The herbarium of Trinity College, Dublin: its history and contents

The herbarium was established in 1840, with the personal herbarium of Thomas Coulter as its nucleus. Extensive purchases were made by him and by his successor, W. H. Harvey, whose personal herbarium was also incorporated. Harvey also received numerous donations, partly through his friendship with W. J. Hooker and Asa Gray, but also from his position as joint author of Flora Capensis. After Harvey's death in 1866 growth continued at a slower rate till 1950, when it once more accelerated. The herbarium contains c. 206000 specimens in all: 166000 seed plants, 8000 pteridophytes, 8000 bryophytes, 20 000 algae and 4000 lichens. An analysis of the geographical origin of the specimens is given, and a list of the chief collectors. The regions most fully represented are Europe (especially the west and south), India, South Africa, North and South America. There is relatively little from China and Tropical Africa. Among the largest collections are those of Spruce (Amazon and Andes), Harvey (world-wide, especially Australian algae), A. F. G. Kerr (Thailand), Drege (South Africa) and Kotschy (Orient).     

Biological collections in an ever changing world: Herbaria as tools for biogeographical and environmental studies

Plant specimens stored in herbaria are being used as never before to document the impacts of global change on humans and nature. However, published statistics on the use of biological collections are rare, and ecologists lack quantitative data demonstrating the relevance to science of herbarium specimens. I found 382 studies with original data that used herbarium specimens to document biogeographical patterns or environmental changes. Most studies are less than 10 years old, and only 1.4% of the herbarium specimens worldwide have been used to answer biogeographical or environmental questions. The vast majority (82%) of papers dealt with vascular plants, but some studies also used bryophytes, lichens, seaweeds and fungi. The herbarium specimens were collected from all continents, but most of the studies used specimens from North America (40% of studies) or Europe (28%). Many types of researches (conservation, plant disease, plant invasion, pollution, etc.) can be conducted using herbarium specimens. Climate change, and especially phenological reconstructions, are clearly emerging research topics. By group, small herbaria (<100,000 specimens) are consulted as often as very large herbaria (>1,000,000 specimens) for biogeographical and environmental research, but in most cases, only large facilities provide specimens collected worldwide. The median number of specimens per study in papers using computerized collections (15,295) was much higher than for papers that did not include electronic data (226). The use of molecular analyses to investigate herbarium specimens is still relatively unexplored, at least from biogeographical and environmental points of view. Combined with recently developed procedures to correct biases, herbarium specimens might provide in the near future exciting additional spatio-temporal insights that are currently unimaginable.     

Metagenomic analysis of historical herbarium specimens reveals a postmortem microbial community

Advances in DNA extraction and next‐generation sequencing have made a vast number of historical herbarium specimens available for genomic investigation. These specimens contain not only genomic information from the individual plants themselves, but also from associated microorganisms such as bacteria and fungi. These microorganisms may have colonized the living plant (e.g., pathogens or host‐associated commensal taxa) or may result from postmortem colonization that may include decomposition processes or contamination during sample handling. Here we characterize the metagenomic profile from shotgun sequencing data from herbarium specimens of two widespread plant species (Ambrosia artemisiifolia and Arabidopsis thaliana) collected up to 180 years ago. We used blast searching in combination with megan and were able to infer the metagenomic community even from the oldest herbarium sample. Through comparison with contemporary plant collections, we identify three microbial species that are nearly exclusive to herbarium specimens, including the fungus Alternaria alternata, which can comprise up to 7% of the total sequencing reads. This species probably colonizes the herbarium specimens during preparation for mounting or during storage. By removing the probable contaminating taxa, we observe a temporal shift in the metagenomic composition of the invasive weed Am. artemisiifolia. Our findings demonstrate that it is generally possible to use herbarium specimens for metagenomic analyses, but that the results should be treated with caution, as some of the identified species may be herbarium contaminants rather than representing the natural metagenomic community of the host plant.     

DNA from herbarium specimens settles a controversy about origins of the European potato

Landrace potato cultivars are native to two areas in South America: the high Andes from eastern Venezuela to northern Argentina and the lowlands of south-central Chile. Potato first appeared outside of South America in Europe in 1567 and rapidly diffused worldwide. Two competing hypotheses suggested the origin of the "European" potato from the Andes or from lowland Chile, but the Andean origin has been widely accepted over the last 60 years. All modern potato cultivars predominantly have Chilean germplasm, explained as originating from breeding with Chilean landraces subsequent to the late blight epidemics beginning in 1845 in the UK. The Andean origin has been questioned recently through examination of landraces in India and the Canary Islands, but this evidence is inferential. Through a plastid DNA deletion marker from historical herbarium specimens, we report that the Andean potato predominated in the 1700s, but the Chilean potato was introduced into Europe as early as 1811 and became predominant long before the late blight epidemics in the UK. Our results provide the first direct evidence of these events and change the history of introduction of the European potato. They shed new light on the value of past breeding efforts to recreate the European potato from Andean forms and highlight the value of herbarium specimens in investigating origins of crop plants.     

C. S. Rafinesque’s North American vascular plants at the Academy of Natural Sciences of Philadelphia

Constantine Samuel Rafinesque (1783–1840) proposed about 2700 generic names and over 6700 binomials in approximately 1000 known publications. His herbarium at one time supposedly contained some 50,000 specimens, but after his death part of it was destroyed by rats, and Elias Durand, who eventually purchased the collection, discarded virtually all of the specimens. Because of these circumstances, plant taxonomists have had difficulty in typifying Rafinesque’s names. This paper summarizes the information on the labels of 275 specimens of Rafinesque’s vascular plants from the United States and Canada that are known to exist at the Academy of Natural Sciences in Philadelphia. These specimens come from four sources: (1) Rafinesque’s own herbarium, (2) Charles Wilkins Short’s herbarium, (3) the William Hembel collection, and (4) the herbarium of Rev. Lewis David von Schweinitz. Of the 275 specimens still extant, 51 (18.5%) are considered to be possible types. These type specimens are enumerated with (1) the complete data on the specimen, (2) the original source herbarium, and in most cases (3) the current accepted name of the taxon.     

Herbarium specimens demonstrate earlier flowering times in response to warming in Boston

Museum specimens collected in the past may be a valuable source of information on the response of species to climate change. This idea was tested by comparing the flowering times during the year 2003 of 229 living plants growing at the Arnold Arboretum in Boston, Massachusetts, USA, with 372 records of flowering times from 1885 to 2002 using herbarium specimens of the same individual plants. During this period, Boston experienced a 1.5°C increase in mean annual temperature. Flowering times became progressively earlier; plants flowered 8 d earlier from 1980 to 2002 than they did from 1900 to 1920. Most of this shift toward earlier flowering times is explained by the influence of temperature, especially temperatures in the months of February, March, April, and May, on flowering time. Plants with a long flowering duration appear to be as useful for detecting responses to changing temperatures as plants with a short flowering duration. Additional studies using herbarium specimens to detect responses to climate change could examine specimens from specific, intensively collected localities, such as mountain peaks, islands, and unique habitats.     

Reconstructing the spread of invasive plants: taking into account biases associated with herbarium specimens

Aim To reconstruct the spread of invasive wetland species using herbarium specimens and to develop a method that accounts for the biases associated with this type of historical record. Location Southern Québec. Methods The temporal and spatial distribution of herbarium specimens of vascular plants was examined. Six invasive species that are mainly found in wetlands were compared with five native, non‐expanding hydrophytes. The cumulative number of locations was plotted against time to construct invasion curves. For native species, this ‘invasion curve’ indicates the spatiotemporal distribution of the sampling for herbarium specimens of wetland plants. It also represents the history of the state of knowledge of the distribution of native species. Deviation from the native species invasion curve can be used to describe the spread of invasive species. For every year on record, the cumulative number of locations of each exotic species was divided by the cumulative number of locations of all native species, and the proportions obtained were plotted against time. Periods of invasiveness were then delineated. Results During the twentieth century, two periods of intensive herbarium specimen collection in Québec can be clearly distinguished, i.e. from 1930 to 1940 and from 1950 to 1985. Several periods of invasiveness were delineated for Butomus umbellatus L. (1922–35), Hydrocharis morsus‐ranae L. (1957–96), Lycopus europaeus L. (1963–2000), Lythrum salicaria L. (1890–1905, 1923–46), Phragmites australis (Cav.) Trin. ex Steudel (1963–84) and Rorippa amphibia (L.) Bess. (1929–34, 1943–52, 1971–79). Main conclusions Accounting for sampling biases associated with herbarium specimens is important in order to objectively delineate periods of invasiveness for exotic species. The spread of wetland vascular plant species can be reconstructed using herbarium specimens, even when the phenomenon is rapid, but the reconstruction is certainly more accurate when the invasion occurred during an active sampling period. The highly variable sampling effort for herbarium specimens in Québec and in other regions strongly cautions against using herbarium data without correction procedures.     

Herbarium tale: the utility of dry specimens for DNA barcoding Juncaceae

Phylogenetic and barcoding studies usually use fresh plant tissues as sources of DNA and have successfully amplified DNA for various loci. The use of dried samples, however, is often necessary due to the frequent inaccessibility of fresh rare plants or their parts for genetic analyses or barcoding. The difficulty in obtaining amplifiable DNA is a major restriction of the use of herbarium specimens for DNA analyses. Recent study has highlighted the crucial issues for comparing herbarium and fresh plants for barcoding. We analysed the performance of samples of the family Juncaceae from various herbarium specimens of different ages with fresh plant material in PCRs and the sequences of seven loci (rbcL, rpoC1, trnL-F intergenic spacer, trnL intron, and psbA-trnH from chloroplast DNA; atp1 from mitochondrial DNA; and ITS1-5.8S-ITS2 from nuclear DNA) using a combination of 28 primers. The herbarium specimens amplified well and may thus be successfully applied for both phylogenetic analyses and barcoding for the Juncaceae family. Amplifying DNA was more difficult from dried herbarium specimens than fresh samples but could be successful in most cases when appropriate internal primers were designed or methods were optimised. Using the set of universal primers recommended by the Consortium for the Barcode of Life and designing specific primers for a particular group of interest were both useful. Specimen age and amplicon length had limited detrimental effects on amplification success for most of the Juncaceae loci tested.     

Photographs and herbarium specimens as tools to document phenological changes in response to global warming

Global warming is affecting natural systems across the world. Of the biological responses to warming, changes in the timing of phenological events such as flowering are among the most sensitive. Despite the recognized importance of phenological changes, the limited number of long-term records of phenological events has restricted research on the topic in most areas of the world. In a previous study in Boston (American Journal of Botany 91: 1260-1264), we used herbarium specimens and one season of field observations to show that plants flowered earlier as the climate warmed over the past 100 yr. In our new study, we found that two extra years of data did not strengthen the explanatory power of the analysis. Analysis of herbarium specimens without any field data yielded results similar to analyses that included field observations. In addition, we found that photographs of cultivated and wild plants in Massachusetts, data similar to that contained in herbarium specimens, show changes in flowering times that closely match independent data on the same species in the same locations. Dated photographs of plants in flower represent a new resource to extend the range of species and localities addressed in global-warming research.     

广西植物标本馆标本数字化信息统计与分析

为更了解广西植物标本馆概况与各类标本构成情况,该文以标本馆信息数据库的标本信息为基础,分别从标本的种类、石山植物标本、采集地、采集年代及采集人等5个方面进行了统计与分析。结果显示,在统计的20万份维管植物标本中,共隶属314科2504属11452种;石山植物标本份数占45.35%,含205科1021属2700种;广西采集的标本份数最多,共100372份占总份数的50.19%;在50年代标本采集量最大,达87997份占总份数的44.00%。并提出了几点建议。     

Is Shape of a Fresh and Dried Leaf the Same?

Plants kept as dried herbarium specimens share many characteristics with their living counterparts, but there are some substantial differences between them. Due to dehydration, leaves of herbarium specimens change not only their mass and colour, but in many cases change their dimensions, too. The present study aimed to determine whether leaf shape changes during the drying process. A total of 794 pairs of fresh and dried leaves or leaflets of 22 plant taxa were studied. The shape of the blades was quantified using elliptic Fourier analysis combined with principal component analysis. In addition, area and mass of the leaves were measured. Statistical tests were applied for comparing fresh and dried leaves. The results indicate that the preservation process of pressing and drying plants for herbarium purposes causes changes in leaf shape. In general, the shape changes were directional. As the shape of fresh and dried plants is different, it is strongly recommended that shape analyses should be performed on datasets containing either of the leaf types.     

DNA damage in plant herbarium tissue

Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4-3.8% of fresh control DNA and 1.0-1.3% after long-term herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of C→T/G→A transitions were observed in old herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term herbarium storage. Our results suggest that reliable sequence data can be obtained from herbarium specimens.     

A deep learning-based approach for detecting plant organs from digitized herbarium specimen images

Herbarium specimens are excellent sources of botanical information to facilitate understanding and monitoring the evolution of plants and their effects on global climate change. Globally, many herbaria have undertaken digitization projects of herbarium specimens to preserve them and make them accessible in online repositories to botanists and ecologists. Automated detection of plant organs such as plant leaves, buds, flowers, and fruits on the digitized herbarium specimen images provides valuable information in various scientific contexts. We developed a deep learning approach based on the refined YOLO-V3 approach to detect plant organs within the digitized herbarium specimen images effectively. The proposed approach combines ResNet and DenseNet architectures to improve feature extraction capabilities. Also, a new scale of feature map is added to the existing scales to address the problem of YOLO-V3's low performance in detecting small plant organs. The experimental results demonstrate that our proposed approach can detect organs of different sizes within different specimens, where the precision and recall reached 94.2% and 95.5%, respectively.     

Digital Herbarium of Moscow State University: The Largest Russian Biodiversity Database

In 2015–2016, 785887 specimens were scanned at the Herbarium of Moscow State University (MW), which comprised 77.7% of the total collection. The metadata of the digital herbarium include the identifier (ID) of each specimen, its species name, and geographical reference (area code). As the largest in Russia database with respect to biodiversity, the Herbarium includes 712925 images of specimens of vascular plants and 72962 specimens of bryophytes. The digital herbarium is interrelated with the Catalogue of Life international database and has enriched it with 160 new species. Images of 781882 specimens have been put online as JPG files (the resolution is 300 dpi) on the web portal of the National Depository Bank of Live Systems (https://plant.depo.msu.ru/). The portal is open for all Russian biological collections.     

Changes in plant collection practices from the 16th to 21st centuries: implications for the use of herbarium specimens in global change research

Background and AimsHerbaria were recently advertised as reliable sources of information regarding historical changes in plant traits and biotic interactions. To justify the use of herbaria in global change research, we asked whether the characteristics of herbarium specimens have changed during the past centuries and whether these changes were due to shifts in plant collection practices.MethodsWe measured nine characteristics from 515 herbarium specimens of common European trees and large shrubs collected from 1558 to 2016. We asked botanists to rank these specimens by their scientific quality, and asked artists to rank these specimens by their beauty.Key ResultsEight of 11 assessed characteristics of herbarium specimens changed significantly during the study period. The average number of leaves in plant specimens increased 3-fold, whereas the quality of specimen preparation decreased. Leaf size negatively correlated with leaf number in specimens in both among-species and within-species analyses. The proportion of herbarium sheets containing plant reproductive structures peaked in the 1850s. The scientific value of herbarium specimens increased until the 1700s, but then did not change, whereas their aesthetic value showed no systematic trends.ConclusionsOur findings strongly support the hypothesis that many characteristics of herbarium specimens have changed systematically and substantially from the 16th to 21st centuries due to changes in plant collection and preservation practices. These changes may both create patterns which could be erroneously attributed to environmental changes and obscure historical trends in plant traits. The utmost care ought to be taken to guard against the possibility of misinterpretation of data obtained from herbarium specimens. We recommend that directional changes in characters of herbarium specimens which occurred during the past 150‒200 years, primarily in specimen size and in the presence of reproductive structures, are accounted for when searching for the effects of past environmental changes on plant traits.     

The Friesner Herbarium (BUT) of Butler University

The Friesner Herbarium (BUT) of Butler University is a collection of over 100,000 specimens built from the personal herbarium of Ray C. Friesner. He and other botanists at Butler amassed one of the largest and most complete collections of Indiana plants. Active exchange from the 1920’s through the 1940’s increased the holdings of plants from other states. Although the collection does not contain many type specimens, it is rich in vouchers from floristic and ecological studies conducted in the first half of the 20th century and published in the scientific journal,Butler University Botanical Studies.     

中国高等植物数字化标本分析

传统上馆藏标本,主要用于植物分类学、植物资源学的研究。数字标本的出现将标本的使用拓展到从研究生物多样性时间空间分布到生态学和进化学理论、生物多样性保护、农业和人类健康等广泛领域。截至目前,从互联网上获取的采自中国的植物标本数量已有1 200多万份。该文通过整理和分析这些数据以了解中国植物标本的数字化精度、采集时间和采集地区规律以及采集空缺等状况。结果表明:中国标本采集形成了4个高峰,即20世纪30年代、60年代、80年代和21世纪初,中国植物标本采集和研究工作主要在20世纪50年代后由中国学者完成。标本采集地区覆盖度在省级较好,县级标本采集则很不平衡; 标本采集类群在科属层面覆盖率高,但近五分之一的物种采集不足; 标本的采集量既与植物分布幅度相关,也与采集地区的知名度、所获科研项目及采集者偏好有关。未来中国植物标本数字化方向应该在继续挖掘馆藏标本的同时,一方面开展对现有数字化标本信息再审核及补充,并加强与欧美大馆的信息共享以获取早期历史标本信息; 另一方面应用数字化标本信息分析结果,指导境内标本的精准采集,包括采集薄弱/空白地区、采集薄弱/空白属种的采集,以进一步增强实体标本馆能力,提高数字化标本质量,为进一步完善植物标本数字化和精准化采集提供依据,更好地服务科学和社会的发展。