Reed S. Beaman

Angiosperm phylogeny: 17 genes, 640 taxa

PREMISE OF THE STUDY Recent analyses employing up to five genes have provided numerous insights into angiosperm phylogeny, but many relationships have remained unresolved or poorly supported. In the hope of improving our understanding of angiosperm phylogeny, we expanded sampling of taxa and genes beyond previous analyses. METHODS We conducted two primary analyses based on 640 species representing 330 families. The first included 25260 aligned base pairs (bp) from 17 genes (representing all three plant genomes, i.e., nucleus, plastid, and mitochondrion). The second included 19846 aligned bp from 13 genes (representing only the nucleus and plastid). KEY RESULTS Many important questions of deep-level relationships in the nonmonocot angiosperms have now been resolved with strong support. Amborellaceae, Nymphaeales, and Austrobaileyales are successive sisters to the remaining angiosperms (Mesangiospermae), which are resolved into Chloranthales + Magnoliidae as sister to Monocotyledoneae + [Ceratophyllaceae + Eudicotyledoneae]. Eudicotyledoneae contains a basal grade subtending Gunneridae. Within Gunneridae, Gunnerales are sister to the remainder (Pentapetalae), which comprises (1) Superrosidae, consisting of Rosidae (including Vitaceae) and Saxifragales; and (2) Superasteridae, comprising Berberidopsidales, Santalales, Caryophyllales, Asteridae, and, based on this study, Dilleniaceae (although other recent analyses disagree with this placement). Within the major subclades of Pentapetalae, most deep-level relationships are resolved with strong support. CONCLUSIONS Our analyses confirm that with large amounts of sequence data, most deep-level relationships within the angiosperms can be resolved. We anticipate that this well-resolved angiosperm tree will be of broad utility for many areas of biology, including physiology, ecology, paleobiology, and genomics.

Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

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.

Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science

Abstract 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.

Diversity and distribution patterns in the flora of Mount Kinabalu

Mount Kinabalu (4,101 m) in northern Borneo, encompassing an area of about 700 km2, has one of the richest floras in the world. The flora includes c. 4,000 species of vascular plants, about one-third of which are known from a single collection. A high percentage of the species have extremely restricted distributions, frequently associated with ultramafic outcrops. Ideal conditions for a diverse flora and rapid evolutionary rates apparently result from several factors including a vast range of climatic conditions, numerous geologically recent habitats on a diversity of substrates (particularly ultramafic outcrops), regularly recurring El Nino droughts that may drive catastrophic selection, precipitous topography resulting in strong reproductive isolation over short distances, and small population size of many species which may be susceptible to genetic drift. Numerous apparent neo-endemics in many genera and families suggest that frequent speciation events in the recent past may have contributed significantly to the great diversity of the flora. Short- and long-range dispersal of some plants pre-adapted to montane environments also may have contributed to the high floristic diversity. Some species may be relictual, but the relict nature of the flora is not considered to be as significant as previously thought. Because 40 percent of the flora is known from a single locality and most species are very restricted in occurrence, the flora is highly endangered by shifting and permanent agriculture, various development projects, and mining activities, notwithstanding the park status of a portion of the mountain.

Whence useful plants? A direct relationship between biodiversity and useful plants among the Dusun of Mt. Kinabalu

Traditionally the Dusun indigenous people of Borneo consider Mt. Kinabalu the home of spirits and ancestors, and they are loath to climb the summit without good cause and plentiful propitiation. In apparent accordance with these beliefs, Projek Etnobotani Kinabalu has recorded few useful plants at high elevations on Mt. Kinabalu. We ask the question: is this an ecological relationship with fewer useful plants being collected at high elevations, or is it an ethnological product of belief with fewer plants collected where people fear to tread? With an indigenous Dusun plant expert (second author) well versed with all areas of Mt. Kinabalu, data on the number and kinds of useful plants were collected for dominant and indicator plant species (168 spp.) among all ecologically identified vegetation types. Results indicate that there are more useful plant species at lower elevations – but there are also more unused species. Once the data are corrected for change in the number of plant species with elevation (useful spp./total spp.), the proportion of useful species are not significantly different over elevation. Thus, useful species are a function of overall biodiversity (i.e., number of useful spp. are correlated with number of plant species, a secondary ecological factor) and not a direct ecological correlate with elevation. The number or kinds of uses also correlates with total number of plant species. In support of direct ecological causation, there is evidence that edaphic conditions (i.e., ultramafic and other poor soils) are associated with reduced proportions of useful species. Ultimately, both ethnological and ecological factors contribute to patterns of peoples use of plants with many implications for conservation and biodiversity.

Clarifying Concepts and Terms in Biodiversity Informatics

“If names be not correct, language is not in accordance with the truth of things. If language be not in accordance with the truth of things, affairs cannot be carried on to success.” - Confucius, Analects, Book XIII, Chapter 3, verses 4-7, translated by James Legge Two workshops (hereafter described as “workshops”) were held in 2012, which brought together domain experts from genomic and biodiversity informatics, information modeling and biology, to clarify concepts and terms at the intersection of these domains. These workshops grew out of efforts sponsored by the NSF funded Resource Coordination Network (RCN) project for GSC [1] (RCN4GSC, hosted at UCSD, with John Wooley as PI) to reconcile terms from the Darwin Core (DwC) [2] vocabulary and with those in the MIxS family of checklists (Minimum Information about Any Type of Sequence) [3]. The original RCN4GSC meetings were able to align many terms between DwC and MIxS, finding both common and complementary terms. However, deciding exactly what constitutes the concept of a sample, a specimen, and an occurrence [4] to satisfy the needs of all use cases proved difficult, especially given the wide variety of sampling strategies employed within and between communities. Further, participants in the initial RCN4GSC workshops needed additional guidance on how to relate these entities to processes that act upon them and the environments in which organisms live. These issues provided the motivation for the workshops described below. The two workshops drew largely from experiences of the Basic Formal Ontology (BFO) [5] and were led by Barry Smith, State University of New York at Buffalo. We chose to interact with Smith based on his successful interactions with the GSC in developing the Environment Ontology (EnvO) [6] and also, on the ability of BFO to unite previously disconnected ontologies in the medical domain [7]. The first workshop addressed term definitions in biodiversity informatics, working within the BFO framework, while the second workshop developed a prototype Bio-Collections Ontology, dealing with samples and processes acting on samples. Concurrent with these workshops were two ongoing efforts involving data acquisition, visualization, and analysis that rely on a solid conceptual understanding of samples, specimens, and occurrences. These implementations are included in this report to show practical applications of term clarification. Finally, this report provides a discussion of some of the next steps discussed during the workshops.

Taxonomic studies in the Miconieae (Melastomataceae). II. Systematics of the miconia subcompressa complex of Hispaniola, including the description of two new species

TheMiconia subcompressa complex containsMiconia subcompressa, M. selleana, M. hypiodes, and two taxa described here:M. septentrionalis (collected mainly at Pico Diego de Ocampo, Cordillera Septentrional) andM. jimenezii (collected at high elevations in the Sierra de Neiba-Montagnes Noires). Members of the group are characterized by a shrubby or arborescent habit; leaves densely covered with ferrugineous, stellate hairs on the abaxial surface; large, actinomorphic flowers with white petals and stamens; and large, globose fruits turning from red to blue as they mature. The taxa comprising the group are compared and their phylogenetic relationships are analyzed. An identification key, along with species descriptions, specimen citations, and eco-geographical characterizations for each taxon, is presented.

Systematics of Tillandsia subgenus Pseudalcantarea (Bromeliaceae)

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, withVriesea subg.Alcantarea employed as the outgroup.Tillandsia subg.Pseudalcantarea is found to be paraphyletic.Tillandsia grandis andT. paniculata are transferred toTillandsia subg.Tillandsia because they are hypothesized to share a more recent common ancestor withT. utriculata, the type of the genus, than they do with the other two species placed in subg.Pseudalcantarea, i.e.,T. baliophylla andT. viridiflora. These latter two species possibly constitute a basal clade withinTillandsia and are provisionally retained within subg.Pseudalcantarea.

A Computational- and Storage-Cloud for Integration of Biodiversity Collections

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.

Miconia zanonii (Melastomataceae: Miconieae), a new species from Hispaniola

Miconia zanonii, which occurs in broad-leaved cloud forests at four localities in the Cordillera Central of the Dominican Republic, is described and illustrated. It is compared withM. krugii andM. samanensis, two probably close relatives withinMiconia sect.Chaenopleura.