scholarly journals Cyberinfrastructure for an integrated botanical information network to investigate the ecological impacts of global climate change on plant biodiversity

Author(s):  
Brian J Enquist ◽  
Rick Condit ◽  
Robert K Peet ◽  
Mark Schildhauer ◽  
Barbara M. Thiers

To answer many of the major questions in comparative botany, ecology, and global change biology it is necessary to extrapolate across enormous geographic, temporal and taxonomic scales. Yet much ecological knowledge is still based on observations conducted within a local area or even a few hundred square meters. Understanding ecological patterns and how plants respond to global warming and human alteration of landscapes and ecosystems necessitates a holistic approach. Such an approach must be conducted at a scale that is commensurate with the breadth of the questions being asked. Further, it requires identification, retrieval, and integration of diverse data from a global confederation of collaborating scientists across a broad range of disciplines. We propose to network core databases and data networks to create a novel resource for quantitative plant biodiversity science. The grand challenge is to assemble and share the world’s rapidly accumulating botanical information from plots and collections to create a distributed, web-accessible, readily analyzable data resource. With such a resource, we will answer major questions of direct relevance to plant ecology, plant evolution, plant geography, conservation, global change biology, and protection of biodiversity and ecosystem services. In particular, how does climate influence the distribution and abundance of plant species, how does the phylogenetic diversity of plants vary across broad environmental and climatic gradients, and how are plants assembled into ecological communities? While these and associated questions are at the core of many research endeavors in comparative botany and ecology, our past collective inability to integrate data on a large scale has significantly limited our ability to address these questions head on. This proposed Grand Challenge team will create a data resource of unprecedented size and scope together with the tools for its use, thereby empowering botanists and the general public to better address fundamental issues in plant ecology and global change biology. Although we will focus on plants of the New World, the infrastructure and protocols developed will be scalable to all geographic regions and all types of organisms. Future steps will enable cross-cutting linkages to emerging networks on plant genomics, physiology, and phylogeny, allowing us to address fundamental genetic and evolutionary questions at unprecedented spatial and temporal scales.

Author(s):  
Brian J Enquist ◽  
Rick Condit ◽  
Robert K Peet ◽  
Mark Schildhauer ◽  
Barbara M. Thiers

To answer many of the major questions in comparative botany, ecology, and global change biology it is necessary to extrapolate across enormous geographic, temporal and taxonomic scales. Yet much ecological knowledge is still based on observations conducted within a local area or even a few hundred square meters. Understanding ecological patterns and how plants respond to global warming and human alteration of landscapes and ecosystems necessitates a holistic approach. Such an approach must be conducted at a scale that is commensurate with the breadth of the questions being asked. Further, it requires identification, retrieval, and integration of diverse data from a global confederation of collaborating scientists across a broad range of disciplines. We propose to network core databases and data networks to create a novel resource for quantitative plant biodiversity science. The grand challenge is to assemble and share the world’s rapidly accumulating botanical information from plots and collections to create a distributed, web-accessible, readily analyzable data resource. With such a resource, we will answer major questions of direct relevance to plant ecology, plant evolution, plant geography, conservation, global change biology, and protection of biodiversity and ecosystem services. In particular, how does climate influence the distribution and abundance of plant species, how does the phylogenetic diversity of plants vary across broad environmental and climatic gradients, and how are plants assembled into ecological communities? While these and associated questions are at the core of many research endeavors in comparative botany and ecology, our past collective inability to integrate data on a large scale has significantly limited our ability to address these questions head on. This proposed Grand Challenge team will create a data resource of unprecedented size and scope together with the tools for its use, thereby empowering botanists and the general public to better address fundamental issues in plant ecology and global change biology. Although we will focus on plants of the New World, the infrastructure and protocols developed will be scalable to all geographic regions and all types of organisms. Future steps will enable cross-cutting linkages to emerging networks on plant genomics, physiology, and phylogeny, allowing us to address fundamental genetic and evolutionary questions at unprecedented spatial and temporal scales.


Author(s):  
Brian J Enquist ◽  
Rick Condit ◽  
Robert K Peet ◽  
Mark Schildhauer ◽  
Barbara M. Thiers

To answer many of the major questions in comparative botany, ecology, and global change biology it is necessary to extrapolate across enormous geographic, temporal and taxonomic scales. Yet much ecological knowledge is still based on observations conducted within a local area or even a few hundred square meters. Understanding ecological patterns and how plants respond to global warming and human alteration of landscapes and ecosystems necessitates a holistic approach. Such an approach must be conducted at a scale that is commensurate with the breadth of the questions being asked. Further, it requires identification, retrieval, and integration of diverse data from a global confederation of collaborating scientists across a broad range of disciplines. We propose to network core databases and data networks to create a novel resource for quantitative plant biodiversity science. The grand challenge is to assemble and share the world’s rapidly accumulating botanical information from plots and collections to create a distributed, web-accessible, readily analyzable data resource. With such a resource, we will answer major questions of direct relevance to plant ecology, plant evolution, plant geography, conservation, global change biology, and protection of biodiversity and ecosystem services. In particular, how does climate influence the distribution and abundance of plant species, how does the phylogenetic diversity of plants vary across broad environmental and climatic gradients, and how are plants assembled into ecological communities? While these and associated questions are at the core of many research endeavors in comparative botany and ecology, our past collective inability to integrate data on a large scale has significantly limited our ability to address these questions head on. This proposed Grand Challenge team will create a data resource of unprecedented size and scope together with the tools for its use, thereby empowering botanists and the general public to better address fundamental issues in plant ecology and global change biology. Although we will focus on plants of the New World, the infrastructure and protocols developed will be scalable to all geographic regions and all types of organisms. Future steps will enable cross-cutting linkages to emerging networks on plant genomics, physiology, and phylogeny, allowing us to address fundamental genetic and evolutionary questions at unprecedented spatial and temporal scales.


2018 ◽  
Vol 374 (1763) ◽  
pp. 20170392 ◽  
Author(s):  
Carrie Andrew ◽  
Jeffrey Diez ◽  
Timothy Y. James ◽  
Håvard Kauserud

For several hundred years, millions of fungal sporocarps have been collected and deposited in worldwide collections (fungaria) to support fungal taxonomy. Owing to large-scale digitization programs, metadata associated with the records are now becoming publicly available, including information on taxonomy, sampling location, collection date and habitat/substrate information. This metadata, as well as data extracted from the physical fungarium specimens themselves, such as DNA sequences and biochemical characteristics, provide a rich source of information not only for taxonomy but also for other lines of biological inquiry. Here, we highlight and discuss how this information can be used to investigate emerging topics in fungal global change biology and beyond. Fungarium data are a prime source of knowledge on fungal distributions and richness patterns, and for assessing red-listed and invasive species. Information on collection dates has been used to investigate shifts in fungal distributions as well as phenology of sporocarp emergence in response to climate change. In addition to providing material for taxonomy and systematics, DNA sequences derived from the physical specimens provide information about fungal demography, dispersal patterns, and are emerging as a source of genomic data. As DNA analysis technologies develop further, the importance of fungarium specimens as easily accessible sources of information will likely continue to grow. This article is part of the theme issue ‘Biological collections for understanding biodiversity in the Anthropocene’.


2019 ◽  
Author(s):  
Sukanya Sasmal ◽  
Léa El Khoury ◽  
David Mobley

The Drug Design Data Resource (D3R) Grand Challenges present an opportunity to assess, in the context of a blind predictive challenge, the accuracy and the limits of tools and methodologies designed to help guide pharmaceutical drug discovery projects. Here, we report the results of our participation in the D3R Grand Challenge 4, which focused on predicting the binding poses and affinity ranking for compounds targeting the beta-amyloid precursor protein (BACE-1). Our ligand similarity-based protocol using HYBRID (OpenEye Scientific Software) successfully identified poses close to the native binding mode for most of the ligands with less than 2 A RMSD accuracy. Furthermore, we compared the performance of our HYBRID-based approach to that of AutoDock Vina and Dock 6 and found that HYBRID performed better here for pose prediction. We also conducted end-point free energy estimates on protein-ligand complexes using molecular mechanics combined with generalized Born surface area method (MM-GBSA). We found that the binding affinity ranking based on MM-GBSA scores have poor correlation with the experimental values. Finally, the main lessons from our participation in D3R Grand Challenge 4 suggest that: i) the generation of the macrocycles conformers is a key step for successful pose prediction, ii) the protonation states of the BACE-1 binding site should be treated carefully, iii) the MM-GBSA method could not discriminate well between different predicted binding poses, and iv) the MM-GBSA method does not perform well at predicting protein-ligand binding affinities here.


Author(s):  
Renata Sõukand ◽  
Julia Prakofjewa ◽  
Andrea Pieroni

AbstractDue to global change and the migration crisis both needing rapid attention, there has been growing debate about the drivers of change in the diet of migrants. Our study aimed to evaluate the consequences of forced resettlement on local ecological knowledge related to wild food plants among forcefully resettled Yaghnobi people in Tajikistan. We conducted 49 semi-structured in-depth interviews and recorded 27 wild food taxa and five unidentified folk taxa used by Yaghnobis and Tajiks in the villages surrounding Yaghnob Valley (including families ressetteled from Yaghnob Valley) in central Tajikitsan. The comparision between the two considered groups showed a high level of Tajikisation among Yaghnobis, both those who live alongside Tajiks as well as those living separately. The few families that still have distinct Yaghnobi plant uses are the ones which were given the opportunity to choose the spot in which to relocate and still visit the Yaghnob Valley regularly. On the basis of our study, we suggest that affording a choice of where to relocate is better than no choice, as the loss of motivation also affects the use of wild food plants. Given the pressure of the possible relocation of many groups of people in the light of global change, we suggest focusing efforts on studying similar cases in order to minimize the damage caused to people by relocation. The trauma of forced relocation, even just a few kilometers away, directly or indirectly affects wild food plant use and with this the food security of the community.


2003 ◽  
Vol 13 (2) ◽  
pp. 101-111 ◽  
Author(s):  
Péter Csontos ◽  
Júlia Tamás

AbstractSince 1969, ten soil seed bank classification systems have been published. Among these systems, the number of recognized seed bank categories varies from three to twelve. Seed longevity is the main factor used for distinguishing categories, but dormancy and germination types are also important. Systems considering relatively few seed bank categories have been the most commonly proposed in contemporary plant ecology. In contrast, systems involving high numbers of categories have received limited interest because the detailed ecological knowledge of individual species required for their successful categorization is usually missing. A comprehensive table on the main features of seed bank classification systems is provided.


Author(s):  
Domenico D'Alelio ◽  
Salvatore Rampone ◽  
Luigi Maria Cusano ◽  
Nadia Sanseverino ◽  
Luca Russo ◽  
...  

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