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Wilf P. Osmoxylon-like fossils from early Eocene South America: West Gondwana-Malesia connections in Araliaceae. AMERICAN JOURNAL OF BOTANY 2025:e70045. [PMID: 40387275 DOI: 10.1002/ajb2.70045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Revised: 03/28/2025] [Accepted: 03/28/2025] [Indexed: 05/20/2025]
Abstract
PREMISE Araliaceae comprise a moderately diverse, predominantly tropical angiosperm family with a limited fossil record. Gondwanan history of Araliaceae is hypothesized in the literature, but no fossils have previously been reported from the former supercontinent. METHODS I describe large (to macrophyll size), palmately compound-lobed leaf fossils and an isolated umbellate infructescence from the early Eocene (52 Ma), late-Gondwanan paleorainforest flora at Laguna del Hunco in Argentine Patagonia. RESULTS The leaf fossils are assigned to Caffapanax canessae gen. et sp. nov. (Araliaceae). Comparable living species belong to five genera that are primarily distributed from Malesia to South China. The most similar genus is Osmoxylon, which is centered in east Malesia and includes numerous threatened species. The infructescence is assigned to Davidsaralia christophae gen. et sp. nov. (Araliaceae) and is also comparable to Osmoxylon. CONCLUSIONS The Caffapanax leaves and Davidsaralia infructescence, potentially representing the same source taxon, are the oldest araliaceous macrofossils and provide direct evidence of Gondwanan history in the family. The new fossils and their large leaves enrich the well-established biogeographic and climatic affinities of the fossil assemblage with imperiled Indo-Pacific, everwet tropical rainforests. The fossils most likely represent shrubs or small trees, adding to the rich record of understory vegetation recovered from Laguna del Hunco.
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Affiliation(s)
- Peter Wilf
- Department of Geosciences and Earth and Environmental Systems Institute, Pennsylvania State University, University Park, 16802, PA, USA
- IUCN/SSC Global Tree Specialist Group, Botanic Gardens Conservation International, Richmond TW9 3BW, UK
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2
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Ahlstrand NI, Primack RB, Austin MW, Panchen ZA, Römermann C, Miller-Rushing AJ. The promise of digital herbarium specimens in large-scale phenology research. THE NEW PHYTOLOGIST 2025. [PMID: 40384489 DOI: 10.1111/nph.70178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2024] [Accepted: 04/08/2025] [Indexed: 05/20/2025]
Abstract
The online mobilization of herbaria has made tens of millions of specimens digitally available, revolutionizing investigations of phenology and plant responses to climate change. We identify two main themes associated with this growing body of research and highlight a selection of recent publications exemplifying: investigating phenology at large spatial and temporal scales and in understudied locations and testing long-standing theories and novel questions in ecology and evolution that were not previously answerable. We explore strengths and limitations of using digitized herbarium specimens in phenology research, including: issues of sampling; reliability, transferability, and biases; and ethical and social justice considerations. This field will see further breakthroughs as herbaria around the world continue to mobilize and digitally interlink their collections. New developments will likely come from advances in technology, international collaborations, and including understudied plant taxa and regions such as the Arctic and the tropics. Advances in technology are already improving digitization workflows and speeding the collection of phenology data from digital specimens.
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Affiliation(s)
| | | | | | - Zoe A Panchen
- Department of Biology, Acadia University, Wolfville, NS, B4P 2R6, Canada
| | - Christine Römermann
- Plant Biodiversity, Friedrich Schiller University Jena, Jena, 07743, Germany
- Senckenberg Institute for Plant Form and Function (SIP), Jena, 07743, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle- Jena- Leipzig, Leipzig, 04103, Germany
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3
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Yuan Y, Feng Y, Wang J, Ulah F, Yuan M, Gao Y. Integrative Taxonomy for Species Delimitation: A Case Study in Two Widely Accepted Yet Morphologically Confounding Rosa Species Within Sect. Pimpinellifoliae (Rosaceae). Mol Ecol 2025:e17779. [PMID: 40285506 DOI: 10.1111/mec.17779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2025] [Revised: 04/09/2025] [Accepted: 04/14/2025] [Indexed: 04/29/2025]
Abstract
The use of morphological traits as a practical approach for delimiting taxa at various ranks has long been regarded as a reliable basis for taxonomy. However, its efficacy has been increasingly called into question in many taxonomic groups due to its inherent limitations, such as failing to account for phenotypic plasticity, ecologically driven variation (e.g., ecotypes), and parallel evolution. These factors often introduce ambiguity or misleading similarities, thereby obscuring the true evolutionary relationships among taxa, particularly in the context of species delimitation. In the present study, we employ an integrated methodology that combines quantitative morphological analyses, whole-genome data, and ecological measurements to resolve the species boundaries of two morphologically similar roses, Rosa sericea and Rosa hugonis, which have long been considered as two distinct species but lack clear morphological boundaries. Our findings reveal that the unbiased analysis of morphological data based on a large and representative sample size was insufficient to identify effective diagnostic traits. However, when complemented with genome-wide population-level sequencing data or integrated with geographic and ecological niche assessments, the delineation of species boundaries was significantly improved. Furthermore, ecological data provide additional insight into the abiotic factors driving interspecific and intraspecific divergence. By integrating multiple lines of evidence-spanning genomic (intrinsic) and phenotypic (extrinsic) traits-and incorporating the interaction between species and their environments, species boundaries can be delineated with greater confidence. A well-defined species can thus be established through the mutual corroboration of diverse datasets, thereby ensuring a more rigorous and comprehensive taxonomic framework.
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Affiliation(s)
- Yumei Yuan
- Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Feng
- Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Jingbo Wang
- Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Fazal Ulah
- College of Life Sciences, Northwest Normal University, Lanzhou, China
| | - Meng Yuan
- Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yundong Gao
- Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
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4
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Kartzinel TR, Hoff HK, Divoll TJ, Littleford-Colquhoun BL, Anderson H, Burak MK, Kuzmina ML, Musili PM, Rogers H, Troncoso AJ, Kartzinel RY. Global Availability of Plant DNA Barcodes as Genomic Resources to Support Basic and Policy-Relevant Biodiversity Research. Mol Ecol 2025; 34:e17712. [PMID: 40018971 DOI: 10.1111/mec.17712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 02/15/2025] [Accepted: 02/19/2025] [Indexed: 03/01/2025]
Abstract
Genetic technologies such as DNA barcoding make it easier and less expensive to monitor biodiversity and its associated ecosystem services, particularly in biodiversity hotspots where traditional assessments are challenging. Successful use of these data-driven technologies, however, requires access to appropriate reference data. We reviewed the >373,584 reference plant DNA barcodes in public repositories and found that they cumulatively cover a remarkable quarter of the ~435,000 extant land plant species (Embryophyta). Nevertheless, coverage gaps in tropical biodiversity hotspots reflect well-documented biases in biodiversity science - most reference specimens originated in the Global North. Currently, at least 17% of plant families lack any reference barcode data whatsoever, affecting tropical and temperate regions alike. Investigators often emphasise the importance of marker choice and the need to ensure protocols are technically capable of detecting and identifying a broad range of taxa. Yet persistent geographic and taxonomic gaps in the reference datasets show that these protocols rely upon risk undermining all downstream applications of the strategy, ranging from basic biodiversity monitoring to policy-relevant objectives - such as the forensic authentication of materials in illegal trade. Future networks of investigators could work strategically to improve data coverage, which will be essential in global efforts to conserve biodiversity while advancing more fair and equitable access to benefits arising from genetic resources.
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Affiliation(s)
- Tyler R Kartzinel
- Department of Ecology, Evolution, & Organismal Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Hannah K Hoff
- Department of Ecology, Evolution, & Organismal Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Timothy J Divoll
- Center for Computation and Visualization, Brown University, Providence, Rhode Island, USA
| | - Bethan L Littleford-Colquhoun
- Department of Ecology, Evolution, & Organismal Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Heidi Anderson
- Yellowstone Center for Resources, Yellowstone National Park, Mammoth Hot Springs, Wyoming, USA
| | - Mary K Burak
- Department of Ecology, Evolution, & Organismal Biology, Brown University, Providence, Rhode Island, USA
- Institute at Brown for Environment and Society, Brown University, Providence, Rhode Island, USA
| | - Maria L Kuzmina
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Ontario, Canada
| | - Paul M Musili
- Botany Department, National Museums of Kenya, Nairobi, Kenya
| | - Haldre Rogers
- Department of Fish and Wildlife Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Alejandra J Troncoso
- Instituto de Ecología y Biodiversidad (IEB), Santiago, Chile
- Departamento de Biología, Universidad de La Serena, La Serena, Chile
| | - Rebecca Y Kartzinel
- Department of Ecology, Evolution, & Organismal Biology, Brown University, Providence, Rhode Island, USA
- Brown University Herbarium, Brown University, Providence, Rhode Island, USA
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5
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Novikov A, Nachychko V. The digitisation workflow of the herbarium of the State Museum of Natural History of the NAS of Ukraine (LWS). Biodivers Data J 2025; 13:e148861. [PMID: 40190478 PMCID: PMC11971642 DOI: 10.3897/bdj.13.e148861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Accepted: 03/21/2025] [Indexed: 04/09/2025] Open
Abstract
The digitisation workflow currently applied at the Herbarium of the State Museum of Natural History of the National Academy of Sciences of Ukraine (LWS) differs from other similar by cascade ('object-to-data-to-image') multilevel organisation. Its application is predicted by the need to preselect specimens by taxon and region, as well as by batched digitisation, which occurs with significant interruptions. Focusing on certain taxonomic groups from specific regions allows us to digitise specimens that could be more valuable for early scientific processing. At the same time, the herbarium benefits from such a digitisation model by revising the existing collection classification and keeping the initial ID system. The presented digitisation workflow can be easily reproduced in any herbarium with a limited budget. The purpose of this paper is to provide detailed description and schemas of the principal digitisation stages applied at the LWS Herbarium and to briefly discuss the steps crucial for a successful result. Provided information should help to maintain the digitisation and choose appropriate equipment and materials. We can conclude that, despite its general complexity, the described workflow demonstrated itself as viable and relevant due to its robust design and focus on data quality. Despite a focus on specialists' involvement, it maintains flexibility that allows combining volunteers and, if needed, outsourced efforts. Moreover, its modularity promotes independence of principal digitisation stages and allows long interruptions between the digitisation batches.
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Affiliation(s)
- Andriy Novikov
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Viktor Nachychko
- Ivan Franko National University of Lviv, Lviv, UkraineIvan Franko National University of LvivLvivUkraine
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6
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Heberling JM, Isaac BL. Making the most of herbaria. A commentary on 'Integrating datasets from herbarium specimens and images to treat a Neotropical myrtle species complex'. ANNALS OF BOTANY 2025:mcaf001. [PMID: 40100288 DOI: 10.1093/aob/mcaf001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/20/2025]
Affiliation(s)
- J Mason Heberling
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, PA, USA
| | - Bonnie L Isaac
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, PA, USA
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7
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Davis CC, Knapp S. Exploring biodiversity through museomics. Nat Rev Genet 2025; 26:149-150. [PMID: 39506143 DOI: 10.1038/s41576-024-00801-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2024]
Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA, USA.
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8
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Vasconcelos T, Boyko JD. mvh: An R tool to assemble and organize virtual herbaria from openly available specimen images. APPLICATIONS IN PLANT SCIENCES 2025; 13:e11631. [PMID: 40308897 PMCID: PMC12038725 DOI: 10.1002/aps3.11631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 11/13/2024] [Accepted: 11/18/2024] [Indexed: 05/02/2025]
Abstract
Premise Recent advances in imaging herbarium specimens have enhanced their use in biodiversity studies. However, user-friendly tools that facilitate the assembly of customized sets of herbarium specimen images on personal devices are still lacking. Methods and Results Here we present the R package mvh ("my virtual herbarium"), which includes functions designed to search and download metadata and openly available images associated with herbarium specimens based on taxon or geography. We tested the functionalities of mvh by searching metadata associated with five sets of 10 vascular plant species and five sets of 10 terrestrial coordinates. The download function had a success rate of 99%, downloading 291 out of the 293 images found in the search. Possible reasons for download failure are discussed. Conclusions As long as an internet connection is available, mvh simplifies the assembly and organization of virtual herbaria, thereby facilitating the investigation of novel empirical questions as well as trends in digitization efforts.
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Affiliation(s)
- Thais Vasconcelos
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn Arbor48109MichiganUSA
- University of Michigan Herbarium, University of MichiganAnn Arbor48108MichiganUSA
| | - James D. Boyko
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn Arbor48109MichiganUSA
- Michigan Institute of Data ScienceUniversity of MichiganAnn Arbor48109MichiganUSA
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9
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Davis CC, Sessa E, Paton A, Antonelli A, Teisher JK. Guidelines for the effective and ethical sampling of herbaria. Nat Ecol Evol 2025; 9:196-203. [PMID: 39333397 DOI: 10.1038/s41559-024-02544-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Accepted: 08/08/2024] [Indexed: 09/29/2024]
Abstract
The use of herbaria for science and conservation is enabling greatly enhanced scopes and scales of discovery, exploration and protection of biodiversity. The availability of digital, open-access herbarium data is, perhaps counter-intuitively, expanding the use of physical collections by researchers who use digital collections to find specimens and then sample physical collections for multiomics investigations, including genomics, transcriptomics, metabolomics, proteomics and microbiomics. These investigations are leading to new scientific insights and supporting the development of conservation actions, but they come with a substantial cost: the partial or complete destruction of often irreplaceable specimens, which constitute a global heritage that should be permanently safeguarded for future reference. Here we provide a set of recommended best practices for the sustainable, equitable and ethical sampling of herbarium specimens. Our recommendations are intended for two complementary and partially overlapping audiences-users and stewards-who together build, use and protect herbarium collections.
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Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA, USA.
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.
- Missouri Botanical Garden, St. Louis, MO, USA.
| | - Emily Sessa
- New York Botanical Garden, New York, NY, USA
| | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, London, UK
- Gothenburg Global Biodiversity Centre, Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Oxford, Oxford, UK
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10
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Rosche C, Broennimann O, Novikov A, Mrázová V, Boiko GV, Danihelka J, Gastner MT, Guisan A, Kožić K, Lehnert M, Müller‐Schärer H, Nagy DU, Remelgado R, Ronikier M, Selke JA, Shiyan NM, Suchan T, Thoma AE, Zdvořák P, Mráz P. Herbarium specimens reveal a cryptic invasion of polyploid Centaurea stoebe in Europe. THE NEW PHYTOLOGIST 2025; 245:392-405. [PMID: 39439296 PMCID: PMC11617643 DOI: 10.1111/nph.20212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Accepted: 10/01/2024] [Indexed: 10/25/2024]
Abstract
Numerous plant species are expanding their native ranges due to anthropogenic environmental change. Because cytotypes of polyploid complexes often show similar morphologies, there may be unnoticed range expansions (i.e. cryptic invasions) of one cytotype into regions where only the other cytotype is native. We critically revised herbarium specimens of diploid and tetraploid Centaurea stoebe, collected across Europe between 1790 and 2023. Based on their distribution in natural and relict habitats and phylogeographic data, we estimated the native ranges of both cytotypes. Diploids are native across their entire European range, whereas tetraploids are native only to South-Eastern Europe and have recently expanded their range toward Central Europe. The proportion of tetraploids has exponentially increased over time in their expanded but not in their native range. This cryptic invasion predominantly occurred in ruderal habitats and enlarged the climatic niche of tetraploids toward a more oceanic climate. We conclude that spatio-temporally explicit assessments of range shifts, habitat preferences and niche evolution can improve our understanding of cryptic invasions. We also emphasize the value of herbarium specimens for accurate estimation of species´ native ranges, with fundamental implications for the design of research studies and the assessment of biodiversity trends.
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Affiliation(s)
- Christoph Rosche
- Institute of GeobotanyMartin Luther University Halle‐WittenbergHalle06108Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzig04103Germany
| | - Olivier Broennimann
- Department of Ecology and EvolutionUniversity of LausanneLausanne1015Switzerland
- Institute of Earth Surface DynamicsUniversity of LausanneLausanne1015Switzerland
| | - Andriy Novikov
- State Museum of Natural History, National Academy of Sciences of UkraineLviv79008Ukraine
| | - Viera Mrázová
- Department of BotanyCharles UniversityPrague12801Czech Republic
| | - Ganna V. Boiko
- M.G. Kholodny Institute of Botany, National Academy of Sciences of UkraineKyiv01601Ukraine
| | - Jiří Danihelka
- Department of Botany and ZoologyMasaryk UniversityBrno60200Czech Republic
- Institute of Botany, Czech Academy of SciencesPrůhonice25243Czech Republic
| | - Michael T. Gastner
- Information and Communication Technology ClusterSingapore Institute of TechnologySingapore828608Singapore
| | - Antoine Guisan
- Department of Ecology and EvolutionUniversity of LausanneLausanne1015Switzerland
- Institute of Earth Surface DynamicsUniversity of LausanneLausanne1015Switzerland
| | - Kevin Kožić
- Institute of GeobotanyMartin Luther University Halle‐WittenbergHalle06108Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzig04103Germany
| | - Marcus Lehnert
- Institute of GeobotanyMartin Luther University Halle‐WittenbergHalle06108Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzig04103Germany
| | - Heinz Müller‐Schärer
- Department of BiologyUniversity of FribourgFribourg1700Switzerland
- College of Resources & EnvironmentHuazhong Agricultural UniversityWuhan430070China
| | - Dávid U. Nagy
- Institute of GeobotanyMartin Luther University Halle‐WittenbergHalle06108Germany
| | - Ruben Remelgado
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzig04103Germany
| | - Michał Ronikier
- W. Szafer Institute of Botany, Polish Academy of SciencesKraków31‐512Poland
| | - Julian A. Selke
- Institute of GeobotanyMartin Luther University Halle‐WittenbergHalle06108Germany
- Faculty of Informatics and Data ScienceUniversity of RegensburgRegensburg93040Germany
| | - Natalia M. Shiyan
- M.G. Kholodny Institute of Botany, National Academy of Sciences of UkraineKyiv01601Ukraine
| | - Tomasz Suchan
- W. Szafer Institute of Botany, Polish Academy of SciencesKraków31‐512Poland
| | - Arpad E. Thoma
- Institute of GeobotanyMartin Luther University Halle‐WittenbergHalle06108Germany
| | - Pavel Zdvořák
- Herbarium collectionsCharles UniversityPrague12801Czech Republic
| | - Patrik Mráz
- Department of BotanyCharles UniversityPrague12801Czech Republic
- Herbarium collectionsCharles UniversityPrague12801Czech Republic
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Tyszka AS, Larson DA, Walker JF. Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life. TRENDS IN PLANT SCIENCE 2024:S1360-1385(24)00305-4. [PMID: 39613559 DOI: 10.1016/j.tplants.2024.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 10/22/2024] [Accepted: 11/04/2024] [Indexed: 12/01/2024]
Abstract
Recent studies have demonstrated that it is a misconception that transcriptome sequencing requires tissue preserved at ultracold temperatures. Here, we outline the potential origins of this misconception and its possible role in biasing the geographic distribution of published plant transcriptomes. We highlight the importance of ensuring diverse sampling by providing an overview of the questions that transcriptomes can answer about the forces shaping the plant tree of life. We discuss how broadening transcriptome sequencing to include existing specimens will allow the field to grow and more fully utilize biological collections. We hope this article encourages the expansion of the current trend in 'herbariomics' research to include whole-transcriptome sequencing of historical RNA.
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Affiliation(s)
- Alexa S Tyszka
- Department of Biological Sciences, The University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Drew A Larson
- Department of Biology, Indiana University, Bloomington, IN 47405, USA.
| | - Joseph F Walker
- Department of Biological Sciences, The University of Illinois at Chicago, Chicago, IL 60607, USA.
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12
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Sadek J, Vlachidis A, Pickering V, Humbel M, Metilli D, Carine M, Nyhan J. Leveraging OCR and HTR cloud services towards data mobilisation of historical plant names. INTERNATIONAL JOURNAL OF DIGITAL HUMANITIES 2024; 6:237-261. [PMID: 40438136 PMCID: PMC12106164 DOI: 10.1007/s42803-024-00091-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 10/28/2024] [Indexed: 06/01/2025]
Abstract
We present our solution to the problem of how to mobilise (that is, extract and enrich) digital data from the analogue, printed book version Sir Hans Sloane's copy of John Ray's Historia Plantarum, to create the first searchable facility of its kind to the plants contained in the Sloane Herbarium, housed in the National History Museum UK. The data mobilisation workflow presented here enables the automatic detection of printed and handwritten marginalia text and annotations in Sir Hans Sloane" personal copy of John Ray's Historia Plantarum. The rationale of adopting AWS Amazon's Textract service and the development of a specialised information extraction workflow for mobilising printed text and handwritten annotations is discussed. Testing of our workflow demonstrates the need for human-checking of outputs to ensure the accuracy of a large set of structured data comprising 7600 plant names and 4540 handwritten marginalia annotation. The links we have created serve as the first digital index to Sloan's Herbarium, a unique development in the longer analogue and digital format-history of these resources.
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Affiliation(s)
- Jawad Sadek
- Department of Information Studies, University College London, London, UK
| | - Andreas Vlachidis
- Department of Information Studies, University College London, London, UK
| | | | - Marco Humbel
- Department of Information Studies, University College London, London, UK
- Technische Universität Darmstadt, Darmstadt, Germany
| | - Daniele Metilli
- Department of Information Studies, University College London, London, UK
| | | | - Julianne Nyhan
- Department of Information Studies, University College London, London, UK
- Technische Universität Darmstadt, Darmstadt, Germany
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13
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Hightower AT, Chitwood DH, Josephs EB. Herbarium specimens reveal links between leaf shape of Capsella bursa-pastoris and climate. AMERICAN JOURNAL OF BOTANY 2024; 111:e16435. [PMID: 39503350 PMCID: PMC11584044 DOI: 10.1002/ajb2.16435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Revised: 08/02/2024] [Accepted: 08/05/2024] [Indexed: 11/13/2024]
Abstract
PREMISE Studies into the evolution and development of leaf shape have connected variation in plant form, function, and fitness. For species with consistent leaf margin features, patterns in leaf architecture are related to both biotic and abiotic factors. However, for species with inconsistent leaf shapes, quantifying variation in leaf shape and the effects of environmental factors on leaf shape has proven challenging. METHODS To investigate leaf shape variation in a species with inconsistently shaped leaves, we used geometric morphometric modeling and deterministic techniques to analyze approximately 500 digitized specimens of Capsella bursa-pastoris collected throughout the continental United States over 100 years. We generated a morphospace of the leaf shapes and modeled leaf shape as a function of environment and time. RESULTS Leaf shape variation of C. bursa-pastoris was strongly associated with temperature over its growing season, with lobing decreasing as temperature increased. While we expected to see changes in variation over time, our results show that the level of leaf shape variation was consistent over the 100 years. CONCLUSIONS Our findings showed that species with inconsistent leaf shape variation can be quantified using geometric morphometric modeling techniques and that temperature is the main environmental factor influencing leaf shape variation.
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Affiliation(s)
- Asia T Hightower
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, 48824-1226, MI, USA
- Ecology, Evolution, & Behavior Program, Michigan State University, 567 Wilson Road, East Lansing, 48824-1226, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, 48824-1226, MI, USA
| | - Daniel H Chitwood
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, 48824-1226, MI, USA
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, 428 S. Shaw Lane, East Lansing, 48824-1226, MI, USA
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, 612 Wilson Road, East Lansing, 48824-1226, MI, USA
- Ecology, Evolution, & Behavior Program, Michigan State University, 567 Wilson Road, East Lansing, 48824-1226, MI, USA
- Plant Resilience Institute, Michigan State University, East Lansing, 48824-1226, MI, USA
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Eckert I, Bruneau A, Metsger DA, Joly S, Dickinson TA, Pollock LJ. Herbarium collections remain essential in the age of community science. Nat Commun 2024; 15:7586. [PMID: 39217174 PMCID: PMC11366035 DOI: 10.1038/s41467-024-51899-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024] Open
Abstract
The past decade has yielded more biodiversity observations from community science than the past century of traditional scientific collection. This rapid influx of data is promising for overcoming critical biodiversity data shortfalls, but we also have vast untapped resources held in undigitized natural history collections. Yet, the ability of these undigitized collections to fill data gaps, especially compared against the constant accumulation of community science data, remains unclear. Here, we compare how well community science (iNaturalist) observations and digitized herbarium specimens represent the diversity, distributions, and modeling needs of vascular plants in Canada. We find that, despite having only a third as many records, herbarium specimens capture more taxonomic, phylogenetic, and functional diversity and more efficiently capture species' environmental niches. As such, the digitization of Canada's 7.3M remaining specimens has the potential to more than quintuple our ability to model biodiversity. In contrast, it would require over 27M more iNaturalist observations to produce similar benefits. Our findings indicate that digitizing Earth's remaining herbarium specimens is likely an efficient, feasible, and potentially critical investment when it comes to improving our ability to predict and protect biodiversity into the future.
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Affiliation(s)
- Isaac Eckert
- Department of Biology, McGill University, Montréal, QC, Canada.
- Québec Centre for Biodiversity Science, Montréal, QC, Canada.
| | - Anne Bruneau
- Québec Centre for Biodiversity Science, Montréal, QC, Canada
- Institut de recherche en biologie végétale & Département de Sciences biologiques, Université de Montréal, Montréal, QC, Canada
| | - Deborah A Metsger
- Green Plant Herbarium, Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
| | - Simon Joly
- Institut de recherche en biologie végétale & Département de Sciences biologiques, Université de Montréal, Montréal, QC, Canada
- Montreal Botanical Garden, Montréal, QC, Canada
| | - T A Dickinson
- Green Plant Herbarium, Department of Natural History, Royal Ontario Museum, Toronto, ON, Canada
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Laura J Pollock
- Department of Biology, McGill University, Montréal, QC, Canada
- Québec Centre for Biodiversity Science, Montréal, QC, Canada
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15
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Edwards EJ, Mishler BD, Davis CD. University herbaria are uniquely important. TRENDS IN PLANT SCIENCE 2024; 29:825-826. [PMID: 38937215 DOI: 10.1016/j.tplants.2024.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/29/2024]
Abstract
University herbaria play critical roles in biodiversity research and training and provide interdisciplinary academic environments that foster innovative uses of natural history collections. Universities have a responsibility to steward these important collections in perpetuity, in alignment with their academic missions and for the good of science and society.
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Affiliation(s)
- Erika J Edwards
- Department of Ecology & Evolutionary Biology, Yale University Herbarium, Yale University, PO Box 208105, New Haven, CT 06520, USA.
| | - Brent D Mishler
- Department of Integrative Biology, University and Jepson Herbaria, University of California, 1001 Valley Life Science Building #2465, Berkeley, CA 94720, USA.
| | - Charles D Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA.
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16
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Haswell ES. What's in a name? NATURE PLANTS 2024; 10:692. [PMID: 38671076 DOI: 10.1038/s41477-024-01687-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
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17
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Jones CB, Stock K, Perkins SE. AI-based discovery of habitats from museum collections. Trends Ecol Evol 2024; 39:323-327. [PMID: 38355366 DOI: 10.1016/j.tree.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Museum collection records are a source of historic data for species occurrence, but little attention is paid to the associated descriptions of habitat at the sample locations. We propose that artificial intelligence methods have potential to use these descriptions for reconstructing past habitat, to address ecological and evolutionary questions.
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Affiliation(s)
- Christopher B Jones
- School of Computer Science and Informatics, Cardiff University, Cardiff, UK.
| | - Kristin Stock
- Massey Geoinformatics Collaboratory, Massey University, Palmerston North, New Zealand
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18
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Wu R, Zou Y, Liao S, Shi K, Nan X, Yan H, Luo J, Xiang Z, Bao Z. Shall we promote natural history collection today?-Answered by reviewing Ernest Henry Wilson's plant collection process in China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 915:170179. [PMID: 38246391 DOI: 10.1016/j.scitotenv.2024.170179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/20/2023] [Accepted: 01/13/2024] [Indexed: 01/23/2024]
Abstract
Plant diversity exploration needs to be accelerated because many species will go extinct before their discovery and description, and many species-rich regions remain poorly studied. However, most contemporary plant collections prefer to focus on a specific group, which hinders the exploration and conservation of plant diversity. Therefore, we need an alternative approach to the dilemma at hand. The comprehensive Natural History Collection (NHC), which existed throughout the pinnacle of biodiversity exploration in the 20th century could be considered. We explore Ernest Henry Wilson's (one of the most successful naturalists in the 20th) plant collections in China as a case to illustrate the advantages of NHC and discuss whether NHC deserves to be promoted again today. From multiple sources, we gathered 19,218 available specimen records of 11,884 collecting numbers assigned and analyzed the collected species, the collection's nature, and restored four routes of his explorations. Results reveal that Wilson's specimens were collected from 28 prefecture-level cities and 38 county-level regions of 7 provinces or municipalities, they belong to 200 families, 1046 genera, 3794 species, and 342 infraspecific taxa, approximately 41 %, 22 %, 10 %, 5 % of Chinese plant families, genera, species, and infraspecific taxa respectively. The Wilson case study shows that NHC is particularly effective in emphasizing species discovery and conservation, recording ecological information, understanding a region's flora, and developing landscape applications. Therefore, we strongly advocate for the expansion of natural history collections in species-rich regions. Furthermore, we recommend the employment of specialized collectors, the enlistment of international cooperation, and the standardization of guidelines for future NHCs.
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Affiliation(s)
- Renwu Wu
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China.
| | - Yongxi Zou
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Shuai Liao
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ke Shi
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinge Nan
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Hai Yan
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Jifan Luo
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhoubing Xiang
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhiyi Bao
- College of Landscape Architecture, Zhejiang A&F University, Hangzhou 311300, China
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19
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Hightower AT, Chitwood DH, Josephs EB. Herbarium specimens reveal links between Capsella bursa-pastoris leaf shape and climate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580180. [PMID: 38405842 PMCID: PMC10888959 DOI: 10.1101/2024.02.13.580180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Studies into the evolution and development of leaf shape have connected variation in plant form, function, and fitness. For species with consistent leaf margin features, patterns in leaf architecture are related to both biotic and abiotic factors. However, for species with inconsistent leaf margin features, quantifying leaf shape variation and the effects of environmental factors on leaf shape has proven challenging. To investigate leaf shape variation in species with inconsistent shapes, we analyzed approximately 500 digitized Capsella bursa-pastoris specimens collected throughout the continental U.S. over a 100-year period with geometric morphometric modeling and deterministic techniques. We generated a morphospace of C. bursa-pastoris leaf shapes and modeled leaf shape as a function of environment and time. Our results suggest C. bursa-pastoris leaf shape variation is strongly associated with temperature over the C. bursa-pastoris growing season, with lobing decreasing as temperature increases. While we expected to see changes in variation over time, our results show that level of leaf shape variation is consistent over the 100-year period. Our findings showed that species with inconsistent leaf shape variation can be quantified using geometric morphometric modeling techniques and that temperature is the main environmental factor influencing leaf shape variation.
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Affiliation(s)
- Asia T Hightower
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824-1226
- Ecology, Evolution, & Behavior Program, Michigan State University, 567 Wilson Rd, East Lansing, MI 48824-1226
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824-1226
| | - Daniel H Chitwood
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824-1226
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, 428 S Shaw Ln, East Lansing, MI 48824-1226
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824-1226
- Ecology, Evolution, & Behavior Program, Michigan State University, 567 Wilson Rd, East Lansing, MI 48824-1226
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824-1226
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20
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Vieira TL, Barbosa-Silva RG, Acosta AL, van den Berg C. Expanding the Distribution of Prosthechea jauana (Orchidaceae) in the Pantepui and Highlighting the Urgent Need for Conservation Strategies in the Region in Face of Climate Change. PLANTS (BASEL, SWITZERLAND) 2024; 13:222. [PMID: 38256775 PMCID: PMC10820582 DOI: 10.3390/plants13020222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/08/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024]
Abstract
Prosthechea jauana has been recognized as an orchid species endemic to the Venezuelan tepui. The first record of P. jauana in Brazil is presented here, also from a tepui in the Southern phytogeographical district of Pantepui in the Serra do Aracá, at the northern border of the Amazonas state. A detailed morphological description and images of the specimen are presented, as well as an updated distribution map, preliminary conservation status assessment, and taxonomic notes about the species. In addition, we provide species' distribution models for P. jauana based on current and future bioclimatic data. Future projections suggest that the geographic distribution of P. jauana will likely be severely affected, with ~79% of its suitable habitat being reduced by 2041-2060 and ~92% by 2061-2080. Prosthechea jauana could represent a flag species and an example of how climate change may affect the endemic Pantepui flora.
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Affiliation(s)
- Tiago L. Vieira
- Harvard University Herbaria, Department of Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Rafael G. Barbosa-Silva
- Biodiversity and Ecosystem Services, Instituto Tecnológico Vale Desenvolvimento Sustentável, Belém 66055-090, Pará, Brazil; (R.G.B.-S.); (A.L.A.)
- Coordenacão Botânica, Museu Paraense Emílio Goeldi, Belém 66077-830, Pará, Brazil
| | - André L. Acosta
- Biodiversity and Ecosystem Services, Instituto Tecnológico Vale Desenvolvimento Sustentável, Belém 66055-090, Pará, Brazil; (R.G.B.-S.); (A.L.A.)
| | - Cássio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana 44036-246, Bahia, Brazil;
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21
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Novikov A, Savytska A, Kuzyarin O, Nachychko V, Susulovska S, Rizun V, Susulovsky A, Hushtan H, Hushtan K, Leleka D. Data mobilisation in the LWS Herbarium: success and prospects. Biodivers Data J 2024; 12:e117292. [PMID: 38249570 PMCID: PMC10797612 DOI: 10.3897/bdj.12.e117292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/08/2024] [Indexed: 01/23/2024] Open
Abstract
Background Digitisation of hosted specimens is a crucial task for all herbaria worldwide and is one of the main streams for today. By digitising their collections and publishing the datasets, the herbaria grant access to essential data to a wide research audience and, as a result, involve their collections in scientific work more actively. Digitisation also allows virtual preservation of the collections, which is especially important in conditions of hostilities, when the entire collection can be destroyed or damaged in one moment. This paper describes two datasets recently published in GBIF in the framework of the LWS herbarium digitisation initiative. It also contains some considerations about further digitisation priorities and plans in the LWS Herbarium in the context of complicated war conditions and limited facilities. New information In total, 2,419 occurrence records from Ukraine mobilised from LWS Herbarium were published. These datasets are planned to be dynamic with the addition of new records along with progress of digitisation work at LWS. At least 6,000 more records are planned to be published through these datasets in 2024.
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Affiliation(s)
- Andriy Novikov
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Anastasiia Savytska
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Oleksandr Kuzyarin
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Viktor Nachychko
- Ivan Franko National University of Lviv, Lviv, UkraineIvan Franko National University of LvivLvivUkraine
| | - Solomia Susulovska
- Ivan Franko National University of Lviv, Lviv, UkraineIvan Franko National University of LvivLvivUkraine
| | - Volodymyr Rizun
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Andrii Susulovsky
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Habriel Hushtan
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Kateryna Hushtan
- State Museum of Natural History of the NAS of Ukraine, Lviv, UkraineState Museum of Natural History of the NAS of UkraineLvivUkraine
| | - Dmytro Leleka
- Institute of Ecology of the Carpathians of the NAS of Ukraine, Lviv, UkraineInstitute of Ecology of the Carpathians of the NAS of UkraineLvivUkraine
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22
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Kim AS, Kreiner JM, Hernández F, Bock DG, Hodgins KA, Rieseberg LH. Temporal collections to study invasion biology. Mol Ecol 2023; 32:6729-6742. [PMID: 37873879 DOI: 10.1111/mec.17176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.
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Affiliation(s)
- Amy S Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia M Kreiner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fernando Hernández
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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23
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Roma-Marzio F, Maccioni S, Dolci D, Astuti G, Magrini N, Pierotti F, Vangelisti R, Amadei L, Peruzzi L. Digitization of the historical Herbarium of Michele Guadagno at Pisa (PI-GUAD). PHYTOKEYS 2023; 234:107-125. [PMID: 37868742 PMCID: PMC10587777 DOI: 10.3897/phytokeys.234.109464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023]
Abstract
The herbarium digitization process is an essential first step in transforming the vast amount of data associated with a physical specimen into flexible digital data formats. In this framework, the Herbarium of the University of Pisa (international code PI), at the end of 2018 started a process of digitization focusing on one of its most relevant collections: the Herbarium of Michele Guadagno (1878-1930). This scholar studied flora and vegetation of different areas of southern Italy, building a large herbarium including specimens collected by himself, plus many specimens obtained through exchanges with Italian and foreign botanists. The Herbarium is composed by 547 packages of vascular plants. Metadata were entered into the online database Virtual Herbaria JACQ and mirrored into a personalized virtual Herbarium of the Botanic Museum. After the completion of the digitization process, the number of sheets preserved in the Herbarium amounts to 44,345. Besides Guadagno, who collected 42% of his specimens, a further 1,102 collectors are represented. Most specimens were collected in Europe (91%), but all the continents are represented. As expected, Italy is the most represented country (59%), followed by France, Spain, Germany, and Greece. The specimens cover a time span of 99 years, from 1830 to 1929, whereas the specimens collected by Guadagno range between 1889 and 1928. Furthermore, we traced 134 herbarium sheets associated with documents, among which 75 drawings handmade by Guadagno, 34 letters from various corresponding authors, 16 copies of publications, and 14 copies of published iconographies.
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Affiliation(s)
- Francesco Roma-Marzio
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Simonetta Maccioni
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - David Dolci
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Giovanni Astuti
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Nicoletta Magrini
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Federica Pierotti
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Roberta Vangelisti
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Lucia Amadei
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Lorenzo Peruzzi
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
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24
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López-Tobar R, Herrera-Feijoo RJ, Mateo RG, García-Robredo F, Torres B. Botanical Collection Patterns and Conservation Categories of the Most Traded Timber Species from the Ecuadorian Amazon: The Role of Protected Areas. PLANTS (BASEL, SWITZERLAND) 2023; 12:3327. [PMID: 37765489 PMCID: PMC10536464 DOI: 10.3390/plants12183327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 09/05/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
The Ecuadorian Amazon is home to a rich biodiversity of woody plant species. Nonetheless, their conservation remains difficult, as some areas remain poorly explored and lack georeferenced records. Therefore, the current study aims predominantly to analyze the collection patterns of timber species in the Amazon lowlands of Ecuador and to evaluate the conservation coverage of these species in protected areas. Furthermore, we try to determine the conservation category of the species according to the criteria of the IUCN Red List. We identified that one third of the timber species in the study area was concentrated in three provinces due to historical botanical expeditions. However, a worrying 22.0% of the species had less than five records of presence, and 29.9% had less than ten records, indicating a possible underestimation of their presence. In addition, almost half of the species evaluated were unprotected, exposing them to deforestation risks and threats. To improve knowledge and conservation of forest biodiversity in the Ecuadorian Amazon, it is recommended to perform new botanical samplings in little-explored areas and digitize data in national herbaria. It is critical to implement automated assessments of the conservation status of species with insufficient data. In addition, it is suggested to use species distribution models to identify optimal areas for forest restoration initiatives. Effective communication of results and collaboration between scientists, governments, and local communities are key to the protection and sustainable management of forest biodiversity in the Amazon region.
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Affiliation(s)
- Rolando López-Tobar
- Facultad de Ciencias Agrarias y Forestales, Universidad Técnica Estatal de Quevedo (UTEQ), Quevedo Av. Quito km, 1 1/2 Vía a Santo Domingo de los Tsáchilas, Quevedo 120550, Ecuador;
- Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, 28040 Madrid, Spain
- Unidad de Posgrado, Universidad Técnica Estatal de Quevedo (UTEQ), Quevedo Av. Quito km, 1 1/2 Vía a Santo Domingo de los Tsáchilas, Quevedo 120550, Ecuador
| | - Robinson J. Herrera-Feijoo
- Facultad de Ciencias Agrarias y Forestales, Universidad Técnica Estatal de Quevedo (UTEQ), Quevedo Av. Quito km, 1 1/2 Vía a Santo Domingo de los Tsáchilas, Quevedo 120550, Ecuador;
- Unidad de Posgrado, Universidad Técnica Estatal de Quevedo (UTEQ), Quevedo Av. Quito km, 1 1/2 Vía a Santo Domingo de los Tsáchilas, Quevedo 120550, Ecuador
- Escuela de Doctorado, Centro de Estudios de Posgrado, Universidad Autónoma de Madrid, C/Francisco Tomás y Valiente, nº 2, 28049 Madrid, Spain
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
| | - Rubén G. Mateo
- Departamento de Biología (Botánica), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain;
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Facultad de Ciencias, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Fernando García-Robredo
- Departamento de Ingeniería y Gestión Forestal y Ambiental, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, C/José Antonio Novais 10, 28040 Madrid, Spain;
| | - Bolier Torres
- Facultad de Ciencia de la Vida, Universidad Estatal Amazónica (UEA), Puyo 160101, Ecuador;
- Ochroma Consulting and Services, Puerto Napo, Tena 150150, Ecuador
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25
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Zhu K, Song Y. Harnessing herbaria to advance plant phenology research under global change. THE NEW PHYTOLOGIST 2023; 239:2057-2059. [PMID: 37376722 DOI: 10.1111/nph.19088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
This article is a Commentary on Park et al. (2023), 239: 2153–2165.
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Affiliation(s)
- Kai Zhu
- Institute for Global Change Biology and School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Yiluan Song
- Institute for Global Change Biology and School for Environment and Sustainability, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Environmental Studies, University of California, Santa Cruz, CA, 95064, USA
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26
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Park DS, Xie Y, Ellison AM, Lyra GM, Davis CC. Complex climate-mediated effects of urbanization on plant reproductive phenology and frost risk. THE NEW PHYTOLOGIST 2023; 239:2153-2165. [PMID: 36942966 DOI: 10.1111/nph.18893] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Urbanization can affect the timing of plant reproduction (i.e. flowering and fruiting) and associated ecosystem processes. However, our knowledge of how plant phenology responds to urbanization and its associated environmental changes is limited. Herbaria represent an important, but underutilized source of data for investigating this question. We harnessed phenological data from herbarium specimens representing 200 plant species collected across 120 yr from the eastern US to investigate the spatiotemporal effects of urbanization on flowering and fruiting phenology and frost risk (i.e. time between the last frost date and flowering). Effects of urbanization on plant reproductive phenology varied significantly in direction and magnitude across species ranges. Increased urbanization led to earlier flowering in colder and wetter regions and delayed fruiting in regions with wetter spring conditions. Frost risk was elevated with increased urbanization in regions with colder and wetter spring conditions. Our study demonstrates that predictions of phenological change and its associated impacts must account for both climatic and human effects, which are context dependent and do not necessarily coincide. We must move beyond phenological models that only incorporate temperature variables and consider multiple environmental factors and their interactions when estimating plant phenology, especially at larger spatial and taxonomic scales.
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Affiliation(s)
- Daniel S Park
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47906, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47906, USA
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | - Yingying Xie
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47906, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47906, USA
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41099, USA
| | - Aaron M Ellison
- Harvard University Herbaria, Harvard University, Cambridge, MA, 02135, USA
- Sound Solutions for Sustainable Science, Boston, MA, 02135, USA
| | - Goia M Lyra
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
- Programa de Pós Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, 40170-115, Brazil
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
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Park DS, Feng X, Akiyama S, Ardiyani M, Avendaño N, Barina Z, Bärtschi B, Belgrano M, Betancur J, Bijmoer R, Bogaerts A, Cano A, Danihelka J, Garg A, Giblin DE, Gogoi R, Guggisberg A, Hyvärinen M, James SA, Sebola RJ, Katagiri T, Kennedy JA, Komil TS, Lee B, Lee SML, Magri D, Marcucci R, Masinde S, Melnikov D, Mráz P, Mulenko W, Musili P, Mwachala G, Nelson BE, Niezgoda C, Novoa Sepúlveda C, Orli S, Paton A, Payette S, Perkins KD, Ponce MJ, Rainer H, Rasingam L, Rustiami H, Shiyan NM, Bjorå CS, Solomon J, Stauffer F, Sumadijaya A, Thiébaut M, Thiers BM, Tsubota H, Vaughan A, Virtanen R, Whitfeld TJS, Zhang D, Zuloaga FO, Davis CC. The colonial legacy of herbaria. Nat Hum Behav 2023:10.1038/s41562-023-01616-7. [PMID: 37308536 DOI: 10.1038/s41562-023-01616-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/27/2023] [Indexed: 06/14/2023]
Abstract
Herbarium collections shape our understanding of Earth's flora and are crucial for addressing global change issues. Their formation, however, is 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 and magnitude of this disparity have not been quantified. Here we examine the colonial legacy of botanical collections, analysing 85,621,930 specimen records and assessing survey responses from 92 herbarium collections across 39 countries. We find an inverse relationship between where plant diversity exists in nature and where it is housed in herbaria. Such disparities persist across physical and digital realms despite overt colonialism ending over half a century ago. We emphasize the need for acknowledging the colonial history of herbarium collections and implementing a more equitable global paradigm for their collection, curation and use.
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Affiliation(s)
- Daniel S Park
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
| | - Xiao Feng
- Department of Geography, Florida State University, Tallahassee, FL, USA
| | - Shinobu Akiyama
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Marlina Ardiyani
- Herbarium Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Neida Avendaño
- Instituto Experimental Jardin Botánico 'Dr. Tobías Lasser', Avenida Salvador Allende, Ciudad Universitaria, Caracas, Venezuela
- Universidad Central de Venezuela, Caracas, Venezuela
| | | | - Blandine Bärtschi
- Herbier LY, FR-BioEEnVis, Université Claude Bernard Lyon 1, Lyon, France
| | | | | | - Roxali Bijmoer
- Botany Section, Naturalis Biodiversity Center, Leiden, the Netherlands
| | | | - Asunción Cano
- Herbario San Marcos, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Jiří Danihelka
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Arti Garg
- Central Regional Centre, Botanical Survey of India, Allahabad, India
| | - David E Giblin
- University of Washington Herbarium, Burke Museum, Seattle, WA, USA
| | - Rajib Gogoi
- Sikkim Himalayan Regional Centre, Botanical Survey of India, Gangtok, India
| | | | - Marko Hyvärinen
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Shelley A James
- Department of Biodiversity, Conservation and Attractions, Western Australian Herbarium, Kensington, Western Australia, Australia
| | - Ramagwai J Sebola
- South African National Biodiversity Institute, Pretoria, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tomoyuki Katagiri
- Department of Biological Sciences, Faculty of Science and Technology, Kochi University, Kochi, Japan
- Hattori Botanical Laboratory, Nichinan, Japan
| | | | - Tojibaev Sh Komil
- Institute of Botany, Uzbekistan Academy of Sciences, Tashkent, Uzbekistan
| | | | - Serena M L Lee
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Donatella Magri
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | | | - Siro Masinde
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Denis Melnikov
- Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Patrik Mráz
- Herbarium Collections & Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Wieslaw Mulenko
- Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Paul Musili
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | | | - Burrell E Nelson
- Rocky Mountain Herbarium, University of Wyoming, Laramie, WY, USA
| | | | - Carla Novoa Sepúlveda
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung München, München, Germany
| | - Sylvia Orli
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Serge Payette
- Herbier Louis-Marie, Université Laval, Québec City, Québec, Canada
| | - Kent D Perkins
- University of Florida Herbarium, Florida Museum, Gainesville, FL, USA
| | - Maria Jimena Ponce
- Instituto Multidisciplinario de Biología Vegetal (UNC-CONICET), Córdoba, Argentina
| | - Heimo Rainer
- Naturhistorisches Museum Wien, Vienna, Austria
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - L Rasingam
- Deccan Regional Centre, Botanical Survey of India, Hyderabad, India
| | - Himmah Rustiami
- Herbarium Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Natalia M Shiyan
- National Herbarium of Ukraine, M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | | | | | - Fred Stauffer
- Conservatory and Botanic Gardens of Geneva, Geneva, Switzerland
| | - Alex Sumadijaya
- Herbarium Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Mélanie Thiébaut
- Herbier LY, FR-BioEEnVis, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Hiromi Tsubota
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Miyajima Natural Botanical Garden, Hiroshima University, Hiroshima, Japan
| | - Alison Vaughan
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Risto Virtanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- University of Oulu Botanical Museum, Oulu, Finland
| | | | - Dianxiang Zhang
- South China Botanical Garden Herbarium, Chinese Academy of Sciences, Guangzhou, China
| | | | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, USA.
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28
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Jenny LA, Shapiro LR, Davis CC, Jonathan Davies T, Pierce NE, Meineke E. Herbarium specimens reveal herbivory patterns across the genus Cucurbita. AMERICAN JOURNAL OF BOTANY 2023; 110:e16126. [PMID: 36633920 DOI: 10.1002/ajb2.16126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
PREMISE Quantifying how closely related plant species differ in susceptibility to insect herbivory is important for understanding the variation in evolutionary pressures on plant functional traits. However, empirically measuring in situ variation in herbivory spanning the geographic range of a plant-insect complex is logistically difficult. Recently, new methods have been developed using herbarium specimens to investigate patterns in plant-insect symbioses across large geographic scales. Such investigations provide insights into how accelerated anthropogenic changes may impact plant-insect interactions that are of ecological or agricultural importance. METHODS Here, we analyze 274 pressed herbarium samples to investigate variation in herbivory damage in 13 different species of the economically important plant genus Cucurbita (Cucurbitaceae). This collection is composed of specimens of wild, undomesticated Cucurbita that were collected from across their native range, and Cucurbita cultivars collected from both within their native range and from locations where they have been introduced for agriculture in temperate North America. RESULTS Herbivory is common on individuals of all Cucurbita species collected throughout their geographic ranges. However, estimates of herbivory varied considerably among individuals, with mesophytic species accruing more insect damage than xerophytic species, and wild specimens having more herbivory than specimens collected from human-managed habitats. CONCLUSIONS Our study suggests that long-term evolutionary changes in habitat from xeric to mesic climates and wild to human-managed habitats may mediate the levels of herbivory pressure from coevolved herbivores. Future investigations into the potential factors that contribute to herbivory may inform the management of domesticated crop plants and their insect herbivores.
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Affiliation(s)
- Laura A Jenny
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - Lori R Shapiro
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
- Department of Applied Ecology, North Carolina State University, Raleigh, North Carolina, 27695, United States
| | - Charles C Davis
- Harvard University Herbaria, Department of Organismal and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - T Jonathan Davies
- Departments of Botany, and Forest & Conservation Sciences, University of British Columbia, Vancouver, British Columbia, BC V6T 1Z4, Canada
- African Centre for DNA Barcoding, University of Johannesburg, Johannesburg, Gauteng, 2028, South Africa
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, 02138, United States
| | - Emily Meineke
- Department of Entomology and Nematology, University of California, Davis, Davis, California, 95616, United States
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