GeoPick ‐ A web application for georeferencing natural history collections following best practices DOI Creative Commons
Arnald Marcer, Agustí Escobar, Arthur D. Chapman

et al.

Ecography, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 30, 2024

Georeferencing is a key process in the digitization of natural history collections as it assigns spatial coordinates to preserved specimen collecting locations, facilitating their use ecological, evolutionary and conservation research. Georeference data public repositories such GBIF often missing or incomplete, jeopardising research limiting return on investment made by institutions. Despite existence guidelines for best practices georeferencing widely accepted standards biodiversity data, there lack simple yet effective software tool that offers implementation both concepts. We present GeoPick with aim offer community standards‐compliant eases process, making more cost‐effective, which, applying practices, contributes betterment occurrence repositories. also possibility collaboration between users institutions through sharing georeferences. The hosted at https://geopick.gbif.org , open source. Its code available GitHub repository ( https://github.com/rtdeb/GeoPick ). Keywords: Darwin Core, georeferencing, collections, point‐radius method, web application, Well Known Text Format, WKT

Language: Английский

The colonial legacy of herbaria DOI
Daniel Park, Xiao Feng,

Shinobu Akiyama

et al.

Nature Human Behaviour, Journal Year: 2023, Volume and Issue: 7(7), P. 1059 - 1068

Published: June 12, 2023

Language: Английский

Citations

41
Strengthening Partnerships to Safeguard the Future of Herbaria DOI Creative Commons
Barbara M. Thiers

Diversity, Journal Year: 2024, Volume and Issue: 16(1), P. 36 - 36

Published: Jan. 5, 2024

Herbaria remain the primary means of documenting plant life on earth, and number herbaria worldwide specimens they hold continues to grow. Digitization herbarium specimens, though far from complete, has increased discoverability holdings range studies which data can be used. The rather large about no current information is available a source concern, as consolidation removal offsite storage facilities. Partnerships are key future health herbaria. Benefits could accrue reimagining world’s global resource than collection independent, often competing institutions. extend reach their by joining nascent effort link species occurrence manage other biological environmental sources deepen our ability understand interrelationships earth’s biota. To assure that held contribute conservation-related projects for relevant, should embrace tenets Team Science play more proactive role in promoting relevant research conservation projects.

Language: Английский

Citations

13
Herbarium collections remain essential in the age of community science DOI Creative Commons
Isaac Eckert, Anne Bruneau,

Deborah A. Metsger

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Aug. 31, 2024

The past decade has yielded more biodiversity observations from community science than the century of traditional scientific collection. This rapid influx data is promising for overcoming critical shortfalls, but we also have vast untapped resources held in undigitized natural history collections. Yet, ability these collections to fill gaps, especially compared against constant accumulation data, remains unclear. Here, compare how well (iNaturalist) and digitized herbarium specimens represent diversity, distributions, modeling needs vascular plants Canada. We find that, despite having only a third as many records, capture taxonomic, phylogenetic, functional diversity efficiently species' environmental niches. As such, digitization Canada's 7.3M remaining potential quintuple our model biodiversity. In contrast, it would require over 27M iNaturalist produce similar benefits. Our findings indicate that digitizing Earth's likely an efficient, feasible, potentially investment when comes improving predict protect into future. authors found specimens, finding with one-third herbaria still by several metrics.

Language: Английский

Citations

10
Achieving zero extinction for land plants DOI Open Access
Richard T. Corlett

Trends in Plant Science, Journal Year: 2023, Volume and Issue: 28(8), P. 913 - 923

Published: May 2, 2023

Language: Английский

Citations

20
From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2 DOI Creative Commons
William N. Weaver, Stephen A. Smith

Applications in Plant Sciences, Journal Year: 2023, Volume and Issue: 11(5)

Published: Sept. 1, 2023

Abstract Premise Quantitative plant traits play a crucial role in biological research. However, traditional methods for measuring morphology are time consuming and have limited scalability. We present LeafMachine2, suite of modular machine learning computer vision tools that can automatically extract base set leaf from digital data sets. Methods LeafMachine2 was trained on 494,766 manually prepared annotations 5648 herbarium images obtained 288 institutions representing 2663 species; it employs component detection segmentation algorithms to isolate individual leaves, petioles, fruits, flowers, wood samples, buds, roots. Our landmarking network identifies measures nine pseudo‐landmarks occur most broadleaf taxa. Text labels barcodes identified by an archival detector optical character recognition or natural language processing algorithms. Results trait at least 245 angiosperm families calculate pixel‐to‐metric conversion factors 26 commonly used ruler types. Discussion is highly efficient tool generating large quantities data, even occluded overlapping field images, non‐archival project, along with similar initiatives, has made significant progress removing the bottleneck acquisition specimens shifted focus toward task revision quality control.

Language: Английский

Citations

17
Complex climate‐mediated effects of urbanization on plant reproductive phenology and frost risk DOI Creative Commons
Daniel Park, Yingying Xie, Aaron M. Ellison

et al.

New Phytologist, Journal Year: 2023, Volume and Issue: 239(6), P. 2153 - 2165

Published: March 21, 2023

Urbanization can affect the timing of plant reproduction (i.e. flowering and fruiting) associated ecosystem processes. However, our knowledge how phenology responds to urbanization its environmental changes is limited. Herbaria represent an important, but underutilized source data for investigating this question. We harnessed phenological from herbarium specimens representing 200 species collected across 120 yr eastern US investigate spatiotemporal effects on fruiting frost risk time between last date flowering). Effects reproductive varied significantly in direction magnitude ranges. Increased led earlier colder wetter regions delayed with spring conditions. Frost was elevated increased Our study demonstrates that predictions change impacts must account both climatic human effects, which are context dependent do not necessarily coincide. move beyond models only incorporate temperature variables consider multiple factors their interactions when estimating phenology, especially at larger spatial taxonomic scales.

Language: Английский

Citations

12
AI-based discovery of habitats from museum collections DOI Creative Commons
Christopher B. Jones, Kristin Stock, Sarah E. Perkins

et al.

Trends in Ecology & Evolution, Journal Year: 2024, Volume and Issue: 39(4), P. 323 - 327

Published: Feb. 13, 2024

Museum collection records are a source of historic data for species occurrence, but little attention is paid to the associated descriptions habitat at sample locations. We propose that artificial intelligence methods have potential use these reconstructing past habitat, address ecological and evolutionary questions.

Language: Английский

Citations

5
Data mobilisation in the LWS Herbarium: success and prospects DOI Creative Commons
Andriy Novikov, Anastasiia Savytska,

Oleksandr Kuzyarin

et al.

Biodiversity Data Journal, Journal Year: 2024, Volume and Issue: 12

Published: Jan. 11, 2024

Digitisation of hosted specimens is a crucial task for all herbaria worldwide and one the main streams today. By digitising their collections publishing datasets, grant access to essential data wide research audience and, as result, involve in scientific work more actively. also allows virtual preservation collections, which especially important conditions hostilities, when entire collection can be destroyed or damaged moment. This paper describes two datasets recently published GBIF framework LWS herbarium digitisation initiative. It contains some considerations about further priorities plans Herbarium context complicated war limited facilities.

Language: Английский

Citations

4
Shall we promote natural history collection today?—Answered by reviewing Ernest Henry Wilson’s plant collection process in China DOI
Renwu Wu,

Yongxi Zou,

Shuai Liao

et al.

The Science of The Total Environment, Journal Year: 2024, Volume and Issue: 915, P. 170179 - 170179

Published: Jan. 19, 2024

Language: Английский

Citations

4
Old meets new: Innovative and evolving uses of herbaria over time as revealed by a literature review DOI Creative Commons
Macarena Marín‐Rodulfo,

Katy V. Rondinel‐Mendoza,

Isabel Martín Girela

et al.

Plants People Planet, Journal Year: 2024, Volume and Issue: 6(6), P. 1261 - 1271

Published: July 15, 2024

Societal Impact Statement Herbaria, as collections of preserved plants, contain large amounts data both in the labels and specimens themselves, which can be applied different study fields. A literature review was conducted to discover how uses herbaria have evolved over time since records began. This analysis revealed insights into are presently used. Uses include traditional taxonomic review, well advanced technological tools, being material address societal global challenges therefore contribute decision‐making conservation. Summary Herbaria plants prominent information, on themselves. There 400 million worldwide, with great potential for studies conservation effects change plants. (1) In this paper, we investigate array through a systematic scientific SCOPUS covering period 1842–2022. (2) We reviewed total 2900 papers classified them areas knowledge, level studied. (3) Our results show that use is most relevant time. use, together primary source plant diversity data, essential documenting, planning, acting threatened Furthermore, our shown new diverse emerged 1990, mostly related ecological issues, provide historical record distribution, their evolutionary responses, allowing scientists track changes (4) contributes improve knowledge biodiversity increase effectiveness strategies policies, priority going change. Therefore, shows relevance ecology, including or forthcoming uses, from originally intended by collectors. Thus, preservation critical unique exceptional space

Language: Английский

Citations

4