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Recent Publications

Emily K. Meineke, Charles C. Davis, and Jonathan Davies. Forthcoming. “The unrealized potential of herbaria for global change biology.” Ecological Monographs, Pp. 1-21.Abstract


Plant and fungal specimens in herbaria are becoming primary resources for investigat-

ing how plant phenology and geographic distributions shift with climate change, greatly expanding

inferences across spatial, temporal, and phylogenetic dimensions. However, these specimens contain a

wealth of additional data, including nutrients, defensive compounds, herbivore damage, disease

lesions, and signatures of physiological processes, that capture ecological and evolutionary responses

to the Anthropocene but which are less frequently utilized. Here, we outline the diversity of herbarium

data, global change topics to which they have been applied, and new hypotheses they could inform.

We find that herbarium data have been used extensively to study impacts of climate change and inva-

sive species, but that such data are less commonly used to address other drivers of biodiversity loss,

including habitat conversion, pollution, and overexploitation. In addition, we note that fungal speci-

mens are under-explored relative to vascular plants. To facilitate broader application of plant and fun-

gal specimens in global change research, we consider the limitations of these data and modern

sampling and statistical tools that may be applied to surmount challenges they present. Using a case

study of insect herbivory, we illustrate how novel herbarium data may be employed to test hypotheses

for which few data exist. With the goal of positioning herbaria as hubs for global change research, we

suggest future research directions and curation priorities.

Key words: climate change; extinction; global change; habitat conversion; herbarium; historical data; invasive

species; museum specimens.


W. patrick Sweeney, Binil Starly, Paul J. Morris, Yiming Xy, Aimee Jones, Sridhar Radhakrishnan, Christopher J. Grassa, and Charles C. Davis. 6/3/2018. “Large-scale digitization of herbarium specimens: Development and usage of an automated, high-throughput conveyor system.” International Association for Plant Taxonomy, 67, 1, Pp. 165-178. Publisher's VersionAbstract
The billions of specimens housed in natural science collections provide a tremendous source of under-utilized data that are useful for scientific research, conservation, commerce, and education. Digitization and mobilization of specimen data and images promises to greatly accelerate their utilization. While digitization of natural science collection specimens has been occurring for decades, the vast majority of specimens remain un-digitized. If the digitization task is to be completed in the near future, innovative, high-throughput approaches are needed. To create a dataset for the study of global change in New England, we designed and implemented an industrial-scale, conveyor-based digitization workflow for herbarium specimen sheets. The workflow is a variation of an object-to-image-to-data workflow that prioritizes imaging and the capture of storage container-level data. The workflow utilizes a novel conveyor system developed specifically for the task of imaging flattened herbarium specimens. Using our workflow, we imaged and transcribed specimen-level data for almost 350,000 specimens over a 131-week period; an additional 56 weeks was required for storage container-level data capture. Our project has demonstrated that it is possible to capture both an image of a specimen and a core database record in 35 seconds per herbarium sheet (for intervals between images of 30 minutes or less) plus some additional overhead for container-level data capture. This rate was in line with the pre-project expectations for our approach. Our throughput rates are comparable with some other similar, high-throughput approaches focused on digitizing herbarium sheets and is as much as three times faster than rates achieved with more conventional non-automated approaches used during the project. We report on challenges encountered during development and use of our system and discuss ways in which our workflow could be improved. The conveyor apparatus software, database schema, configuration files, hardware list, and conveyor schematics are available for download on GitHub.
Andrea S. Meseguer, Jorge M. Lobo, Josselin Cornualt, Davis Beerling, Brad R. Ruhfel, Charles C. Davis, Emmanuelle Jousellin, and Isabel Sanmartin. 5/2018. “Reconstructing deep‐time palaeoclimate legacies in the clusioid Malpighiales unveils their role in the evolution and extinction of the boreotropical flora.” Global Ecology and Biogeography, 27, 5, Pp. 616-628. Publisher's VersionAbstract

During its entire history, the Earth has gone through periods of climate change similar in scale and pace to the warming trend observed today in the Anthropocene. The impact of these ancient climatic events on the evolutionary trajectories of organisms provides clues on the organismal response to climate change, including extinction, migration and persistence. Here, we examine the evolutionary response to climate cooling/warming events of the clusioid families Calophyllaceae, Podostemaceae and Hypericaceae (CPH clade) and the genus Hypericum as test cases.