Rapid enhancement of biodiversity occurrence records using unconventional specimen data

Pearson, Katelin D.

doi:10.1007/s10531-018-1584-0

Cited by 7 publications

(5 citation statements)

References 18 publications

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“…Specimens of different species that were collected together could be compared or considered in analyses. Similarly, "associated species" are frequently provided by collectors on specimen labels (Landrum and Lafferty 2015;Pearson 2018). These metadata are mostly unused.…”

Section: Addressing Effects Of Microsite Variationmentioning

confidence: 99%

Herbaria as Big Data Sources of Plant Traits

Heberling

2022

International Journal of Plant Sciences

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Herbarium specimens have long been a cornerstone of taxonomic research but are only recently being recognized for their potential as a source of spatially and temporally extensive data on plant functional traits. Many researchers in trait-based disciplines remain surprisingly unaware of this powerful use of herbaria, including functional ecologists and evolutionary biologists alike. This review brings together disparate studies to synthesize the past, current, and potential future uses of specimens as functional trait data sources, answering: 1) What insights have been made to date using specimens? (including traits measured, approaches used, research questions answered); 2) What new trait-based insights can be made from herbarium specimens? (including potential contributions to global trait databases and recent advancements such as machine learning and high throughput phenotyping); and 3) How can inherent limitations and collection biases be addressed when using specimens in unanticipated ways? (including new analytical approaches and improved methods for collecting). I conclude by identifying what is needed to foster the future of herbaria as big data sources of plant traits. Most notably, plant collecting must be continued, expanded beyond predominantly systematists, and intentionally revised with downstream trait measurements in mind. Further, community-wide standards are needed to integrate otherwise disconnected data and directly link newly derived measurements back to specimen records. Specimens serve as reliable (and necessary) sources of phenotypic data, enabling us to answer questions across phylogenetic, temporal, and spatial dimensions otherwise not possible. Herbaria should be embraced as centers for functional trait research.

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Section: Addressing Effects Of Microsite Variationmentioning

confidence: 99%

Herbaria as Big Data Sources of Plant Traits

Heberling

2022

International Journal of Plant Sciences

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“…In examining sampling bias in Australia, New England (U.S.A.), and South Africa from ~5 million digitized herbarium records, Daru et al (2018) found that graminoid specimens in Australia and South Africa were overrepresented compared to New England, which overrepresented herbs and trees. In examining co-associated taxa compared to specimen data for the Robert K. Godfrey Herbarium (FSU), Pearson (2018) found that fewer graminoids were included as associated taxa records (20.9%) compared to specimen records (26.8%), showing that graminoids are underrepresented as co-associated taxa. In comparison to arctic herbarium collection bias in Nunavut, Canada, eastern Arkansas also exhibits under-collection of Asteraceae, Fabaceae, and Ranunculaceae (Panchen et al 2019).…”

Section: Resultsmentioning

confidence: 99%

An exploration of the vascular flora of Pine City Natural Area, Monroe County, Arkansas, U.S.A., in comparison to the Mississippi Alluvial Plain in eastern Arkansas (U.S.A.)

Soteropoulos

Ledvina

Marsico

2022

J. Bot. Res. Inst. Texas

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The Mississippi Alluvial Plain (MAP) ecoregion in eastern Arkansas has had >90% of its land area converted to agriculture and has historically been under-collected floristically, including the ecologically unique site, Pine City Natural Area (PCNA). Actively managed by the Arkansas Natural Heritage Commission, PCNA contains diverse loblolly pine-post oak flatwoods and some of the last known saline barrens in the MAP. Our inventory of the vascular flora in and around PCNA resulted in the documentation of 113 families, 308 genera, and 576 taxa (including infraspecific taxa); 482 (83.7%) are native, 9 (1.6%) are of state conservation concern, and 184 (31.9%) represent county records. The total taxa known for Monroe County, Arkansas, increased from 583 to 767. The most taxa-rich families included Poaceae (92 taxa), Asteraceae (65), Cyperaceae (48), and Fabaceae (42). In the surrounding ten-county region, 27 taxa (4.7%) documented at PCNA had not been vouchered, and 196 taxa (34.0%) are known from half or fewer surrounding MAP counties. We examined families in need of additional exploration in the MAP to better understand county-level floristic richness. The richest graminoid families, the Poaceae, Cyperaceae, and Juncaceae, are apparently the most understudied in the MAP, based on low relative numbers of herbarium specimens. The richness in the PCNA flora, in comparison to the broader MAP, demonstrates the need for continued floristic inventory in eastern Arkansas to locate areas of high conservation value in need of protection.

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“…We prefer the ‘ResourceRelationship’ field but agree with Downey (1998) that a field for ‘host plant’ in databases and specimen labels would eliminate confusion with species that are only associated. An extension to the Darwin Core controlled vocabulary framework for parasitic plants with standardized terms for these important interrelationships would provide a more information‐rich description of their ecologies and greater accuracy for web‐based applications and data analysis protocols (Myltsev & Mozzherin, 2016; Pearson, 2018) that extract taxon information from digitized records. It is crucial, however, that both the original voucher label and the digitized specimen host taxa are annotated similarly, as to avoid confusion.…”

Section: Best Practices For Collecting Preparing and Curating Parasit...mentioning

confidence: 99%

Parasitic flowering plant collections embody the extended specimen

et al. 2022

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The widespread digitization of natural history collections, combined with novel tools and approaches is revolutionizing biodiversity science. The ‘extended specimen’ concept advocates a more holistic approach in which a specimen is framed as a diverse stream of interconnected data. Herbarium specimens that by their very nature capture multispecies relationships, such as certain parasites, fungi and lichens, hold great potential to provide a broader and more integrative view of the ecology and evolution of symbiotic interactions. This particularly applies to parasite–host associations, which owing to their interconnectedness are especially vulnerable to global environmental change. Here, we present an overview of how parasitic flowering plants is represented in herbarium collections. We then discuss the variety of data that can be gathered from parasitic plant specimens, and how they can be used to understand global change impacts at multiple scales. Finally, we review best practices for sampling parasitic plants in the field, and subsequently preparing and digitizing these specimens. Plant parasitism has evolved 12 times within angiosperms, and similar to other plant taxa, herbarium collections represent the foundation for analysing key aspects of their ecology and evolution. Yet these collections hold far greater potential. Data and metadata obtained from parasitic plant specimens can inform analyses of co‐distribution patterns, changes in eco‐physiology and species plasticity spanning temporal and spatial scales, chemical ecology of tripartite interactions (e.g. host–parasite–herbivore), and molecular data critical for species conservation. Moreover, owing to the historic nature and sheer size of global herbarium collections, these data provide the spatiotemporal breadth essential for investigating organismal response to global change. Parasitic plant specimens are primed to serve as ideal examples of extended specimen concept and help motivate the next generation of creative and impactful collection‐based science. Continued digitization efforts and improved curatorial practices will contribute to opening these specimens to a broader audience, allowing integrative research spanning multiple domains and offering novel opportunities for education.

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Rapid enhancement of biodiversity occurrence records using unconventional specimen data

Cited by 7 publications

References 18 publications

Herbaria as Big Data Sources of Plant Traits

Herbaria as Big Data Sources of Plant Traits

An exploration of the vascular flora of Pine City Natural Area, Monroe County, Arkansas, U.S.A., in comparison to the Mississippi Alluvial Plain in eastern Arkansas (U.S.A.)

Parasitic flowering plant collections embody the extended specimen

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