Nuclear DNA from a 180‐year‐old study skin reveals the phylogenetic position of the Kinglet Calyptura Calyptura cristata (Passeriformes: Tyrannides)

The Kinglet Calyptura Calyptura cristata is one of the most enigmatic bird species in South America, known only from specimens collected in the 19th century and a few recent observations. Knowledge of its biology is scanty and its systematic position is obscure. Traditionally, Calyptura was placed in the Cotingidae, but associated with genera that are now known to fall outside the Cotingidae. In an attempt to clarify its phylogenetic position, sequence data from four nuclear markers were obtained from a 180‐year‐old museum study skin of Calyptura, and incorporated into a comprehensive dataset of tyrant flycatchers, cotingas, manakins and allies. Our analyses demonstrate that Calyptura is most closely related to Platyrinchus and Neopipo and that these three genera constitute a deep branch in the clade containing the Rhynchocyclidae (tody‐tyrants and flatbills) and Tyrannidae (typical tyrant flycatchers). The Calyptura specimen is one of the oldest avian museum specimens from which a substantial amount of nuclear DNA sequence data have been obtained, and highlights the immense value of museum collections for DNA‐based phylogenetic studies.     

Distinguishing range expansions from previously undocumented populations using background data from museum records

Aim Knowledge of the distribution of a species is fundamental to understanding the species’ biology, and changes in known distribution may reflect response to environmental change. However, in many cases, purported range expansions are not adequately justified and extra‐limital records may simply reflect previously undocumented populations. Thus, it is critical to distinguish between these hypotheses. This study aimed to provide a simple, conceptual framework for evaluating these hypotheses that depends on the use of museum background data to assess the adequacy of historical sampling. Location American Southwest and worldwide. Methods Background data are records of species other than the taxon of interest that are likely to be documented using the same sampling methods. If evaluation of the background group determines that the taxon of interest would have been documented if present, then the extra‐limital record can be considered a range expansion. Conversely, if evaluation of the background group indicates that historical sampling was inadequate to have documented the taxon of interest, then the most parsimonious explanation for the extra‐limital record is an undocumented population, which should be presented as a range extension. As an example, I applied the methods to a purported range expansion of the yellow‐nosed cotton rat (Sigmodon ochrognathus) in the Rincon Mountains in south‐eastern Arizona. Results Evaluation of the background group revealed that sampling was inadequate to have documented S. ochrognathus in the Rincon Mountains if present. Thus, the record of S. ochrognathus in the Rincon Mountains was interpreted as a previously undocumented population rather than a range expansion. Main conclusion Range expansions can reflect factors that are of important conservation concern, such as climate change or habitat modification. Thus, it is essential that the cause of extra‐limital records be accurately interpreted. The method provides a simple means for testing between hypotheses of range extension and range expansion.     

Biological collections and ecological/environmental research: a review,some observations and a look to the future

Housed worldwide, mostly in museums and herbaria, is a vast collection of biological specimens developed over centuries. These biological collections, and associated taxonomic and systematic research, have received considerable long‐term public support. The work remaining in systematics has been expanding as the estimated total number of species of organisms on Earth has risen over recent decades, as have estimated numbers of undescribed species. Despite this increasing task, support for taxonomic and systematic research, and biological collections upon which such research is based, has declined over the last 30‐40 years, while other areas of biological research have grown considerably, especially those that focus on environmental issues. Reflecting increases in research that deals with ecological questions (e.g. what determines species distribution and abundance) or environmental issues (e.g. toxic pollution), the level of research attempting to use biological collections in museums or herbaria in an ecological/environmental context has risen dramatically during about the last 20 years. The perceived relevance of biological collections, and hence the support they receive, should be enhanced if this trend continues and they are used prominently regarding such environmental issues as anthropogenic loss of biodiversity and associated ecosystem function, global climate change, and decay of the epidemiological environment. It is unclear, however, how best to use biological collections in the context of such ecological/environmental issues or how best to manage collections to facilitate such use. We demonstrate considerable and increasingly realized potential for research based on biological collections to contribute to ecological/environmental understanding. However, because biological collections were not originally intended for use regarding such issues and have inherent biases and limitations, they are proving more useful in some contexts than in others. Biological collections have, for example, been particularly useful as sources of information regarding variation in attributes of individuals (e.g. morphology, chemical composition) in relation to environmental variables, and provided important information in relation to species' distributions, but less useful in the contexts of habitat associations and population sizes. Changes to policies, strategies and procedures associated with biological collections could mitigate these biases and limitations, and hence make such collections more useful in the context of ecological/environmental issues. Haphazard and opportunistic collecting could be replaced with strategies for adding to existing collections that prioritize projects that use biological collections and include, besides taxonomy and systematics, a focus on significant environmental/ecological issues. Other potential changes include increased recording of the nature and extent of collecting effort and information associated with each specimen such as nearby habitat and other individuals observed but not collected. Such changes have begun to occur within some institutions. Institutions that house biological collections should, we think, pursue a mission of ‘understanding the life of the planet to inform its stewardship’ ( Krishtalka & Humphrey, 2000 ), as such a mission would facilitate increased use of biological collections in an ecological/environmental context and hence lead to increased appreciation, encouragement and support from the public for these collections, their associated research, and the institutions that house them.     

Recovering full DNA barcodes from natural history collections of Tephritid fruitflies (Tephritidae, Diptera) using mini barcodes

The family of Tephritid fruit flies (Tephritidae, Diptera) is composed of more than 4000 species and more than 350 are of economic importance (EI). The Tephritid Barcoding Initiative (TBI) aims at obtaining DNA barcodes for all EI species and the majority of their congeners. Dry pinned specimens from natural history collections are an important resource for reference material, but were often collected decades ago. We observed a strong decrease in the success rate of obtaining a full COX1 DNA barcode (658 bp), with an increasing age of the specimens. Obtaining full barcodes is often not possible using standard protocols. We developed a universal Tephritid primer set for multiple overlapping mini-barcodes that allows reconstructing the full COX1 DNA barcode. These newly developed primers and the corresponding protocol will facilitate the utilization of the extensive natural history collection by the TBI consortium.     

Investigating the timing of origin and evolutionary processes shaping regional species diversity: Insights from simulated data and neotropical butterfly diversification rates

Different diversification scenarios have been proposed to explain the origin of extant biodiversity. However, most existing meta‐analyses of time‐calibrated phylogenies rely on approaches that do not quantitatively test alternative diversification processes. Here, I highlight the shortcomings of using species divergence ranks, which is a method widely used in meta‐analyses. Divergence ranks consist of categorizing cladogenetic events to certain periods of time, typically to either Pleistocene or to pre‐Pleistocene ages. This approach has been claimed to shed light on the origin of most extant species and the timing and dynamics of diversification in any biogeographical region. However, interpretations drawn from such method often confound two fundamental questions in macroevolutionary studies, tempo (timing of evolutionary rate shifts) and mode (“how” and “why” of speciation). By using simulated phylogenies under four diversification scenarios, constant‐rate, diversity‐dependence, high extinction, and high speciation rates in the Pleistocene, I showed that interpretations based on species divergence ranks might have been seriously misleading. Future meta‐analyses of dated phylogenies need to be aware of the impacts of incomplete taxonomic sampling, tree topology, and divergence time uncertainties, as well as they might be benefited by including quantitative tests of alternative diversification models that acknowledge extinction and diversity dependence.     

The effect of anoxic treatment on the larvae of six species of dermestids (Coleoptera)

Abstract: Based on surveys of species of museum pest insects commonly found in Finland, Norway, Denmark and Sweden, six species were selected for a study of the effect of exposure to anoxic treatment on the larval stage. An oxygen level of 0.3% (the rest, nitrogen) was applied and lethal exposure times were determined. Anthrenus museorum L. was the most susceptible species (LT₉₉ = 32.2 h), while Attagenus woodroffei Halst. & Green and Attagenus smirnovi Zhantiev (LT₉₉ = 88.1 h) were the most tolerant species. The LT₉₉ value of At. woodroffei was not calculated, as only 50% of the larvae were killed by the treatment. The results indicate that large intraspecific variation is present in these two Attagenus species. Larvae of Anthrenus verbasci (L.) (LT₉₉ = 43.9 h), Reesa vespulae (Milliron) (LT₉₉ = 53.6 h), and Trogoderma angustum (Solier) (LT₉₉ = 57.2 h) showed intermediate tolerance.     

Age distribution,sex ratio and mortality of the red foxVulpes vulpes in Tochigi,central Japan: an estimation using a museum collection

One hundred and thirty carcasses of the red fox were collected in Tochigi Prefecture, by the Tochigi Prefectural Museum, from 1981 to 1991. The young/adult ratio of the sample was 1.60, which suggests that the hunting pressure has been relatively low in this area. Six percent of the animals were 5 years or older which compares to those taken in Hokkaido, but is higher than those in Europe and North America. The sex ratio for all specimens had a tendency towards male bias (0.587), but this bias was higher for the adult (0.605) than for the young (0.576). Among young (0 year-old) foxes, more individuals were killed on roads than by trapping or shooting (P<0.02, chisquare test). This mortality pattern was caused by high mortality of young males (P<0.02). The proportions of adults killed by the three mortality factors were similar, though only one of the 14 foxes older than 4 years old was shot, probably due to age-linked activity patterns. Most road-kills of young foxes occurred in May when juveniles began exploiting and in November when sub-adults began dispersal. The ratios of road-kills for the whole sample and for adults alone were 42% and 34%, respectively. These high rates of road-kills suggest that the mortality pattern in Tochigi has been affected by factors characteristic of urban environments.     

The Earth's Magnetic Field: A Simple Measurement of its Strength

Although most teachers agree that a field trip is an important educational experience for their students, many struggle with finding a way to make it connect with their classroom curriculum. Creating an effective field trip involves creating an effective lesson plan and using the resources of the museum, zoo, or aquarium to foster inquiry and learning. By incorporating the learning cycle into their field trip, students are able to use their explorations with animal-based exhibits to develop basic life science concepts.