Article
Ecology
Rafael Molina-Venegas, Miguel A. Rodriguez, Manuel Pardo-de-Santayana, Cristina Ronquillo, David J. Mabberley
Summary: The divergent nature of evolution may require relying on different lineages of the Tree of Life to secure human benefits directly provided by biodiversity, with quantitative evidence still lacking. However, a global review of plant-use records shows that maximum levels of phylogenetic diversity capture significantly more plant-use records than random selection of taxa. This study establishes an empirical foundation linking evolutionary history to human wellbeing, serving as a basis for promoting well-grounded discussions on services directly provided by biodiversity.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Multidisciplinary Sciences
R. W. McDowell, A. Noble, P. Pletnyakov, P. M. Haygarth
Summary: Soil phosphorus is crucial for food production to support the growing global population. However, the knowledge of plant available phosphorus stocks at a global scale is limited, hindering the efficient use of phosphorus fertilizers. This study compiled and analyzed a database of thousands of soil samples to generate a model that predicts the distribution and global stock of plant available phosphorus. These findings can inform strategies to optimize phosphorus use and mitigate environmental degradation.
Article
Multidisciplinary Sciences
Francesco Maria Sabatini, Borja Jimenez-Alfaro, Ute Jandt, Milan Chytry, Richard Field, Michael Kessler, Jonathan Lenoir, Franziska Schrodt, Susan K. Wiser, Mohammed A. S. Arfin Khan, Fabio Attorre, Luis Cayuela, Michele De Sanctis, Jurgen Dengler, Sylvia Haider, Mohamed Z. Hatim, Adrian Indreica, Florian Jansen, Anibal Pauchard, Robert K. Peet, Petr Petrik, Valerio D. Pillar, Brody Sandel, Marco Schmidt, Zhiyao Tang, Peter van Bodegom, Kiril Vassilev, Cyrille Violle, Esteban Alvarez-Davila, Priya Davidar, Jiri Dolezal, Bruno Herault, Antonio Galan-de-Mera, Jorge Jimenez, Stephan Kambach, Sebastian Kepfer-Rojas, Holger Kreft, Felipe Lezama, Reynaldo Linares-Palomino, Abel Monteagudo Mendoza, Justin K. N'Dja, Oliver L. Phillips, Gonzalo Rivas-Torres, Petr Sklenar, Karina Speziale, Ben J. Strohbach, Rodolfo Vasquez Martinez, Hua-Feng Wang, Karsten Wesche, Helge Bruelheide
Summary: “Global patterns of regional plant diversity are relatively well known, but whether they hold for local communities is debated. This study created multi-grain global maps of alpha diversity for vascular plants to provide a nuanced understanding of plant diversity hotspots and improve predictions of global change effects on biodiversity.”
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Guignon Valentin, Toure Abdel, Droc Gaetan, Dufayard Jean-Francois, Conte Matthieu, Rouard Mathieu
Summary: Comparative genomics is the analysis of genomic relationships among different species, with GreenPhylDB providing a database for exploring gene families and homologous relationships among plant genomes. By harnessing multiple genome sequences by species, GreenPhylDBv5 introduces the concept of comparative pangenomics to predict homologous relationships and support community curation efforts.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Junhao Zhuge, Xiang Zhou, Lifeng Zhou, Jiafu Hu, Kai Guo
Summary: This study developed the Plant Parasitic Nematodes Database (PPND), a platform that provides genomic, transcriptomic, protein, and functional annotation data for plant parasitic nematode research.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Multidisciplinary Sciences
Michael Getachew Tadesse, Thomas Wahl
Summary: Storm surges are one of the deadliest coastal hazards, and understanding their impact is crucial. By using data-driven modeling and climate reconstruction, valuable information for future preparation and robust extreme value analysis can be provided.
Article
Biochemistry & Molecular Biology
Jingjing Jin, Peng Lu, Yalong Xu, Jiemeng Tao, Zefeng Li, Shuaibin Wang, Shizhou Yu, Chen Wang, Xiaodong Xie, Junping Gao, Qiansi Chen, Lin Wang, Wenxuan Pu, Peijian Cao
Summary: The emergence of single-cell sequencing has revolutionized transcriptomic and genomic research. The lack of a comprehensive database of cell markers for plant research community has been addressed by the development of PCMDB, providing a valuable resource for researchers to annotate cell types and predict the biological function of individual cells.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Computer Science, Information Systems
Theerawat Whairit, Boonyarat Phadermrod, Varunya Attasena
Summary: This paper proposes JINDEX, a JSON and index-based search system for plant germplasm database. By using a hybrid key-value/document data model, the system offers flexible structure and efficient retrieval, resulting in improved query response time. The practical deployment of the system since 2020 demonstrates its feasibility.
JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES
(2023)
Article
Multidisciplinary Sciences
Etienne Fluet-Chouinard, Benjamin D. Stocker, Zhen Zhang, Avni Malhotra, Joe R. Melton, Benjamin Poulter, Jed O. Kaplan, Kees Klein Goldewijk, Stefan Siebert, Tatiana Minayeva, Gustaf Hugelius, Hans Joosten, Alexandra Barthelmes, Catherine Prigent, Filipe Aires, Alison M. Hoyt, Nick Davidson, C. Max Finlayson, Bernhard Lehner, Robert B. Jackson, Peter B. McIntyre
Summary: Wetlands have been drained for human use, causing significant impact on multiple aspects including greenhouse gas fluxes, flood control, nutrient cycling, and biodiversity. However, the extent of natural wetland loss globally has remained uncertain. In this study, the researchers reconstructed the spatial distribution and timing of wetland loss from 1700 to 2020, and estimated that approximately 3.4 million km2 of inland wetlands, primarily for croplands, have been lost since 1700, accounting for a net loss of 21% of global wetland area. The study highlights the concentration of wetland loss in Europe, the United States, and China, and provides a valuable historical baseline for assessing the impact of wetland loss and guiding conservation planning and restoration efforts.
Article
Ecology
Na Huang, Xinyuan Sun, Yanfang Song, Zhiyong Yuan, Weiwei Zhou
Summary: This article discusses two issues: the decline of amphibian populations and the lack of morphological trait data for amphibians. To address these problems, the authors collected morphological trait data for global amphibians and created a database.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2023)
Article
Multidisciplinary Sciences
Giselle Muschett, Francisco E. Fonturbel
Summary: This study compiled information on pollinators, flower visitors, and plant-pollinator interactions in Chile to contribute to the agricultural industry and unique biodiversity of the country. The database created provides the first systematic information on pollination in Chile, which can be used for future studies and conservation strategies for pollinators.
Article
Biochemistry & Molecular Biology
Yongrong Cao, Dongmei Tian, Zhixin Tang, Xiaonan Liu, Weijuan Hu, Zhang Zhang, Shuhui Song
Summary: This article presents the Open Plant Image Archive (OPIA), an open archive of plant images and image-based phenotypic traits derived from high-throughput phenotyping platforms. OPIA houses a large number of plant images and i-traits, providing useful tools and resources that are crucial for facilitating artificial intelligence-assisted breeding research.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Daniel Falster, Rachael Gallagher, Elizabeth H. Wenk, Ian J. Wright, Dony Indiarto, Samuel C. Andrew, Caitlan Baxter, James Lawson, Stuart Allen, Anne Fuchs, Anna Monro, Fonti Kar, Mark A. Adams, Collin W. Ahrens, Matthew Alfonzetti, Tara Angevin, Deborah M. G. Apgaua, Stefan Arndt, Owen K. Atkin, Joe Atkinson, Tony Auld, Andrew Baker, Maria von Balthazar, Anthony Bean, Chris J. Blackman, Keith Bloomfeld, David M. J. S. Bowman, Jason Bragg, Timothy J. Brodribb, Genevieve Buckton, Geof Burrows, Elizabeth Caldwell, James Camac, Raymond Carpenter, JaneA Catford, Gregory R. Cawthray, Lucas A. Cernusak, Gregory Chandler, Alex R. Chapman, David Cheal, Alexander W. Cheesman, Si-Chong Chen, Brendan Choat, Brook Clinton, Peta L. Clode, Helen Coleman, William K. Cornwell, Meredith Cosgrove, Michael Crisp, Erika Cross, Kristine Y. Crous, Saul Cunningham, Timothy Curran, Ellen Curtis, Matthew Daws, Jane L. DeGabriel, Matthew D. Denton, Ning Dong, Pengzhen Du, Honglang Duan, David H. Duncan, Richard P. Duncan, Marco Duretto, John M. Dwyer, Cheryl Edwards, Manuel Esperon-Rodriguez, John R. Evans, Susan E. Everingham, Claire Farrell, Jennifer Firn, Carlos Roberto Fonseca, Ben J. French, Doug Frood, Jennifer L. Funk, Sonya R. Geange, Oula Ghannoum, Sean M. Gleason, Carl R. Gosper, Emma Gray, Philip K. Groom, Saskia Grootemaat, Caroline Gross, Greg Guerin, Lydia Guja, Amy K. Hahs, Matthew Tom Harrison, Patrick E. Hayes, Martin Henery, Dieter Hochuli, Jocelyn Howell, Guomin Huang, Lesley Hughes, John Huisman, Jugoslav Ilic, Ashika Jagdish, Daniel Jin, Gregory Jordan, Enrique Jurado, John Kanowski, Sabine Kasel, Jurgen Kellermann, Belinda Kenny, Michele Kohout, Robert M. Kooyman, Martyna M. Kotowska, Hao Ran Lai, Etienne Laliberte, Hans Lambers, Byron B. Lamont, Robert Lanfear, Frank van Langevelde, Daniel C. Laughlin, Bree-Anne Laugier-kitchener, Susan Laurance, Caroline E. R. Lehmann, Andrea Leigh, Michelle R. Leishman, Tanja Lenz, Brendan Lepschi, James D. Lewis, Felix Lim, Udayangani Liu, Janice Lord, Christopher H. Lusk, Cate Macinnis-Ng, Hannah McPherson, Susana Magallon, Anthony Manea, Andrea Lopez-Martinez, Margaret Mayfeld, James K. McCarthy, Trevor Meers, Marlien van der Merwe, Daniel J. Metcalfe, Per Milberg, Karel Mokany, Angela T. Moles, Ben D. Moore, Nicholas Moore, John W. Morgan, William Morris, Annette Muir, Samantha Munroe, Aine Nicholson, Dean Nicolle, Adrienne B. Nicotra, Ulo Niinemets, Tom North, Andrew O'Reilly-Nugent, Odhran S. O'Sullivan, Brad Oberle, Yusuke Onoda, Mark K. J. Ooi, Colin P. Osborne, Grazyna Paczkowska, Burak Pekin, Caio Guilherme Pereira, Catherine Pickering, Melinda Pickup, Laura J. Pollock, Pieter Poot, Jef R. Powell, SallyA Power, Iain Colin Prentice, Lynda Prior, Suzanne M. Prober, Jennifer Read, Victoria Reynolds, Anna E. Richards, Ben Richardson, Michael L. Roderick, Julieta A. Rosell, Maurizio Rossetto, Barbara Rye, Paul D. Rymer, MichaelA Sams, Gordon Sanson, Herve Sauquet, Susanne Schmidt, Juerg Schoenenberger, Ernst-Detlef Schulze, Kerrie Sendall, Steve Sinclair, Benjamin Smith, Renee Smith, Fiona Soper, Ben Sparrow, Rachel J. Standish, Timothy L. Staples, Ruby Stephens, Christopher Szota, Guy Taseski, Elizabeth Tasker, Freya Thomas, David T. Tissue, Mark G. Tjoelker, David Yue Phin Tng, Felix de Tombeur, Kyle Tomlinson, Neil C. Turner, Erik J. Veneklaas, Susanna Venn, Peter Vesk, Carolyn Vlasveld, Maria S. Vorontsova, Charles A. Warren, Nigel Warwick, Lasantha K. Weerasinghe, Jessie Wells, Mark Westoby, Matthew White, Nicholas S. G. Williams, Jarrah Wills, Peter G. Wilson, Colin Yates, Amy E. Zanne, Graham Zemunik, Kasia Zieminska
Summary: AusTraits is a database compiling values of plant traits for taxa in the Australian flora, encompassing data from various sources and traits ranging from physiological to morphological aspects. It provides curated data and contextual information, serving as a template for similar initiatives globally.
Article
Biochemistry & Molecular Biology
Zhaohui He, Yuting Luo, Xinkai Zhou, Tao Zhu, Yangming Lan, Dijun Chen
Summary: This study presents a systematic approach to construct a plant single-cell database (scPlantDB) by integrating high-quality single-cell transcriptomic profiles from different plant species. The database allows interactive visualization and comparison of cell types.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Multidisciplinary Sciences
Robert van Woesik, Chelsey Kratochwill
Summary: Coral reefs, the most diverse marine ecosystems, are facing increased thermal stress events leading to coral bleaching. The severity of bleaching varies depending on species, location, historical conditions, and local/regional influences. The Global Coral-Bleaching Database compiles over 34,000 records from 93 countries, providing crucial information on bleaching presence, site exposure, and environmental factors.
Article
Biodiversity Conservation
Luciano Pataro, Rafael Molina-Venegas, Joaquin Calatayud, Juan Carlos Moreno-Saiz, Miguel A. Rodriguez
Summary: Classical bioregionalizations may have underestimated the importance of historical factors in shaping biogeographic regions, particularly for lineages with long evolutionary histories like ferns. A new method based on phylogenetic relatedness was used to define six distinct fern phyloregions in Europe, revealing a primary divide between northeastern and southwestern Europe. The study highlights the preference of ancient fern lineages for northern latitudes and sheds light on the evolutionary history of the group, providing a fresh regional delineation.
BIODIVERSITY AND CONSERVATION
(2021)
Article
Green & Sustainable Science & Technology
Rufino Acosta-Naranjo, Ramon Rodriguez-Franco, Antonio Jesus Guzman-Troncoso, Manuel Pardo-de-Santayana, Laura Aceituno-Mata, Jose Gomez-Melara, Pablo Dominguez, Isabel Diaz-Reviriego, Jessica Gonzalez-Nateras, Victoria Reyes-Garcia
Summary: This study examines the differences in men's and women's relations with wild edible plants in various regions of Spain, showcasing a geographical pattern influenced by the construction and distribution of agrarian spaces. The study suggests that gendered differences in natural resource use can be better understood when contextualized within a larger socioecological framework.
Article
Multidisciplinary Sciences
Alje van Dam, Mark Dekker, Ignacio Morales-Castilla, Miguel A. Rodriguez, David Wichmann, Mara Baudena
Summary: This article reexamines correspondence analysis (CA) as a classical method for revealing structures in high-dimensional data from a network perspective. The poorly-known equivalence of CA to spectral clustering and graph embedding techniques is presented. The multiple interpretations of CA results, beyond its traditional interpretation as an ordination technique, are discussed, with emphasis on their relation to the underlying structure of networks.
SCIENTIFIC REPORTS
(2021)
Article
Plant Sciences
Luis Gorriz, Manuel Pardo-de-Santayana
Summary: This study aims to explore the incorporation of Traditional Ecological Knowledge in nature conservation in the context of global biodiversity loss. By investigating traditional ecological knowledge in a Spanish natural reserve, the research found that local ecological knowledge is accurate and applicable for the management of Sierra de Andia's grazing pastures.
BOLETIN DE LA SOCIEDAD ARGENTINA DE BOTANICA
(2021)
Article
Ecology
Rafael Molina-Venegas, Miguel A. Rodriguez, Manuel Pardo-de-Santayana, Cristina Ronquillo, David J. Mabberley
Summary: The divergent nature of evolution may require relying on different lineages of the Tree of Life to secure human benefits directly provided by biodiversity, with quantitative evidence still lacking. However, a global review of plant-use records shows that maximum levels of phylogenetic diversity capture significantly more plant-use records than random selection of taxa. This study establishes an empirical foundation linking evolutionary history to human wellbeing, serving as a basis for promoting well-grounded discussions on services directly provided by biodiversity.
NATURE ECOLOGY & EVOLUTION
(2021)
Article
Ecology
Ignacio Ramos-Gutierrez, Herlander Lima, Santiago Pajaron, Carlos Romero-Zarco, Llorenc Saez, Luciano Pataro, Rafael Molina-Venegas, Miguel A. Rodriguez, Juan Carlos Moreno-Saiz
Summary: The study compiled a comprehensive species list of the Iberian-Balearic terrestrial vascular flora and generated AFLIBER, an accurate floristic database of georeferenced plant occurrence records, totaling over 1.8 million plant occurrence records. The spatial scope covered the western Mediterranean with a resolution of 10 km UTM quadrangular grid cells, including inland territories of Spain, Portugal, Andorra, as well as adjacent archipelagos. The time period for the database consisted of distributional trustable records dating mostly from the 1960s onwards, focusing on terrestrial vascular plant species and subspecies.
GLOBAL ECOLOGY AND BIOGEOGRAPHY
(2021)
Article
Ecology
Sonia Llorente-Culebras, Rafael Molina-Venegas, A. Marcia Barbosa, Silvia B. Carvalho, Miguel A. Rodriguez, Ana M. C. Santos
Summary: Protected areas are created to preserve biodiversity and act as refuges from human activities. This study focused on evaluating the representation of functional, phylogenetic, and taxonomic diversity of tetrapod assemblages in national and natural parks of the Iberian Peninsula. The results suggest that these parks effectively capture the diversity components of most tetrapod assemblages present at the regional level.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Plant Sciences
Victoria Reyes-Garcia, Petra Benyei, Laura Aceituno-Mata, Airy Gras, Maria Molina, Javier Tardio, Manuel Pardo-de-Santayana
Summary: In Spain, two innovative initiatives have been implemented to document and protect traditional knowledge related to biodiversity, with over 131,066 uses and 152,246 local names documented so far. These initiatives contribute to the maintenance and sharing of traditional knowledge through open data and copyleft licenses, but more efforts are needed to ensure data sovereignty for knowledge holders.
JOURNAL OF ETHNOPHARMACOLOGY
(2021)
Article
Plant Sciences
Guillermo Benitez, Manuel Pardo de Santayana, Diego Rivera, Alonso Verde, Airy Gras, Rosario G. Gavilan
Summary: In this new era of Mediterranean Botany, the editorial team has opened up the opportunity for manuscripts to be submitted for evaluation to the ethnobotany/ethnopharmacology section of the journal. We have compiled a set of minimum standards that manuscripts based on field research should meet in order to pass the review process and meet the minimum quality requirement. We specifically focus on the method and results sections, which often encounter issues with format, style, or content. While not exhaustive, we believe these recommendations will assist authors in presenting their texts and reviewers in evaluating them.
MEDITERRANEAN BOTANY
(2022)
Article
Food Science & Technology
Cristina Tamayo-Vives, Patricia Garcia-Herrera, Maria Cortes Sanchez-Mata, Rosa M. M. Camara-Hurtado, Maria Luisa Perez-Rodriguez, Laura Aceituno, Manuel Pardo-de-Santayana, Maria Ines Dias, Lillian Barros, Patricia Morales
Summary: Hawthorn and whitebeam are wild species traditionally used as ethnic foods in the Mediterranean area. This study analyzed the composition and properties of the epidermis of the fruits of these species, specifically focusing on phenolic compounds and antioxidant capacity. The results provide new insights into the composition of these wild fruits and confirm their potential as ingredients for the food industry.
Letter
Plant Sciences
Rafael Molina-Venegas, Ignacio Morales-Castilla, Miguel A. Rodriguez
Article
Food Science & Technology
Laura Aceituno-Mata, Javier Tardio, Manuel Pardo-de-Santayana
Summary: Despite the global cultural erosion of traditional knowledge on wild food plants, a study in Sierra Norte de Madrid, Spain revealed that out of 252 useful wild flora species, 74 were culturally important for human food use. Vegetables were found to be the most culturally important category, while beverages and condiments had the lowest erosion rate, indicating factors influencing the abandonment of traditional agricultural practices and shepherding.
FRONTIERS IN SUSTAINABLE FOOD SYSTEMS
(2021)
Article
Social Issues
Petra Benyei, Manuel Pardo-de-Santayana, Laura Aceituno-Mata, Laura Calvet-Mir, Maria Carrascosa-Garcia, Marta Rivera-Ferre, Antonio Perdomo-Molina, Victoria Reyes-Garcia
Summary: This study aims to understand the participation dynamics, barriers, and drivers in citizen science. Findings suggest that overcoming participation barriers related to education, age, and residence is challenging, while participants' alliance with project objectives and trust relationships with the project team are important drivers of participation.
SCIENCE TECHNOLOGY & HUMAN VALUES
(2021)