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Parker EJ, Weiskopf SR, Oliver RY, Rubenstein MA, Jetz W. Insufficient and biased representation of species geographic responses to climate change. GLOBAL CHANGE BIOLOGY 2024; 30:e17408. [PMID: 38984769 DOI: 10.1111/gcb.17408] [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: 07/20/2023] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 07/11/2024]
Abstract
The geographic redistributions of species due to a rapidly changing climate are poised to perturb ecological communities and significantly impact ecosystems and human livelihoods. Effectively managing these biological impacts requires a thorough understanding of the patterns and processes of species geographic range shifts. While substantial recent redistributions have been identified and recognized to vary by taxon, region, and range geometry, there are large gaps and biases in the available evidence. Here, we use the largest compilation of geographic range change observations to date, comprised of 33,016 potential redistributions across 12,009 species, to formally assess within- and cross-species coverage and biases and to motivate future data collection. We find that species coverage varies strongly by taxon and underrepresents species at high and low latitudes. Within species, assessments of potential redistributions came from parts of their geographic range that were highly uneven and non-representative. For most species and taxa, studies were strongly biased toward the colder parts of species' distributions and thus significantly underrepresented populations that might get pushed beyond their maximum temperature limits. Coverage of potential leading and trailing geographic range edges under a changing climate was similarly uneven. Only 8% of studied species were assessed at both high and low latitude and elevation range edges, with most only covered at one edge. This suggests that substantial within-species biases exacerbate the considerable geographic and taxonomic among-species unevenness in evidence. Our results open the door for a more quantitative accounting for existing knowledge biases in climate change ecology and a more informed management and conservation. Our findings offer guidance for future data collection that better addresses information gaps and provides a more effective foundation for managing the biological impacts of climate change.
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Affiliation(s)
- Evan J Parker
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
| | - Sarah R Weiskopf
- U.S. Geological Survey National Climate Adaptation Science Center, Reston, Virginia, USA
| | - Ruth Y Oliver
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
- Bren School of Environmental Science & Management, UC Santa Barbara, Santa Barbara, California, USA
| | - Madeleine A Rubenstein
- U.S. Geological Survey National Climate Adaptation Science Center, Reston, Virginia, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
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2
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Onyango B, Copeland R, Mbogholi J, Wamalwa M, Kibet C, Tonnang HEZ, Senagi K. WiPFIM: A digital platform for interlinking biocollections of wild plants, fruits, associated insects, and their molecular barcodes. Ecol Evol 2024; 14:e11457. [PMID: 38826163 PMCID: PMC11143469 DOI: 10.1002/ece3.11457] [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: 09/15/2023] [Revised: 04/12/2024] [Accepted: 05/07/2024] [Indexed: 06/04/2024] Open
Abstract
The current knowledge on insects feeding on fruits is limited, and some of the scarce existing data on the fruit-associated insects are secluded within the host institutions. Consequently, their value is not fully realized. Moreover, in countries like Kenya, the integration of biocollections data within a digital framework has not been fully exploited. To address these gaps, this article presents a description of the development of a web-based platform for data sharing and integrating biodiversity historical data of wild plants, fruits, associated insects, and their molecular barcodes (WiPFIM) while leveraging data science technologies. The barcodes corresponding to the biocollections data were retrieved from BOLD database. The platform is an online resource about fruit-insect interactions that can be of interest to a worldwide community of users and can be useful in building innovative tools. The platform is accessible online at https://test-dmmg.icipe.org/wpfhi.
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Affiliation(s)
- Bonface Onyango
- Data Management, Modeling and Geo‐Information (DMMG) UnitInternational Centre of Insect Physiology and EcologyNairobiKenya
- Biochemistry and Biotechnology DepartmentPwani UniversityKilifiKenya
| | - Robert Copeland
- Data Management, Modeling and Geo‐Information (DMMG) UnitInternational Centre of Insect Physiology and EcologyNairobiKenya
| | - John Mbogholi
- Biochemistry and Biotechnology DepartmentPwani UniversityKilifiKenya
| | - Mark Wamalwa
- Data Management, Modeling and Geo‐Information (DMMG) UnitInternational Centre of Insect Physiology and EcologyNairobiKenya
| | - Caleb Kibet
- Data Management, Modeling and Geo‐Information (DMMG) UnitInternational Centre of Insect Physiology and EcologyNairobiKenya
| | - Henri E. Z. Tonnang
- Data Management, Modeling and Geo‐Information (DMMG) UnitInternational Centre of Insect Physiology and EcologyNairobiKenya
| | - Kennedy Senagi
- Data Management, Modeling and Geo‐Information (DMMG) UnitInternational Centre of Insect Physiology and EcologyNairobiKenya
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3
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MacNeill BN, Ortiz-Brunel JP, Rodríguez A, Ruiz-Sánchez E, Navarro-Moreno J, Hofford NP, McKain MR. Floral Diversity and Pollination Syndromes in Agave subgenus Manfreda. Integr Comp Biol 2023; 63:1376-1390. [PMID: 37673672 DOI: 10.1093/icb/icad118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 08/09/2023] [Accepted: 08/19/2023] [Indexed: 09/08/2023] Open
Abstract
The genus Agave is an ecological keystone of American deserts and both culturally and economically important in Mexico. Agave is a large genus of about 250 species. The radiation of Agave is marked by an initial adaptation to desert environments and then a secondary diversification of species associated with pollinator groups, such as hummingbirds and nocturnal moths. Phylogenetic analyses place Agave subgenus Manfreda, or the "herbaceous agaves," in a monophyletic clade that likely evolved in part as an adaptation to novel pollination vectors. Here, we present a morphological and observational study assessing the evolution of floral form in response to pollinator specialization within this understudied group. We found significant visitation by hummingbirds and nocturnal moths to several species within the Agave subgenus Manfreda. These observations also align with our morphological analyses of floral organs and support the evolution of distinct pollination syndromes. We found that not all floral morphology is consistent within a pollination syndrome, suggesting hidden diversity in the evolution of floral phenotypes in Agave. We also characterize the morphological variation between herbarium and live specimens, demonstrating that special consideration needs to be made when combining these types of data. This work identifies the potential for studying the functional evolution of diverse floral forms within Agave and demonstrates the need to further explore ecological and evolutionary relationships to understand pollinator influence on diversification in the genus.
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Affiliation(s)
- Bryan N MacNeill
- Department of Biological Sciences, The University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | | | - Aarón Rodríguez
- Department of Botany and Zoology, University of Guadalajara, Zapopan, Jal. 45200 , Mexico
| | - Eduardo Ruiz-Sánchez
- Department of Botany and Zoology, University of Guadalajara, Zapopan, Jal. 45200 , Mexico
| | - Jesús Navarro-Moreno
- Department of Botany and Zoology, University of Guadalajara, Zapopan, Jal. 45200 , Mexico
| | - Nathaniel P Hofford
- Department of Biological Sciences, The University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
| | - Michael R McKain
- Department of Biological Sciences, The University of Alabama, 300 Hackberry Lane, Tuscaloosa, AL 35487, USA
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4
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Quatela AS, Cangren P, Jafari F, Michel T, de Boer HJ, Oxelman B. Retrieval of long DNA reads from herbarium specimens. AOB PLANTS 2023; 15:plad074. [PMID: 38130422 PMCID: PMC10735254 DOI: 10.1093/aobpla/plad074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 11/06/2023] [Indexed: 12/23/2023]
Abstract
High-throughput sequencing of herbarium specimens' DNA with short-read platforms has helped explore many biological questions. Here, for the first time, we investigate the potential of using herbarium specimens as a resource for long-read DNA sequencing technologies. We use target capture of 48 low-copy nuclear loci in 12 herbarium specimens of Silene as a basis for long-read sequencing using SMRT PacBio Sequel. The samples were collected between 1932 and 2019. A simple optimization of size selection protocol enabled the retrieval of both long DNA fragments (>1 kb) and long on-target reads for nine of them. The limited sampling size does not enable statistical evaluation of the influence of specimen age to the DNA fragmentation, but our results confirm that younger samples, that is, collected after 1990, are less fragmented and have better sequencing success than specimens collected before this date. Specimens collected between 1990 and 2019 yield between 167 and 3403 on-target reads > 1 kb. They enabled recovering between 34 loci and 48 (i.e. all loci recovered). Three samples from specimens collected before 1990 did not yield on-target reads > 1 kb. The four other samples collected before this date yielded up to 144 reads and recovered up to 25 loci. Young herbarium specimens seem promising for long-read sequencing. However, older ones have partly failed. Further exploration would be necessary to statistically test and understand the potential of older material in the quest for long reads. We would encourage greatly expanding the sampling size and comparing different taxonomic groups.
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Affiliation(s)
- Anne-Sophie Quatela
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden
| | - Patrik Cangren
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
| | - Farzaneh Jafari
- Department of Biology, Faculty of Basic Sciences, Lorestan University, P.O. BOX 6815144316, Khorramabad, Iran
- Department of Plant Science, Center of Excellence in Phylogeny of Living Organisms, School of Biology, College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran
| | - Thibauld Michel
- Tropical Diversity Research Department, Royal Botanic Garden of Edinburgh, 20A Inverleith Row, Edinburgh, EH3 5LRUK
| | - Hugo J de Boer
- Natural History Museum, University of Oslo, P.O. Box 1172 Blindern, 0318 Oslo, Norway
| | - Bengt Oxelman
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, 405 30, Gothenburg, Sweden
- Gothenburg Global Biodiversity Center, Gothenburg, Box 463, 405 30, Sweden
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5
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Buldrini F, Alessandrini A, Mossetti U, Muzzi E, Pezzi G, Soldano A, Nascimbene J. Botanical memory: five centuries of floristic changes revealed by a Renaissance herbarium (Ulisse Aldrovandi, 1551-1586). ROYAL SOCIETY OPEN SCIENCE 2023; 10:230866. [PMID: 38026021 PMCID: PMC10645095 DOI: 10.1098/rsos.230866] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 08/09/2023] [Indexed: 12/01/2023]
Abstract
We analysed the spatially explicit floristic information available in the herbarium of Ulisse Aldrovandi (1551-1586) to track floristic changes in the surroundings of Bologna across five centuries. Aldrovandi's data were compared with the Flora della Provincia di Bologna by Girolamo Cocconi (1883) and the Floristic Database of Emilia-Romagna (1965-2021). We explored potential variations in native range and life forms composition, and habitat affinity of the species in the three floras, also contrasting between native and alien species. Native species, mainly in terms of variations of hydro-hygrophytes, chamaephytes and therophytes, provide clear signals of human disturbance and habitat loss. Signals of climate change are provided by the high-mountain species, that were comparably rare between Aldrovandi and current flora and more represented in Cocconi, probably reflecting the effect of the Little Ice Age. Our findings also indicate the increasing importance of alien species from the Renaissance onwards. In this perspective, Aldrovandi's herbarium preserves the memory of the first signs of a radical transformation of the European flora and habitats. Finally, the study warns about the risk of dismissing herbaria and herbarium specimens collection, which would cause irreparable lacunas in our botanical memory, hindering our ability to predict biodiversity trajectories.
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Affiliation(s)
- Fabrizio Buldrini
- BIOME Lab - Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Via Irnerio 42, 40126 Bologna, Italy
- Sistema Museale di Ateneo, Università di Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | | | - Umberto Mossetti
- Sistema Museale di Ateneo, Università di Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - Enrico Muzzi
- Dipartimento di Scienze e Tecnologie Agrarie e Alimentari, Università di Bologna, Viale G. Fanin 44, 40127 Bologna, Italy
| | - Giovanna Pezzi
- BIOME Lab - Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Via Irnerio 42, 40126 Bologna, Italy
| | - Adriano Soldano
- Independent Researcher, Largo Brigata Cagliari 6, 13100 Vercelli, Italy
| | - Juri Nascimbene
- BIOME Lab - Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Via Irnerio 42, 40126 Bologna, Italy
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6
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Burbano HA, Gutaker RM. Ancient DNA genomics and the renaissance of herbaria. Science 2023; 382:59-63. [PMID: 37797028 DOI: 10.1126/science.adi1180] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 08/02/2023] [Indexed: 10/07/2023]
Abstract
Herbaria are undergoing a renaissance as valuable sources of genomic data for exploring plant evolution, ecology, and diversity. Ancient DNA retrieved from herbarium specimens can provide unprecedented glimpses into past plant communities, their interactions with biotic and abiotic factors, and the genetic changes that have occurred over time. Here, we highlight recent advances in the field of herbarium genomics and discuss the challenges and opportunities of combining data from modern and time-stamped historical specimens. We also describe how integrating herbarium genomics data with other data types can yield substantial insights into the evolutionary and ecological processes that shape plant communities. Herbarium genomic analysis is a tool for understanding plant life and informing conservation efforts in the face of dire environmental challenges.
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Affiliation(s)
- Hernán A Burbano
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Rafal M Gutaker
- Royal Botanic Gardens, Kew, Kew Green, Richmond, Surrey TW9 3AE, UK
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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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8
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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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Weaver WN, Smith SA. FieldPrism: A system for creating snapshot vouchers from field images using photogrammetric markers and QR codes. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11545. [PMID: 37915427 PMCID: PMC10617303 DOI: 10.1002/aps3.11545] [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: 01/15/2023] [Revised: 04/18/2023] [Accepted: 05/26/2023] [Indexed: 11/03/2023]
Abstract
Premise Field images are important sources of information for research in the natural sciences. However, images that lack photogrammetric scale bars, including most iNaturalist observations, cannot yield accurate trait measurements. We introduce FieldPrism, a novel system of photogrammetric markers, QR codes, and software to automate the curation of snapshot vouchers. Methods and Results Our photogrammetric background templates (FieldSheets) increase the utility of field images by providing machine-readable scale bars and photogrammetric reference points to automatically correct image distortion and calculate a pixel-to-metric conversion ratio. Users can generate a QR code flipbook derived from a specimen identifier naming hierarchy, enabling machine-readable specimen identification for automatic file renaming. We also developed FieldStation, a Raspberry Pi-based mobile imaging apparatus that records images, GPS location, and metadata redundantly on up to four USB storage devices and can be monitored and controlled from any Wi-Fi connected device. Conclusions FieldPrism is a flexible software tool designed to standardize and improve the utility of images captured in the field. When paired with the optional FieldStation, researchers can create a self-contained mobile imaging apparatus for quantitative trait data collection.
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Affiliation(s)
- William N. Weaver
- Department of Ecology and Evolutionary BiologyUniversity of Michigan1105 N. University Ave.Ann Arbor48109MichiganUSA
| | - Stephen A. Smith
- Department of Ecology and Evolutionary BiologyUniversity of Michigan1105 N. University Ave.Ann Arbor48109MichiganUSA
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10
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Zheng Y, Yuan C, Matsushita N, Lian C, Geng Q. Analysis of the distribution pattern of the ectomycorrhizal fungus Cenococcum geophilum under climate change using the optimized MaxEnt model. Ecol Evol 2023; 13:e10565. [PMID: 37753310 PMCID: PMC10518754 DOI: 10.1002/ece3.10565] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 09/06/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Cenococcum geophilum (C. geophilum) is a widely distributed ectomycorrhizal fungus that plays a crucial role in forest ecosystems worldwide. However, the specific ecological factors influencing its global distribution and how climate change will affect its range are still relatively unknown. In this study, we used the MaxEnt model optimized with the kuenm package to simulate changes in the distribution pattern of C. geophilum from the Last Glacial Maximum to the future based on 164 global distribution records and 17 environmental variables and investigated the key environmental factors influencing its distribution. We employed the optimal parameter combination of RM = 4 and FC = QPH, resulting in a highly accurate predictive model. Our study clearly shows that the mean temperature of the coldest quarter and annual precipitation are the key environmental factors influencing the suitable habitats of C. geophilum. Currently, appropriate habitats of C. geophilum are mainly distributed in eastern Asia, west-central Europe, the western seaboard and eastern regions of North America, and southeastern Australia, covering a total area of approximately 36,578,300 km2 globally. During the Last Glacial Maximum and the mid-Holocene, C. geophilum had a much smaller distribution area, being mainly concentrated in the Qinling-Huaihe Line region of China and eastern Peninsular Malaysia. As global warming continues, the future suitable habitat for C. geophilum is projected to shift northward, leading to an expected expansion of the suitable area from 9.21% to 21.02%. This study provides a theoretical foundation for global conservation efforts and biogeographic understanding of C. geophilum, offering new insights into its distribution patterns and evolutionary trends.
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Affiliation(s)
- Yexu Zheng
- College of ForestryShandong Agricultural UniversityTai'anChina
- College of Grassland Science and TechnologyChina Agricultural UniversityBeijingChina
| | - Chao Yuan
- College of ForestryFujian Agriculture and Forestry UniversityFuzhouChina
| | - Norihisa Matsushita
- Graduate School of Agricultural and Life SciencesThe University of TokyoTokyoJapan
| | - Chunlan Lian
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life SciencesThe University of TokyoNishitokyo‐shiTokyoJapan
| | - Qifang Geng
- College of ForestryShandong Agricultural UniversityTai'anChina
- Asian Research Center for Bioresource and Environmental Sciences, Graduate School of Agricultural and Life SciencesThe University of TokyoNishitokyo‐shiTokyoJapan
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11
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Melbourne LA, Brodie J, Rayfield EJ, Titelboim D, Lord OT, Schmidt DN. Environmental impacts on the structural integrity of British rhodoliths. Sci Rep 2023; 13:13473. [PMID: 37596363 PMCID: PMC10439216 DOI: 10.1038/s41598-023-40292-5] [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: 09/15/2022] [Accepted: 08/08/2023] [Indexed: 08/20/2023] Open
Abstract
Coralline algae form complex habitats which are biodiversity hotspots. Experimental studies suggest that climate change will decrease coralline algal structural integrity. These experiments, however, lack information on local morphological variability and how much structural change would be needed to threaten habitat formation. Here, using finite element modelling, we assess variability in cellular structure and chemical composition of the carbonate skeleton of four coralline algal species from Britain in contemporary and historical specimens collected over the last 130 years. Cellular and mineral properties are highly variable within species, between sites and through time, with structurally weaker cells in the southern species and contemporary material compared to northern taxa and historical material. Yet, temporal differences in strength were smaller than spatial differences. Our work supports long term experiments which show the adaptation potential of this group. Our results suggest that future anthropogenic climate change may lead to loss of habitat complexity in the south and expansion of structurally weaker southern species into northern sites.
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Affiliation(s)
- Leanne A Melbourne
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK.
- Earth and Planetary Sciences, American Museum of Natural History, New York, NY, 10024, USA.
| | - Juliet Brodie
- Department of Life Sciences, Natural History Museum, London, SW7 5BD, UK
| | - Emily J Rayfield
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
| | - Danna Titelboim
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
- Department of Earth Sciences, University of Oxford, Oxford, OX1 3AN, UK
| | - Oliver T Lord
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
| | - Daniela N Schmidt
- School of Earth Sciences, University of Bristol, Bristol, BS8 1RJ, UK
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12
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Azevedo-Schmidt L, Swain A, Shoemaker LG, Currano ED. Landscape-level variability and insect herbivore outbreak captured within modern forests provides a framework for interpreting the fossil record. Sci Rep 2023; 13:9701. [PMID: 37322107 PMCID: PMC10272219 DOI: 10.1038/s41598-023-36763-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 06/09/2023] [Indexed: 06/17/2023] Open
Abstract
Temporal patterns of plant-insect interactions are readily observed within fossil datasets but spatial variability is harder to disentangle without comparable modern methods due to limitations in preservation. This is problematic as spatial variability influences community structure and interactions. To address this we replicated paleobotanical methods within three modern forests, creating an analogous dataset that rigorously tested inter- and intra-forest plant-insect variability. Random mixed effects models, non-metric multidimensional scaling (NMDS) ordinations, and bipartite network- and node-level metrics were used. Total damage frequency and diversity did not differ across forests but differences in functional feeding groups (FFGs) were observed across forests, correlating with plant diversity, evenness, and latitude. Overall, we found higher generalized herbivory within the temperate forests than the wet-tropical, a finding also supported by co-occurrence and network analyses at multiple spatial scales. Intra-forest analyses captured consistent damage type communities, supporting paleobotanical efforts. Bipartite networks captured the feeding outbreak of Lymantria dispar caterpillars; an exciting result as insect outbreaks have long been unidentifiable within fossil datasets. These results support paleobotanical assumptions about fossil insect herbivore communities, provide a comparative framework between paleobotanical and modern communities, and suggest a new analytical framework for targeting modern and fossil outbreaks of insect feeding.
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Affiliation(s)
- Lauren Azevedo-Schmidt
- Climate Change Institute, University of Maine, Orono, 04469, USA.
- Department of Botany, University of Wyoming, Laramie, 82071, USA.
| | - Anshuman Swain
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, 02138, USA
| | | | - Ellen D Currano
- Department of Botany, University of Wyoming, Laramie, 82071, USA
- Department of Geology and Geophysics, University of Wyoming, Laramie, 82071, USA
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13
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Daru BH, Rodriguez J. Mass production of unvouchered records fails to represent global biodiversity patterns. Nat Ecol Evol 2023:10.1038/s41559-023-02047-3. [PMID: 37127769 DOI: 10.1038/s41559-023-02047-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 03/26/2023] [Indexed: 05/03/2023]
Abstract
The ever-increasing human footprint even in very remote places on Earth has inspired efforts to document biodiversity vigorously in case organisms go extinct. However, the data commonly gathered come from either primary voucher specimens in a natural history collection or from direct field observations that are not traceable to tangible material in a museum or herbarium. Although both datasets are crucial for assessing how anthropogenic drivers affect biodiversity, they have widespread coverage gaps and biases that may render them inefficient in representing patterns of biodiversity. Using a large global dataset of around 1.9 billion occurrence records of terrestrial plants, butterflies, amphibians, birds, reptiles and mammals, we quantify coverage and biases of expected biodiversity patterns by voucher and observation records. We show that the mass production of observation records does not lead to higher coverage of expected biodiversity patterns but is disproportionately biased toward certain regions, clades, functional traits and time periods. Such coverage patterns are driven by the ease of accessibility to air and ground transportation, level of security and extent of human modification at each sampling site. Conversely, voucher records are vastly infrequent in occurrence data but in the few places where they are sampled, showed relative congruence with expected biodiversity patterns for all dimensions. The differences in coverage and bias by voucher and observation records have important implications on the utility of these records for research in ecology, evolution and conservation research.
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Affiliation(s)
- Barnabas H Daru
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - Jordan Rodriguez
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
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14
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Li Y, Hopkins AJM, Davis RA. Going, Going, Gone The Diminishing Capacity of Museum Specimen Collections to Address Global Change Research: A Case Study on Urban Reptiles. Animals (Basel) 2023; 13:ani13061078. [PMID: 36978619 PMCID: PMC10044672 DOI: 10.3390/ani13061078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/14/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023] Open
Abstract
It has been increasingly popular to use natural history specimens to examine environmental changes. As the current functionality of museum specimens has extended beyond their traditional taxonomic role, there has been a renewed focus on the completeness of biological collections to provide data for current and future research. We used the collections of the Western Australian Museum to answer questions about the change in occurrence of five common reptile species due to the rapid urbanization of Perth. We recorded a significant decline in collection effort from the year 2000 onwards (F = 7.65, p < 0.01) compared to the period 1990–1999. Spatial analysis revealed that only 0.5% of our study region was well sampled, 8.5% were moderately sampled and the majority of the regions (91%) were poorly sampled. By analysing the trend of specimen acquisition from 1950 to 2010, we discovered a significant inconsistency in specimen sampling effort for 13 common reptile species across time and space. A large proportion of past specimens lacked information including the place and time of collection. An increase in investment to museums and an increase in geographically and temporally systematic collecting is advocated to ensure that collections can answer questions about environmental change.
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Affiliation(s)
- Yanlin Li
- School of Science, Edith Cowan University, 100 Joondalup Drive, Joondalup, WA 6027, Australia
| | - Anna J. M. Hopkins
- School of Science, Edith Cowan University, 100 Joondalup Drive, Joondalup, WA 6027, Australia
| | - Robert A. Davis
- School of Science, Edith Cowan University, 100 Joondalup Drive, Joondalup, WA 6027, Australia
- Department of Terrestrial Zoology, Western Australia Museum, 49 Kew St, Welshpool, WA 6106, Australia
- Correspondence:
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15
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Barnes M, Sulé-Suso J, Millett J, Roach P. Fourier transform infrared spectroscopy as a non-destructive method for analysing herbarium specimens. Biol Lett 2023; 19:20220546. [PMID: 36946131 PMCID: PMC10031417 DOI: 10.1098/rsbl.2022.0546] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
Dried plant specimens stored in herbaria are an untapped treasure chest of information on environmental conditions, plant evolution and change over many hundreds of years. Owing to their delicate nature and irreplaceability, there is limited access for analysis to these sensitive samples, particularly where chemical data are obtained using destructive techniques. Fourier transform infrared (FTIR) spectroscopy is a chemical analysis technique which can be applied non-destructively to understand chemical bonding information and, therefore, functional groups within the sample. This provides the potential for understanding geographical, spatial and species-specific variation in plant biochemistry. Here, we demonstrate the use of mid-FTIR microspectroscopy for the chemical analysis of Drosera rotundifolia herbarium specimens, which were collected 100 years apart from different locations. Principal component and hierarchical clustering analysis enabled differentiation between three main regions on the plant (lamina, tentacle stalk and tentacle head), and between the different specimens. Lipids and protein spectral regions were particularly sensitive differentiators of plant tissues. Differences between the different sets of specimens were smaller. This study demonstrates that relevant information can be extracted from herbarium specimens using FTIR, with little impact on the specimens. FTIR, therefore, has the potential to be a powerful tool to unlock historic information within herbaria.
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Affiliation(s)
- M Barnes
- Department of Chemistry, Loughborough University, Loughborough, UK
| | - J Sulé-Suso
- School of Pharmacy and Bioengineering, Guy Hilton Research Centre, Keele University, Keele, UK
- Cancer Centre, University Hospitals of North Midlands, Stoke-on-Trent, UK
| | - J Millett
- Department of Geography and Environment, Loughborough University, Loughborough, UK
| | - P Roach
- Department of Chemistry, Loughborough University, Loughborough, UK
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16
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Conti M, Nimis PL, Tretiach M, Muggia L, Moro A, Martellos S. The Italian lichens dataset from the TSB herbarium (University of Trieste). Biodivers Data J 2023; 11:e96466. [PMID: 38327327 PMCID: PMC10848505 DOI: 10.3897/bdj.11.e96466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 02/13/2023] [Indexed: 03/02/2023] Open
Abstract
Background The "Herbarium Universitatis Tergestinae" (TSB), with a total of ca. 50,000 specimens, includes the largest modern collection of lichens in Italy, with 25,796 samples collected from all over the country since 1984, representing 74% of all taxa known to occur in Italy. Almost all specimens have been georeferenced "a posteriori". The dataset is available through GBIF, as well as in ITALIC, the Information System of Italian Lichens. New information The TSB Herbarium hosts the largest modern lichen collection in Italy, with a total of ca. 50,000 specimens. This dataset contains all of the 25,796 specimens collected within the administrative borders of Italy. Amongst them, 98% are georeferenced and 87% have the date of collection. The dataset includes several type specimens (isotypes and holotypes) and exsiccata.
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Affiliation(s)
- Matteo Conti
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
| | - Pier Luigi Nimis
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
| | - Mauro Tretiach
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
| | - Lucia Muggia
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
| | - Andrea Moro
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
| | - Stefano Martellos
- Dept. Of Life Sciences, University of Trieste, Trieste, ItalyDept. Of Life Sciences, University of TriesteTriesteItaly
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17
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Bradshaw MJ, Carey J, Liu M, Bartholomew HP, Jurick WM, Hambleton S, Hendricks D, Schnittler M, Scholler M. Genetic time traveling: sequencing old herbarium specimens, including the oldest herbarium specimen sequenced from kingdom Fungi, reveals the population structure of an agriculturally significant rust. THE NEW PHYTOLOGIST 2023; 237:1463-1473. [PMID: 36385249 DOI: 10.1111/nph.18622] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/07/2022] [Indexed: 06/16/2023]
Abstract
Sequencing herbarium specimens can be instrumental in answering ecological, evolutionary, and taxonomic inquiries. We developed a protocol for sequencing herbarium specimens of rust fungi (Pucciniales) and proceeded to sequence specimens ranging from 4 to 211 yr old from five different genera. We then obtained sequences from an economically important biological control agent, Puccinia suaveolens, to highlight the potential of sequencing herbarium specimens in an ecological sense and to evaluate the following hypotheses: (1) The population structure of a plant pathogen changes over time, and (2) introduced pathogens are more diverse in their native range. Our efforts resulted in sequences from 87 herbarium specimens that revealed a high level of diversity with a population structure that exhibited spatial-temporal patterns. The specimens sequenced from Europe showed more diversity than the ones from North America, uncovering an invasion pattern likely related to its European native host in North America. Additionally, to the best of our knowledge, the specimen from France collected in c. 1811 is the oldest herbarium specimen sequenced from kingdom Fungi. In conclusion, sequencing old herbarium specimens is an important tool that can be extrapolated to better understand plant-microbe evolution and to evaluate old type specimens to solidify the taxonomy of plant pathogenic fungi.
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Affiliation(s)
- Michael J Bradshaw
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Julie Carey
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Miao Liu
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Holly P Bartholomew
- Food Quality Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Wayne M Jurick
- Food Quality Laboratory, Agricultural Research Service, US Department of Agriculture, Beltsville, MD, 20705, USA
| | - Sarah Hambleton
- Biodiversity and Bioresources, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, ON, K1A 0C6, Canada
| | - Dylan Hendricks
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Martin Schnittler
- General Botany and Plant Systematics, Institute of Botany and Landscape Ecology, Ernst Moritz Arndt University Greifswald, 17487, Greifswald, Germany
| | - Markus Scholler
- Staatliches Museum für Naturkunde, Abteilung Biowissenschaften, D-76133, Karlsruhe, Germany
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18
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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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19
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Geissler C, Davidson A, Niesenbaum RA. The influence of climate warming on flowering phenology in relation to historical annual and seasonal temperatures and plant functional traits. PeerJ 2023; 11:e15188. [PMID: 37101791 PMCID: PMC10124540 DOI: 10.7717/peerj.15188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 03/15/2023] [Indexed: 04/28/2023] Open
Abstract
Climate warming has the potential to influence plant flowering phenology which in turn can have broader ecological consequences. Herbarium collections offer a source of historical plant data that makes possible the ability to document and better understand how warming climate can influence long-term shifts in flowering phenology. We examined the influence of annual, winter, and spring temperatures on the flowering phenology of herbarium specimens for 36 species collected from 1884-2015. We then compared the response to warming between native and non-native, woody and herbaceous, dry and fleshy fruit, and spring vs summer blooming species. Across all species, plants flowered 2.26 days earlier per 1 °C increase in annual average temperatures and 2.93 days earlier per 1 °C increase in spring onset average temperatures. Winter temperatures did not significantly influence flowering phenology. The relationship of temperature and flowering phenology was not significantly different between native and non-native species. Woody species flowered earlier than herbaceous species only in response to increasing annual temperatures. There was no difference in the phenological response between species with dry fruits and those fleshy fruits for any of the temperature periods. Spring blooming species exhibited a significantly greater phenological response to warming yearly average temperatures than summer blooming species. Although herbarium specimens can reveal climate change impacts on phenology, it is also evident that the phenological responses to warming vary greatly among species due to differences in functional traits such as those considered here, as well as other factors.
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Affiliation(s)
- Cole Geissler
- Department of Biology, Muhlenberg College, Allentown, PA, United States of America
| | - Allison Davidson
- Department of Mathematics, Muhlenberg College, Allentown, PA, United States of America
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20
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Davis CC. The herbarium of the future. Trends Ecol Evol 2022; 38:412-423. [PMID: 36549958 DOI: 10.1016/j.tree.2022.11.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022]
Abstract
The ~400 million specimens deposited across ~3000 herbaria are essential for: (i) understanding where plants have lived in the past, (ii) forecasting where they may live in the future, and (iii) delineating their conservation status. An open access 'global metaherbarium' is emerging as these specimens are digitized, mobilized, and interlinked online. This virtual biodiversity resource is attracting new users who are accelerating traditional applications of herbaria and generating basic and applied scientific innovations, including e-monographs and floras produced by diverse, interdisciplinary, and inclusive teams; robust machine-learning algorithms for species identification and phenotyping; collection and synthesis of ecological trait data at large spatiotemporal and phylogenetic scales; and exhibitions and installations that convey the beauty of plants and the value of herbaria in addressing broader societal issues.
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Affiliation(s)
- Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, 22 Divinity Avenue, Cambridge, MA 02138, USA.
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21
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Vogt-Schilb H, Richard F, Malaval JC, Rapior S, Fons F, Bourgade V, Schatz B, Buentgen U, Moreau PA. Climate-induced long-term changes in the phenology of Mediterranean fungi. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101166] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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22
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Zettlemoyer MA, Wilson JE, DeMarche ML. Estimating phenological sensitivity in contemporary vs. historical data sets: Effects of climate resolution and spatial scale. AMERICAN JOURNAL OF BOTANY 2022; 109:1981-1990. [PMID: 36321486 DOI: 10.1002/ajb2.16087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/13/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
PREMISE Phenological sensitivity, or the degree to which a species' phenology shifts in response to warming, is an important parameter for comparing and predicting species' responses to climate change. Phenological sensitivity is often measured using herbarium specimens or local studies in natural populations. These approaches differ widely in spatiotemporal scales, yet few studies explicitly consider effects of the geographic extent and resolution of climate data when comparing phenological sensitivities quantified from different data sets for a given species. METHODS We compared sensitivity of flowering phenology to growing degree days of the alpine plant Silene acaulis using two data sets: herbarium specimens and a 6 yr observational study in four populations at Niwot Ridge, Colorado, USA. We investigated differences in phenological sensitivity obtained using variable spatial scales and climate data sources. RESULTS Herbarium specimens underestimated phenological sensitivity compared to observational data, even when herbarium samples were limited geographically or to nearby weather station data. However, when observational data were paired with broader-scale climate data, as is typically used in herbarium data sets, estimates of phenological sensitivity were more similar. CONCLUSIONS This study highlights the potential for variation in data source, geographic scale, and accuracy of macroclimate data to produce very different estimates of phenological responses to climate change. Accurately predicting phenological shifts would benefit from comparisons between methods that estimate climate variables and phenological sensitivity over a variety of spatial scales.
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Affiliation(s)
- Meredith A Zettlemoyer
- Department of Plant Biology, University of Georgia, 120 Carlton Street, 2502 Miller Plant Sciences, Athens, Georgia, 30602-5004, USA
| | - Jill E Wilson
- Department of Plant Biology, University of Georgia, 120 Carlton Street, 2502 Miller Plant Sciences, Athens, Georgia, 30602-5004, USA
| | - Megan L DeMarche
- Department of Plant Biology, University of Georgia, 120 Carlton Street, 2502 Miller Plant Sciences, Athens, Georgia, 30602-5004, USA
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Kothari S, Beauchamp‐Rioux R, Laliberté E, Cavender‐Bares J. Reflectance spectroscopy allows rapid, accurate and non‐destructive estimates of functional traits from pressed leaves. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shan Kothari
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
- Institut de recherche en biologie végétale, Département de sciences biologiques Université de Montréal Montréal QC Canada
| | - Rosalie Beauchamp‐Rioux
- Institut de recherche en biologie végétale, Département de sciences biologiques Université de Montréal Montréal QC Canada
| | - Etienne Laliberté
- Institut de recherche en biologie végétale, Département de sciences biologiques Université de Montréal Montréal QC Canada
| | - Jeannine Cavender‐Bares
- Department of Plant and Microbial Biology University of Minnesota St. Paul MN USA
- Department of Ecology, Evolution, and Behavior University of Minnesota St. Paul MN USA
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24
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Rosche C, Baasch A, Runge K, Brade P, Träger S, Parisod C, Hensen I. Tracking population genetic signatures of local extinction with herbarium specimens. ANNALS OF BOTANY 2022; 129:857-868. [PMID: 35670810 PMCID: PMC9292615 DOI: 10.1093/aob/mcac061] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness, which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management. METHODS We studied the population genetic signatures of the local extinction of Biscutella laevigata subsp. gracilis populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as a surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations. KEY RESULTS Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both the spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as a powerful predictor of functional connectivity which may promote decision-making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination. CONCLUSIONS Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex situ population and a germination trial underlines the need for genetic rescue measures to prevent extinction of B. laevigata in Central Germany.
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Affiliation(s)
| | | | - Karen Runge
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg (Saale), Germany
| | - Philipp Brade
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg (Saale), Germany
| | - Sabrina Träger
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Große Steinstraße 79/80, 06108 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Christian Parisod
- University of Fribourg, Department of Biology, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Isabell Hensen
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Große Steinstraße 79/80, 06108 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
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25
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Cai L, Zhang H, Davis CC. PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data. APPLICATIONS IN PLANT SCIENCES 2022; 10:e11475. [PMID: 35774988 PMCID: PMC9215275 DOI: 10.1002/aps3.11475] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 06/15/2023]
Abstract
PREMISE The application of high-throughput sequencing, especially to herbarium specimens, is rapidly accelerating biodiversity research. Low-coverage sequencing of total genomic DNA (genome skimming) is particularly promising and can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here, we introduce PhyloHerb, a bioinformatic pipeline to efficiently assemble phylogenomic data sets derived from genome skimming. METHODS AND RESULTS PhyloHerb uses either a built-in database or user-specified references to extract orthologous sequences from all three genomes using a BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, partitioning, concatenation, and phylogeny inference. The program is freely available at https://github.com/lmcai/PhyloHerb/. CONCLUSIONS We demonstrate that PhyloHerb can accurately identify genes using a published data set from Clusiaceae. We also show via simulations that our approach is effective for highly fragmented assemblies from herbarium specimens and is scalable to thousands of species.
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Affiliation(s)
- Liming Cai
- Harvard University Herbaria22 Divinity Avenue, CambridgeMassachusetts02138USA
- Department of Integrative BiologyUniversity of Texas at AustinAustinTexas78712USA
- Department of Botany and Plant SciencesUniversity of CaliforniaRiversideCalifornia92507USA
| | - Hongrui Zhang
- Harvard University Herbaria22 Divinity Avenue, CambridgeMassachusetts02138USA
| | - Charles C. Davis
- Harvard University Herbaria22 Divinity Avenue, CambridgeMassachusetts02138USA
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Teixeira‐Costa L, Heberling JM, Wilson CA, Davis CC. Parasitic flowering plant collections embody the extended specimen. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13866] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Luiza Teixeira‐Costa
- Harvard University Herbaria Cambridge MA USA
- Hanse‐Wissenschaftskolleg – Institute for Advanced Study, Lehmkuhlenbusch 4, 27753 Delmenhorst Germany
| | | | - Carol A. Wilson
- University and Jepson Herbaria University of California, Berkeley, 1001 Valley Life Sciences Building Berkeley CA USA
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Nobis M, Klichowska E, Wolanin M, Nobis A, Nowak A. Typification of five plant names described based on specimens collected by Józef Warszewicz in Central and South America. PHYTOKEYS 2022; 192:45-61. [PMID: 35437384 PMCID: PMC8930917 DOI: 10.3897/phytokeys.192.78409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/19/2022] [Indexed: 06/14/2023]
Abstract
Józef Warszewicz (1812-1864) was one of the first Polish naturalists to explore the flora of the tropical New World. During two expeditions to Central and South America (1844-1850 and 1850-1853) he collected and delivered to Europe up to twenty thousand plant specimens. To honour his service and his achievements in plant collections, different taxonomists described more than 100 taxa using the surname Warszewicz, for example in the genus name (Warszewiczia) and the species epithets (warszewiczii, warscewiczii, warszewicziana). Unfortunately, a large part of Warszewicz's collection of plant species deposited in the Berlin Herbarium (B), including many type specimens was destroyed during World War II. During digitisation of herbarium collections preserved in the Herbarium of the Jagiellonian University (KRA), we reviewed more than 650 herbarium sheets with plant specimens collected by Warszewicz and originating from his trips to Central and South America. In this paper, we present the typification of five names of species, described base on Warszewicz's plant material. We select lectotypes for Berberiswarszewiczii, Esenbeckiawarscewiczii, Psammisiaramiflora, Remijiainvolucrata and Rondeletiaorthoneura, and provide data on the presence of 17 specimens (isotypes) representing Esenbeckiacornuta, an extremely rare species, that to date is known only from the type locality in Peru. A list of all Warszewicz's specimens preserved at KRA herbarium is also presented. Additionally, in the result of the revision of syntypes of Berberismultiflora and Rondeletiareflexa we designated here the lectotypes for these taxa.
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Affiliation(s)
- Marcin Nobis
- Institute of Botany, Jagiellonian University, Gronostajowa 3, 30–387 Kraków, PolandJagiellonian UniversityKrakówPoland
| | - Ewelina Klichowska
- Institute of Botany, Jagiellonian University, Gronostajowa 3, 30–387 Kraków, PolandJagiellonian UniversityKrakówPoland
| | - Mateusz Wolanin
- Institute of Biology and Biotechnology, Rzeszów University, Zelwerowicza 4, 35–601 Rzeszów, PolandRzeszów UniversityRzeszówPoland
| | - Agnieszka Nobis
- Institute of Botany, Jagiellonian University, Gronostajowa 3, 30–387 Kraków, PolandJagiellonian UniversityKrakówPoland
| | - Arkadiusz Nowak
- Institute of Biology, University of Opole, 45–052 Opole, PolandUniversity of OpoleOpolePoland
- Botanical Garden, Center for Biological Diversity Conservation, Polish Academy of Sciences, 02–976 Warszawa, PolandCenter for Biological Diversity Conservation, Polish Academy of SciencesWarszawaPoland
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Alfonso B, Sansón M, Sangil C, Expósito FJ, Díaz JP, Hernández JC. Herbarium macroalgae specimens reveal a rapid reduction of thallus size and reproductive effort related with climate change. MARINE ENVIRONMENTAL RESEARCH 2022; 174:105546. [PMID: 34968841 DOI: 10.1016/j.marenvres.2021.105546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/12/2021] [Accepted: 12/18/2021] [Indexed: 06/14/2023]
Abstract
Understanding and forecasting the effects of climate changes on vulnerable species are leading concerns for ecologists and conservation biologists. Herbaria are invaluable for use in long-term data series, and one of the few available methods for quantifying biodiversity changes over large periods of time. Gelidium canariense is an endemic and habitat-forming macroalga of the Canary Islands that coexists with two other habitat-forming Gelidiales: G. arbuscula and Pterocladiella capillacea. This study assesses long-term changes in thallus size and reproductive effort of all specimens deposited in the Herbarium of Universidad de La Laguna of these three Gelidiales species. Also assessed were the effects of seawater temperature and increased incident light on net primary production (NPP), and the effects of extreme desiccation conditions on the relative water content and NPP of the three Gelidiales species. The length of the thallus of the endemic species G. canariense was halved during the past 40 years. The shortening of the thallus coincided with a significant decrease in the number of reproductive structures in both Gelidium species. These morphological changes coincide with a significant increase of the sea surface temperature, air temperature above sea surface and ultraviolet radiation in the studied area. The experiments have revealed the deleterious effects of extreme desiccation and extreme irradiance on all three species. Hence, these results suggest that air temperature and irradiance are related with these morphological changes over time in the habitat-forming Gelidium species and that are most likely compromising the survival of their populations which are already declining.
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Affiliation(s)
- B Alfonso
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, Canary Islands, Spain.
| | - M Sansón
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, Canary Islands, Spain
| | - C Sangil
- Departamento de Botánica, Ecología y Fisiología Vegetal, Universidad de La Laguna, Canary Islands, Spain
| | - F J Expósito
- Departamento de Física, Universidad de La Laguna, Canary Islands, Spain
| | - J P Díaz
- Departamento de Física, Universidad de La Laguna, Canary Islands, Spain
| | - J C Hernández
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, Canary Islands, Spain
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Love NLR, Bonnet P, Goëau H, Joly A, Mazer SJ. Machine Learning Undercounts Reproductive Organs on Herbarium Specimens but Accurately Derives Their Quantitative Phenological Status: A Case Study of Streptanthus tortuosus. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112471. [PMID: 34834835 PMCID: PMC8623300 DOI: 10.3390/plants10112471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Machine learning (ML) can accelerate the extraction of phenological data from herbarium specimens; however, no studies have assessed whether ML-derived phenological data can be used reliably to evaluate ecological patterns. In this study, 709 herbarium specimens representing a widespread annual herb, Streptanthus tortuosus, were scored both manually by human observers and by a mask R-CNN object detection model to (1) evaluate the concordance between ML and manually-derived phenological data and (2) determine whether ML-derived data can be used to reliably assess phenological patterns. The ML model generally underestimated the number of reproductive structures present on each specimen; however, when these counts were used to provide a quantitative estimate of the phenological stage of plants on a given sheet (i.e., the phenological index or PI), the ML and manually-derived PI's were highly concordant. Moreover, herbarium specimen age had no effect on the estimated PI of a given sheet. Finally, including ML-derived PIs as predictor variables in phenological models produced estimates of the phenological sensitivity of this species to climate, temporal shifts in flowering time, and the rate of phenological progression that are indistinguishable from those produced by models based on data provided by human observers. This study demonstrates that phenological data extracted using machine learning can be used reliably to estimate the phenological stage of herbarium specimens and to detect phenological patterns.
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Affiliation(s)
- Natalie L. R. Love
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA;
- Biological Sciences Department, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Pierre Bonnet
- Botany and Modeling of Plant Architecture and Vegetation (AMAP), French Agricultural Research Centre for International Development (CIRAD), French National Centre for Scientific Research (CNRS), French National Institute for Agriculture, Food and Environment (INRAE), Research Institute for Development (IRD), University of Montpellier, 34398 Montpellier, France; (P.B.); (H.G.)
| | - Hervé Goëau
- Botany and Modeling of Plant Architecture and Vegetation (AMAP), French Agricultural Research Centre for International Development (CIRAD), French National Centre for Scientific Research (CNRS), French National Institute for Agriculture, Food and Environment (INRAE), Research Institute for Development (IRD), University of Montpellier, 34398 Montpellier, France; (P.B.); (H.G.)
| | - Alexis Joly
- ZENITH Team, Laboratory of Informatics, Robotics and Microelectronics-Joint Research Unit, Institut National de Recherche en Informatique et en Automatique (INRIA) Sophia-Antipolis, CEDEX 5, 34095 Montpellier, France;
| | - Susan J. Mazer
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA;
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Lofgren LA, Stajich JE. Fungal biodiversity and conservation mycology in light of new technology, big data, and changing attitudes. Curr Biol 2021; 31:R1312-R1325. [PMID: 34637742 PMCID: PMC8516061 DOI: 10.1016/j.cub.2021.06.083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Fungi have successfully established themselves across seemingly every possible niche, substrate, and biome. They are fundamental to biogeochemical cycling, interspecies interactions, food production, and drug bioprocessing, as well as playing less heroic roles as difficult to treat human infections and devastating plant pathogens. Despite community efforts to estimate and catalog fungal diversity, we have only named and described a minute fraction of the fungal world. The identification, characterization, and conservation of fungal diversity is paramount to preserving fungal bioresources, and to understanding and predicting ecosystem cycling and the evolution and epidemiology of fungal disease. Although species and ecosystem conservation are necessarily the foundation of preserving this diversity, there is value in expanding our definition of conservation to include the protection of biological collections, ecological metadata, genetic and genomic data, and the methods and code used for our analyses. These definitions of conservation are interdependent. For example, we need metadata on host specificity and biogeography to understand rarity and set priorities for conservation. To aid in these efforts, we need to draw expertise from diverse fields to tie traditional taxonomic knowledge to data obtained from modern -omics-based approaches, and support the advancement of diverse research perspectives. We also need new tools, including an updated framework for describing and tracking species known only from DNA, and the continued integration of functional predictions to link genetic diversity to functional and ecological diversity. Here, we review the state of fungal diversity research as shaped by recent technological advancements, and how changing viewpoints in taxonomy, -omics, and systematics can be integrated to advance mycological research and preserve fungal biodiversity.
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Affiliation(s)
- Lotus A Lofgren
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA.
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California-Riverside, Riverside, CA 92521, USA
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Meineke EK, Daru BH. Bias assessments to expand research harnessing biological collections. Trends Ecol Evol 2021; 36:1071-1082. [PMID: 34489117 DOI: 10.1016/j.tree.2021.08.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/22/2022]
Abstract
Biological collections are arguably the most important resources for investigations into the impacts of human activities on biodiversity. However, the apparent opportunities presented by museum-derived datasets have not resulted in consistent or widespread use of specimens in ecology outside phenological research and species distribution modeling. We attribute this gap between opportunity and application to biases introduced by collectors, curators, and preservation practices and an imperfect understanding of these biases and how to mitigate them. To facilitate broader use of specimen-based data, we characterize collection biases across key axes and explore interactions among them. We then present a framework for determining the bias assessments needed when extracting data from biological collections. We show that bias assessments required by particular ecological studies will depend on the response variables being measured and the predictor axes of interest. We argue that quantification of biases in specimen-derived datasets is needed to facilitate the widespread application of these data.
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Affiliation(s)
- Emily K Meineke
- Department of Entomology and Nematology, University of California, Davis 95616, CA, USA.
| | - Barnabas H Daru
- Department of Life Sciences, Texas A&M University-Corpus Christi, Corpus Christi, TX 78412, USA.
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Miller TK, Gallinat AS, Smith LC, Primack RB. Comparing fruiting phenology across two historical datasets: Thoreau's observations and herbarium specimens. ANNALS OF BOTANY 2021; 128:159-170. [PMID: 33830225 PMCID: PMC8324031 DOI: 10.1093/aob/mcab019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 02/10/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Fruiting remains under-represented in long-term phenology records, relative to leaf and flower phenology. Herbarium specimens and historical field notes can fill this gap, but selecting and synthesizing these records for modern-day comparison requires an understanding of whether different historical data sources contain similar information, and whether similar, but not equivalent, fruiting metrics are comparable with one another. METHODS For 67 fleshy-fruited plant species, we compared observations of fruiting phenology made by Henry David Thoreau in Concord, Massachusetts (1850s), with phenology data gathered from herbarium specimens collected across New England (mid-1800s to 2000s). To identify whether fruiting times and the order of fruiting among species are similar between datasets, we compared dates of first, peak and last observed fruiting (recorded by Thoreau), and earliest, mean and latest specimen (collected from herbarium records), as well as fruiting durations. KEY RESULTS On average, earliest herbarium specimen dates were earlier than first fruiting dates observed by Thoreau; mean specimen dates were similar to Thoreau's peak fruiting dates; latest specimen dates were later than Thoreau's last fruiting dates; and durations of fruiting captured by herbarium specimens were longer than durations of fruiting observed by Thoreau. All metrics of fruiting phenology except duration were significantly, positively correlated within (r: 0.69-0.88) and between (r: 0.59-0.85) datasets. CONCLUSIONS Strong correlations in fruiting phenology between Thoreau's observations and data from herbaria suggest that field and herbarium methods capture similar broad-scale phenological information, including relative fruiting times among plant species in New England. Differences in the timing of first, last and duration of fruiting suggest that historical datasets collected with different methods, scales and metrics may not be comparable when exact timing is important. Researchers should strongly consider matching methodology when selecting historical records of fruiting phenology for present-day comparisons.
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Affiliation(s)
- Tara K Miller
- Boston University, Biology Department, Boston, MA 02215, USA
| | - Amanda S Gallinat
- Department of Biology and Ecology Center, Utah State University, Logan, UT 84322, USA
| | - Linnea C Smith
- German Centre for Integrative Biodiversity Research, Leipzig 04103, Germany
- Institute of Biology, Leipzig University, Leipzig 04103, Germany
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33
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Auffret AG. Historical floras reflect broad shifts in flowering phenology in response to a warming climate. Ecosphere 2021. [DOI: 10.1002/ecs2.3683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Alistair G. Auffret
- Department of Ecology Swedish University of Agricultural Sciences Box 7044 Uppsala 75007 Sweden
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34
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Kommineni VK, Tautenhahn S, Baddam P, Gaikwad J, Wieczorek B, Triki A, Kattge J. Comprehensive leaf size traits dataset for seven plant species from digitised herbarium specimen images covering more than two centuries. Biodivers Data J 2021; 9:e69806. [PMID: 34316273 PMCID: PMC8292298 DOI: 10.3897/bdj.9.e69806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/30/2021] [Indexed: 11/12/2022] Open
Abstract
Background Morphological leaf traits are frequently used to quantify, understand and predict plant and vegetation functional diversity and ecology, including environmental and climate change responses. Although morphological leaf traits are easy to measure, their coverage for characterising variation within species and across temporal scales is limited. At the same time, there are about 3100 herbaria worldwide, containing approximately 390 million plant specimens dating from the 16th to 21st century, which can potentially be used to extract morphological leaf traits. Globally, plant specimens are rapidly being digitised and images are made openly available via various biodiversity data platforms, such as iDigBio and GBIF. Based on a pilot study to identify the availability and appropriateness of herbarium specimen images for comprehensive trait data extraction, we developed a spatio-temporal dataset on intraspecific trait variability containing 128,036 morphological leaf trait measurements for seven selected species. New information After scrutinising the metadata of digitised herbarium specimen images available from iDigBio and GBIF (21.9 million and 31.6 million images for Tracheophyta; accessed date December 2020), we identified approximately 10 million images potentially appropriate for our study. From the 10 million images, we selected seven species (Salixbebbiana Sarg., Alnusincana (L.) Moench, Violacanina L., Salixglauca L., Chenopodiumalbum L., Impatienscapensis Meerb. and Solanumdulcamara L.) , which have a simple leaf shape, are well represented in space and time and have high availability of specimens per species. We downloaded 17,383 images. Out of these, we discarded 5779 images due to quality issues. We used the remaining 11,604 images to measure the area, length, width and perimeter on 32,009 individual leaf blades using the semi-automated tool TraitEx. The resulting dataset contains 128,036 trait records. We demonstrate its comparability to trait data measured in natural environments following standard protocols by comparing trait values from the TRY database. We conclude that the herbarium specimens provide valuable information on leaf sizes. The dataset created in our study, by extracting leaf traits from the digitised herbarium specimen images of seven selected species, is a promising opportunity to improve ecological knowledge about the adaptation of size-related leaf traits to environmental changes in space and time.
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Affiliation(s)
- Vamsi Krishna Kommineni
- Max Planck Institute for Biogeochemistry, Jena, Germany Max Planck Institute for Biogeochemistry Jena Germany.,Ernst-Abbe-Hochschule Jena, Jena, Germany Ernst-Abbe-Hochschule Jena Jena Germany
| | - Susanne Tautenhahn
- Max Planck Institute for Biogeochemistry, Jena, Germany Max Planck Institute for Biogeochemistry Jena Germany
| | - Pramod Baddam
- Max Planck Institute for Biogeochemistry, Jena, Germany Max Planck Institute for Biogeochemistry Jena Germany.,Ernst-Abbe-Hochschule Jena, Jena, Germany Ernst-Abbe-Hochschule Jena Jena Germany
| | - Jitendra Gaikwad
- Friedrich Schiller University Jena, Jena, Germany Friedrich Schiller University Jena Jena Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
| | - Barbara Wieczorek
- Ernst-Abbe-Hochschule Jena, Jena, Germany Ernst-Abbe-Hochschule Jena Jena Germany
| | - Abdelaziz Triki
- University of Sfax, Sfax, Tunisia University of Sfax Sfax Tunisia
| | - Jens Kattge
- Max Planck Institute for Biogeochemistry, Jena, Germany Max Planck Institute for Biogeochemistry Jena Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig Leipzig Germany
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Hussein BR, Malik OA, Ong WH, Slik JWF. Automated Extraction of Phenotypic Leaf Traits of Individual Intact Herbarium Leaves from Herbarium Specimen Images Using Deep Learning Based Semantic Segmentation. SENSORS (BASEL, SWITZERLAND) 2021; 21:4549. [PMID: 34283110 PMCID: PMC8271859 DOI: 10.3390/s21134549] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 12/16/2022]
Abstract
With the increase in the digitization efforts of herbarium collections worldwide, dataset repositories such as iDigBio and GBIF now have hundreds of thousands of herbarium sheet images ready for exploration. Although this serves as a new source of plant leaves data, herbarium datasets have an inherent challenge to deal with the sheets containing other non-plant objects such as color charts, barcodes, and labels. Even for the plant part itself, a combination of different overlapping, damaged, and intact individual leaves exist together with other plant organs such as stems and fruits, which increases the complexity of leaf trait extraction and analysis. Focusing on segmentation and trait extraction on individual intact herbarium leaves, this study proposes a pipeline consisting of deep learning semantic segmentation model (DeepLabv3+), connected component analysis, and a single-leaf classifier trained on binary images to automate the extraction of an intact individual leaf with phenotypic traits. The proposed method achieved a higher F1-score for both the in-house dataset (96%) and on a publicly available herbarium dataset (93%) compared to object detection-based approaches including Faster R-CNN and YOLOv5. Furthermore, using the proposed approach, the phenotypic measurements extracted from the segmented individual leaves were closer to the ground truth measurements, which suggests the importance of the segmentation process in handling background noise. Compared to the object detection-based approaches, the proposed method showed a promising direction toward an autonomous tool for the extraction of individual leaves together with their trait data directly from herbarium specimen images.
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Affiliation(s)
- Burhan Rashid Hussein
- Digital Science, Faculty of Science, Universiti Brunei Darussalam, Tungku Link, Gadong BE1410, Brunei; (B.R.H.); (W.-H.O.)
| | - Owais Ahmed Malik
- Digital Science, Faculty of Science, Universiti Brunei Darussalam, Tungku Link, Gadong BE1410, Brunei; (B.R.H.); (W.-H.O.)
| | - Wee-Hong Ong
- Digital Science, Faculty of Science, Universiti Brunei Darussalam, Tungku Link, Gadong BE1410, Brunei; (B.R.H.); (W.-H.O.)
| | - Johan Willem Frederik Slik
- Department of Environmental Life Sciences, Faculty of Science, Universiti Brunei Darussalam, Tungku Link, Gadong BE1410, Brunei;
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Kozlov MV, Sokolova IV, Zverev V, Zvereva EL. Changes in plant collection practices from the 16th to 21st centuries: implications for the use of herbarium specimens in global change research. ANNALS OF BOTANY 2021; 127:865-873. [PMID: 33556168 PMCID: PMC8225282 DOI: 10.1093/aob/mcab016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 02/05/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND AND AIMS Herbaria were recently advertised as reliable sources of information regarding historical changes in plant traits and biotic interactions. To justify the use of herbaria in global change research, we asked whether the characteristics of herbarium specimens have changed during the past centuries and whether these changes were due to shifts in plant collection practices. METHODS We measured nine characteristics from 515 herbarium specimens of common European trees and large shrubs collected from 1558 to 2016. We asked botanists to rank these specimens by their scientific quality, and asked artists to rank these specimens by their beauty. KEY RESULTS Eight of 11 assessed characteristics of herbarium specimens changed significantly during the study period. The average number of leaves in plant specimens increased 3-fold, whereas the quality of specimen preparation decreased. Leaf size negatively correlated with leaf number in specimens in both among-species and within-species analyses. The proportion of herbarium sheets containing plant reproductive structures peaked in the 1850s. The scientific value of herbarium specimens increased until the 1700s, but then did not change, whereas their aesthetic value showed no systematic trends. CONCLUSIONS Our findings strongly support the hypothesis that many characteristics of herbarium specimens have changed systematically and substantially from the 16th to 21st centuries due to changes in plant collection and preservation practices. These changes may both create patterns which could be erroneously attributed to environmental changes and obscure historical trends in plant traits. The utmost care ought to be taken to guard against the possibility of misinterpretation of data obtained from herbarium specimens. We recommend that directional changes in characters of herbarium specimens which occurred during the past 150‒200 years, primarily in specimen size and in the presence of reproductive structures, are accounted for when searching for the effects of past environmental changes on plant traits.
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Affiliation(s)
| | - Irina V Sokolova
- Herbarium, V. L. Komarov Botanical Institute, Professora Popova Str. 2, 197376, St. Petersburg, Russia
| | - Vitali Zverev
- Department of Biology, University of Turku, Turku, Finland
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Meineke EK, Davis CC, Davies TJ. Phenological sensitivity to temperature mediates herbivory. GLOBAL CHANGE BIOLOGY 2021; 27:2315-2327. [PMID: 33735502 DOI: 10.1111/gcb.15600] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 02/18/2021] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
Species interactions drive ecosystem processes and are a major focus of global change research. Among the most consequential interactions expected to shift with climate change are those between insect herbivores and plants, both of which are highly sensitive to temperature. Insect herbivores and their host plants display varying levels of synchrony that could be disrupted or enhanced by climate change, yet empirical data on changes in synchrony are lacking. Using evidence of herbivory on herbarium specimens collected from the northeastern United States and France from 1900 to 2015, we provide evidence that plant species with temperature-sensitive phenologies experience higher levels of insect damage in warmer years, while less temperature-sensitive, co-occurring species do not. While herbivory might be mediated by interactions between warming and phenology through multiple pathways, we suggest that warming might lengthen growing seasons for phenologically sensitive plant species, exposing their leaves to herbivores for longer periods of time in warm years. We propose that elevated herbivory in warm years may represent a previously underappreciated cost to phenological tracking of climate change over longer timescales.
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Affiliation(s)
- Emily K Meineke
- Department of Entomology and Nematology, University of California, Davis, Davis, CA, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Cambridge, MA, USA
| | - T Jonathan Davies
- Departments of Botany, Forest & Conservation Sciences, University of British Columbia, Vancouver, BC, Canada
- African Centre for DNA Barcoding, University of Johannesburg, Johannesburg, South Africa
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38
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Zettlemoyer MA, Renaldi K, Muzyka MD, Lau JA. Extirpated prairie species demonstrate more variable phenological responses to warming than extant congeners. AMERICAN JOURNAL OF BOTANY 2021; 108:958-970. [PMID: 34133754 DOI: 10.1002/ajb2.1684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/20/2021] [Indexed: 06/12/2023]
Abstract
PREMISE Shifting phenology in response to climate is one mechanism that can promote population persistence and geographic spread; therefore, species with limited ability to phenologically track changing environmental conditions may be more susceptible to population declines. Alternatively, apparently nonresponding species may demonstrate divergent responses to multiple environmental conditions experienced across seasons. METHODS Capitalizing on herbarium records from across the midwestern United States and on detailed botanical surveys documenting local extinctions over the past century, we investigated whether extirpated and extant taxa differ in their phenological responses to temperature and precipitation during winter and spring (during flowering and the growing season before flowering) or in the magnitude of their flowering time shift over the past century. RESULTS Although warmer temperatures across seasons advanced flowering, extirpated and extant species differed in the magnitude of their phenological responses to winter and spring warming. Extirpated species demonstrated inconsistent phenological responses to warmer spring temperatures, whereas extant species consistently advanced flowering in response to warmer spring temperatures. In contrast, extirpated species advanced flowering more than extant species in response to warmer winter temperatures. Greater spring precipitation tended to delay flowering for both extirpated and extant taxa. Finally, both extirpated and extant taxa delayed flowering over time. CONCLUSIONS This study highlights the importance of understanding phenological responses to seasonal warming and indicates that extirpated species may demonstrate more variable phenological responses to temperature than extant congeners, a finding consistent with the hypothesis that appropriate phenological responses may reduce species' likelihood of extinction.
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Affiliation(s)
- Meredith A Zettlemoyer
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060-9505, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824-6406, USA
- Department of Plant Biology, University of Georgia, Athens, GA, 30602-5004, USA
| | | | | | - Jennifer A Lau
- Kellogg Biological Station, Michigan State University, Hickory Corners, MI, 49060-9505, USA
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824-6406, USA
- Department of Biology, Indiana University, Bloomington, IN, 47405-7005, USA
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Albani Rocchetti G, Armstrong CG, Abeli T, Orsenigo S, Jasper C, Joly S, Bruneau A, Zytaruk M, Vamosi JC. Reversing extinction trends: new uses of (old) herbarium specimens to accelerate conservation action on threatened species. THE NEW PHYTOLOGIST 2021; 230:433-450. [PMID: 33280123 DOI: 10.1111/nph.17133] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/22/2020] [Indexed: 05/29/2023]
Abstract
Although often not collected specifically for the purposes of conservation, herbarium specimens offer sufficient information to reconstruct parameters that are needed to designate a species as 'at-risk' of extinction. While such designations should prompt quick and efficient legal action towards species recovery, such action often lags far behind and is mired in bureaucratic procedure. The increase in online digitization of natural history collections has now led to a surge in the number new studies on the uses of machine learning. These repositories of species occurrences are now equipped with advances that allow for the identification of rare species. The increase in attention devoted to estimating the scope and severity of the threats that lead to the decline of such species will increase our ability to mitigate these threats and reverse the declines, overcoming a current barrier to the recovery of many threatened plant species. Thus far, collected specimens have been used to fill gaps in systematics, range extent, and past genetic diversity. We find that they also offer material with which it is possible to foster species recovery, ecosystem restoration, and de-extinction, and these elements should be used in conjunction with machine learning and citizen science initiatives to mobilize as large a force as possible to counter current extinction trends.
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Affiliation(s)
| | | | - Thomas Abeli
- Department of Science, University Roma Tre, Viale G. Marconi 446, Roma, 00154, Italy
| | - Simone Orsenigo
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, 27100, Italy
| | - Caroline Jasper
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Simon Joly
- Montreal Botanical Garden, Montréal, QC, H1X 2B2, Canada
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Anne Bruneau
- Département de Sciences Biologiques and Institut de Recherche en Biologie Végétale, Université de Montréal, Montréal, QC, H1X 2B2, Canada
| | - Maria Zytaruk
- Department of English, University of Calgary, Calgary, AB, T2N 1N4, Canada
| | - Jana C Vamosi
- Department of Biological Sciences, University of Calgary, Calgary, AB, T2N 1N4, Canada
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Sullivan CN, Koski MH. The effects of climate change on floral anthocyanin polymorphisms. Proc Biol Sci 2021; 288:20202693. [PMID: 33653138 DOI: 10.1098/rspb.2020.2693] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Pigmentation affords resistance to abiotic stressors, and thus can respond adaptively or plastically to drought and extreme temperatures associated with global change. Plants frequently display variability in flower coloration that is underlain by anthocyanin pigmentation. While anthocyanin polymorphisms impact plant-animal interactions, they also impact reproductive performance under abiotic stress. We used descriptions of flower colour from over 1900 herbarium records representing 12 North American species spanning 124 years to test whether anthocyanin-based flower colour has responded to global change. Based on demonstrated abiotic associations with performance of anthocyanin colour morphs, we predicted pigmentation would increase in species experiencing increased aridity, but decline in those experiencing larger increases in temperature. We found that the frequency of reports of pigmented morphs increased temporally in some taxa but displayed subtle declines in others. Pigmentation was negatively associated with temperature and positively associated with vapour pressure deficit (a metric of aridity) across taxa. Species experiencing larger temperature increases over time displayed reductions in pigmentation, while those experiencing increases in aridity displayed increases in pigmentation. Change in anthocyanin-based floral colour was thus linked with climatic change. Altered flower coloration has the strong potential to impact plant-animal interactions and overall plant reproductive performance.
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Affiliation(s)
- Cierra N Sullivan
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
| | - Matthew H Koski
- Department of Biological Sciences, Clemson University, Clemson, SC, USA
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41
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Hussein BR, Malik OA, Ong WH, Slik JWF. Reconstruction of damaged herbarium leaves using deep learning techniques for improving classification accuracy. ECOL INFORM 2021. [DOI: 10.1016/j.ecoinf.2021.101243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Manzano S, Julier ACM. How FAIR are plant sciences in the twenty-first century? The pressing need for reproducibility in plant ecology and evolution. Proc Biol Sci 2021; 288:20202597. [PMID: 33563121 DOI: 10.1098/rspb.2020.2597] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The need for open, reproducible science is of growing concern in the twenty-first century, with multiple initiatives like the widely supported FAIR principles advocating for data to be Findable, Accessible, Interoperable and Reusable. Plant ecological and evolutionary studies are not exempt from the need to ensure that the data upon which their findings are based are accessible and allow for replication in accordance with the FAIR principles. However, it is common that the collection and curation of herbarium specimens, a foundational aspect of studies involving plants, is neglected by authors. Without publicly available specimens, huge numbers of studies that rely on the field identification of plants are fundamentally not reproducible. We argue that the collection and public availability of herbarium specimens is not only good botanical practice but is also fundamental in ensuring that plant ecological and evolutionary studies are replicable, and thus scientifically sound. Data repositories that adhere to the FAIR principles must make sure that the original data are traceable to and re-examinable at their empirical source. In order to secure replicability, and adherence to the FAIR principles, substantial changes need to be brought about to restore the practice of collecting and curating specimens, to educate students of their importance, and to properly fund the herbaria which house them.
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Affiliation(s)
- Saúl Manzano
- Plant Conservation Unit, Department of Biological Sciences, HW Pearson Building, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa
| | - Adele C M Julier
- Plant Conservation Unit, Department of Biological Sciences, HW Pearson Building, University of Cape Town, Private Bag X3, Rondebosch 7701, South Africa
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Brussel T, Brewer SC. Functional Paleoecology and the Pollen-Plant Functional Trait Linkage. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2020.564609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Paleoecological investigations using the pollen-plant functional trait linkage are increasing in value as new insights to past ecological function and dynamics are revealed. These retrospective approaches link pollen sequences to plant functional trait measurements to reveal long-term changes in ecosystem properties that are difficult to resolve using traditional paleoecological methods. Despite these methodological improvements and the newfound perspectives, there has yet to be thorough testing of whether transforming pollen to ecological function tracks functional trait distributions in geographic space. We assess this in North America by linking surface pollen samples to measurements of three functional traits that represent major axes of plant ecological strategy. Pollen-derived estimates of function were first used to investigate occupied trait space at different scales. These estimates were used to reconstruct the latitudinal functional diversity gradient of North America, and results were compared to the continent’s functional diversity gradient estimated from tree assemblages and gradients based on pollen richness and evenness. Results indicated that the patterns in pollen-based function sufficiently track ecological function in trait and geographic space and the macroecological biodiversity pattern was reconstructed, although there were minor differences between the slopes of the functional diversity and each of the pollen index gradients. Taken together, the outcomes of our investigation indicate reliability in extending the pollen-plant functional trait linkage into deeper time, at least for examining North American functional dynamics.
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Shultz AJ, Adams BJ, Bell KC, Ludt WB, Pauly GB, Vendetti JE. Natural history collections are critical resources for contemporary and future studies of urban evolution. Evol Appl 2021; 14:233-247. [PMID: 33519967 PMCID: PMC7819571 DOI: 10.1111/eva.13045] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/04/2020] [Accepted: 06/09/2020] [Indexed: 12/30/2022] Open
Abstract
Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re-visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community-from practicing biologists to funding agencies and professional societies-must make adjustments that prioritize the collection and deposition of urban specimens.
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Affiliation(s)
- Allison J. Shultz
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Ornithology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Benjamin J. Adams
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Entomology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Department of Biological SciencesGeorge Washington UniversityWashingtonDCUSA
| | - Kayce C. Bell
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Mammalogy DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - William B. Ludt
- Ichthyology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Gregory B. Pauly
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Herpetology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
| | - Jann E. Vendetti
- Urban Nature Research CenterNatural History Museum of Los Angeles CountyLos AngelesCAUSA
- Malacology DepartmentNatural History Museum of Los Angeles CountyLos AngelesCAUSA
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45
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Raes N, Casino A, Goodson H, Islam S, Koureas D, Schiller E, Schulman L, Tilley L, Robertson T. White paper on the alignment and interoperability between the Distributed System of Scientific Collections (DiSSCo) and EU infrastructures - The case of the European Environment Agency (EEA). RESEARCH IDEAS AND OUTCOMES 2020. [DOI: 10.3897/rio.6.e62361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The Distributed System of Scientific Collections (DiSSCo) Research Infrastructure (RI) is presently in its preparatory phase. DiSSCo is developing a new distributed RI to operate as a one-stop-shop for the envisaged European Natural Science Collection (NSC) and all its derived information. Through mass digitisation, DiSSCo will transform the fragmented landscape of NSCs, including an estimated 1.5 billion specimens, into an integrated knowledge base that will provide interconnected evidence of the natural world. Data derived from European NSCs underpin countless discoveries and innovations, including tens of thousands of scholarly publications and official reports annually (supporting legislative and regulatory processes on sustainability, environmental change, land use, societal infrastructure, health, food, security, etc.); base-line biodiversity data; inventions and products essential to bio-economy; databases, maps and descriptions of scientific observations; educational material for students; and instructive and informative resources for the public. To expand the user community, DiSSCo will strengthen capacity building across Europe for maximum engagement of stakeholders in the biodiversity-related field and beyond, including industry and the private sector, but also policy-driving entities. Hence, it is opportune to reach out to relevant stakeholders in the European environmental policy domain represented by the European Environment Agency (EEA). The EEA aims to support sustainable development by helping to achieve significant and measurable improvement in Europe's environment, through the provision of timely, targeted, relevant and reliable information to policy-making agents and the public. The EEA provides information through the European Environment Information and Observation System (Eionet). The aim of this white paper is to open the discussion between DiSSCo and the EEA and identify the common service interests that are relevant for the European environmental policy domain. The first section describes the significance of (digital) Natural Science Collections (NHCs). Section two describes the DiSSCo programme with all DiSSCo aligned projects. Section three provides background information on the EEA and the biodiversity infrastructures that are developed and maintained by the EEA. The fourth section illustrates a number of use cases where the DiSSCo consortium sees opportunities for interaction between the DiSSCo RI and the Eionet portal of the EEA. Opening the discussion with the EEA in this phase of maturity of DiSSCo will ensure that the infrastructural design of DiSSCo and the development of e-Services accommodate the present and future needs of the EEA and assure data interoperability between the two infrastructures.
The aim of this white paper is to present benefits from identifying the common service interests of DiSSCo and the EEA. A brief introduction to natural science collections as well as the two actors is given to facilitate the understanding of the needs and possibilities in the alignment of DiSSCo with the EEA.
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Abstract
Dead museum specimens are finding new life, providing critical data about otherwise hidden impacts of human-caused environmental change. New research powerfully leverages decades of plant collections to uncover global responses in floral pigmentation linked to ozone and climate change.
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Affiliation(s)
- J Mason Heberling
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, PA 15213, USA.
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47
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Perez TM, Rodriguez J, Mason Heberling J. Herbarium-based measurements reliably estimate three functional traits. AMERICAN JOURNAL OF BOTANY 2020; 107:1457-1464. [PMID: 32945535 DOI: 10.1002/ajb2.1535] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/25/2020] [Indexed: 06/11/2023]
Abstract
PREMISE The use of functional traits has surged in recent decades, providing new insights ranging from individual plant fitness to ecosystem processes. Global plant trait databases have advanced our understanding of plant functional diversity, but they remain incomplete because of geographic and taxonomic biases. Herbarium specimens may help fill these gaps by providing trait information across space and time. We tested whether herbarium specimen-derived measurements are reliable estimates of three important, commonly measured functional traits-specific leaf area (SLA), branch wood specific gravity, and leaf thickness. METHODS Leaves and branches were collected from species cultivated at Fairchild Tropical Botanic Garden and Florida International University in Miami, FL, USA. Fresh components of SLA (area), branch wood specific gravity (volume), and leaf thickness were measured following standard trait measurement protocols. We compared these trait values to corresponding measurements using plant tissues dried in a plant press following standard herbarium plant collecting protocols. RESULTS Herbarium-derived trait measurements (dried tissues) were highly correlated with those measured using fresh tissues following standard protocols (SLA: R2 = 0.72-0.97, p < 0.01; wood specific gravity: R2 = 0.74-0.75, p < 0.01; leaf thickness: R2 = 0.96, p < 0.01). However, except for leaf thickness, linear model slope or intercept coefficients differed from 1, indicating herbarium-derived trait measurements may provide biased estimates of fresh traits without the use of correction factors. CONCLUSIONS Herbarium-derived traits cannot always be used interchangeably with those measured from fresh tissues because of tissue shrinkage. However, herbarium-derived trait data still have the potential to drastically expand the temporal, geographic, and taxonomic scope of global trait databases.
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Affiliation(s)
- Timothy M Perez
- Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
- Fairchild Tropical Botanic Garden, Coral Gables, FL, 33156, USA
| | - Jessica Rodriguez
- Department of Earth and Environment, Florida International University, Miami, FL, 33199, USA
| | - J Mason Heberling
- Section of Botany, Carnegie Museum of Natural History, Pittsburgh, PA, 15213, USA
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Koski MH, MacQueen D, Ashman TL. Floral Pigmentation Has Responded Rapidly to Global Change in Ozone and Temperature. Curr Biol 2020; 30:4425-4431.e3. [PMID: 32946752 DOI: 10.1016/j.cub.2020.08.077] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/03/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022]
Abstract
Across kingdoms, organisms ameliorate UV stress by increasing UV-absorbing pigmentation. Rapid ozone degradation during the 20th century resulted in elevated UV incidence, but pigmentation responses to this aspect of global change have yet to be demonstrated. In flowering plants, UV exposure favors larger areas of UV-absorbing pigmentation on petals, which protects pollen from UV-damage. Pigmentation also affects floral thermoregulation, suggesting climate warming may additionally impact pigmentation. We used 1,238 herbarium specimens collected from 1941 to 2017 to test whether change in UV floral pigmentation was associated with altered ozone and temperature in 42 species spanning three continents. We tested three predictions: first, UV-absorbing pigmentation will increase temporally and be correlated with reduced ozone (higher UV) when accounting for effects of temperature; second, taxa that experienced larger ozone declines will display larger increases in pigmentation; and third, taxa with anthers exposed to ambient UV will respond more strongly than those with anthers protected by petals. Globally, the extent of petal UV pigmentation increased significantly across taxa by ∼2% per year. However, temporal change was species specific-increasing in some taxa but declining in others. Species with exposed anthers experiencing larger declines in ozone displayed more dramatic pigmentation increases. For taxa with anthers enclosed within petals, pigmentation declined with increases in temperature, supporting a thermoregulatory role of UV pigmentation. Results document a rapid phenotypic response of floral pigmentation to anthropogenic climatic change, suggesting that global change may alter pollination through its impact on floral color, with repercussions for plant reproductive fitness.
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Affiliation(s)
- Matthew H Koski
- Clemson University, Department of Biological Sciences, Clemson, SC 29631, USA; University of Virginia, Department of Biology, Charlottesville, VA 22904, USA.
| | - Drew MacQueen
- University of Virginia Library Scholars Lab, PO Box 40010, Charlottesville, VA 22904-4129, USA
| | - Tia-Lynn Ashman
- University of Pittsburgh, Department of Biological Sciences, Pittsburgh, PA 15260, USA
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Biederman LA, Weldon SM, Anderson DS, Leoschke MJ. Precipitation contributes to plant height, but not reproductive effort, for western prairie fringed orchid ( Platanthera praeclara Sheviak & Bowles): Evidence from herbarium records. Ecol Evol 2020; 10:9532-9537. [PMID: 32953081 PMCID: PMC7487221 DOI: 10.1002/ece3.6647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/10/2020] [Accepted: 07/17/2020] [Indexed: 11/07/2022] Open
Abstract
The western fringed prairie orchid (WFPO) is a rare plant found in mesic to wet tallgrass prairies in the Great Plains and Midwest regions of the United States. The size of WFPO populations varies considerably from year to year, and studies have suggested that population size is dependent on precipitation during critical periods in the plant's annual development. We hypothesized that plant height and reproductive effort would also be controlled by precipitation, either during these periods or over a broader period. We acquired available images of WFPO from 21 herbaria, and of these 141 individual plants had information adequate for analysis, although some population/year combinations were represented multiple times. For each specimen, we measured plant height (cm) and reproductive effort (as measured by total flower and bud count). We used bootstrapped linear regression, randomly selecting one individual from each population/year combination, to compare precipitation models, both during critical periods and the various summaries. We found that precipitation during the phenologically critical periods was a poor predictor of plant height and reproductive effort. Of the broader precipitation variables, accumulated precipitation from January 1 to collection date best described plant height. We also used correlations to detect a relationship among the variables WFPO height, reproductive effort, precipitation, latitude, and year of collection. Year of specimen collection was negatively correlated with WFPO plant height and accumulated precipitation, suggesting that both have declined in more recent years. Negative correlations with latitude also suggest height and precipitation decrease in the northern part of WFPO's range. Reproductive effort was not related to tested precipitation variables; however, it was weakly correlated with plant height. Although the results are limited, this study leverages available data and makes inferences on WFPO biology over broad ranges of time (1894-2012) and latitude (37.5°-49.9°).
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Affiliation(s)
- Lori A. Biederman
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIowaUSA
| | - Sydney M. Weldon
- Department of Ecology, Evolution and Organismal BiologyIowa State UniversityAmesIowaUSA
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Pérez-Escobar OA, Richardson JE, Howes MJR, Lucas E, Álvarez de Róman N, Collemare J, Graham IA, Gratzfeld J, Kersey PJ, Leitch IJ, Paton A, Hollingsworth PM, Antonelli A. Untapped resources for medical research. Science 2020; 369:781-782. [DOI: 10.1126/science.abc8085] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
| | - James E. Richardson
- Department of Biology, Faculty of Natural Sciences, Universidad del Rosario, Bogotá, Colombia
- Royal Botanic Garden Edinburgh, Edinburgh, EH3 5LR, UK
| | - Melanie-Jayne R. Howes
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Institute of Pharmaceutical Science, Faculty of Life Sciences & Medicine, King's College London, SE1 9NH, UK
| | - Eve Lucas
- Royal Botanic Gardens, Kew, TW9 3AE, UK
| | | | | | - Ian A. Graham
- Department of Biology, Centre for Novel Agricultural Products, University of York, York, YO10 5DD, UK
| | | | | | | | | | | | - Alexandre Antonelli
- Royal Botanic Gardens, Kew, TW9 3AE, UK
- Gothenburg Global Biodiversity Centre and University of Gothenburg, Gothenburg, Sweden
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