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Zhang J, Xiao C, Duan X, Gao X, Zeng H, Dong R, Feng G, Ma K. Species' geographical range, environmental range and traits lead to specimen collection preference of dominant plant species of grasslands in Northern China. PLANT DIVERSITY 2024; 46:353-361. [PMID: 38798734 PMCID: PMC11119519 DOI: 10.1016/j.pld.2024.02.001] [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: 09/01/2023] [Revised: 01/19/2024] [Accepted: 02/01/2024] [Indexed: 05/29/2024]
Abstract
Many different factors, such as species traits, socio-economic factors, geographical and environmental factors, can lead to specimen collection preference. This study aims to determine whether grassland specimen collection in China is preferred by species traits (i.e., plant height, flowering and fruiting period), environmental range (i.e., the temperature and precipitation range) and geographical range (i.e., distribution range and altitudinal range). Ordinary least squares models and phylogenetic generalized linear mixed models were used to analyze the relationships between specimen number and the explanatory variables. Random Forest models were then used to find the most parsimonious multivariate model. The results showed that interannual variation in specimen number between 1900 and 2020 was considerable. Specimen number of these species in southeast China was notably lower than that in northwest China. Environmental range and geographical range of species had significant positive correlations with specimen number. In addition, there were relatively weak but significant associations between specimen number and species trait (i.e., plant height and flowering and fruiting period). Random Forest models indicated that distribution range was the most important variable, followed by flowering and fruiting period, and altitudinal range. These findings suggest that future floristic surveys should pay more attention to species with small geographical range, narrow environmental range, short plant height, and short flowering and fruiting period. The correction of specimen collection preference will also make the results of species distribution model, species evolution and other works based on specimen data more accurate.
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Affiliation(s)
- Jingya Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Cui Xiao
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Xiaoyu Duan
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Xin Gao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Hao Zeng
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Rong'an Dong
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Gang Feng
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot 010021, China
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
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Yim C, Bellis ES, DeLeo VL, Gamba D, Muscarella R, Lasky JR. Climate biogeography of Arabidopsis thaliana: linking distribution models and individual variation. JOURNAL OF BIOGEOGRAPHY 2024; 51:560-574. [PMID: 38596256 PMCID: PMC11000247 DOI: 10.1111/jbi.14737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 09/19/2023] [Indexed: 04/11/2024]
Abstract
AIM Patterns of individual variation are key to testing hypotheses about the mechanisms underlying biogeographic patterns. If species distributions are determined by environmental constraints, then populations near range margins may have reduced performance and be adapted to harsher environments. Model organisms are potentially important systems for biogeographical studies, given the available range-wide natural history collections, and the importance of providing biogeographical context to their genetic and phenotypic diversity. LOCATION Global. TAXON Arabidopsis thaliana ("Arabidopsis"). METHODS We fit occurrence records to climate data, and then projected the distribution of Arabidopsis under last glacial maximum, current, and future climates. We confronted model predictions with individual performance measured on 2,194 herbarium specimens, and we asked whether predicted suitability was associated with life-history and genomic variation measured on ~900 natural accessions. RESULTS The most important climate variables constraining the Arabidopsis distribution were winter cold in northern and high elevation regions and summer heat in southern regions. Herbarium specimens from regions with lower habitat suitability in both northern and southern regions were smaller, supporting the hypothesis that the distribution of Arabidopsis is constrained by climate-associated factors. Climate anomalies partly explained interannual variation in herbarium specimen size, but these did not closely correspond to local limiting factors identified in the distribution model. Late-flowering genotypes were absent from the lowest suitability regions, suggesting slower life histories are only viable closer to the center of the realized niche. We identified glacial refugia farther north than previously recognized, as well as refugia concordant with previous population genetic findings. Lower latitude populations, known to be genetically distinct, are most threatened by future climate change. The recently colonized range of Arabidopsis was well-predicted by our native-range model applied to certain regions but not others, suggesting it has colonized novel climates. MAIN CONCLUSIONS Integration of distribution models with performance data from vast natural history collections is a route forward for testing biogeographical hypotheses about species distributions and their relationship with evolutionary fitness across large scales.
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Affiliation(s)
- Christina Yim
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Emily S. Bellis
- Department of Biology, Pennsylvania State University, University Park, USA
- Department of Computer Science, Arkansas State University, Jonesboro, USA
| | - Victoria L. DeLeo
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Diana Gamba
- Department of Biology, Pennsylvania State University, University Park, USA
| | - Robert Muscarella
- Plant Ecology and Evolution, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
| | - Jesse R. Lasky
- Department of Biology, Pennsylvania State University, University Park, USA
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3
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Jones CB, Stock K, Perkins SE. AI-based discovery of habitats from museum collections. Trends Ecol Evol 2024; 39:323-327. [PMID: 38355366 DOI: 10.1016/j.tree.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/21/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024]
Abstract
Museum collection records are a source of historic data for species occurrence, but little attention is paid to the associated descriptions of habitat at the sample locations. We propose that artificial intelligence methods have potential to use these descriptions for reconstructing past habitat, to address ecological and evolutionary questions.
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Affiliation(s)
- Christopher B Jones
- School of Computer Science and Informatics, Cardiff University, Cardiff, UK.
| | - Kristin Stock
- Massey Geoinformatics Collaboratory, Massey University, Palmerston North, New Zealand
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Patten NN, Gaynor ML, Soltis DE, Soltis PS. Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs): An R package and workflow for processing biodiversity data. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11575. [PMID: 38638614 PMCID: PMC11022233 DOI: 10.1002/aps3.11575] [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: 05/24/2023] [Revised: 01/07/2024] [Accepted: 01/14/2024] [Indexed: 04/20/2024]
Abstract
Premise Digitized biodiversity data offer extensive information; however, obtaining and processing biodiversity data can be daunting. Complexities arise during data cleaning, such as identifying and removing problematic records. To address these issues, we created the R package Geographic And Taxonomic Occurrence R-based Scrubbing (gatoRs). Methods and Results The gatoRs workflow includes functions that streamline downloading records from the Global Biodiversity Information Facility (GBIF) and Integrated Digitized Biocollections (iDigBio). We also created functions to clean downloaded specimen records. Unlike previous R packages, gatoRs accounts for differences in download structure between GBIF and iDigBio and allows for user control via interactive cleaning steps. Conclusions Our pipeline enables the scientific community to process biodiversity data efficiently and is accessible to the R coding novice. We anticipate that gatoRs will be useful for both established and beginning users. Furthermore, we expect our package will facilitate the introduction of biodiversity-related concepts into the classroom via the use of herbarium specimens.
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Affiliation(s)
- Natalie N. Patten
- Department of MathematicsUniversity of FloridaGainesville32611FloridaUSA
- Present address:
Department of MathematicsThe Ohio State UniversityColumbus43210OhioUSA
| | - Michelle L. Gaynor
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
- Department of BiologyUniversity of FloridaGainesville32611FloridaUSA
| | - Douglas E. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
- Department of BiologyUniversity of FloridaGainesville32611FloridaUSA
| | - Pamela S. Soltis
- Florida Museum of Natural HistoryUniversity of FloridaGainesville32611FloridaUSA
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Ramirez-Parada TH, Park IW, Record S, Davis CC, Ellison AM, Mazer SJ. Plasticity and not adaptation is the primary source of temperature-mediated variation in flowering phenology in North America. Nat Ecol Evol 2024; 8:467-476. [PMID: 38212525 DOI: 10.1038/s41559-023-02304-5] [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: 07/01/2023] [Accepted: 12/08/2023] [Indexed: 01/13/2024]
Abstract
Phenology varies widely over space and time because of its sensitivity to climate. However, whether phenological variation is primarily generated by rapid organismal responses (plasticity) or local adaptation remains unresolved. Here we used 1,038,027 herbarium specimens representing 1,605 species from the continental United States to measure flowering-time sensitivity to temperature over time (Stime) and space (Sspace). By comparing these estimates, we inferred how adaptation and plasticity historically influenced phenology along temperature gradients and how their contributions vary among species with different phenology and native climates and among ecoregions differing in species composition. Parameters Sspace and Stime were positively correlated (r = 0.87), of similar magnitude and more frequently consistent with plasticity than adaptation. Apparent plasticity and adaptation generated earlier flowering in spring, limited responsiveness in late summer and delayed flowering in autumn in response to temperature increases. Nonetheless, ecoregions differed in the relative contributions of adaptation and plasticity, from consistently greater importance of plasticity (for example, southeastern United States plains) to their nearly equal importance throughout the season (for example, Western Sierra Madre Piedmont). Our results support the hypothesis that plasticity is the primary driver of flowering-time variation along temperature gradients, with local adaptation having a widespread but comparatively limited role.
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Affiliation(s)
- Tadeo H Ramirez-Parada
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA.
| | - Isaac W Park
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Sydne Record
- Department of Wildlife, Fisheries and Conservation Biology, University of Maine, Orono, ME, USA
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Aaron M Ellison
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Sound Solutions for Sustainable Science, Boston, MA, USA
| | - Susan J Mazer
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
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Hightower AT, Chitwood DH, Josephs EB. Herbarium specimens reveal links between Capsella bursa-pastoris leaf shape and climate. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580180. [PMID: 38405842 PMCID: PMC10888959 DOI: 10.1101/2024.02.13.580180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Studies into the evolution and development of leaf shape have connected variation in plant form, function, and fitness. For species with consistent leaf margin features, patterns in leaf architecture are related to both biotic and abiotic factors. However, for species with inconsistent leaf margin features, quantifying leaf shape variation and the effects of environmental factors on leaf shape has proven challenging. To investigate leaf shape variation in species with inconsistent shapes, we analyzed approximately 500 digitized Capsella bursa-pastoris specimens collected throughout the continental U.S. over a 100-year period with geometric morphometric modeling and deterministic techniques. We generated a morphospace of C. bursa-pastoris leaf shapes and modeled leaf shape as a function of environment and time. Our results suggest C. bursa-pastoris leaf shape variation is strongly associated with temperature over the C. bursa-pastoris growing season, with lobing decreasing as temperature increases. While we expected to see changes in variation over time, our results show that level of leaf shape variation is consistent over the 100-year period. Our findings showed that species with inconsistent leaf shape variation can be quantified using geometric morphometric modeling techniques and that temperature is the main environmental factor influencing leaf shape variation.
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Affiliation(s)
- Asia T Hightower
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824-1226
- Ecology, Evolution, & Behavior Program, Michigan State University, 567 Wilson Rd, East Lansing, MI 48824-1226
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824-1226
| | - Daniel H Chitwood
- Department of Horticulture, Michigan State University, 1066 Bogue Street, East Lansing, MI 48824-1226
- Department of Computational Mathematics, Science, and Engineering, Michigan State University, 428 S Shaw Ln, East Lansing, MI 48824-1226
| | - Emily B Josephs
- Department of Plant Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824-1226
- Ecology, Evolution, & Behavior Program, Michigan State University, 567 Wilson Rd, East Lansing, MI 48824-1226
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824-1226
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Folk RA, Guralnick RP, LaFrance RT. FloraTraiter: Automated parsing of traits from descriptive biodiversity literature. APPLICATIONS IN PLANT SCIENCES 2024; 12:e11563. [PMID: 38369975 PMCID: PMC10873814 DOI: 10.1002/aps3.11563] [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: 06/06/2023] [Revised: 09/13/2023] [Accepted: 10/01/2023] [Indexed: 02/20/2024]
Abstract
Premise Plant trait data are essential for quantifying biodiversity and function across Earth, but these data are challenging to acquire for large studies. Diverse strategies are needed, including the liberation of heritage data locked within specialist literature such as floras and taxonomic monographs. Here we report FloraTraiter, a novel approach using rule-based natural language processing (NLP) to parse computable trait data from biodiversity literature. Methods FloraTraiter was implemented through collaborative work between programmers and botanical experts and customized for both online floras and scanned literature. We report a strategy spanning optical character recognition, recognition of taxa, iterative building of traits, and establishing linkages among all of these, as well as curational tools and code for turning these results into standard morphological matrices. Results Over 95% of treatment content was successfully parsed for traits with <1% error. Data for more than 700 taxa are reported, including a demonstration of common downstream uses. Conclusions We identify strategies, applications, tips, and challenges that we hope will facilitate future similar efforts to produce large open-source trait data sets for broad community reuse. Largely automated tools like FloraTraiter will be an important addition to the toolkit for assembling trait data at scale.
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Affiliation(s)
- Ryan A. Folk
- Department of Biological SciencesMississippi State UniversityMississippi StateMississippiUSA
| | - Robert P. Guralnick
- Florida Museum of Natural HistoryUniversity of FloridaGainesvilleFloridaUSA
- Biodiversity InstituteUniversity of FloridaGainesvilleFloridaUSA
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8
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Kim AS, Kreiner JM, Hernández F, Bock DG, Hodgins KA, Rieseberg LH. Temporal collections to study invasion biology. Mol Ecol 2023; 32:6729-6742. [PMID: 37873879 DOI: 10.1111/mec.17176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/07/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023]
Abstract
Biological invasions represent an extraordinary opportunity to study evolution. This is because accidental or deliberate species introductions have taken place for centuries across large geographical scales, frequently prompting rapid evolutionary transitions in invasive populations. Until recently, however, the utility of invasions as evolutionary experiments has been hampered by limited information on the makeup of populations that were part of earlier invasion stages. Now, developments in ancient and historical DNA technologies, as well as the quickening pace of digitization for millions of specimens that are housed in herbaria and museums globally, promise to help overcome this obstacle. In this review, we first introduce the types of temporal data that can be used to study invasions, highlighting the timescale captured by each approach and their respective limitations. We then discuss how ancient and historical specimens as well as data available from prior invasion studies can be used to answer questions on mechanisms of (mal)adaptation, rates of evolution, or community-level changes during invasions. By bridging the gap between contemporary and historical invasive populations, temporal data can help us connect pattern to process in invasion science. These data will become increasingly important if invasions are to achieve their full potential as experiments of evolution in nature.
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Affiliation(s)
- Amy S Kim
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Julia M Kreiner
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Fernando Hernández
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Dan G Bock
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn A Hodgins
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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Xie Y, Thammavong HT, Berry LG, Huang CH, Park DS. Sex-dependent phenological responses to climate vary across species' ranges. Proc Natl Acad Sci U S A 2023; 120:e2306723120. [PMID: 37956437 PMCID: PMC10691327 DOI: 10.1073/pnas.2306723120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/27/2023] [Indexed: 11/15/2023] Open
Abstract
Anthropogenic climate change has significantly altered the flowering times (i.e., phenology) of plants worldwide, affecting their reproduction, survival, and interactions. Recent studies utilizing herbarium specimens have uncovered significant intra- and inter-specific variation in flowering phenology and its response to changes in climate but have mostly been limited to animal-pollinated species. Thus, despite their economic and ecological importance, variation in phenological responses to climate remain largely unexplored among and within wind-pollinated dioecious species and across their sexes. Using both herbarium specimens and volunteer observations of cottonwood (Populus) species, we examined how phenological sensitivity to climate varies across species, their ranges, sexes, and phenophases. The timing of flowering varied significantly across and within species, as did their sensitivity to spring temperature. In particular, male flowering generally happened earlier in the season and was more sensitive to warming than female flowering. Further, the onset of flowering was more sensitive to changes in temperature than leaf out. Increased temporal gaps between male and female flowering time and between the first open flower date and leaf out date were predicted for the future under two climate change scenarios. These shifts will impact the efficacy of sexual reproduction and gene flow among species. Our study demonstrates significant inter- and intra-specific variation in phenology and its responses to environmental cues, across species' ranges, phenophases, and sex, in wind-pollinated species. These variations need to be considered to predict accurately the effects of climate change and assess their ecological and evolutionary consequences.
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Affiliation(s)
- Yingying Xie
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN47907
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY41099
| | - Hanna T. Thammavong
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
| | - Lily G. Berry
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN47907
| | - Chingyan H. Huang
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
| | - Daniel S. Park
- Department of Biological Sciences, Purdue University, West Lafayette, IN47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN47907
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Ramírez-Barahona S, Cuervo-Robayo AP, Magallón S. Assessing digital accessible botanical knowledge and priorities for exploration and discovery of plant diversity across Mesoamerica. THE NEW PHYTOLOGIST 2023; 240:1659-1672. [PMID: 37571871 DOI: 10.1111/nph.19190] [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: 03/17/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023]
Abstract
Digital accessible biodiversity knowledge has the potential to greatly advance botanical research and guide conservation efforts. Evaluating its shortfalls is key to understanding its limits and prioritising regions in need of renewed survey efforts. We used the Royal Botanical Gardens Kew's World Checklist of Vascular Plants to parse publicly available occurrence data downloaded from the Global Biodiversity Information Facility and quantify the spatial distribution of spatial, phylogenetic, and temporal data shortfalls across Mesoamerica. After processing 3578 777 occurrence records for 32 522 species of vascular plants across Mesoamerica, we found evidence of poor data coverage: incomplete characterisation of species diversity, old occurrence records, and low phylogenetic representation. One-third of the region showed large gaps for at least one of these dimensions (hotspots) and < 15% had adequate data coverage across dimensions. Overall, the shortfalls we identified compromise the quality of digitally available occurrence data and hamper research on spatial phylogenetics and species dynamics under anthropogenic disturbances. Our analyses identified areas of opportunity for increased efforts in data digitisation, botanical exploration, sequencing, and biodiversity monitoring. These efforts would serve to increase and rejuvenate knowledge on the geographic distribution of vascular plants in Mesoamerica.
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Affiliation(s)
- Santiago Ramírez-Barahona
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico, 04510, Mexico
| | - Angela P Cuervo-Robayo
- Departamento de Zoología, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico, 04510, Mexico
| | - Susana Magallón
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, Mexico, 04510, Mexico
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Roma-Marzio F, Maccioni S, Dolci D, Astuti G, Magrini N, Pierotti F, Vangelisti R, Amadei L, Peruzzi L. Digitization of the historical Herbarium of Michele Guadagno at Pisa (PI-GUAD). PHYTOKEYS 2023; 234:107-125. [PMID: 37868742 PMCID: PMC10587777 DOI: 10.3897/phytokeys.234.109464] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 09/29/2023] [Indexed: 10/24/2023]
Abstract
The herbarium digitization process is an essential first step in transforming the vast amount of data associated with a physical specimen into flexible digital data formats. In this framework, the Herbarium of the University of Pisa (international code PI), at the end of 2018 started a process of digitization focusing on one of its most relevant collections: the Herbarium of Michele Guadagno (1878-1930). This scholar studied flora and vegetation of different areas of southern Italy, building a large herbarium including specimens collected by himself, plus many specimens obtained through exchanges with Italian and foreign botanists. The Herbarium is composed by 547 packages of vascular plants. Metadata were entered into the online database Virtual Herbaria JACQ and mirrored into a personalized virtual Herbarium of the Botanic Museum. After the completion of the digitization process, the number of sheets preserved in the Herbarium amounts to 44,345. Besides Guadagno, who collected 42% of his specimens, a further 1,102 collectors are represented. Most specimens were collected in Europe (91%), but all the continents are represented. As expected, Italy is the most represented country (59%), followed by France, Spain, Germany, and Greece. The specimens cover a time span of 99 years, from 1830 to 1929, whereas the specimens collected by Guadagno range between 1889 and 1928. Furthermore, we traced 134 herbarium sheets associated with documents, among which 75 drawings handmade by Guadagno, 34 letters from various corresponding authors, 16 copies of publications, and 14 copies of published iconographies.
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Affiliation(s)
- Francesco Roma-Marzio
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Simonetta Maccioni
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - David Dolci
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Giovanni Astuti
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Nicoletta Magrini
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Federica Pierotti
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Roberta Vangelisti
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Lucia Amadei
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
| | - Lorenzo Peruzzi
- Orto e Museo Botanico, Sistema Museale d’Ateneo, Università di Pisa, via Ghini 13, 56126 Pisa, ItalyUniversità di PisaPisaItaly
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Bisang I, Ehrlén J, Hedenäs L. Life-history characteristics and historical factors are important to explain regional variation in reproductive traits and genetic diversity in perennial mosses. ANNALS OF BOTANY 2023; 132:29-42. [PMID: 36928083 PMCID: PMC10550275 DOI: 10.1093/aob/mcad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 03/15/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND AND AIMS Plants have evolved an unrivalled diversity of reproductive strategies, including variation in the degree of sexual vs. clonal reproduction. This variation has important effects on the dynamics and genetic structure of populations. We examined the association between large-scale variation in reproductive patterns and intraspecific genetic diversity in two moss species where sex is manifested in the dominant haploid generation and sex expression is irregular. We predicted that in regions with more frequent realized sexual reproduction, populations should display less skewed sex ratios, should more often express sex and should have higher genetic diversity than in regions with largely clonal reproduction. METHODS We assessed reproductive status and phenotypic sex in the dioicous long-lived Drepanocladus trifarius and D. turgescens, in 248 and 438 samples across two regions in Scandinavia with frequent or rare realized sexual reproduction, respectively. In subsets of the samples, we analysed genetic diversity using nuclear and plastid sequence information and identified sex with a sex-specific molecular marker in non-reproductive samples. KEY RESULTS Contrary to our predictions, sex ratios did not differ between regions; genetic diversity did not differ in D. trifarius and it was higher in the region with rare sexual reproduction in D. turgescens. Supporting our predictions, relatively more samples expressed sex in D. trifarius in the region with frequent sexual reproduction. Overall, samples were mostly female. The degree of sex expression and genetic diversity differed between sexes. CONCLUSIONS Sex expression levels, regional sex ratios and genetic diversity were not directly associated with the regional frequency of realized sexual reproduction, and relationships and variation patterns differed between species. We conclude that a combination of species-specific life histories, such as longevity, overall degree of successful sexual reproduction and recruitment, and historical factors are important to explain this variation. Our data on haploid-dominated plants significantly complement plant reproductive biology.
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Affiliation(s)
- Irene Bisang
- Department of Botany, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
| | - Johan Ehrlén
- Department of Ecology, Environment and Plant Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Lars Hedenäs
- Department of Botany, Swedish Museum of Natural History, Box 50007, SE-104 05 Stockholm, Sweden
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13
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Schmidt RJ, King MR, Aronson MFJ, Struwe L. Hidden cargo: The impact of historical shipping trade on the recent-past and contemporary non-native flora of northeastern United States. AMERICAN JOURNAL OF BOTANY 2023; 110:e16224. [PMID: 37551431 DOI: 10.1002/ajb2.16224] [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: 12/22/2022] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 08/09/2023]
Abstract
PREMISE Understanding establishment and spread of non-native plants is important in the face of a homogenizing global flora. While many studies focus on successful, invasive species, fewer have studied failed plant introductions. Until the early 1900s, large quantities of ship ballast, often containing foreign plant propagules, were deposited in New Jersey (USA). The resulting ballast flora is documented in extensive herbarium records, providing us a unique opportunity to analyze successes and failures of novel plant species introductions. METHODS We used digitized specimens from 75 herbaria to study 264 non-native species introduced into New Jersey through 19th century ballast deposition. We used spatial (density-based clustering; HDBSCAN) and temporal analyses of species retention and geographic spread to quantify disappearance rate, survival, and dispersion through time and define trajectory groups. RESULTS Four distinct trajectory groups were identified: waif (only present during import; 32% of species), short-term (disappeared quickly; 20%), established-limited spread (survives locally, 30%), and established-widespread (widespread, 18%). Species disappearance rate was highest during ballast deposition and decreased soon after deposition stopped around 1900. Spatial patterns showed a strong association with 19th century railroads for inland dispersal from ports. The disappearance rate and spatial analyses are robust to herbarium collection bias. CONCLUSIONS This study using New Jersey as a model is one of the few documenting multispecies successes and failures in inadvertent plant introductions. Results reveal distinct trends in species establishment and geographic spread and highlight the utility of herbarium specimens in answering questions that span large time scales.
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Affiliation(s)
- Ryan J Schmidt
- Department of Ecology, Evolution & Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, 08901-8551, USA
- Graduate Program in Ecology and Evolution, School of Graduate Studies, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, 08901-8551, USA
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA, 02138, USA
| | - Megan R King
- Department of Ecology, Evolution & Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, 08901-8551, USA
- Graduate Program in Ecology and Evolution, School of Graduate Studies, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, 08901-8551, USA
| | - Myla F J Aronson
- Department of Ecology, Evolution & Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, 08901-8551, USA
| | - Lena Struwe
- Department of Ecology, Evolution & Natural Resources, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, 08901-8551, USA
- Department of Plant Biology, Rutgers, The State University of New Jersey, 59 Dudley Road, New Brunswick, NJ, 08901-8551, USA
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14
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Park DS, Xie Y, Ellison AM, Lyra GM, Davis CC. Complex climate-mediated effects of urbanization on plant reproductive phenology and frost risk. THE NEW PHYTOLOGIST 2023; 239:2153-2165. [PMID: 36942966 DOI: 10.1111/nph.18893] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 03/07/2023] [Indexed: 06/18/2023]
Abstract
Urbanization can affect the timing of plant reproduction (i.e. flowering and fruiting) and associated ecosystem processes. However, our knowledge of how plant phenology responds to urbanization and its associated environmental changes is limited. Herbaria represent an important, but underutilized source of data for investigating this question. We harnessed phenological data from herbarium specimens representing 200 plant species collected across 120 yr from the eastern US to investigate the spatiotemporal effects of urbanization on flowering and fruiting phenology and frost risk (i.e. time between the last frost date and flowering). Effects of urbanization on plant reproductive phenology varied significantly in direction and magnitude across species ranges. Increased urbanization led to earlier flowering in colder and wetter regions and delayed fruiting in regions with wetter spring conditions. Frost risk was elevated with increased urbanization in regions with colder and wetter spring conditions. Our study demonstrates that predictions of phenological change and its associated impacts must account for both climatic and human effects, which are context dependent and do not necessarily coincide. We must move beyond phenological models that only incorporate temperature variables and consider multiple environmental factors and their interactions when estimating plant phenology, especially at larger spatial and taxonomic scales.
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Affiliation(s)
- Daniel S Park
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47906, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47906, USA
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
| | - Yingying Xie
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47906, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, 47906, USA
- Department of Biological Sciences, Northern Kentucky University, Highland Heights, KY, 41099, USA
| | - Aaron M Ellison
- Harvard University Herbaria, Harvard University, Cambridge, MA, 02135, USA
- Sound Solutions for Sustainable Science, Boston, MA, 02135, USA
| | - Goia M Lyra
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
- Programa de Pós Graduação em Biodiversidade e Evolução, Instituto de Biologia, Universidade Federal da Bahia, Salvador, Bahia, 40170-115, Brazil
| | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, 02138, USA
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15
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Weaver WN, Smith SA. From leaves to labels: Building modular machine learning networks for rapid herbarium specimen analysis with LeafMachine2. APPLICATIONS IN PLANT SCIENCES 2023; 11:e11548. [PMID: 37915430 PMCID: PMC10617304 DOI: 10.1002/aps3.11548] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/28/2023] [Accepted: 07/17/2023] [Indexed: 11/03/2023]
Abstract
Premise Quantitative plant traits play a crucial role in biological research. However, traditional methods for measuring plant morphology are time consuming and have limited scalability. We present LeafMachine2, a suite of modular machine learning and computer vision tools that can automatically extract a base set of leaf traits from digital plant data sets. Methods LeafMachine2 was trained on 494,766 manually prepared annotations from 5648 herbarium images obtained from 288 institutions and representing 2663 species; it employs a set of plant component detection and segmentation algorithms to isolate individual leaves, petioles, fruits, flowers, wood samples, buds, and roots. Our landmarking network automatically identifies and measures nine pseudo-landmarks that occur on most broadleaf taxa. Text labels and barcodes are automatically identified by an archival component detector and are prepared for optical character recognition methods or natural language processing algorithms. Results LeafMachine2 can extract trait data from at least 245 angiosperm families and calculate pixel-to-metric conversion factors for 26 commonly used ruler types. Discussion LeafMachine2 is a highly efficient tool for generating large quantities of plant trait data, even from occluded or overlapping leaves, field images, and non-archival data sets. Our project, along with similar initiatives, has made significant progress in removing the bottleneck in plant trait data acquisition from herbarium specimens and shifted the focus toward the crucial task of data revision and quality control.
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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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16
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Feeley KJ, Bernal-Escobar M, Fortier R, Kullberg AT. Tropical Trees Will Need to Acclimate to Rising Temperatures-But Can They? PLANTS (BASEL, SWITZERLAND) 2023; 12:3142. [PMID: 37687387 PMCID: PMC10490527 DOI: 10.3390/plants12173142] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/10/2023]
Abstract
For tropical forests to survive anthropogenic global warming, trees will need to avoid rising temperatures through range shifts and "species migrations" or tolerate the newly emerging conditions through adaptation and/or acclimation. In this literature review, we synthesize the available knowledge to show that although many tropical tree species are shifting their distributions to higher, cooler elevations, the rates of these migrations are too slow to offset ongoing changes in temperatures, especially in lowland tropical rainforests where thermal gradients are shallow or nonexistent. We also show that the rapidity and severity of global warming make it unlikely that tropical tree species can adapt (with some possible exceptions). We argue that the best hope for tropical tree species to avoid becoming "committed to extinction" is individual-level acclimation. Although several new methods are being used to test for acclimation, we unfortunately still do not know if tropical tree species can acclimate, how acclimation abilities vary between species, or what factors may prevent or facilitate acclimation. Until all of these questions are answered, our ability to predict the fate of tropical species and tropical forests-and the many services that they provide to humanity-remains critically impaired.
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Affiliation(s)
- Kenneth J. Feeley
- Department of Biology, University of Miami, Coral Gables, FL 33146, USA; (M.B.-E.); (R.F.); (A.T.K.)
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17
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Park DS, Feng X, Akiyama S, Ardiyani M, Avendaño N, Barina Z, Bärtschi B, Belgrano M, Betancur J, Bijmoer R, Bogaerts A, Cano A, Danihelka J, Garg A, Giblin DE, Gogoi R, Guggisberg A, Hyvärinen M, James SA, Sebola RJ, Katagiri T, Kennedy JA, Komil TS, Lee B, Lee SML, Magri D, Marcucci R, Masinde S, Melnikov D, Mráz P, Mulenko W, Musili P, Mwachala G, Nelson BE, Niezgoda C, Novoa Sepúlveda C, Orli S, Paton A, Payette S, Perkins KD, Ponce MJ, Rainer H, Rasingam L, Rustiami H, Shiyan NM, Bjorå CS, Solomon J, Stauffer F, Sumadijaya A, Thiébaut M, Thiers BM, Tsubota H, Vaughan A, Virtanen R, Whitfeld TJS, Zhang D, Zuloaga FO, Davis CC. The colonial legacy of herbaria. Nat Hum Behav 2023:10.1038/s41562-023-01616-7. [PMID: 37308536 DOI: 10.1038/s41562-023-01616-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/27/2023] [Indexed: 06/14/2023]
Abstract
Herbarium collections shape our understanding of Earth's flora and are crucial for addressing global change issues. Their formation, however, is not free from sociopolitical issues of immediate relevance. Despite increasing efforts addressing issues of representation and colonialism in natural history collections, herbaria have received comparatively less attention. While it has been noted that the majority of plant specimens are housed in the Global North, the extent and magnitude of this disparity have not been quantified. Here we examine the colonial legacy of botanical collections, analysing 85,621,930 specimen records and assessing survey responses from 92 herbarium collections across 39 countries. We find an inverse relationship between where plant diversity exists in nature and where it is housed in herbaria. Such disparities persist across physical and digital realms despite overt colonialism ending over half a century ago. We emphasize the need for acknowledging the colonial history of herbarium collections and implementing a more equitable global paradigm for their collection, curation and use.
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Affiliation(s)
- Daniel S Park
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- Purdue Center for Plant Biology, Purdue University, West Lafayette, IN, USA.
| | - Xiao Feng
- Department of Geography, Florida State University, Tallahassee, FL, USA
| | - Shinobu Akiyama
- Department of Botany, National Museum of Nature and Science, Tsukuba, Japan
| | - Marlina Ardiyani
- Herbarium Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Neida Avendaño
- Instituto Experimental Jardin Botánico 'Dr. Tobías Lasser', Avenida Salvador Allende, Ciudad Universitaria, Caracas, Venezuela
- Universidad Central de Venezuela, Caracas, Venezuela
| | | | - Blandine Bärtschi
- Herbier LY, FR-BioEEnVis, Université Claude Bernard Lyon 1, Lyon, France
| | | | | | - Roxali Bijmoer
- Botany Section, Naturalis Biodiversity Center, Leiden, the Netherlands
| | | | - Asunción Cano
- Herbario San Marcos, Museo de Historia Natural, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - Jiří Danihelka
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
- Institute of Botany of the Czech Academy of Sciences, Průhonice, Czech Republic
| | - Arti Garg
- Central Regional Centre, Botanical Survey of India, Allahabad, India
| | - David E Giblin
- University of Washington Herbarium, Burke Museum, Seattle, WA, USA
| | - Rajib Gogoi
- Sikkim Himalayan Regional Centre, Botanical Survey of India, Gangtok, India
| | | | - Marko Hyvärinen
- Botany Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland
| | - Shelley A James
- Department of Biodiversity, Conservation and Attractions, Western Australian Herbarium, Kensington, Western Australia, Australia
| | - Ramagwai J Sebola
- South African National Biodiversity Institute, Pretoria, South Africa
- School of Animal, Plant and Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tomoyuki Katagiri
- Department of Biological Sciences, Faculty of Science and Technology, Kochi University, Kochi, Japan
- Hattori Botanical Laboratory, Nichinan, Japan
| | | | - Tojibaev Sh Komil
- Institute of Botany, Uzbekistan Academy of Sciences, Tashkent, Uzbekistan
| | | | - Serena M L Lee
- National Parks Board, Singapore Botanic Gardens, Singapore, Singapore
| | - Donatella Magri
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | | | - Siro Masinde
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Denis Melnikov
- Komarov Botanical Institute, Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Patrik Mráz
- Herbarium Collections & Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Wieslaw Mulenko
- Institute of Biological Sciences, Maria Curie-Skłodowska University, Lublin, Poland
| | - Paul Musili
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | | | - Burrell E Nelson
- Rocky Mountain Herbarium, University of Wyoming, Laramie, WY, USA
| | | | - Carla Novoa Sepúlveda
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Botanische Staatssammlung München, München, Germany
| | - Sylvia Orli
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | | | - Serge Payette
- Herbier Louis-Marie, Université Laval, Québec City, Québec, Canada
| | - Kent D Perkins
- University of Florida Herbarium, Florida Museum, Gainesville, FL, USA
| | - Maria Jimena Ponce
- Instituto Multidisciplinario de Biología Vegetal (UNC-CONICET), Córdoba, Argentina
| | - Heimo Rainer
- Naturhistorisches Museum Wien, Vienna, Austria
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - L Rasingam
- Deccan Regional Centre, Botanical Survey of India, Hyderabad, India
| | - Himmah Rustiami
- Herbarium Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
| | - Natalia M Shiyan
- National Herbarium of Ukraine, M.G. Kholodny Institute of Botany, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | | | | | - Fred Stauffer
- Conservatory and Botanic Gardens of Geneva, Geneva, Switzerland
| | - Alex Sumadijaya
- Herbarium Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency (BRIN), Cibinong, Indonesia
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Mélanie Thiébaut
- Herbier LY, FR-BioEEnVis, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Hiromi Tsubota
- Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Miyajima Natural Botanical Garden, Hiroshima University, Hiroshima, Japan
| | - Alison Vaughan
- Royal Botanic Gardens Victoria, Melbourne, Victoria, Australia
| | - Risto Virtanen
- Ecology and Genetics Research Unit, University of Oulu, Oulu, Finland
- University of Oulu Botanical Museum, Oulu, Finland
| | | | - Dianxiang Zhang
- South China Botanical Garden Herbarium, Chinese Academy of Sciences, Guangzhou, China
| | | | - Charles C Davis
- Department of Organismic and Evolutionary Biology, Harvard University Herbaria, Harvard University, Cambridge, MA, USA.
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18
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Knapp S. The past is a foreign country. Nat Hum Behav 2023:10.1038/s41562-023-01622-9. [PMID: 37308537 DOI: 10.1038/s41562-023-01622-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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19
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Nitta JH. Machine learning methods reveal processes affecting abundance at multiple scales. A commentary on 'Global and regional drivers of abundance patterns in the hart's tongue fern complex (Aspleniaceae)'. ANNALS OF BOTANY 2023; 131:i-ii. [PMID: 36847248 PMCID: PMC10184431 DOI: 10.1093/aob/mcad024] [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: 05/16/2023]
Abstract
This article comments on:
Namjoo Heo, Donald J. Leopold, Mark V. Lomolino, Seona Yun and Danilo D. Fernando. Global and regional drivers of abundance patterns in the hart’s tongue fern complex (Aspleniaceae), Annals of Botany, Volume 131, Issue 5, 11 April 2023, Pages 737–750, https://doi.org/10.1093/aob/mcac129
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Affiliation(s)
- Joel H Nitta
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
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20
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Specimens trump field observations in capturing biodiversity trends. Nat Ecol Evol 2023:10.1038/s41559-023-02051-7. [PMID: 37127768 DOI: 10.1038/s41559-023-02051-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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21
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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: 2] [Impact Index Per Article: 2.0] [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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22
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Wu Y, Hipp AL, Fargo G, Stith N, Ricklefs RE. Improving species delimitation for effective conservation: a case study in the endemic maple-leaf oak (Quercus acerifolia). THE NEW PHYTOLOGIST 2023; 238:1278-1293. [PMID: 36707920 DOI: 10.1111/nph.18777] [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: 08/24/2022] [Accepted: 01/22/2023] [Indexed: 06/18/2023]
Abstract
Species delimitation is challenging in lineages that exhibit both high plasticity and introgression. This challenge can be compounded by collection biases, which may downweight specimens morphologically intermediate between traditional species. Additionally, mismatch between named species and observable phenotypes can compromise species conservation. We studied the species boundaries of Quercus acerifolia, a tree endemic to Arkansas, U.S. We performed morphometric analyses of leaves and acorns from 527 field and 138 herbarium samples of Q. acerifolia and its close relatives, Q. shumardii and Q. rubra. We employed two novel approaches: sampling ex situ collections to detect phenotypic plasticity caused by environmental variation and comparing random field samples with historical herbarium samples to identify collection biases that might undermine species delimitation. To provide genetic evidence, we also performed molecular analyses on genome-wide SNPs. Quercus acerifolia shows distinctive morphological, ecological, and genomic characteristics, rejecting the hypothesis that Q. acerifolia is a phenotypic variant of Q. shumardii. We found mismatches between traditional taxonomy and phenotypic clusters. We detected underrepresentation of morphological intermediates in herbarium collections, which may bias species discovery and recognition. Rare species conservation requires considering and addressing taxonomic problems related to phenotypic plasticity, mismatch between taxonomy and morphological clusters, and collection biases.
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Affiliation(s)
- Yingtong Wu
- Biology Department, University of Missouri - St Louis, St Louis, MO, 63121, USA
- Whitney R. Harris World Ecology Center, University of Missouri - St Louis, St Louis, MO, 63121, USA
| | - Andrew L Hipp
- The Morton Arboretum, 4100 Illinois Route 53, Lisle, IL, 60532, USA
- The Field Museum, Integrative Research Center, 1400S Lake Shore Dr., Chicago, IL, 60605, USA
| | - Gregory Fargo
- Biology Department, University of Missouri - St Louis, St Louis, MO, 63121, USA
| | - Nora Stith
- Biology Department, University of Missouri - St Louis, St Louis, MO, 63121, USA
| | - Robert E Ricklefs
- Biology Department, University of Missouri - St Louis, St Louis, MO, 63121, USA
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23
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Beiter CM, Crimmins TM. How consistently do species leaf-out or flower in the same order? Understanding the factors that shape this characteristic of plant communities. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023:10.1007/s00484-023-02477-5. [PMID: 37186257 DOI: 10.1007/s00484-023-02477-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 04/05/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Plant species are frequently reported to undergo leaf-out and flowering in a consistent order from 1 year to the next; however, only a limited number of these findings arise from studies encompassing many species or sites. Here, we evaluate the consistency in the order species leafed out in the northeastern United States using observations contributed to the USA National Phenology Network's Nature's Notebook platform. We repeated this analysis for flowering, evaluating a total of 132 species across 84 sites. We documented a relatively high degree of consistency in the order of both events among individual plants, with higher consistency in flowering. A small number of species pairs exhibited very high consistency in phenological order across several sites. The majority of species pairs exhibited variability in how consistently they underwent either leaf-out or flowering from site to site, which could be the result of either plastic or locally adaptive responses. Our investigation revealed that neither functional type nor seasonal position played a major role in shaping how consistently species leafed out or flowered in the same order. Instead, we found the number of days separating the events and interannual variability in timing to be the most influential factors driving the consistency in ordering.
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Affiliation(s)
- Caryn M Beiter
- Department of Biology, Miami University, 501 E High St, Oxford, OH, 45056, USA.
| | - Theresa M Crimmins
- USA National Phenology Network, School of Natural Resources and the Environment University of Arizona, 1311 E. 4Th. St., Suite 325, Tucson, AZ, 85721, USA
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Cisternas-Fuentes A, Koski MH. Drivers of strong isolation and small effective population size at a leading range edge of a widespread plant. Heredity (Edinb) 2023:10.1038/s41437-023-00610-z. [PMID: 37016137 DOI: 10.1038/s41437-023-00610-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 04/06/2023] Open
Abstract
Climate change has influenced species distributions worldwide with upward elevational shifts observed in many systems. Leading range edge populations, like those at upper elevation limits, are crucial for climate change responses but can exhibit low genetic diversity due to founder effects, isolation, or limited outbreeding. These factors can hamper local adaptation at range limits. Using the widespread herb, Argentina anserina, we measured ecological attributes (population density on the landscape, area of population occupancy, and plant and flower density) spanning a 1000 m elevation gradient, with high elevation populations at the range limit. We measured vegetative clonal potential in the greenhouse for populations spanning the gradient. We combined these data with a ddRAD-seq dataset to test the hypotheses that high elevation populations would exhibit ecological and genomic signatures of leading range edge populations. We found that population density on the landscape declined towards the high elevation limit, as is expected towards range edges. However, plant density was elevated within edge populations. In the greenhouse, high elevation plants exhibited stronger clonal potential than low elevation plants, likely explaining increased plant density in the field. Phylogeographic analysis supported more recent colonization of high elevation populations which were also more genetically isolated, had more extreme heterozygote excess and had smaller effective population size than low. Results support that colonization of high elevations was likely accompanied by increased asexuality, contributing to a decline in effective population size. Despite high plant density in leading edge populations, their small effective size, isolation and clonality could constrain adaptive potential.
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Affiliation(s)
- Anita Cisternas-Fuentes
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA.
| | - Matthew H Koski
- Department of Biological Sciences, Clemson University, 132 Long Hall, Clemson, SC, 29634, USA.
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25
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Wood CL, Vanhove MPM. Is the world wormier than it used to be? We'll never know without natural history collections. J Anim Ecol 2023; 92:250-262. [PMID: 35959636 DOI: 10.1111/1365-2656.13794] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 07/25/2022] [Indexed: 11/28/2022]
Abstract
Many disease ecologists and conservation biologists believe that the world is wormier than it used to be-that is, that parasites are increasing in abundance through time. This argument is intuitively appealing. Ecologists typically see parasitic infections, through their association with disease, as a negative endpoint, and are accustomed to attributing negative outcomes to human interference in the environment, so it slots neatly into our worldview that habitat destruction, biodiversity loss and climate change should have the collateral consequence of causing outbreaks of parasites. But surprisingly, the hypothesis that parasites are increasing in abundance through time remains entirely untested for the vast majority of wildlife parasite species. Historical data on parasites are nearly impossible to find, which leaves no baseline against which to compare contemporary parasite burdens. If we want to know whether the world is wormier than it used to be, there is only one major research avenue that will lead to an answer: parasitological examination of specimens preserved in natural history collections. Recent advances demonstrate that, for many specimen types, it is possible to extract reliable data on parasite presence and abundance. There are millions of suitable specimens that exist in collections around the world. When paired with contemporaneous environmental data, these parasitological data could even point to potential drivers of change in parasite abundance, including climate, pollution or host density change. We explain how to use preserved specimens to address pressing questions in parasite ecology, give a few key examples of how collections-based parasite ecology can resolve these questions, identify some pitfalls and workarounds, and suggest promising areas for research. Natural history specimens are 'parasite time capsules' that give ecologists the opportunity to test whether infectious disease is on the rise and to identify what forces might be driving these changes over time. This approach will facilitate major advances in a new sub-discipline: the historical ecology of parasitism.
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Affiliation(s)
- Chelsea L Wood
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, USA
| | - Maarten P M Vanhove
- Centre for Environmental Sciences, Research Group Zoology: Biodiversity & Toxicology, Hasselt University, Diepenbeek, Belgium
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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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How to use natural history collections to resurrect information on historical parasite abundances. J Helminthol 2023; 97:e6. [PMID: 36633512 DOI: 10.1017/s0022149x2200075x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Many of the most contentious questions that concern the ecology of helminths could be resolved with data on helminth abundance over the past few decades or centuries, but unfortunately these data are rare. A new sub-discipline - the historical ecology of parasitism - is resurrecting long-term data on the abundance of parasites, an advancement facilitated by the use of biological natural history collections. Because the world's museums hold billions of suitable specimens collected over more than a century, these potential parasitological datasets are broad in scope and finely resolved in taxonomic, temporal and spatial dimensions. Here, we set out best practices for the extraction of parasitological information from natural history collections, including how to conceive of a project, how to select specimens, how to engage curators and receive permission for proposed projects, standard operating protocols for dissections and how to manage data. Our hope is that other helminthologists will use this paper as a reference to expand their own research programmes along the dimension of time.
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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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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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Buldrini F, Alessandrini A, Muzzi E, Krebs P, Conedera M, Pezzi G. Historical Floras: addressing their genesis in order to be viewed from a modern-day perspective. A case study from Northern Italy. RENDICONTI LINCEI. SCIENZE FISICHE E NATURALI 2022. [DOI: 10.1007/s12210-022-01116-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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McClinton JD, Kulpa SM, Grames EM, Leger EA. Field observations and remote assessment identify climate change, recreation, invasive species, and livestock as top threats to critically imperiled rare plants in Nevada. FRONTIERS IN CONSERVATION SCIENCE 2022. [DOI: 10.3389/fcosc.2022.1070490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
IntroductionRare plant species comprise >36.5% of the world’s flora and disproportionately support ecosystem function and resilience. However, rare species also lead global plant extinctions, and unique ecological characteristics can make them vulnerable to anthropogenic pressure. Despite their vulnerability, many rare plants receive less monitoring than is needed to inform conservation efforts due to limited capacity for field surveys.MethodsWe used field observations and geospatial data to summarize how 128 imperiled, rare vascular plant species in Nevada are affected by various threats. We assessed correlations between threats predicted by geospatial data and threats observed on the ground and asked how historic and current threats compare.ResultsThe most commonly observed threats were from recreation, invasive and non-native/alien species, and livestock farming and ranching. Threat prevalence varied by elevation (e.g., a greater variety of threats at lower elevations, greater threat from climate change observed at higher elevations) and land management. There was a 28.1% overall correlation between predicted and observed threats, which was stronger for some threats (e.g., development of housing and urban areas, livestock farming and ranching) than others. All species experienced extreme climatic differences during 1990-2020 compared to baseline conditions, with the most extreme change in southern Nevada. The average number of threats observed per occurrence increased by 0.024 each decade.DiscussionWhile geospatial data did not perfectly predict observed threats, many of these occurrences have not been visited in over 30 years, and correlations may be stronger than we were able to detect here. Our approach can be used to help guide proactive monitoring, conservation, and research efforts for vulnerable species.
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Ralimanana H, Perrigo AL, Smith RJ, Borrell JS, Faurby S, Rajaonah MT, Randriamboavonjy T, Vorontsova MS, Cooke RSC, Phelps LN, Sayol F, Andela N, Andermann T, Andriamanohera AM, Andriambololonera S, Bachman SP, Bacon CD, Baker WJ, Belluardo F, Birkinshaw C, Cable S, Canales NA, Carrillo JD, Clegg R, Clubbe C, Crottini A, Damasco G, Dhanda S, Edler D, Farooq H, de Lima Ferreira P, Fisher BL, Forest F, Gardiner LM, Goodman SM, Grace OM, Guedes TB, Hackel J, Henniges MC, Hill R, Lehmann CER, Lowry PP, Marline L, Matos-Maraví P, Moat J, Neves B, Nogueira MGC, Onstein RE, Papadopulos AST, Perez-Escobar OA, Phillipson PB, Pironon S, Przelomska NAS, Rabarimanarivo M, Rabehevitra D, Raharimampionona J, Rajaonary F, Rajaovelona LR, Rakotoarinivo M, Rakotoarisoa AA, Rakotoarisoa SE, Rakotomalala HN, Rakotonasolo F, Ralaiveloarisoa BA, Ramirez-Herranz M, Randriamamonjy JEN, Randrianasolo V, Rasolohery A, Ratsifandrihamanana AN, Ravololomanana N, Razafiniary V, Razanajatovo H, Razanatsoa E, Rivers M, Silvestro D, Testo W, Torres Jiménez MF, Walker K, Walker BE, Wilkin P, Williams J, Ziegler T, Zizka A, Antonelli A. Madagascar’s extraordinary biodiversity: Threats and opportunities. Science 2022; 378:eadf1466. [DOI: 10.1126/science.adf1466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Madagascar’s unique biota is heavily affected by human activity and is under intense threat. Here, we review the current state of knowledge on the conservation status of Madagascar’s terrestrial and freshwater biodiversity by presenting data and analyses on documented and predicted species-level conservation statuses, the most prevalent and relevant threats, ex situ collections and programs, and the coverage and comprehensiveness of protected areas. The existing terrestrial protected area network in Madagascar covers 10.4% of its land area and includes at least part of the range of the majority of described native species of vertebrates with known distributions (97.1% of freshwater fishes, amphibians, reptiles, birds, and mammals combined) and plants (67.7%). The overall figures are higher for threatened species (97.7% of threatened vertebrates and 79.6% of threatened plants occurring within at least one protected area). International Union for Conservation of Nature (IUCN) Red List assessments and Bayesian neural network analyses for plants identify overexploitation of biological resources and unsustainable agriculture as the most prominent threats to biodiversity. We highlight five opportunities for action at multiple levels to ensure that conservation and ecological restoration objectives, programs, and activities take account of complex underlying and interacting factors and produce tangible benefits for the biodiversity and people of Madagascar.
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Affiliation(s)
- Hélène Ralimanana
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Allison L. Perrigo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Rhian J. Smith
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | | | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Mamy Tiana Rajaonah
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | | | - Robert S. C. Cooke
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- UK Centre for Ecology and Hydrology, Wallingford, UK
| | - Leanne N. Phelps
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Ferran Sayol
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Niels Andela
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, Wales, UK
| | - Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Organismal Biology, SciLifeLab, Uppsala University, Uppsala, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | | | - Christine D. Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | | | - Francesco Belluardo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Chris Birkinshaw
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
- Missouri Botanical Garden, St. Louis, MO, USA
| | - Stuart Cable
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Nataly A. Canales
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Juan D. Carrillo
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- CR2P, Muséum National d’Histoire Naturelle, Paris, France
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Rosie Clegg
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Geography, University of Exeter, Exeter, Devon, UK
| | - Colin Clubbe
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Angelica Crottini
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Gabriel Damasco
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Departamento de Botânica e Zoologia, Universidade Federal do Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Sonia Dhanda
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Daniel Edler
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Integrated Science Lab, Department of Physics, Umeå University, Umeå, Sweden
| | - Harith Farooq
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Faculty of Natural Sciences, Lúrio University, Pemba, Cabo Delgado Province, Mozambique
| | - Paola de Lima Ferreira
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | | | - Félix Forest
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Lauren M. Gardiner
- Cambridge University Herbarium, Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Steven M. Goodman
- Association Vahatra, Antananarivo, Madagascar
- Field Museum of Natural History, Chicago, IL, USA
| | | | - Thaís B. Guedes
- Instituto de Biologia, Universidade Estadual de Campinas, Unicamp, Campinas, São Paulo, Brazil
| | - Jan Hackel
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Marie C. Henniges
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Rowena Hill
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Caroline E. R. Lehmann
- School of GeoSciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | - Porter P. Lowry
- Missouri Botanical Garden, St. Louis, MO, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Lovanomenjanahary Marline
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Association Vahatra, Antananarivo, Madagascar
| | - Pável Matos-Maraví
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Biology Centre CAS, Institute of Entomology, České Budějovice, Czech Republic
| | - Justin Moat
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | - Beatriz Neves
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matheus G. C. Nogueira
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Museu Nacional, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Renske E. Onstein
- Naturalis Biodiversity Center, Leiden, Netherlands
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | | | - Peter B. Phillipson
- Missouri Botanical Garden, St. Louis, MO, USA
- Institut de Systématique, Évolution, et Biodiversité (ISYEB), Muséum National d’Histoire Naturelle, Paris, France
| | - Samuel Pironon
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- UN Environment Programme World Conservation Monitoring Centre (UNEP-WCMC), Cambridge, UK
| | - Natalia A. S. Przelomska
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Anthropology, Smithsonian National Museum of Natural History, Washington, DC, USA
| | | | - David Rabehevitra
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Fano Rajaonary
- Missouri Botanical Garden, Madagascar Program, Antananarivo, Madagascar
| | - Landy R. Rajaovelona
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Mijoro Rakotoarinivo
- Department of Plant Biology and Ecology, University of Antananarivo, Antananarivo, Madagascar
| | - Amédée A. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Solofo E. Rakotoarisoa
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Herizo N. Rakotomalala
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Franck Rakotonasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | - Myriam Ramirez-Herranz
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Instituto de Ecología y Biodiversidad, University of La Serena, La Serena, Chile
- Programa de Doctorado en Biología y Ecología Aplicada, Universidad Católica del Norte, Universidad de La Serena, La Serena, Chile
| | | | - Vonona Randrianasolo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | | | | | | | - Velosoa Razafiniary
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Henintsoa Razanajatovo
- Royal Botanic Gardens, Kew, Kew Madagascar Conservation Centre, Antananarivo, Madagascar
| | - Estelle Razanatsoa
- Plant Conservation Unit, Department of Biological Sciences, University of Cape Town, South Africa
| | - Malin Rivers
- Botanic Gardens Conservation International, Kew, Richmond, Surrey, UK
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Weston Testo
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Field Museum of Natural History, Chicago, IL, USA
| | - Maria F. Torres Jiménez
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Institute of Biosciences, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| | - Kim Walker
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Royal Holloway, University of London, Egham, Surrey, UK
| | | | - Paul Wilkin
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
| | | | - Thomas Ziegler
- Cologne Zoo, Cologne, Germany
- Institute of Zoology, University of Cologne, Cologne, Germany
| | - Alexander Zizka
- Department of Biology, Philipps-University Marburg, Marburg, Germany
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
- Royal Botanic Gardens, Kew, Richmond, Surrey, UK
- Department of Biology, University of Oxford, Oxford, UK
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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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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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The invasion history of Elodea canadensis and E. nuttallii (Hydrocharitaceae) in Italy from herbarium accessions, field records and historical literature. Biol Invasions 2022. [DOI: 10.1007/s10530-022-02949-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
AbstractWe analysed the invasion history of two North American macrophytes (Elodea canadensis and E. nuttallii) in Italy, through an accurate census of all available herbarium and field records, dating between 1850 and 2019, and a rich literature collection describing the initial introduction and naturalisation phase that supports the results obtained by the occurrence records. Elodea canadensis arrived in Italy before 1866 and had two invasion phases, between the 1890s and 1920s and between the 1990s and 2000s; E. nuttallii, probably arrived in the 1970s, started invading in 2000 and the invasion is still ongoing. Botanical gardens and fish farming played a crucial role in dispersal and naturalisation of both species. The current invasion range of both species is centred in northern Italy, with scattered occurrences of E. canadensis in central and southern regions. River Po represents a dispersal barrier to the Mediterranean region and a strategic monitoring site to prevent the invasion in the peninsula. The study detects differences in the niches of the two species during the introduction and naturalisation phase and a habitat switch occurred after 1980 in E. canadensis and after 2000 in E. nuttallii, during their expansion phases. For E. canadensis the switch corresponds to the second invasion round. Further research can clarify whether the second invasion round is due to confusion of the recently introduced E. nuttallii with E. canadensis, to a cryptic introduction of a new genotype, to post-introduction evolution, or just to an increased scientific interest in biological invasions.
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Bertin RI, Spind CG. Are Rare Northern Plant Species Retreating from the Southern Edge of Their Ranges in Southern New England? Northeast Nat (Steuben) 2022. [DOI: 10.1656/045.029.0401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Robert I. Bertin
- Biology Department, College of the Holy Cross, Worcester, MA 01610
| | - Caitlin G. Spind
- Biology Department, College of the Holy Cross, Worcester, MA 01610
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Xie Y, Thammavong HT, Park DS. The ecological implications of intra- and inter-species variation in phenological sensitivity. THE NEW PHYTOLOGIST 2022; 236:760-773. [PMID: 35801834 PMCID: PMC9796043 DOI: 10.1111/nph.18361] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
Plant-pollinator mutualisms rely upon the synchrony of interacting taxa. Climate change can disrupt this synchrony as phenological responses to climate vary within and across species. However, intra- and interspecific variation in phenological responses is seldom considered simultaneously, limiting our understanding of climate change impacts on interactions among taxa across their ranges. We investigated how variation in phenological sensitivity to climate can alter ecological interactions simultaneously within and among species using natural history collections and citizen science data. We focus on a unique system, comprising a wide-ranged spring ephemeral with varying color morphs (Claytonia virginica) and its specialist bee pollinator (Andrena erigeniae). We found strongly opposing trends in the phenological sensitivities of plants vs their pollinators. Flowering phenology was more sensitive to temperature in warmer regions, whereas bee phenology was more responsive in colder regions. Phenological sensitivity varied across flower color morphs. Temporal synchrony between flowering and pollinator activity was predicted to change heterogeneously across the species' ranges in the future. Our work demonstrates the complexity and fragility of ecological interactions in time and the necessity of incorporating variation in phenological responses across multiple axes to understand how such interactions will change in the future.
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Affiliation(s)
- Yingying Xie
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47906USA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteIN47906USA
| | | | - Daniel S. Park
- Department of Biological SciencesPurdue UniversityWest LafayetteIN47906USA
- Purdue Center for Plant BiologyPurdue UniversityWest LafayetteIN47906USA
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Primack RB, Miller-Rushing AJ, Miller TK. Was Henry David Thoreau a Good Naturalist? An Approach for Assessing Data from Historical Natural History Records. Bioscience 2022. [DOI: 10.1093/biosci/biac063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
abstract
Ecologists are increasingly combining historical observations made by naturalists with modern observations to detect the ecological effects of climate change. This use of historical observations raises the following question: How do we know that historical data are appropriate to use to answer current ecological questions? In the present article, we address this question for environmental philosopher Henry David Thoreau, author of Walden. Should we trust his observations? We qualitatively and quantitatively evaluate Thoreau's observations using a three-step framework: We assess the rigor, accuracy, and utility of his observations to investigate changes in plants and animals over time. We conclude that Thoreau was an accurate observer of nature and a reliable scientist. More importantly, we describe how this simple three-step approach could be used to assess the accuracy of other scientists and naturalists.
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Affiliation(s)
- Richard B Primack
- Department of Biology, Boston University , Boston, Massachusetts, United States
| | - Abraham J Miller-Rushing
- US National Park Service, science coordinator for Acadia National Park , Bar Harbor, Maine, United States
| | - Tara K Miller
- Department of Biology, Boston University , Boston, Massachusetts, United States
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New directions in tropical phenology. Trends Ecol Evol 2022; 37:683-693. [PMID: 35680467 DOI: 10.1016/j.tree.2022.05.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 03/08/2022] [Accepted: 05/04/2022] [Indexed: 11/21/2022]
Abstract
Earth's most speciose biomes are in the tropics, yet tropical plant phenology remains poorly understood. Tropical phenological data are comparatively scarce and viewed through the lens of a 'temperate phenological paradigm' expecting phenological traits to respond to strong, predictably annual shifts in climate (e.g., between subfreezing and frost-free periods). Digitized herbarium data greatly expand existing phenological data for tropical plants; and circular data, statistics, and models are more appropriate for analyzing tropical (and temperate) phenological datasets. Phylogenetic information, which remains seldom applied in phenological investigations, provides new insights into phenological responses of large groups of related species to climate. Consistent combined use of herbarium data, circular statistical distributions, and robust phylogenies will rapidly advance our understanding of tropical - and temperate - phenology.
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Morales-Marroquín JA, Solis Miranda R, Baldin Pinheiro J, Zucchi MI. Biodiversity Research in Central America: A Regional Comparison in Scientific Production Using Bibliometrics and Democracy Indicators. Front Res Metr Anal 2022; 7:898818. [PMID: 35910707 PMCID: PMC9329674 DOI: 10.3389/frma.2022.898818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/20/2022] [Indexed: 11/13/2022] Open
Abstract
Central America science production on biodiversity topics is important in planning future adaptive and conservation policies in a climate-related risk region that is considered a biodiversity hotspot but has the lowest Human Development Index of Latin America. Science production on biodiversity is related to geo-referenced species occurrence records, but the accessibility depends on political frameworks and science funding. This paper aims at foregrounding how the democratic shifts throughout the years have had an impact on science production on biodiversity research, and species records. For this exploration we developed a novel systematic scientometric analysis of science production on biodiversity topics, we used Bio-Dem (open-source software of biodiversity records and socio-political variables) and briefly analyzed the history—from 1980 to 2020—of Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica, and Panama. With a data set of 16,304 documents, our analysis shows the significant discrepancies between the low science production of Central American Northern countries (Guatemala, El Salvador, Honduras, and Nicaragua), the prolific production from the Southern (Costa Rica and Panama), and how this relates to democratic stability. Scientific production tends to be more abundant when democratic conditions are guaranteed. The state capture phenomenon and colonial-rooted interactions worldwide have an effect on the conditions under which science is being produced in Central America. Democracy, science production, funding, and conservation are core elements that go hand in hand, and that need to be nourished in a region that struggles with the protection of life and extractive activities in a climate change scenario.
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Affiliation(s)
- Jonathan A. Morales-Marroquín
- Genetics and Molecular Biology Department, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
- *Correspondence: Jonathan A. Morales-Marroquín
| | - Regina Solis Miranda
- School of Languages and Cultures, University of Sheffield, Sheffield, United Kingdom
| | - José Baldin Pinheiro
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Maria Imaculada Zucchi
- Genetics and Molecular Biology Department, Biology Institute, University of Campinas (UNICAMP), Campinas, Brazil
- Department of Genetics, “Luiz de Queiroz” College of Agriculture, University of São Paulo, Piracicaba, Brazil
- Unidade Regional de Pesquisa e Desenvolvimento (APTA), Secretaria de Agricultura, São Paulo, Brazil
- Maria Imaculada Zucchi
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Willems FM, Scheepens JF, Bossdorf O. Forest wildflowers bloom earlier as Europe warms: lessons from herbaria and spatial modelling. THE NEW PHYTOLOGIST 2022; 235:52-65. [PMID: 35478407 DOI: 10.1111/nph.18124] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Today plants often flower earlier due to climate warming. Herbarium specimens are excellent witnesses of such long-term changes. However, the magnitude of phenological shifts may vary geographically, and the data are often clustered. Therefore, large-scale analyses of herbarium data are prone to pseudoreplication and geographical biases. We studied over 6000 herbarium specimens of 20 spring-flowering forest understory herbs from Europe to understand how their phenology had changed during the last century. We estimated phenology trends with or without taking spatial autocorrelation into account. On average plants now flowered over 6 d earlier than at the beginning of the last century. These changes were strongly associated with warmer spring temperatures. Flowering time advanced 3.6 d per 1°C warming. Spatial modelling showed that, in some parts of Europe, plants flowered earlier or later than expected. Without accounting for this, the estimates of phenological shifts were biased and model fits were poor. Our study indicates that forest wildflowers in Europe strongly advanced their phenology in response to climate change. However, these phenological shifts differ geographically. This shows that it is crucial to combine the analysis of herbarium data with spatial modelling when testing for long-term phenology trends across large spatial scales.
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Affiliation(s)
- Franziska M Willems
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, 72076, Tübingen, Germany
- Conservation Biology, Department of Biology, University of Marburg, 35032, Marburg, Germany
| | - J F Scheepens
- Plant Evolutionary Ecology, Faculty of Biological Sciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany
| | - Oliver Bossdorf
- Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, 72076, Tübingen, Germany
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Zhitomirsky-Geffet M, Kizhner I, Minster S. What do they make us see: a comparative study of cultural bias in online databases of two large museums. JOURNAL OF DOCUMENTATION 2022. [DOI: 10.1108/jd-02-2022-0047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
PurposeLarge cultural heritage datasets from museum collections tend to be biased and demonstrate omissions that result from a series of decisions at various stages of the collection construction. The purpose of this study is to apply a set of ethical criteria to compare the level of bias of six online databases produced by two major art museums, identifying the most biased and the least biased databases.Design/methodology/approachAt the first stage, the relevant data have been automatically extracted from all six databases and mapped to a unified ontological scheme based on Wikidata. Then, the authors applied ethical criteria to the results of the geographical distribution of records provided by two major art museums as online databases accessed via museums' websites, API datasets and datasets submitted to Wikidata.FindingsThe authors show that the museums use different artworks in each of its online databases and each data-base has different types of bias reflected by the study variables, such as artworks' country of origin or the creator's nationality. For most variables, the database behind the online search system on the museum's website is more balanced and ethical than the API dataset and Wikidata databases of the two museums.Originality/valueBy applying ethical criteria to the analysis of cultural bias in various museum databases aimed at different audiences including end users, researchers and commercial institutions, this paper shows the importance of explicating bias and maintaining integrity in cultural heritage representation through different channels that potentially have high impact on how culture is perceived, disseminated, contextualized and transformed.
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43
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Hussein BR, Malik OA, Ong WH, Slik JWF. Applications of computer vision and machine learning techniques for digitized herbarium specimens: A systematic literature review. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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44
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Rodrigues AV, Nakamura G, Staggemeier VG, Duarte L. Species misidentification affects biodiversity metrics: Dealing with this issue using the new R package naturaList. ECOL INFORM 2022. [DOI: 10.1016/j.ecoinf.2022.101625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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45
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Austin MW, Cole PO, Olsen KM, Smith AB. Climate change is associated with increased allocation to potential outcrossing in a common mixed mating species. AMERICAN JOURNAL OF BOTANY 2022; 109:1085-1096. [PMID: 35699252 PMCID: PMC9544429 DOI: 10.1002/ajb2.16021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
PREMISE Although the balance between cross- and self-fertilization is driven by the environment, no long-term study has documented whether anthropogenic climate change is affecting reproductive strategy allocation in species with mixed mating systems. Here, we test whether the common blue violet (Viola sororia; Violaceae) has altered relative allocation to the production of potentially outcrossing flowers as the climate has changed throughout the 20th century. METHODS Using herbarium records spanning from 1875 to 2015 from the central United States, we quantified production of obligately selfing cleistogamous (CL) flowers and potentially outcrossing chasmogamous (CH) flowers by V. sororia, coupled these records with historic temperature and precipitation data, and tested whether changes to the proportion of CL flowers correlate with temporal climate trends. RESULTS We find that V. sororia progressively produced lower proportions of CL flowers across the past century and in environments with lower mean annual temperature and higher total annual precipitation. We also find that both CL and CH flower phenology has advanced across this time period. CONCLUSIONS Our results suggest that V. sororia has responded to lower temperatures and greater water availability by shifting reproductive strategy allocation away from selfing and toward potential outcrossing. This provides the first long-term study of how climate change may affect relative allocation to potential outcrossing in species with mixed mating systems. By revealing that CL flowering is associated with low water availability and high temperature, our results suggest the production of obligately selfing flowers is favored in water limited environments.
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Affiliation(s)
- Matthew W. Austin
- Living Earth CollaborativeWashington University in St. LouisSt. LouisMOUSA
| | - Piper O. Cole
- Division of Natural SciencesNew College of FloridaSarasotaFLUSA
| | - Kenneth M. Olsen
- Department of BiologyWashington University in St. LouisSt. LouisMOUSA
| | - Adam B. Smith
- Center for Conservation and Sustainable DevelopmentMissouri Botanical GardenSt. LouisMOUSA
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Climate Niche Modelling for Mapping Potential Distributions of Four Framework Tree Species: Implications for Planning Forest Restoration in Tropical and Subtropical Asia. FORESTS 2022. [DOI: 10.3390/f13070993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
Selecting tree species to plant for forest ecosystem restoration is critical but problematic. Knowing tree species’ climatic niches can help, but such information is limited for most tropical tree species. Consequently, the research presented here explored the use of climate and species record location data, to map the potential distribution of four tree species across tropical and subtropical Asia based on their modelled climatic niches. All were framework species, of proven effectiveness for forest restoration: Choerospondias axillaris (Roxb.) B.L. Burtt and A.W. Hill, Ficus hispida L.f., Hovenia dulcis Thunb., and Prunus cerasoides Buch.-Ham. ex D. Don. Potential species distributions were projected onto maps of known climatic conditions using the maximum entropy algorithm in Maxent software to predict where the climate is conducive for including each species in forest restoration trials. The models predicted species location very well for F. hispida and H. dulcis and fairly well for P. cerasoides and C. axillaris. Climatically suitable areas for C. axillaris were located mostly north of the equator, whilst those of F. hispida, H. dulcis and P. cerasoides extended south of the equator. The importance of each climatic niche variable differed among species. Driest-month precipitation was critical for F. hispida, as well as mean dry-season temperature for C. axillaris and P. cerasoides and cold-season precipitation for H. dulcis. In addition to aiding species selection for forest restoration, potential distribution maps based on climatic niche models can indicate where novel species for tree plantations might be successful and where species might become invasive. Applying such techniques to a large number of species will be needed to significantly improve species selection for forest ecosystem restoration.
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Boyd RJ, Aizen MA, Barahona‐Segovia RM, Flores‐Prado L, Fontúrbel FE, Francoy TM, Lopez‐Aliste M, Martinez L, Morales CL, Ollerton J, Pescott OL, Powney GD, Saraiva AM, Schmucki R, Zattara EE, Carvell C. Inferring trends in pollinator distributions across the Neotropics from publicly available data remains challenging despite mobilization efforts. DIVERS DISTRIB 2022. [DOI: 10.1111/ddi.13551] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Affiliation(s)
| | - Marcelo A. Aizen
- Grupo de Ecología de la Polinización INIBIOMA, Universidad Nacional del Comahue‐CONICET Bariloche Argentina
| | - Rodrigo M. Barahona‐Segovia
- Departamento de Ciencias Biológicas y Biodiversidad Universidad de Los Lagos Osorno Chile
- Moscas Florícolas de Chile Citizen Science Program, Patricio Lynch Valdivia Chile
| | - Luis Flores‐Prado
- Instituto de Entomología Universidad Metropolitana de Ciencias de la Educación Ñuñoa Chile
| | - Francisco E. Fontúrbel
- Instituto de Biología, Facultad de Ciencias Pontificia Universidad Católica de Valparaíso Valparaíso Chile
| | - Tiago M. Francoy
- Escola de Artes, Ciências e Humanidades Universidade de São Paulo. Rua Arlindo Béttio São Paulo Brazil
| | - Manuel Lopez‐Aliste
- Instituto de Biología, Facultad de Ciencias Pontificia Universidad Católica de Valparaíso Valparaíso Chile
| | - Lican Martinez
- Grupo de Ecología de la Polinización INIBIOMA, Universidad Nacional del Comahue‐CONICET Bariloche Argentina
| | - Carolina L. Morales
- Grupo de Ecología de la Polinización INIBIOMA, Universidad Nacional del Comahue‐CONICET Bariloche Argentina
| | - Jeff Ollerton
- Faculty of Arts, Science and Technology University of Northampton Northampton UK
| | | | | | | | | | - Eduardo E. Zattara
- Grupo de Ecología de la Polinización INIBIOMA, Universidad Nacional del Comahue‐CONICET Bariloche Argentina
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Borowiec ML, Dikow RB, Frandsen PB, McKeeken A, Valentini G, White AE. Deep learning as a tool for ecology and evolution. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13901] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marek L. Borowiec
- Entomology, Plant Pathology and Nematology University of Idaho Moscow ID USA
- Institute for Bioinformatics and Evolutionary Studies (IBEST) University of Idaho Moscow ID USA
| | - Rebecca B. Dikow
- Data Science Lab, Office of the Chief Information Officer Smithsonian Institution Washington DC USA
| | - Paul B. Frandsen
- Data Science Lab, Office of the Chief Information Officer Smithsonian Institution Washington DC USA
- Department of Plant and Wildlife Sciences Brigham Young University Provo UT USA
| | - Alexander McKeeken
- Entomology, Plant Pathology and Nematology University of Idaho Moscow ID USA
| | | | - Alexander E. White
- Data Science Lab, Office of the Chief Information Officer Smithsonian Institution Washington DC USA
- Department of Botany, National Museum of Natural History Smithsonian Institution Washington DC USA
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Shirey V, Khelifa R, M’Gonigle LK, Guzman LM. Occupancy‐detection models with museum specimen data: promise and pitfalls. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13896] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vaughn Shirey
- Department of Biology Georgetown University Washington DC United States
| | - Rassim Khelifa
- Department of Zoology, University of British Columbia 6270 University Blvd Vancouver United States
| | - Leithen K. M’Gonigle
- Department of Biological Sciences, Simon Fraser University 8888 University Drive Burnaby BC Canada
| | - Laura Melissa Guzman
- Department of Biological Sciences, Simon Fraser University 8888 University Drive Burnaby BC Canada
- Marine and Environmental Biology Section at the Department of Biological Sciences University of Southern California Los Angeles CA United States
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Iwanycki Ahlstrand N, Primack RB, Tøttrup AP. A comparison of herbarium and citizen science phenology datasets for detecting response of flowering time to climate change in Denmark. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2022; 66:849-862. [PMID: 35235036 PMCID: PMC9042978 DOI: 10.1007/s00484-022-02238-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 12/23/2021] [Accepted: 01/03/2022] [Indexed: 06/14/2023]
Abstract
Phenology has emerged as a key metric to measure how species respond to changes in climate. Innovative means have been developed to extend the temporal and spatial range of phenological data by obtaining data from herbarium specimens, citizen science programs, and biodiversity data repositories. These different data types have seldom been compared for their effectiveness in detecting environmental impacts on phenology. To address this, we compare three separate phenology datasets from Denmark: (i) herbarium specimen data spanning 145 years, (ii) data collected from a citizen science phenology program over a single year observing first flowering, and (iii) data derived from incidental biodiversity observations in iNaturalist over a single year. Each dataset includes flowering day of year observed for three common spring-flowering plant species: Allium ursinum (ramsons), Aesculus hippocastanum (horse chestnut), and Sambucus nigra (black elderberry). The incidental iNaturalist dataset provided the most extensive geographic coverage across Denmark and the largest sample size and recorded peak flowering in a way comparable to herbarium specimens. The directed citizen science dataset recorded much earlier flowering dates because the program objective was to report the first flowering, and so was less compared to the other two datasets. Herbarium data demonstrated the strongest effect of spring temperature on flowering in Denmark, possibly because it was the only dataset measuring temporal variation in phenology, while the other datasets measured spatial variation. Herbarium data predicted the mean flowering day of year recorded in our iNaturalist dataset for all three species. Combining herbarium data with iNaturalist data provides an even more effective method for detecting climatic effects on phenology. Phenology observations from directed and incidental citizen science initiatives will increase in value for climate change research in the coming years with the addition of data capturing the inter-annual variation in phenology.
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Affiliation(s)
| | | | - Anders P Tøttrup
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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