More Like this

1. Small herbaria contribute unique biogeographic records to county, locality, and temporal scales

   https://doi.org/10.1002/ajb2.1563  

   Marsico, Travis D. ; Krimmel, Erica R. ; Carter, J. Richard ; Gillespie, Emily L. ; Lowe, Phillip D. ; McCauley, Ross ; Morris, Ashley B. ; Nelson, Gil ; Smith, Michelle ; Soteropoulos, Diana L. ; et al ( November 2020 , American Journal of Botany)

   With digitization and data sharing initiatives underway over the last 15 years, an important need has been prioritizing specimens to digitize. Because duplicate specimens are shared among herbaria in exchange and gift programs, we investigated the extent to which unique biogeographic data are held in small herbaria vs. these data being redundant with those held by larger institutions. We evaluated the unique specimen contributions that small herbaria make to biogeographic understanding at county, locality, and temporal scales.

   We sampled herbarium specimens of 40 plant taxa from each of eight states of the United States of America in four broad status categories: extremely rare, very rare, common native, and introduced. We gathered geographic information from specimens held by large (≥100,000 specimens) and small (<100,000 specimens) herbaria. We built generalized linear mixed models to assess which features of the collections may best predict unique contributions of herbaria and used an Akaike information criterion‐based information‐theoretic approach for our model selection to choose the best model for each scale.

   Small herbaria contributed unique specimens at all scales in proportion with their contribution of specimens to our data set. The best models for all scales were the full models that included the factors of species status and herbarium size when accounting for state as a random variable.

   We demonstrated that small herbaria contribute unique information for research. It is clear that unique contributions cannot be predicted based on herbarium size alone. We must prioritize digitization and data sharing from herbaria of all sizes.

    

   more » « less
2. Herbarium specimens reveal increasing herbivory over the past century

   https://doi.org/10.1111/1365-2745.13057  

   Meineke, Emily K. ; Classen, Aimée T. ; Sanders, Nathan J. ; Jonathan Davies, T. ( September 2018 , Journal of Ecology)

   1. Predicting how ecological interactions will respond to global change is a major challenge. Plants and their associated insect herbivores compose much of macroscopic diversity, yet how their interactions have been altered by recent environmental change remains underexplored. 2. To address this gap, we quantified herbivory on herbarium specimens of four plant species with records extending back 112 years. Our study focused on the northeastern US, where temperatures have increased rapidly over the last few decades. This region also represents a range of urban development, a form of global change that has shown variable effects on herbivores in the past studies. 3. Herbarium specimens collected in the early 2000s were 23% more likely to be damaged by herbivores than those collected in the early 1900s. Herbivory was greater following warmer winters and at low latitudes, suggesting that climate warming may drive increasing insect damage over time. In contrast, human population densities were negatively associated with herbivore damage. 4. To explore whether changes in insect occurrence or abundance might explain shifts in herbivory, we used insect observational records to build climate occupancy models for lepidopteran herbivores (butterflies and moths) of our focal plant species. 5. These models show that higher winter temperatures were associated with higher probability of insect herbivore presence, while urbanization was associated with reduced probability of herbivore presence, supporting a link between insect herbivore occurrence and herbivory mediated through environment. 6. Synthesis. Using a temporal record of plant herbivory that spans over a century, we show that both temperature and urbanization influence insect damage to plants, but in very different ways. Our results indicate that damage to plants by insect herbivores will likely continue to increase through time in the northeastern US as global temperatures rise, but that urbanization may disrupt local effects of winter warming on herbivory by excluding certain herbivores. These changes may scale to shape ecosystem processes that are driven by herbivory, including plant productivity. 

   more » « less
3. Integrating herbarium specimen observations into global phenology data systems

   https://doi.org/10.1002/aps3.1231  

   Brenskelle, Laura ; Stucky, Brian J. ; Deck, John ; Walls, Ramona ; Guralnick, Rob P. ( March 2019 , Applications in Plant Sciences)

   The Plant Phenology Ontology (PPO) was originally developed to integrate phenology observations of whole plants across different global observation networks. Here we describe a new release of thePPOand associated data pipelines that supports integration of phenology observations from herbarium specimens, which provide historical and modern phenology data.

   Critical changes to thePPOinclude key terms that describe how measurements from parts of plants, which are captured in most imaged herbarium specimens, relate to whole plants. We provide proof of concept for ingesting annotations from imaged herbarium sheets ofPrunus serotina, the common black cherry. We then provide an example analysis of changes in flowering timing over the past 125 years, demonstrating the value of integrating herbarium and observational phenology data sets.

   These conceptual and technical advances will support the addition of phenology data from herbaria, but also could be expanded upon to facilitate the inclusion of data from photograph‐based citizen science platforms. With the incorporation of herbarium phenology data, new historical baseline data will strengthen the capability to monitor, model, and forecast plant phenology changes.

    

   more » « less
4. An algorithm competition for automatic species identification from herbarium specimens

   https://doi.org/10.1002/aps3.11365  

   Little, Damon P. ; Tulig, Melissa ; Tan, Kiat Chuan ; Liu, Yulong ; Belongie, Serge ; Kaeser‐Chen, Christine ; Michelangeli, Fabián A. ; Panesar, Kiran ; Guha, R. V. ; Ambrose, Barbara A. ( June 2020 , Applications in Plant Sciences)

   Plant biodiversity is threatened, yet many species remain undescribed. It is estimated that >50% of undescribed species have already been collected and are awaiting discovery in herbaria. Robust automatic species identification algorithms using machine learning could accelerate species discovery.

   To encourage the development of an automatic species identification algorithm, we submitted our Herbarium 2019 data set to the Fine‐Grained Visual Categorization sub‐competition (FGVC6) hosted on the Kaggle platform. We chose to focus on the flowering plant family Melastomataceae because we have a large collection of imaged herbarium specimens (46,469 specimens representing 683 species) and taxonomic expertise in the family. As is common for herbarium collections, some species in this data set are represented by few specimens and others by many.

   In less than three months, the FGVC6 Herbarium 2019 Challenge drew 22 teams who entered 254 models for Melastomataceae species identification. The four best algorithms identified species with >88% accuracy.

   The FGVC competitions provide a unique opportunity for computer vision and machine learning experts to address difficult species‐recognition problems. The Herbarium 2019 Challenge brought together a novel combination of collections resources, taxonomic expertise, and collaboration between botanists and computer scientists.

    

   more » « less
5. The colonial legacy of herbaria

   https://doi.org/2021.2010.2027.466174  

   Park ; D. S. ; Feng ; X. ; Akiyama ; S. ; Ardiyani ; M. ; Avendaño ; N. ; et al ( November 2021 , bioRxiv)

   Herbarium collections shape our understanding of the world’s flora and are crucial for addressing global change and biodiversity conservation. The formation of such natural history collections, however, are not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the global North, the extent of this disparity has not been rigorously quantified to date. Here, by analyzing over 85 million specimen records and surveying herbaria across the globe, we assess the colonial legacy of botanical collections and how we may move towards a more inclusive future. We demonstrate that colonial exploitation has contributed to an inverse relationship between where plant biodiversity exists in nature and where it is housed in herbaria. Such disparities persist in herbaria across physical and digital realms despite overt colonialism having ended over half a century ago, suggesting ongoing digitization and decolonization efforts have yet to alleviate colonial-era discrepancies. We emphasize the need for acknowledging the inconvenient history of herbarium collections and the implementation of a more equitable, global paradigm for their collection, curation, and use. 

   more » « less