Zack E. Murrell

The notes from nature tool for unlocking biodiversity records from museum records through citizen science

Abstract Legacy data from natural history collections contain invaluable and irreplaceable information about biodiversity in the recent past, providing a baseline for detecting change and forecasting the future of biodiversity on a human-dominated planet. However, these data are often not available in formats that facilitate use and synthesis. New approaches are needed to enhance the rates of digitization and data quality improvement. Notes from Nature provides one such novel approach by asking citizen scientists to help with transcription tasks. The initial web-based prototype of Notes from Nature is soon widely available and was developed collaboratively by biodiversity scientists, natural history collections staff, and experts in citizen science project development, programming and visualization. This project brings together digital images representing different types of biodiversity records including ledgers , herbarium sheets and pinned insects from multiple projects and natural history collections. Experts in developing web-based citizen science applications then designed and built a platform for transcribing textual data and metadata from these images. The end product is a fully open source web transcription tool built using the latest web technologies. The platform keeps volunteers engaged by initially explaining the scientific importance of the work via a short orientation, and then providing transcription “missions” of well defined scope, along with dynamic feedback, interactivity and rewards. Transcribed records, along with record-level and process metadata, are provided back to the institutions. While the tool is being developed with new users in mind, it can serve a broad range of needs from novice to trained museum specialist. Notes from Nature has the potential to speed the rate of biodiversity data being made available to a broad community of users.

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.

The US Virtual Herbarium: working with individual herbaria to build a national resource

Abstract The goal of the US Virtual Herbarium (USVH) project is to digitize (database, image, georeference) all specimens in all US herbaria, enabling them to be made available through a single portal. Herbaria house specimens of plants, fungi, and algae, so USVH will offer a rich portrait of biodiversity in the US and in the other countries represented in US herbaria. Equally importantly, working towards this goal will engage people with herbaria and the organisms they house, expanding their appreciation of both the power of biodiversity informatics and the demands that it places on data providers while developing improved communication among those working in and with herbaria. The project is not funded but has strong support among those working in herbaria. It works through regional herbarium networks, some of which existed prior to the USVH project, while others are still in gestation. It differs from most digitization projects in its emphasis on helping those involved with herbaria become part of a national enterprise, an aspect that is seen as critical to creating the resources needed to develop and sustain the project. In this paper, we present some of the lessons we have learned and the difficulties we have encountered during the first few years of the project.

Digitization Workflows for Flat Sheets and Packets of Plants, Algae, and Fungi

Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.S. National Science Foundations (NSF) coordinating center and national resource for the digitization of public, nonfederal U.S. collections, launched several working groups to address this deficiency. Here, we report the development of 14 workflow modules with 7–36 tasks each. These workflows represent the combined work of approximately 35 curators, directors, and collections managers representing more than 30 herbaria, including 15 NSF-supported plant-related Thematic Collections Networks and collaboratives. The workflows are provided for download as Portable Document Format (PDF) and Microsoft Word files. Customization of these workflows for specific institutional implementation is encouraged.

Patterns of native and exotic vascular plant richness along an elevational gradient from sea level to the summit of the Appalachian Mountains, U.S.A.

Abstract We used floristic studies from the state of North Carolina to compare the patterns of total, native and exotic plant species richness from sea level (Atlantic coast) to the summit of the Appalachian Mountains. Few studies have investigated how patterns of native and exotic species richness differ along environmental gradients, and these studies have yielded contrasting results. We compare our results with those few published studies, and demonstrate that there is a need for future studies examining exotic richness along gradients. We modeled the effects of size of study area, year of study, and elevation on species richness using a dataset of sixty-eight floristic studies. Native and exotic species richness showed a positive relationship with area and year. Exotic species showed a steeper slope than native species for the species-area relationship. Richness of both groups was positively but weakly related to year of study. After accounting for area and year, native species displayed a hump-shaped pattern along the elevational gradient. Exotic species richness was weakly related to elevation, which was not a significant variable in the model. This contrasts with the few previous studies that have examined exotic richness patterns along elevational gradients that have found either a strong linear decline, or a strong hump-shaped pattern. Both native and exotic species showed high variation in richness at elevations below 400 m. We conclude that different processes may govern native and exotic plant richness patterns and that exotic richness patterns along gradients may in fact be idiosyncratic due to factors such as disturbance history.

Vascular Flora of Mount Jefferson State Natural Area and Environs, Ashe County, North Carolina

Abstract A qualitative inventory of the vascular plant species of Mount Jefferson State Natural Area and contiguous areas was conducted from fall 2004–summer 2008. The 368 ha site is the most southeastern peak within the Amphibolite Mountains Macrosite of northwestern North Carolina. The study area is near equidistant from the towns of Jefferson and West Jefferson in central Ashe County, and lies within the Blue Ridge Range of the Southern Section of the Blue Ridge Physiographic Province. Nine major communities were recognized, including a High Elevation Mafic Glade, which is only the second documentation of such a community in North Carolina or globally. Vascular plants consist of 706 specific and infraspecific taxa in 383 genera from 109 families. Plants represented were one Equisetophyta, six Lycopodiophyta, twenty-four Polypodiophyta, five Pinophyta, and 670 Magnoliophyta. The largest families in taxa richness were the Asteraceae (96), Poaceae (82), Rosaceae (37), Cyperaceae (32), Fabaceae (30), and Lamiaceae (25). One-hundred and sixty taxa (22.7%) were exotic. Thirty-four taxa were on the “NC Watch List” and an additional sixteen were regarded as “Significantly Rare” in North Carolina. One hundred and twenty-nine taxa were Ashe County records. Eight taxa were documented for the first time in North Carolina.

A Bibliography of North Carolina Local Floras

Abstract Vascular plant checklists (floras) supply key information for biodiversity studies by providing a comprehensive picture of the floristic composition of a specific study area. A bibliography of floras conducted within the state of North Carolina was compiled. Eighty-six floras were completed within North Carolina between the years 1834 and 2009. Floras conducted in North Carolina cover areas of varying size, from small islands and state parks to entire counties. These studies include journal articles, government publications, technical reports and Masters theses. More than half of the flora citations were not published in scientific journals and were often difficult to discover or obtain.

Fourteen Polymorphic Microsatellite Markers for a Widespread Limestone Endemic, Carex eburnea (Cyperaceae: Carex sect. Albae)

Premise of the study: Microsatellite primers were developed for a widespread limestone endemic sedge, Carex eburnea, to facilitate investigation of the genetic diversity and phylogeography of this taxon and its closest relative, C. mckittrickensis. Methods and Results: Forty-eight primer pairs were designed from Illumina sequence data and screened for suitability. Fourteen of these primer pairs were polymorphic and generated one to seven alleles per locus. Cross-species amplifications were conducted for all four members of Carex sect. Albae. Conclusions: These primer pairs can be used to assess the genetic diversity and population structure in future studies of C. eburnea and C. mckittrickensis, and likely in other members of Carex sect. Albae.

Sixteen Polymorphic Microsatellite Markers for a Federally Threatened Species, Hexastylis naniflora (Aristolochiaceae), and Co-Occurring Congeners

Premise of the study: Twenty microsatellite loci were developed for the federally threatened species Hexastylis naniflora (Aristolochiaceae) to examine genetic diversity and to distinguish this species from co-occurring congeners, H. heterophylla and H. minor. Methods and Results: Next-generation sequencing approaches were used to identify microsatellite loci and design primers. One hundred fifty-two primer pairs were screened for repeatability, and 20 of these were further characterized for polymorphism. In H. naniflora, the number of alleles identified for polymorphic loci ranged from two to 23 (mean ∼8.8), with a mean heterozygosity of 0.39. Conclusions: These 16 polymorphic primers for H. naniflora will be useful tools in species identification and quantifying genetic diversity within the genus.