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Wang X, Xiao Y, Lv YW, He ZH, Yeh FC, Hu XS. A Community-Based Framework Integrates Interspecific Interactions into Forest Genetic Conservation. PLANTS (BASEL, SWITZERLAND) 2024; 13:435. [PMID: 38337968 PMCID: PMC10856838 DOI: 10.3390/plants13030435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Forest genetic conservation is typically species-specific and does not integrate interspecific interaction and community structure. It mainly focuses on the theories of population and quantitative genetics. This approach depicts the intraspecific patterns of population genetic structure derived from genetic markers and the genetic differentiation of adaptive quantitative traits in provenance trials. However, it neglects possible interspecific interaction in natural forests and overlooks natural hybridization or subspeciation. We propose that the genetic diversity of a given species in a forest community is shaped by both intraspecific population and interspecific community evolutionary processes, and expand the traditional forest genetic conservation concept under the community ecology framework. We show that a community-specific phylogeny derived from molecular markers would allow us to explore the genetic mechanisms of a tree species interacting with other resident species. It would also facilitate the exploration of a species' ecological role in forest community assembly and the taxonomic relationship of the species with other species specific to its resident forest community. Phylogenetic β-diversity would assess the similarities and differences of a tree species across communities regarding ecological function, the strength of selection pressure, and the nature and extent of its interaction with other species. Our forest genetic conservation proposal that integrates intraspecific population and interspecific community genetic variations is suitable for conserving a taxonomic species complex and maintaining its evolutionary potential in natural forests. This provides complementary information to conventional population and quantitative genetics-based conservation strategies.
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Affiliation(s)
- Xi Wang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yu Xiao
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Yan-Wen Lv
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Zi-Han He
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
| | - Francis C. Yeh
- Department of Renewable Resources, University of Alberta, 751 General Service Building, Edmonton, AB T6G 2H1, Canada;
| | - Xin-Sheng Hu
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.W.); (Y.X.); (Y.-W.L.); (Z.-H.H.)
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou 510642, China
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Catarino S, Goyder D, Darbyshire I, Costa E, Figueira R, Duarte MC, Romeiras MM. Species Diversity and Endemicity in the Angolan Leguminosae Flora. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.871261] [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
Angola has a great diversity of species and ecosystems and a high level of endemism. However, knowledge of the native flora remains very incomplete and outdated. Leguminosae is the largest family in the country, including many species which are of local or more regional economic importance. Based on an extensive review of bibliographic sources, natural history collections, and online databases, the checklist of Angolan Leguminosae plants was updated, including data on their native distribution, conservation status, and principal uses. The endemic taxa were the subject of additional investigation, including the main habitat, the number of collections preserved in herbaria, and the locality of the first collection. We identified 953 Leguminosae taxa occurring in Angola, of which 165 are endemic to the country. Among the 180 genera found, Crotalaria (136) and Indigofera (96) have the highest number of taxa. Almost half of the studied species have important applications, mainly in traditional medicine (385), forage (267), timber (188), and food (120). Nevertheless, only 27.7% have been assessed according to the IUCN Red List and 10 species are classified as threatened. Thirty-three endemics are known only from the type specimen, revealing the lack of knowledge on these species and the need for further field research. More than 30 type specimens were collected in the Serra da Chela, which highlights the importance of this region for biodiversity conservation.
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Vidaković A, Šatović Z, Tumpa K, Idžojtić M, Liber Z, Pintar V, Radunić M, Runjić TN, Runjić M, Rošin J, Gaunt D, Poljak I. Phenotypic Variation in European Wild Pear (Pyrus pyraster (L.) Burgsd.) Populations in the North-Western Part of the Balkan Peninsula. PLANTS 2022; 11:plants11030335. [PMID: 35161316 PMCID: PMC8837925 DOI: 10.3390/plants11030335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/03/2022]
Abstract
Leaves play a central role in plant fitness, allowing efficient light capture, gas exchange and thermoregulation, ensuring optimal growing conditions for the plant. Phenotypic variability in leaf shape and size has been linked to environmental heterogeneity and habitat characteristics. Therefore, the study of foliar morphology in plant populations can help us to identify the environmental factors that may have influenced the process of species diversification. In this study, we used European wild pear (Pyrus pyraster (L.) Burgsd., Rosaceae) as a model species to investigate the phenotypic variability of leaves under different environmental conditions. Using leaf morphometric data from 19 natural populations from the north-western part of the Balkan Peninsula, a high level of variability among and within populations were found. Leaf traits related to leaf size were more variable compared to leaf shape traits, with both influenced by geographic and environmental factors. Consequently, patterns of isolation by environment (IBE) and distance (IBD) were identified, with IBE showing a stronger influence on leaf variability. Multivariate statistical analysis revealed that European wild pear populations from the north-western part of the Balkan Peninsula can be divided into two morphological clusters, consistent with their geographical distance and environmental conditions. Our results confirm a high level of phenotypic variability in European wild pear populations, providing additional data on this poorly studied species, emphasizing phenotypic plasticity as a major driver in the adaptation of this noble hardwood species to rapid climate change.
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Affiliation(s)
- Antonio Vidaković
- Institute of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska cesta 23, HR-10000 Zagreb, Croatia; (A.V.); (K.T.); (M.I.); (D.G.)
| | - Zlatko Šatović
- Department for Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia;
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia; (Z.L.); (M.R.)
| | - Katarina Tumpa
- Institute of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska cesta 23, HR-10000 Zagreb, Croatia; (A.V.); (K.T.); (M.I.); (D.G.)
| | - Marilena Idžojtić
- Institute of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska cesta 23, HR-10000 Zagreb, Croatia; (A.V.); (K.T.); (M.I.); (D.G.)
| | - Zlatko Liber
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia; (Z.L.); (M.R.)
- Department of Biology, Faculty of Science, University of Zagreb, Marulićev trg 9a, HR-10000 Zagreb, Croatia
| | - Valentino Pintar
- Ministry of Economy and Sustainable Development, Institute for Environment and Nature, Nature Sector, Radnička cesta 80, HR-10000 Zagreb, Croatia;
| | - Mira Radunić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska cesta 25, HR-10000 Zagreb, Croatia; (Z.L.); (M.R.)
- Institute for Adriatic Crops and Karst Reclamation, Put Duilova 11, HR-21000 Split, Croatia; (T.N.R.); (M.R.); (J.R.)
| | - Tonka Ninčević Runjić
- Institute for Adriatic Crops and Karst Reclamation, Put Duilova 11, HR-21000 Split, Croatia; (T.N.R.); (M.R.); (J.R.)
| | - Marko Runjić
- Institute for Adriatic Crops and Karst Reclamation, Put Duilova 11, HR-21000 Split, Croatia; (T.N.R.); (M.R.); (J.R.)
| | - Jakša Rošin
- Institute for Adriatic Crops and Karst Reclamation, Put Duilova 11, HR-21000 Split, Croatia; (T.N.R.); (M.R.); (J.R.)
| | - Daniel Gaunt
- Institute of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska cesta 23, HR-10000 Zagreb, Croatia; (A.V.); (K.T.); (M.I.); (D.G.)
| | - Igor Poljak
- Institute of Forest Genetics, Dendrology and Botany, Faculty of Forestry and Wood Technology, University of Zagreb, Svetošimunska cesta 23, HR-10000 Zagreb, Croatia; (A.V.); (K.T.); (M.I.); (D.G.)
- Correspondence: ; Tel.: +385-1-2352547
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Ramon GD, Green BJ, Levetin E, Makra L, Bielory L. The Importance of Binomial Nomenclature for the Identification of Pollen Aeroallergens. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2021; 9:2642-2644. [PMID: 33741508 DOI: 10.1016/j.jaip.2021.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/23/2021] [Accepted: 03/01/2021] [Indexed: 10/21/2022]
Abstract
The diagnosis and treatment of atopic disorders associated with specific aerobiological triggers require basic botanical training. However, the identification of specific pollen can often be confounded by broad naming conventions that range from categorized colloquial to scientific names based on either higher taxonomic levels or, in some cases, binomial nomenclature. Physicians specializing in allergy often lack a comprehensive understanding with respect to plant taxonomy and botanical nomenclature that are critical skills required for clinical practice and research programs evaluating pollen and airborne fungal spores. In addition, binomial and current family designation and synonyms, including author citation are often misused, causing a misinterpretation of existing plants species or pollen types. It is critical that the correct botanical name is linked to a validated specimen and scientific naming conventions are used where possible by the clinician and researcher. In relation to pollen identification, we propose that clinicians and researchers should provide the currently accepted binomial nomenclature, offer relevant synonyms, and use the Angiosperm Phylogeny Group names.
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Affiliation(s)
- German Dario Ramon
- Instituto de Alergia e Inmunología del Sur, Hospital Italiano Regional del Sur, Bahía Blanca, Buenos Aires, Argentina.
| | - Brett James Green
- Office of the Director, Health Effects Laboratory Division, National Institute for Occupational Safety and Health, Centers for Disease Control and Prevention, Morgantown, Va
| | - Estelle Levetin
- Department of Biological Science, University of Tulsa, Tulsa, Okla
| | - László Makra
- University of Szeged, Faculty of Agriculture, Institute of Economics and Rural Development, Hódmezővásárhely, Hungary
| | - Leonard Bielory
- Department of Medicine and Ophthalmology, Hackensack Meridian School of Medicine, Seton Hall University, Nutley Center for Environmental Prediction, Department of Environmental Sciences, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ
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Freiberg M, Winter M, Gentile A, Zizka A, Muellner-Riehl AN, Weigelt A, Wirth C. LCVP, The Leipzig catalogue of vascular plants, a new taxonomic reference list for all known vascular plants. Sci Data 2020; 7:416. [PMID: 33243996 PMCID: PMC7693275 DOI: 10.1038/s41597-020-00702-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 09/23/2020] [Indexed: 12/23/2022] Open
Abstract
The lack of comprehensive and standardized taxonomic reference information is an impediment for robust plant research, e.g. in systematics, biogeography or macroecology. Here we provide an updated and much improved reference list of 1,315,562 scientific names for all described vascular plant species globally. The Leipzig Catalogue of Vascular Plants (LCVP; version 1.0.3) contains 351,180 accepted species names (plus 6,160 natural hybrids), within 13,460 genera, 564 families and 84 orders. The LCVP a) contains more information on the taxonomic status of global plant names than any other similar resource, and b) significantly improves the reliability of our knowledge by e.g. resolving the taxonomic status of ~181,000 names compared to The Plant List, the up to date most commonly used plant name resource. We used ~4,500 publications, existing relevant databases and available studies on molecular phylogenetics to construct a robust reference backbone. For easy access and integration into automated data processing pipelines, we provide an ‘R’-package (lcvplants) with the LCVP. Measurement(s) | Plant Taxonomy | Technology Type(s) | digital curation | Sample Characteristic - Organism | Tracheophyta |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.13013651
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Affiliation(s)
- Martin Freiberg
- Systematic Botany and Functional Biodiversity / Botanical Garden, Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany.
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, sDiv - Synthesis Centre, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Alessandro Gentile
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, sDiv - Synthesis Centre, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Alexander Zizka
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, sDiv - Synthesis Centre, Deutscher Platz 5e, Leipzig, 04103, Germany.,Naturalis Biodiversity Center, Darwinweg 2, 2333, CR, Leiden, The Netherlands
| | - Alexandra Nora Muellner-Riehl
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, sDiv - Synthesis Centre, Deutscher Platz 5e, Leipzig, 04103, Germany.,Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany
| | - Alexandra Weigelt
- Systematic Botany and Functional Biodiversity / Botanical Garden, Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, sDiv - Synthesis Centre, Deutscher Platz 5e, Leipzig, 04103, Germany
| | - Christian Wirth
- Systematic Botany and Functional Biodiversity / Botanical Garden, Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, sDiv - Synthesis Centre, Deutscher Platz 5e, Leipzig, 04103, Germany.,Molecular Evolution and Plant Systematics & Herbarium (LZ), Institute of Biology, Leipzig University, Johannisallee 21-23, 04103, Leipzig, Germany.,Max Planck Institute for Biogeochemistry, PO Box 100164, 07701, Jena, Germany
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Seeland M, Rzanny M, Boho D, Wäldchen J, Mäder P. Image-based classification of plant genus and family for trained and untrained plant species. BMC Bioinformatics 2019; 20:4. [PMID: 30606100 PMCID: PMC6318858 DOI: 10.1186/s12859-018-2474-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 11/08/2018] [Indexed: 11/26/2022] Open
Abstract
Background Modern plant taxonomy reflects phylogenetic relationships among taxa based on proposed morphological and genetic similarities. However, taxonomical relation is not necessarily reflected by close overall resemblance, but rather by commonality of very specific morphological characters or similarity on the molecular level. It is an open research question to which extent phylogenetic relations within higher taxonomic levels such as genera and families are reflected by shared visual characters of the constituting species. As a consequence, it is even more questionable whether the taxonomy of plants at these levels can be identified from images using machine learning techniques. Results Whereas previous studies on automated plant identification from images focused on the species level, we investigated classification at higher taxonomic levels such as genera and families. We used images of 1000 plant species that are representative for the flora of Western Europe. We tested how accurate a visual representation of genera and families can be learned from images of their species in order to identify the taxonomy of species included in and excluded from learning. Using natural images with random content, roughly 500 images per species are required for accurate classification. The classification accuracy for 1000 species amounts to 82.2% and increases to 85.9% and 88.4% on genus and family level. Classifying species excluded from training, the accuracy significantly reduces to 38.3% and 38.7% on genus and family level. Excluded species of well represented genera and families can be classified with 67.8% and 52.8% accuracy. Conclusion Our results show that shared visual characters are indeed present at higher taxonomic levels. Most dominantly they are preserved in flowers and leaves, and enable state-of-the-art classification algorithms to learn accurate visual representations of plant genera and families. Given a sufficient amount and composition of training data, we show that this allows for high classification accuracy increasing with the taxonomic level and even facilitating the taxonomic identification of species excluded from the training process. Electronic supplementary material The online version of this article (10.1186/s12859-018-2474-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Seeland
- Institute for Computer and Systems Engineering, Technische Universität Ilmenau, Helmholtzplatz 5, Ilmenau, 98693, Germany.
| | - Michael Rzanny
- Max-Planck-Institute for Biogeochemistry, Department Biogeochemical Integration, Hans-Knöll-Str. 10, Jena, 07745, Germany
| | - David Boho
- Institute for Computer and Systems Engineering, Technische Universität Ilmenau, Helmholtzplatz 5, Ilmenau, 98693, Germany
| | - Jana Wäldchen
- Max-Planck-Institute for Biogeochemistry, Department Biogeochemical Integration, Hans-Knöll-Str. 10, Jena, 07745, Germany
| | - Patrick Mäder
- Institute for Computer and Systems Engineering, Technische Universität Ilmenau, Helmholtzplatz 5, Ilmenau, 98693, Germany
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Stork NE. How Many Species of Insects and Other Terrestrial Arthropods Are There on Earth? ANNUAL REVIEW OF ENTOMOLOGY 2018; 63:31-45. [PMID: 28938083 DOI: 10.1146/annurev-ento-020117-043348] [Citation(s) in RCA: 423] [Impact Index Per Article: 70.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In the last decade, new methods of estimating global species richness have been developed and existing ones improved through the use of more appropriate statistical tools and new data. Taking the mean of most of these new estimates indicates that globally there are approximately 1.5 million, 5.5 million, and 7 million species of beetles, insects, and terrestrial arthropods, respectively. Previous estimates of 30 million species or more based on the host specificity of insects to plants now seem extremely unlikely. With 1 million insect species named, this suggests that 80% remain to be discovered and that a greater focus should be placed on less-studied taxa such as many families of Coleoptera, Diptera, and Hymenoptera and on poorly sampled parts of the world. DNA tools have revealed many new species in taxonomically intractable groups, but unbiased studies of previously well-researched insect faunas indicate that 1-2% of species may be truly cryptic.
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Affiliation(s)
- Nigel E Stork
- Environmental Futures Research Institute, Griffith School of Environment, Griffith University, Queensland 4111, Australia;
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Di Camillo CG, Gravili C, De Vito D, Pica D, Piraino S, Puce S, Cerrano C. The importance of applying Standardised Integrative Taxonomy when describing marine benthic organisms and collecting ecological data. INVERTEBR SYST 2018. [DOI: 10.1071/is17067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The decline of morphologically based taxonomy is mainly linked to increasing species redundancy, which probably contributed to a worldwide disinterest in taxonomy, and to a reduction of funding for systematic biology and for expertise training. The present trend in the study of biodiversity is integrated taxonomy, which merges morphological and molecular approaches. At the same time, in many cases new molecular techniques have eclipsed the morphological approach. The application of Standardised Integrative Taxonomy, i.e. a rigorous, common method of description based on the integration between ecological and morphological characteristics, may increase the precision, accessibility, exploitability and longevity of the collected data, and favour the renaissance of taxonomy by new investments in biodiversity exploration.
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Abstract
A new species, Lysimachia huangsangensis (Primulaceae), from Hunan, China is described and illustrated. The new species is closely related to L. carinata because of the crested calyx, but differs in the leaf blades that are ovate to elliptic and (3-)4.5-9 × 2-3.4 cm, 2-5-flowered racemes, and the calyx lobes that are ovate-lanceolate and 5-6 × 3-4 mm. The systematic placement and conservation status are also discussed.
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Gaudeul M, Rouhan G. A plea for modern botanical collections to include DNA-friendly material. TRENDS IN PLANT SCIENCE 2013; 18:184-5. [PMID: 23312146 DOI: 10.1016/j.tplants.2012.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Revised: 11/28/2012] [Accepted: 12/11/2012] [Indexed: 05/12/2023]
Abstract
Botanists have long collected herbarium specimens during their expeditions, and the importance of such collections is broadly acknowledged nowadays. It is largely recognized that material for molecular studies must be accompanied by herbarium material to be deposited in a recognized herbarium (vouchers). By contrast, the collection of herbarium specimens with no material for genetic analyses is unfortunately still common. The evolution of science and the need to face new environmental challenges require some changes in the way science is planned and performed. Here, we highlight some key scientific areas which could greatly benefit from such DNA-friendly collections, and we make a plea - and a call to all botanists - for the routine collection of DNA-friendly material together with herbarium specimens.
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Affiliation(s)
- Myriam Gaudeul
- Muséum National d'Histoire Naturelle, Herbier National (P), UMR CNRS 7205 Origine, Structure et Evolution de la Biodiversité, 16 rue Buffon, CP39, 75231 Paris Cedex 05, France.
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