New information technologies have enabled the scientific collections community and its stakeholders to adapt, adopt, and leverage novel approaches for a nearly 300 years old scientific discipline. ...Now, few can credibly question the transformational impact of technology on efforts to digitize scientific collections, as IT now reaches into almost every nook and cranny of society. Five to ten years ago this was not the case. Digitization is an activity that museums and academic institutions increasingly recognize, though many still do not embrace, as a means to boost the impact of collections to research and society through improved access. The acquisition and use of scientific collections is a global endeavor, and digitization enhances their value by improved access to core biodiversity information, increases use, relevance and potential downstream value, for example, in the management of natural resources, policy development, food security, and planetary and human health. This paper examines new opportunities to design and implement infrastructure that will support not just mass digitization efforts, but also a broad range of research on biological diversity and physical sciences in order to make scientific collections increasingly relevant to societal needs and interest.
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Identifying physical and ecological boundaries that limit where species can occur is important for predicting how those species will respond to global change. The island of Borneo encompasses a wide ...range of habitats that support some of the highest richness on Earth, making it an ideal location for investigating ecological mechanisms underlying broad patterns of species distribution. We tested variation in richness and range‐size in relation to edaphic specialization and vegetation zone boundaries using 3060 plant species from 193 families centered around the elevational gradient of Mt Kinabalu, Borneo. Across species, average range‐size increased with elevation, consistent with Rapoport's rule. However, plants associated with ultramafic soil, which is low in nutrient and water availability and often has high concentrations of heavy metals, had larger range‐sizes and greater richness than expected along the elevational gradient, as compared to a null model with randomization of edaphic association. In contrast, non‐ultramafic species had smaller range‐sizes and lower richness than expected. These results suggest that tolerance of resource limitation may be associated with wider range‐sizes, whereas species intolerant of edaphic stress may have narrower range‐sizes, possibly owing to more intense competition in favorable soil types. Using elevation as a predictor of average range‐sizes, we found that piece‐wise models with breakpoints at vegetation zone transitions explained species distributions better than models that did not incorporate ecological boundaries. The greatest relative increases in range‐size with respect to elevation occurred mid‐elevation, within the montane cloud forest vegetation zone. Expansion of average range‐size across an area without physical boundaries may indicate a shift in ecological strategy and importance of biotic versus abiotic stressors. Our results indicate that elevational range‐size patterns are structured by ecological constraints such as species' edaphic association, which may limit the ability of species to migrate up or down mountains in response to climate change.
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The development of biological informatics infrastructure capable of supporting growing data management and analysis environments is an increasing need within the systematics biology community. ...Although significant progress has been made in recent years on developing new algorithms and tools for analyzing and visualizing large phylogenetic data and trees, implementation of these resources is often carried out by bioinformatics experts, using one-off scripts. Therefore, a gap exists in providing data management support for a large set of non-technical users. The TOLKIN project (Tree of Life Knowledge and Information Network) addresses this need by supporting capabilities to manage, integrate, and provide public access to molecular, morphological, and biocollections data and research outcomes through a collaborative, web application. This data management framework allows aggregation and import of sequences, underlying documentation about their source, including vouchers, tissues, and DNA extraction. It combines features of LIMS and workflow environments by supporting management at the level of individual observations, sequences, and specimens, as well as assembly and versioning of data sets used in phylogenetic inference. As a web application, the system provides multi-user support that obviates current practices of sharing data sets as files or spreadsheets via email.
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Pollination of Rafflesia (Rafflesiaceae) Beaman, Reed S.; Decker, Pamla J.; Beaman, John H.
American journal of botany,
August 1988, Volume:
75, Issue:
8
Journal Article
Peer reviewed
The genus Rafflesia includes about 13 species of parasitic flowering plants, among which are the largest known flowers. The flower with subtending scales is the only part of the plant external to the ...host and is produced solitary on roots (rarely stems) of the genus Tetrastigma (Vitaceae). Field studies were made of the pollination process in R. pricei, a species endemic to the Crocker Range in the Malaysian state of Sabah (northern Borneo). Pollination is mediated by carrion (bluebottle) flies of the genera Lucilia and Chrysomya. Experimental data indicate that both visual and olfactory cues are important in attracting flies to flowers. Flies (mostly female L. papuensis) obtain loads of the viscous liquid pollen matrix by visiting male flowers and entering anther grooves on the central column of the flower, precisely guided by ridges armed with hairs that force the fly into a position in which the pollen is positioned on the dorsal part of the thorax. "Windows" on the inside of the perigone diaphragm apparently help orient their flight inside flowers. Pollen-loaded flies visiting female flowers may enter the infradiscoidal sulcus formed by a broad ring of stigmatic tissue above and the expanded base of the column below. On entering the sulcus the fly is wedged in so tightly that pollen is rubbed off the thorax onto the stigma. Only large flies could be effective in picking up pollen from male flowers and transferring it to female flowers. The pollination syndrome is sapromyophily, in which the flower closely parallels trap flowers of several other plant families, although it is not a trap. The flower provides no reward for pollinators but deceives them by an apparent offering of food and possibly brood place. Rafflesia plants are extremely rare, perhaps in part because of infrequency of pollination, which requires neighboring male and female flowers simultaneously in bloom.
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Pollination of Rafflesia (Rafflesiaceae) Beaman, Reed S.; Decker, Pamla J.; Beaman, John H.
American journal of botany,
08/1988, Volume:
75, Issue:
8
Journal Article
Peer reviewed
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Thesis (Ph. D.)--University of Florida, 2000.
Title from first page of PDF file. Document formatted into pages; contains ix, 264 p.; also contains graphics. Vita. Includes bibliographical references ...(p. 255-262).
A core mission of the Integrated Digitized Biocollections (iDigBio) project is the building and deployment of a cloud computing environment customized to support the digitization workflow and ...integration of data from all U.S. non-federal biocollections. iDigBio chose to use cloud computing technologies to deliver a cyber infrastructure that is flexible, agile, resilient, and scalable to meet the needs of the biodiversity community. In this context, this paper describes the integration of open source cloud middleware, applications, and third party services using standard formats, protocols, and services. In addition, this paper demonstrates the value of the digitized information from collections in a broader scenario involving multiple disciplines.
Tillandsia subg. Pseudalcantarea (Bromeliaceae) includes four species as currently delimited. The phylogenetic relationships of the species in this group are investigated by a cladistic analysis ...using 16 morphological characters, with Vriesea subg. Alcantarea employed as the outgroup. Tillandsia subg. Pseudalcantarea is found to be paraplyletic. Tillandsia grandis and T. paniculata are transferred to Tillandsia subg. Tillandsia because they are hypothesized to share a more recent common ancestor with T. utriculata, the type of the genus, than they do with the other two species placed in subg. Pseudalcantarea, i.e., T. baliophylla and T. viridiflora. These latter two species possibly constitute a basal clade within Tillandsia and are provisionally retained within subg. Pseudalcantarea.
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The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by ...information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.
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