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Unlocking historical plant interactions in herbarium collections

Nature Reviews Biodiversity volume 1, pages 627–643 (2025)Cite this article

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Abstract

Herbaria have a rich history dating back to the sixteenth century and have grown over time to house specimens that represent global plant diversity. Although herbaria have been the foundation for research in plant taxonomy and systematics, their use has expanded to include fundamental ecological disciplines, such as species interactions. Plants engage with other organisms in a complex web of interactions, which can be mutually beneficial (such as pollination) or competitive or consumptive (such as herbivory, pathogen attacks or competition with other plants for limited resources). Understanding the long-term trends of these species interactions requires historical data, which might best be obtained from herbarium specimens. Herbarium specimens are increasingly being used to study long-term trends in plant biotic interactions, and new developments in genomic methodologies are further expanding the use of herbarium specimens for studying plant interactions across time and space. These approaches enable targeted sequencing of highly degraded DNA. Climate change might be disrupting these interactions in a way that can lead to loss of beneficial interactions in favour of antagonistic interactions, which can potentially reduce the functioning of biodiversity at regional scales.

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Fig. 1: Global distribution and historical proliferation of active herbaria.
Fig. 2: Investigating herbivory and plant defence strategies using herbarium specimens.
Fig. 3: Investigating historical plant–pollinator interactions and temporal mismatches using herbarium specimens.
Fig. 4: Investigating historical plant–microorganism interactions using herbarium specimens.
Fig. 5: Investigating past plant competition using herbarium specimens.
Fig. 6: A framework for analysing plant competition using herbarium specimens, imaging and computer vision.

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Acknowledgements

The authors thank Stanford University for logistical support. B.H.D. was supported by grants from the US National Science Foundation (awards 2345994 and 2416314) and Alfred P. Sloan Foundation.

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Authors and Affiliations

  1. Department of Biology, Stanford University, Stanford, CA, USA

    Barnabas H. Daru

  2. Department of Plant Sciences, Gombe State University, Tudun Wada, Nigeria

    Daniel A. Zhigila

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The study was conceived and designed by B.H.D. The manuscript was written and revised by B.H.D. and D.A.Z. Final approval of the submitted version: B.H.D. and D.A.Z.

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Glossary

Allelopathy

The chemical inhibition of one plant by another through the release of allelochemicals into the environment.

Climate change

Long-term shifts in temperature, precipitation and other climate variables that affect plant distribution, growth, reproduction and survival.

Competition

A non-trophic interaction between either individuals of different species (interspecific) or those of a single species (intraspecific) for shared resources. Plants compete for water, nutrients and space and for access to light and mates.

Fungal endophytes

Fungi that live within plant tissues without causing harm to the host.

Herbarium

A collection or repository of preserved plant specimens that are typically dried, mounted on sheets and labelled with metadata. Herbaria often include type specimens, which are the reference examples of formally described species.

Herbivory

The ecological interaction in which animals, known as herbivores, feed on plants. This process can involve the consumption of any part of the plant, including leaves, stems, roots, seeds or fruits.

Invasive species

A non-native organism that is introduced into a new environment, in which it establishes, spreads rapidly and causes harm to native ecosystems, biodiversity, human health or the economy.

Metabarcoding

A DNA-based method that uses universal genetic markers to identify multiple species within a mixed environmental sample.

Microorganisms

Microscopic organisms, including bacteria, fungi and protists.

Nematodes

A microscopic, worm-like organism that is found in a wide range of environments. Nematodes can be free-living or parasitic and are important in soil health, nutrient cycling and the regulation of plant and insect populations.

Pathogens

Organisms, typically microorganisms such as fungi, bacteria and viruses, that cause diseases in multicellular organisms, such as plants.

Phenology

The study of the timing of cyclical and seasonal events, particularly in relation to climate and plant and animal life cycles.

Pollination

The process by which pollen is transferred from the male reproductive organs (anthers) to the female reproductive organs (stigma) of a flower of the same species to enable fertilization and the production of seeds.

Pollination syndromes

Flower traits, such as colour, shape, scent and nectar, that have evolved in response to natural selection by specific pollinators.

Secondary metabolites

Organic compounds produced by plants that are not directly involved in growth or reproduction but serve ecological functions, such as defence.

Species interaction

The various relationships between living organisms in an ecosystem. For plants, this can include interactions with herbivores (grazing), pollinators and microbial partners, such as mycorrhizal fungi.

Symbiosis

A close and often long-term interaction between two species.

Systematics

The study of the diversity of organisms and their evolutionary relationships; includes both evolutionary history (phylogenetics) and taxonomy.

Taxonomy

The branch of science concerned with the classification, naming and identification of organisms, including their biology. Taxonomy involves organizing organisms into a hierarchical system of groups (taxa) based on shared characteristics, from domain to species level, to reflect their evolutionary relationships.

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Daru, B.H., Zhigila, D.A. Unlocking historical plant interactions in herbarium collections. Nat. Rev. Biodivers. 1, 627–643 (2025). https://doi.org/10.1038/s44358-025-00071-8

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