Enthesopathy formation in the humerus: Data from known age‐at‐death and known occupation skeletal collections

Enthesopathies, in the guise of musculoskeletal skeletal stress markers (MSM), have been widely used to reconstruct activity levels in human skeletal populations. In general, studies have focused on their presence in the upper limb, which is used in the majority of daily activities. The aim of this study was to use some of the attachment sites on the humerus to explore the relationship between enthesopathy formation, activity, and the ageing process. The skeletal sample used in this study comprised male adult skeletons with known age‐at‐death and known occupations from the late‐19th and early‐20th century cemeteries in Portugal. The enthesopathies were recorded as either present or absent. Statistical analysis using Fishers exact tests and logistic regression was undertaken to determine whether associations could be found between specific activities or socioeconomic status (manual or nonmanual workers), and age and enthesopathy presence. Left and right sides were analyzed separately. Fisher's exact tests were used to determine the relationship between activity and enthesopathy, and they demonstrated no association between activity and enthesopathies (P > 0.01). The results of the logistic regression established that age was the single most significant factor in enthesopathy formation (P > 0.05). This study found that, in these samples, age‐at‐death, and therefore age‐related degeneration rather than degeneration caused by activities, was the primary cause of enthesopathy formation. Considering the difficulties of reliably ageing adult human skeletal remains, this is a major issue for studies of activity using enthesopathies. Am J Phys Anthropol, 2010. © 2009 Wiley‐Liss, Inc.     

Analysing botanical collecting effort in Amazonia and correcting for it in species range estimation

Aim The aim of this study is to analyse the distribution pattern of the botanical collecting effort in Amazonia so that it can be accounted for when interpreting phytogeographical patterns such as inferred species ranges. We also develop a mechanistic and transparent method for taking into account the bias in collecting effort when estimating likelihoods of species occurrences. Location Amazonia, Neotropics. Methods We utilized electronic data sets of georeferenced herbarium collections (1,063,530 in total). We plotted collecting localities (68,246 in total) on maps overlaid with 1° and 0.5° square grids, and analysed collecting effort using a geographical information system (GIS). We also drew a map of Thiessen polygons, using collecting localities as polygon centres, to visualize collecting density in a scale‐independent way. We then created a ‘collecting activity landscape’ in which well‐collected areas appear as peaks and poorly studied areas as valleys. We demonstrate how this surface can be utilized when estimating species distributions. Results The data available to us confirm that botanical collecting activity is still severely biased in Amazonia. The uncollected area represents 43% of the total area of Amazonia, while another 28% is poorly collected and only 2% can be considered relatively well collected. The Thiessen polygon network represents an improvement in the presentation of collecting intensity compared with square grids. Main conclusions The maps of botanical collecting effort in the Neotropics should be used for visually correcting phytogeographical interpretations. With the help of GIS applications the observed spatial bias in collecting effort can be utilized in estimating the likelihood of occurrence of species in a repeatable manner. These estimates, in turn, can be used for various purposes in basic and applied science as well as in decision‐making. The biased collecting effort should, in the long run, be corrected by further field work in unexplored areas, which can be identified with the maps presented here.     

Representation of DNA sequences in recombinant DNA libraries prepared by restriction enzyme partial digestion

We present a theoretical study of the fraction of sequences incorporated in a recombinant DNA partial digest library as a function of the size of the library. The fraction incorporated depends on the degree of restriction enzyme partial digestion. If all restriction sites in the target DNA can be cleaved with the same rate, optimum incorporation of sequences is observed when the number average length of the digested DNA equals the desired average length of the cloned insert. Overdigestion severely reduces the fraction of sequences present in a sample of clones. Heterogeneity in restriction enzyme cleavage rates also reduces the fraction incorporated, and underdigestion improves sequence representation in the face of cleavage rate heterogeneity. Practical methods for determining the number average length of partially digested DNAs are also presented.     

The ‘Frank J. Myers Rotifera Collection’ at the Academy of Natural Sciences of Philadelphia

The Academy of Natural Sciences of Philadelphia (ANSP) houses the world’s most comprehensive collection of Rotifera on microscope slides. A particular strength of this major reference collection and type repository lies in the excellent preparation of specimens in life-like extended state and its balanced coverage of the phylum. The collection is almost worldwide in scope, and currently comprises 774 valid taxa, equalling a taxon coverage of 88.2% (families), 75.4% (genera), and 39.1% (species) compared to taxon numbers currently known to occur worldwide. A searchable database plus illustrated catalog has now been published on CD-ROM and on the Academy’s website. The poor representation of Rotifera in natural history collections and their generally poor curation and conservation is commented upon.     

新世纪的中国昆虫系统学

对未来我国昆虫系统学在能力建设、物种编目、理论研究、技术创新和国际合作等方面提出一系列建议。在昆虫系统学能力建设方面,政府和科学家应该在生物分类学能力评估、基础硬件建设、各级生物标本馆中建立伙伴关系（包括标本采集、标本馆管理、 科学研究、 知识共享和标本与资料交换）等方面重点开展工作。在物种编目方面,我国的昆虫物种编目有赖于各级政府和机构继续关注标本的收集和保藏,继续启动一些考察项目,以满足发现和认识昆虫物种的实际需求。在物种水平上研究以往昆虫系统学家的工作,进行地区性和世界性的昆虫类群的订正更是非常必要的。在理论研究方面,我国昆虫系统应该在下列方面积极探索：物种概念、进化理论、比较生物学理论和高级分类系统研究。在技术创新方面,我国的昆虫系统学家应该在数据库与网络技术应用、图形图像处理技术、专家鉴定系统技术、分类性状分析技术、分子生物学技术、系统发育推断程序、信息统一管理技术和知识传播技术等方面进行深入研究,以满足昆虫系统学的发展需求。在国际合作方面,要进一步推动我国昆虫系统学研究机构加入生物分类学全球战略联盟、加入各种相关国际相关组织,要促进物种信息管理系统的建立与共享,要推动研究项目国际化。     

Testing the use of specimen collection data and GIS in biodiversity exploration and conservation decision making in Guyana

This paper presents the results of a study conducted at the request of the Government of Guyana by the Centre for the Study of Biological Diversity at the University of Guyana, and the Smithsonian Institution. The purpose of the study was to evaluate the utility of using systematic collections in identifying areas with a high priority for conservation. A biodiversity database and a gazetteer were assembled and interpreted primarily through the use of maps generated in ARC/INFO and ArcView. The data were examined to determine coverage and completeness, and while in general the results support a continued use of the methodology for making informed decisions in conservation related issues, several recommendations are offered in order to enhance the data. The primary use of the results of this study is in the identification of areas of interest for conservation and in the location of eleven areas covering most ecoregions in Guyana that are in need of additional study. The eleven areas have been chosen to avoid areas that are already allocated to logging and mining concessions or Amerindian lands. While it is true that this study would benefit from additional data and further analysis of those data, it is also true that decisions concerning areas for conservation in Guyana are being made in the near future, and if any data are to be used in this process, it will be those data presented in this paper.     

Morphometric measurements of dragonfly?wings: the accuracy of pinned,scanned and detached?measurement methods

Large-scale digitization of museum specimens, particularly of insect collections, is becoming commonplace. Imaging increases the accessibility of collections and decreases the need to handle individual, often fragile, specimens. Another potential advantage of digitization is to make it easier to conduct morphometric analyses, but the accuracy of such methods needs to be tested. Here we compare morphometric measurements of scanned images of dragonfly wings to those obtained using other, more traditional, methods. We assume that the destructive method of removing and slide-mounting wings provides the most accurate method of measurement because it eliminates error due to wing curvature. We show that, for dragonfly wings, hand measurements of pinned specimens and digital measurements of scanned images are equally accurate relative to slide-mounted hand measurements. Since destructive slide-mounting is unsuitable for museum collections, and there is a risk of damage when hand measuring fragile pinned specimens, we suggest that the use of scanned images may also be an appropriate method to collect morphometric data from other collected insect species.     

FORMIDABEL: The Belgian Ants Database

FORMIDABEL is a database of Belgian Ants containing more than 27.000 occurrence records. These records originate from collections, field sampling and literature. The database gives information on 76 native and 9 introduced ant species found in Belgium. The collection records originated mainly from the ants collection in Royal Belgian Institute of Natural Sciences (RBINS), the ‘Gaspar’ Ants collection in Gembloux and the zoological collection of the University of Liège (ULG). The oldest occurrences date back from May 1866, the most recent refer to August 2012. FORMIDABEL is a work in progress and the database is updated twice a year.The latest version of the dataset is publicly and freely accessible through this url: http://ipt.biodiversity.be/resource.do?r=formidabel. The dataset is also retrievable via the GBIF data portal through this link: http://data.gbif.org/datasets/resource/14697A dedicated geo-portal, developed by the Belgian Biodiversity Platform is accessible at: http://www.formicidae-atlas.bePurpose: FORMIDABEL is a joint cooperation of the Flemish ants working group “Polyergus” (http://formicidae.be) and the Wallonian ants working group “FourmisWalBru” (http://fourmiswalbru.be). The original database was created in 2002 in the context of the preliminary red data book of Flemish Ants (Dekoninck et al. 2003). Later, in 2005, data from the Southern part of Belgium; Wallonia and Brussels were added. In 2012 this dataset was again updated for the creation of the first Belgian Ants Atlas (Figure 1) (Dekoninck et al. 2012). The main purpose of this atlas was to generate maps for all outdoor-living ant species in Belgium using an overlay of the standard Belgian ecoregions. By using this overlay for most species, we can discern a clear and often restricted distribution pattern in Belgium, mainly based on vegetation and soil types.Open in a separate windowFigure 1.www.formicidae-atlas.be     

Museum genomics: low-cost and high-accuracy genetic data from historical specimens

Natural history collections are unparalleled repositories of geographical and temporal variation in faunal conditions. Molecular studies offer an opportunity to uncover much of this variation; however, genetic studies of historical museum specimens typically rely on extracting highly degraded and chemically modified DNA samples from skins, skulls or other dried samples. Despite this limitation, obtaining short fragments of DNA sequences using traditional PCR amplification of DNA has been the primary method for genetic study of historical specimens. Few laboratories have succeeded in obtaining genome-scale sequences from historical specimens and then only with considerable effort and cost. Here, we describe a low-cost approach using high-throughput next-generation sequencing to obtain reliable genome-scale sequence data from a traditionally preserved mammal skin and skull using a simple extraction protocol. We show that single-nucleotide polymorphisms (SNPs) from the genome sequences obtained independently from the skin and from the skull are highly repeatable compared to a reference genome.