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.     

The Henry Parker Sartwell herbarium of Hamilton College

H. P. Sartwell's private herbarium was donated to the New York Botanical Garden in 1983 by Hamilton College of Clinton, New York. This herbarium was assembled by Dr. Sartwell (1792–1867) throughout his carcer and was eventually sold to Hamilton College. The collection is particularly rich in type material, western New York plants, and carices. Dr. Sartwell had an active exchange program with his contemporaries and, therefore, his herbarium also has collections from many parts of the world. An index to collectors is presented, as well as a list of verified and probable types.     

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.     

Amplification of cox2 (approximately 620 bp) from 2 mg of up to 129 years old herbarium specimens, comparing 19 extraction methods and 15 polymerases

During the past years an increasing number of studies have focussed on the use of herbarium specimens for molecular phylogenetic investigations and several comparative studies have been published. However, in the studies reported so far usually rather large amounts of material (typically around 100 mg) were sampled for DNA extraction. This equals an amount roughly equivalent to 8 cm(2) of a medium thick leaf. For investigating the phylogeny of plant pathogens, such large amounts of tissue are usually not available or would irretrievably damage the specimens. Through systematic comparison of 19 DNA extraction protocols applied to only 2 mg of infected leaf tissue and testing 15 different DNA polymerases, we could successfully amplify a mitochondrial DNA region (cox2; approximately 620 bp) from herbarium specimens well over a hundred years old. We conclude that DNA extraction and the choice of DNA polymerase are crucial factors for successful PCR amplification from small samples of historic herbarium specimens. Through a combination of suitable DNA extraction protocols and DNA polymerases, only a fraction of the preserved plant material commonly used is necessary for successful PCR amplification. This facilitates the potential use of a far larger number of preserved specimens for molecular phylogenetic investigation and provides access to a wealth of genetic information in preserved in specimens deposited in herbaria around the world without reducing their scientific or historical value.     

地黄属的分类学修订

地黄属特产于我国,本文对该属进行了分类修订。根据地黄属的腊叶标本和活体植物研究,结合地黄属的野外调查,确认地黄属有5个种,并将高地黄Rehmannia elata N.E.Brown ex Prain处理为裂叶地黄R.piasezkii Maxim的一个异名。同时给出地黄属每个种的描述、分布和分种检索表。     

Amplification of cox2 (～620 bp) from 2 mg of Up to 129 Years Old Herbarium Specimens,Comparing 19 Extraction Methods and 15 Polymerases

During the past years an increasing number of studies have focussed on the use of herbarium specimens for molecular phylogenetic investigations and several comparative studies have been published. However, in the studies reported so far usually rather large amounts of material (typically around 100 mg) were sampled for DNA extraction. This equals an amount roughly equivalent to 8 cm² of a medium thick leaf. For investigating the phylogeny of plant pathogens, such large amounts of tissue are usually not available or would irretrievably damage the specimens. Through systematic comparison of 19 DNA extraction protocols applied to only 2 mg of infected leaf tissue and testing 15 different DNA polymerases, we could successfully amplify a mitochondrial DNA region (cox2; ∼620 bp) from herbarium specimens well over a hundred years old. We conclude that DNA extraction and the choice of DNA polymerase are crucial factors for successful PCR amplification from small samples of historic herbarium specimens. Through a combination of suitable DNA extraction protocols and DNA polymerases, only a fraction of the preserved plant material commonly used is necessary for successful PCR amplification. This facilitates the potential use of a far larger number of preserved specimens for molecular phylogenetic investigation and provides access to a wealth of genetic information in preserved in specimens deposited in herbaria around the world without reducing their scientific or historical value.     

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.     

长白山高山冻原种子植物的调查

通过多次对长白山高山冻原的实地考察,统计得到冻原种子植物共计34科、94属、146种,有6种属的分布区类型(包括3个变型),北温带分布类型最多,占总属数的68.09%。在整个冻原上,草本有125种,占总数的85.62%,其中多年生草本124种。高山冻原植物中具有多种生态,生理适应方式,低矮平卧状植株、极矮小草本、密集丛生是植物的重要适应方式,细长密集须根是冻原上主要的适应方式,占植物总数的54.94%。果实中干果共计137种,其中蒴果56种。由于高山冻原上生态环境十分残酷,极易受人为因素的影响。     

New World Podostemaceae: Ecological and evolutionary enigmas

The largely tropical Podostemaceae occur in a unique habitat for angiosperms: attached to rocks in river rapids and waterfalls. Little taxonomic work has been published on New World Podostemaceae since Van Royen's monograph in the early 1950s. A paucity of complete herbarium material severely limits taxonomic study and precludes addressing a range of enigmatic ecological and evolutionary issues that relate to the family. The size, high level of endemism, and life history of the family are discussed. The distributions of two species in Mexico are used to illustrate the need for concerted collecting efforts. Recommendations for collection strategies are made that reflect the unusual habitat and life history of these plants.     

中国长江中下游地区贝母属的修订

本文对长江中下游地区的贝母属进行了修订,确认该地区有3种1变种,新归并14种5变种。     

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).     

Sources of information about botanic gardens and herbaria

Botany is the study of living plants in the garden and the wild and of dead plants in the herbarium and laboratory. The value of a botanic garden for teaching purposes became evident in the 16th century with the founding between 1543 and 1600 of botanic gardens at Pisa, Padua, Florence, Bologna, Leyden, Leipzig, Paris, Montpellier and Heidelberg: indeed most of the major European botanic gardens were founded during this and the next two centuries. Associated with the study of living plants in botanic gardens was the invention of the herbarium by Luca Ghini (1490–1556) and the subsequent making of many private herbaria, out of which have developed the large institutional herbaria, mostly in the 18th and 19th centuries. The continuous enrichment of European gardens by the introduction of new plants resulting from European exploration and colonization created many problems of classification and naming, and so led to the development of taxonomic methods and the adoption of consistent binomial nomenclature for species, following Linnaeus, during the 18th century. The fashion for collecting in the 17th and 18th centuries resulted in the amassing of big private collections which later became the basis of institutional collections. The increase of such public collections by making available material for study from all over the world has, in turn, increased the publications relating to this. Thus the botanic garden and the herbarium, with their associated libraries, have become complementary repositories of botanical information invaluable to the taxonomist, the plant geographer, the economic botanist and the student of evolution. Some useful publications relating to botanic gardens, herbaria and botanical and horticultural collectors are listed.     

滇西北高山流石滩植物多样性

通过多次对滇西北高山流石滩野外实地考察、标本鉴定并查阅有关献,建立数据库统计得到流石滩种子植物共计29科、103属、519种。其中中国特有植物295种,占总数的56．8％,滇西北特有植物54种,占10．4％。有10种属的分布区类型(包括7个变型),北温带分布类型最多,占总属数的47．5％。在整个高山流石滩中,草本有455种,占总数的87．7％,其中多年生草本421种。流石滩植物中具有多种生态、生理适应方式,低矮平卧状植株、莲座状、垫状、极矮小草本、密集丛生是植物的重要适应方式。根茎及发达的肉质根或木质根是典型流石滩上的主要适应方式,分别占植物总数的19．7％,31．0％。果实中干果共计518种,其中蒴果298种。由于流石滩处于生态脆弱区,人为干扰易对生态系统造成危害。本对流石滩种子植物多样性组成分析,为合理保护和利用流石滩植物资源提供基础资料。     

The uses ofAtuna racemosa Raf. (Chrysobalanaceae) in Samoa

The Uses of Atuna racemosaRaf. (Chrysobalanaceae) in Samoa. Economic Botany 58(3):470-475, 2004. An ethnobotanical study was made of the uses ofAtuna racemosa subsp.racemosa (Chrysobalanaceae) in Samoa. The main use is of the cotyledons to extract an anti-inflammatory massage oil and a putty to caulk boats. Minor uses as a medicinal and of the wood are reported and a survey of herbarium material shows that the fruit of Atuna is widely used throughout the Pacific region.     

Historical herbarium specimens in plant molecular systematics — an example from the fern genus <Emphasis Type="Italic">Lindsaea</Emphasis> (Lindsaeaceae)

We extracted, amplified and sequenced DNA from historical herbarium specimens and silica-dried samples of the fern genus Lindsaea in order to study the sequencing success between the two kinds of samples. High quality sequences were obtained from 57% of the herbarium samples. The specimens age was found to be of little importance for sequencing success when less than 75 years, but the colour of a specimen was found more indicative of sequencing success. Shorter DNA fragments were sequenced successfully twice as often as longer fragments from the herbarium material; in relatively recently collected silica-dried material longer sequences were obtained almost as frequently as short ones. No obvious differences in sequencing success between material originating from different herbaria was observed. We conclude that by using specifically designed DNA extraction protocols and by sequencing short DNA fragments from carefully selected specimens, herbarium material and type specimens can be successfully used in molecular systematics. Typical material or specimens from the type locality (topotypes) should be preferred, when placing a species in a phylogeny.     

A Revision of Fritillaria L. (Liliaceae) in the Hengduan Mountains and Adjacent Regions,China ( 1 )—A Study of Fritillaria cirrhosa D. Don and Its Related Species

A study was made on Fritillaria cirrhosa D．Don and its related species based on both field observation and herbarium material．As a result,four species are recognized and 16 specific names and 18 variety names are reduced as synonyms．     

中国横断山区及其邻近地区贝母属的研究(一)——川贝母及其近缘种的初步研究

本文根据笔者在陕西、甘肃、四川等地的野外观察,以及查阅各有关标本馆的馆藏标本,对川贝母Fritillaria cirrhosa D．Don及其近缘种进行了初步研究,认为与川贝母关系密切的有3个种,并且归并了16种18变种。