Microsatellite (SSR) markers reveal genetic identities, genetic diversity and relationships in a Malus×domestica borkh. core subset collection

 A collection of 66 Malus×domestica Borkh. accessions from the USDA-ARS Plant Genetic Resources Unit’s core collection was screened with a set of eight SSR (simple sequence repeat) primers developed at the PGRU in order to determine genetic identities, estimate genetic diversity, and to identify genetic relationships among these accessions. All eight primer pairs generated multiple fragments when used in amplification reactions with DNA from these accessions. High levels of variation were detected with a mean of 12.1 alleles per locus and a mean heterozygosity across all eight loci of 0.693. The eight primer pairs utilized in this study unambiguously differentiated all but seven pairs of accessions in this collection of 66 M.×domestica Borkh. genotypes. The probability of matching any two genotypes at all eight loci in this study was approximately 1 in 1 billion. The markers detected two misnamed accessions in the collection. Genetic-identity data produced a genetic-relatedness phenogram which was concordant with geographic origins and/or known pedigree information. These SSR markers show great promise as tools for managing Malus ex situ germplasm collections as well as for collection and preservation strategies concerning wild Malus populations in situ. Received: 28 March 1998 / Accepted: 29 April 1998     

Systematics,biological knowledge and environmental conservation

Systematics and taxonomy are essential: they respectively elucidate life's history, and organize and verify biological knowledge. This knowledge is built of interrelated concepts which are ultimately accounted for by biological specimens. Such knowledge is essential to decide how much and what biodiversity survives human onslaughts. The preservation of specimens in natural history collections is the essential part of the process which builds and maintains biological knowledge. These collections and the human expertise essential to interpret specimens are the taxonomic resources which maintain accurate and verifiable concepts of biological entities. Present and future knowledge of the complexities and diversity of the biosphere depends on the integrity of taxonomic resources, vet widespread ignorance and disregard for their fundamental value has created a global crisis. Preservation of specimens in natural history collections is chronically neglected and support to study and manage collections is very insufficient. The knowledge held by experienced taxonomists is not being passed on to younger recruits. Neglect of collections has destroyed countless specimens and threatens millions more. These threats to taxonomic resources not only impinge on systematics but all biology: this tragedy jeopardizes the integrity of biological knowledge. The consequences for environmental conservation and therefore humanity are also of dire severity and the biodiversity crisis adds unprecedented weight to the barely recognized crisis in taxonomy and systematics.Where correspondence should     

The relevance,biases, and importance of digitising opportunistic non-standardised collections: A case study in Iberian harvestmen fauna with BOS Arthropod Collection datasets (Arachnida,Opiliones)

In this study, we analyse the relevance of harvestmen distribution data derived from opportunistic, unplanned, and non-standardised collection events in an area in the north of the Iberian Peninsula. Using specimens deposited in the BOS Arthropod Collection at the University of Oviedo, we compared these data with data from planned, standardised, and periodic collections with pitfall traps in several locations in the same area. The Arthropod Collection, begun in 1977, includes specimens derived from both sampling types, and its recent digitisation allows for this type of comparative analysis. Therefore, this is the first data-paper employing a hybrid approach, wherein subset metadata are described alongside a comparative analysis. The full dataset can be accessed through Spanish GBIF IPT at http://www.gbif.es:8080/ipt/archive.do?r=Bos-Opi, and the metadata of the unplanned collection events at http://www.gbif.es:8080/ipt/resource.do?r=bos-opi_unplanned_collection_events. We have mapped the data on the 18 harvestmen species included in the unplanned collections and provided records for some species in six provinces for the first time. We have also provided the locations of Phalangium opilio in eight provinces without published records. These results highlight the importance of digitising data from unplanned biodiversity collections, as well as those derived from planned collections, especially in scarcely studied groups and areas.     

Alpine lichen diversity in an isolated sky island in the Colorado Plateau,USA—Insight from an integrative biodiversity inventory

Lichens are major components of high altitude/latitude ecosystems. However, accurately characterizing their biodiversity is challenging because these regions and habitats are often underexplored, there are numerous poorly known taxonomic groups, and morphological variation in extreme environments can yield conflicting interpretations. Using an iterative taxonomic approach based on over 800 specimens and incorporating both traditional morphology‐based identifications and information from the standard fungal DNA barcoding marker, we compiled a voucher‐based inventory of biodiversity of lichen‐forming fungi in a geographically limited and vulnerable alpine community in an isolated sky island in the Colorado Plateau, USA—the La Sal Mountains. We used the newly proposed Assemble Species by Automatic Partitioning (ASAP) approach to empirically delimit candidate species‐level lineages from family‐level multiple sequence alignments. Specimens comprising DNA‐based candidate species were evaluated using traditional taxonomically diagnostic phenotypic characters to identify specimens to integrative species hypotheses and link these, where possible, to currently described species. Despite the limited alpine habitat (ca. 3,250 ha), we document the most diverse alpine lichen community known to date from the southern Rocky Mountains, with up to 240 candidate species/species‐level lineages of lichen‐forming fungi. 139 species were inferred using integrative taxonomy, plus an additional 52 candidate species within 29 different putative species complexes. Over 68% of sequences could not be assigned to species‐level rank with statistical confidence, corroborating the limited utility of current sequence repositories for species‐level DNA barcoding of lichen‐forming fungi. By integrating vouchered specimens, DNA sequence data, and photographic documentation, we provide an important baseline of lichen‐forming fungal diversity for the limited alpine habitat in the Colorado Plateau. These data provide an important resource for subsequent research in the ecology and evolution of lichens alpine habitats, including DNA barcodes for most putative species/species‐level lineages occurring in the La Sal Mountains, and vouchered collections representing any potentially undescribed species that can be used for future taxonomic studies.     

Spatiotemporal distribution and dynamic changes of myxomycetes in subtropical forests of China

The spatiotemporal distribution and dynamic changes of species composition of myxomycetes in humid subtropical forests of Houhe National Nature Reserve in southern China were studied by collecting samples of bark and ground litter within four seasons for isolation of myxomycetes in moist chamber cultures and by collecting fruiting bodies in the field from June to October. A total of 725 specimens of myxomycete fruiting bodies representing 77 species of 25 genera were registered, among them 302 records/51 species from field collections and 423 records obtained from 600 moist chamber cultures of ground litter and bark of living trees, which resulted in 35 and 39 species, respectively. Cornuvia serpula and Perichaena microspora were recorded for the first time in China. Both myxomycete species richness and diversity were significantly different in ground litter among sites and field collections among months. NMDS combined with Permanova indicated that the site had a greater impact on the myxomycete community of bark and litter than the season, while the month of field collections had a greater impact than the sampling sites. CCA and VPA analysis showed that the bark-inhabiting myxomycete species were mainly affected by spatial variables, while the litter-inhabiting and field collected species were more affected by climatic factors.     

Mass digitization of scientific collections: New opportunities to transform the use of biological specimens and underwrite biodiversity science

New information technologies have enabled the scientific collections community and its stakeholders to adapt, adopt, and leverage novel approaches for a nearly 300 years old scientific discipline. Now, few can credibly question the transformational impact of technology on efforts to digitize scientific collections, as IT now reaches into almost every nook and cranny of society. Five to ten years ago this was not the case. Digitization is an activity that museums and academic institutions increasingly recognize, though many still do not embrace, as a means to boost the impact of collections to research and society through improved access. The acquisition and use of scientific collections is a global endeavor, and digitization enhances their value by improved access to core biodiversity information, increases use, relevance and potential downstream value, for example, in the management of natural resources, policy development, food security, and planetary and human health. This paper examines new opportunities to design and implement infrastructure that will support not just mass digitization efforts, but also a broad range of research on biological diversity and physical sciences in order to make scientific collections increasingly relevant to societal needs and interest.     

The relative importance of deforestation,precipitation change,and temperature sensitivity in determining the future distributions and diversity of Amazonian plant species

Tropical forests are threatened by many human disturbances – two of the most important of which are deforestation and climate change. To mitigate the impacts of these disturbances, it is important to understand their potential effects on the distributions of species. In the tropics, such understanding has been hindered by poor knowledge of the current distributions and range limits of most species. Here, we use herbarium collection records to model the current and future distributions of ca. 3000 Amazonian plant species. We project these distributions into the future under a range of different scenarios related to the magnitude of climate change and extent of deforestation as well as the response of species to changes in temperature, precipitation, and atmospheric concentrations of CO₂ . We find that the future of Amazonian diversity will be dependant primarily on the ability of species to tolerate or adapt to rising temperatures. If the thermal niches of tropical plant species are fixed and incapable of expanding under rapid warming, then the negative effects of climate change will overshadow the effects of deforestation, greatly reducing the area of suitable habitat available to most species and potentially leading to massive losses of biodiversity throughout the Amazon. If tropical species are generally capable of tolerating warmer temperatures, rates of habitat loss will be greatly reduced but many parts of Amazonia may still experience rapid losses of diversity, with the effects of enhanced seasonal water stress being similar in magnitude to the effects of deforestation.     

Experimental taphonomy in museums: Preparation protocols for skeletons and fossil vertebrates under the scanning electron microscopy

Natural history institutions use different standards and methods to prepare and preserve skeletons of both modern and fossil vertebrates. These standards and treatments may be considered as taphonomic agents of museum collections. Modifications may occur during preparation, affecting the integrity of bone tissues and skeletons or their molecular and geochemical composition. The present evaluation uses a Scanning Electron Microscope (SEM) to analyze the most common preparation methods and standards. The aim of this paper is to evaluate preparation methods to determine those that provide the best SEM observations and those that best preserve osseous tissues and least damage fossil surfaces. In addition, the study of these alterations, produced under known conditions, provides criteria, which aids recognition of modifications that may occur in nature.