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... pot being blown over and spilling the soil could have ruined the experiment. Gerard (1633) illustrated a planted pot sunk in the ground (Figure 2) so it seems likely gardeners of Helmont's time knew of one or more of the practical advantages. Sinking the pot may have also prevented the roots from being killed by subfreezing temperatures (Hershey, 1991). ...
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... of photos or line-draws of the organisms studied that would help the reader who is not familiar with group. This would be particularly useful in chapter 8 to illustrate the diverse patterns of forms. Simple diagrammatic schemes to shows the variations in columnar cactus branching would be sufficient. The graphics and maps are clear, except for Fig. 2- 3 where the floristic provinces of Mexico are illustrated by gray tones. Finally, it is unclear if birds and insects have less importance in pollination, or if the few references to them indicates the lack of a specialist in these ...
Citations
... Herbaria serve as an important source of primary data for many studies, including taxonomic, biogeographic and phylogenetic ones (Holmes et al. 2016, Soltis 2017, James et al. 2018, Ball-Damerow et al. 2019. The herbarium management is a responsible task during which the curators face several issues, including organisation of permanent access, long-term preservation of the collection, unintentional damage to specimens and, occasionally, vandalism (Funk 2002, Pennock 2017, Rabeler et al. 2019. Moreover, processing of the natural history collections, including the herbarium collections, by researchers in person is laborious and expensive (Suarez and Tsutsui 2004, Bradley et al. 2014, Popov et al. 2021. ...
Digitisation of hosted specimens is a crucial task for all herbaria worldwide and is one of the main streams for today. By digitising their collections and publishing the datasets, the herbaria grant access to essential data to a wide research audience and, as a result, involve their collections in scientific work more actively. Digitisation also allows virtual preservation of the collections, which is especially important in conditions of hostilities, when the entire collection can be destroyed or damaged in one moment. This paper describes two datasets recently published in GBIF in the framework of the LWS herbarium digitisation initiative. It also contains some considerations about further digitisation priorities and plans in the LWS Herbarium in the context of complicated war conditions and limited facilities.
In total, 2,419 occurrence records from Ukraine mobilised from LWS Herbarium were published. These datasets are planned to be dynamic with the addition of new records along with progress of digitisation work at LWS. At least 6,000 more records are planned to be published through these datasets in 2024.
... Herbaria serve as an important source of primary data for many studies, including taxonomic, biogeographic, and phylogenetic ones (Holmes et al. 2016, Soltis 2017, James et al. 2018, Ball-Damerow et al. 2019. The herbarium management is a responsible task during which the curators face several issues, including organization of permanent access, long-term preservation of the collection, unintentional damage to specimens and, occasionally, vandalism (Funk 2002, Pennock 2017, Rabeler et al. 2019. Moreover, processing of the natural history collections, including the herbarium collections, by researchers in person is laborious and expensive (Suarez and Tsutsui 2004, Bradley et al. 2014, Popov et al. 2021. ...
Digitization of hosted specimens is a crucial task for all herbaria worldwide and is one of the main streams for today. By digitizing their collections and publishing the datasets, the herbaria grant access to essential data to a wide research audience and, as a result, involve their collections in scientific work more actively. Digitization also allows virtual preservation of the collections, which is especially important in conditions of hostilities, when the entire collection can be destroyed or damaged in one moment. This paper describes two datasets recently published in GBIF in frames of the LWS herbarium digitization initiative. It also contains some considerations about further digitization priorities and plans in the LWS herbarium in the context of complicated war conditions and limited facilities.
In total, 2,419 occurrence records from Ukraine mobilized from LWS herbarium were published. These datasets are planned to be dynamic with the addition of new records along with progress of digitization work at LWS. At least 6,000 more records are planned to be published through these datasets in 2024.
... Thanks to the digitisation of herbarium collections, images of sheets with plant specimens are available on websites of many herbaria, making them available to a wide audience. Herbaria provide material samples for biological research in diverse fields (Funk 2003), including global change biology (Meineke et al. 2018;Lang et al. 2019), and are an important source of species discovery (Bebber et al. 2010). They play an integral role in a modern additive research process (Henning et al. 2018) that aims to describe and understand the evolution and diversity of organisms worldwide (Harris and Marsico 2017;Borsch et al. 2020). ...
Józef Warszewicz (1812–1864) was one of the first Polish naturalists to explore the flora of the tropical New World. During two expeditions to Central and South America (1844–1850 and 1850–1853) he collected and delivered to Europe up to twenty thousand plant specimens. To honour his service and his achievements in plant collections, different taxonomists described more than 100 taxa using the surname Warszewicz, for example in the genus name ( Warszewiczia ) and the species epithets ( warszewiczii , warscewiczii , warszewicziana ). Unfortunately, a large part of Warszewicz’s collection of plant species deposited in the Berlin Herbarium (B), including many type specimens was destroyed during World War II. During digitisation of herbarium collections preserved in the Herbarium of the Jagiellonian University (KRA), we reviewed more than 650 herbarium sheets with plant specimens collected by Warszewicz and originating from his trips to Central and South America. In this paper, we present the typification of five names of species, described base on Warszewicz’s plant material. We select lectotypes for Berberis warszewiczii , Esenbeckia warscewiczii , Psammisia ramiflora , Remijia involucrata and Rondeletia orthoneura , and provide data on the presence of 17 specimens (isotypes) representing Esenbeckia cornuta , an extremely rare species, that to date is known only from the type locality in Peru. A list of all Warszewicz’s specimens preserved at KRA herbarium is also presented. Additionally, in the result of the revision of syntypes of Berberis multiflora and Rondeletia reflexa we designated here the lectotypes for these taxa.
... Herbaria, like other natural history collections, are immense primary data repositories documenting biodiversity across space and time over the last 500 years (Stefanaki et al., 2019). Each specimen contains a wealth of information including geographic occurrence data, phenotype, genotype, phenological status, and biotic interactions (Funk, 2003;Heberling and Burke, 2019). Collectively herbarium specimens are analyzed for studies in taxonomy, systematics, floristics, ecology, phenology, conservation, and global environmental change (Funk, 2003;Calinger et al., 2013;Willis et al., 2017;Lang et al., 2019;Albani Rocchetti et al., 2021). ...
... Each specimen contains a wealth of information including geographic occurrence data, phenotype, genotype, phenological status, and biotic interactions (Funk, 2003;Heberling and Burke, 2019). Collectively herbarium specimens are analyzed for studies in taxonomy, systematics, floristics, ecology, phenology, conservation, and global environmental change (Funk, 2003;Calinger et al., 2013;Willis et al., 2017;Lang et al., 2019;Albani Rocchetti et al., 2021). ...
Herbarium sheets present a unique view of the world's botanical history, evolution, and biodiversity. This makes them an all–important data source for botanical research. With the increased digitization of herbaria worldwide and advances in the domain of fine–grained visual classification which can facilitate automatic identification of herbarium specimen images, there are many opportunities for supporting and expanding research in this field. However, existing datasets are either too small, or not diverse enough, in terms of represented taxa, geographic distribution, and imaging protocols. Furthermore, aggregating datasets is difficult as taxa are recognized under a multitude of names and must be aligned to a common reference. We introduce the Herbarium 2021 Half–Earth dataset: the largest and most diverse dataset of herbarium specimen images, to date, for automatic taxon recognition. We also present the results of the Herbarium 2021 Half–Earth challenge, a competition that was part of the Eighth Workshop on Fine-Grained Visual Categorization (FGVC8) and hosted by Kaggle to encourage the development of models to automatically identify taxa from herbarium sheet images.
... Los herbarios se consideran sitios donde se deposita material vegetal seco que proveen información sobre las plantas (Katinas, 2001;Funk, 2003a). Los primeros herbarios eran libros de plantas medicinales y sus usos, basada en plantas silvestres o cultivadas (Sprague y Nelmes, 1931). ...
... Los primeros herbarios eran libros de plantas medicinales y sus usos, basada en plantas silvestres o cultivadas (Sprague y Nelmes, 1931). Los herbarios se han usado para estudios de sistemática, taxonomía, palinología, filogenia basada en datos morfológicos y moleculares, anatomía, fitogeografìa, ecofisiología, entre otros (Funk, 2003a;Funk, 2003b; ...
RESUMEN El Herbario Paul R. House tiene como finalidad albergar la flora útil de Honduras. Se realizo el registro y la actualización de nombres y familias y su vez, elaborar una base de datos en Access de plantas con importancia económica con basada en la colección del Herbario de Plantas Útiles de Honduras, Paul R. House. Este cuenta con 1547 especímenes depositados distribuidos en 144 familias pertenecientes a 447 géneros y 712 especies vegetales. Se registra un 80% de especies son nativas y el 20% introducidas. La mayoría de las especies registradas son medicinales (68%), comestibles (8%), representada por la familia Fabaceae, Malvaceae y Rubiaceae. Además, se enlistan los principales colectores y sitios de colecta. Esta información será el apoyo para estudios morfológicos, genéticos, florísticos, etnobotánicos, asimismo, para educación formal y técnica para estudiantes e investigadores. ABSTRACT The purpose of the Paul R. House Herbarium is to house the useful flora of Honduras. The register and updating of names and families was carried out and, likewise, a database in Access of plants with economic importance was created based on the collection of the Herbarium of Useful Plants of Honduras, Paul R. House. This has 1547 deposited specimens distributed in 144 families belonging to 447 genera and 712 plant species. 80% of species are native and 20% introduced. Most of the registered species are medicinal (68%), edible (8%), represented by the Fabaceae, Malvaceae and Rubiaceae families. In addition, the main collectors and collection sites are listed. This information will be the support for morphological, genetic, floristic, ethnobotanical studies, as well as for formal education and technical for students and researchers.
... museums and herbaria) are essential for studying biodiversity (Graham et al., 2004). Taxonomists use these collections to describe new species, produce taxonomic revisions and species checklists, among other important uses (Bebber et al., 2010;Besnard et al., 2018;Funk, 2003). In macroecology, biogeography and conservation, biological collections are often the main source of species records, which are used to study spatial patterns of biodiversity, species ecological niches, endemism levels and conservation status (Dauby et al., 2017;Graham et al., 2004;Lima et al., 2020;Ulloa et al., 2017). ...
Species records from biological collections are becoming increasingly available online. This unprecedented availability of records has largely supported recent studies in taxonomy, biogeography, macroecology and biodiversity conservation. Biological collections vary in their documentation and notation standards, which have changed through time. For different reasons, neither collections nor data repositories perform the editing, formatting and standardisation of the data, leaving these tasks to the final users of the species records (e.g. taxonomists, ecologists and conservationists). These tasks are challenging, particularly when working with millions of records from hundreds of biological collections.
To help collection curators and final users perform those tasks, we introduce plantR, an open‐source package that provides a comprehensive toolbox to manage species records from biological collections. The package is accompanied by the proposal of a reproducible workflow to manage this type of data in taxonomy, ecology and biodiversity conservation. It is implemented in R and designed to handle relatively large datasets as fast as possible. Initially designed to handle plant species records, many of the plantR features also apply to other groups of organisms, given that the data structure is similar.
The plantR workflow includes tools to (a) download records from different data repositories, (b) standardise typical fields associated with species records, (c) validate the locality, geographical coordinates, taxonomic nomenclature and species identifications, including the retrieval of duplicates across collections, and (d) summarise and export records, including the construction of species lists with vouchers.
Other R packages provide tools to tackle some of the workflow steps described above. But in addition to the new tools and resources related to data standardisation and validation, the greatest strength of plantR is to provide a comprehensive and user‐friendly workflow in one single environment, performing all tasks from data retrieval to export. Thus, plantR can help researchers better assess data quality and avoid data leakage in a wide variety of studies using species records.
... Herbarium specimens have been collected from all over the world for hundreds of years and serve as a rich source of crucial data for studying plant biodiversity and ecology [12]. Expanding access to specimen types across digitization is essential in maintaining specimens and making relevant knowledge readily available to researchers and the public. ...
Pattern Recognition Letters
Available online 21 July 2021
In Press, Journal Pre-proofWhat are Journal Pre-proof articles?
Deep Leaf: Mask R-CNN based leaf Detection and Segmentation from digitized herbarium specimen images
Author links open overlay panelAbdelazizTrikiaWalidMahdia
https://doi.org/10.1016/j.patrec.2021.07.003
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Highlights
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A modified mask RCNN named Deep Leaf is developed to identify the leaves from the digitized herbarium specimens.
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Deep Leaf measures automatically the morphological traits of the extracted leaves.
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Deep features are extracted through an improved ResNet50/101, which is chosen as the backbone network of the feature extraction.
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We achieved better performance compared with the original mask RCNN algorithm for leaves detection.
Abstract
The generation of morphological traits of plants such as the leaf length, width, perimeter, area, and petiole length are fundamental features of herbarium specimens, thus providing high-quality data to investigate plant responses to ongoing climatic change and plant history evolution. However, the existing measurement methods are primarily associated with manual analysis, which is labor-intensive and inefficient. This paper proposes a deep learning-based approach, called Deep Leaf, for detecting and pixel-wise segmentation of leaves based on the improved state-of-the-art instance segmentation approach, Mask Region Convolutional Neural Network (Mask R-CNN). Deep Leaf can accurately detect each leaf in the herbarium specimen and measure the associated morphological traits. The experimental results indicate that our automated approach can segment the leaves of different families. Compared to manual measurement done by ecologist and botanist experts, the average relative error of leaf length is 4.6%, while the average relative error of leaf width is 5.7%.
... They are also useful for examining historical distribution and abundance of species, providing insight into actual and potential effects of anthropogenic environmental change (Araujo and Rahbek 2006;Feeley and Silman 2011). The benefits of museum and herbaria collections are many, ranging from niche modeling to food safety to medicine (Funk 2003;Funk 2018). As amateur scientists collect data they provide invaluable resources for professionals to further analyze, and some of the amateur scientists become experts or professionals themselves. ...
Citizen science, which has contributed greatly to scientific understanding, works through partnerships between non-governmental and governmental organizations, academia, and most importantly, volunteers. In the United States, Master Naturalist training programs prepare adults as knowledgeable environmental stewards. Once certified, Master Naturalists are encouraged to log annual volunteer activity hours involving scientific research and education. Compared to untrained volunteers, individuals who have completed Master Naturalist training (or similar programs) exhibit greater project involvement and efficiency at collecting data. These traits align well with the goals of citizen science and point to a symbiotic relationship between citizen science and Master Naturalist programs. Here, we convey how Master Naturalist programs benefit citizen science and provide guidelines for individuals who wish to pursue citizen science projects or programming to produce high quality citizen scientists.
... Atualmente, existem 4.217 herbários no mundo, dos quais 272 estão localizados no Brasil, mas apenas 37 sediados na Amazônia brasileira (SBB 2020;Thiers 2020). Um herbário resguarda espécimes de plantas, fungos e algas, possibilitando diversas aplicações didáticas e científicas, principalmente relacionadas com estudos em taxonomia, sistemática, ecologia, anatomia, morfologia, etnobotânica, paleobiologia e biologia da conservação (Funk 2003;Peixoto & Maia 2013;Heberling & Burke 2019). A disponibilização pública de dados e imagens de espécimes em escala global vem sendo realizada e é essencial para o reconhecimento de endemismos, para a adoção de medidas conservacionistas ou à detecção de áreas que necessitam de expedições adicionais de coleta (Funk 2018;Barberena et al. 2019;Rabeler et al. 2019). ...
Resumo: O herbário da Universidade Federal Rural da Amazônia-campus Capitão Poço (HCP), localizado no nordeste do estado do Pará, abriga 19 gêneros, 26 espécies e 49 espécimes de Orchidaceae, que correspondem a 7,4% do acervo. Os principais coletores são integrantes do grupo de pesquisa "Núcleo de Pesquisas em Epífitas". Notylia lyrata e Catasetum macrocarpum são as espécies mais bem documentadas, com sete e cinco espécimes, respectivamente. A consolidação desse novo herbário possibilitará o apoio aos projetos florístico-taxonômicos e ecológicos em desenvolvimento na mesorregião do nordeste paraense, que tendem a suprir as lacunas de coletas botânicas, tornando o HCP uma fonte regional de conhecimento da flora amazônica. Abstract: The herbarium of the Universidade Federal Rural da Amazônia-campus Capitão Poço (HCP), located in the northeast of the state of Pará, houses 19 genera, 26 species and 49 specimens of Orchidaceae, which correspond to 7.4% of the collection. The main collectors are members of the research group "Núcleo de Pesquisas em Epífitas". Notylia lyrata and Catasetum macrocarpum are the best documented species, with seven and five specimens, respectively. The consolidation of this new herbarium will make it possible to support the floristic-taxonomic and ecological projects under development in the northeastern region of Pará, which tends to fill the gaps of the botanical collection, thus making HCP a regional source for knowledge of Amazonian flora.
... Herbarium collections contain invaluable information about the evolutionary history of living and extinct species, and therefore represent a key source of knowledge for science (Funk, 2003;Raedig et al., 2010). Notwithstanding this, on the one hand, by the year 2000 the majority of data on Neotropical plants from herbarium collections were yet to be digitized (Morawetz and Raedig, 2007). ...
Brazil has high levels of biodiversity and has received strong criticism for the increasing country-wide deforestation that threatens it. Although a significant percentage of land area in Brazil is protected, the areas are insufficient and unevenly distributed. Many studies have contributed to the biogeographical knowledge of Brazilian flora, but no endemicity analysis (EA) has been conducted including all endemic angiosperms. We investigated the spatial component, drawing on a huge and taxonomically diverse dataset based on 827 016 records collected over the last two centuries. We conducted an EA for 15 034 species from 173 families using an optimality criterion with 2° and 3° grid sizes, in order to search for distributional concordance, to identify the biogeographical units and discuss the implications for conservation. Six analyses were run for basal angiosperms,
monocots and eudicots. The EA recovered 66 consensus areas (CAs). The concordance of CAs enabled the identification of five best-supported areas of endemism––three in the Atlantic and Parana Forest and two areas in the Cerrado province––supported
by species of 120 families. The age of divergence for some genera that contributed significantly to the identification of areas
recovered in the Cerrado coincides with the recent, <10 Ma, estimated age of that province. By contrast, the areas in the Atlantic and Parana Forest are supported by genera with earlier diversification >30 Ma, supporting an ancient origin. Most areas in
the Atlantic Forest are partially superimposed with the limits of the protected areas, however, big gaps were identified in the Cerrado. Protecting Brazilian biomes was at the heart of Brazil’s environmental policy. Regrettably, this scenario has radically
changed based on misleading divergences in conservation policy. Areas of endemism are pivotal for biodiversity conservation due to the common evolutionary history shared by their endemic taxa. Thus, we hope that these congruent patterns of endemism
support the establishment of biodiversity priorities.
