Searching for DNA in museum specimens: a comparison of sources in a mammal species

The number of genetic studies that use preserved specimens as sources of DNA has been steadily increasing during the last few years. Therefore, selecting the sources that are more likely to provide a suitable amount of DNA of enough quality to be amplified and at the minimum cost to the original specimen is an important step for future research. We have compared different types of tissue (hides vs. bones) from museum specimens of Iberian lynx and multiple alternative sources within each type (skin, footpad, footpad powder, claw, diaphysis, maxilloturbinal bone, mastoid process and canine) for DNA yield and probability of amplification of both mitochondrial and nuclear targets. Our results show that bone samples yield more and better DNA than hides, particularly from sources from skull, such as mastoid process and canines. However, claws offer an amplification success as high as bone sources, which makes them the preferred DNA source when no skeletal pieces have been preserved. Most importantly, these recommended sources can be sampled incurring minimal damage to the specimens while amplifying at a high success rate for both mitochondrial and microsatellite markers.     

Museum specimens reveal changes in the population structure of northern Fennoscandian domestic reindeer in the past one hundred years

Traditional reindeer herding of northern Fennoscandia has been based on seasonal movements independent of national borders. At the beginning of the 19th century, these yearly movements of reindeer were excessive, but during that century the borders between the Fennoscandian countries were closed. By analysing a 190‐base pair fragment of the mitochondrial DNA control region in 79 museum samples, we show that the reindeer of northern Fennoscandia were one homogenous population shortly after the national borders were closed. However, anthropogenic activity has effectively ended genetic exchange within northern Fennoscandia and has made the reindeer population within this region heterogeneous. Genetic input of eastern origin is also suggested within the extant Russian reindeer of the Kola Peninsula.     

昆虫数字化博物馆的建设

数字化博物馆是博物馆现代化的一个重要标志。国外博物馆从20世纪90年代就开始进行数字化建设,国内的博物馆数字化建设起步较晚,同国外的先进技术相比还有一定的差距,但发展较快。目前,国内外已有的昆虫数字化博物馆各具特色,有以展示昆虫图片为主的,有以介绍昆虫知识为主的,也有以营利为目的的,但仍有不少需要改进的地方。为了满足中小学生的求知欲和探索欲,适应他们喜欢自己动手操作和活泼好动的性格,昆虫数字化博物馆网站建设在技术上应采用J2EE三层体系结构,采用动态网站内容管理与发布系统构建的后台管理系统,将昆虫数字化博物馆分成后台管理和前台展示与交互两部分,从而实现网站内容与表现形式的分离,加快网页更新的速度。在数据库建设上,应采用功能强大的数据库软件,以满足大量图片、声音、动画、视频等多种类型的数据库的有效存储和高效的检索功能。在网站的内容上应有实体展厅的数字化、昆虫学术交流与知识集锦、中小学生互动教育等板块。在网站的后期维护上应做到由全社会的昆虫爱好者共同维护和管理。     

Please don't misuse the museum: ‘declines’ may be statistical

Detecting declines in populations at broad spatial scales takes enormous effort, and long‐term data are often more sparse than is desired for estimating trends, identifying drivers for population changes, framing conservation decisions, or taking management actions. Museum records and historic data can be available at large scales across multiple decades, and are therefore an attractive source of information on the comparative status of populations. However, changes in populations may be real (e.g. in response to environmental covariates) or resulting from variation in our ability to observe the true population response (also possibly related to environmental covariates). This is a (statistical) nuisance in understanding the true status of a population. Evaluating statistical hypotheses alongside more interesting ecological ones is important in the appropriate use of museum data. Two statistical considerations are generally applicable to use of museum records: first without initial random sampling, comparison with contemporary results cannot provide inference to the entire range of a species, and second the availability of only some individuals in a population may respond to environmental changes. Changes in the availability of individuals may reduce the proportion of the population that is present and able to be counted on a given survey event, resulting in an apparent decline even when population size is stable.     

Primers for identification of type and other archived specimens of Aphrodes leafhoppers (Hemiptera, Cicadellidae)

Primers were developed for leafhoppers of the genus Aphrodes amplifying 84-244 bp fragments of the mitochondrial cytochrome oxidase subunit I gene. DNA was extracted from legs of over 100-year-old archived museum specimens, amplified and sequenced. The fragments contain sufficient variation to unequivocally identify the different species. The majority of the analysed museum specimens, including three specimens of the syntype series for the UK endemic species A. aestuarina (Edwards 1908), were found to have been assigned to the wrong species. This work clearly underlines the need to validate museum specimens using molecular methods where identity is in doubt, based on reliable standards for species discrimination.     

Historical DNA from museum type specimens clarifies diversity of Asian leaf turtles (Cyclemys)

Species boundaries in Asian leaf turtles of the genus Cyclemys are difficult to define on the basis of morphology, primarily because many populations exhibit considerable ontogenetic variation in shell and head coloration. Two recent molecular phylogenetic hypotheses of Cyclemys species relationships, based largely on market and pet-trade samples of uncertain provenance, were highly incongruent. We used historical DNA methods to sequence fragments of the mitochondrial cytochrome  b gene from eight type specimens of Cyclemys (including one collected by Alfred Russel Wallace), and phylogenetically placed these type sequences into the context of published cytochrome  b variation. Our phylogenetic hypothesis supports the recognition of four named species ( Cyclemys atripons , Cyclemys dentata , Cyclemys oldhamii , and C. pulchristriata ), as well as a fifth species of unknown geographical provenance obtained from the Hong Kong pet trade. The type sequences show that previous molecular phylogenetic studies were hampered by misidentifications, supporting the notion that Cyclemys of unknown provenance are not reliably identified to species solely on the basis of morphology.  © 2008 The Linnean Society of London, Biological Journal of the Linnean Society , 2008, 94 , 131–141.     

Amazonian biodiversity: assessing conservation priorities with taxonomic data

Data from 3991 records of museum collections representing 421 species of plants, arthropods, amphibians, fish, and primates were analyzed with GIS to identify areas of high species diversity and endemism in Amazonia. Of the 472 1 × 1° grid cells in Amazonia, only nine cells are included in the highest species diversity category (43–67 total species) and nine in the highest endemic species diversity category (4–13 endemic species). Over one quarter of the grid cells have no museum records of any of the organisms in our study. Little correspondence exists between the centers of species diversity identified by our collections-based data and those areas recommended for conservation in an earlier qualitative study of Amazonian biodiversity. Museum collections can play a vital role in identifying species-rich areas for potential conservation in Amazonia, but a concerted and structured effort to increase the number and distribution of collections is needed to take maximum advantage of the information they contain.     

Unlocking avian museum collections to enable and advance environmental change research

The rate and magnitude of contemporary changes in natural systems is unprecedented in the Earth's history. Studies of wild birds have been critically important in helping us understand and address these environmental changes. Avian collections provide a potentially unique perspective on change through time, but their role in environmental change research is limited by the availability of collections data. Here we describe how avian collections might be unlocked to enable environmental change research, and discuss the opportunities and constraints associated with this. We use the concept of the extended specimen to describe the types of data that could be unlocked from basic data for discoverability to enhanced data that might be directly applied to environmental change questions. We illustrate the type of environmental change research these data might support. We argue that data creation and access is currently limited by funding for digitization, a rather patchy understanding of the needs of the research community and less than adequate data-sharing by institutions and researchers. We develop a blueprint for addressing these issues which includes (1) improvements in sharing the data we are already creating and (2) building a better case for digitization at scale. As one of the largest avian collections in the world, the Natural History Museum, UK, is committed to unlocking our collections, but we will need input and support from the avian research community to do so.     

Records of ocean sunfish Mola mola along the Norwegian coast spanning two centuries, 1801–2015

Records of the ocean sunfish Mola mola along the Norwegian coast were compiled from all possible sources: literature, media, databases and museums. A total of 216 records were found between 1801 and 2015. They were distributed along the whole coast, except for the most north‐eastern part. Nearly all years with more than five records were after 2000, with 1985 as the only exception and with a maximum of 23 records in 2014. Most, 92·4%, were from July to December. Records from before 1979 were more incidental and random and no sunfish were recorded in 54 separate years between 1879 and 2015. The northernmost record was from 70° 44′ N in December 1881. No relationship between year and latitude was found. Forty‐four per cent of the records were of sunfish caught in fishing gear, 27% were found stranded and 30% were observed alive at sea. A trend of a decrease in numbers of observations of living individuals and an increase in numbers of strandings as dead individuals as autumn progressed was found. Geographical differences in the three categories of observation were also found. Among the specimens whose size was recorded, most were small, <30 kg and 70 cm in total length. Only 10 were heavier than 100 kg, all these were from before 1960. Annual numbers correlated weakly with sea temperatures. This was supported by a weak negative correlation with the North Atlantic Oscillation (NAO) index, because the majority of years since 2000 had a negative NAO.