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664 results on '"Royal Botanic Garden [Edinburgh]"'

1. Photograph of Delegates

Author: Royal Botanic Garden Edinburgh
Subjects: Botany, QK1-989
Abstract: Photograph of Delegates
Published: 2018
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2. Categorization of plant uses utilized by the inhabitants of urban and rural areas of Peru

Author: Albán-Castillo, Joaquina, Departamento de Etnobotánica y Botánica Económica. Museo de Historia Natural. Universidad Nacional Mayor de San Marcos. Apartado 14-0434, Lima 14, Chilquillo Torres, Eder, Departamento de Etnobotánica y Botánica Económica. Museo de Historia Natural. Universidad Nacional Mayor de San Marcos. Apartado 14-0434, Lima 14, PERÚ. Programa de Pós-Graduação em Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, BRAZIL, Melchor-Castro, Briggitthe, Departamento de Etnobotánica y Botánica Económica. Museo de Historia Natural. Universidad Nacional Mayor de San Marcos. Apartado 14-0434, Lima 14, PERÚ. Institute of Molecular Plant Sciences. School of Biological Sciences, The University of Edinburgh, Edinburgh, UNITED KINGDOM Tropical Diversity Section, Royal Botanic Garden Edinburgh, 20A Inverleith Row, Edinburgh, UNITED KINGDOM, Cochachin Guerrero, Elizabeth, Castillo Vera, Hellen, Hurtado-Huarcaya, José, Departamento de Etnobotánica y Botánica Económica. Museo de Historia Natural. Universidad Nacional Mayor de San Marcos. Apartado 14-0434, Lima 14, PERÚ Departamento de Biología. Facultad de Ciencias. Universidad Nacional Agraria La Molina. Av. Universidad S/N, La Molina, Lima., and Cruz-Ríos, Isabeu
Subjects: Use of plant resources, categorization, traditional knowledge, Peru, uso de recursos vegetal, categorización, conocimiento tradicional, Perú
Abstract: En la actualidad el uso y aprovechamiento de los recursos vegetales ha derivado en numerosas investigaciones etnobotánicas, las cuales vienen documentando una rápida erosión de conocimientos tradicionales en las culturas nativas peruanas, incentivando su preservación y consecuente revalorización. Con el fin de facilitar el análisis de la data obtenida en los múltiples estudios realizados, esta investigación constituye una aproximación de los criterios de clasificación de las categorías de uso de las especies vegetales asociadas a la vida y cultura del poblador peruano. La definición de las categorías de uso presentes en este documento constituye el resultado de 130 expediciones de campo realizadas por los autores en comunidades costeras, andinas y amazónicas peruanas, así como en la evaluación de 17 281 registros de usos documentados en nueve herbarios peruanos y extranjeros. Se proponen nueve categorías de usos, subdivididas en 60 subcategorías: medicinal (21), social (8), alimento humano (3), alimento para animales (3), materiales (10), tóxicas (4), etnoveterinario (2), ambiental (6) y combustible (3). Se concluye que la propuesta de una estandarización de categorías de uso facilitará la compilación y análisis del uso de plantas dentro de una comunidad, y a la vez permitirá realizar comparaciones entre ecosistemas y/o comunidades. Nowadays, the use and harnessing of vegetal resources has resulted in much ethnobotanical research, which has documented a rapid erosion of traditional knowledge in native Peruvian cultures, encouraging its preservation and consequent revaluation. In order to ease the analysis of the data obtained in the multiple studies that have been made, this proposal constitutes an approximation of the classification criteria for the categories of plant uses associated with the life and culture of Peruvian inhabitants. These use categories’ definitions are the result of 130 field expeditions carried out by the authors, in coastal, Andean and Amazon Peruvian communities, as well as the evaluation of 17 281-use registries documented in nine foreign and Peruvian herbaria. The nine use categories proposed in this article, are divided in 60 subcategories: medicinal (21), social (8), human food (3), animal food (3), materials (10), toxic (4), ethnoveterinary medicine (2), environmental (6) and fuel (3). The authors conclude that the proposal of the use categories standardization will simplify the compilation and analysis of plant uses in a community, and it will allow making comparisons between different ecosystems and communities.
Published: 2021

3. [Dr. Hope's elementa botanici]

Author: Hope, John 1725-1786, Linné, Carl von, 1707-1778, Wright, William, 1735-1819, Royal Botanic Garden, Edinburgh, Royal Botanic Garden Edinburgh, Hope, John 1725-1786, Linné, Carl von, 1707-1778, Wright, William, 1735-1819, and Royal Botanic Garden, Edinburgh
Subjects: Botanic gardens, History of science, Plant catalogues, Royal Botanic Garden Edinburgh

4. [Dr. Hope's elementa botanici]

Author: Hope, John 1725-1786, Linné, Carl von, 1707-1778, Wright, William, 1735-1819, Royal Botanic Garden, Edinburgh, Royal Botanic Garden Edinburgh, Hope, John 1725-1786, Linné, Carl von, 1707-1778, Wright, William, 1735-1819, and Royal Botanic Garden, Edinburgh
Subjects: Botanic gardens, History of science, Plant catalogues, Royal Botanic Garden Edinburgh

5. List of seeds collected during ...

Author: Royal Botanic Garden, Edinburgh, Missouri Botanical Garden, Peter H. Raven Library, and Royal Botanic Garden, Edinburgh
Subjects: Catalogs, Catalogs and collections, Edinburgh, Royal Botanic Garden, Edinburgh, Scotland, Seeds
Published: 1888

6. List of seeds collected during ...

Author: Royal Botanic Garden, Edinburgh, Missouri Botanical Garden, Peter H. Raven Library, and Royal Botanic Garden, Edinburgh
Subjects: Catalogs, Catalogs and collections, Edinburgh, Royal Botanic Garden, Edinburgh, Scotland, Seeds

7. List of seeds collected during ...

Author: Royal Botanic Garden, Edinburgh, Missouri Botanical Garden, Peter H. Raven Library, and Royal Botanic Garden, Edinburgh
Subjects: Catalogs, Catalogs and collections, Edinburgh, Royal Botanic Garden, Edinburgh, Scotland, Seeds

8. List of seeds collected during ...

Author: Royal Botanic Garden, Edinburgh, Missouri Botanical Garden, Peter H. Raven Library, and Royal Botanic Garden, Edinburgh
Subjects: Catalogs, Catalogs and collections, Edinburgh, Royal Botanic Garden, Edinburgh, Scotland, Seeds

9. Notes from the Royal Botanic Garden, Edinburgh.

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals
Published: 1900

10. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

11. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

12. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

13. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

14. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

15. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

16. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

17. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

18. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

19. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

20. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

21. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

22. Notes from the Royal Botanic Garden, Edinburgh

Author: Royal Botanic Garden, Edinburgh and Missouri Botanical Garden, Peter H. Raven Library
Subjects: Botany, Periodicals

23. A genome size and phylogenetic survey of Mediterranean Tripleurospermum and Matricaria (Anthemideae, Asteraceae)

Author: Dirección General de Investigación Científica y Técnica, DGICT (España), Generalitat de Catalunya, The Scientific and Technological Research Council of Turkey, Ministerio de Economía y Competitividad (España), Royal Botanic Garden Edinburgh, Inceer, Huseyin, Garnatje, Teresa, Hayõrlõoğlu-Ayaz, Sema, Pascual-Díaz, Joan Pere, Vallès, Joan, Garcia, Sònia, Dirección General de Investigación Científica y Técnica, DGICT (España), Generalitat de Catalunya, The Scientific and Technological Research Council of Turkey, Ministerio de Economía y Competitividad (España), Royal Botanic Garden Edinburgh, Inceer, Huseyin, Garnatje, Teresa, Hayõrlõoğlu-Ayaz, Sema, Pascual-Díaz, Joan Pere, Vallès, Joan, and Garcia, Sònia
Abstract: The study of genome size variation can contribute valuable information on species relationships as well as correlate to several morphological or ecological features, among others. Here we provide an extensive report on genome sizes on genus Tripleurospermum and its closely related genus Matricaria, which are two typically Mediterranean genera particularly widespread and diverse in Turkey, the origin of most of the populations here studied. We analyse and discuss genome size variation in the first relatively complete molecular phylogenetic framework of Tripleurospermum (based on ITS and ETS ribosomal DNA–rDNA–regions). We find cases of intraspecific genome size variation, which could be taxonomically significant. Genome downsizing is also detected as the typical response to polyploidisation in Tripleurospermum taxa, being most conspicuous at the tetraploid level. Several positive correlations with genome size, including those with pollen and stomatal size or cypsela length, among others, are also found. Remarkably, taxa presenting rhizomes tend to present higher genome sizes, confirming a trend to accumulate nuclear DNA in such species, which could be explained by the nutrient reserves availability in their storage organs, allowing genome expansion, or by the lower rates of sexual reproduction in rhizomatous taxa.
Published: 2018

24. エジンバラ植物園における野外実習 : 本学「植物学野外実習」との比較

Author: Louis Ronse De Craene, IWAMOTO,Akitoshi, Louis Ronse De Craene(Royal Botanic Garden Edinburgh), and IWAMOTO,Akitoshi(Department of Biology, Tokyo Gakugei University)
Subjects: field trip, Royal Botanic Garden Edinburgh, Tokyo Gakugei University, plant taxonomy, STYP:大学, ETYP:教育関連論文
Published: 2014

25. Using Model Analysis to Unveil Hidden Patterns in Tropical Forest Structures

Author: N. Ayyappan, Frédéric Mortier, David Harris, Faustin Boyemba Bosela, Thomas W. Crowther, Alfred Ngomanda, Pierre Couteron, Nestor Laurier Engone Obiang, Géraldine Derroire, Sylvie Gourlet-Fleury, John R. Poulsen, Nicolas Picard, Bonaventure Sonké, Connie J. Clark, Eric Forni, Pierre Ploton, Fabrice Bénédet, Jingjing Liang, Jean-François Bastin, Groupement d'Interêt Public Ecosystèmes Forestiers GIP ECOFOR (GIP ECOFOR ), Forêts et Sociétés (UPR Forêts et Sociétés), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Département Environnements et Sociétés (Cirad-ES), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Purdue University [West Lafayette], Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Institut Français de Pondichéry (IFP), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), Université de Kisangani, Duke University [Durham], Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Centre National de la Recherche Scientifique et Technologique (CNRST), Royal Botanic Garden [Edinburgh], University of Yaoundé [Cameroun], ANR-18-CE02-0025,GAMBAS,Nouvelles avancées dans la modélisation de la biodiversité et des services écosystémiques : améliorations statistiques et pertinences écologiques des modèles de distribution multi-espèces(2018), and Royal Botanic Garden Edinburgh
Subjects: 0106 biological sciences, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 01 natural sciences, Allométrie, K01 - Foresterie - Considérations générales, parcelle, Forêt tropicale humide, QH540-549.5, Ecology, type forestier (composition botanique), U10 - Informatique, mathématiques et statistiques, Null model, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Correlation, Forest typology, Geography, forest structure, F40 - Écologie végétale, Evolution, 010603 evolutionary biology, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, QH359-425, Ordination, Ecology, Evolution, Behavior and Systematics, 010604 marine biology & hydrobiology, Rain forest, 15. Life on land, Tropical forest, Structure du peuplement, forest typology, null model, pattern and process, rain forest, correlation, ordination, Modélisation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Modèle végétal, Pattern and process
Abstract: When ordinating plots of tropical rain forests using stand-level structural attributes such as biomass, basal area and the number of trees in different size classes, two patterns often emerge: a gradient from poorly to highly stocked plots and high positive correlations between biomass, basal area and the number of large trees. These patterns are inherited from the demographics (growth, mortality and recruitment) and size allometry of trees and tend to obscure other patterns, such as site differences among plots, that would be more informative for inferring ecological processes. Using data from 133 rain forest plots at nine sites for which site differences are known, we aimed to filter out these patterns in forest structural attributes to unveil a hidden pattern. Using a null model framework, we generated the anticipated pattern inherited from individual allometric patterns. We then evaluated deviations between the data (observations) and predictions of the null model. Ordination of the deviations revealed site differences that were not evident in the ordination of observations. These sites differences could be related to different histories of large-scale forest disturbance. By filtering out patterns inherited from individuals, our model analysis provides more information on ecological processes., Frontiers in Ecology and Evolution, 9, ISSN:2296-701X
Published: 2021

26. Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Author: Couvreur, Thomas, Dauby, Gilles, Blach-Overgaard, Anne, Deblauwe, Vincent, Dessein, Steven, Droissart, Vincent, Hardy, Oliver, Harris, David, Janssens, Steven, Ley, Alexandra, Mackinder, Barbara, Sonké, Bonaventure, Sosef, Marc, Stévart, Tariq, Svenning, Jens-Christian, Wieringa, Jan, Faye, Adama, Missoup, Alain, Tolley, Krystal, Nicolas, Violaine, Ntie, Stéphan, Fluteau, Frédéric, Robin, Cécile, Guillocheau, Francois, Barboni, Doris, Sepulchre, Pierre, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aarhus University [Aarhus], University of California [Los Angeles] (UCLA), University of California (UC), Meise Botanic Garden [Belgium] (Plantentuin), Université libre de Bruxelles (ULB), Université de Yaoundé I, Missouri Botanical Garden, Royal Botanic Garden [Edinburgh], Martin-Luther-University Halle-Wittenberg, Naturalis Biodiversity Center [Leiden], LNRPV Laboratoire National de Recherches et de Productions Végétales, Institut Sénégalais de Recherches Agricoles [Dakar] (ISRA), LPF, University of Douala, South African National Biodiversity Institute, University of the Witwatersrand [Johannesburg] (WITS), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Université des Sciences et Techniques de Masuku (USTM), Institut de Physique du Globe de Paris (IPGP (UMR_7154)), Institut national des sciences de l'Univers (INSU - CNRS)-Université de La Réunion (UR)-Institut de Physique du Globe de Paris (IPG Paris)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Géosciences Rennes (GR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Centre européen de recherche et d'enseignement des géosciences de l'environnement (CEREGE), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Collège de France (CdF (institution))-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire des Sciences du Climat et de l'Environnement [Gif-sur-Yvette] (LSCE), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Modélisation du climat (CLIM), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), ANR-15- CE02-0002-01, Agence Nationale de la Recherche, RAINBIO, Fondation pour la Recherche sur la Biodiversite, ANR-15-CE02-0002,AFRODYN,Forêts tropicales humides d'Afrique Centrale : dynamiques passées et résiliences futures(2015), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), University of California, Botanic Garden Meise, Royal Botanic Garden Edinburgh, Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université des Sciences et Techniques de Masuku [Franceville, Gabon] (USTM), Institut de Physique du Globe de Paris (IPGP), Institut national des sciences de l'Univers (INSU - CNRS)-IPG PARIS-Université de La Réunion (UR)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Centre National de la Recherche Scientifique (CNRS), Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), and Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)
Subjects: [SDU.STU.TE]Sciences of the Universe [physics]/Earth Sciences/Tectonics, tropical Africa, Cenozoic, dated molecular phylogenies, palaeoclimate models, African geology, speciation models, Original Articles, Biodiversity, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Plants, [SDU.STU.CL]Sciences of the Universe [physics]/Earth Sciences/Climatology, Animals, Original Article, fossils, Biologie, Ecosystem, Phylogeny, ComputingMilieux_MISCELLANEOUS
Abstract: Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context., SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2021

27. Metadata standards and practical guidelines for specimen and DNA curation when building barcode reference libraries for aquatic life

Author: Magali Schweizer, Frederik Leliaert, Jan Pawlowski, Rodolphe Rougerie, Frédéric Rimet, Torbjørn Ekrem, Alexis Canino, Teofana Chonova, David G. Mann, Agnès Bouchez, Régis Lionel Vivien, Christian Chauvin, Chloé Goulon, Valentin Vasselon, Romain Gastineau, Rosa Trobajo, Christophe Laplace-Treyture, Jonas Zimmermann, Eva Aylagas, Wolf-Henning Kusber, Andrzej Witkowski, Vona Méléder, Frédéric Marchand, Sinziana F. Rivera, Maria Kahlert, Muriel Gugger, Filipe O. Costa, Maria Holzmann, Benoît J.D. Ferrari, Serena Rasconi, Alexander M. Weigand, Regine Jahn, Fedor Čiampor, Florian Leese, Ángel Borja, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), King Abdullah University of Science and Technology (KAUST), Basque Research and Technology Alliance (BRTA), King Abdulaziz University, Ecosystèmes aquatiques et changements globaux (UR EABX), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Slovak Academy of Science [Bratislava] (SAS), Universidade do Minho, Swiss Centre for Applied Ecotoxicology (Ecotox Center), Ecole Polytechnique Fédérale de Lausanne (EPFL), Technical university of Szczecin, Collection des Cyanobactéries, Institut Pasteur [Paris], University of Geneva [Switzerland], Freie Universität Berlin, Swedish University of Agricultural Sciences (SLU), Universitat Duisberg-Essen, Botanic Garden Meise, Institute of Agrifood Research and Technology [Sant Carles de la Ràpita] (IRTA), Institute of Agrifood Research and Technology (IRTA), Royal Botanic Garden Edinburgh, Unité Expérimentale d'Ecologie et d'Ecotoxicologie Aquatique - U3E (Rennes, France) (U3E ), Université de Nantes (UN), Polish Academy of Sciences (PAN), ID-Gene ecodiagnostics [Geneva], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Laboratoire de Planétologie et Géodynamique [UMR 6112] (LPG), Université d'Angers (UA)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), SCIMABIO Interface SAS, Musée National d'Histoire Naturelle de Luxembourg (MNHN), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), This paper was written under COST Action DNAqua-Net. The European COST Action DNAqua-Net (CA 15219 collaborative network which gathers several hundreds of scientists and water managers, with the objective of developing new genetic tools for bioassessment and monitoring of aquatic ecosystems (Leese et al. 2016)., European Project, West Pomeranian University of Technology in Szczecin (ZUT), Universidade do Minho = University of Minho [Braga], Université de Genève = University of Geneva (UNIGE), Institut Pasteur [Paris] (IP), Meise Botanic Garden [Belgium] (Plantentuin), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Royal Botanic Garden [Edinburgh], Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Producció Animal, and Aigües Marines i Continentals
Subjects: 0106 biological sciences, 0301 basic medicine, Computer science, [SDV]Life Sciences [q-bio], Ciências Biológicas [Ciências Naturais], computer.software_genre, Barcode, 01 natural sciences, DNA barcoding, law.invention, law, QH540-549.5, aquatic organisms, media_common, Database, Ecology, Quality, Voucher, Identification (information), Aquatic organisms, quality, Biologie, Traceability, media_common.quotation_subject, reference library, Engenharia e Tecnologia::Engenharia do Ambiente, 010603 evolutionary biology, 03 medical and health sciences, Genetics (medical genetics to be 30107 and agricultural genetics to be 40402), Genetics, Quality (business), Relevance (information retrieval), 14. Life underwater, Molecular Biology, Nature and Landscape Conservation, Engenharia do Ambiente [Engenharia e Tecnologia], Metadata, Ciências Naturais::Ciências Biológicas, metadata, barcode, Reference library, DNA, 030104 developmental biology, traceability, Animal Science and Zoology, computer
Abstract: DNA barcoding and metabarcoding is increasingly used to effectively and precisely assess and monitor biodiversity in aquatic ecosystems. As these methods rely on data availability and quality of barcode reference libraries, it is important to develop and follow best practices to ensure optimal quality and traceability of the metadata associated with the reference barcodes used for identification. Sufficient metadata, as well as vouchers, corresponding to each reference barcode must be available to ensure reliable barcode library curation and, thereby, provide trustworthy baselines for downstream molecular species identification. This document (1) specifies the data and metadata required to ensure the relevance, the accessibility and traceability of DNA barcodes and (2) specifies the recommendations for DNA harvesting and for the storage of both voucher specimens/samples and barcode data, (undefined)
Published: 2021

28. DNA barcoding identifies cryptic animal tool materials

Author: Steele, Matthew, Neaves, Linda, Klump, Barbara, St Clair, James, Fernandes, Joana, Hequet, Vanessa, Shaw, Phil, Hollingsworth, Peter, Rutz, Christian, University of St Andrews [Scotland], Royal Botanic Garden Edinburgh, School of Biology [University of St Andrews], Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche pour le Développement (IRD [Nouvelle-Calédonie]), and Royal Botanic Garden [Edinburgh]
Subjects: Crow, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, New Caledonian, Animal construction behavior, DNA barcoding, Tool use, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Nest building
Abstract: International audience; Some animals fashion tools or constructions out of plant materials to aid foraging, reproduction, self-maintenance, or protection. Their choice of raw materials can affect the structure and properties of the resulting artifacts, with considerable fitness consequences. Documenting animals’ material preferences is challenging, however, as manufacture behavior is often difficult to observe directly, and materials may be processed so heavily that they lack identifying features. Here, we use DNA barcoding to identify, from just a few recovered tool specimens, the plant species New Caledonian crows (Corvus moneduloides) use for crafting elaborate hooked stick tools in one of our long-term study populations. The method succeeded where extensive fieldwork using an array of conventional approaches—including targeted observations, camera traps, radio-tracking, bird-mounted video cameras, and behavioral experiments with wild and temporarily captive subjects—had failed. We believe that DNA barcoding will prove useful for investigating many other tool and construction behaviors, helping to unlock significant research potential across a wide range of study systems.DNA sequence data have been deposited in GenBank (MT366813–MT366824 and MT366951–MT366962). Sequence alignments and resulting phylogenetic trees are deposited in Dryad (https://doi.org/10.5061/dryad.d7wm37q1v) (19), including GenBank accession numbers.
Published: 2021

29. Genome-enabled phylogenetic and functional reconstruction of an araphid pennate diatom Plagiostriata sp. CCMP470, previously assigned as a radial centric diatom, and its bacterial commensal

Author: Elena Kazamia, Shinya Sato, Fabio Rocha Jimenez Vieira, Patrick Wincker, Zoltán Füssy, Deepak Nanjappa, Jean-Marc Aury, Olivier Jaillon, David G. Mann, Miroslav Oborník, Sergio A. Muñoz-Gómez, Leila Tirichine, Adriana Zingone, Chris Bowler, Alaguraj Veluchamy, Richard G. Dorrell, Roland Heilig, Fukui Prefectural University [Fukui, Japon], Stazione Zoologica Anton Dohrn (SZN), Stony Brook University [SUNY] (SBU), State University of New York (SUNY), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Unité de fonctionnalité et ingénierie de protéines (UFIP), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute of Parasitology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Charles University [Prague] (CU), University of South Bohemia, Dalhousie University [Halifax], Royal Botanic Garden [Edinburgh], Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), D.N. acknowledges a fellowship funded by the Stazione Zoologica Anton Dohrn (SZN) within the SZN-Open University Ph.D. program. R.G.D. was supported by a CNRS Momentum Fellowship and E.K. was supported by the Marie Curie Postdoctoral Fellowship IRONCOMM. Work in the Bowler lab is supported by the Investissements d’Avenir programmes PSL and MEMOLIFE: MEMO LIFE (ANR-10-LABX-54), and PSL*Research University (ANR-11-IDEX-0001-02)., ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Royal Botanic Garden Edinburgh, Institute of Agrifood Research and Technology (IRTA), Producció Animal, Aigües Marines i Continentals, Bodescot, Myriam, Memory in living systems: an integrated approach - - MEMOLIFE2010 - ANR-10-LABX-0054 - LABX - VALID, and INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE - - Amidex2011 - ANR-11-IDEX-0001 - IDEX - VALID
Subjects: 0106 biological sciences, 0301 basic medicine, Science, Lineage (evolution), [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Microbiology, 01 natural sciences, Genome, Article, Evolution, Molecular, 03 medical and health sciences, Algae, Phylogenetics, Genus, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 14. Life underwater, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Phylogeny, Diatoms, Multidisciplinary, Ecology, biology, Phylogenetic tree, Gene Expression Profiling, fungi, biology.organism_classification, Biological Evolution, Rhodobacterales, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, 030104 developmental biology, Diatom, Evolutionary biology, Medicine, Transcriptome, 010606 plant biology & botany
Abstract: Diatoms are an ecologically fundamental and highly diverse group of algae, dominating marine primary production in both open-water and coastal communities. The diatoms include both centric species, which may have radial or polar symmetry, and the pennates, which include raphid and araphid species and arose within the centric lineage. Here, we use combined microscopic and molecular information to reclassify a diatom strain CCMP470, previously annotated as a radial centric species related to Leptocylindrus danicus, as an araphid pennate species in the staurosiroid lineage, within the genus Plagiostriata. CCMP470 shares key ultrastructural features with Plagiostriata taxa, such as the presence of a sternum with parallel striae, and the presence of a highly reduced labiate process on its valve; and this evolutionary position is robustly supported by multigene phylogenetic analysis. We additionally present a draft genome of CCMP470, which is the first genome available for a staurosiroid lineage. 270 Pfams (19%) found in the CCMP470 genome are not known in other diatom genomes, which otherwise does not hold big novelties compared to genomes of non-staurosiroid diatoms. Notably, our DNA library contains the genome of a bacterium within the Rhodobacterales, an alpha-proteobacterial lineage known frequently to associate with algae. We demonstrate the presence of commensal alpha-proteobacterial sequences in other published algal genome and transcriptome datasets, which may indicate widespread and persistent co-occurrence.
Published: 2020

30. Cradles and museums of generic plant diversity across tropical Africa

Author: Dagallier, Léo-Paul, Janssens, Steven, Dauby, Gilles, Blach-Overgaard, Anne, MacKinder, Barbara, Droissart, Vincent, Svenning, Jens-Christian, Sosef, Marc, Stévart, Tariq, Harris, David, Sonké, Bonaventure, Wieringa, Jan, Hardy, Olivier, Couvreur, Thomas, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Botanic Garden Meise, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aarhus University [Aarhus], Royal Botanic Garden Edinburgh, Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), ANR-15-CE02-0002,AFRODYN,Forêts tropicales humides d’Afrique Centrale : dynamiques passées et résiliences futures(2015), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université libre de Bruxelles (ULB), Missouri Botanical Garden, Université de Yaoundé I, ANR-15-CE02-0002,AFRODYN,Forêts tropicales humides d'Afrique Centrale : dynamiques passées et résiliences futures(2015), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Meise Botanic Garden [Belgium] (Plantentuin), and Royal Botanic Garden [Edinburgh]
Subjects: Full Paper, Research, Museums, Biodiversity, mountains, Full Papers, Plants, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, CANAPE, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, East Africa, humanities, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, endemism, Africa, phylogenetic diversity, protected areas, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, angiosperms, Biologie, Phylogeny
Abstract: International audience; Determining where species diversify (cradles) and persist (museums) over evolutionary time is fundamental to understanding the distribution of biodiversity and for conservation prioriti-zation. Here, we identify cradles and museums of angiosperm generic diversity across tropical Africa, one of the most biodiverse regions on Earth. Regions containing nonrandom concentrations of young (neo-) and old (paleo-) endemic taxa were identified using distribution data of 1719 genera combined with a newly generated time-calibrated mega-phylogenetic tree. We then compared the identified regions with the current network of African protected areas (PAs). At the generic level, phylogenetic diversity and endemism are mainly concentrated in the biogeographically complex region of Eastern Africa. We show that mountainous areas are centres of both neo-and paleo-endemism. By contrast, the Guineo-Congolian lowland rain forest region is characterized by widespread and old lineages. We found that the overlap between centres of phylogenetic endemism and PAs is high (> 85%). We show the vital role played by mountains acting simultaneously as cradles and museums of tropical African plant biodiversity. By contrast, lowland rainforests act mainly as museums for generic diversity. Our study shows that incorporating large-scale taxonomically verified distribution datasets and mega-phylogenies lead to an improved understanding of tropical plant biodiversity evolution.
Published: 2020

31. The Treasure Vault Can be Opened : Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material

Author: Mihai Pușcaș, Sébastien Lavergne, Bogdan-Iuliu Hurdu, Martí Boleda, Niklaus E. Zimmermann, Inger Greve Alsos, Iva Pitelkova, Adriana Alberti, Peter M. Hollingsworth, Charles Pouchon, Cristina Roquet, Youri Lammers, Marie Kristine Føreid Merkel, Wilfried Thuiller, Eric Coissac, National Centre for Biosystematics [Oslo], Natural History Museum [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Génomique métabolique (UMR 8030), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institut Fédéral de Recherches sur la Forêt, la Neige et le Paysage (WSL), Institut Fédéral de Recherches [Suisse], Royal Botanic Garden [Edinburgh], UMR, Lab Ecol Alpine, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Royal Botanic Garden Edinburgh
Subjects: 0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Plant Science, rbcL, 01 natural sciences, Genome, DNA barcoding, chemistry.chemical_compound, chloroplast DNA, lcsh:Botany, Environmental DNA, VDP::Mathematics and natural science: 400, Ecology, biology, Silica gel, Nuclear ribosomal DNA, Boraginaceae, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], lcsh:QK1-989, Chloroplast DNA, Rbcl, Polar, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Plant DNA barcode, 010603 evolutionary biology, Article, 03 medical and health sciences, matK, Botany, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, polar, Phylogenomic, Ribosomal DNA, Ecology, Evolution, Behavior and Systematics, MatK, phylogenomic, alpine, plant DNA barcode, VDP::Matematikk og Naturvitenskap: 400, nuclear ribosomal DNA, biology.organism_classification, environmental DNA, Alpine, 030104 developmental biology, Herbarium, chemistry, ITS
Abstract: Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was &gt, 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
Published: 2020

32. The global abundance of tree palms

Author: Ekananda Paudel, Katrin Böhning-Gaese, Erika Berenguer, Edilson J. Requena-Rojas, Xinghui Lu, Luciana F. Alves, Yves Laumonier, Matt Bradford, Keith C. Hamer, Heike Culmsee, Robert M. Ewers, Jan Reitsma, Natacha Nssi Bengone, Anne Mette Lykke, Kuswata Kartawinata, Michael J. Lawes, Géraldine Derroire, Martin Gilpin, Jean-François Bastin, Rodolfo Vásquez Martínez, Laszlo Nagy, José Luís Camargo, Gabriella Fredriksson, Esteban Álvarez-Dávila, Casimiro Mendoza Bautista, Swapan Kumar Sarker, Jhon del Aguila-Pasquel, Ida Theilade, Erny Poedjirahajoe, Bonaventure Sonké, Jefferson S. Hall, Naret Seuaturien, Shin-ichiro Aiba, Simon L. Lewis, Francesco Rovero, Carlos Mariano Alvez-Valles, Donald R. Drake, Agustín Rudas Lleras, Lee J. T. White, Gerardo A.Aymard Corredor, Damien Catchpole, Tariq Stévart, Samuel Almeida, Janet Franklin, Mohammad Shah Hussain, Nicholas J. Berry, Jon C. Lovett, Hirma Ramírez-Angulo, Rafael de Paiva Salomão, Beatriz Schwantes Marimon, Onrizal Onrizal, Ted R. Feldpausch, Wannes Hubau, Ima Célia Guimarães Vieira, Thomas L. P. Couvreur, José Luís Marcelo Peña, Juliana Schietti, Ana Andrade, Anand Roopsind, Javier E. Silva-Espejo, Carlos Alfredo Joly, Fabrício Alvim Carvalho, Connie J. Clark, Kofi Affum-Baffoe, William E. Magnusson, Shengbin Chen, K. Anitha, Ni Putu Diana Mahayani, Flávia R. C. Costa, John R. Poulsen, Faridah Hanum Ibrahim, Aurélie Dourdain, Irie Casimir Zo-Bi, Heriberto David-Higuita, Rahmad Zakaria, Mario Percy Núñez Vargas, Karina Melgaço, Marcelo Trindade Nascimento, Damien Bonal, Murray Collins, Jos Barlow, Emilio Vilanova, Yadvinder Malhi, Andes Hamuraby Rozak, Timothy J. S. Whitfeld, Badru Mugerwa, Terry L. Erwin, John Pipoly, Bruno Hérault, Ervan Rutishauser, Anthony Di Fiore, William F. Laurance, Luzmila Arroyo, Jean-Louis Doucet, Lilian Blanc, Henrik Balslev, Percival Cho, Priya Davidar, Sonia Palacios-Ramos, John Terborgh, Peter M. Umunay, Shijo Joseph, Robert Muscarella, Massiel Corrales Medina, Rueben Nilus, Robert Steinmetz, Everton Cristo de Almeida, Rhett D. Harrison, Thomas E. Lovejoy, Peter S. Ashton, Sophie Fauset, Adriana Prieto, Christelle Gonmadje, Wolf L. Eiserhardt, Andreas Hemp, R. Nazaré O. de Araújo, Markus Fischer, Hoang Van Sam, Ferry Slik, Jianwei Tang, Luiz Menini Neto, Plínio Barbosa de Camargo, Tran Van Do, Hidetoshi Nagamasu, Aisha Sultana, Marc P. E. Parren, Carlos Reynel Rodriguez, Frans Bongers, Campbell O. Webb, Lan Qie, Jean Claude Razafimahaimodison, Justin Kassi, Kanehiro Kitayama, Francis Q. Brearley, Peter van der Hout, Nigel C. A. Pitman, Georgia Pickavance, Jérôme Millet, Joice Ferreira, Zorayda Restrepo Correa, Manichanh Satdichanh, Carlos Gabriel Hidalgo Pizango, Rodrigo Sierra, Oliver L. Phillips, Vianet Mihindou, William Milliken, Walter A. Palacios, Fernando Alzate Guarin, Charles E. Zartman, Abel Monteagudo Mendoza, Arachchige Upali Nimal Gunatilleke, Eddy Nurtjahya, Susan G. Laurance, Marcos Silveira, Janvier Lisingo, Nobuo Imai, Asyraf Mansor, Kenneth R. Young, Serge A. Wich, Ruwan Punchi-Manage, Christine B. Schmitt, Simone Aparecida Vieira, D. Mohandass, Thaise Emilio, Gemma Rutten, Fabian Brambach, Steven W. Brewer, Timothy R. Baker, Carolina V. Castilho, Timothy J. Killeen, Terry Sunderland, Lourens Poorter, Martin van de Bult, Feyera Senbeta, Eileen Larney, Bente B. Klitgård, Phourin Chhang, Hans ter Steege, Runguo Zang, Simon Willcock, Wendeson Castro, María Uriarte, Jean Philippe Puyravaud, Andrew R. Marshall, R. Toby Pennington, Jens-Christian Svenning, Jonathan Timberlake, Eurídice N. Honorio Coronado, Douglas Sheil, Susan K. Wiser, Lila Nath Sharma, Raman Sukumar, Jeanneth Villalobos Cayo, Andy Hector, Luis E.O.C. Aragao, Wanlop Chutipong, David Harris, Carlos A. Quesada, Thomas W. Gillespie, Alejandro Araujo Murakami, Edmund V. J. Tanner, Carlos E. Cerón Martínez, William J. Baker, Corneille E. N. Ewango, Nicolas Labrière, Paulo S. Morandi, Armando Torres-Lezama, David A. Neill, Edward L. Webb, Andreas Ensslin, David Campbell, Khalid Rehman Hakeem, Robert M. Kooyman, Aurora Levesley, Edmar Almeida de Oliveira, James A. Comiskey, Ben Hur Marimon-Junior, Hebbalalu S. Suresh, Ophelia Wang, Leandro Valle Ferreira, Luis Valenzuela Gamarra, Marc K. Steininger, P. Rama Chandra Prasad, Systems Ecology, Robert Muscarella, Uppsala University / Aarhus University, Thomas L. P. Couvreur, University of Montpellier, Luzmila Arroyo, Gabriel René Moreno Autonomous University, Plinio Barbosa de Camargo, CENA-USP, Jos Barlow, Lancaster University, Jean-François Bastin, ETH Zürich, Natacha Nssi Bengone, National Agency of National Parks of Gabon, Erika Berenguer, Lancaster University / University of Oxford, Nicholas Berry, The Landscapes and Livelihoods Group, Lilian Blanc, CIRAD / University of Montpellier, Katrin Böhning-Gaese, Senckenberg Biodiversity and Climate Research Centre / Goethe University, Damien Bonal, Université de Lorraine, Frans Bongers, Wageningen University & Research, Matt Bradford, CSIRO Land and Water, Percival Cho, Forest Department, Connie Clark, Duke University, Murray Collins, University of Edinburgh, James A. Comiskey, National Park Service / Smithsonian Institution, Flávia R. C. Costa, INPA, Géraldine Derroire, CIRAD, Anthony Di Fiore, University of Texas at Austin, Tran Van Do, Vietnamese Academy of Forest Sciences, Jean-Louis Doucet, Liège University, Aurélie Dourdain, CIRAD, Andreas Ensslin, University of Bern, Terry Erwin, Smithsonian Institution, Corneille E. N. Ewango, University of Kisangani, JOICE NUNES FERREIRA, CPATU, David J. Harris, Royal Botanic Garden Edinburgh, Rhett D. Harrison, World Agroforestry, East and Southern Africa Region, Andrew Hector, University of Oxford, Wannes Hubau, University of Leeds / Royal Museum for Central Africa, Mohammad Shah Hussain, University of Delhi, Faridah-Hanum Ibrahim, Universiti Putra Malaysia Bintulu Campus, Nobuo Imai, Tokyo University of Agriculture, Carlos A. Joly, UNICAMP, Shijo Joseph, Kerala University of Fisheries and Ocean Studies, Anitha K, Rainforest Traditions, Kuswata Kartawinata, The Field Museum of Natural History / Indonesian Institute of Sciences, Justin Kassi, Université Félix Houphouët-Boigny, Timothy J. Killeen, Universidad Autonoma Gabriel Rene Moreno, Kanehiro Kitayama, Kyoto University, Bente Bang Klitgård, Royal Botanic Gardens Kew, Michael J. Lawes, University of KwaZulu-Natal, Aurora Levesley, University of Leeds, Janvier Lisingo, Kisangani University, Thomas Lovejoy, George Mason University, Jon C. Lovett, University of Leeds / Royal Botanic Gardens Kew, Xinghui Lu, Liaocheng University, Anne Mette Lykke, Aarhus University, William E. Magnusson, INPA, Casimiro Mendoza Bautista, Universidad Mayor de San Simón, Vianet Mihindou, Agence Nationale des Parcs Nationaux / Ministère de la Forêt et de l’Environnement, Jérôme Millet, French Agency for Biodiversity, William Milliken, Royal Botanic Gardens Kew, D. Mohandass, Novel Research Academy, David A. Neill, Universidad Estatal Amazónica, Luiz Menini Neto, Universidade Federal de Juiz de Fora, Rueben Nilus, Forest Research Centre, Sabah Forestry Department, Mario Percy Núñez Vargas, Universidad Nacional de San Antonio Abad del Cusco, Eddy Nurtja, Universitas Bangka Belitung, R. Nazaré O. de Araújo, INPA, Onrizal Onrizal, Universitas Sumatera Utara, Walter A. Palacios, Herbario Nacional del Ecuador, Universidad Técnica del Norte, Sonia Palacios-Ramos, Universidad Nacional Agraria La Molina, Marc Parren, Wageningen University & Research, Ekananda Paudel, Nepal Academy of Science and Technology, Paulo S. Morandi, Universidade do Estado de Mato Grosso, R. Toby Pennington, Royal Botanic Garden Edinburgh / University of Exeter, Georgia Pickavance, University of Leeds, John J. Pipoly III, Broward County Parks and Recreation Division, Nigel C. A. Pitman, Field Museum, Erny Poedjirahajoe, Universitas Gadjah Mada, Lourens Poorter, Université de Lorraine, AgroParisTech, INRAE, John R. Poulsen, Duke University, P. Rama Chandra Prasad, International Institute of Information Technology, Adriana Prieto, Universidad Nacional de Colombia, Jean-Philippe Puyravaud, Sigur Nature Trust, Lan Qie, University of Lincoln, Carlos A. Quesada, INPA, Hirma Ramírez-Angulo, INDEFOR, Universidad de Los Andes, Ervan Rutishauser, Smithsonian Tropical Research Institute, Gemma Rutten, University of Bern, Ruwan Punchi-Manage, University of Peradeniya, Rafael P. Salomão, MPEG / UFRA, Hoang Van Sam, Vietnam National University of Forestry, Swapan Kumar Sarker, Shahjalal University of Science & Technology, Manichanh Satdichanh, hinese Academy of Sciences / World Agroforestry Centre, Juliana Schietti, INPA, Jianwei Tang, Chinese Academy of Sciences, Edmund Tanner, University of Cambridge, Hans ter Steege, Naturalis Biodiversity Center / Systems Ecology, Jeanneth Villalobos Cayo, Universidad Mayor Real and Pontifical de San Francisco Xavier de Chuquisaca, Ophelia Wang, Northern Arizona University, Campbell O. Webb, University of Alaska, Edward L. Webb, National University of Singapore, Lee White, Agence Nationale des Parcs Nationaux / Institut de Recherche en Ecologie Tropicale / University of Stirling, Timothy J. S. Whitfeld, University of Minnesota, Serge Wich, Liverpool John Moores University / University of Amsterdam, Simon Willcock, Bangor University, Wanlop Chutipong, King Mongut's Institute of Technology Thonburi, Douglas Sheil, Norwegian University of Life Sciences, Rodrigo Sierra, GeoIS, Andreas Hemp, University of Bayreuth, Bruno Herault, CIRAD / Institut National Polytechnique Félix Houphouët-Boigny, Carlos Gabriel Hidalgo Pizango, IIAP, Eurídice N. Honorio Coronado, IIAP, Wolf L. Eiserhardt, Aarhus University / Royal Botanic Gardens Kew, Jens-Christian Svenning, Aarhus University, Kofi Affum-Baffoe, Ghana Forestry Commission, Shin-Ichiro Aiba, Hokkaido University Sapporo, Everton C. de Almeida, UFOPA, Samuel S. de Almeida, MPEG, Edmar Almeida de Oliveira, UFMT, Esteban Álvarez-Dávila, Universidad Nacional Abierta y a Distancia, Luciana F. Alves, University of California, Carlos Mariano Alvez-Valles, Universidad Nacional Mayor de San Marcos, Fabrício Alvim Carvalho, Universidade Federal de Juiz de Fora, Fernando Alzate Guarin, Universidad de Antioquia, Ana Andrade, INPA, Luis E. O. C. Aragão, INPE / University of Exeter, Alejandro Araujo Murakami, Universidad Autonoma Gabriel Rene Moreno, Peter S. Ashton, Harvard University, Gerardo A. Aymard Corredor, Compensation International Progress / UNELLEZ-Guanare, Timothy R. Baker, University of Leeds, Fabian Brambach, University of Goettingen, Francis Q. Brearley, Manchester Metropolitan University, Steven W. Brewer, Wild Earth Allies, Jose L. C. Camargo, INPA, David G. Campbell, Grinnell College, CAROLINA VOLKMER DE CASTILHO, CPAF-RR, Wendeson Castro, SOS Amazônia, Damien Catchpole, University of Tasmania, Carlos E. Cerón Martínez, Universidad Central del Ecuador, Shengbin Chen, Chengdu University of Technology, Phourin Chhang, Forestry Administration, Massiel Nataly Corrales Medina, Universidad Nacional de San Agustín de Arequipa, Heike Culmsee, German Federal Foundation for the Environment, Heriberto David-Higuita, Universidad de Antioquia, Priya Davidar, Sigur Nature Trust, Jhon del Aguila-Pasquel, IIAP, Robert M. Ewers, Imperial College London, Sophie Fauset, University of Plymouth, Ted R. Feldpausch, University of Exeter, Leandro Valle Ferreira, MPEG, Markus Fischer, University of Bern, Janet Franklin, University of California, Gabriella M. Fredriksson, Pro Natura Foundation, Thomas W. Gillespie, University of California, Martin Gilpin, University of Leeds, Christelle Gonmadje, University of Yaoundé / National Herbarium, Arachchige Upali Nimal Gunatilleke, University of Peradeniya, Khalid Rehman Hakeem, King Abdulaziz University, Jefferson S. Hall, Smithsonian Tropical Research Institute, Keith C. Hamer, University of Leeds, Lila Nath Sharma, ForestAction Nepal, Robert Kooyman, Macquarie University / Royal Botanic Gardens, Nicolas Labrière, CNRS, Eileen Larney, TEAM / Zoological Society of London, Yves Laumonier, CIRAD, Susan G. Laurance, James Cook University, William F. Laurance, James Cook University, Ni Putu Diana Mahayani, Universitas Gadjah Mada, Yadvinder Malhi, University of Oxford, Asyraf Mansor, Universiti Sains Malaysia / Universiti Sains Malaysia, Jose Luis Marcelo Peña, Universidad Nacional Agraria La Molina / ESALQ-USP, Ben H. Marimon-Junior, UNEMAT, Andrew R. Marshall, University of the Sunshine Coast / University of York / Flamingo Land, Karina Melgaco, University of Leeds, Abel Lorenzo Monteagudo Mendoza, Universidad Nacional de San Antonio Abad del Cusco, Badru Mugerwa, Mbarara University of Science and Technology, Hidetoshi Nagamasu, Kyoto University, Laszlo Nagy, UNICAMP, Naret Seuaturien, WWF Thailand, Marcelo T. Nascimento, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Jean Claude Razafimahaimodison, University of Fianarantsoa, Jan Meindert Reitsma, Bureau Waardenburg BV, Edilson J. Requena-Rojas, Universidad Continental, Zorayda Restrepo Correa, Ecosystems Services and Climate Change (SECC) Group, COL-TREE Corporatio, Carlos Reynel Rodriguez, Universidad Nacional Agraria La Molina, Anand Roopsind, Boise State University, Francesco Rovero, University of Florence / Museo delle Scienze, Andes Rozak, Indonesian Institute of Sciences (LIPI), Agustín Rudas Lleras, Universidad Nacional de Colombia, Christine B. Schmitt, University of Bonn / University of Freiburg, Beatriz Schwantes Marimon, UNEMAT, Feyera Senbeta, Addis Ababa University, Javier E. Silva-Espejo, Universidad de La Serena, Marcos Silveira, UFAC, Bonaventure Sonké, University of Yaoundé, Robert Steinmetz, WWF Thailand, Tariq Stévart, Missouri Botanical Garden, Raman Sukumar, Indian Institute of Science, Aisha Sultana, University of Delhi, Terry C. H. Sunderland, University of British Columbia / CIFOR, Hebbalalu Satyanarayana Suresh, Indian Institute of Science, John W. Terborgh, University of Florida / James Cook University, Ida Theilade, University of Copenhagen, Jonathan Timberlake, Warren Lane, Armando Torres-Lezama, Universidad de Los Andes, Peter Umunay, Yale University, María Uriarte, Columbia University, Luis Valenzuela Gamarra, Jardín Botánico de Missouri, Martin van de Bult, Doi Tung Development Project, Social Development Department, Peter van der Hout, Van der Hout Förestry Consulting, Rodolfo Vasquez Martinez, Herbario Selva Central Oxapampa, Ima Célia Guimarães Vieira, MPEG, Simone A. Vieira, UNICAMP, Emilio Vilanova, University of California, Susan K. Wiser, Manaaki Whenua, Landcare Research, Kenneth R. Young, University of Texas at Austin, Rahmad Zakaria, Universiti Sains Malaysia, Runguo Zang, Chinese Academy of Forestry, Charles E. Zartman, INPA, Irié Casimir Zo-Bi, Institut National Polytechnique Félix Houphouët-Boigny, Henrik Balslev, Aarhus University., Donald R. Drake, University of Hawai'i at M?noa, Marc K. Steininger, University of Maryland, Thaise Emilio, UNICAMP / Royal Botanic Gardens Kew, Oliver L. Phillips, University of Leeds, Simon L. Lewis, University of Leeds / University College London, Ferry Slik, Universiti Brunei Darussalam, William J. Baker, Royal Botanic Gardens Kew, Uppsala University, SILVA (SILVA), AgroParisTech-Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Rainforest Research Sdn Bhd
Subjects: 0106 biological sciences, DIVERSITY, Biomasa, Biomassa, Arecaceae, AFRICAN, 580 Plants (Botany), 01 natural sciences, BIOMASS, purl.org/pe-repo/ocde/ford#4.01.02 [http], biomasse aérienne des arbres, Abundance (ecology), CARBON STORAGE, Floresta Tropical, Densité, Silvicultura, Biomass, Forêt tropicale humide, ALLOMETRY, above-ground biomass, Global and Planetary Change, Biomass (ecology), GE, Condições abióticas locais, biology, Ecology, Inventaire forestier, abundance patterns, tropical, Facteur du milieu, wood density, PE&RC, Geography, Physical, 0501 Ecological Applications, Geography, Biogeografia, Physical Sciences, [SDE]Environmental Sciences, Biodiversité, C180 Ecology, 0406 Physical Geography and Environmental Geoscience, Variance génétique, Life Sciences & Biomedicine, pantropical biogeography, Neotropics, F40 - Écologie végétale, Zona tropical, Biogéographie, Environmental Sciences & Ecology, Subtropics, 010603 evolutionary biology, Bois, local abiotic conditions, Bosecologie en Bosbeheer, Ecosystem, Relative species abundance, Ecology, Evolution, Behavior and Systematics, Densidade da Madeira, Ekologi, Science & Technology, 0602 Ecology, 010604 marine biology & hydrobiology, QK, Diameter at breast height, Biology and Life Sciences, facteurs abiotiques, DIVERSIFICATION HISTORY, 15. Life on land, biology.organism_classification, EVOLUTION, Forest Ecology and Forest Management, AMAZONIAN FOREST, Physical Geography, 13. Climate action, Earth and Environmental Sciences, PATTERNS, tropical rainforest, Tropical rainforest
Abstract: Aim Palms are an iconic, diverse and often abundant component of tropical ecosystems that provide many ecosystem services. Being monocots, tree palms are evolutionarily, morphologically and physiologically distinct from other trees, and these differences have important consequences for ecosystem services (e.g., carbon sequestration and storage) and in terms of responses to climate change. We quantified global patterns of tree palm relative abundance to help improve understanding of tropical forests and reduce uncertainty about these ecosystems under climate change. Location Tropical and subtropical moist forests. Time period Current. Major taxa studied Palms (Arecaceae). Methods We assembled a pantropical dataset of 2,548 forest plots (covering 1,191ha) and quantified tree palm (i.e., ≥10cm diameter at breast height) abundance relative to co‐occurring non‐palm trees. We compared the relative abundance of tree palms across biogeographical realms and tested for associations with palaeoclimate stability, current climate, edaphic conditions and metrics of forest structure. Results On average, the relative abundance of tree palms was more than five times larger between Neotropical locations and other biogeographical realms. Tree palms were absent in most locations outside the Neotropics but present in >80% of Neotropical locations. The relative abundance of tree palms was more strongly associated with local conditions (e.g., higher mean annual precipitation, lower soil fertility, shallower water table and lower plot mean wood density) than metrics of long‐term climate stability. Life‐form diversity also influenced the patterns; palm assemblages outside the Neotropics comprise many non‐tree (e.g., climbing) palms. Finally, we show that tree palms can influence estimates of above‐ground biomass, but the magnitude and direction of the effect require additional work. Conclusions Tree palms are not only quintessentially tropical, but they are also overwhelmingly Neotropical. Future work to understand the contributions of tree palms to biomass estimates and carbon cycling will be particularly crucial in Neotropical forests.
Published: 2020

33. Multiple innovations underpinned branching form diversification in mosses

Author: Neil E. Bell, Claude Edelin, C. Jill Harrison, Yoan Coudert, University of Bristol [Bristol], Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Department of Plant Sciences, University of Cambridge, Royal Botanic Garden Edinburgh, Institut Français de Pondichéry (IFP), Ministère de l'Europe et des Affaires étrangères (MEAE)-Centre National de la Recherche Scientifique (CNRS), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of Cambridge [UK] (CAM), and Royal Botanic Garden [Edinburgh]
Subjects: 0301 basic medicine, plant architecture, Branching, Physiology, Lineage (evolution), Modularity, Bryophyta, Plant Science, Apical cell, Diversification (marketing strategy), [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, mosses, Branching (linguistics), pleurocarpy, 03 medical and health sciences, Convergent evolution, Mosses, convergent evolution, Phylogeny, modularity, Full Paper, biology, Ecology, Research, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Plant architecture, Full Papers, 15. Life on land, biology.organism_classification, Biological Evolution, Moss, Pleurocarpy, 030104 developmental biology, Gametophore, Bryophyte
Abstract: •Broad scale evolutionary comparisons have shown that branching forms arose by convergence in vascular plants and bryophytes, but the trajectory of branching form diversification in bryophytes is unclear. Mosses are the most species rich bryophyte lineage and two sub-groups are circumscribed by alternative reproductive organ placements. In one, reproductive organs form apically, terminating growth of the primary shoot (gametophore) axis. In the other, reproductive organs develop on very short lateral branches. A switch from apical to lateral reproductive organ development is proposed to have primed branching form diversification. •Moss gametophores have modular development and each module develops from a single apical cell. Here we define the architectures of 175 mosses by the number of module classes, branching patterns and the pattern in which similar modules repeat. Using ancestral character state reconstruction we identify two stages of architectural diversification. •During a first stage there were sequential changes in the module repetition pattern, reproductive organ position, branching pattern and number of module classes. During a second stage, vegetative changes occurred independently of reproductive fate. •The results pinpoint the nature of developmental change priming branching form diversification in mosses and provide a framework for mechanistic studies of architectural diversification.
Published: 2017

34. Comment on 'The global tree restoration potential'

Author: Thomas W. Boutton, Jayashree Ratnam, Forrest Fleischman, Reed F. Noss, Nicola Stevens, Michele de Sá Dechoum, Grégory Mahy, Swanni T. Alvarado, Josep G. Canadell, Christine B. Schmitt, Catherine L. Parr, Juli G. Pausas, A. Carla Staver, Fernando A. O. Silveira, Gerhard E. Overbeck, J. Morgan Varner, Caroline E. R. Lehmann, Alessandra Fidelis, Milton H. Díaz-Toribio, Elise Buisson, Isabel Belloni Schmidt, William J. Bond, Soizig Le Stradic, Nicholas P. Zaloumis, Joseph W. Veldman, John J. Ewel, William A. Hoffmann, Caroline A.E. Strömberg, Ashish N. Nerlekar, Daniel M. Griffith, R. Toby Pennington, Julie C. Aleman, Stephen P. Good, Nina Buchmann, G. Wilson Fernandes, Mahesh Sankaran, Jesse B. Nippert, Colin P. Osborne, Francis E. Putz, Michael P. Perring, T. Michael Anderson, Sally Archibald, Christopher J. Still, Giselda Durigan, Vicky M. Temperton, Julia-Maria Hermann, Texas A&M University [College Station], Université de Montréal (UdeM), Universidade Estadual do Maranhão = State University of Maranhão (UEMA), University of the Witwatersrand [Johannesburg] (WITS), Department of Biological Sciences, University of Cape Town, Cape Town, South Africa, Institute of Agricultural Sciences [Zürich], Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Oceans and Atmosphere Flagship (CSIRO), CSIRO Oceans and Atmosphere Flagship, Instituto Florestal do Estado de São Paulo, Universidade Federal de Minas Gerais = Federal University of Minas Gerais [Belo Horizonte, Brazil] (UFMG), Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), University of Edinburgh, Gembloux Agro-Bio Tech [Gembloux], Université de Liège, Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), University of Liverpool, Center for Desertification Research (CIDE), Universitat de València (UV), Royal Botanic Garden [Edinburgh], The University of Western Australia (UWA), University of Florida [Gainesville] (UF), Natural Resource Ecology Laboratory [Fort Collins] (NREL), Colorado State University [Fort Collins] (CSU), Universidade de Brasilia [Brasília] (UnB), University of Freiburg [Freiburg], Universität Bonn = University of Bonn, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Yale University [New Haven], Leuphana Universität Lüneburg, Swiss National Science Foundation, Centre National de la Recherche Scientifique (France), Conselho Nacional de Desenvolvimento Científico e Tecnológico (Brasil), National Science Foundation (US), Fundação de Amparo à Pesquisa do Estado de São Paulo Minas Gerais, Royal Society (UK), German Research Foundation, Food and Agriculture Organization of the United Nations, Pausas, J. G. [0000-0003-3533-5786], Universidade Estadual de Maranhão, Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UMR237-Aix Marseille Université (AMU)-Avignon Université (AU), Federal University of Minas Gerais (UFMG), Royal Botanic Garden Edinburgh, University of Bonn, and Pausas, J. G.
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, Tree planting, [SDE.MCG]Environmental Sciences/Global Changes, Climate change, 010603 evolutionary biology, 01 natural sciences, Shrubland, Latitude, Afforestation, ComputingMilieux_MISCELLANEOUS, Organic carbon, 0105 earth and related environmental sciences, 2. Zero hunger, geography, Multidisciplinary, geography.geographical_feature_category, Forestry, Soil carbon, 15. Life on land, [SDE.ES]Environmental Sciences/Environmental and Society, Tree (data structure), Climate change mitigation, Ecosystems Research, 13. Climate action, Restoration, [SDE]Environmental Sciences, Environmental science, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, grassland
Abstract: Bastin et al.’s estimate (Reports, 5 July 2019, p. 76) that tree planting for climate change mitigation could sequester 205 gigatonnes of carbon is approximately five times too large. Their analysis inflated soil organic carbon gains, failed to safeguard against warming from trees at high latitudes and elevations, and considered afforestation of savannas, grasslands, and shrublands to be restoration., Funding: Supported by the Texas A&M Sid Kyle Global Savanna Research Initiative (T.W.B.); Swiss National Science Foundation (20FI20_173691) (N.B.); Centre National pour la Recherche Scientifique CNRS PICS 2018-2020 (RESIGRASS) (E.B.); CNPq (Brazil, 303179/2016-3) (G.D.); CNPq (Brazil) (G.W.F.); CNPq (Brazil, 303988/2018-5) (A.F.); NASA award NNX17AK14G (F.F.); NSF award 1354943 (W.A.H.); Fundação de Amparo à Pesquisa do Estado de Minas Gerais (Brazil, 2016/13232-5) (S.L.S.); the Office of the Royal Society (IC170015) (C.E.R.L.); CNPq (Brazil, 310345/2018-9) (G.E.O.); the Spanish Government (FIROTIC, PGC2018-096569-B-I00) (J.G.P.); the National Research Foundation (ACCESS, 114695) (N.S.); CNPq (Brazil, 303568/2017-8) (F.A.O.S.); NSF awards 1342703 and 1926431 (C.J.S. and D.M.G.); NSF award EAR-1253713 (C.A.E.S.); Deutsche Forschungsgemeinschaft grant 5579 POEM (V.M.T.); and USDA-NIFA Sustainable Agricultural Systems Grant 12726253 (J.W.V.)
Published: 2019

35. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes

Author: Martin Kolisko, Bente Edvardsen, Conrad L. Schoch, Christopher E. Lane, Edward A. D. Mitchell, Satoshi Shimano, Frederick W. Spiegel, Guifré Torruella, Qianqian Zhang, Jan Pawlowski, Sina M. Adl, Sabine Agatha, Vladimír Hampl, Lora L. Shadwick, Daniel J. G. Lahr, Jong Soo Park, Denis H. Lynn, David Bass, Aaron A. Heiss, Sergey Karpov, Anna Karnkowska, Timothy Y. James, Julius Lukeš, Sonja Rueckert, Fabien Burki, Alexey V. Smirnov, Daniel J. Richter, Javier del Campo, Cédric Berney, Alexander Kudryavtsev, Line Le Gall, Martha J. Powell, Laure Guillou, Lyudmila V. Chistyakova, Paco Cárdenas, Noha H. Youssef, Christine Morrow, David G. Mann, Vasily V. Zlatogursky, Yana Eglit, Eunsoo Kim, Ramon Massana, Mona Hoppenrath, Ivan Čepička, Matthew Brown, Enrique Lara, Micah Dunthorn, University of Saskatchewan [Saskatoon] (U of S), The Natural History Museum [London] (NHM), University of Rhode Island (URI), Institute of Parasitology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), National Institutes of Health [Bethesda] (NIH), Saint Petersburg State University (SPBU), Universität Salzburg, Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Mississippi State University [Mississippi], Uppsala University, Biologie des Organismes et Ecosystèmes Aquatiques (BOREA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Charles University [Prague] (CU), University of British Columbia (UBC), University of Kaiserslautern [Kaiserslautern], University of Oslo (UiO), Dalhousie University [Halifax], Unité de Catalyse et Chimie du Solide - UMR 8181 (UCCS), Université d'Artois (UA)-Centrale Lille-Institut de Chimie du CNRS (INC)-Université de Lille-Centre National de la Recherche Scientifique (CNRS), American Museum of Natural History (AMNH), German Centre for Marine Biodiversity Research [Wilhelmshaven, Allemagne] (DZMB), Senckenberg am Meer, University of Michigan [Ann Arbor], University of Michigan System, Division of Invertebrate Zoology [New York], Czech Academy of Sciences [Prague] (CAS), Universidade de São Paulo = University of São Paulo (USP), Université de Neuchâtel (UNINE), Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), University of Guelph, Royal Botanic Garden [Edinburgh], Centro de Investigaciones Biológicas (CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), National Museums Northern Ireland (NMNI), Kyungpook National University [Daegu] (KNU), Université de Genève = University of Geneva (UNIGE), University of Alabama [Tuscaloosa] (UA), Edinburgh Napier University, University of Arkansas [Fayetteville], Hosei University, Université Paris-Sud - Paris 11 (UP11), Oklahoma State University [Stillwater] (OSU), Chinese Academy of Sciences [Beijing] (CAS), Gordon and Betty Moore Foundation, Natural Sciences and Engineering Research Council of Canada, Generalitat de Catalunya, Comunidad de Madrid, European Commission, Science for Life Laboratory, National Institutes of Health (US), Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Sorbonne Université (SU)-Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU), Laboratoire de catalyse de Lille - UMR 8010 (LCL), Université de Lille, Sciences et Technologies-Centrale Lille-Centre National de la Recherche Scientifique (CNRS), University of São Paulo (USP), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Royal Botanic Garden Edinburgh, Kyungpook National University [Daegu], University of Geneva [Switzerland], Hosei University [Chiyoda], Oklahoma State University [Stillwater], Producció Animal, and Aigües Marines i Continentals
Subjects: 0301 basic medicine, Flagellate, [SDV]Life Sciences [q-bio], ciliate, Marine and Freshwater Biology, Evolutionsbiologi, protozoa, taxonomy, SponGES, Eukaryotes, protists, phylogenetic analyses, environmental sampling, Nomenclature, Phylogeny, biodiversity, Fungus, Environmental microbiology, Ecology, Deep-sea Sponge Grounds Ecosystems of the North Atlantic: an integrated approach towards their preservation and sustainable exploitation, plankton, fungus, Eukaryota, Amoebae, QR Microbiology, Biodiversity, 030108 mycology & parasitology, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Plankton, 3. Good health, Parasite, 579 Microorganisms, fungi & algae, parasite, Original Article, Taxonomy (biology), ecology, Animal and Plant Science Research Group, Biologie, amoebae, Algae, Culture and Communities, Biodiversity and conservation, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, Microbiology, flagellate, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Terminology as Topic, Systematics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Protozoa, systematics, Taxonomy, Horizon 2020, Evolutionary Biology, Ciliates, microbiology, Grant Agreement No 679849, Original Articles, 030104 developmental biology, Evolutionary biology, European Union (EU)
Abstract: 116 pages, 1 figure, 4 tables, 3 appendices, This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users, Research support was provided as follows: SMA by NSERC 249889‐2007; DB by NERC NE/H009426/1 and NE/H000887/1; MWB by NSF 1456054; FB by a Fellowship from Science for Life Laboratory and VR/2017‐04563; PC by EU‐Horizon 2020 research and innovation program through the SponGES project 679849 [...]; IC by CSF 18‐18699S; BE by RCN TaxMArc 268286/GMR; LG by ANR HAPAR (ANR‐14‐CE02‐0007); VH MK JL by ERDF; MEYS with ERC 771592 CZ 1.05/1.1.00/02.0109 BIOCEV; SK by RSF 16‐14‐10302; MK by CSF GA18‐28103S; CEL by NSF 1541510 and NIH‐AI124092; EL by CAM: 2017‐T1/AMB‐5210; and by grant 2017‐T1/AMB‐5210 from the program >Atracción de talentos> from the Consejería de Educación, Juventud y Deporte, Comunidad de Madrid; JL by ERC CZ LL1601 and OPVVV 16_019/0000759; MP by NSF DEB‐1455611; DJR by the Beatriu de Pinós postdoctoral programme of the Government of Catalonia's Secretariat for Universities and Research of the Ministry of Economy and Knowledge; CLS by the intramural research program of the National Library of Medicine, National Institutes of Health; AS by RSF 17‐14‐01391 and RFBR 16‐04‐01454 NY by NSF DEB 1557102; VZ by RFBR 16‐34‐60102 mol‐a‐dk; UniEuk and EukRef by the Gordon and Betty Moore Foundation
Published: 2019

36. North Andean origin and diversification of the largest ithomiine butterfly genus OPEN

Author: Carlos E. Giraldo, Sandra Knapp, James Mallet, Keith R. Willmott, Karina L. Silva-Brandão, Ricardo Mallarino, Luz Miryam Gómez Piñerez, Luísa L. Mota, Gerardo Lamas, Mathieu Joron, Nicolas Chazot, Chris D. Jiggins, André V. L. Freitas, Sandra Uribe, Tiina Särkinen, Marianne Elias, Donna Lisa De‐Silva, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Harvard University [Cambridge], Universidade Estadual de Campinas (UNICAMP), Universidad Nacional Mayor de San Marcos (UNMSM), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Department of Organismic and Evolutionary Biology [Cambridge] (OEB), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Lund University [Lund], Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Universidad Nacional de Colombia (Sede Medellín), Universidad Nacional de Colombia, Grupo de investigacion Ciencias Forenses y Salud, Technologico de Antioquia, Medellin, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Universidad catolica de Oriente, Rionegro, Royal Botanic Garden Edinburgh, The Natural History Museum [London] (NHM), University of Cambridge [UK] (CAM), University of Florida [Gainesville] (UF), Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Biologie Intégrative des Populations, École pratique des hautes études (EPHE)-Centre National de la Recherche Scientifique (CNRS), University of Florida [Gainesville], Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Universidade Estadual de Campinas = University of Campinas (UNICAMP), Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Harvard University, Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Royal Botanic Garden [Edinburgh], Jiggins, Chris [0000-0002-7809-062X], and Apollo - University of Cambridge Repository
Subjects: 0106 biological sciences, 0301 basic medicine, Time Factors, Genetic Speciation, Fauna, Biogeography, [SDV]Life Sciences [q-bio], Biodiversity, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Nymphalidae, Article, 03 medical and health sciences, Species Specificity, Genus, Animals, Phylogeny, 030304 developmental biology, 0303 health sciences, Likelihood Functions, Multidisciplinary, Ecology, Species diversity, 15. Life on land, biology.organism_classification, Ithomiini, phylogenetics, Phylogeography, Geography, 030104 developmental biology, Habitat, evolutionary ecology, Butterfly, Calibration, Biological dispersal, Butterflies
Abstract: The Neotropics harbour the most diverse flora and fauna on Earth. The Andes are a major centre of diversification and source of diversity for adjacent areas in plants and vertebrates, but studies on insects remain scarce, even though they constitute the largest fraction of terrestrial biodiversity. Here, we combine molecular and morphological characters to generate a dated phylogeny of the butterfly genus Pteronymia (Nymphalidae: Danainae), which we use to infer spatial, elevational and temporal diversification patterns. We first propose six taxonomic changes that raise the generic species total to 53, making Pteronymia the most diverse genus of the tribe Ithomiini. Our biogeographic reconstruction shows that Pteronymia originated in the Northern Andes, where it diversified extensively. Some lineages colonized lowlands and adjacent montane areas, but diversification in those areas remained scarce. The recent colonization of lowland areas was reflected by an increase in the rate of evolution of species’ elevational ranges towards present. By contrast, speciation rate decelerated with time, with no extinction. The geological history of the Andes and adjacent regions have likely contributed to Pteronymia diversification by providing compartmentalized habitats and an array of biotic and abiotic conditions, and by limiting dispersal between some areas while promoting interchange across others.
Published: 2017

37. Diversity and carbon storage across the tropical forest biome

Author: Connie J. Clark, Kofi Affum-Baffoe, Lan Qie, Timothy R. Baker, Abel Monteagudo-Mendoza, Lise Zemagho, Yadvinder Malhi, Javier Silva Espejo, Patricia Alvarez-Loayza, Lindsay F. Banin, Jefferson S. Hall, Ima Célia Guimarães Vieira, H. Priyadi, Jérôme Chave, Fernando Cornejo Valverde, Peter M. Umunay, J. W. Ferry Slik, Martin Gilpin, Ana Andrade, Andrew R. Marshall, Alvaro Cogollo Pacheco, Bonaventure Sonké, Rodrigo Sierra, Jan Bogaert, Emanuel Gloor, Christopher Baraloto, Guido Pardo, Nicholas J. Berry, Simon L. Lewis, Georgia Pickavance, Axel Dalberg Poulsen, Ismayadi Samsoedin, Vincent A. Vos, Carlos Cerón, Jean-Louis Doucet, Peter S. Ashton, William F. Laurance, Wannes Hubau, Thomas E. Lovejoy, Eric Chezeaux, Zorayda Restrepo, Aida Cuni-Sanchez, Kanehiro Kitayama, Everton Cristo de Almeida, Luiz E. O. C. Aragão, Sophie Fauset, Nadir Pallqui Camacho, Jan Reitsma, Corneille E. N. Ewango, Percy Núñez Vargas, Hans ter Steege, John Terborgh, Roel J. W. Brienen, Jean-François Bastin, Kamariah Abu Salim, Jon C. Lovett, Beatriz Schwantes Marimon, Simon Willcock, Marisol Toledo, Ben Hur Marimon Junior, Serge K. Begne, Greta C. Dargie, Carlos A. Quesada, Terese B. Hart, Martin J. P. Sullivan, Terry Sunderland, Ted R. Feldpausch, Eurídice N. Honorio Coronado, Stuart J. Davies, Lera Miles, Sean C. Thomas, Lip Khoon Kho, Lisa Steel, Jaques Mukinzi, Marie Noel Djuikouo K., Rafael de Paiva Salomão, Terry L. Erwin, Ervan Rutishauser, Edmar Almeida de Oliveira, Rafael Herrera, Shin-ichiro Aiba, Faustin Mpanya Lukasu, Damien Bonal, Sylvester Tan, Esteban Alvarez Dávila, Marielos Peña-Claros, José Luís Camargo, Lee J. T. White, James A. Comiskey, Hermann Taedoumg, Maxime Réjou-Méchain, Pascal Petronelli, Jean-Remy Makana, Ophelia Wang, Richard B. Primack, Gerardo A. Aymard C, Charles De Cannière, Luis Valenzuela Gamarra, Gabriela Lopez-Gonzalez, Leandro Maracahipes, Kuswata Kartawinata, Michael Balinga, Victor Chama Moscoso, Susan G. Laurance, Marcos Silveira, David Harris, Miguel E. Leal, Paulo S. Morandi, John Tshibamba Mukendi, Frans Bongers, Joey Talbot, Douglas Sheil, Reuben Nilus, John R. Poulsen, Oliver L. Phillips, Sch Geog, University of Nottingham, Dept Geog, University College of London [London] (UCL), Plant Systemat & Ecol Lab, Université de Yaoundé, Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS), Instituto Nacional de Pesquisas da Amazônia (INPA), United Nations Environment Programme World Conservation Monitoring Centre, Missouri Botanical Garden (USA), Universidad Nacional San Antonio Abad del Cusco, Center for International Forestry Research (CIFOR), Coll Marine & Environm Sci, James Cook University, Leiden University, Agence Nationale des Parcs Nationaux du Gabon, Ecole de Terrain en Ecologie Tropicale (ECOTROP), Mensurat Unit, Forestry Research Institute of Ghana, Grad Sch Sci & Engn, Kagoshima University, Inst Biodiversidade & Floresta, Universidade Federal do Oeste do Pará, Universidade Federal do Mato Grosso (UFMT), Ctr Trop Conservat, Duke University [Durham], Universidad Nacional de Colombia, Coll Life & Environm Sci, University of Exeter, Dept Organism & Evolutionary Biol, Harvard University [Cambridge], Programa Ciencias Agro & Mar, Herbario Universitario PORT, Ctr Ecol & Hydrol, Dept Biol Sci, Int Ctr Trop Bot, Florida International University (FIU), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biens et services des écosystèmes forestiers tropicaux : l'enjeu du changement global (Cirad-Es-UPR 105 BSEF), Département Environnements et Sociétés (Cirad-ES), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Sch Geosci, University of Edinburgh, Biodivers & Landscape Unit, Université de Liège, Gembloux Agro-Bio Tech [Gembloux], Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Forest Ecol & Forest Management Grp, Wageningen University and Research Centre [Wageningen] (WUR), Projeto Dinam Biol Fragmentos Florestais, Herbario Alfredo Paredes, Universidad Agraria del Ecuador, Rougier Gabon, Nicholas Sch Environm, Duke University, Jardín Botánico de Medellín, Inventory & Monitoring Program, National Park Service, Smithsonian Institution, Andes to Amazon Biodiversity Program, Instituto de Investigaciones de la Amazonía Peruana, Smithsonian Tropical Research Institute, Landscape Ecol & Vegetal Prod Syst Unit, Université Libre de Bruxelles [Bruxelles] (ULB), Dept Bot & Plant Physiol, Fac Sci, University of Buea, Wildlife Conservation Society, Centre de Formation et de Recherche en Conservation Forestière (CEFRECOF), Department of Biology [Copenhagen], Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Ctr Ecol, Instituto Venezolano de Investigaciones Cientificas (IVIC), Inst Geog & Reg Forsch, University of Vienna, Royal Botanic Garden Edinburgh, Lukuru Wildlife Res Fdn, Div Vertebrate Zool, National Museum of Natural History, Herbarium Bogoriense, Indonesian Institute of Sciences, Integrat Res Ctr, Field Museum of Natural History [Chicago, USA], Trop Peat Res Inst, Biol Res Div, Malaysian Palm Oil Board, Kyoto University, Ctr Trop Environm & Sustainabil Sci, Coll Sci & Engn, Dept Environm Sci & Policy, George Mason University, Fac Sci Agron, University of Kisangani, Sch Geog & Environm, University of Oxford, Universidade Federal de Goiás [Goiânia] (UFG), Flamingo Land LTD, Dept Environm, CIRCLE, University of York, Salonga Natl Pk, sabah Parks, Universidad Autonoma del Beni, Inst Boliviano Invest Forestal, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Natural History Museum [Oslo], University of Oslo (UiO), Southern Swedish Forest Res Ctr, Swedish University of Agricultural Sciences (SLU), Bur Waarderburg, Fundación Con-Vida, CarboForExpert, Fac Sci, Environm & Life Sci, University of Brunei Darussalam (Biology Department), Museu Paraense Emílio Goeldi, Forestry Research and Development Agency (FORDA), Norwegian University of Life Sciences (NMBU), Geoinformática y Sistemas , Cia. Ltda (GeoIS), Museu Univ, Universidade Federal do Acre (UFAC), World Wide Fund for Nature, CTFS AA Asia Program, Fac Forestry, University Stefan cel Mare of Suceava (USU), Sch Forestry & Environm Studies, Yale University [New Haven], Centro de Investigación y Promoción del Campesinado Norte Amazónico, Sch Earth Sci & Environm Sustainabil, Northern Arizona University [Flagstaff], Biol Sci, Liverpool John Moore University (ljmu), Sch Environm Nat Resources & Geog, Bangor University, European Research Council (ERC), Gordon and Betty Moore Foundation, David and Lucile Packard Foundation, European Union's Seventh Framework Programme 283080, 282664, Natural Environment Research Council (NERC) Urgency Grants, NERC Consortium Grant 'AMAZONICA' NE/F005806/1, NERC Consortium Grant 'TROBIT' NE/D005590/1, NERC Consortium Grant 'BIO-RED' NE/N012542/1, NERC New Investigators Grant, Royal Society, Centre for International Forestry (CIFOR), Gabon's National Parks Agency (ANPN), NERC PhD Studentship, UNEP-WCMC, NERC research fellowship NE/I021160/1, Royal Society University Research Fellowship ERC Advanced Grant (T-FORCES), Phillip Leverhulme Prize, Royal Society Wolfson Research Merit Award, NERC studentship, RGS-IBG Henrietta Hutton Grant, National Council for Science and Technology Development of Brazil (CNPq) PELD/403725/2012-7, CNPq/PPBio/457602/2012-0, National Council for Science and Technology Development of Brazil (CNPq) Productivity Grant, Leverhulme Trust under the Valuing the Arc project, Missouri Botanical Garden, Sullivan, Martin J. P., Université de Yaoundé I, Universidad Nacional de San Antonio Abad del Cusco (UNSAAC), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), Florida International University [Miami] (FIU), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), Biens et services des écosystèmes forestiers tropicaux : l'enjeu du changement global (UPR BSEF), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Wageningen University and Research [Wageningen] (WUR), Instituto de Investigaciones de la Amazonía Peruana (IIAP), Université libre de Bruxelles (ULB), University of Vienna [Vienna], Indonesian Institute of Sciences (LIPI), University of Oxford [Oxford], Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Southern Swedish Forest Research Centre, Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Université de Toulouse (UT), James Cook University (JCU), Universiteit Leiden, Agence Nationale des Parcs Nationaux du Gabon (ANPN), Harvard University, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), and Royal Botanic Garden [Edinburgh]
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, INCREASES, ALPHA-DIVERSITY, [SDV]Life Sciences [q-bio], Biome, Biodiversity, COMPLEMENTARITY, forêt tropicale, Forests, 01 natural sciences, AMAZONIAN FORESTS, Tropic Climate, biodiversité, biomasse aérienne des arbres, conservation des forêts, Tropical climate, stockage du carbone, Biomass (ecology), Multidisciplinary, PRODUCTIVITY, Agroforestry, Ecology, Plants, PE&RC, Classification, Tropical ecology, Chemistry, séquestration du carbone, biome, diversité variétale, protection de la forêt, P01 - Conservation de la nature et ressources foncières, ABOVEGROUND BIOMASS, tropical forest, Asia, F60 - Physiologie et biochimie végétale, TREE ALPHA-DIVERSITY, forêt amazonienne, CONSERVATION, 010603 evolutionary biology, Article, Ecology and Environment, Phénomènes atmosphériques, Forest ecology, Life Science, Bosecologie en Bosbeheer, Forest, AFRICAN RAIN-FORESTS, WOOD PRODUCTION, BIODIVERSITY, CLIMATE, K70 - Dégâts causés aux forêts et leur protection, atténuation des effets du changement climatique, 0105 earth and related environmental sciences, Tropical Climate, Western Hemisphere, TREE SPECIES RICHNESS, Tropics, Plant, 15. Life on land, Forest Ecology and Forest Management, Carbon, biodiversité forestière, DOMINANCE, 13. Climate action, Earth and Environmental Sciences, Africa, Alpha diversity, Americas, structure de la canopée
Abstract: Tropical forests are global centres of biodiversity and carbon storage. Many tropical countries aspire to protect forest to fulfil biodiversity and climate mitigation policy targets, but the conservation strategies needed to achieve these two functions depend critically on the tropical forest tree diversity-carbon storage relationship. Assessing this relationship is challenging due to the scarcity of inventories where carbon stocks in aboveground biomass and species identifications have been simultaneously and robustly quantified. Here, we compile a unique pan-Tropical dataset of 360 plots located in structurally intact old-growth closed-canopy forest, surveyed using standardised methods, allowing a multi-scale evaluation of diversity-carbon relationships in tropical forests. Diversity-carbon relationships among all plots at 1 ha scale across the tropics are absent, and within continents are either weak (Asia) or absent (Amazonia, Africa). A weak positive relationship is detectable within 1 ha plots, indicating that diversity effects in tropical forests may be scale dependent. The absence of clear diversity-carbon relationships at scales relevant to conservation planning means that carbon-centred conservation strategies will inevitably miss many high diversity ecosystems. As tropical forests can have any combination of tree diversity and carbon stocks both require explicit consideration when optimising policies to manage tropical carbon and biodiversity., 0, SCOPUS: ar.j, info:eu-repo/semantics/published
Published: 2017

38. A botanical inventory of forest on karstic limstone and metamorphic substrate in the Chiquibul Forest, Belize, with focus on woody taxa

Author: S. Chicas, R. Chance, Tiina Särkinen, W. D. R. Bayly, David Harris, C. Pennil, H. M. Baden, H. Vandrot, A. C. Matthews, Dalia Amor Conde, S. Bridgewater, University of Southern Denmark (SDU), Royal Botanic Garden Edinburgh, National Institute of Water and Atmospheric Research [Auckland] (NIWA), Institut Agronomique Néo-Calédonien (IAC), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), University of Belize, Geisel School of Medicine at Dartmouth, University of Edinburgh, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Royal Botanic Garden [Edinburgh]
Subjects: 0106 biological sciences, Watershed, Mesoamerica, Plant Science, Conservation, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Karstic terrain, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, La Selva Maya, Maya Forest, Mesoamerica, floristic affinity, conservation, threatened species, limestone forest, karstic terrain, Limestone forest, Ecology, Evolution, Behavior and Systematics, Floristic affinity, Ecology, National park, Diameter at breast height, Vegetation, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Belize, Threatened species, Geography, Taxon, Maya Forest, Liana, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, La Selva Maya, 010606 plant biology & botany
Abstract: International audience; The Chiquibul Forest Reserve and National Park in Belize is a priority conservation area within the ‘Maya Forest’ in Central America. Although taxonomic data are essential for the development of conservation plans in the region, there is limited knowledge of the existing species in the area. Here we present a botanical species list of mostly woody taxa based on voucher specimens, with particular focus on the Raspaculo watershed in the eastern part of the National Park. Within the Raspaculo watershed, a comparison is made between 0.1 ha of valley floor and 0.1 ha of hilltop vegetation, sampling trees, shrubs, palms and lianas ≥2.5 cm diameter at breast height. Additionally, a 1 ha plot was established in the Upper Raspaculo watershed. Our study shows 38 new species records for the region, and important additions to the flora of Belize. New records were recorded from forests on both metamorphic and karstic substrate, including previously overlooked hilltop forest elements. Quantitative assessment of vegetation across elevation zones shows distinct elements dominating on valley floors and hilltops. Our results show that the Chiquibul contains at least 58% of Belize’s threatened plant species, and represent a source of information for the management and conservation of the area.
Published: 2016

39. Assessing Hotspots of Evolutionary History with Data from Multiple Phylogenies: An Analysis of Endemic Clades from New Caledonia

Author: Philippe Grandcolas, Peter M. Hollingsworth, Roseli Pellens, Antje Ahrends, Royal Botanic Garden Edinburgh, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Royal Botanic Garden [Edinburgh], Muséum national d'Histoire naturelle (MNHN)-Université Pierre et Marie Curie - Paris 6 (UPMC)-École Pratique des Hautes Études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Ws, 0303 health sciences, Resampling, [SDV]Life Sciences [q-bio], Tree of life, 15. Life on land, Biology, 010603 evolutionary biology, 01 natural sciences, Biodiversity hotspot, 03 medical and health sciences, Phylogenetic diversity, Meta-analysis, Taxon, Evolutionary biology, Phylogenetics, [SDE]Environmental Sciences, Rarefaction, Rarefaction (ecology), Species richness, Clade, 030304 developmental biology
Abstract: International audience; The great bulk of the present knowledge of the Tree of Life comes from many phylogenies, each with relatively few tips, but with lots of diversity concerning taxa and characters sampled and methods of analysis used. For several biodiversity hotspots this is the kind of data available and ready to be used to have a better understanding on the evolutionary patterns and to identify areas with remarkable evolutionary history. But relying on data coming from independent studies raises some methodological challenges of standardization, comparability and assessments of bias to make the best use of the currently available information. To bring light to this subject here we analyzed the distribution of phylogenetic diversity in New Caledonia, a biodiversity hotspot characterized by strong rates of regional and internal endemicity. We used a dataset with 18 phylogenies distributed in 16 study sites, and based our analysis on the measure Ws sum. Our study comprises the analysis of (1) the role of the number of phylogenies on site' scores and a strategy of standardization of the dataset by the number of phylogenies; (2) the infl uence of species richness on site scores and the design of the measure Ws ranks to focus on the most divergent species of each phylogeny; (3) an assessment of the infl uence of individual phylogenies; (4) a resampling strategy using multiple phylogenies to verify the results' stability.
Published: 2016

40. Phylogenetic diversity of Amazonian tree communities

Author: Esteban Álvarez, Gabriela Lopez-Gonzalez, Alejandro Araujo-Murakami, William F. Laurance, Oliver L. Phillips, Abel Monteagudo Mendoza, Ben Hur Marimon-Junior, Iêda Leão do Amaral, Atila Alves de Oliveira, Hans ter Steege, Emilio Vilanova Torre, Walter Palacios Cuenca, John Terborgh, David A. Neill, Maria Cristina Peñuela Mora, Eric Arets, Hirma Ramírez Angulo, Susan G. Laurance, Wilson Roberto Spironello, Carlos A. Quesada, Ted R. Feldpausch, Ademir Roberto Ruschel, Adriana Prieto, Niro Higuchi, Miguel Alexiades, Christopher Baraloto, Simon L. Lewis, Luis Valenzuela Gamarra, Vincent A. Vos, Ana Andrade, Isau Huamantupa-Chuquimaco, Carlos Cerón, Fernando Cornejo Valverde, Gerardo Aymard, Anthony Di Fiore, Nigel C. A. Pitman, R. Toby Pennington, Rafael de Paiva Salomão, Roel J. W. Brienen, Beatriz Schwantes Marimon, Jérôme Chave, Norma Salinas Revilla, Damien Bonal, Eurídice N. Honorio Coronado, Kyle G. Dexter, Ima Célia Guimarães Vieira, Marisol Toledo, William Farfan-Rios, Agustín Rudas, Miles R. Silman, School of Geography [Leeds], University of Leeds, School of Geosciences [Edinburgh], University of Edinburgh, Royal Botanic Garden [Edinburgh], Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), University of Kent [Canterbury], Instituto Nacional de Pesquisas da Amazônia (INPA), Projeto TEAM-Manaus, Universidad Autonoma Gabriel René Moreno (UAGRM), Jardín Botánico de Medellín, Wageningen University and Research [Wageningen] (WUR), Programa Cienclas Agro & Mar, UNELLEZ Guanare, Herbario Universitario PORT, Ecologie des forêts de Guyane (UMR ECOFOG), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-AgroParisTech-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Herbario Nacional del Ecuador, Andes to Amazon Biodiversity Program [Madre de Dios], University of Texas at Austin [Austin], Universidad Nacional de San Antonio Abad del Cusco (UNSAAC), James Cook University (JCU), Universidade do Estado de Mato Grosso (UNEMAT), Chercheur indépendant, Missouri Botanical Garden, Universidad Estatal Amazonica, Duke University [Durham], Universidad Nacional de Colombia [Bogotà] (UNAL), Instituto de Investigaciones para el Desarrollo Forestal, Universidad de los Andes [Bogota] (UNIANDES), EMBRAPA Amazonia Oriental, Brazilian Agricultural Research Corporation (Embrapa), Museu Paraense Emílio Goeldi [Belém, Brésil] (MPEG), Naturalis Biodiversity Center [Leiden], Utrecht University [Utrecht], Inst Boliviano Invest Forestal, Santa Cruz 10260, Bolivia, Instituto Boliviano de Investigacion Forestal (IBIF), Museu Paraense Emílio Goeldi, Federal University of Para - Universidade Federal do Pará - UFPA [Belém, Brazil] (UFPA), European Project: 282664,EC:FP7:ENV,FP7-ENV-2011,AMAZALERT(2011), Royal Botanic Garden Edinburgh, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research Centre [Wageningen] (WUR), Universidad Nacional San Antonio Abad del Cusco, Missouri Botanical Garden (USA), Universidad de los Andes [Bogota], Federal University of Para - Universidade Federal do Para [Belem - Brésil], Fitzpatrick, Matthew C., Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Eurídice N. Honorio Coronado, University of Leeds, Kyle G. Dexter, University of Edinburgh / Royal Botanic Garden Edinburgh, R. Toby Pennington, Royal Botanic Garden Edinburgh, Jérôme Chave, CNRS & Université Paul Sabatier, Simon L. Lewis, University of Leeds / University College London, Miguel N. Alexiades, University of Kent, Esteban Alvarez, Jardín Botânico de Medellín, Atila Alves de Oliveira, Projeto TEAM - INPA, Iêda L. Amaral, PROJETO TEAM - INPA, Alejandro Araujo-Murakami, Museo de Historia Natural Noel Kempff Mercado & Universidad Autonoma Gabriel Rene Moreno, Eric J. M. M. Arets, Alterra, Wageningen University and Research Centre, Gerardo A. Aymard, UNELLEZ-Guanare, Programa del Agro y el Mar, Herbario Universitario (PORT), Christopher Baraloto, Institut National de la Recherche Agronomique / Florida International University, Damien Bonal, INRA-Université de Lorraine, Roel Brienen, University of Leeds, Carlos Cerón, Universidad Central del Ecuador, Fernando Cornejo Valverde, Andes to Amazon Biodiversity Program, Anthony Di Fiore, University of Texas, William Farfan-Rios, Wake Forest University, Ted R. Feldpausch, University of Exeter, Niro Higuchi, INPA, Isau Huamantupa-Chuquimaco, Universidad Nacional San Antonio Abad del Cusco, Susan G. Laurance, Centre for Tropical Environmental and Sustainability Science (TESS) and School of Marine and Tropical Biology, James Cook University, William F. Laurance, Centre for Tropical Environmental and Sustainability Science (TESS) and School of Marine and Tropical Biology, James Cook University, Gabriela López-Gonzalez, University of Leeds, Beatriz S. Marimon, Universidade do Estado de Mato Grosso, Ben Hur Marimon-Junior, Universidade do Estado de Mato Grosso, Abel Monteagudo Mendoza, JardíN Botánico de Missouri, David Neill, Universidad Estatal Amazónica, Walter Palacios Cuenca, Universidad Técnica del Norte & Herbario Nacional del Ecuador, Maria Cristina Peñuela Mora, Universidad Regional Amazónica Ikiam, Nigel C. A. Pitman, Duke University / The Field Museum, Adriana Prieto, Universidad Nacional de Colombia, Carlos A. Quesada, INPA, Hirma Ramirez Angulo, Universidad de Los Andes, Agustín Rudas, Universidad Nacional de Colombia, ADEMIR ROBERTO RUSCHEL, CPATU, Norma Salinas Revilla, Universidad Nacional San Antonio Abad del Cusco / University of Oxford, Rafael P. Salomão, MPEG, Ana Segalin de Andrade, INPA, Miles R. Silman, Wake Forest University, Wilson Spironello, PROJETO TEAM - INPA, Hans ter Steege, Naturalis Biodiversity Center / Utrecht University, John Terborgh, Duke University, Marisol Toledo, Instituto Boliviano de Investigación Forestal / Universidad Autónoma Gabriel René Moreno, Luis Valenzuela Gamarra, Jardín Botánico de Missouri, Ima C. G. Vieira, MPEG, Emilio Vilanova Torre, Universidad de Los Andes, Vincent Vos, Universidad Autónoma del Beni, Oliver L. Phillips, University of Leeds., and Université des Antilles (UA)-Université de Guyane (UG)-Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Lineage (evolution), [SDV]Life Sciences [q-bio], Bos- en Landschapsecologie, Liliopsida, Árvore, Monocots, Biology, 010603 evolutionary biology, 01 natural sciences, Filogenética, Magnoliophyta, Phylogenetic diversity, 03 medical and health sciences, Plant Community, Forest and Landscape Ecology, species richness, Clade, Vegetatie, Monocotyledon, Ecology, Evolution, Behavior and Systematics, Taxonomy, 030304 developmental biology, 0303 health sciences, Vegetation, Forest inventory, Phylogenetic tree, Amazon rainforest, Ecology, Magnoliids, Amazonia, 15. Life on land, Phylogenetics, Taxon, Dicotyledon, Diversidade, phylogenetic diversity, Vegetatie, Bos- en Landschapsecologie, Vegetation, Forest and Landscape Ecology, Species richness, Amazon basin, Eudicots
Abstract: Aim: To examine variation in the phylogenetic diversity (PD) of tree communities across geographical and environmental gradients in Amazonia. Location: Two hundred and eighty-three c. 1 ha forest inventory plots from across Amazonia. Methods: We evaluated PD as the total phylogenetic branch length across species in each plot (PDss), the mean pairwise phylogenetic distance between species (MPD), the mean nearest taxon distance (MNTD) and their equivalents standardized for species richness (ses.PDss, ses.MPD, ses.MNTD). We compared PD of tree communities growing (1) on substrates of varying geological age; and (2) in environments with varying ecophysiological barriers to growth and survival. Results: PDss is strongly positively correlated with species richness (SR), whereas MNTD has a negative correlation. Communities on geologically young- and intermediate-aged substrates (western and central Amazonia respectively) have the highest SR, and therefore the highest PDss and the lowest MNTD. We find that the youngest and oldest substrates (the latter on the Brazilian and Guiana Shields) have the highest ses.PDss and ses.MNTD. MPD and ses.MPD are strongly correlated with how evenly taxa are distributed among the three principal angiosperm clades and are both highest in western Amazonia. Meanwhile, seasonally dry tropical forest (SDTF) and forests on white sands have low PD, as evaluated by any metric. Main conclusions: High ses.PDss and ses.MNTD reflect greater lineage diversity in communities. We suggest that high ses.PDss and ses.MNTD in western Amazonia results from its favourable, easy-to-colonize environment, whereas high values in the Brazilian and Guianan Shields may be due to accumulation of lineages over a longer period of time. White-sand forests and SDTF are dominated by close relatives from fewer lineages, perhaps reflecting ecophysiological barriers that are difficult to surmount evolutionarily. Because MPD and ses.MPD do not reflect lineage diversity per se, we suggest that PDss, ses.PDss and ses.MNTD may be the most useful diversity metrics for setting large-scale conservation priorities. © 2015 John Wiley & Sons Ltd.
Published: 2015

41. The botanist in Berwickshire : an annotated check-list of the flowering plants and ferns of Berwickshire /

Author: Braithwaite, Michael E., Royal Botanic Garden Edinburgh, and Braithwaite, Michael E.
Subjects: Berwickshire, Botany, Bryophytes, England, Pteridophyta
Published: 1990

42. The botanist in Berwickshire : an annotated check-list of the flowering plants and ferns of Berwickshire and an annotated check-list of the bryophytes of Berwickshire with introductory sections giving an overview of the flora

Author: Braithwaite, M.E.; Long, David Geoffrey, Royal Botanic Garden Edinburgh, and Braithwaite, M.E.; Long, David Geoffrey
Subjects: Berwickshire, Floras, Scotland
Published: 1990

43. Problèmes et perspectives de l'histoire globale de l'environnement depuis 1990

Author: Dufoix, Stéphane, Mcneill, John, Sociologie, philosophie et anthropologie politiques (SOPHIAPOL), Université Paris Nanterre (UPN), Royal Botanic Garden, Edinburgh, Royal Botanic Garden-Royal Botanic Garden, Caillé, Alain and Dufoix, Stéphane, and Royal Botanic Garden [Edinburgh]
Subjects: Sociologie, [SHS.PHIL]Humanities and Social Sciences/Philosophy, Épistémologie des sciences sociales, Mondialisation
Abstract: no abstract
Published: 2013

44. Permanent genetic resources added to Molecular Ecology Resources database 1 December 2011 - 31 January 2012

Author: Mark A. Renshaw, M. C. Arias, Haydée A. Cunha, Abel Bernadou, Terrence L. Miller, Shuzhen Wang, Christopher M. Hollenbeck, F. Piatscheck, F. A. M. Volckaert, E.L. Souche, M. P. Dubois, Chunxiao Zhang, Jan R. McDOWELL, D. J. Harris, Jie Xiao, Bingfang Liu, Shengli Jing, Kimberly S. Reece, Céline M. O. Reisser, Chiara Papetti, E. D’Alençon, John R. Gold, E. Françoso, R. Blatrix, Lili Zhu, C. Djieto-Lordon, Sergine Ponsard, C. Eraud, Jonathan P. A. Gardner, Xinxin Peng, D. McKEY, Yan Zhao, B. Hellemans, Yi Ding, Xi Zhou, Antonio Sole-Cava, Giorgia Bino, Lorenzo Zane, S. Garnier, Hangjin Yu, Anne-Laure Clamens, M. Garcia, Erica Newton, Barbara Zannato, J. Peccoud, Katrina M. Pagenkopp Lohan, Anderson Vasconcellos, Ian G. Paterson, Daniel E. Ruzzante, Cecilia Carrea, M. Sauve, Jeffrey D. Shields, E. Arnoux, G. J. Kergoat, P. Dumas, Guangcun He, S. Gimenez, F. O. Francisco, Tyler S. Zemlak, Denis Bourguet, B. Faivre, James J. Bell, J. K. J. Van Houdt, Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo (USP), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre for Marine Environmental and Economic Research, Victoria University of Wellington, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Department of Biology, Universita degli Studi di Padova, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Dalhousie University [Halifax], Laboratório de Biodiversidade Molecular, Universidade Federal do Rio de Janeiro (UFRJ), Laboratório de Mamíferos Aquáticos e Bioindicadores (MAQUA), Universidade do Estado do Rio de Janeiro [Rio de Janeiro] (UERJ), Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] (DGIMI), Université de Montpellier (UM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA), State Key Laboratory of Hybrid Rice, Wuhan University [China], Laboratory of Zoology, Yaoundé University, CNERA Avifaune migratrice - Station de Chizé, Office National de la Chasse et de la Faune Sauvage, Center for Biosystematics and Biodiversity, Texas A&M University [College Station], Royal Botanic Garden Edinburgh, Laboratory of Biodiversity and Evolutionary Genomics, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Virginia Institute of Marine Science (VIMS), Environmental and Life Sciences Department, Trent University, Unit of Ecology and Evolution, Albert-Ludwigs-Universität Freiburg, Intégration et Analyse Génomique (Plate-Forme 4) (PF4), Institut Pasteur [Paris], Laboratory for Cytogenetics and Genome Research, Department of Microbiology & Immunology, Universidade de São Paulo = University of São Paulo (USP), Biogéosciences [UMR 6282] (BGS), Université de Bourgogne (UB)-Centre National de la Recherche Scientifique (CNRS), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Università degli Studi di Padova = University of Padua (Unipd), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM), Royal Botanic Garden [Edinburgh], Institut Pasteur [Paris] (IP), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Universidade de São Paulo ( USP ), Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Evolution et Diversité Biologique ( EDB ), Institut de Recherche pour le Développement ( IRD ) -Université Paul Sabatier - Toulouse 3 ( UPS ) -Centre National de la Recherche Scientifique ( CNRS ), Universita degli Studi di Padova = University of Padua = Université de Padoue, Centre d’Ecologie Fonctionnelle et Evolutive ( CEFE ), Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Centre National de la Recherche Scientifique ( CNRS ) -Université de Montpellier ( UM ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -École pratique des hautes études ( EPHE ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Université Paul-Valéry - Montpellier 3 ( UM3 ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Centre de Biologie pour la Gestion des Populations ( CBGP ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Institut de Recherche pour le Développement ( IRD [France-Sud] ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Universidade Federal do Rio de Janeiro, Laboratório de Mamíferos Aquáticos e Bioindicadores ( MAQUA ), Universidade do Estado do Rio de Janeiro, Diversité, Génomes & Interactions Microorganismes - Insectes [Montpellier] ( DGIMI ), Institut National de la Recherche Agronomique ( INRA ) -Université Montpellier 2 - Sciences et Techniques ( UM2 ) -Université de Montpellier ( UM ), Catholic University of Leuven ( KU Leuven ), The Virginia Institute of Marine Science, The College of William & Mary, University of Fribourg, and Intégration et Analyse Génomique (Plate-Forme)
Subjects: 0106 biological sciences, Biology, Bioinformatics, Polymorphism, Single Nucleotide, 010603 evolutionary biology, 01 natural sciences, Molecular ecology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Genetic resources, Databases, Genetic, Genetics, Ecology, Evolution, Behavior and Systematics, DNA Primers, 030304 developmental biology, 0303 health sciences, Ecology, business.industry, Environmental resource management, [ SDV.GEN.GA ] Life Sciences [q-bio]/Genetics/Animal genetics, Biota, GENÉTICA, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [ SDV.GEN.GPL ] Life Sciences [q-bio]/Genetics/Plants genetics, business, Microsatellite Repeats, Biotechnology
Abstract: 3 pages; International audience; This article documents the addition of 473 microsatellite marker loci and 71 pairs of single-nucleotide polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Barteria fistulosa, Bombus morio, Galaxias platei, Hematodinium perezi, Macrocentrus cingulum Brischke (a.k.a. M. abdominalis Fab., M. grandii Goidanich or M. gifuensis Ashmead), Micropogonias furnieri, Nerita melanotragus, Nilaparvata lugens Stål, Sciaenops ocellatus, Scomber scombrus, Spodoptera frugiperda and Turdus lherminieri. These loci were cross-tested on the following species: Barteria dewevrei, Barteria nigritana, Barteria solida, Cynoscion acoupa, Cynoscion jamaicensis, Cynoscion leiarchus, Cynoscion nebulosus, Cynoscion striatus, Cynoscion virescens, Macrodon ancylodon, Menticirrhus americanus, Nilaparvata muiri and Umbrina canosai. This article also documents the addition of 116 sequencing primer pairs for Dicentrarchus labrax.
Published: 2012

45. Carpeloidy in flower evolution and diversification: a comparative study in Carica papaya and Arabidopsis thaliana

Author: Christophe Trehin, Louis P. Ronse De Craene, Ioan Negrutiu, Patrice Morel, Royal Botanic Garden [Edinburgh], Reproduction et développement des plantes (RDP), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Royal Botanic Garden Edinburgh, Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon)
Subjects: 0106 biological sciences, sup1 mutants, Gynoecium, Meristem, Ovary (botany), Stamen, Arabidopsis, Plant Science, Flowers, Biology, 01 natural sciences, feminization, 03 medical and health sciences, sex conversion, Locule, Botany, Arabidopsis thaliana, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, 030304 developmental biology, bisexual flowers, 0303 health sciences, Carica papaya, Arabidopsis Proteins, Carica, fungi, food and beverages, evo-devo, Articles, biology.organism_classification, Biological Evolution, floral development, ectopic ovules, carpeloidy, Mutation, Microscopy, Electron, Scanning, 010606 plant biology & botany, Transcription Factors
Abstract: Annals of Botany, 107 (9) Supplement 1; International audience; Background and Aims Bisexual flowers of Carica papaya range from highly regular flowers to morphs with various fusions of stamens to the ovary. Arabidopsis thaliana sup1 mutants have carpels replaced by chimeric carpel-stamen structures. Comparative analysis of stamen to carpel conversions in the two different plant systems was used to understand the stage and origin of carpeloidy when derived from stamen tissues, and consequently to understand how carpeloidy contributes to innovations in flower evolution. Methods Floral development of bisexual flowers of Carica was studied by scanning electron microscopy and was compared with teratological sup mutants of A. thaliana. Key Results In Carica development of bisexual flowers was similar to wild (unisexual) forms up to locule initiation. Feminization ranges from fusion of stamen tissue to the gynoecium to complete carpeloidy of antepetalous stamens. In A. thaliana, partial stamen feminization occurs exclusively at the flower apex, with normal stamens forming at the periphery. Such transformations take place relatively late in development, indicating strong developmental plasticity of most stamen tissues. These results are compared with evo-devo theories on flower bisexuality, as derived from unisexual ancestors. The Arabidopsis data highlight possible early evolutionary events in the acquisition of bisexuality by a patchy transformation of stamen parts into female parts linked to a flower axis-position effect. The Carica results highlight tissue-fusion mechanisms in angiosperms leading to carpeloidy once bisexual flowers have evolved. We show two different developmental routes leading to stamen to carpel conversions by late re-specification. The process may be a fundamental aspect of flower development that is hidden in most instances by developmental homeostasis.
Published: 2011

46. Whole genome genotyping reveals discrete genetic diversity in north‐east Atlantic maerl beds

Author: Heidi L. Burdett, Jamie R. Stevens, Tom L. Jenkins, Viviana Peña, Cornelia Simon-Nutbrown, Marie-Laure Guillemin, University of Exeter, Universidad Austral de Chile, Evolutionary Biology and Ecology of Algae (EBEA), Pontificia Universidad Católica de Chile (UC)-Sorbonne Université (SU)-Universidad Austral de Chile-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff (SBR), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Heriot-Watt University [Edinburgh] (HWU), Royal Botanic Garden Edinburgh, and Universidade da Coruña
Subjects: 0106 biological sciences, 0301 basic medicine, Evolution, [SDV]Life Sciences [q-bio], Rhodolith, 010603 evolutionary biology, 01 natural sciences, Population genomics, 03 medical and health sciences, single nucleotide polymorphism, QH359-425, Genetics, population genetic structure, 14. Life underwater, Maerl, Ecology, Evolution, Behavior and Systematics, Genetic diversity, rhodolith, mitogenome, biology, Ecology, Marine reserve, Original Articles, 15. Life on land, plastome, biology.organism_classification, conservation management, 030104 developmental biology, Habitat, Threatened species, Biological dispersal, Original Article, maerl, General Agricultural and Biological Sciences, coralline algae
Abstract: International audience; Maerl beds are vital habitats for a diverse array of marine species across trophic levels, but they are increasingly threatened by human activities and climate change. Furthermore, little is known about the genetic diversity of maerl‐forming species and the population structure of maerl beds, both of which are important for understanding the ability of these species to adapt to changing environments and for informing marine reserve planning. In this study, we used a whole genome genotyping approach to explore the population genomics of Phymatolithon calcareum, a maerl‐forming red algal species, whose geographic distribution spans the north‐east Atlantic, from Norway to Portugal. Our results, using 14,150 genome‐wide SNPs (single nucleotide polymorphisms), showed that P. calcareum maerl beds across the north‐east Atlantic are generally structured geographically, a pattern likely explained by low dispersal potential and limited connectivity between regions. Additionally, we found that P. calcareum from the Fal Estuary, south‐west England, is genetically distinct from all other P. calcareum sampled, even from The Manacles, a site located only 13 km away. Further analysis revealed that this finding is not the result of introgression from two closely related species, P. purpureum or Lithothamnion corallioides. Instead, this unique diversity may have been shaped over time by geographical isolation of the Fal Estuary maerl bed and a lack of gene flow with other P. calcareum populations. The genomic data presented in this study suggest that P. calcareum genetic diversity has accumulated over large temporal and spatial scales, the preservation of which will be critical for maximising the resilience of this species to changes in climate and the environment. Moreover, our findings underline the importance of managing the conservation of maerl beds across western Europe as distinct units, at a site‐by‐site level.
Published: 2021

47. Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire

Author: R. Toby Pennington, Rosaura Grether, Luciano Paganucci de Queiroz, Colin E. Hughes, Marcelo F. Simon, Cynthia Skema, MARCELO FRAGOMENI SIMON, Cenargen, ROSAURA GRETHER, UNIVERSIDADE AUTÓNOMA METROPOLITANA-IZTAPALAPA, LUCIANO P. DE QUEIROZ, UNIVERSIDADE ESTADUAL DE FEIRA DE SANTANA, CYNTHIA SKEMA, ROYAL BOTANIC GARDEN EDINBURGH, R. TOBY PENNINGTON, ROYAL BOTANIC GARDEN EDINBURGH, and COLIN E. HUGHES, UNIVERSITY OF OXFORD.
Subjects: Biome, Molecular Sequence Data, Biodiversity, Adaptation, Biological, Plant Development, Tropical and subtropical grasslands, savannas, and shrublands, Biology, Grassland, Fires, Tropical savanna climate, Phylogeny, geography, Multidisciplinary, geography.geographical_feature_category, Base Sequence, Models, Genetic, Ecology, Species diversity, Cerrado, Fogo, Sequence Analysis, DNA, Plants, South America, Biological Sciences, Biological Evolution, Tropical savana, Biological dispersal, Species richness
Abstract: The relative importance of local ecological and larger-scale historical processes in causing differences in species richness across the globe remains keenly debated. To gain insight into these questions, we investigated the assembly of plant diversity in the Cerrado in South America, the world's most species-rich tropical savanna. Time-calibrated phylogenies suggest that Cerrado lineages started to diversify less than 10 Mya, with most lineages diversifying at 4 Mya or less, coinciding with the rise to dominance of flammable C4 grasses and expansion of the savanna biome worldwide. These plant phylogenies show that Cerrado lineages are strongly associated with adaptations to fire and have sister groups in largely fire-free nearby wet forest, seasonally dry forest, subtropical grassland, or wetland vegetation. These findings imply that the Cerrado formed in situ via recent and frequent adaptive shifts to resist fire, rather than via dispersal of lineages already adapted to fire. The location of the Cerrado surrounded by a diverse array of species-rich biomes, and the apparently modest adaptive barrier posed by fire, are likely to have contributed to its striking species richness. These findings add to growing evidence that the origins and historical assembly of species-rich biomes have been idiosyncratic, driven in large part by unique features of regional- and continental-scale geohistory and that different historical processes can lead to similar levels of modern species richness.
Published: 2009

48. Molecular phylogenetics of Euploca (Boraginaceae): homoplasy in many characters, including the C4 photosynthetic pathway

Author: Michael W Frohlich, Rowan F Sage, Lyn A Craven, Sebastian Schuster, Guillaume Gigot, Hartmut H Hilger, Hossein Akhani, Parastoo Mahdavi, Federico Luebert, Maximilian Weigend, Mats Thulin, Jeff J Doyle, Jane L Doyle, Patrick Vogan, Alan Forrest, Timothy K Fulcher, Dion S Devey, Mark W Chase, Royal Botanic Gardens [Kew], École normale supérieure de Lyon (ENS de Lyon), University of Toronto, Australian National Herbarium, Patrimoine naturel (PatriNat), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Office français de la biodiversité (OFB), Freie Universität Berlin, University of Tehran, University of Oldenburg, Rheinische Friedrich-Wilhelms-Universität Bonn, Universidad de Chile = University of Chile [Santiago] (UCHILE), Uppsala University, Cornell University [New York], and Royal Botanic Garden [Edinburgh]
Subjects: contagious distribution, C-2 photosynthesis, C-3, C3–C4 intermediate, desert flora, Botany, Botanik, Plant Science, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, C2 photosynthesis, seed set modelling, [SDE]Environmental Sciences, inflorescence plant, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, C-4 intermediate, Heliotropium section Orthostachys, Ecology, Evolution, Behavior and Systematics
Abstract: We present a phylogenetic analysis using plastid (matK, rbcL) and nuclear (nrITS) DNA for diverse Euploca spp. (formerly Heliotropium section Orthostachys) from the worldwide distribution of a genus and including species encompassing the wide physiological and morphological diversity of the genus. Our results indicate that some remarkably complex features arose multiple times in parallel in Euploca, including attributes of its subsections under section Orthostachys, notably plants that, above ground, consist almost entirely of inflorescences. To elucidate in greater detail the distribution of C4 species in Euploca and Heliotropium s.s., we made > 800 δ 13C determinations, including some from the traditional genus Tournefortia. We greatly increase the number of proven C4 species in Euploca, but found none outside Euploca. Of the tested Euploca spp., c. 28% are C3 or intermediate in carbon fixation pathway. Our phylogenetic results indicate four parallel/convergent acquisitions of C4 photosynthesis or fewer origins with subsequent loss in some species.
Published: 2022

49. Envisaging a global infrastructure to exploit the potential of digitised collections

Author: Quentin Groom, Mathias Dillen, Wouter Addink, Arturo H. Ariño, Christian Bölling, Pierre Bonnet, Lorenzo Cecchi, Elizabeth R. Ellwood, Rui Figueira, Pierre-Yves Gagnier, Olwen Grace, Anton Güntsch, Helen Hardy, Pieter Huybrechts, Roger Hyam, Alexis Joly, Isabel Larridon, Vamsi Krishna Kommineni, Laurence Livermore, Ricardo Jorge Lopes, Jeremy Miller, Sofie Meeus, Kenzo Milleville, Marc Pignal, Renato Panda, Jorrit H. Poelen, Blagoj Ristevski, Tim Robertson, Cristina Rufino, Joaquim Santos, Maarten Schermer, Katja Seltmann, Ben Scott, Heliana Teixeira, Maarten Trekels, Jitendra Gaikwad, Meise Botanic Garden [Belgium] (Plantentuin), Naturalis Biodiversity Center [Leiden], Museum für Naturkunde [Berlin], Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université de Montpellier (UM), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Museo di Storia Naturale di Firenze, Università degli Studi di Firenze = University of Florence (UniFI), Instituto Superior de Agronomia [Lisboa] (ISA), Universidade de Lisboa = University of Lisbon (ULISBOA), Muséum national d'Histoire naturelle (MNHN), Royal Botanic Garden [Edinburgh], Scientific Data Management (ZENITH), Inria Sophia Antipolis - Méditerranée (CRISAM), Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Royal Botanic Gardens [Kew], Friedrich-Schiller-Universität = Friedrich Schiller University Jena [Jena, Germany], Universidade do Porto = University of Porto, Internet Technology and Data Science Lab (IDLab), Universiteit Antwerpen = University of Antwerpen [Antwerpen]-Universiteit Gent = Ghent University (UGENT), Global Biodiversity Information Facility (GBIF), and Universidade de Aveiro
Subjects: [INFO.INFO-LG]Computer Science [cs]/Machine Learning [cs.LG], [INFO.INFO-MM]Computer Science [cs]/Multimedia [cs.MM], [INFO.INFO-CV]Computer Science [cs]/Computer Vision and Pattern Recognition [cs.CV], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, [SDE.ES]Environmental Sciences/Environmental and Society, [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract: Tens of millions of images from biological collections have become available online in the last two decades. In parallel, there has been a dramatic increase in the capabilities of image analysis technologies, especially those involving machine learning and computer vision. Whilst image analysis has become mainstream in consumer applications, it is still only used on an artisanal basis in the biological collections community, largely because the image corpora are dispersed. Yet, there is massive untapped potential for novel applications and research if the images of collection objects could be made accessible as a single corpus. In this paper, we make the case for building infrastructure that could support image analysis of collection objects. We show that such an infrastructure is entirely feasible and well worth the investment.
Published: 2022

50. MASTREE+ : time-series of plant reproductive effort from six continents

Author: Andrew Hacket‐Pain, Jessie J. Foest, Ian S. Pearse, Jalene M. LaMontagne, Walter D. Koenig, Giorgio Vacchiano, Michał Bogdziewicz, Thomas Caignard, Paulina Celebias, Joep van Dormolen, Marcos Fernández‐Martínez, Jose V. Moris, Ciprian Palaghianu, Mario Pesendorfer, Akiko Satake, Eliane Schermer, Andrew J. Tanentzap, Peter A. Thomas, Davide Vecchio, Andreas P. Wion, Thomas Wohlgemuth, Tingting Xue, Katharine Abernethy, Marie‐Claire Aravena Acuña, Marcelo Daniel Barrera, Jessica H. Barton, Stan Boutin, Emma R. Bush, Sergio Donoso Calderón, Felipe S. Carevic, Carolina Volkmer de Castilho, Juan Manuel Cellini, Colin A. Chapman, Hazel Chapman, Francesco Chianucci, Patricia da Costa, Luc Croisé, Andrea Cutini, Ben Dantzer, R. Justin DeRose, Jean‐Thoussaint Dikangadissi, Edmond Dimoto, Fernanda Lopes da Fonseca, Leonardo Gallo, Georg Gratzer, David F. Greene, Martín A. Hadad, Alejandro Huertas Herrera, Kathryn J. Jeffery, Jill F. Johnstone, Urs Kalbitzer, Władysław Kantorowicz, Christie A. Klimas, Jonathan G. A. Lageard, Jeffrey Lane, Katharina Lapin, Mateusz Ledwoń, Abigail C. Leeper, Maria Vanessa Lencinas, Ana Cláudia Lira‐Guedes, Michael C. Lordon, Paula Marchelli, Shealyn Marino, Harald Schmidt Van Marle, Andrew G. McAdam, Ludovic R. W. Momont, Manuel Nicolas, Lúcia Helena de Oliveira Wadt, Parisa Panahi, Guillermo Martínez Pastur, Thomas Patterson, Pablo Luis Peri, Łukasz Piechnik, Mehdi Pourhashemi, Claudia Espinoza Quezada, Fidel A. Roig, Karen Peña Rojas, Yamina Micaela Rosas, Silvio Schueler, Barbara Seget, Rosina Soler, Michael A. Steele, Mónica Toro‐Manríquez, Caroline E. G. Tutin, Tharcisse Ukizintambara, Lee White, Biplang Yadok, John L. Willis, Anita Zolles, Magdalena Żywiec, Davide Ascoli, CAROLINA VOLKMER DE CASTILHO, CPAF-RR, PATRICIA DA COSTA, CNPMA, ANA CLAUDIA LIRA GUEDES, CPAF-AP, FERNANDA LOPES DA FONSECA, CPAF-AC, LUCIA HELENA DE OLIVEIRA WADT, CPAF-RO., Hacket-Pain, Andrew [0000-0003-3676-1568], Foest, Jessie J [0000-0002-8236-4646], Pearse, Ian S [0000-0001-7098-0495], LaMontagne, Jalene M [0000-0001-7713-8591], Koenig, Walter D [0000-0001-6207-1427], Vacchiano, Giorgio [0000-0001-8100-0659], Bogdziewicz, Michał [0000-0002-6777-9034], Caignard, Thomas [0000-0001-5009-4613], Celebias, Paulina [0000-0001-9916-2904], Fernández-Martínez, Marcos [0000-0002-5661-3610], Moris, Jose V [0000-0003-0241-7910], Palaghianu, Ciprian [0000-0003-2496-2135], Pesendorfer, Mario [0000-0002-7994-7090], Satake, Akiko [0000-0002-0831-8617], Schermer, Eliane [0000-0001-7302-2241], Tanentzap, Andrew J [0000-0002-2883-1901], Thomas, Peter A [0000-0003-3115-3301], Wion, Andreas P [0000-0002-0701-2843], Wohlgemuth, Thomas [0000-0002-4623-0894], Abernethy, Katharine [0000-0002-0393-9342], Aravena Acuña, Marie-Claire [0000-0002-4493-4396], Daniel Barrera, Marcelo [0000-0002-9207-8109], Barton, Jessica H [0000-0002-2016-4278], Boutin, Stan [0000-0001-6317-038X], Bush, Emma R [0000-0003-4036-125X], Donoso Calderón, Sergio [0000-0002-4599-4702], Carevic, Felipe S [0000-0002-6137-2057], de Castilho, Carolina Volkmer [0000-0002-1064-2758], Manuel Cellini, Juan [0000-0002-7870-5751], Chapman, Colin A [0000-0002-8827-8140], Chapman, Hazel [0000-0001-8509-703X], Chianucci, Francesco [0000-0002-5688-2060], da Costa, Patricia [0000-0002-5192-6685], Cutini, Andrea [0000-0002-7033-2399], Dantzer, Ben [0000-0002-3058-265X], Justin DeRose, R [0000-0002-4849-7744], da Fonseca, Fernanda Lopes [0000-0001-7289-6684], Gratzer, Georg [0000-0002-6355-6562], Hadad, Martín A [0000-0002-9334-064X], Herrera, Alejandro Huertas [0000-0003-2229-6714], Johnstone, Jill F [0000-0001-6131-9339], Kalbitzer, Urs [0000-0002-6289-7971], Kantorowicz, Władysław [0000-0002-2474-0113], Klimas, Christie A [0000-0001-9362-1305], Lageard, Jonathan GA [0000-0001-8971-0444], Lapin, Katharina [0000-0003-4462-2058], Ledwoń, Mateusz [0000-0003-3017-6376], Vanessa Lencinas, Maria [0000-0002-2123-3976], Lira-Guedes, Ana Cláudia [0000-0001-9200-4727], Marchelli, Paula [0000-0002-6949-0656], McAdam, Andrew G [0000-0001-7323-2572], Nicolas, Manuel [0000-0002-0885-1227], de Oliveira Wadt, Lúcia Helena [0000-0002-5018-7550], Panahi, Parisa [0000-0002-5295-9534], Martínez Pastur, Guillermo [0000-0003-2614-5403], Patterson, Thomas [0000-0002-3498-893X], Luis Peri, Pablo [0000-0002-5398-4408], Piechnik, Łukasz [0000-0002-3958-7393], Pourhashemi, Mehdi [0000-0002-8918-6336], Roig, Fidel A [0000-0003-0987-0486], Peña Rojas, Karen [0000-0001-6795-1503], Micaela Rosas, Yamina [0000-0001-7476-399X], Schueler, Silvio [0000-0003-0155-5692], Seget, Barbara [0000-0002-7872-926X], Soler, Rosina [0000-0002-5799-1672], Toro-Manríquez, Mónica [0000-0001-6492-1333], White, Lee [0000-0002-4595-5981], Yadok, Biplang [0000-0001-5926-9897], Willis, John L [0000-0003-0238-0003], Zolles, Anita [0000-0003-3476-3172], Żywiec, Magdalena [0000-0002-5992-4051], Ascoli, Davide [0000-0002-0546-4467], Apollo - University of Cambridge Repository, Department of Geography and Planning, School of Environmental Sciences, University of Liverpool, US Geological Survey [Fort Collins], United States Geological Survey [Reston] (USGS), Department of Biological Sciences [Chicago], University of Illinois [Chicago] (UIC), University of Illinois System-University of Illinois System, University of California [Berkeley] (UC Berkeley), University of California (UC), Department of Agricultural and Environmental Sciences, Università degli Studi di Milano = University of Milan (UNIMI), Laboratoire des EcoSystèmes et des Sociétés en Montagne (UR LESSEM), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biodiversité, Gènes & Communautés (BioGeCo), Université de Bordeaux (UB)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universitatea Stefan cel Mare Suceava (USU), Department of Forest and Soil Sciences, Universität für Bodenkultur Wien = University of Natural Resources and Life [Vienne, Autriche] (BOKU), Kyushu University, Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), ECOSYSTEMS AND GLOBAL CHANGE GROUP DEPARTMENT OF PLANT SCIENCES UNIVERSITY OF CAMBRIDGE GBR, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), School of Life Sciences, University of Northumbria at Newcastle [United Kingdom], Faculty of Natural Sciences [Stirling], University of Stirling, Universidad Nacional de la Plata [Argentine] (UNLP), Department of Biological Sciences [Edmonton], University of Alberta, Royal Botanic Garden [Edinburgh], Brazilian Agricultural Research Corporation (Embrapa), Department of Anthropology [George Washington University] (GW), The George Washington University (GW), School of biological Sciences [Christchurch], University of Canterbury [Christchurch], Centro di Viticoltura ed Enologia [CREA], Consiglio per la Ricerca in Agricoltura e l’analisi dell’economia agraria = Council for Agricultural Research and Economics (CREA), Département Recherche-Développement-Innovation, Office National des Forêts (ONF), Agence Nationale des Parcs Nationaux du Gabon (ANPN), Centro de Investigación en Ecosistemas de la Patagonia (CIEP), Universidad Austral de Chile, Institute of Arctic Biology, University of Alaska [Fairbanks] (UAF), Department of Biology, University of Konstanz, Konstanz, forest research institute, Department of silviculture and genetics of forest trees, Austrian Research Centre for Forests (BFW), Department of Ecology and Evolutionary Biology [Boulder], University of Colorado [Boulder], Instituto Nacional de Tecnología Agropecuaria, and Universidad Nacional de la Patagonia Austral (UNPA)
Subjects: Plantas Perennes, Reclutamiento, demography, Seed production, Regeneración, Regeneration (biological), Q1, Perennials, Flowering, Plant Propagation, Evolución de las Estrategias Reproductivas, Ecología Vegetal, flowering, general flowering, masting, plant reproduction, recruitment, regeneration, Propagación de Plantas, General Environmental Science, Global and Planetary Change, Ecology, Ecosistemas de Tierras Secas, Reproduction, R735, Plants, [SDE]Environmental Sciences, Seeds, General flowering, Recruitment, Strategies, FOS: Medical biotechnology, demography, flowering, general flowering, masting, plant reproduction, recruitment, regeneration, Dryland Ecosystems, Plant reproduction, ddc:570, Environmental Chemistry, Demografía, Regeneration, Floración, Time Series Analysis, Ecosystem, Demography, Plant Ecology, Masting, QR, Evolution of Reproductive Strategies, FOS: Biological sciences, Análisis de Series Temporales, Estrategias
Abstract: Significant gaps remain in understanding the response of plant reproduction to environmental change. This is partly because measuring reproduction in long-lived plants requires direct observation over many years and such datasets have rarely been made publicly available. Here we introduce MASTREE+, a data set that collates reproductive time-series data from across the globe and makes these data freely available to the community. MASTREE+ includes 73,828 georeferenced observations of annual reproduction (e.g. seed and fruit counts) in perennial plant populations worldwide. These observations consist of 5971 population-level time-series from 974 species in 66 countries. The mean and median time-series length is 12.4 and 10 years respectively, and the data set includes 1122 series that extend over at least two decades (≥20 years of observations). For a subset of well-studied species, MASTREE+ includes extensive replication of time-series across geographical and climatic gradients. Here we describe the open-access data set, available as a.csv file, and we introduce an associated web-based app for data exploration. MASTREE+ will provide the basis for improved understanding of the response of long-lived plant reproduction to environmental change. Additionally, MASTREE+ will enable investigation of the ecology and evolution of reproductive strategies in perennial plants, and the role of plant reproduction as a driver of ecosystem dynamics. EEA Santa Cruz Fil: Hacket-Pain, Andrew. University of Liverpool. School of Environmental Sciences. Department of Geography and Planning; Reino Unido Fil: Foest, Jessie J. University of Liverpool. School of Environmental Sciences. Department of Geography and Planning; Reino Unido Fil: Pearse, Ian S. U.S. Fort Collins Science Center. Geological Survey; Estados Unidos Fil: LaMontagne, Jalene M. DePaul University. Department of Biological Sciences; Estados Unidos Fil: Koenig, Walter D. University of California Berkeley. Hastings Reservation; Estados Unidos Fil: Vacchiano, Giorgio. University of Milan. Milan Department of Agricultural and Environmental Sciences; Italia. Fil: Bogdziewicz, Michał. Adam Mickiewicz University. Faculty of Biology. Institute of Environmental Biology; Polonia Fil: Bogdziewicz, Michał. University Grenoble Alpes. INRAE, LESSEM; Francia Fil: Caignard, Thomas. Université Bordeaux. INRAE, BIOGECO; Francia Fil: Celebias, Paulina. Adam Mickiewicz University. Faculty of Biology. Institute of Environmental Biology; Polonia Fil: Peri, Pablo Luis. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Santa Cruz; Argentina. Fil: Peri, Pablo Luis. Universidad Nacional de la Patagonia Austral; Argentina. Fil: Peri, Pablo Luis. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Fil: Ascoli, Davide. University of Torino. Department of Agricultural. Forest and Food Sciences (DISAFA); Italia Fil: Gallo, Leonardo Ariel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; Argentina Fil: Gallo, Leonardo Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina Fil: Marchelli, Paula. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Bariloche; Argentina Fil: Marchelli, Paula. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Instituto de Investigaciones Forestales y Agropecuarias Bariloche; Argentina
Published: 2022

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