Supporting information
advertisement
Supporting Information for The COMPADRE Plant Matrix Database an Open Online Repository for Plant Demography Roberto Salguero-Gómez, Owen R. Jones, C. Ruth Archer, Yvonne M. Buckley, Judy Che-Castaldo, Hal Caswell, David Hodgson, Alexander Scheuerlein, Dalia A. Conde, Erik Brinks, Hendrik de Buhr, Fränce Gottschalk, Claudia Farack, Alexander Hartmann, Anne Henning, Gabriel Hoppe, Gesa Römer, Jens Runge, Tara Ruoff, Julia Wille, Stefan Zeh, Dirk Vieregg, Raziel Davison, Annette Baudisch, Res Altwegg, Fernando Colchero, Ming Dong, Hans de Kroon, JeanDominique Lebreton, Jessica C. Metcalf, Maile Neel, Ingrid Parker, Bernt-Erik Sæther, Takenori Takada, Teresa Valverde, Luis Antonio Vélez-Espino, Glenda M. Wardle, Miguel Franco & James W. Vaupel 1 Table of Contents Appendix S1. Constituents of COMPADRE .................................................................. 3 Appendix S2. COMPADRE user’s guide ........................................................................ 6 Appendix S3. COMPADRE R scripts............................................................................... 7 Appendix S4. Extended literature used in COMPADRE 3.0 .................................. 9 Appendix S5. COMPADRE phylogeny ........................................................................ 55 Appendix S6. COMPADRE funding support and extended acknowledgements ......................................................................................................... 64 Appendix S7. Author contributions........................................................................... 67 Appendix S8. Supporting Information References .............................................. 71 2 Appendix S1. Constituents of COMPADRE The COMPADRE Plant Matrix Database is developed and supported by two committees and a digitization team. Their constituent members, whose tenure is revisited every two years, are located worldwide, assuring that COMPADRE reaches all continents, and that published information is sent back to COMPADRE from white and gray literature. Member Institution Country University of Queensland Australia Max Planck Institute for Demographic Germany Roberto Salguero-Gómez Research (MPIDR) Owen Jones Trinity College Dublin Ireland University of Southern Denmark Denmark Trinity College Dublin Ireland University of Queensland Australia Core committee Yvonne Buckley National Socio-Environmental Judy Che-Castaldo USA Synthesis Center (SESYNC) Dalia Conde University of Southern Denmark Denmark David Hodgson University of Exeter UK Alexander Scheuerlein MPIDR Germany Woods Hole Oceanographic Institute USA MPIDR Germany University of Amsterdam The Netherlands Hal Caswell 3 MPIDR Germany Duke University USA University of Southern Denmark Denmark Res Altwegg University of Cape Town South Africa Fernando Colchero University of Southern Denmark Denmark Ming Dong The Chinese Academy of Sciences China Miguel Franco University of Plymouth UK Hans de Kroon Radboud University The Netherlands Jean-Dominique Centre National de la Recherche James Vaupel Science committee France Lebreton Scientifique Jessica Metcalf Princeton University UK Maile Neel University of Maryland USA Ingrid Parker University of California Santa Cruz USA Norwegian University of Science and Bernt-Erik Sæther Norway Technology Juan Silva Universidad de los Andes Venezuela Jonathan Silvertown Open University UK Takenori Takada Hokkaido University Japan Universidad Nacional Autonoma de Teresa Valverde Mexico Mexico Luis Antonio VelezFisheries and Oceans Canada Canada University of Sydney Australia Espino Glenda Wardle 4 Digitization team Ruth Archer MPIDR Germany Hendrik de Buhr MPIDR Germany Fränce Gottschalk MPIDR Germany Claudia Farack MPIDR Germany Alexander Hartmann MPIDR Germany Anna Henning MPIDR Germany Gesa Römer MPIDR Germany Tara Ruoff University of Maryland USA Julia Wille MPIDR Germany Stefan Zeh MPIDR Germany Past compadrinos: Erik Brinks (MPIDR), Gabriela Cosma (University of Pennsylvania), Elisabeth McCuaig (University of Pennsylvania), Vuong Nguyen (University of Sydney). Henry Tai (University of Pennsylvania), Bonnie Waring (University of Pennsylvania), and Angela Zeng (University of Pennsylvania) 5 Appendix S2. COMPADRE user’s guide The COMPADRE Plant Matrix Database user’s guide, which contains all the variables available in COMPADRE, the organization of the “COMPADRE Data_MONTH_DAY_YEAR.csv file, and the range of options for each variable, is available here: http://www.compadre-db.org/Download/guide.pdf 6 Appendix S3. COMPADRE R scripts The COMPADRE Plant Matrix Database team wishes to make publicly available the following R scripts as a service to the community. The usage of these materials is at the user’s discretion and responsibility. Regrettably, no member of the COMPADRE team holds a grant to provide technical support on their implementation. Various textbooks (Caswell, 2001; Morris & Doak, 2002) and R libraries (Metcalf et al., 2013; Stubben 2007; Stott et al., 2012) have been developed for these purposes. Nonetheless, we trust that the commented R scripts below will be of help to the community. Next to their name, and brief description, the user can find the URL for download. https://github.com/jonesor/compadreDB/tree/master/Scripts - COMPADRE_Update_Taxonomy_TPL.R: script to update the taxonomy with the names used by the authors (see Table 1, SpeciesAuthor variable) based on the R library Taxonstand (http://cran.rproject.org/web/packages/Taxonstand/index.html). - subsettingCOMPADRE.R: script to implement basic conditional searches on the matrices, to perform basic MPM manipulations, and to obtain basic demographic output from them based on methodologies developed by some of the coauthors and elsewhere (Cochran & Ellner 1992; Caswell 2001; Metcalf et al., 2013; Stubben 2007; Stott et al., 2012). - COMPADRE_Author_Citations.R: script to generate full citations based on the variable DOI/ISBN (See Table 1) using the R libraries rmetadata (https://github.com/ropensci/rmetadata), ropensci (http://ropensci.org) 7 and rplos (https://github.com/ropensci/rplos). See also Supporting Information Appendix S4. 8 Appendix S4. Extended literature used in COMPADRE 3.0 Below we provide the full list of citations used in the information compiled in the first release of COMPADRE (3.0). Users of these materials are strongly encouraged to credit the work of the specific studies by citing the publications whose information they may use. The name “SpeciesAuthor” corresponds to the exact taxonomic name used by the author in the publication, as detailed in Table 1, with a sequential numerical suffix if more than one study exists for the same species (e.g. Rhododendron_ponticum, Rhododendron_ponticum_2). SpeciesAuthor Authors Journal 1 Abies_concolor van Mantgem; Stephenson J Ecol 2 Abies_homolepis Nakashizuka J Veg Sci 3 4 5 6 van Mantgem; Stephenson Kubota Hiura; Fujiwara Westerman; Liebman; J Ecol Eco Research J Veg Sci Weed Sci Abies_magnifica Abies_sachalinensis Abies_sachalinensis_2 Abutilon_theophrasti 9 YearPublication DOI.ISBN 0.1111/j.13652005 2745.2005.01007.x 10.1658/11009233(2007)18[379:VIJSAR]2.0.CO 1991 ;2 0.1111/j.13652005 2745.2005.01007.x 1997 10.1007/BF02523604 1999 10.2307/3237309 2005 10.3719/weed.50.60 7 Acacia_aneura 8 Acacia_bilimekii 9 Acacia_pennatula 10 Acacia_victoriae 11 Acer_amoenum 12 Acer_mono 13 Acer_rufinerve 14 Acer_saccharum 15 Achillea_millefolium Achnatherum_calamagrosti 16 s Menalled; Heggenstaller Rosenberg; Boland; Tiver; Watson Jiménez-Lobato; Valverde Somarriba Internet J Arid Env Agrofor Syst Grice; Westoby; Torpy Tanaka; Shibata; Masaki; Iida; Niiyama; Abe; Kominomi; Nokashizuka Tanaka; Shibata; Masaki; Iida; Niiyama; Abe; Kominomi; Nokashizuka Tanaka; Shibata; Masaki; Iida; Niiyama; Abe; Kominami; Nokashizuka Lin; Augspurger Fréville; Silvertown Austral Ecol None 2006 10.1016/j.jaridenv.2005.07.002 2012 10.1007/s10457-011-9447-7 10.1111/j.14421994 9993.1994.tb01537.x J Veg Sci 2008 10.3170/2007-8-18342 J Veg Sci 2008 10.3170/2007-8-18342 J Veg Sci Forest Ecol Manag Plant Ecol Guardia; Raventos; Caswell J Ecol 2008 10.3170/2007-8-18342 2008 10.1016/j.foreco.2008.02.040 2005 10.1007/s11258-004-0017-1 10.1046/j.13652000 2745.2000.00504.x 10.1890/00129658(2000)081[0694:SSSAAN]2.0 2000 .CO;2 2010 10.1007/s00442-010-1809-8 2003 10.1139/B03-099 http://dx.doi.org/10.1590/S1516 2013 -89132013000100009Ê 17 Aconitum_noveboracense_2 Easterling; Ellner; Dixon 18 Actaea_elata Mayberry; Elle 19 Actaea_spicata Fröborg; Eriksson Bianchini; de Araújo; Green; 20 Actinostemon_concolor Pimenta Ecology Oecologia Can J Bot Braz Arch Biol Technol 10 NA 21 Adenocarpus_gibbsianus 22 Adenophora_lobophylla 23 Adenophora_potaninii Iriondo; Albert; Giménez; Lozano; Escudero Wenhui; Yuangang Wenhui; Yuangang Book J For Res J For Res 24 25 26 27 Cipriotti; Aguiar Ticktin; Nantel Sampaio; Pico; Scarano Griffith; Forseth Appl Veg Sci Biol Cons Am J Bot Ecol Appl Kaneko; Takada; Kawano Jiménez-Valdés; GodínezAlvarez; Caballero; Lira Kiviniemi Plant Spp Biol Hansen; Wilson Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Bullock; White; Prudhomme; Tansey; Perea; Hooftman Pfister; Wang J Appl Ecol Meekins; McCarthy Am Mid Nat Adesmia_volckmanni Aechmea_magdalenae Aechmea_nudicaulis Aeschynomene_virginica 28 Aesculus_turbinata 29 Agave_marmorata 30 Agrimonia_eupatoria 31 Agropyron_cristatum 32 Ailanthus_altissima 33 Ailanthus_altissima_2 34 Alaria _nana 35 Alliaria_petiolata 36 Alliaria_petiolata_2 37 Alliaria_petiolata_3 2009 978-84-8014-746-0 1998 10.1007/BF02856444 1998 10.1007/BF02856444 10.1111/j.16542012 109X.2011.01138.x 2004 10.1016/j.biocon.2004.03.019 2005 10.3732/ajb.92.4.674 2005 10.1890/02-5219 10.1046/j.14421999 1984.1999.00007.x Econ Bot Plant Ecol 2010 10.1007/s12231-010-9117-0 2002 None 10.1111/j.13652006 2664.2006.01145.x Ecology J Ecol Ecology NA Burns; Pardini; Schutzenhofer; Chung; Ecology 11 2013 10.1890/12-1310.1 10.1111/j.13652012 2745.2011.01910.x 2005 10.1890/04-1952 10.1674/00030031(2002)147[0256:EOPDOT]2. 2002 0.CO;2 None 2013 10.1890/12-1310.1 48 Andropogon_brevifolius 49 Andropogon_semiberbis Seidler; Knight Evans; Davis; Raghu; Ragavendran; Landis; Schemske Kawano; Takada; Nakayama; Hiratsuka Kawano; Takada; Nakayama; Hiratsuka Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Nault; Gagnon Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Huenneke; Marks Goldberg; Turner Miriti; Wright; Howe Iriondo; Albert; Giménez; Lozano; Escudero Canales; Trevisan; Silva; Caswell Silva; Raventos; Caswell 50 Androsace_elongata 51 Androsace_vitaliana Dostál Iriondo; Albert; 38 Alliaria_petiolata_4 39 Allium_monanthum 40 Allium_monanthum_2 41 Allium_sativum 42 Allium_tricoccum 43 44 45 46 Allium_vineale Alnus_incana_subsp._rugosa Ambrosia_deltoidea Ambrosia_dumosa 47 Anarrhinum_fruticosum Ecol Appl 2012 10.1890/11-1291.1 Book 1987 None Book 1987 None Ecology J Ecol 2013 10.1890/12-1310.1 1993 10.2307/2261228 Ecology Ecology Ecology Ecol Monog 2013 1987 1986 2001 Book 2009 978-84-8014-746-1 Acta Oeco J Ecol 1994 None 1991 10.2307/2260717 10.1111/j.16542007 1103.2007.tb02519.x 2009 978-84-8014-746-2 J Veg Sci Book 12 10.1890/12-1310.1 10.2307/1939207 10.2307/1937693 10.2307/3100033 Giménez; Lozano; Escudero 52 53 54 55 56 Anemone_patens Annamocarya_sinensis Anthericum_liliago Anthericum_ramosum Anthoxanthum_odoratum 57 Anthyllis_vulneraria 58 Anthyllis_vulneraria_2 59 Anthyllis_vulneraria_3 60 Antirrhinum_lopesianum 61 Antirrhinum_subbaeticum 62 63 64 65 66 67 Aquilaria_crassna Aquilaria_malaccensis Aquilaria_microcarpa Aquilegia_chrysantha Aquilegia_sp. Arabis_fecunda Williams; Crone Chien; Zuidema; Nghia Černá; Münzbergová Černá; Münzbergová Fréville; Silvertown Bastrenta; Lebreton; Thompson Bastrenta; Lebreton; Thompson Davison Iriondo; Albert; Giménez; Lozano; Escudero Iriondo; Albert; Giménez; Lozano; Escudero Zhang; Brockelman; Allen Soehartono; Newton Soehartono; Newton Stubben Stubben; Milligan Lesica; Shelly 13 10.1890/00129658(2006)87[3200:TIOIGO]2.0.C O;2 10.1007/s10144-008-0079-3 10.1371/journal.pone.0075563 10.1371/journal.pone.0075563 10.1007/s11258-004-0017-1 Ecology Popul Ecol PLoS ONE PLoS ONE Plant Ecol 2006 2008 2013 2013 2005 J Ecol 1995 10.2307/2261628 J Ecol PhD thesis 1995 10.2307/2261628 2011 None Book 2009 978-84-8014-746-3 Book 2009 978-84-8014-746-4 Biol Cons Biol Cons Biol Cons PhD thesis J Stat Soft Am J Bot 2008 2001 2001 2007 2007 1995 10.1016/j.biocon.2008.04.015 10.1016/S0006-3207(00)00089-6 10.1016/S0006-3207(00)00089-6 None None 10.2307/2445615 68 Araucaria_araucana Bekessy; Newton; Fox; Lara et al. Book 69 Araucaria_cunninghamii Enright; Ogden Aust J Ecol 70 Araucaria_hunsteinii Aust J Ecol 76 Arenaria_bolosii Enright Rigg; Enright; Jaffré; Perry Enright; Miller; Perry; Goldblum; Jaffré Rautiainen; Laine; Aikio; Aspi; Siira; Hyvärinen Koop; Horvitz Pascarella; Horvitz Iriondo; Albert; Giménez; Lozano; Escudero 77 Arenaria_serpyllifolia 78 Argyroxiphium_sandwicense Dostál Forsyth J Veg Sci Oecologia 79 Arisaema_serratum 80 Arisaema_triphyllum 81 Aristida_bipartita Kinoshita Bierzychudek O'Connor Lefebvre; ChandlerMortimer Plant Spp Biol Ecol Monog J Appl Ecol 2009 978-84-8014-746-5 10.1658/11009233(2007)18[91:PDOAIP]2.0.CO 2007 ;2 2003 10.1007/s00442-003-1295-3 10.1111/j.14421987 1984.1987.tb00030.x 1982 10.2307/2937350 1993 10.2307/2404276 J Appl Ecol 1984 10.2307/2403051 71 Araucaria_laubenfelsii 72 Araucaria_muelleri 73 Arctophila_fulva_var._pendulina 74 Ardisia_elliptica 75 Ardisia_escallonioides 82 Armeria_maritima 14 Biotrop Aust Ecol Appl Veg Sci Ecology Ecology Book 2004 None 10.1111/j.14421979 9993.1979.tb01195.x 10.1111/j.14421982 9993.1982.tb01304.x 10.1111/j.17442010 7429.2009.00615.x 2014 10.1111/aec.12045 10.1111/j.16542004 109X.2004.tb00613.x 2005 10.1890/04-1483 1998 10.2307/176952 83 Armeria_merinoi Iriondo; Albert; Giménez; Lozano; Escudero Book 84 Arnica_angustifolia Jäkäläniemi Env and Exp Bot 85 Asarum_canadense 86 Asclepias_meadii 87 Aspasia_principissa Damman; Cain Bell; Bowles; McEachern Zotz; Schmidt Bucharová; Münzbergová; Tájek Bucharová; Münzbergová; Tájek Bremer; Jongejans Münzbergová Iriondo; Albert; Giménez; Lozano; Escudero Nicolè Maschinski; Frye; Rutman Wall; Hoffmann; Wentworth; Gray; Hohmann Martin; Meinke Lesica Crone; Lesica J Ecol Book Biol Cons 2009 978-84-8014-746-6 10.1016/j.envexpbot.2011.03.01 2011 3 10.1046/j.13651998 2745.1998.00242.x 2003 978-3-642-07869-9 2006 10.1016/j.biocon.2005.07.022 Am J Bot 2010 10.3732/ajb.0900351 Am J Bot Popul Ecol Am J Bot 2010 10.3732/ajb.0900351 2010 10.1007/s10144-009-0143-7 2007 10.1093/aob/mcm204 Book Cons Biol 2009 978-84-8014-746-7 None 10.1046/j.15231997 1739.1997.96159.x Plant Ecol Popul Ecol Great Bas Nat Ecology 2012 2012 1995 2004 88 Asplenium_adulterinum 89 Asplenium_cuneifolium 90 Asplenium_scolopendrium 91 Aster_amellus 92 Aster_pyrenaeus 93 Astragalus_alopecurus Astragalus_cremnophylax_var._cre 94 mnophylax 95 96 97 98 Astragalus_michauxii Astragalus_peckii Astragalus_scaphoides Astragalus_scaphoides_2 15 NA 10.1007/s11258-012-0068-7 10.1007/s10144-012-0318-5 10.2307/2445615 10.1890/03-0256 99 Astragalus_tremolsianus Iriondo; Albert; Giménez; Lozano; Escudero Ecology Biodivers Conserv 2010 10.1007/s10531-010-9846-5 Ecology 1984 10.2307/2259545 Oecologia 2008 10.1007/s00442-008-0980-7 104 Atriplex_canescens Kaye; Pyke Portela; Bruna; dos Santos Pinero; Martinez; Sarukhan Verhulst; Montaña; Mandujano; Franco Verhulst; Montaña; Mandujano; Franco 2009 978-84-8014-746-8 10.1890/00129658(2003)084[1464:TEOSTO]2. 2003 0.CO;2 Oecologia 105 Atriplex_vesicaria Hunt J Appl Ecol 106 Attalea_humilis Biodivers Conserv Glob Change Biol 10.1111/j.13652010 2486.2010.02292.x 108 Avicennia_germinans 109 Avicennia_marina_2 Souza; Martins Godfree; Lepschi; Rside; Bolger; Robertson; Marshall; Carnegie López-Hoffman; Ackerly; Anten; Denoyer;Ramos Clarke 2008 10.1007/s00442-008-0980-7 10.1046/j.13652001 2664.2001.00586.x 10.1023/B:BIOC.0000029326.446 2004 47.7f 110 Balsamorhiza_sagittata Crone; Marler; Pearson J Appl Ecol 100 Astragalus_tyghensis 101 Astrocaryum_aculeatissimum 102 Astrocaryum_mexicanum 103 Atriplex_acanthocarpa 107 Austrostipa_aristiglumis Book 16 J Ecol Hydrobiol 10.1111/j.13652007 2745.2007.01298.x 1995 10.1007/978-94-011-0289-6_11 10.1111/j.13652009 2664.2009.01635.x 111 Banksia_ericifolia 112 Bertholletia_excelsa 113 Betula_nana 114 Betula_pubescens_subsp._tortuosa 115 Boltonia_decurrens 116 Borassus_aethiopum 117 Borderea_chouardii 118 119 120 121 Boswellia_papyrifera Bothriochloa_insculpta Bothriochloa_ischaemum Bouteloua_rigidiseta 122 123 124 125 126 127 128 Brassica_insularis Brassica_napus_2 Braya_fernaldii Braya_longii Bromus_tectorum Brosimum_alicastrum Bursera_glabrifolia Bradstock; O'Connell Zuidema; Boot Ebert; Ebert Lehtilä; Tuomi; Sulkinoja Smith; Caswell; MettlerCherry Barot; Gignoux; Vuattoux Garcia Groenendijk; Eshete; Sterck; Zuidema; Bongers O'Connor Gabbard Fowler; Overath; Pease Noel; Maurice; Mignot; Glémin; Carbonell; Justy; Guyot; Olivieri; Petit Aust J Ecol J Trop Ecol Vegetatio 10.1111/j.14421988 9993.1988.tb00999.x 2002 10.1017/S0266467402002018 1989 10.1007/BF00042253 Ecology 1994 10.2307/1939418 Ecol Appl 2005 10.1890/04-0434 J Trop Ecol Cons Biol 2000 10.1017/S0266467400001620 2003 10.1016/S0006-3207(01)00113-6 10.1111/j.13652664.2011.02078.x 10.2307/2404276 None 10.1890/05-1197 J Appl Ecol J Appl Ecol PhD thesis Ecology 2012 1993 2003 2006 Cons Genet 2010 10.1007/s10592-010-0056-1 NA Squires Squires Griffith Peters Hernández-Apolinor; PhD thesis PhD thesis Ecology PhD thesis Forest Ecol Manag 17 2010 2010 2010 1989 2006 None None 10.1890/08-1446.1 None 10.1016/j.foreco.2005.10.072 129 130 131 132 Calamagrostis_canescens Calamus_platyacanthus Calamus_rhabdocladus Calathea_marantifolia 133 134 135 136 Calathea_micans Calathea_ovandensis Callitris_intratropica Calluna_vulgaris 137 138 139 140 141 142 143 144 145 Calocedrus_decurrens Calocedrus_macrolepis Calochortus_albus Calochortus_lyallii Calochortus_lyallii_2 Calochortus_macrocarpus Calochortus_obispoensis Calochortus_pulchellus Calochortus_tiburonensis 146 Camellia_japonica 147 Camellia_japonica_2 148 Campanula_americana 149 Carduus_nutans Valverde; Purata Logofet; Ulanova; Klochkova; Demidova Binh Binh Matlaga Le Corff; Horvitz Horvitz; Schemske Price; Bowman Scandrett; Gimmingham van Mantgem; Stephenson Chien; Zuidema; Nghia Fiedler Miller; Antos; Allen Miller; Antos; Allen Miller; Antos; Allen Fiedler Fiedler Fiedler Shimatani; Kubota; Araki; Aikawa; Manobe Ecol Model PhD thesis PhD thesis PhD thesis 2006 2009 2009 2008 Ecol Model Ecol Monog J Biogeog Vegetatio 2005 1995 1994 1989 J Ecol Popul Ecol J Ecol PhD thesis PhD thesis PhD thesis J Ecol J Ecol J Ecol 2005 2008 1987 2004 2004 2004 1987 1987 1987 Plant Spp Biol 2007 NA Wardle Jongejans; Sheppard; Shea 18 Ecology 1998 J Appl Ecol 2006 10.1016/j.ecolmodel.2005.07.02 0 None None None 10.1016/j.ecolmodel.2005.05.00 9 10.2307/2937136 10.2307/2846032 10.1007/BF00036515 10.1111/j.13652745.2005.01007.x 10.1007/s10144-008-0079-3 10.2307/2260308 None None None 10.2307/2260308 10.2307/2260308 10.2307/2260308 10.1111/j.14421984.2007.00190.x None 10.2307/176842 10.1111/j.13652664.2006.01228.x 150 Carduus_nutans_2 151 Carduus_nutans_3 152 Carex_aquatilis_subsp._stans 153 Carex_bigelowii 154 Carex_humilis 155 Carex_membranacea 156 157 158 159 Carlina_vulgaris Carnegiea_gigantea Carum_carvi Cassia_nemophila 160 Catopsis_compacta 161 Catopsis_sessiliflora 162 Cecropia_obtusifolia 163 Centaurea_corymbosa 164 Centaurea_horrida Shea; Kelly Shea; Kelly; Sheppard; Woodburn Tolvanen; Schroderus; Henry Carlsson; Callaghan Wikberg; Svensson Tolvanen; Schroderus; Henry Lofgren; Eriksson; Lehtila Steenbergh; Lowe Kiviniemi Silander del Castillo; TrujilloArgueta; Rivera-Garcia; Gómez-Ocampo; Mondragón-Chaparro Winkler; Hülber; Hietz Alvarez-Buylla Fréville; Colas; Riba; Caswell; Mignot; Imbert; Olivieri Pisanu; Farris; Filigheddu; García 19 Ecol Appl 10.1890/10510761(1998)008[0824:EBAIWM]2. 1998 0.CO;2 Ecology 2005 10.1890/05-0195 J Veg Sci Oikos Plant Ecol 2001 10.2307/3236906 1991 10.2307/3544870 2006 10.1007/s11258-005-9006-2 J Veg Sci 2001 10.2307/3236906 Ann Bot Fen Ecology Popul Ecol Oecologia 2000 1969 2009 1983 Ecol and Evol Bas and Appl Ecol Am Nat 2013 10.1002/ece3.765 2007 10.1016/j.baae.2006.05.003 1994 10.1086/285599 Ecology 2004 10.1890/03-0119 Plant Ecol 2012 10.1007/s11258-012-0110-9 None 10.2307/1933696 10.1007/s10144-008-0096-2 10.1007/BF00379524 165 Centaurea_jacea Jongejans; de Kroon J Ecol 166 Centaurea_maculosa Emery; Gross Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Pérez-Farrera; Vovides; Octavio-Aguilar; González-Astorga; CruzRodriguez; HernandezJonapa; VillalobosMendez Martínez-Meléndez Magda; Duru; Theau Liu; Menges; QuintanaAscencio Valverde; HernándezApolinor; MendozaAmarom Endress; Gorchov; Robert; Noble Berry; Gorchov; Endress; Stevens J Appl Ecol 10.1111/j.13652005 2745.2005.01003.x 10.1111/j.13652005 2664.2004.00990.x Ecology 2013 10.1890/12-1310.1 Ecology 2013 10.1890/12-1310.1 Plant Ecol BSc thesis Weed Sci 2006 10.1007/s11258-006-9135-2 2012 None 2004 10.1614/P2202-067 Ecol Appl 2005 10.1890/03-5382 J Sust Forestry 2006 10.1300/J091v23n01_05 Ecol Appl 2004 10.1890/02-5365 Ecology 2008 10.1007/s10144-007-0067-z 167 Cerastium_fontanum 168 Cerastium_pumilum 169 Ceratozamia_mirandae 170 Ceratozamia_norstogii 171 Chaerophyllum_aureum 172 Chamaecrista_keyensis 173 Chamaedorea_elegans 174 Chamaedorea_radicalis 175 Chamaedorea_radicalis_2 20 176 Chamaelirium_luteum 177 Cheirolophus_metlesicsii 178 Chlorocardium_rodiei 179 Choerospodnias_axillaris 180 Cimicifuga_elata 181 Cimicifuga_rubifolia 182 Cirsium_acaule 183 Cirsium_acaule_2 184 Cirsium_arvense 185 186 187 188 Cirsium_dissectum Cirsium_palustre Cirsium_pannonicum Cirsium_perplexans Meagher; Antonovics Iriondo; Albert; Giménez; Lozano; Escudero ter Steege; Boot; Brouwer; Hammond; Vanderhout; Jetten; Khan; Polak; Raaimakers; Zagt Brodie; Helmy; Brockelman; Maron Ecology 1982 10.2307/1940111 Book 2009 978-84-8014-746-9 Ecol Appl 1995 10.2307/2269341 Ecol Appl Kaye; Pyke Cook; Lyons Münzbergová Bullock; White; Prudhomme; Tansey; Perea; Hooftman Ecology PhD thesis Am J Bot 2009 10.1890/08-0111.1 10.1890/00129658(2003)084[1464:TEOSTO]2. 2003 0.CO;2 1993 None 2005 10.3732/ajb.92.12.1987 Ecol Appl 10.1111/j.13652012 2745.2011.01910.x 10.1890/10510761(2006)016[2399:DMISOB]2. 2006 0.CO;2 Plant Ecol Acta Oeco Am J Bot PhD thesis 2008 2008 2005 2005 J Ecol Davis; Landis; Nuzzo; Blossey; Gerber; Hinz Jongejans; de Vere; de Kroon Ramula Münzbergová Dodge 21 10.1007/s11258-008-9397-y 10.1016/j.actao.2007.11.005 10.3732/ajb.92.12.1987 None 189 Cirsium_perplexans_2 193 194 195 196 Cirsium_pitcheri_4 Cirsium_pitcheri_5 Cirsium_scariosum Cirsium_scariosum_2 Dodge Louda; Rand; Arnett; McClay; Shea; McEachern Bell; Bowles; McEachern Bell; Bowles; McEachern Ellis; Williams; Lesica; Bell; Bierzychudek; Bowles; Crone; Doak; Ehrlen; Ellis-Adam; McEachern; Ganesan; Latham; Luijten; Kaye; Knight; Menges; Morris; Den Nijs; Oostermeijer; Quintana-Ascencio; Shelly; Stanley; Thorpe; Ticktin; Valverde; Weekley Ellis Dodge Dodge 197 198 199 200 201 Cirsium_undulatum Cirsium_undulatum_2 Cirsium_undulatum_var._tracyi Cirsium_undulatum_var._tracyi_2 Cirsium_vulgare Dalgleish; Koons; Adler Adler; Byrne; Leiker Dodge Dodge Bullock; Hill; Silvertown 190 Cirsium_pitcheri 191 Cirsium_pitcheri_2 192 Cirsium_pitcheri_3 22 PhD thesis 2005 None Ecol Appl Book Book 2005 10.1890/03-5212 2003 None 2003 None Ecology Ecology PhD thesis PhD thesis 2012 2012 2005 2005 J Ecol Glob Change Biol PhD thesis PhD thesis J Ecol 2010 2013 2005 2005 1994 10.1890/11-1052.1 10.1890/11-1052.1 None None 10.1111/j.13652745.2009.01585.x 10.1111/gcb.12168 None None 10.2307/2261390 202 Cirsium_vulgare_2 203 204 205 206 207 208 209 210 211 212 213 214 215 Cirsium_vulgare_3 Cleistes_varicata_var._bifaria Cleistes_varicata_var._divaricata Cleome_droserifolia Cleome_droserifolia_2 Clidemia_hirta Clintonia_borealis Coccothrinax_readii Cochlearia_bavarica Cochlearia_pyrenaica Collinsia_verna Commelina_benghalensis Commelina_bracteosa 216 Conyza_canadensis 217 Corallorhiza_trifida 218 Cornus_florida 219 Coryphanta_robbinsorum 220 Coryphanta_werdermannii Tenhumberg; Louda; Eckberg; Takahashi Forcella; Wood Wells; Willems Wells; Willems Wells; Willems Hegazy DeWalt Pitelka; Hansen; Ashmun Olmsted; Alvarez-Buylla Abs Abs Kalisz; McPeek Burns Burns Bullock; White; Prudhomme; Tansey; Perea; Hooftman Iriondo; Albert; Giménez; Lozano; Escudero Vejdani Schmalzel; Reichenbacher; Rutman Portilla-Alonso; Martorell 23 10.1111/j.13652664.2007.01427.x 10.1111/j.13653180.1986.tb00697.x 10.2307/2261246 10.2307/2261246 10.1016/0006-3207(93)90656-L None 10.1007/s10530-005-5277-8 10.2307/2259776 10.2307/1942038 10.1007/BF02803075 10.1007/BF02803075 10.2307/1940182 10.1890/07-0568.1 10.1890/07-0568.1 J Appl Ecol 2008 Weed Res Book Book Book J Arid Env Biol Inv J Ecol Ecol Appl Folia Geobot Folia Geobot Ecology Ecol Appl Ecol Appl 1986 1991 1991 1991 1990 2006 1985 1995 1999 1999 1992 2008 2008 J Ecol 10.1111/j.13652012 2745.2011.01910.x Book PhD thesis 2009 978-84-8014-746-10 2006 None Madrono 1995 None J Arid Env 2011 10.1016/j.jaridenv.2011.01.015 10.1111/j.13652745.2007.01350.x 10.1111/j.14698137.1984.tb03596.x 10.1111/j.14421984.1993.tb00062.x 10.1111/j.13652745.2005.01010.x 10.1111/j.15231739.2010.01466.x 10.1111/j.15231739.2010.01466.x 221 Cryptantha_flava Lucas; Casper; Forseth J Ecol 2008 222 Cynoglossum_officinale New Phyto 1984 Plant Spp Biol 1993 224 Cypripedium_calceolus Boorman; Fuller Cipollini; Whigham; O'Neill Nicolè; Brzosko; TillBottraud J Ecol 2005 225 Cypripedium_calceolus_2 Garcı́a; Goñi; Guzmán Cons Biol 2010 226 Cypripedium_calceolus_3 Garcia; Goñi; Guzmán Thorpe; Stanley; Kayne; Latham Zhongjian; Rao Wenhui; Liqiang; Yuting Cons Biol 2010 Report 2011 None Acta Ecol Sinica Neubert; Parker Chien; Zuidema; Nghia Sletvold; Øien; Moen Sletvold; Dahlgren; Øien; Moen; Ehrlén Moloney Risk Anal Popul Ecol Biol Cons 2008 10.1016/S1872-2032(08)60021-9 10.1111/j.02722004 4332.2004.00481.x 2008 10.1007/s10144-008-0079-3 2010 10.1016/j.biocon.2009.12.017 Verkaar; Schenkeveld Shimatani; Kubota; Araki; Aikawa; Manobe New Phyto 223 Cynoglossum_virginianum 227 Cypripedium_fasciculatum 228 Cypripedium_lentiginosum 229 Cytisus_scoparius 230 Dacrydium_elatum 231 Dactylorhiza_lapponica 232 Dactylorhiza_lapponica_2 233 Danthonia_sericea 234 Daucus_carota 235 Dendropanax_trifidus Glob Change Biol Ecology Plant Spp Biol 24 2013 10.1111/gcb.12167 1988 10.3354/meps045001 10.1111/j.14691984 8137.1984.tb04155.x 10.1111/j.14422007 1984.2007.00190.x 236 Dicerandra_frutescens 237 Dicorynia_guianensis 238 Dicymbe_altsonii 239 Digitalis_purpurea 240 Digitalis_purpurea_2 241 Digitaria_eriantha 242 Dioon_caputoi 243 Dioon_edule 244 Dioon_merolae 245 Dioon_sonorense 246 Dioon_spinulosum 247 Dipsacus_sylvestris_2 248 Disporum_sessile 249 Disporum_sessile_2 Menges; QuintanaAscencio; Weekley; Gaoue Picard; Mortier; Chagneau Zagt; Boot Baalen; Prins Biol Cons J Ecol J Appl Ecol PhD thesis 2006 10.1016/j.biocon.2005.08.002 10.1016/j.ecolmodel.2010.06.01 2010 0 1997 None 1983 10.1007/BF00384546 10.1111/j.13652007 2745.2007.01287.x 1993 10.2307/2404276 2009 None Bot J Lin Soc 2008 None Forest Ecol Manag 2011 10.1016/j.foreco.2010.10.028 Biol Cons MSc thesis Ecology 2011 10.1016/j.biocon.2010.08.007 2008 None 1977 10.2307/1936930 Book 1987 None Book 1987 None Ecol Model PhD thesis Oecologia Sletvold; Rydgren O'Connor Cabrera-Toledo Octavio-Aguilar; Gonzalez-Astorga; Vovides Lázaro-Zermeño; González -Espinosa; Mendoza; MartínezRamos; QuintanaAscencio Álvarez-Yépiz Dovčiak; Búrquez Castaneda Werner; Caswell Kawano; Takada; Nakayama; Hiratsuka Kawano; Takada; Nakayama; Hiratsuka 25 250 Disporum_smilacinum 251 Disporum_smilacinum_2 252 Dodonaea_angustifolia 253 254 255 256 Dorycnium_spectabile Dracaena_cinnabari Duguetia_neglecta Echeveria_longissima 257 Echinacea_angustifolia 258 Echinacea_angustifolia_2 259 Echinocactus_platyacanthus 260 261 262 263 264 Echinospartum_algibicum Echium_vulgare Encephalartos_cycadifolius Encephalartos_villosus Encyclia_tampensis 265 Entandrophragma_cylindricum 266 Eperua_falcata Kawano; Takada; Nakayama; Hiratsuka Kawano; Takada; Nakayama; Hiratsuka Bekele Iriondo; Albert; Giménez; Lozano; Escudero Habrova; Cermak; Pavlis Zagt; Boot Martorell Dalgleish; Koons; Adler Hurlburt Jiménez-Sierra; Mandujano; Eguiarte Iriondo; Albert; Giménez; Lozano; Escudero Klemow; Raynal Raimondo; Donoldson Raimondo; Donoldson Larson Picard; Yalibanda; Namkosserena; Baya Chagneau; Mortier; Picard Book 1987 None Book PhD thesis 1987 None 2000 None Book Biol Cons PhD thesis Popul Ecol 2009 2009 1997 2007 J Ecol PhD thesis 978-84-8014-746-12 10.1016/j.biocon.2008.12.022 None 10.1007/s10144-012-0307-8 10.1111/j.13652010 2745.2009.01585.x 1999 None Biol Cons 2007 10.1016/j.biocon.2006.10.038 Book J Ecol Biol Cons Biol Cons Selbyana 2009 1985 2003 2003 1992 Forest Ecol Manag 2008 10.1016/j.foreco.2008.02.041 10.1111/j.14672009 9876.2008.00657.x J Roy Stat Soc 26 978-84-8014-746-13 10.2307/2259775 10.1016/S0006-3207(02)00303-8 10.1016/S0006-3207(02)00303-8 None 267 Epilobium_latifolium 268 269 270 271 Epipactis_atrorubens Eremophila_forrestii Eremophila_maitlandii Eremosparton_songoricum 272 Eremospatha_macrocarpa 273 Erica_ciliaris 274 Erigeron_kachinensis Eriogonum_longifolium_var._gnaph 275 alifolium_2 Eriophorum_angustifolium_subsp._ 276 triste 277 Erodium_paularense 278 Eryngium_alpinum 279 Eryngium_cuneifolium 280 Eryngium_maritimum Doak Jäkäläniemi; Crone; Närhi; Tuomi Watson; Westoby; Holm Watson; Westoby; Holm Zhang; Wang; Shi Kouassi; Barot; Gignoux; Bi Bullock; White; Prudhomme; Tansey; Perea; Hooftman Allphin; Harper Satterthwaite; Menges; Quintana-Ascencio Tolvanen; Schroderus; Henry Iriondo; Albert; Giménez; Lozano; Escudero Andrello; Bizoux; Barbet-Massin; Gaudeul; Nicolè; Till-Bottraud Menges; QuintanaAscencio Curie; Stabbetorp; Nordal 27 Ecology 1992 10.2307/1941457 Ecology J Ecol J Ecol Chin J Plant Ecol 2011 1997 1997 2009 J Trop Ecol 2008 10.1017/S0266467408005312 10.1890/10-1957.1 10.2307/2960604 10.2307/2960604 None Ecol Appl 10.1111/j.13652012 2745.2011.01910.x 1997 10.2307/2426659 10.1890/10510761(2002)012[1672:ASBPVI]2.0. 2002 CO;2 J Veg Sci 2001 10.2307/3236906 Book 2009 978-84-8014-746-14 Biol Cons 2012 10.1016/j.biocon.2011.12.012 Ecol Monog 2004 10.1890/03-4029 Nord J Bot 2007 None J Ecol Am Mid Nat 286 Espeletia_timotensis Kawano; Takada; Nakayama; Hiratsuka Kawano; Takada; Nakayama; Hiratsuka Takada; Nakayama; Kawano Ortega-Baes Silva; Trevisan; Estrada; Monosterio Silva; Trevisan; Estrada; Monosterio 287 Eupatorium_perfoliatum Byers; Meagher Ecol Appl 288 Eupatorium_resinosum Byers; Meagher Iriondo; Albert; Giménez; Lozano; Escudero Ecol Appl 281 Erythronium_japonicum 282 Erythronium_japonicum_2 283 Erythronium_japonicum_3 284 Escontria_chiotilla 285 Espeletia_spicata 289 Euphorbia_fontqueriana 290 Euterpe_edulis 291 Euterpe_edulis_2 292 Euterpe_oleracea 293 Euterpe_precatoria Book 1987 None Book 1987 None 10.1111/j.14421998 1984.1998.tb00253.x 2001 None 10.1046/j.13652000 2699.2000.00187.x 10.1046/j.13652000 2699.2000.00187.x 10.1890/10510761(1997)007[0519:ACODCI]2.0 1997 .CO;2 10.1890/10510761(1997)007[0519:ACODCI]2.0 1997 .CO;2 Plant Spp Biol PhD thesis Global Ecol Biogeogr Global Ecol Biogeogr Book Silva-Matos; Freckleton; Watkinson Freckleton; Matos; Bovi; Watkinson Arango; Duque; Muñoz Zuidema 28 Ecology 2009 978-84-8014-746-15 10.1890/00129658(1999)080[2635:TRODDI]2.0 1999 .CO;2 J Appl Ecol Int J Trop Biol Ecol Bolivia 2003 None 2010 None 2000 None 294 Fabiana_imbricata 295 Fagus_crenata 296 Fagus_grandifolia 297 Fagus_sylvatica 298 Festuca_gracillima 299 Fragaria_vesca 300 Frasera_speciosa 301 Fritillaria_camtschatcensis 302 Fritillaria_meleagris 303 Fucus_distichus 304 Fumana_procumbens 305 Garcinia_lucida 306 Gardenia_actinocarpa Gaura_neomexicana_subsp._colora 307 densis 308 Gelidium_sesquipedale 309 Gentiana_pneumonanthe Ruete Nakashizuka Batista; Platt; Macchiavelli López; Ortuño; Martín; Fullano Oliva; Collantes; Humano Schulze; Rufener; Erharft; Stoll Taylor; Inouye Shimizu; Hatanaka; Zentoh; Yashima; Kinoshita; Watano; Shimizu BSc thesis J Veg Sci 2006 None 1991 None Ecology 1998 10.2307/176863 Ann For Sci Rang Ecol Manag 2007 10.1051/forest:2007037 10.2111/15515028(2005)58[466:DOGTGP]2.0. 2005 CO;2 Popul Ecol Ecology 2012 10.1007/s10144-012-0338-1 1985 10.2307/1940400 Zhang; Hytteborn Ang; de Wreede Bengtsson Guedje; Zuidema; During; Foahom; Lejoly Osunkoya Hol Ecol Mar Ecol Prog Ser J Ecol 10.1046/j.14401998 1703.1998.00245.x 10.1111/j.16001985 0587.1985.tb01174.x 1993 10.3354/meps093253 1993 10.2307/2261672 Forest Ecol Manag Biol Cons 2007 10.1016/j.foreco.2006.09.029 2003 10.1016/S0006-3207(02)00417-2 Floyd; Ranker Santos; Nyman Oostermeijer; Brugman; Int J Plant Sci J Appl Phyco J Ecol 1998 10.1086/297607 1998 None 1996 10.2307/2261351 Ecol Research 29 310 Gentianella_campestris de Boer; den Nijs Lennartsson; Oostermeijer J Ecol 2001 311 Geonoma_brevispatha Souza; Martins Aust Ecol 2006 Ecol Appl Plant Ecol 2007 2002 Forest Ecol Manag J Trop Ecol 2005 10.1016/j.foreco.2005.02.052 2010 10.1017/S0266467409990599 Int J Plant Sci 2007 10.1086/512040 10.1111/j.13652006 2745.2006.01134.x 2002 None 10.1111/j.13652008 2745.2008.01375.x 1991 None 2008 None 10.1111/j.14422009 1984.2009.00230.x 2010 10.1890/09-0480.1 10.1890/00129658(2003)084[1464:TEOSTO]2. 2003 0.CO;2 312 Geonoma_deversa 313 Geonoma_macrostachys 314 Geonoma_orbignyana 315 Geonoma_schottiana 316 Geranium_sylvaticum 317 Geum_reptans 318 Geum_rivale Zuidema; de Kroon; Werger Svenning Rodríguez-Buriticá; Orjuela; Galeano Sampaio; Scariot Ramula; Toivonen; Mutikainen J Ecol Plant Ecol 319 Gilia_tenuiflora_subsp._hoffmannii 320 Grias_peruviana 321 Guaiacum_sanctum Weppler; Stoll; Stocklin Kiviniemi Levine; McEachern; Cowan Peters CITES 322 Guarianthe_aurantiaca 323 Guettarda_viburnoides Mondragon Loayza; Knight Plant Spp Biol Ecology 324 Haplopappus_radiatus Kaye; Pyke Ecology J Ecol Book Plants Committee 30 10.1046/j.13652745.2001.00566.x 10.1111/j.14429993.2006.01650.x 10.1890/10510761(2007)017[0118:TSBPAR]2.0 .CO;2 10.1023/A:1015520116260 325 Harrisia_fragrans Rae; Ebert Int J Plant Sci 326 Hedyotis_nigricans 327 Helenium_virginicum J Ecol Biol Cons Biol Cons 2007 10.1016/j.biocon.2007.01.010 Book 2009 978-84-8014-746-16 330 Helianthemum_teneriffae Dalgleish; Koons; Adler Adams; Marsh; Knox Marrero-Gómez; Oostermeijer; CarquéÁlamo; Bañares-Baudet Iriondo; Albert; Giménez; Lozano; Escudero Iriondo; Albert; Giménez; Lozano; Escudero 2002 10.1086/339719 10.1111/j.13652010 2745.2009.01585.x 2003 10.1016/j.biocon.2005.02.001 Book 331 Helianthus_divaricatus Nantel; Gagnon Ecology 332 Heliconia_acuminata Bruna Schleuning; Huamán; Matthies Nehrbass; Winkler; Pergl; Perglová; Pyšek Wells; Rothery; Cox; Bamford O'Connor Thomas; Dale Vega; Montaña Ecology 2009 978-84-8014-746-17 10.1046/j.13651999 2745.1999.00388.x 10.1890/00129658(2003)084[0932:APPIFH]2.0. 2003 CO;2 10.1111/j.13652008 2745.2008.01416.x 328 Helianthemum_juliae 329 Helianthemum_polygonoides 333 Heliconia_metallica 334 Heracleum_mantegazzianum 335 336 337 338 Herminium_monorchis Heteropogon_contortus Hieracium_floribundum Hilaria_mutica J Ecol Pers Plant Ecol Evol Syst Bot J Lin Soc J Appl Ecol Can J Bot Plant Ecol 31 2006 10.1016/j.ppees.2005.11.001 10.1111/j.10951998 8339.1998.tb02514.x 1993 10.2307/2404276 1975 10.1139/b75-331 2004 10.1023/B:VEGE.0000048094.21 J Appl Ecol 994.74 10.1111/j.13652006 2664.2006.01148.x J Ecol 10.1111/j.13652012 2745.2011.01910.x 343 Hudsonia_montana Pfeifer; Wiegand; Heinrich; Jetschke Bullock; White; Prudhomme; Tansey; Perea; Hooftman Satterthwaite; Holl; Hayes; Barber Kaye; Benfield Gross; Lockwood; Frost; Morris 344 345 346 347 Hara; Kanno; Hirabuki; Takehara Christensen; Gorchov Christensen; Gorchov Sinclair J Veg Sci Plant Ecol Plant Ecol PhD thesis 348 Hylocomium_splendens 349 Hymenoxys_herbacea Okland Campbell; Husband Oikos Heredity 350 Hyparrhenia_diplandra Garnier; Dajoz Quintana-Ascencio; Menges; Weekley Ellis; Williams; Lesica; Bell; Bierzychudek; J Ecol 339 Himantoglossum_hircinum 340 Himantoglossum_hircinum_2 341 Holocarpha_macradenia 342 Horkelia_congesta Hydrangea_paniculata Hydrastis_canadensis Hydrastis_canadensis_2 Hydrastis_canadensis_3 351 Hypericum_cumulicola 352 Hypericum_cumulicola_2 32 Biol Cons Report Cons Biol 2007 10.1016/j.biocon.2006.09.018 2004 None 10.1111/j.15231998 1739.1998.97285.x 10.1658/11009233(2004)015[0475:PDOFUS]2. 2004 0.CO;2 2010 10.1007/s11258-010-9749-2 2010 10.1007/s11258-010-9749-2 2002 None 10.1034/j.16002000 0706.2000.880301.x 2005 10.1038/sj.hdy.6800653 10.1890/00129658(2001)082[1720:ESOALV]2.0 2001 .CO;2 10.1046/j.15232003 1739.2003.01431.x Ecology 2012 10.1890/11-1052.1 Cons Biol Bowles; Crone; Doak; Ehrlén; Ellis-Adam; McEachern; Ganesan; Latham; Luijten; Kaye; Knight; Menges; Morris; Den Nijs; Oostermeijer; Quintana-Ascencio; Shelly; Stanley; Thorpe; Ticktin; Valverde; Weekley 10.1111/j.13652745.2005.01003.x 10.1086/518178 10.2307/2426148 10.1111/j.2007.00301299.15705.x 10.1086/510758 10.2307/2388974 353 Hypochaeris_radicata 354 Impatiens_capensis 355 Ipomoea_leptophylla Jongejans; de Kroon Steets; Knight; Ashman Keeler J Ecol Am Nat Am Mid Nat 2005 2007 1991 356 Ipomopsis_aggregata 357 Ipomopsis_tenuituba 358 Iriartea_deltoidea Brody; Price; Waser Campbell; Waser Pinard Ang; de Wreede; Shaughnessy; Dyck Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Pathikonda; Ackleh; Hasenstein; Mopper Farah; Tanaka; West Couralet; Sass-Klaassen; Oikos Am Nat Biotrop 2007 2007 1993 Hydrobiol 1990 10.1007/978-94-009-2049-1_27 Ecology 2013 10.1890/12-1310.1 10.1111/j.15232009 1739.2008.01073.x 1988 10.3719/weed.33.Suppl_103 2005 10.1016/j.foreco.2005.05.065 359 Iridaea_splendens 360 Iris_germanica 361 Iris_hexagona 362 Isatis_tinctoria 363 Juniperus_procera 33 Cons Biol Weed Sci Forest Ecol Manag 364 Jurinea_fontqueri 365 Khaya_senegalensis 366 Khaya_senegalensis_2 367 Koeleria_macrantha 368 Kosteletzkya_pentacarpos 369 Kunkeliella_subsucculenta 370 Laccosperma_secundiflorum 371 Lactuca_serriola 372 Lactuca_serriola_2 373 Lactuca_virosa 374 Laminaria_digitata 375 Lantana_camara Sterck; Bekele; Zuidema Iriondo; Albert; Giménez; Lozano; Escudero Gaoue; Ticktin Gaoue; Horvitz; Ticktin; Steiner; Tuljapurkar Dalgleish; Kula; Hartnett; Sandercook Cons Biol 2009 978-84-8014-746-18 10.1111/j.15232010 1739.2009.01345.x J Ecol 2013 10.1111/1365-2745.12140 Am J Bot Pino; Picó; Roa Iriondo; Albert; Giménez; Lozano; Escudero Kouassi; Barot; Gignoux; Bi Prevéy; Germino; Huntly Bullock; White; Prudhomme; Tansey; Perea; Hooftman Bot J Lin Soc 2008 10.3732/ajb.2007277 10.1111/j.10952007 8339.2007.00628.x Book 2009 978-84-8014-746-19 J Trop Ecol 2008 10.1017/S0266467408005312 Ecol Appl 2010 10.1890/09-0750 Boorman; Fuller Chapman Osunkoya; Perrett; Fernando; Clark; Raghu New Phyto Hydrobiol 10.1111/j.13652012 2745.2011.01910.x 10.1111/j.14691984 8137.1984.tb03596.x 1993 10.1007/978-94-011-1998-6_31 Popul Ecol 2013 10.1007/s10144-013-0364-7 34 Book J Ecol 376 377 378 379 380 381 Laserpitium_longiradium Lathyrus_vernus Lepanthes_eltoroensis Lepanthes_rubripetala Lepanthes_rupestris Lepidium_davisii 382 Leptocoryphium_lanatum 383 Lespedeza_cuneata 384 Lesquerella_ovalifolia 385 Liatris_scariosa 386 Limonium_carolinianum 387 Limonium_delicatulum 388 Limonium_erectum 389 Limonium_geronense 390 Limonium_malacitanum 391 Lindera_benzoin Iriondo; Albert; Giménez; Lozano; Escudero Ehrlen Tremblay; Ackerman Tremblay; Ackerman Tremblay; Ackerman Bernatus Raventos; Segarra; Acevedo Schutzenhofer; Knight Dalgleish; Koons; Adler Ellis Baltzer; Reekie; Hewlin; Taylor; Boates Hegazy Iriondo; Albert; Giménez; Lozano; Escudero Iriondo; Albert; Giménez; Lozano; Escudero Iriondo; Albert; Giménez; Lozano; Escudero Cipollini; Wallace-Senft; 35 Book J Ecol Biol J Linn Soc Biol J Linn Soc Biol J Linn Soc Report 2009 1995 2001 2001 2001 1995 978-84-8014-746-20 None 10.1006/bijl.2000.0485 10.1006/bijl.2000.0485 10.1006/bijl.2000.0485 None 10.1016/j.ecolmodel.2003.12.04 4 10.1890/06-1282 10.1111/j.13652745.2009.01585.x 10.1890/11-1052.1 Ecol Model Ecol Appl 2004 2007 J Ecol Ecology 2010 2012 Can J Bot J Appl Ecol 2002 10.1139/b02-070 1992 10.2307/2404462 Book 2009 978-84-8014-746-21 Book 2009 978-84-8014-746-22 Book J Ecol 2009 978-84-8014-746-23 1994 10.2307/2261269 Whigham 10.1658/11009233(2004)015[0475:PDOFUS]2. 0.CO;2 10.1111/j.14698137.1984.tb04155.x 10.1111/plb.12007 10.1111/plb.12007 10.1890/11-0948.1 None 10.1890/00129658(2002)083[1991:AEFAFS]2.0 .CO;2 10.1890/00129658(2003)084[1464:TEOSTO]2. 0.CO;2 10.1890/10510761(2001)011[1366:TEOFOT]2. 0.CO;2 10.1890/00129658(2003)084[1464:TEOSTO]2. 0.CO;2 392 Lindera_umbellata Hara; Kanno; Hirabuki; Takehara J Veg Sci 2004 393 394 395 396 397 Verkaar; Schenkeveld Münzbergová Münzbergová Bricker; Maron Lacey; Royo; Bates; Herr New Phyto Plant Biology Plant Biology Ecology Castanea 1984 2013 2013 2012 2001 398 Lobularia_maritima Picó; de Kroon; Retana Ecology 2002 399 Lomatium_bradshawii Kaye; Pyke Ecology 2003 400 Lomatium_bradshawii_2 Kaye; Pendergrass; Finley; Kauffman Ecol Appl 2001 Ecology 2003 Ecology 2013 10.1890/12-1310.1 Book 2009 978-84-8014-746-25 Linum_catharticum Linum_flavum Linum_tenuifolium Lithospermum_ruderale Lobelia_boykinii 401 Lomatium_cookii 402 Lonicera_maackii 403 Lotus_arinagensis Kaye; Pyke Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Iriondo; Albert; Gime Giménez; Lozano; 36 404 405 406 407 408 Lotus_corniculatus Lupinus_arboreus Lupinus_tidestromii Lythrum_salicaria Machaerium_cuspidatum 409 Macrocystis_pyrifera 410 Magnolia_dealbata 411 Magnolia_salicifolia 412 Malacothrix_indecora 413 Mammillaria_crucigera 414 Mammillaria_gaumeri 415 Mammillaria_huitzilopochtli 416 Mammillaria_magnimamma 417 Mammillaria_pectinifera 418 Manglietia_fordiana Escudero Emery; Beuselinck; English Kauffman; Maron Dangremond; Knight Lacroix Nabe-Nielsen Nyman; Brown; Neushul; Keogh Sánchez-Velásquez; Pineda-López Hara; Kanno; Hirabuki; Takehara Levine; McEachern; Cowan Contreras; Valverde Ferrer; Duran; Méndez; Dorantes; Dzib Flores-Martinez; Manzanero-Medino; Golubov; Montaña; Mandujano Valverde; Quijas; LopezVillavicencio; Castillo Valverde; ZavalaHurtado Chien; Zuidema; Nghia 37 10.1046/j.14698137.1999.00540.x 10.1086/507877 10.1890/09-0418.1 None 10.1017/S0266467404001609 New Phyto Am Nat Ecology PhD thesis J Trop Ecol 1999 2006 2010 2004 2004 J Appl Phyco 1990 10.1007/BF02179782 Popul Ecol J Ecol J Arid Env 2010 10.1007/s10144-009-0161-5 10.1111/j.16542004 1103.2004.tb02286.x 10.1111/j.13652008 2745.2008.01375.x 2002 10.1006/jare.2001.0926 Bol Soc Bot Mex 2011 None Plant Ecol Plant Ecol 2010 10.1007/s11258-010-9737-6 10.1023/B:VEGE.0000021662.78 2004 634.de J Arid Env Popul Ecol 2006 10.1016/j.jaridenv.2005.06.001 2008 10.1007/s10144-008-0079-3 J Veg Sci 419 Manilkara_zapota Cruz-Rodriguez; LópezVillavicencio; Valverde Biotrop 424 Miconia_prasina 425 Microberlinia_bisulcata Holm; Miller; Cropper Crowley; Garnett; Shephard Ramula Hoffmann Pascarella; Alde; Zimmerman Norghauer; Newbery 426 Mimulus_cardinalis Angert Ecology 427 Mimulus_guttatus Elderd; Doak J Ecol 428 Mimulus_lewisii 429 Minuartia_obtusiloba Ecology Am J Bot Ecology 2013 10.1890/12-1310.1 431 Molinia_caerulea Angert Forbis; Doak Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Jacquemyn; Brys; Neubert 2009 10.1017/S0266467408005713 10.1111/j.17442008 7429.2008.00412.x 10.1111/j.14422009 9993.2008.01921.x 2008 10.1016/j.actao.2007.11.005 1999 10.2307/177080 10.1111/j.17442007 7429.2006.00220.x 2011 10.1890/10-2268.1 10.1890/00129658(2006)87[2014:DOCAMP]2. 2006 0.CO;2 10.1111/j.13652006 2745.2006.01115.x 10.1890/00129658(2006)87[2014:DOCAMP]2. 2006 0.CO;2 2004 10.3732/ajb.91.7.1147 Ecol Appl 432 Mulinum_spinosum Cipriotti; Aguiar Appl Veg Sci 2005 10.1890/04-1762 10.1111/j.16542012 109X.2011.01138.x 420 Mauritia_flexuosa 421 Melaleuca_viridiflora 422 Melampyrum_pratense 423 Miconia_albicans 430 Mircothlaspi_perfoliatum J Trop Ecol Aust Ecol Bas and Appl Ecol Ecology Biotrop Ecol Monog 38 433 Murdannia_nudiflora 434 Murdannia_simplex Burns Burns Ecol Appl Ecol Appl 435 Myosotis_ramosissima 436 Myrsine_guianensis J Veg Sci Ecology Ecology J Ecol 2013 10.1890/12-1310.1 1980 10.2307/2259425 J Appl Ecol 10.1111/j.13652008 2664.2007.01375.x 445 Neodypsis_decaryi Dostal Hoffmann Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Barkham Ghimire; Gimenez; Pradel; McKey; Aumeeruddy-Thomas Esparza-Olguin; Valverde; Mandujano Godínez-Alvarez; Valiente-Banuet Esparza-Olguin; Valverde; Mandujano Esparza-Olguin; Valverde; Mandujano Godínez-Alvarez; Valiente-Banuet Ratsirarson; Silander; Richard 2008 10.1890/07-0568.1 2008 10.1890/07-0568.1 10.1111/j.16542007 1103.2007.tb02519.x 1999 10.2307/177080 446 Neotinea_ustulata 447 Nothofagus_fusca Shefferson; Tali Enright; Ogden J Ecol Aust J Ecol 437 Narcissus_poeticus 438 Narcissus_pseudonarcissus 439 Nardostachys_grandiflora 440 Neobuxbaumia_macrocephala 441 Neobuxbaumia_macrocephala_2 442 Neobuxbaumia_mezcalaensis 443 Neobuxbaumia_tetetzo 444 Neobuxbaumia_tetetzo_2 Popul Ecol Plant Ecol 2005 10.1007/s10144-005-0230-3 10.1023/B:VEGE.0000046052.35 2004 390.59 Popul Ecol 2005 10.1007/s10144-005-0230-3 Popul Ecol 2005 10.1007/s10144-005-0230-3 10.1023/B:VEGE.0000046052.35 2004 390.59 10.1046/j.15231996 1739.1996.10010040.x 10.1111/j.13652007 2745.2006.01195.x 1979 10.1111/j.1442- Plant Ecol Cons Biol 39 448 Oenothera_deltoides 449 Ophrys_sphegodes 450 Opuntia_macrocentra 451 Opuntia_macrorhiza 452 Opuntia_rastrera 453 Orchis_purpurea 454 Oxalis_acetosella 455 Oxandra_asbeckii 456 Oxytropis_jabalambrensis 457 Panax_quinquefolium 458 459 460 461 Panax_quinquefolium_2 Panax_quinquefolium_3 Panax_quinquefolium_4 Parashorea_chinensis 462 Parkinsonia_aculeata Thomson Wells; Willems Mandujano; Golubov; Huenneke Keeler; Tenhumberg Mandujano; Montaña; Franco; Golubov; FloresMartinez Jacquemyns; Brys; Jongejans Cons Biol Book 9993.1979.tb01195.x 10.1111/j.15232005 1739.2005.004108.x 1991 10.2307/2261246 Popul Ecol Southw Nat 2007 10.1007/s10144-006-0032-2 2011 10.1894/F02-JB-17.1 Ecology 2001 10.2307/2679864 Ecology Berg Chagneau; Mortier; Picard Iriondo; Albert; Giménez; Lozano; Escudero Van de Voort; McGraw Ecography 2010 10.1890/08-2321.1 10.1034/j.16002002 0587.2002.250211.x 10.1111/j.14672009 9876.2008.00657.x Nantel; Gagnon; Nault Shahi Charron; Gagnon Chien; Zuidema; Nghia Raghu; Wilson; Dhileepan Cons Biol PhD thesis J Ecol Popul Ecol J R Stat Soc C Book Biol Cons Aust J Entomol 40 2009 978-84-8014-746-26 2006 10.1016/j.biocon.2006.01.010 10.1046/j.15231996 1739.1996.10020608.x 2007 None 1991 10.2307/2260724 2008 10.1007/s10144-008-0079-3 10.1111/j.14402006 6055.2006.00556.x 463 Parolinia_glabriuscula Iriondo; Albert; Giménez; Lozano; Escudero Book 464 Paronychia_jamesii 465 Paronychia_pulvinata Dalgleish; Koons; Adler Forbis; Doak J Ecol Am J Bot 466 467 468 469 470 Menges Hartshorn Hoffmann; Solbrig Garcı́a; Guzman; Goñi Garcı́a Cons Biol PhD thesis Forest Ecol Manag Biol Cons Biol Cons Bradstock; O'Connell Levine; McEachern; Cowan Degreef; Baudoin; Rocha Sinha; Brault Ticktin; Ganesan; Paramesha; Setty Ellis; Williams; Lesica; Bell; Bierzychudek; Bowles; Crone; Doak;Ehrlén; EllisAdam; McEachern; Ganesan; Latham; Luijten; Kaye; Knight; Aust J Bot Pedicularis_furbishiae Pentaclethra_macroloba Periandra_mediterranea Petrocoptis_pseudoviscosa Petrocoptis_pseudoviscosa_2 471 Petrophile_pulchella 472 Phacelia_insularis_var._insularis 473 Phaseolus_lunatus 474 Phyllanthus_emblica 475 Phyllanthus_emblica_2 476 Phyllanthus_emblica_3 41 J Appl Ecol 2009 978-84-8014-746-27 10.1111/j.13652010 2745.2009.01585.x 2004 10.3732/ajb.91.7.1147 10.1111/j.15231990 1739.1990.tb00267.x 1972 None 2003 10.1016/S0378-1127(02)00566-2 2002 10.1016/S0006-3207(01)00113-6 2002 10.1016/S0006-3207(01)00113-6 10.1111/j.14421988 9993.1988.tb00999.x 10.1111/j.13652008 2745.2008.01375.x 1997 10.1023/A:1008623521755 2005 10.1007/s10531-004-0827-4 10.1111/j.13652012 2664.2012.02156.x Ecology 2012 10.1890/11-1052.1 J Ecol Gen Res Crop Evol Biodivers Conserv 477 Phyllanthus_indofischeri 478 479 480 481 Phytelephas_seemannii Picea_glehnii Picea_jezoensis Picris_hieracioides 482 Pinguicula_alpina 483 Pinguicula_ionantha 484 Pinguicula_villosa 485 Pinguicula_vulgaris 486 Pinus_albicaulis 487 Pinus_albicaulis_2 488 Pinus_jeffreyi 489 Pinus_kwangtungensis 490 Pinus_lambertiana Menges; Morris; Den Nijs; Oostermeijer; Quintana-Ascencio; Shelly; Stanley; Thorpe; Ticktin; Valverde; Weekley Ticktin; Ganesan; Paramesha; Setty Bernal Kubota Kubota Klemow; Raynal Svennson; Carlsson; Karlsson; Nordell Kesler; Trusty; Hermann; Guyer Svennson; Carlsson; Karlsson; Nordell Svennson; Carlsson; Karlsson; Nordell Ettl; Cottone Ettl; Cottone van Mantgem; Stephenson Chien; Zuidema; Nghia van Mantgem; 42 10.1111/j.13652664.2012.02156.x 10.1046/j.13652664.1998.00280.x 10.1007/BF02523604 10.1007/BF02523604 10.2307/2259775 J Appl Ecol 2012 J Appl Ecol Eco Research Eco Research J Ecol 1998 1997 1997 1985 J Ecol 1993 10.2307/2261662 Oecologia 2008 10.1007/s00442-008-1022-1 J Ecol 1993 10.2307/2261662 J Ecol Book Book 1993 10.2307/2261662 2004 None 2004 None 10.1111/j.13652005 2745.2005.01007.x 2008 10.1007/s10144-008-0079-3 2005 10.1111/j.1365- J Ecol Popul Ecol J Ecol 491 Pinus_lambertiana_2 492 Pinus_maximartinezii 493 Pinus_nigra 494 Pinus_palustris 495 Pinus_ponderosa 496 497 498 499 500 Pinus_strobus Pinus_sylvestris Pityopsis_aspera_var._aspera Plantago_coronopus Plantago_media 501 Platanthera_hookeri 502 Platymiscium_filipes 503 504 505 506 Poa_alpina Podococcus_barteri Podophyllum_peltatum Polemonium_vanbruntiae Stephenson Maloney; Vogler; Eckert; Jensen; Neale 2745.2005.01007.x Forest Ecol Manag 2011 10.1016/j.foreco.2011.05.011 http://dx.doi.org/10.1016/j.acta 2013 o.2013.02.010 López-Mata Buckley; Brockerhoff; Langer; Ledgard; North; Rees Platt; Evans; Rathbun van Mantgem; Stephenson Münzbergová; Hadincová; Wild; Kindlmannová Usher Gornish Waite Eriksson; Eriksson Acta Oeco Reddoch; Reddoch Fortini; Zarin Marcante; Winkler; Erschbamer Bullock Sohn; Policansky Bermingham J Torrey Bot Soc Forest Ecol Manag 10.1371/journal.pone.0056953 10.2307/2401258 10.1093/aobpla/plt041 10.2307/2259533 10.2307/3236803 10.3159/10955674(2007)134[369:PEOPHO]2.0. 2007 CO;2 2010 10.1016/j.foreco.2010.11.007 Annals Bot Biotrop Ecology Plant Ecol 2009 1980 1977 2010 43 J Ecol 10.1111/j.13652005 2664.2005.01100.x 1988 10.1086/284803 10.1111/j.13652005 2664.2005.01100.x PLoS ONE Biom AoB Plants J Ecol J Veg Sci 2013 1966 2013 1984 2000 J Appl Ecol Am Nat 10.1093/aob/mcp047 10.2307/2387694 10.2307/1935088 10.1007/s11258-010-9762-5 507 508 509 510 Polygonum_perfoliatum Polystichum_aculeatum Polystichum_setiferum Potentilla_anserina Hyatt; Araki de Groot de Groot Eriksson Biol Inv PhD thesis PhD thesis J Ecol Invasive Plant Science and Manag Ecology 511 Potentilla_recta 512 Primula_elatior Lesica; Ellis Jacquemyn; Brys 513 Primula_farinosa Lindborg; Ehrlén Ehrlén; Syrjänen; Leimu; Garcia; Lehtilä Lehtilä; Syrjänen; Leimu; Garcia; Ehrlén Jacquemyn; Brys; Davison; Tuljapurkar; Jongejans Endels; Jacquemyn; Brys; Hermy Brys; Jacquemyn; Endels; de Blust; Hermy Valverde; Silvertown Endels; Jacquemyn; Brys; Hermy Condit Golubov; Mandujano; Franco; Montaña; Eguiarte; Lopez-Portillo 514 Primula_veris 515 Primula_veris_2 516 Primula_veris_3 517 Primula_veris_4 518 Primula_veris_5 519 Primula_vulgaris 520 Primula_vulgaris_2 521 Prioria_copaifera 522 Prosopis_glandulosa 44 2006 2011 2011 1988 10.1007/s10530-004-5572-9 None None 10.2307/2260610 Cons Biol 2010 10.1614/IPSM-08-135.1 2008 10.1016/j.biocon.2006.07.016 10.1046/j.15232002 1739.2002.00509.x 10.1111/j.13652005 2664.2005.01015.x 10.1111/j.15232006 1739.2006.00368.x Oikos 10.1111/j.16002011 0706.2011.19774.x Cons Biol J Appl Ecol Plant Ecol J Ecol Forest Ecol Manag 2005 10.1007/s11258-004-0026-0 10.1111/j.15232005 1739.2005.00216.x 1998 None 10.1111/j.13652007 2745.2007.01279.x 1993 10.1016/0378-1127(93)90045-O J Ecol 10.1046/j.13651999 2745.1999.00420.x Cons Biol J Ecol 523 Prosopis_laevigata 524 Prunus_africana 525 Prunus_serotina 526 527 528 529 Pseudomisopates_rivas-martinezii Pseudophoenix_sargentii Pseudophoenix_sargentii_2 Psidium_guajava 530 Psoralea_tenuiflora 531 Pterocarpus_angolensis 532 Pterocarya_rhoifolia 533 Pterocereus_gaumeri 534 Ptychosperma_macarthurii 535 Purshia_subintegra 536 Pyrrocoma_radiata 537 Pyxidanthera_brevifolia Bernal Stewart Sebert-Cuvillier; Paccaut; Chabrerie; Endels; Goubet; Decocq Iriondo; Albert; Giménez; Lozano; Escudero Duran; Franco Maschinski; Duquesnel Somarriba PhD thesis PhD thesis 2004 None 2001 None Ecol Model 10.1016/j.ecolmodel.2006.09.00 2007 5 Book PhD thesis Biol Cons Agrofor Syst 2009 1992 2006 1988 Dalgleish; Koons; Adler Desmet; Shackleton; Robinson Kaneko; Kawano Méndez; Duran; Olmsted Liddle; Brook; Matthews; Taylor; Caley Maschinski; Baggs; Quintana-Ascencio; Menges Pfingsten Wall; Hoffmann; Wentworth; Gray; Hohmann J Ecol 978-84-8014-746-28 10.1016/j.biocon.2006.07.012 10.1016/j.biocon.2006.07.012 10.1007/BF02344742 10.1111/j.13652010 2745.2009.01585.x S African J Bot J Plant Res 1996 None 2002 10.1007/s10265-002-0042-x Biotrop 2004 10.1646/1601 Biol Cons 2006 10.1016/j.biocon.2006.04.028 Cons Biol PhD thesis 10.1111/j.15232006 1739.2006.00272.x 2013 None Plant Ecol 2012 10.1007/s11258-012-0068-7 45 538 539 540 541 542 543 544 Quercus_crispula Quercus_rugosa Ramonda_myconi Ranunculus_acris Ranunculus_bulbosus Ranunculus_peltatus Ranunculus_repens Hiura; Fujiwara Bonfil; Valverde Picó; Riba Sarukhan; Harper Sarukhan; Harper Idestam-Almquist Sarukhan; Harper J Veg Sci Unpublished Plant Ecol J Ecol J Ecol PhD thesis J Ecol J Ecol PhD thesis 552 Rhododendron_ponticum_2 Dalgleish; Koons; Adler Mendoza; Franco López -Hoffman; Ackerly; Anten; DeNoyer;Ramos McGraw McGraw McGraw Salguero-Gómez Travis; Harris; Park; Bullock 553 Rhopalostylis_sapida 554 Rhopalostylis_sapida_2 555 Rhus_aromatica 556 Rhus_copallinum 545 Ratibida_columnifera 546 Reinhardtia_gracilis 547 548 549 550 551 Rhizophora_mangle Rhododendron_maximum Rhododendron_maximum_2 Rhododendron_maximum_3 Rhododendron_ponticum 557 Rosa_multiflora NA 1999 10.2307/3237309 None 2002 10.1023/A:1020310609348 1973 10.2307/2258643 1973 10.2307/2258643 1998 None 1973 10.2307/2258643 10.1111/j.13652010 2745.2009.01585.x 1993 None 10.1111/j.13652745.2007.01298.x 10.2307/2444780 10.2307/2444780 10.2307/2444780 None 10.1111/j.2041210X.2011.00104.x 10.1080/0028825X.1992.104128 83 10.1080/0028825X.1992.104128 83 None None J Ecol Am J Bot Am J Bot Am J Bot MSc thesis 2007 1989 1989 1989 2004 Methods Ecol Evol 2011 Enright; Watson New Zealand J Bot 1992 Enright; Watson Nantel; Gagnon Thaxton Burns; Pardini; Schutzenhofer; Chung; New Zealand J Bot J Ecol PhD thesis 1992 1999 2003 Ecology 2013 10.1890/12-1310.1 46 558 Rosmarinus_tomentosus 559 Roupala_montana 560 Rourea_induta 561 Rubus_discolor 562 Rubus_saxatilis 563 Rubus_ursinus Seidler; Knight Iriondo; Albert; Giménez; Lozano; Escudero Hoffmann Hoffmann Lambrecht-McDowell; Radosevich Eriksson Lambrecht-McDowell; Radosevich Book Ecology Ecology 2009 978-84-8014-746-30 1999 10.2307/177080 1999 10.2307/177080 Biol Inv Ecol Research 2005 10.1007/s10530-004-0870-9 1994 10.1007/BF02348412 Biol Inv Weed Res Book PhD thesis 2009 978-84-8014-746-31 1989 None J Trop Ecol 2007 10.1017/S0266467406003877 Evol Ecol 2002 10.1007/978-94-017-1345-0_12 Evol Ecol 570 Salsola_australis Pino; Sans; Masalles Iriondo; Albert; Giménez; Lozano; Escudero Ramp Pulido; Valverde; Caballero Tolvanen; Schroderus; Henry Tolvanen; Schroderus; Henry Borger; Scott; Renton; Walsh; Powles 2005 10.1007/s10530-004-0870-9 10.1046/j.13651998 3180.1998.00068.x 571 Sanicula_europaea Gustafsson; Ehrlén Oikos 2002 10.1007/978-94-017-1345-0_12 10.1111/j.13652009 3180.2009.00703.x 10.1034/j.16002003 0706.2003.11493.x 564 Rumex_obtusifolius 565 Rumex_rupestris 566 Sabal_minor 567 Sabal_yapa 568 Salix_arctica 569 Salix_arctica_2 Weed Res 47 581 Saxifraga_aizoides 582 Saxifraga_cotyledon Iriondo; Albert; Giménez; Lozano; Escudero Renne Csergő; Molnár; Garcia Salinas; Suárez; Blanca Salinas; Suárez; Blanca Salinas; Suárez; Blanca Brewer Gotelli; Ellison Law; Salick; Knight Marcante; Winkler; Erschbamer Dinnetz; Nilsson 583 Saxifraga_tridactylites Dostal J Veg Sci 584 Scabiosa_columbaria New Phyto 585 Scaphium_borneense 586 Sclerocarya_birrea 587 Scorzonera_hispanica Verkaar; Schenkeveld Yamada; Zuidema; Itoh; et al. Emanuel Münzbergová 588 Scorzonera_humilis Colling; Matthies J Ecol 589 Senecio_filaginoides 590 Senecio_jacobaea Cipriotti; Aguiar Forbes Appl Veg Sci Weed Res 572 573 574 575 576 577 578 579 580 Santolina_melidensis Sapium_sebiferum Saponaria_bellidifolia Sarcocapnos_baetica Sarcocapnos_enneaphylla Sarcocapnos_pulcherrima Sarracenia_alata Sarracenia_purpurea Saussurea_medusa 48 Book PhD thesis Popul Ecol Can J Bot Can J Bot Can J Bot Am J Bot Ecol Appl Plant Ecol 2009 2001 2011 2002 2002 2002 2001 2006 2010 Annals Bot Plant Ecol 2009 10.1093/aob/mcp047 2002 10.1023/A:1015593311183 10.1111/j.16542007 1103.2007.tb02519.x 10.1111/j.14691984 8137.1984.tb04155.x 10.1111/j.13652007 2745.2006.01209.x 2005 10.1016/j.foreco.2005.03.066 2006 10.1007/bf02806475 10.1111/j.13652006 2745.2006.01147.x 10.1111/j.16542012 109X.2011.01138.x 1977 10.1111/j.1365- J Ecol Forest Ecol Manag Folia Geobot 978-84-8014-746-32 None 10.1007/s10144-010-0249-y 10.1139/b02-013 10.1139/b02-013 10.1139/b02-013 10.2307/3558336 10.1890/04-0479 10.1007/s11258-010-9761-6 PhD thesis Am Nat Science Acta Biotheo Ecol Appl J Appl Ecol J Appl Ecol Am J Bot 1995 2004 1993 1993 1998 599 Silene_acaulis_2 600 Silene_douglasii_var._oraria Crider Namkoong; Roberds Bosch Jarry; khaladi; HossaertMcKey; McKey Davis; Dixon; Liebman O'Connor O'Connor Morris; Doak Gross; Morris; Wolosin; Doak Kephart; Paladino 3180.1977.tb00498.x 2009 None 1974 10.1086/282913 1971 10.1126/science.172.3981.345 Popul Ecol Am J Bot 601 Silene_regia Menges; Dolan J Ecol 602 Silene_spaldingii Lesica; Crone J Ecol 603 Solidago_mollis 604 Spartina_alterniflora Dalgleish; Koons; Adler Hastings; Hall; Tylor J Ecol Theor Popul Biol 605 Sphaeralcea_coccinea Dalgleish; Koons; Adler Dalgleish; Kula; Hartnett; Sandercook Abe; Wada; Nokagoshi Hartshorn Abe; Nokashizuka; J Ecol 2006 10.1007/s10144-005-0247-7 1997 10.2307/2446079 10.1046/j.13651998 2745.1998.00234.x 10.1111/j.13652007 2745.2007.01291.x 10.1111/j.13652010 2745.2009.01585.x 2006 10.1016/j.tpb.2006.05.003 10.1111/j.13652010 2745.2009.01585.x Am J Bot Plant Ecol PhD thesis J Veg Sci 2008 2008 1972 1998 591 Senecio_jacobaea_2 592 Sequoia_sempervirens 593 Sequoia_sempervirens_2 594 595 596 597 598 606 607 608 609 Sesbania_vesicaria Setaria_faberi Setaria_incrassata Setaria_incrassata_2 Silene_acaulis Sporobolus_heterolepis Stachyurus_macrocarpus Stryphnodendron_excelsum Styrax_obassia 49 10.1007/BF00709433 10.1890/02-5385 10.2307/2404276 10.2307/2404276 None 10.3732/ajb.2007277 10.1007/s11258-007-9393-7 None 10.2307/3237044 610 Styrax_obassia_2 Tanoka Abe; Nokashizuka; Tanoka J Ecol PhD thesis Biol Cons J Appl Ecol Biol Cons 10.1111/j.13652008 2664.2008.01564.x 2012 10.1016/j.biocon.2012.03.018 620 Taraxacum_officinale_2 621 Taxus_brevifolia Jongejans; de Kroon Milden Pavlik; Barbour Verwer; Peña-Claros; van der Staak; OhlsonKiehn; Sterck Schmidt; Ticktin Shen; Santiago; Ma; Lin; Lian; Cao; Ye Poorter; Zuidema; PenoClaros; Boot Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Vavrek; McGraw; Yang Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Busing; Spies 1998 10.2307/3237044 10.1111/j.13652005 2745.2005.01003.x 2005 None 1988 10.1016/0006-3207(88)90069-9 622 Taxus_floridana 623 Tetraberlinia_bifoliolata 624 Tetramolopium_arenarium Kwit; Horvitz; Platt Norghauer; Newbery Aplet; Laven; Shaw Cons Biol Ecol Monog Nat Areas J 611 Succisa_pratensis 612 Succisa_pratensis_3 613 Swallenia_alexandrae 614 Swietenia_macrophylla 615 Syngonanthus_nitens 616 Syzgium_rehderianum 617 Tachigali_vasquezii 618 Taraxacum_erythrospermum 619 Taraxacum_officinale J Veg Sci 50 J Trop Ecol J Ecol 2013 10.1017/S0266467413000059 10.1111/j.13652005 2745.2005.00958.x Ecology J Ecol 2013 10.1890/12-1310.1 1997 10.2307/2960501 Ecology USDAResearchNate 2013 10.1890/12-1310.1 1995 None 10.1111/j.15232004 1739.2004.00567.x 2011 10.1890/10-2268.1 1994 None 625 626 627 628 Thelesperma_megapotamicum Themeda_triandra Themeda_triandra_2 Thrinax_radiata 629 Thymus_webbianus 630 Tillandsia_brachycaulos 631 Tillandsia_deppeana 632 Tillandsia_juncea 633 634 635 636 637 638 Tillandsia_macdougallii Tillandsia_multicaulis Tillandsia_punctulata Tillandsia_recurvata Tillandsia_violacea Tolumnia_variegata 639 640 641 642 643 Torreya_taxifolia Tradescantia_blossfeldiana Tradescantia_brevifolia Tradescantia_fluminensis Tradescantia_zebrina 644 Tragopogon_dubius 10.1111/j.13652745.2009.01585.x 10.2307/2404276 10.2307/2404276 10.2307/1942038 Dalgleish; Koons; Adler O'Connor; Pickett O'Connor; Pickett Olmsted; Alvarez-Buylla Iriondo; Albert; Giménez; Lozano; Escudero Mondragón; Durán; Ramírez; Valverde Winkler; Hülber; Hietz Winkler; Hülber; Hietz J Ecol J Appl Ecol J Appl Ecol Ecol Appl 2010 1992 1992 1995 Book 2009 978-84-8014-746-34 J Trop Ecol Bas and Appl Ecol Bas and Appl Ecol Mondragón; Ticktin Winkler; Hülber; Hietz Winkler; Hülber; Hietz Valverde; Bernal Mondragón; Ticktin Calvo Schwartz; Hermann; Mantgem Burns Burns Burns Burns Prevéy; Germino; Huntly Cons Biol Bas and Appl Ecol Bas and Appl Ecol Bol Soc Bot Mex Cons Biol Ecology Cons Biol Ecol Appl Ecol Appl Ecol Appl Ecol Appl 2004 10.1017/S0266467403001287 2007 10.1016/j.baae.2006.05.003 2007 10.1016/j.baae.2006.05.003 10.1111/j.15232011 1739.2011.01691.x 2007 10.1016/j.baae.2006.05.003 2007 10.1016/j.baae.2006.05.003 2010 0366-2128 2011 None 1993 10.2307/1940473 10.1046/j.15232000 1739.2000.98393.x 2008 10.1890/07-0568.1 2008 10.1890/07-0568.1 2008 10.1890/07-0568.1 2008 10.1890/07-0568.1 Ecol Appl 2010 10.1890/09-0750.1 51 645 Tragopogon_pratensis Milden; Eriksson Ann Bot Fen 646 Trifolium_montanum 647 Trifolium_pratense Schleuning; Matthies Fréville; Silvertown Cons Biol Plant Ecol 648 Trillium_apetalon Ohara; Takada; Kawano Ohara; Tomimatsu; 649 Trillium_camschatcense Takada; Kawano 650 Trillium_grandiflorum Knight 651 Trillium_grandiflorum_2 Rooney; Gross 652 Trollius_laxus Scanga; Leopold 653 Tsuga_canadensis Lamar; McGraw Stokes; Bullok; 654 Ulex_gallii Watkinson Stokes; Bullok; 655 Ulex_minor Watkinson 656 Vatica_hainanensis Hu; Wang Iriondo; Albert; Giménez; Lozano; 657 Vella_pseudocytisus_subsp._paui Escudero Iriondo; Albert; Vella_pseudocytisus_subsp._pseudo Giménez; Lozano; 658 cytisus Escudero Iriondo; Albert; Giménez; Lozano; 659 Verbascum_fontqueri Escudero 660 Veronica_arvensis Dostal 52 J Ecol Acta Ecol Sinica 2007 None 10.1111/j.15232009 1739.2008.01054.x 2005 10.1007/s11258-004-0017-1 10.1046/j.14422001 1984.2001.00062.x 10.1111/j.14422006 1984.2006.00145.x 2003 10.3732/ajb.90.8.1207 2003 10.1023/A:1024486606698 2012 10.1016/j.biocon.2012.01.061 2005 10.1016/j.foreco.2005.02.056 10.1111/j.13652004 2745.2004.00844.x 10.1111/j.13652004 2745.2004.00844.x 1988 None Book 2009 978-84-8014-746-35 Book 2009 978-84-8014-746-36 Book J Veg Sci 2009 978-84-8014-746-37 2007 10.1658/1100- Plant Spp Biol Plant Spp Biol Am J Bot Plant Ecol Biol Cons Forest Ecol Manag J Ecol 9233(2007)18[91:PDOAIP]2.0.CO ;2 661 Veronica_arvensis_2 Verticosa_staminosa_subsp._stami 662 nosa 663 Viburnum_furcatum 664 Viola_elatior 665 Viola_fimbriatula 666 Viola_pumila 667 Viola_stagnina 668 Vochysia_ferruginea 669 Vouacapoua_americana 670 Werauhia_sanguinolenta 671 Zamia_amblyphyllidia 672 Zea_diploperennis Burns; Pardini; Schutzenhofer; Chung; Seidler; Knight Yates; Ladd; Coates; McArthur Hara; Kanno; Hirabuki; Takehara Eckstein; Otte Solbrig; Sarandon; Bossert Eckstein; Danihelka; Otte Eckstein; Danihelka; Otte Boucher; Mallono Chagneau; Mortier; Picard Zotz Negron-Ortiz; Gorchov; Breckon Sanchez-Velazquez; Ezcurra; MartinezRamos; Alvarez-Buylla; Lorente 53 Ecology 2013 10.1890/12-1310.1 Aust J Bot J Veg Sci Flora 2007 10.1071/BT06032 10.1658/11009233(2004)015[0475:PDOFUS]2. 2004 0.CO;2 2004 10.1078/0367-2530-00151 Am Nat 1988 10.1086/284796 Biol 2009 10.2478/s11756-009-0002-1 Biol Forest Ecol Manag J R Stat Soc C Acta Oeco 2009 10.2478/s11756-009-0002-1 1997 10.1016/S0378-1127(96)03890-X 10.1111/j.14672009 9876.2008.00657.x 2005 10.1016/j.actao.2005.05.009 Int J plant Sci 1996 10.1086/297381 J Ecol 10.1046/j.13652002 2745.2002.00702.x 54 Appendix S5. COMPADRE phylogeny In order to facilitate broader demographic comparative analyses, we are making publically available a phylogenetic tree for the species released in COMPADRE 3.0. To construct the tree, the identity of each species and its corresponding taxonomic family were checked in The Plant List website (http://www.theplantlist.org/). The specific names used by the authors (SpeciesAuthor instead of SpeciesAccepted in Table 1 in the main manuscript), however, were used here for direct reference to the COMPADRE data. Second, we obtained an approximate phylogeny with PHYLOMATIC (Webb 2005). Resolution below the level provided by phylomatic, which varies from family to family, was achieved by manually sorting individuals species in MESQUITE (Maddison 2009) by reference to published sources of phylogenetic information (Blomberg 2003; Schlichting 2002) (See separate reference list for each taxonomic family below). This is because many species did not have information in GenBank to allow us to construct a phylogeny from DNA data. Moreover, closely related species that could be used as temporary surrogates could often not be obtained. Also, because “in every case, the ultimate authoritative source for the nomenclature and classification is the primary taxonomic literature itself” (Federhen 2012), we decided to follow Federhen’s practice at NCBI (“… the NCBI taxonomy is not generated automatically from the sequence data – rather, we try to reflect the current consensus in the systematics literature”) and use the available published information to determine the topological position of each species in the tree. Once the maximally resolved topology that we produced with the available information was obtained, branch lengths were interpolated 55 employing the function bladj of PHYLOCOM (Webb 2008) given the node ages provided by Wikstrom and colleagues (2001). The link to the nexus phylogeny file can be found in the COMPADRE database github site. This file will be updated as more information is periodically released. This file may contain species currently in the working version of COMPADRE, but whose demographic information has not yet been released. https://github.com/jonesor/compadreDB/tree/master/Phylogeny 56 Taxonomic group Angiosperms Amaranthaceae Apiaceae Araucariaceae Arecaceae Asparagaceae/Asparagales Reference Angiosperm Phylogeny Group III. An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Botanical Journal of the Linnean Society 161, 105 (2009). P.F. Stevens onwards. Angiosperm Phylogeny Website. Version 12, July 2012. http://www.mobot.org/MOBOT/research/APweb/ (2001). O.T. Ogundipe, M. Chase. Phylogenetic analyses of Amaranthaceae based on matK DNA sequence data with emphasis on West African species. Turkish Journal of Botany 33, 153 (2009). C.I. Calviño, S.R. Downie. Circumscription and phylogeny of Apiaceae subfamily Saniculoideae based on chloroplast DNA sequences. Molecular Phylogenetics and Evolution 44, 175 (2007). S.R. Downie, D.S. Katz-Downie, M.F. Watson. A phylogeny of the flowering plant family Apiaceae based on chloroplast DNA rpl16 and rpoC1 intron sequences: Towards a suprageneric classification of subfamily Apioideae. American Journal of Botany 87, 273 (2000). S. Gilmore, K.D. Hill. Relationships of the Wollemi Pine (Wollemia nobilis) and a molecular phylogeny of the Araucariaceae. Telopea 7, 275 (1997). C.B. Asmussen, J. Dransfield, V. Deickmann, A.S. Barfod, J.-C. Pintaud, W.J. Baker. A new subfamily classification of the palm family (Arecaceae): evidence from plastid DNA phylogeny. Botanical Journal of the Linnean Society 151, 15 (2006). W.J. Baker, V. Savolainen, C.B. Asmussen-Lange, M.W. Chase, J. Dransfield, F. Forest, M.M. Harley, N.W. Uhl, M. Wilkinson, M. Complete Generic-Level Phylogenetic Analyses of Palms (Arecaceae) with Comparisons of Supertree and Supermatrix Approaches. Systematic Biology 58, 240 (2009). M.W. Chase, J.L. Reveal, M.F. Fay. A subfamilial classification for the expanded asparagalean families Amaryllidaceae, Asparagaceae and Xanthorrhoeaceae. Botanical Journal of the Linnean Society 161, 132 (2009). J.-H. Kim, D.-K. Kim, F. Forest, M.F. Fay, M.W. Chase. Molecular phylogenetics of Ruscaceae sensu lato and related families (Asparagales) based on plastid and nuclear DNA sequences. 57 Asteraceae Boraginaceae Brassicaceae Annals of Botany 106, 775 (2010). V.A. Funk, A. Susanna, T. Stuessy, H. Robinson. Classification of Compositae. In: Funk, V.A., Susanna, A., Stuessy, T. & Bayer R. (eds), Systematics, Evolution, and Biogeography of Compositae, pp. 171-189. International Association for Plant Taxonomy, Vienna (2009). V.A. Funk, A.A. Anderberg, B.G. Baldwin, R.J. Bayer, J.M Bonifacino, J.M., I. Breitwieser, L. Brouillet, R. Carbajal, R. Chan, A.X.P. Coutinho, D.J. Crawford, J.V. Crisci, M.O. Dillon, S.E. Freire, J. Galbany-Casals, N. Garcia-Jacas, B. Gemeinholzer, M. Gruenstaeudl, H.V. Hansen, S. Himmelreich, J.W. Kadereit, M. Källersjö, V. Karaman-Castro, P.O. Karis, L. Katinas, S.C. Keeley, N. Kilian, R.T. Kimball, T.K. Lowrey, J. Lundberg, R.J. McKenzie, M. Tadesse, M.E. Mort, B. Nordenstam, C. Oberprieler, S. Ortiz, P.B. Pelser, C.P. Randle, H. Robinson, N. Roque, G. Sancho, J.C. Semple, M. Serrano, T.F. Stuessy, A. Susanna, M. Unwin, L. Urbatsch, E. Urtubey, J. Vallès, R. Vogt, S. Wagstaff, J. Ward, L.E. Watson. Compositae metatrees: the next generation. In: Funk, V.A., Susanna, A., Stuessy, T. & Bayer, R. (eds), Systematics, Evolution, and Biogeography of Compositae, pp. 747-777. International Association for Plant Taxonomy, Vienna (2009). L.R. Goertzen, J.J. Cannone, R.R. Gutell, K. Robert, R.K. Jansen. ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the Asteraceae. Molecular Phylogenetics and Evolution 29, 216 (2003). J.L. Panero, V.A. Funk. Toward a phylogenetic subfamilial classification for the Compositae (Asteraceae). Proceedings of the Biological Society of Washington 115, 760 (2002). M. Nazaire, L. Hufford. A Broad Phylogenetic Analysis of Boraginaceae: Implications for the Relationships of Mertensia. Systematic Botany 37, 758 (2012). C.D. Bailey, M.A. Koch, M. Mayer, K. Mummenhoff, S.L. O'Kane, S.I. Warwick, M.D. Windham, I.A. Al-Shehbaz. Toward a Global Phylogeny of the Brassicaceae. Molecular Biology and Evolution 23, 2142 (2006). M.A. Beilstein, I.A. Al-Shehbaz, E.A. Kellogg. Brassicaceae phylogeny and trichome evolution. American Journal of Botany 93, 607 (2006). J.C. Hall, K.J. Sytsma, H.H. Iltis. Phylogeny of Capparaceae and Brassicaceae based on chloroplast sequence data. American Journal of Botany 89, 1826 (2002). 58 Bromeliaceae Campanulaceae Caprifoliaceae/Dipsacaceae Caryophyllaceae Cistaceae Commelinaceae Cupressaceae Cycadales M.H.J. Barfuss, R. Samuel, W. Till, T.F. Stuessy. Phylogenetic relationships in subfamily Tillandsioideae (Bromeliaceae) based on DNA sequence data from seven plastid regions. American Journal of Botany 92, 337 (2005). R.G. Terry, G.K. Brown, R.G. Olmstead. Examination of subfamilial phylogeny in Bromeliaceae using comparative sequencing of the plastid locus ndhF. American Journal of Botany 84, 664 (1997). W.M.M.Eddie, T. Shulkina, J. Gaskin, R.C. Haberle, R.K. Jansen. Phylogeny of Campanulaceae S. Str. inferred from its sequences of nuclear ribosomal DNA. Annals of the Missouri Botanical Garden 90, 554 (2003). A. Backlund, B. Bremer. Phylogeny of the Asteridae s. str. based on rbcL sequences, with particular reference to the Dipsacales. Plant Systematics and Evolution 207, 225 (1997). S. Fior, P.O. Karis, G. Casazza, L. Minuto, F. Sala. Molecular phylogeny of the Caryophyllaceae (Caryophyllales) inferred from chloroplast matK and nuclear rDNA ITS sequences. American Journal of Botany 93, 399 (2006). B. Guzmán & P. Vargas. Historical biogeography and character evolution of Cistaceae (Malvales) based on analysis of plastid rbcL and trnL-trnF sequences. Organisms, Diversity and Evolution 9, 83 (2009). T.M. Evans, R.B. Faden, M.G. Simpson, K.J. Sytsma. Phylogenetic Relationships in the Commelinaceae: I. A Cladistic Analysis of Morphological Data. Systematic Botany 25, 668 (2000). P.A. Gadek, D.L. Alpers, M.M. Heslewood, C.J. Quinn. Relationships within Cupressaceae sensu lato: a combined morphological and molecular approach. American Journal of Botany 87, 1044 (2000). D. González, A.P. Vovides, C. Bárcenas. Phylogenetic relationships of the Neotropical genus Dioon (Cycadales, Zamiaceae) based on nuclear and chloroplast DNA sequence data. Systematic Botany 33, 229 (2008). D. Gonzalez, A.P. Vovides. A modification to the SCAR (Sequence Characterized Amplified Region) method provides phylogenetic insights within Ceratozamia (Zamiaceae). Revista Mexicana de Biodiversidad 83, 929 (2012). 59 Dipsacales Ericaceae Fabaceae Fagaceae Gymnosperms Lauraceae Liliales/Liliaceae S.-M. Chaw, T.W. Walters, C.-C. Chang, S.-H. Hu, S.-H. Chen. A phylogeny of cycads (Cycadales) inferred from chloroplast matK gene, trnK intron, and nuclear rDNA ITS region. Molecular Phylogenetics and Evolution 37, 214 (2005). M.J. Donoghue, R.G. Olmstead, J.F. Smith, J.D. Palmer. Phylogenetic relationships of Dipsacales based on rbcL sequences. Annals of the Missouri Botanical Garden 79, 333 (1992). M.J. Donoghue, T. Eriksson, P.A. Reeves, R.G. Olmstead. Phylogeny and phylogenetic taxonomy of Dipsacales, with special reference to Sinadoxa and Tetradoxa (Adoxaceae). Harvard Papers in Botany 6, 459 (2001). K.A. Kron, W.S. Judd, P.F. Stevens, D.M. Crayn, A.A. Anderberg, P.A. Gadek, C.J. Quinn, J.L. Luteyn. Phylogenetic classification of Ericaceae: molecular and morphological evidence. Botanical Review 68, 335 (2002). P.S. Herendeen, A. Bruneau. Advances in legume systematics 9. Royal Botanic Gardens, Kew (2000). B.B. Klitgaard, A. Bruneau. Advances in legume systematics 10: Higher level systematics. Royal Botanic Gardens, Kew (2003). P.S. Manos, Z.-K. Zhou, C.H. Cannon. Systematics of Fagaceae: phylogenetic tests of reproductive trait evolution. International Journal of Plant Sciences 162, 1361 (2001). S.-M. Chaw, C.L. Parkinson, Y. Cheng, T.M. Vincent, J.D. Palmer. Seed plant phylogeny inferred from all three plant genomes: Monophyly of extant gymnosperms and origin of Gnetales from conifers. Proceedings of the National Academy of Sciences 97, 4086 (2000). S.-M. Chaw, A. Zharkikh, H.-M. Sung, T.-C. Lau, W.-H. Li. Molecular phylogeny of extant gymnosperms and seed plant evolution: analysis of nuclear 18S rRNA sequences. Molecular Biology and Evolution 14, 56 (1997). A.S. Chanderbali, H. van der Werff, S.S. Renner. Phylogeny and historical biogeography of Lauraceae: evidence from the chloroplast and nuclear genomes. Annals of the Missouri Botanical garden 88, 104 (2001). G. Petersen, O. Seberg, J.I. Davis. Phylogeny of the Liliales (Monocotyledons) with special emphasis on data partition congruence and RNA editing. Cladistics 29, 274 (2013). A. Vinnersten, K. Bremer. Age and biogeography of major clades in Liliales. American Journal of 60 Meliaceae Orchidaceae Pinaceae Plantaginaceae Poaceae Botany 88, 1695 (2001). A.N. Muellner, R. Samuel, S.A. Johnson, M. Cheek, T.D. Pennington, M.W. Chase. Molecular phylogenetics of Meliaceae (Sapindales) based on nuclear and plastid DNA sequences. American Journal of Botany 90, 471 (2003). K.M. Cameron, M.W. Chase, W.M. Whitten, P.J. Kores, D.C. Jarrell, V.A. Albert, T. Yukawa, H.G. Hills, D.H. Goldman. A phylogenetic analysis of the Orchidaceae: evidence from rbcL nucleotide sequences. American Journal of Botany 86, 208 (1999). J.V. Freudenstein, C. van den Berg, D.H. Goldman, P.J. Kores, J. Molvray, M.W. Chase. An expanded plastid DNA phylogeny of Orchidaceae and analysis of jackknife branch support strategy. American Journal of Botany 91, 149 (2004). J.-H. Li, Z.-J. Liu, G.A. Salazar, P. Bernhardt, H. Perner, Y. Tomohisa, X.-H. Jin, S.-W. Chung, Y.B. Luo. Molecular phylogeny of Cypripedium (Orchidaceae: Cypripedioideae) inferred from multiple nuclear and chloroplast regions. Molecular Phylogenetics and Evolution 61, 308 (2011). É. Aguirre-Planter, J.P. Jaramillo-Correa, S. Gómez-Acevedo, D.P. Khasa, J. Bousquet, L.E. Eguiarte. Phylogeny, diversification rates and species boundaries of Mesoamerican firs (Abies, Pinaceae) in a genus-wide context. Molecular Phylogenetics and Evolution 62, 263 (2012). A.J. Eckert, B.D. Hall. Phylogeny, historical biogeography, and patterns of diversification for Pinus (Pinaceae): Phylogenetic tests of fossil-based hypotheses. Molecular Phylogenetics and Evolution 40, 166 (2006). D.S. Gernandt, G.G. López, S.O. García, A. Liston. Phylogeny and classification of Pinus. Taxon 54, 29 (2005). D.C. Albach, H.M. Meudt, B. Oxelman. Piecing together the ‘‘new’’ Plantaginaceae. American Journal of Botany 92, 297 (2005). Y. Bouchenak-Khelladi, N. Salamin, V. Savolainen, F. Forest, M.V.D. Bank, M.W. Chase, T.R. Hodkinson. Large multi-gene phylogenetic trees of the grasses (Poaceae): Progress towards complete tribal and generic level sampling. Molecular Phylogenetics and Evolution 47, 488 (2008). 61 Polemoniaceae Polygonaceae Proteaceae Ranunculaceae Rosaceae/Rosales L.M. Giussani, J.H. Cota-Sánchez, F.O. Zuloaga, E.A. Kellogg. A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis. American Journal of Botany 88: 1993 (2001). GPWG. Phylogeny and subfamilial classification of the grasses (Poaceae). Annals of the Missouri Botanical Garden 88, 373 (2001). P.M. Peterson, K. Romaschenko, G. Johnson. A classification of the Chloridoideae (Poaceae) based on multi-gene phylogenetic trees. Molecular Phylogenetics and Evolution 55, 580 (2010). A. Teerawatananon, S.W.L. Jacobs, T.R. Hodkinson. Phylogenetics of Panicoideae (Poaceae) based on chloroplast and nuclear DNA sequences. Telopea 13, 115 (2011). W. Zhang. Phylogeny of the Grass Family (Poaceae) from rpl16 Intron Sequence Data. Molecular Phylogenetics and Evolution 15, 135 (2000). L.A. Prather, C.J. Ferguson & R.K. Jansen. Polemoniaceae phylogeny and classification: implications of sequence data from the chloroplast gene ndhF. American Journal of Botany 87, 1300 (2000). A. Sanchez, T.M. Schuster, K.A. Kron. A Large-Scale Phylogeny of Polygonaceae Based on Molecular Data. International Journal of Plant Sciences 170, 1044 (2009). P.H. Weston, N.P. Barker. A new suprageneric classification of the Proteaceae, with an annotated checklist of genera. Telopea 11, 314 (2006). Y.-F. Cai, S.-W. Li, Y. Liu, S. Quan, M. Chen, Y.-F. Xie, H.-Z. Jiang, E.-Z. Wei, N.-W. Yin, L. Wang, R. Zhang, C.-I. Huang, X.-H. He, M.-F. Jiang. Molecular phylogeny of Ranunculaceae based on internal transcribed spacer sequences. African Journal of Biotechnology 8, 5215 (2009). K. Emadzade, C. Lehnebach, P. Lockhart, E Hörandl. A molecular phylogeny, morphology and classification of genera of Ranunculeae (Ranunculaceae). Taxon 59: 809 (2010). W. Wang, A. Lu, Y. Ren, M.E. Endress, Z. Chen. Phylogeny and classification of Ranunculales: evidence from four molecular loci and morphological data. Perspectives in Plant Ecology, Evolution and Systematics 11, 81 (2009). D. Potter, T. Eriksson, R.C. Evans, S. Oh, J.E.E. Smedmark, D.R. Morgan, M. Kerr, K.R. 62 Rubiaceae Sapindaceae Taxaceae Robertson, M. Arsenault, T.-A. Dickinson, C.S. Campbell. Phylogeny and classification of Rosaceae. Plant Systematics and Evolution 266, 5 (2007). S.-D. Zhang, D.E. Soltis, Y. Yang, D.-Z. Li, T.-S. Yi. Multi-gene analysis provides a well-supported phylogeny of Rosales. Molecular Phylogenetics and Evolution 60, 21 (2011). B. Bremer, T. Eriksson. Time Tree of Rubiaceae: Phylogeny and Dating the Family, Subfamilies, and Tribes. International Journal of Plant Sciences 170, 766 (2009). S. Buerki, P.P. Lowry, N. Alvarez, S.G. Razafimandimbison, P. Küpfer, M.W. Callmander. Phylogeny and circumscription of Sapindaceae revisited: molecular sequence data, morphology and biogeography support recognition of a new family, Xanthoceraceae. Plant Ecology and Evolution 143, 148 (2010). R.A. Price. Generic and familial relationships of the Taxaceae from rbcL and matK sequence comparisons. Acta Horticulturae 615, 235 (2003). 63 Appendix S6. COMPADRE funding support and extended acknowledgements We acknowledge the following funding agencies in the support of the COMPADRE Plant Matrix Database: Period Financial support Leader/recipient 1989-1994 The British Council (UK) Jonathan Silvertown 1990-1992 Consejo Nacional de Ciencia y Tecnologia (Mexico) Miguel Franco 1993-1996 Academia Mexicana de Ciencias (Mexico) Miguel Franco 1994-1996 The Royal Society of London (UK) Jonathan Silvertown 1999-2000 The Ferguson Trust. Open University (UK) Jonathan Silvertown & Miguel Franco 1999-2000 Consejo Nacional de Ciencia y Tecnología (Mexico) Miguel Franco Dirección General Asuntos del Personal Académico, Universidad Nacional 1994-1996 Miguel Franco Autónoma de México (Mexico) 2006-2007 Natural Environment Research Council (UK) Dave Hodgson 64 2006-2008 Personal funds Roberto Salguero-Gómez 2007-2010 Australian Research Council (Australia) Yvonne Buckley Australian & New Zealand Vegetation Function Network (Australia & New 2007-2010 Yvonne Buckley Zealand) 2008-2010 Reese Family Foundation (USA) Roberto Salguero-Gómez 2009-2012 European Social Fund (Europe) Dave Hodgson & Stuart Townley 2011 Max Planck Institute for Demographic Research (Germany) Roberto Salguero-Gómez Strategic Environmental Research and Development Program, Department of 2011-2013 Maile Neel & William Fagan Defense (US) 2012-2014 Australian Research Council (Australia) Yvonne Buckley & Glenda Wardle 2012-2014 Max Planck Institute for Demographic Research (Germany) Roberto Salguero-Gómez & Owen Jones 2014-2016 Australian Research Council (Australia) Roberto Salguero-Gómez 2014-2017 Natural Environmental Research Council (UK) David Hodgson 65 The following is a list of extended acknowledgement to funding agencies that supported the time each researcher allocated to the preparation of the present manuscript: R.S.-G. was supported by the Australian Research Council DECRA fellowship and the Max Planck Institute for Demographic Research. J.C.-C. was supported by the National Socio-Environmental Synthesis Center. Y.M.B. was supported by a Marie Curie Reintegration grant. H.C. was supported by an ERC Advanced Grant 322989 and National Science Foundation Grant DEB-1257545. T.T. was supported by a Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science, KAKENHI 25340115. G.M.W was supported by an Australian Research Council Discovery grant. 66 Appendix S7. Author contributions The authorship and authorship order of this manuscript was determined following the ICMJE authorship standards (http://www.icmje.org/recommendations/browse/roles-and-responsibilities/defining-the-role-of-authors-and-contributors.html), aided by the table of contributions (below). The first two positions correspond to the leaders of this project, followed by the core committee members (See Supporting Information Appendix S1) in order of decreasing contributions, followed by the digitization team in alphabetic order, followed by the science committee members in alphabetic order; last, senior authorship is shared among the founders of COMPADRE and its current grand-vision exponent. The authors below are organized in alphabetical last name order. The definitions of each task are: - Project vision and scope: Founded, developed and/or organized the current staff and database structure. - Digitization of data: digitization of information into COMPADRE Plant Matrix Database v. 3.0, previous versions, and any other independent database that has been since integrated into COMPADRE. - Data error check: Implementation of protocols for error checking and of “hand” error checking of digitized data. - Organization of database: Set the standards for what variables, with what options and in what ways to archive information in COMPADRE. 67 - Online portal: Outlined the organization of the portal, the rules of access and distribution of sub-sites, as well as its oversaw its programming outcomes. - Phylogenetic tree: Construction of phylogenetic tree of species released in COMPADRE v. 3.0, pruning and integration into database. - R scripts: Developed R scripts to manipulated matrices in COMPADRE and ancillary information. - Analyses: Carried out analyses presented for summary statistics in the manuscript. - Wrote paper: Wrote the first full draft of the manuscript, including tables, figures and references, and integrated posterior comments by coauthors. - Edited paper: Provided significant comments to the paper, as described by the authorship standards of the ICMJE. - Compiled Supporting Information Appendixes: Organized and wrote the first full draft of the SOM, and integrated posterior comments by coauthors. 68 Altwegg Archer Baudisch Buckley Caswell Che-Castaldo Colchero Conde Brinks de Buhr de Kroon Davison Dong Farack Franco Gottschalk 3 4 2§ 2 2 2 3 2 5 4 3 Hartmann Henning Hodgson 4 4 3 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * 69 Edited SIAs Compiled SIAs Edited paper Wrote paper Analyses R scripts Phylogenetic tree Online portal Organization of database Data error check * * * § 3 4 3 4 Digitization of data Project vision and scope Database role Authors * * * * * * * * Hoppe Jens Jones Lebreton Metcalf Neel Parker Römer Ruoff Salguero-Gómez Scheuerlein Takada Valverde Vaupel Velez-Espino Dirk Vieregg Wardle Wille Zeh 5 5 1,2 3 3 3 3 4 4 1,2 2 3 3 2 3 6 3 4 4 * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * Values for database role: 1 COMPADRE team leader; 2 COMPADRE Core Committee member; 3 COMPADRE Science Committee member; 4 COMPADRE Digitization Team member; 5 Past COMPADRE Digitization Team member; 6 IT support. See Supporting Information Appendix S1. §No longer an active member of COMPADRE. 70 Appendix S8. Supporting Information References Caswell, H. (2001) Matrix Population Models: Construction, Analysis, and Interpretation, 2nd edition edn. Sinauer Associates, Inc. Cochran, M.E. & Ellner, S. (1992) Simple methods for calculating age-based lifehistory parameters for stage-structured populations. Ecological Monographs, 62, 345-364. Morris, W.F. & Doak, D.F. (2002) Quantitative Conservation Biology: Theory and Practice of Population Viability Analysis. Sinauer Associates, Sunderland, MA, USA. Metcalf, C.J.E., S. McMahon, R. Salguero-Gómez, and E. Jongejans. (2013) IPMpack: an R package for integral projection models. Methods in Ecology and Evolution 4: 195-200. Stubben, C. & Milligan, B. (2007) Estimating and analyzing demographic models using the popbio package in R. Journal of Statistical Software, 22, 1-23. Stott, I., Hodgson, D.J. & Townley, S. (2012) popdemo: an R package for population demography using projection matrix analysis. Methods in Ecology and Evolution, 3, 797-802. 71
