de la Ville de Genève (CJBG). Table des matières Préface 11 Introduction 13 Méthodologie 25 Liste Rouge 37 Résultats 85 Bibliographie 107 Liste des contributeurs 110 Préface car là où des moyens techniques, financiers et humains sont investis pour recréer des Pierre-André Loizeau milieux naturels, adapter leur gestion et, Directeur des CJBG pour quelques espèces, mettre en œuvre un plan d’action, les espèces les plus sensibles Bertrand von Arx bénéficient de cette assistance particulière. Directeur de la biodiversité, OCAN Par contre, environ 10% des espèces non menacées en 2006 (LC) se rapprochent dan- Il y a presque 15 ans, une première Liste gereusement du statut «Probabilité d’être en Rouge du canton était publiée sur la base de danger dans un futur proche» ou le sont déjà. plus de 170 ans d’observations de terrain, Les espèces communes souffrent principale- réunies dans les herbiers des Conservatoire ment du grignotage des petites surfaces natu- et Jardin botaniques de la Ville de Genève relles converties en surfaces imperméables (CJBG), dans des publications ou par le fait minérales. Si les causes principales des pertes d’observations directes récentes. Cette publi- étaient évidentes dans les années cinquante cation faisait le constat de l’état de santé de (drainages agricoles, endiguement et enterre- notre flore et, par extension, de nos milieux ment des cours d’eau, destruction des marais naturels. Elle constituait par ailleurs un point et des prairies sèches), ce rétrécissement des de référence pour toute observation future zones naturelles est aujourd’hui plus insi- de l’évolution de la biodiversité végétale. dieux. À ce propos, la carte des milieux natu- Nous commencions à cette époque à décou- rels du canton nous révèle qu’entre 2015 et vrir le terme de biodiversité, la complexité 2019, 144 hectares ont été imperméabilisés, de son analyse et la difficulté à obtenir des soit la disparition de l’équivalent de quatre valeurs absolues permettant le suivi de sa terrains de football chaque mois... qualité. Nous tenons à saluer l’énorme travail d’obser- Alors où en sommes-nous dans notre canton vations sur le terrain et d’analyse des données depuis cette première édition? réalisés par les botanistes experts et amateurs éclairés. Leur engagement a permis de confir- Malheureusement, nous devons constater mer scientifiquement que si l’on se donne que, malgré de gros efforts de protection les moyens de conserver notre patrimoine et de gestion de la nature, des espèces dis- d’une manière ciblée, les résultats sont là. De paraissent aussi dans notre canton, comme même, le tandem collaboratif et complémen- dans le reste du monde. Ce ne sont pas moins taire, en place depuis bientôt deux décennies, de 31 taxons qui ont disparu depuis la der- que forment une institution scientifique (les nière Liste Rouge (soit en moyenne plus de CJBG) et l’autorité gestionnaire (l’OCAN), deux par an…)! reste une valeur sûre pour œuvrer en faveur de la biodiversité. Nous n’arrivons donc pas à endiguer l’érosion de la biodiversité végétale. Un petit réconfort En conclusion, rappelons-nous qu’au-delà des néanmoins: 19 taxons qui étaient considérés espèces qui diminuent ou disparaissent, ce sont comme éteints au niveau régional (RE) en les milieux naturels qu’elles constituent qui 2006 ont été à nouveau observés. sont également en diminution. Et s’il est certes dommage de ne plus pouvoir observer telle Au-delà de ce constat, deux autres tendances orchidée ou telle autre fleur spectaculaire, ce se dégagent. Premièrement, il est réjouis- sont aussi les services (écosystémiques) rendus sant d’observer que les espèces menacées par ces espèces et ces milieux naturels qui vont se portent globalement un peu mieux. Les nous manquer. La chlorophylle portée par les mesures mises en place se montrent utiles, feuilles ne produit-elle pas l’air que nous respi- 11 rons? Le son du vent dans les feuilles en forêt verons à éviter les affrontements stériles (la ne calme-t-il pas notre esprit en nous incitant flore ou les panneaux solaires, la nature ou à la rêverie? L’«herbe» n’est-elle pas simple- la construction, etc.). ment la base de la pyramide alimentaire des espèces, de même que beaucoup de plantes Les solutions ne sont finalement pas si com- qui font partie de notre propre alimentation? pliquées à trouver: laissons un espace à la Alors soyons inquiets et réagissons! Les Nature sauvage. S’il faut parfois lui donner indices contenus dans cette Liste Rouge un coup de pouce pour réparer les impacts ne sont que l’arbre qui cache la forêt. Le anthropiques, c’est très généralement en la «réflexe biodiversité» doit s’instaurer au sein laissant s’occuper d’elle-même qu’elle nous de toutes les activités et corps de métier qui rendra les plus grands services. interviennent sur les milieux naturels et le sol. Chaque politique publique est concer- À l’heure où nous comptons sur les espèces et née, comme le souligne la Stratégie Biodi- surtout leur résilience pour nous accompagner versité Genève et son Plan d’action. Et c’est, dans les changements climatiques, il est impor- notamment, par le biais du développement tant de promouvoir la plus grande diversité intégratif de notre infrastructure écologique possible de taxons aux populations généti- cantonale et transfrontalière que nous arri- quement riches partout sur notre territoire. 12 Introduction Présentation du canton gny, le Salève, au sud-est, atteint 1379 m (Grand Piton) et le massif des Voirons, à l’est, Situé à l’extrême ouest de la Suisse, le canton culmine à 1480 m au niveau du Signal des de Genève occupe une superficie de 282,5 Voirons. Le canton est donc entouré de mas- kilomètres carrés dont 36,8 entièrement sifs montagneux mais demeure néanmoins lacustres. Bien que de faible superficie, le ter- largement ouvert en direction du Léman situé ritoire est densément peuplé avec 2032 habi- au nord-est de son territoire. Le bassin gene- tants par km2 en 2018 (OCSTAT, 2019) faisant vois possède en outre une petite ouverture de Genève le deuxième canton suisse, après sur le sud via le Défilé de l’Écluse. Bâle-Ville, en terme de densité de population. Malgré le fait qu’il représente un peu moins Le climat qui prédomine sur le territoire est de 1% du territoire helvétique et en dépit de de type subocéanique dégradé (Theurillat & la forte pression anthropique à laquelle il est al., 2011) caractérisé par des hivers relative- soumis, le canton héberge plus d’un tiers de ment humides et doux et des étés relative- la flore vasculaire indigène du pays, soit 1126 ment secs et chauds. Avec une pluviométrie taxons sur les 2712 recensés en Suisse (Bor- annuelle de 945 mm, selon une moyenne nand & al., 2016). Cette richesse s’explique établie entre 1961 et 2018 (OCSTAT, 2019), entre autres par la localisation géographique il s’agit de l’un des cantons les plus secs de du territoire, ses conditions climatiques mais Suisse.
Recommended publications
  • The Selfing Syndrome Overshadows Other Differences When Comparing
    bioRxiv preprint doi: https://doi.org/10.1101/2020.11.26.398016; this version posted November 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 The selfing syndrome overshadows other differences when 2 comparing fitness across Capsella species 3 4 5 Marion Orsucci1, Theofilos Vanikiotis2, Maria Guerrina1, Tianlin Duan1, Sylvain Glémin3, Martin 6 Lascoux1 7 8 1 Department of Ecology and Genetics, Evolutionary Biology Centre and Science for Life 9 Laboratory, Uppsala University, 75236 Uppsala, Sweden 10 2 Department of Biological Applications & Technology, University of Ioannina, Leof. S. 11 Niarchou GR-451 10, Ioannina, Greece 12 3 UMR CNRS 6553 ECOBIO, Campus Beaulieu, bât 14a, p.118, CS 74205, 35042 Rennes, 13 France 14 15 16 Corresponding authors: Martin Lascoux ([email protected]), Marion Orsucci 17 ([email protected]) 18 19 20 Running title: Influence of mating system on life history traits in Capsella spp. 21 22 23 Key words: mating system, ploidy, life history traits, environmental disturbance 24 25 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.11.26.398016; this version posted November 27, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 26 SUMMARY 27 Self-fertilization has recurrently evolved from outcrossing. Self-fertilization provides an advantage 28 in the short-term as individuals do not require a mate to reproduce, but self-fertilization is also 29 associated with both decreased genetic diversity and accumulation of weakly deleterious mutations, 30 which could, however, be alleviated in polyploid selfers.
    [Show full text]
  • Functional Role of Polymerase IV During Pollen Development in Capsella
    bioRxiv preprint doi: https://doi.org/10.1101/863522; this version posted December 3, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Functional role of Polymerase IV during pollen development in Capsella 2 Zhenxing Wang1*, Nicolas Butel1*, Juan Santos-González1, Filipe Borges2,3, Jun Yi1, 3 Robert A. Martienssen2, German Martinez1, Claudia Köhler1 4 1 Department of Plant Biology, Swedish University of Agricultural Sciences and Linnean 5 Center for Plant Biology, Uppsala 75007, Sweden 6 2 Howard Hughes Medical Institute and Cold Spring Harbor Laboratory, 1 Bungtown 7 Road, Cold Spring Harbor, New York 11724, USA. 8 3 Present address: Institut Jean-Pierre Bourgin, INRA, AgroParisTech, Université Paris- 9 Saclay, 78000, Versailles, France 10 *both authors contributed equally to this work 11 Corresponding Author: [email protected] 12 13 Short title: Requirement of Polymerase IV in Capsella pollen. 14 One-sentence summary: Loss of Polymerase IV function in Capsella rubella causes 15 microspore arrest, revealing an important functional role of Polymerase IV during pollen 16 development. 17 The author responsible for distribution of materials integral to the findings presented in 18 this article in accordance with the policy described in the Instructions for Authors 19 (www.plantcell.org) is: Claudia Köhler ([email protected]) 20 21 22 23 1 bioRxiv preprint doi: https://doi.org/10.1101/863522; this version posted December 3, 2019.
    [Show full text]
  • Evolution of Flowering Time in the Tetraploid Capsella Bursa-Pastoris (Brassicaceae)
    Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology 367 Evolution of Flowering Time in the Tetraploid Capsella bursa-pastoris (Brassicaceae) TANJA SLOTTE ACTA UNIVERSITATIS UPSALIENSIS ISSN 1651-6214 UPPSALA ISBN 978-91-554-7024-1 2007 urn:nbn:se:uu:diva-8311 ! " #$$" $%$$ & & & ' ( ) * ( + )( #$$"( & ! * ) ) ,-( . ( /0"( 1$ ( ( 2+ 3" 4345514"$#14( . 6 & &* & * ( 2 2 & & * * & * & ( ! * & ( . 7 & * . * & & & & & * ( & & * & * 8 & ( ) & & * * ( . 4 4& * && * * && & * ( + * 9) ,9 ) - & & * : ( ) !"!#$% ,%- & 9) &!'$()* &! ,&- * & * ( && & * & * & ; ( ) % & * & && & * ( 2 8 & & * +, - & * 8 9) . / $ / * / $ * / ) %0/ / $ 12345 / , < ) 6 + #$$" 2++ 0540#1 2+ 3" 4345514"$#14 % %%% 4 / , %== (:(= > ? % %%% 4 /- looking carefully, a shepherd’s purse is blooming under the fence Bash List of papers This thesis is based on the following papers, which are referred to by their Roman numerals: I Slotte, T., Ceplitis, A., Neuffer, B., Hurka, H., and M. Lascoux. 2006. Intrageneric phylogeny of Capsella (Brassicaceae) and the
    [Show full text]
  • Genetic Control of Plastidic L-Glutamate Dehydrogenase Isozymes in the Genus Apsella (Brassicaceae)
    Heredityl2 (1994) 126—131 Received 1 June 1993 Genetical Society of Great Britain Genetic control of plastidic L-glutamate dehydrogenase isozymes in the genus apsella (Brassicaceae) HERBERT HURKA* & SABINE DURING University of Osnabruck, Faculty of Biology/Chemistry, Botany, Barbarastr. 11, D-49069 Osnabrück, Germany Leafextracts of three Capsella species (Brassicaceae), two diploids and one tetraploid, have been analysed for isozymes of L-glutamate dehydrogenase on polyacrylamide gels. A plastidic GDH (EC 1.4.1.4.) consisted of at least seven bands. Progeny analyses and crossing experiments revealed that within the two diploid species two genetic loci code for this pattern. One of the loci, Gdhl, appeared to be monomorphic. The other locus Gdh2, is polymorphic and segregates for three alleles determining allozymes in accordance with Mendelian inheritance. Estimates of out- crossing rates based on segregation at the Gdh2 locus support the view that one of the diploid species is highly inbred whereas the other is an obligate outbreeder. In the tetraploid species, both loci are apparently duplicated so that four instead of two genes determine the polypeptide structure of plastidic GDH. These loci share the same alleles with the diploid species and no additional allozymes have been detected. Keywords:Capsella,GDH, gene duplication, isozyme loci, polymorphism, subcellular location. Introduction reveals a seven or even more banded pattern (Srivastava & Singh, 1987 for reference). Its subcellular Glutamatedehydrogenase, GDH, EC 1.4.1.2-4, has location and the underlying genetics have not been been found in almost all types of organisms. In higher clearly resolved. Two genes are thought to be respon- plants, organ and tissue specificity as well as subcellular sible for the polypeptide structure of GDH.
    [Show full text]
  • Independent FLC Mutations As Causes of Flowering-Time Variation in Arabidopsis Thaliana and Capsella Rubella
    INVESTIGATION Independent FLC Mutations as Causes of Flowering-Time Variation in Arabidopsis thaliana and Capsella rubella Ya-Long Guo,*,† Marco Todesco,* Jörg Hagmann,* Sandip Das,*,1 and Detlef Weigel*,2 *Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany, and †State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China ABSTRACT Capsella rubella is an inbreeding annual forb closely related to Arabidopsis thaliana, a model species widely used for studying natural variation in adaptive traits such as flowering time. Although mutations in dozens of genes can affect flowering of A. thaliana in the laboratory, only a handful of such genes vary in natural populations. Chief among these are FRIGIDA (FRI) and FLOWERING LOCUS C (FLC). Common and rare FRI mutations along with rare FLC mutations explain a large fraction of flowering-time variation in A. thaliana. Here we document flowering time under different conditions in 20 C. rubella accessions from across the species’ range. Similar to A. thaliana, vernalization, long photoperiods and elevated ambient temperature generally promote flowering. In this collection of C. rubella accessions, we did not find any obvious loss-of-function FRI alleles. Using mapping-by-sequencing with two strains that have contrasting flowering behaviors, we identified a splice-site mutation in FLC as the likely cause of early flowering in accession 1408. However, other similarly early C. rubella accessions did not share this mutation. We conclude that the genetic basis of flowering-time variation in C. rubella is complex, despite this very young species having undergone an extreme genetic bottleneck when it split from C.
    [Show full text]
  • Hybrid Origins and the Earliest Stages of Diploidization in the Highly Successful Recent Polyploid Capsella Bursa-Pastoris
    Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris Gavin M. Douglasa,1, Gesseca Gosa,1, Kim A. Steigeb,1, Adriana Salcedoa, Karl Holmb, Emily B. Josephsa, Ramesh Arunkumara, J. Arvid Ågrena, Khaled M. Hazzouria,c, Wei Wanga, Adrian E. Plattsd, Robert J. Williamsona, Barbara Neuffere, Martin Lascouxb,2, Tanja Slotteb,f,2, and Stephen I. Wrighta,2 aDepartment of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2; bDepartment of Ecology and Genetics, Evolutionary Biology Centre, Science for Life Laboratory, Uppsala University, 75236 Uppsala, Sweden; cCenter for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates 129188; dMcGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada H3G 0B1; eDepartment of Botany, University of Osnabruck, 49076 Osnabruck, Germany; and fDepartment of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 10691 Stockholm, Sweden Edited by Michael Lynch, Indiana University, Bloomington, IN, and approved January 28, 2015 (received for review June 30, 2014) Whole-genome duplication (WGD) events have occurred repeat- occur rapidly upon polyploid formation or following a longer edly during flowering plant evolution, and there is growing time scale of genome rearrangement and evolution. evidence for predictable patterns of gene retention and loss Studying the early stages of gene degeneration and loss should following polyploidization.
    [Show full text]
  • A Chromosome-Scale Reference Genome of Lobularia Maritima, An
    Huang et al. Horticulture Research (2020) 7:197 Horticulture Research https://doi.org/10.1038/s41438-020-00422-w www.nature.com/hortres ARTICLE Open Access A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance Li Huang1,YazhenMa1, Jiebei Jiang1,TingLi1, Wenjie Yang1,LeiZhang1,LeiWu1,LandiFeng1, Zhenxiang Xi1, Xiaoting Xu1, Jianquan Liu 1,2 and Quanjun Hu 1 Abstract Lobularia maritima (L.) Desv. is an ornamental plant cultivated across the world. It belongs to the family Brassicaceae and can tolerate dry, poor and contaminated habitats. Here, we present a chromosome-scale, high-quality genome assembly of L. maritima based on integrated approaches combining Illumina short reads and Hi–C chromosome conformation data. The genome was assembled into 12 pseudochromosomes with a 197.70 Mb length, and it includes 25,813 protein-coding genes. Approximately 41.94% of the genome consists of repetitive sequences, with abundant long terminal repeat transposable elements. Comparative genomic analysis confirmed that L. maritima underwent a species-specific whole-genome duplication (WGD) event ~22.99 million years ago. We identified ~1900 species-specific genes, 25 expanded gene families, and 50 positively selected genes in L. maritima. Functional annotations of these genes indicated that they are mainly related to stress tolerance. These results provide new insights into the stress tolerance of L. maritima, and this genomic resource will be valuable for further genetic improvement of this important ornamental plant. 1234567890():,; 1234567890():,; 1234567890():,; 1234567890():,; Introduction ancestral species, WGDs can also promote reproductive Whole-genome duplication (WGD), or polyploidy, has isolation and thus facilitate speciation13.
    [Show full text]
  • Group Code Species Code Species Common Name Classification
    group code species code species common name classification genome version source transcript version Source website EUD Aco Aquilegia coerulea columbine Eudicotyledons (Ranunculales) JGI v1 Phytozome 11 JGI v1.1 https://phytozome.jgi.doe.gov/pz/portal.html BRA Aly Arabidopsis lyrata lyrate rockcress Eudicotyledons (Rosids – Malvids – Brassicales) JGI v1 Phytozome 11 JGI V1.0 https://phytozome.jgi.doe.gov/pz/portal.html BRA Ath Arabidopsis thaliana (Columbia) thale cress Eudicotyledons (Rosids – Malvids – Brassicales) TAIR10 Araport Araport11 https://araport.org EUD Bvu Beta vulgaris sugar beet Eudicotyledons (Caryophyllales) RefBeet-1.2.2 Ensembl RefBeet-1.2.2 https://plants.ensembl.org/info/website/ftp/index.html BRA Bst Boechera stricta drummond's rockcress Eudicotyledons (Rosids – Malvids – Brassicales) JGI v1 Phytozome 10 JGI v1.3 https://phytozome.jgi.doe.gov/pz/portal.html BRA Bra Brassica rapa turnip mustard Eudicotyledons (Rosids – Malvids – Brassicales) JGI v1 Phytozome 10 JGI v1.2 https://phytozome.jgi.doe.gov/pz/portal.html BRA Cgr Capsella grandiflora Eudicotyledons (Rosids – Malvids – Brassicales) JGI v1 Phytozome 10 JGI v1.1 https://phytozome.jgi.doe.gov/pz/portal.html BRA Cru Capsella rubella red shepherd's purse Eudicotyledons (Rosids – Malvids – Brassicales) JGI v1 Phytozome 10 ASGPB v0.4 https://phytozome.jgi.doe.gov/pz/portal.html BRA Cpa Carica papaya papaya Eudicotyledons (Rosids – Malvids - Brassicales) JGI v1 Phytozome 11 JGI v1.0 https://phytozome.jgi.doe.gov/pz/portal.html MAL Ccl Citrus clementina clementine Eudicotyledons
    [Show full text]
  • Transposable Element Evolution in the Allotetraploid Capsella Bursa-Pastoris And
    bioRxiv preprint doi: https://doi.org/10.1101/042325; this version posted March 3, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Transposable Element Evolution in the Allotetraploid Capsella bursa-pastoris and 2 the Perfect Storm Hypothesis 3 J. Arvid Ågren1,2, Hui-Run Huang3, Stephen I. Wright1 4 5 1 Department of Ecology and Evolutionary Biology, University of Toronto 6 2 Present address: Department of Molecular Biology and Genetics, Cornell University 7 3 Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South 8 China Botanical Garden, the Chinese Academy of Sciences 9 10 Key words: C-value; genome size; mating system; polyploidy 11 Running head: Capsella transposons and the perfect storm hypothesis 12 Word count: 2009 13 Abstract word count: 248 14 Number of figures: 3 15 Number of tables: 1 16 17 18 19 20 21 22 23 bioRxiv preprint doi: https://doi.org/10.1101/042325; this version posted March 3, 2016. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Abstract 2 Premise of the study 3 Shifts in ploidy level will affect the evolutionary dynamics of genomes in a myriad of 4 ways. Population genetic theory predicts that transposable element (TE) proliferation may 5 follow because the genome wide efficacy of selection should be reduced and the increase 6 in gene copies may mask the deleterious effects of TE insertions.
    [Show full text]
  • Recent Speciation of Capsella Rubella from Capsella Grandiflora, Associated with Loss of Self-Incompatibility and an Extreme Bottleneck
    Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck Ya-Long Guoa,1, Jesper S. Bechsgaardb,1, Tanja Slottec, Barbara Neufferd, Martin Lascouxc, Detlef Weigela,2, and Mikkel H. Schierupb,2 aDepartment of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tu¨bingen, Germany; bEcology and Genetics, Institute of Biological Sciences, University of Aarhus, 8000 Aarhus C, Denmark; cProgram in Evolutionary Functional Genomics, Uppsala University, 75326 Uppsala, Sweden; and dDepartment of Systematic Botany, University of Osnabru¨ck, 49076 Osnabru¨ck, Germany Edited by Spencer C. H. Barrett, University of Toronto, Toronto, Canada, and accepted by the Editorial Board January 26, 2009 (received for review August 13, 2008) Flowering plants often prevent selfing through mechanisms of thaliana, the work horse for much of plant molecular genetics, self-incompatibility (S.I.). The loss of S.I. has occurred many times has become self-compatible relatively recently, apparently by the independently, because it provides short-term advantages in sit- gradual fixation of multiple, independent mutations that weak- uations where pollinators or mates are rare. The genus Capsella, ened or disabled the S.I. system throughout its geographical which is closely related to Arabidopsis, contains a pair of closely range (15, 16). related diploid species, the self-incompatible Capsella grandiflora We set out to investigate the breakdown of S.I. in Capsella and the self-compatible Capsella rubella. To elucidate the transi- rubella to test the generality of the pattern described for A. tion to selfing and its relationship to speciation of C. rubella,we thaliana.
    [Show full text]
  • Mating System Shifts and Transposable Element Evolution in the Plant
    Ågren et al. BMC Genomics 2014, 15:602 http://www.biomedcentral.com/1471-2164/15/602 RESEARCH ARTICLE Open Access Mating system shifts and transposable element evolution in the plant genus Capsella J Arvid Ågren1*, Wei Wang1, Daniel Koenig2, Barbara Neuffer3, Detlef Weigel2 and Stephen I Wright1 Abstract Background: Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora. Results: We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species. Conclusion: Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale.
    [Show full text]
  • Divergence Population Genetics of the Genus Capsella Pádraic Corcoran
    Divergence Population Genetics ofthe Genus Capsella Pádraic Corcoran Degree project inbiology, Master ofscience (2years), 2009 Examensarbete ibiologi 45 hp tillmasterexamen, 2009 Biology Education Centre and Department ofEvolutionary Functional Genomics, Uppsala University Supervisor: Prof. Martin Lascoux 1 "A contrary pancake surely, a fingerish atrocity but not without a queer charm all its own" (Flann O'Brien, The Third Policeman) 2 Abstract The population genetic study of diverging species or populations has seen many advances in recent years. Likelihood or Bayesian methods based on coalescent theory offer researchers the opportunity to estimate important parameters for the history of the species or populations under consideration. The divergence population genetics approach was utilized here at both the interspecific and intraspecific levels. In this study, fourteen nuclear loci were sequenced in the species Capsella bursa-pastoris sampled in Europe and the Far East. Seven loci were sequenced in the species Capsella rubella found in southern Europe and Israel. Phylogenetic methods were utilized to identify haplotype sharing between these species and the causes of this haplotype sharing were investigated using and divergence population genetics methods. The fitting of the Isolation-with-Migration model to the data identified post divergent gene flow as the cause of haplotype sharing between these species. It was also found that the origin of the polyploid C. bursa-pastoris was an extreme bottleneck event. At the intraspecific level of this study in C. bursa-pastoris, nucleotide diversity estimates for the Far Eastern populations were found to be lower than those in Europe. However, the Russian population appears to have diverged relatively recently from the European population of C.
    [Show full text]