The GenTree Platform: growth traits and tree-level environmental data in 12 European forest tree species

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Abstract

Background

Progress in the field of evolutionary forest ecology has been hampered by the huge challenge of phenotyping trees across their ranges in their natural environments, and the limitation in high-resolution environmental information.

Findings

The GenTree Platform contains phenotypic and environmental data from 4,959 trees from 12 ecologically and economically important European forest tree species: Abies alba Mill. (silver fir), Betula pendula Roth. (silver birch), Fagus sylvatica L. (European beech), Picea abies (L.) H. Karst (Norway spruce), Pinus cembra L. (Swiss stone pine), Pinus halepensis Mill. (Aleppo pine), Pinus nigra Arnold (European black pine), Pinus pinaster Aiton (maritime pine), Pinus sylvestris L. (Scots pine), Populus nigra L. (European black poplar), Taxus baccata L. (English yew), and Quercus petraea (Matt.) Liebl. (sessile oak). Phenotypic (height, diameter at breast height, crown size, bark thickness, biomass, straightness, forking, branch angle, fructification), regeneration, environmental in situ measurements (soil depth, vegetation cover, competition indices), and environmental modeling data extracted by using bilinear interpolation accounting for surrounding conditions of each tree (precipitation, temperature, insolation, drought indices) were obtained from trees in 194 sites covering the species’ geographic ranges and reflecting local environmental gradients.

Conclusion

The GenTree Platform is a new resource for investigating ecological and evolutionary processes in forest trees. The coherent phenotyping and environmental characterization across 12 species in their European ranges allow for a wide range of analyses from forest ecologists, conservationists, and macro-ecologists. Also, the data here presented can be linked to the GenTree Dendroecological collection, the GenTree Leaf Trait collection, and the GenTree Genomic collection presented elsewhere, which together build the largest evolutionary forest ecology data collection available.

Related collections

Most cited references 31

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Climatologies at high resolution for the earth’s land surface areas

Dirk Karger, Olaf Conrad, Jürgen Böhner … (2017)

High-resolution information on climatic conditions is essential to many applications in environmental and ecological sciences. Here we present the CHELSA (Climatologies at high resolution for the earth’s land surface areas) data of downscaled model output temperature and precipitation estimates of the ERA-Interim climatic reanalysis to a high resolution of 30 arc sec. The temperature algorithm is based on statistical downscaling of atmospheric temperatures. The precipitation algorithm incorporates orographic predictors including wind fields, valley exposition, and boundary layer height, with a subsequent bias correction. The resulting data consist of a monthly temperature and precipitation climatology for the years 1979–2013. We compare the data derived from the CHELSA algorithm with other standard gridded products and station data from the Global Historical Climate Network. We compare the performance of the new climatologies in species distribution modelling and show that we can increase the accuracy of species range predictions. We further show that CHELSA climatological data has a similar accuracy as other products for temperature, but that its predictions of precipitation patterns are better.

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System for Automated Geoscientific Analyses (SAGA) v. 2.1.4

J Böhner, M. Bock, H. Dietrich … (2015)

The System for Automated Geoscientific Analyses (SAGA) is an open source geographic information system (GIS), mainly licensed under the GNU General Public License. Since its first release in 2004, SAGA has rapidly developed from a specialized tool for digital terrain analysis to a comprehensive and globally established GIS platform for scientific analysis and modeling. SAGA is coded in C++ in an object oriented design and runs under several operating systems including Windows and Linux. Key functional features of the modular software architecture comprise an application programming interface for the development and implementation of new geoscientific methods, a user friendly graphical user interface with many visualization options, a command line interpreter, and interfaces to interpreted languages like R and Python. The current version 2.1.4 offers more than 600 tools, which are implemented in dynamically loadable libraries or shared objects and represent the broad scopes of SAGA in numerous fields of geoscientific endeavor and beyond. In this paper, we inform about the system's architecture, functionality, and its current state of development and implementation. Furthermore, we highlight the wide spectrum of scientific applications of SAGA in a review of published studies, with special emphasis on the core application areas digital terrain analysis, geomorphology, soil science, climatology and meteorology, as well as remote sensing.

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The velocity of climate change.

Scott Loarie, Philip B. Duffy, Healy Hamilton … (2009)

The ranges of plants and animals are moving in response to recent changes in climate. As temperatures rise, ecosystems with 'nowhere to go', such as mountains, are considered to be more threatened. However, species survival may depend as much on keeping pace with moving climates as the climate's ultimate persistence. Here we present a new index of the velocity of temperature change (km yr(-1)), derived from spatial gradients ( degrees C km(-1)) and multimodel ensemble forecasts of rates of temperature increase ( degrees C yr(-1)) in the twenty-first century. This index represents the instantaneous local velocity along Earth's surface needed to maintain constant temperatures, and has a global mean of 0.42 km yr(-1) (A1B emission scenario). Owing to topographic effects, the velocity of temperature change is lowest in mountainous biomes such as tropical and subtropical coniferous forests (0.08 km yr(-1)), temperate coniferous forest, and montane grasslands. Velocities are highest in flooded grasslands (1.26 km yr(-1)), mangroves and deserts. High velocities suggest that the climates of only 8% of global protected areas have residence times exceeding 100 years. Small protected areas exacerbate the problem in Mediterranean-type and temperate coniferous forest biomes. Large protected areas may mitigate the problem in desert biomes. These results indicate management strategies for minimizing biodiversity loss from climate change. Montane landscapes may effectively shelter many species into the next century. Elsewhere, reduced emissions, a much expanded network of protected areas, or efforts to increase species movement may be necessary.

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Author and article information

Contributors

Lars Opgenoorth:

ORCID: https://orcid.org/0000-0003-0737-047X

Benjamin Dauphin:

ORCID: https://orcid.org/0000-0003-0982-4252

Raquel Benavides:

ORCID: https://orcid.org/0000-0003-2328-5371

Katrin Heer:

ORCID: https://orcid.org/0000-0002-1036-599X

Paraskevi Alizoti:

ORCID: https://orcid.org/0000-0002-5656-8434

Elisabet Martínez-Sancho

Ricardo Alía:

ORCID: https://orcid.org/0000-0002-9426-0967

Olivier Ambrosio

Albet Audrey

Francisco Auñón

Camilla Avanzi:

ORCID: https://orcid.org/0000-0003-1632-5304

Evangelia Avramidou:

ORCID: https://orcid.org/0000-0002-5932-1189

Francesca Bagnoli:

ORCID: https://orcid.org/0000-0001-6909-0006

Evangelos Barbas:

ORCID: https://orcid.org/0000-0002-5760-605X

Cristina C Bastias:

ORCID: https://orcid.org/0000-0002-2479-2001

Catherine Bastien:

ORCID: https://orcid.org/0000-0002-9391-6637

Eduardo Ballesteros

Giorgia Beffa

Frédéric Bernier

Henri Bignalet

Guillaume Bodineau

Damien Bouic

Sabine Brodbeck:

ORCID: https://orcid.org/0000-0002-4481-7348

William Brunetto

Jurata Buchovska

Melanie Buy

Ana M Cabanillas-Saldaña

Bárbara Carvalho

Nicolas Cheval

José M Climent

Marianne Correard

Eva Cremer

Darius Danusevičius:

ORCID: https://orcid.org/0000-0002-1196-9293

Fernando Del Caño

Jean-Luc Denou

Nicolas di Gerardi

Bernard Dokhelar

Alexis Ducousso

Anne Eskild Nilsen

Anna-Maria Farsakoglou:

ORCID: https://orcid.org/0000-0002-1906-2813

Patrick Fonti:

ORCID: https://orcid.org/0000-0002-7070-3292

Ioannis Ganopoulos:

ORCID: https://orcid.org/0000-0001-7967-5702

José M García del Barrio:

ORCID: https://orcid.org/0000-0001-7267-6286

Olivier Gilg:

ORCID: https://orcid.org/0000-0002-9083-4492

Santiago C González-Martínez:

ORCID: https://orcid.org/0000-0002-4534-3766

René Graf

Alan Gray

Delphine Grivet:

ORCID: https://orcid.org/0000-0001-8168-4456

Felix Gugerli:

ORCID: https://orcid.org/0000-0003-3878-1845

Christoph Hartleitner

Enja Hollenbach

Agathe Hurel

Bernard Issehut

Florence Jean

Veronique Jorge:

ORCID: https://orcid.org/0000-0002-5016-3006

Arnaud Jouineau

Jan-Philipp Kappner

Katri Kärkkäinen

Robert Kesälahti

Florian Knutzen

Sonja T Kujala:

ORCID: https://orcid.org/0000-0003-0949-6156

Timo A Kumpula:

ORCID: https://orcid.org/0000-0002-6124-8929

Mariaceleste Labriola

Celine Lalanne:

ORCID: https://orcid.org/0000-0003-1877-1703

Johannes Lambertz

Martin Lascoux:

ORCID: https://orcid.org/0000-0003-1699-9042

Vincent Lejeune

Gregoire Le-Provost

Joseph Levillain

Mirko Liesebach

David López-Quiroga

Benjamin Meier

Ermioni Malliarou

Jérémy Marchon

Nicolas Mariotte

Antonio Mas

Silvia Matesanz:

ORCID: https://orcid.org/0000-0003-0060-6136

Helge Meischner

Célia Michotey

Pascal Milesi:

ORCID: https://orcid.org/0000-0001-8580-4291

Sandro Morganti

Daniel Nievergelt

Eduardo Notivol:

ORCID: https://orcid.org/0000-0003-4272-4536

Geir Ostreng

Birte Pakull:

ORCID: https://orcid.org/0000-0003-0921-6732

Annika Perry:

ORCID: https://orcid.org/0000-0002-7889-7597

Andrea Piotti:

ORCID: https://orcid.org/0000-0002-3324-5325

Christophe Plomion:

ORCID: https://orcid.org/0000-0002-3176-2767

Nicolas Poinot

Mehdi Pringarbe

Luc Puzos

Tanja Pyhäjärvi:

ORCID: https://orcid.org/0000-0001-6958-5172

Annie Raffin:

ORCID: https://orcid.org/0000-0003-2459-4264

José A Ramírez-Valiente:

ORCID: https://orcid.org/0000-0002-5951-2938

Christian Rellstab:

ORCID: https://orcid.org/0000-0002-0221-5975

Dourthe Remi

Sebastian Richter

Juan J Robledo-Arnuncio:

ORCID: https://orcid.org/0000-0002-3909-8928

Sergio San Segundo

Outi Savolainen:

ORCID: https://orcid.org/0000-0001-9851-7945

Silvio Schueler:

ORCID: https://orcid.org/0000-0003-0155-5692

Volker Schneck

Ivan Scotti:

ORCID: https://orcid.org/0000-0002-8951-2680

Vladimir Semerikov

Lenka Slámová

Jørn Henrik Sønstebø:

ORCID: https://orcid.org/0000-0002-3204-1283

Ilaria Spanu

Jean Thevenet

Mari Mette Tollefsrud:

ORCID: https://orcid.org/0000-0002-5939-7845

Norbert Turion:

ORCID: https://orcid.org/0000-0003-4095-1399

Giovanni Giuseppe Vendramin:

ORCID: https://orcid.org/0000-0001-9921-7872

Marc Villar:

ORCID: https://orcid.org/0000-0001-9210-7072

Georg von Arx:

ORCID: https://orcid.org/0000-0002-8566-4599

Johan Westin

Bruno Fady:

ORCID: https://orcid.org/0000-0003-2379-7617

Tor Myking

Fernando Valladares:

ORCID: https://orcid.org/0000-0002-5374-4682

Filippos A Aravanopoulos:

ORCID: https://orcid.org/0000-0001-7194-2642

Stephen Cavers:

ORCID: https://orcid.org/0000-0003-2139-9236

Journal

Journal ID (nlm-ta): Gigascience

Journal ID (iso-abbrev): Gigascience

Journal ID (publisher-id): gigascience

Title: GigaScience

Publisher: Oxford University Press

ISSN (Electronic): 2047-217X

Publication date (Electronic): 18 March 2021

Publication date Collection: March 2021

Publication date PMC-release: 18 March 2021

Volume: 10

Issue: 3

Electronic Location Identifier: giab010

Affiliations

Philipps University Marburg , Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

LINCGlobal, Department of Biogeography and Global Change , Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain

Philipps University Marburg , Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany

Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement , 54124, Thessaloniki, Greece

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR) , Ctra. de la Coruña km 7.5, 28040, Madrid, Spain

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR) , Ctra. de la Coruña km 7.5, 28040, Madrid, Spain

Institute of Biosciences and BioResources , National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy

Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement , 54124, Thessaloniki, Greece

Institute of Biosciences and BioResources , National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy

Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement , 54124, Thessaloniki, Greece

departmentCentre d'Ecologie Fonctionnelle et Evolutive (CEFE) , CNRS, UMR 5175, 34090, Montpellier, France

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), Dept ECOFA, 45075, Orléans, France

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR) , Ctra. de la Coruña km 7.5, 28040, Madrid, Spain

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), GBFOR, 45075, Orléans, France

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France

Vytautas Magnus University , Studentu Street 11, 53361, Akademija, Lithuania

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France

Departamento de Agricultura, Ganadería y Medio Ambiente , Gobierno de Aragón, P. Mª Agustín 36, 50071, Zaragoza, Spain

LINCGlobal, Department of Biogeography and Global Change , Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR) , Ctra. de la Coruña km 7.5, 28040, Madrid, Spain

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France

Bavarian Institute for Forest Genetics , Forstamtsplatz 1, 83317, Teisendorf, Germany

Vytautas Magnus University , Studentu Street 11, 53361, Akademija, Lithuania

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR) , Ctra. de la Coruña km 7.5, 28040, Madrid, Spain

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France

INRAE, Univsité de Bordeaux , BIOGECO, 33770, Cestas, France

Division of Forestry and Forest Resources , departmentNorwegian Institute of Bioeconomy Research (NIBIO) , P.O. Box 115, 1431, Ås, Norway

Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement , 54124, Thessaloniki, Greece

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

Institute of Plant Breeding and Genetic Resources , Hellenic Agricultural Organization DEMETER (ex NAGREF), 57001, Thermi, Greece

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR) , Ctra. de la Coruña km 7.5, 28040, Madrid, Spain

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

UK Centre for Ecology and Hydrology, Bush Estate Penicuik , EH26 0QB, Edinburgh, UK

Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria - Centro de Investigación Forestal (INIA-CIFOR) , Ctra. de la Coruña km 7.5, 28040, Madrid, Spain

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

LIECO GmbH & Co KG

Philipps University Marburg , Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), UEFP, 33610, Cestas, France

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), ONF, BIOFORA, 45075, Orléans, France

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France

Philipps University Marburg , Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany

Natural Resources Institute Finland, Paavo Havaksentie 3, 90014, University of Oulu , Finland

University of Oulu, Pentti Kaiteran katu 1, 90014, University of Oulu , Finland

Bavarian Institute for Forest Genetics , Forstamtsplatz 1, 83317, Teisendorf, Germany

Natural Resources Institute Finland, Paavo Havaksentie 3, 90014, University of Oulu , Finland

University of Oulu, Pentti Kaiteran katu 1, 90014, University of Oulu , Finland

Institute of Biosciences and BioResources , National Research Council (CNR), via Madonna del Piano 10, 50019, Sesto, Fiorentino, Italy

INRAE, Univsité de Bordeaux , BIOGECO, 33770, Cestas, France

Philipps University Marburg , Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany

Department of Ecology & Genetics, EBC, Uppsala University , Norbyvägen 18D, 75236, Uppsala, Sweden

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), GBFOR, 45075, Orléans, France

INRAE, Univsité de Bordeaux , BIOGECO, 33770, Cestas, France

Université de Lorraine, AgroParisTech , INRAE, SILVA, 54000, Nancy, France

Thünen Institute of Forest Genetics , Sieker Landstr. 2, 22927, Grosshansdorf, Germany

LINCGlobal, Department of Biogeography and Global Change , Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

Aristotle University of Thessaloniki, School of Forestry and Natural Environment, Laboratory of Forest Genetics and Tree Improvement , 54124, Thessaloniki, Greece

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), Domaine Saint Paul, Site Agroparc, 84914, Avignon, France

LINCGlobal, Department of Biogeography and Global Change , Museo Nacional de Ciencias Naturales, CSIC, Serrano 115 dpdo, 28006, Madrid, Spain

Área de Biodiversidad y Conservación , Universidad Rey Juan Carlos, Calle Tulipán s/n, 28933, Móstoles, Spain

Philipps University Marburg , Faculty of Biology, Plant Ecology and Geobotany, Karl-von-Frisch Strasse 8, 35043, Marburg, Germany

Institut National de Recherche en Agriculture , Alimentation et Environment (INRAE), URGI, Versailles, France

Department of Ecology & Genetics, EBC, Science for Life Laboratory, Uppsala University , 75236, Uppsala, Sweden

Swiss Federal Research Institute WSL , Zürcherstrasse 111, 8903, Birmensdorf, Switzerland

Centro de Investigación y Tecnología Agroalimentaria de Aragón - Unidad de Recursos Forestales (CITA), Avda. Montañana 930, 50059, Zaragoza, Spain