Bryophytes and lichens in 16th-century herbaria

The diversity of bryophyte and lichen collections in 9 of the oldest preserved herbaria (dating from ca 1542 to 1577) was compared, including the first reports of bryophytes and lichens from the ‘En Tibi’ herbarium (possibly 1542–1544) and the herbarium of Leonhard Rauwolf (1560–1563). Bryophytes and lichens formed only a minority in each herbarium compared to the numbers of vascular plant specimens; numbers ranged from representatives of 21 genera in the herbarium of Ulisse Aldrovandi to the single genus Conocephalum in the Rauwolf herbarium. The focus was on large, handsome species of bryophytes and macrolichens, apart from small amounts of additional species collected as ‘by-catch’ in mixed collections. All herbaria together included 34 genera of bryophytes (36 species and 10 specimens identified to genus level) and 13 genera of lichens (24 species and 4 specimens identified to genus level). The diversity of mosses was higher than that of liverworts, and pleurocarpous mosses were more diverse than acrocarpous mosses. The collectors probably aimed at selecting material that was either characteristic of the vegetation in the respective areas of collecting or used for certain purposes (or both). The former hypothesis is supported by the small overlap in taxonomic diversity between the herbaria, and the latter by the fact that several moss, liverwort, and lichen genera are included whose traditional uses are well documented.     

The pseudoscorpions of New Zealand,Norfolk, and Lord Howe

Nearly 20 000 specimens of pseudoscorpions from a full range of habitats have been examined. For New Zealand, 70 species and subspecies in 28 genera are recognised, and for Norfolk and Lord Howe Islands, 11 species in 9 genera. Endemism is very high in this area: in New Zealand, 13 out of 25 indigenous genera are endemic; 2 others (Apatochernes, Nesochernes) are shared with Norfolk Island; and 4 (Sathrochthonius, Austrochthonius, Synsphyronus, Protochelifer) extend their distribution to Australia (Austrochthonius is known also from South America and South Africa). The rest of the native genera have a wider distribution in the Pacific. Three species (Lamprochernes savignyi, Withius subruber, Chelifer cancroides) have a wide and disjunct distribution induced by human traffic, and are considered to be an introduced element.     

Phylogenetic Diversity of New Zealand Gelidiales as Revealed by rbcL Sequence Data

Diversity and phylogenetic relationships of New Zealand representatives of the red algal order Gelidiales have been examined using rbcL sequence data. Extensive field collections have been made from throughout the New Zealand region. Six genera have been reported previously from New Zealand (Capreolia, Gelidium, Pterocladia, Pterocladiella, Pterocladiastrum, Ptilophora). This research has revealed species with very restricted local distributions, as well as the discovery of several undescribed, cryptic taxa. The common and widespread Gelidium caulacantheum is confirmed to be more closely related to Capreolia than to other species of Gelidium. The generic concept of Capreolia, based on life history characters, will need to be modified to accommodate additional species possessing “Gelidium” life histories. A species endemic to New Zealand, Gelidium ceramoides, has been found to differ significantly from all other members of the Gelidiales and requires reclassification in another genus and order. Examination of field collections and herbarium specimens in addition to molecular sequence data have led us to conclude that specimens previously placed in the genera Ptilophora and Pterocladiastrum belong within Pterocladia lucida.     

New records of two deep-sea eels collected from the Western Pacific Ocean based on COI and 16S rRNA genes

Background

Two deep-sea eels collected from the Western Pacific Ocean are described in this study. Based on their morphological characteristics, the two deep-sea eel specimens were assumed to belong to the cusk-eel family Ophidiidae and the cutthroat eel family Synaphobranchidae.

Methods and results

To accurately identify the species of the deep-sea eel specimens, we sequenced the mitochondrial genes (cytochrome c oxidase subunit I [COI] and 16S ribosomal RNA [16S rRNA]). Through molecular phylogenetic analysis based on mtDNA COI and 16S rRNA gene sequences, these species clustered with the genera Bassozetus and Synaphobranchus, suggesting that the deep-sea eel specimens collected are two species from the genera Bassozetus and Synaphobranchus in the Western Pacific Ocean, respectively.

Conclusions

This is the first study to report new records of the genera Bassozetus and Synaphobranchus from the Western Pacific Ocean based on COI and 16S rRNA genes

     

广西被子植物二新记录属

在第四次中药资源普查中采集了大量标本,经过对这些标本进行仔细鉴定并查阅相关资料,确定其中两号标本为香茜属(Carlemannia Benth.)和粘腺果属(Commicarpus Standl.)植物。这两属植物在广西尚无报道,为首次记录。香茜属植物叶对生,子房下位,无托叶,雄蕊仅有2枚,这和茜草科相似但又不同,系统位置较混乱,以前曾放于茜草科( Rubiaceae)和忍冬科( Caprifoliaceae)中,最近该属和蜘蛛花属独立成香茜科( Car-lemanniaceae)。该属植物共有3种,沿喜马拉雅山脉向东一直分布到缅甸、越南北部。我国西藏东南、云南南部、广西西北部分布一种即香茜( Carlenannia chinenesis Hook. f.)。粘腺果属是紫茉莉科( Nyctaginaceae)主产热带地区的1个属,全世界约25种分布于热带非洲和阿拉伯半岛南部,在南亚、东南亚和墨西哥至热带美洲也有少量分布。中国产2种,其中广西产1种即中华粘腺果[ Commiaicarpus chinensis ( L.) Heim.]。该种植物分布广泛,从南亚次大陆向东至中南半岛、马来半岛,向北到我国西沙群岛、海南岛以及广州附近,在广西首次记录,产凤山县和凌云县。     

Analyzing trait-climate relationships within and among taxa using machine learning and herbarium specimens

Premise

Continental-scale leaf trait studies can help explain how plants survive in different environments, but large data sets are costly to assemble at this scale. Automating the measurement of digitized herbarium collections could rapidly expand the data available to such studies. We used machine learning to identify and measure leaves from existing, digitized herbarium specimens. The process was developed, validated, and applied to analyses of relationships between leaf size and climate within and among species for two genera: Syzygium (Myrtaceae) and Ficus (Moraceae).

Methods

Convolutional neural network (CNN) models were used to detect and measure complete leaves in images. Predictions of a model trained with a set of 35 randomly selected images and a second model trained with 35 user-selected images were compared using a set of 50 labeled validation images. The validated models were then applied to 1227 Syzygium and 2595 Ficus specimens digitized by the National Herbarium of New South Wales, Australia. Leaf area measurements were made for each genus and used to examine links between leaf size and climate.

Results

The user-selected training method for Syzygium found more leaves (9347 vs. 8423) using fewer training masks (218 vs. 225), and found leaves with a greater range of sizes than the random image training method. Within each genus, leaf size was positively associated with temperature and rainfall, consistent with previous observations. However, within species, the associations between leaf size and environmental variables were weaker.

Conclusions

CNNs detected and measured leaves with levels of accuracy useful for trait extraction and analysis and illustrate the potential for machine learning of herbarium specimens to massively increase global leaf trait data sets. Within-species relationships were weak, suggesting that population history and gene flow have a strong effect at this level. Herbarium specimens and machine learning could expand sampling of trait data within many species, offering new insights into trait evolution.     

Ithyoclinostomum yamagutii n. sp. (Digenea: Clinostomidae) in the great blue heron Ardea herodias L. (Aves: Ardeidae) from Mississippi,USA

With only six recognised genera, the family Clinostomidae Lühe, 1901 remains a global research interest of parasitologists and ecologists. Recent efforts have focused on providing molecular data to investigate species diversity, elucidate life-cycles, and make inferences on the group’s evolutionary history. Of the clinostomid genera, the monotypic Ithyoclinostomum Witenberg, 1926 has remained more enigmatic compared to the commonly encountered Clinostomum Leidy, 1856. Recent morphological and molecular evidence from metacercariae suggests a second Ithyoclinostomum species may exist in freshwater cichlids in Central America and Mexico. In a recent survey of great blue herons Ardea herodias L. from commercial catfish production farms in Mississippi, USA, two specimens of an abnormally large (> 20 mm) clinostomid were encountered in the oesophagus of a single bird. These specimens were identified as an Ithyoclinostomum sp. morphologically distinct from the only nominal species Ithyoclinostomum dimorphum (Diesing, 1850). Using morphological and molecular data these adult specimens were confirmed as conspecific with the larval metacercariae previously described from Central America and Mexico and represent the novel species, Ithyoclinostomum yamagutii n. sp.

     

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.     

紫堇属模式标本馆藏现状及分析

模式标本是发表新种的依据,对稳定物种学名至关重要。紫堇属(Corydalis DC.)隶属于罂粟科(Papaveraceae)荷包牡丹亚科(Fumarioideae)紫堇族(Corydaleae),是分类学研究的困难属之一。该研究首先基于《中国植物志》、Flora of China以及全球物种名录查询获得被认可的526个紫堇属物种,然后通过检索全球数字化植物标本数据库(JSTOR)、全球生物多样性信息网络数据库(GBIF)和中国数字植物标本馆(CVH)获得了其中395个物种1 894份模式标本,最后对获得的标本信息进行核实、整理和归纳,提取模式类型、馆藏地、采集人、模式产地和采集时间等关键信息进行统计分析。结果表明:紫堇属每个物种平均仅有约5份模式标本; 该属模式标本散落在全球80个标本馆中,其中超过85%为国外采集者采集。未来应当结合文献,加强对该属模式标本的信息考证和规范化整理。     

Molecular phylogeny and species delimitation of Stachyuraceae: Advocating a herbarium specimen‐based phylogenomic approach in resolving species boundaries

Species concept and delimitation are fundamental to taxonomic and evolutionary studies. Both inadequate informative sites in the molecular data and limited taxon sampling have often led to poor phylogenetic resolution and incorrect species delineation. Recently, the whole chloroplast genome sequences from extensive herbarium specimen samples have been shown to be effective to amend the problem. Stachyuraceae are a small family consisting of only one genus Stachyurus of six to 16 species. However, species delimitation in Stachyurus has been highly controversial because of few and generally unstable morphological characters used for classification. In this study, we sampled 69 individuals of seven species (each with at least three individuals) covering the entire taxonomic diversity, geographic range, and morphological variation of Stachyurus from herbarium specimens for genome‐wide plastid gene sequencing to address species delineation in the genus. We obtained high‐quality DNAs from specimens using a recently developed DNA reconstruction technique. We first assembled four whole chloroplast genome sequences. Based on the chloroplast genome and one nuclear ribosomal DNA sequence of Stachyurus, we designed primers for multiplex polymerase chain reaction and high throughput sequencing of 44 plastid loci for species of Stachyurus. Data of these chloroplast DNA and nuclear ribosomal DNA internal transcribed spacer sequences were used for phylogenetic analyses. The phylogenetic results showed that the Japanese species Stachyurus praecox Siebold & Zucc. was sister to the rest in mainland China, which indicated a typical Sino‐Japanese distribution pattern. Based on diagnostic morphological characters, distinct distributional range, and monophyly of each clade, we redefined seven species for Stachyurus following an integrative species concept, and revised the taxonomy of the family based on previous reports and specimens, in particular the type specimens. Furthermore, our divergence time estimation results suggested that Stachyuraceae split from its sister group Crossosomataceae from the New World at ca. 54.29 Mya, but extant species of Stachyuraceae started their diversification only recently at ca. 6.85 Mya. Diversification time of Stachyurus in mainland China was estimated to be ca. 4.45 Mya. This research has provided an example of using the herbarium specimen‐based phylogenomic approach in resolving species boundaries in a taxonomically difficult genus.     

CHROMOSOME NUMBERS IN UMBELLIFERAE. III

Chromosome numbers are reported for 156 collections representing 100 taxa of Umbelliferae. Approximately two thirds of the collections are from Mexico, Central and South America and indicate a high percentage of polyploid species in certain genera found in this area. Chromosome numbers for plants belonging to 78 taxa are published here for the first time, previously published chromosome numbers are verified for 18 taxa and chromosome numbers differing from those previously published are reported in seven instances. No chromosome counts have been previously published for nine of the genera included here. Further aneuploidy and polyploidy were found in Eryngium, and Lomatium columbianum has been found to be a high polyploid with 2n = 14x. Every chromosome count is referable to a cited herbarium specimen.     

Prospects for the Management of Invasive Alien Weeds Using Co-Evolved Fungal Pathogens: A Latin American Perspective

Invasive alien weeds pose a serious threat to the biodiversity of natural ecosystems and a significant constraint to agricultural production worldwide. The use of co-evolved natural enemies, a strategy referred to as classical biological control (CBC), has proven to be a potentially efficacious, cost-effective, and safe option for the management of alien weeds. An analysis of CBC of invasive weeds in Latin America is presented, which shows that only 5% of the worldwide releases of agents, overwhelmingly arthropod, have been in this region. Fungal pathogens are increasingly being considered in CBC programmes, and there are now 11 examples of Latin American fungi having been released as biocontrol agents in other regions of the world. In contrast, only three weed pathogens have been deliberately released in the region. Possible reasons for the paucity of CBC programmes in Latin America are presented, despite the presence of a significant number of alien weed species (60 are listed). An analysis of these weeds reveals that many of them could be amenable to control using natural enemies, including nine weed species for which CBC programmes have been successfully implemented elsewhere in the world. In addition, for many of these 60 species, a co-evolved and damaging mycobiota has already been recorded. The prospects for management of invasive alien weeds in Latin America, using co-evolved fungal pathogens, are assessed with particular reference to selected species from the genera Ambrosia, Broussonetia, Calotropis, Commelina, Cyperus, Dichrostachys, Echinochloa, Pittosporum, Rottboellia, Rubus, Sonchus and Ulex. This revised version was published online in July 2006 with corrections to the Cover Date.     

Survey of leaf anatomy,especially secretory structures,of tribeCaesalpinieae (Leguminosae,Caesalpinioideae)

We studied leaflet anatomy, emphasizing secretory structures, from herbarium specimens of 128 species of 44 genera of tribeCaesalpinieae, using clearings, resin sections, and scanning electron microscopy. These observations, combined with those from our three earlier papers, provide a survey of 210 species representing all genera. Seventy-three species had secretory structures: 21 had glands or gland-like trichomes, 40 had living mesophyll idioblasts, and nine had cavities (three species each had two different types). Five additional species, all inCercidium (Caesalpinia group), had paired or clustered large spheroidal, thick-walled, empty cells (veinlet idioblasts) interconnected by perforation plate-like gaps. Secretory structures have systematic significance at various taxonomic levels.     

Suitability of dried herbarium specimens for NMR metabolomics of mushrooms. A comparison of four species of the genera Kuehneromyces and Hypholoma (Strophariaceae)

Herbarium specimens are a treasure trove for biochemical studies. However, this implies understanding of the chemical changes during the drying and storage of the specimen. We compared herbarium specimens at different ages and fresh samples of four mushroom species (Kuehneromyces mutabilis, Hypholoma capnoides, Kuehneromyces lignicola, Hypholoma fasciculare) of two genera in the family Strophariaceae by using proton nuclear magnetic resonance (¹H NMR) spectroscopy combined with principal component analysis (PCA). 25 metabolites were identified. No significant alterations were found between herbarium samples at different ages, suggesting that they are stable enough for comparative studies. The most dominant differences between fresh and herbarium samples was that sugars such as α-α-trehalose, and fumaric and malic acids were more abundant in fresh fungi. Total contents of fatty and amino acids, uracil and γ-aminobutyric acid (GABA) were higher in herbarium specimens. In addition, pyroglutamic acid was observed only in Kuehneromyces mutabilis and fasciculic acid E in Hypholomafasciculare. Hence, based on results of the studied taxa, we conclude that NMR metabolomics can be used for both fresh and dried mushrooms when such alterations are properly addressed.     

东北地区木本植物一个新记录属和五个新记录种

东北地区位于我国东北部,地处欧亚大陆东部,地域辽阔,植物种类丰富,共有维管束植物164科928属3 103种。该文根据野外调查结果及相关资料,报道了东北地区木本植物1个新记录属是黄连木属(Pistacia L.)(漆树科Anacardiaceae)和5个新记录种,分别是黄连木(Pistacia chinensis)、野皂荚(Gleditsia microphylla)、东北忍冬(Lonicera elisae)、郁香忍冬(L.fragrantissima)、毛叶水栒子(Cotoneaster submultiflorus)。该文报道的新记录种凭证标本保存于大连自然博物馆植物标本室。这些新记录木本植物的发现,对东北地区生物多样性的研究具有重要意义,为其在我国的地理分布研究提供了新资料。     

Leaf anatomy ofDombeya andNesogordonia (Sterculiaceae), emphasizing epidermal and internal idioblasts

We studied leaf anatomy, using clearings, resin sections, and scanning electron microscopy, from mostly herbarium specimens of 123 species ofDombeya and 11 species ofNesogordonia (Sterculiaceae). Species were placed in seven idioblast categories, ranging from those without any to single and bicelled epidermal forms to multicelled nodules and single mesophyll idioblasts. Idioblast contents are possibly mucilaginous, but were not identified. In these two genera the range of foliar idioblast morphology surpasses that known previously for the entire family. Leaves are dorsiventral with mostly abaxial anomocytic stomata and typical palisade and spongy layers; paraveinal mesophyll is lacking. Miniature glandular (clavates, capitates) and nonglandular (mostly stellate) trichomes occur. Prismatic crystals predominate; epidermal prismatics and mesophyll druses are rare.