博物館だより(6) なぜ保存するのか伝える : 博物館は研究用標本を保存すべきか?

DNA preserved in degraded beetle (Coleoptera) specimens, including those derived from dry-stored museum and ancient permafrost-preserved environments, could provide a valuable resource for researchers interested in species and population histories over timescales from decades to millenia. However, the potential of these samples as genetic resources is currently unassessed. Here, using Sanger and Illumina shotgun sequence data, we explored DNA preservation in specimens of the ground beetle Amara alpina, from both museum and ancient environments. Nearly all museum specimens had amplifiable DNA, with the maximum amplifiable fragment length decreasing with age. Amplification of DNA was only possible in 45% of ancient specimens. Preserved mitochondrial DNA fragments were significantly longer than those of nuclear DNA in both museum and ancient specimens. Metagenomic characterization of extracted DNA demonstrated that parasite-derived sequences, including Wolbachia and Spiroplasma, are recoverable from museum beetle specimens. Ancient DNA extracts contained beetle DNA in amounts comparable to museum specimens. Overall, our data demonstrate that there is great potential for both museum and ancient specimens of beetles in future genetic studies, and we see no reason why this would not be the case for other orders of insect.

Feathers are known to contain amplifiable DNA at their base (calamus) and have provided an important genetic source from museum specimens. However, feathers in subfossil deposits generally only preserve the upper shaft and feather 'vane' which are thought to be unsuitable for DNA analysis. We analyse subfossil moa feathers from Holocene New Zealand rockshelter sites and demonstrate that both ancient DNA and plumage information can be recovered from their upper portion, allowing species identification and a means to reconstruct the appearance of extinct taxa. These ancient DNA sequences indicate that the distal portions of feathers are an untapped resource for studies of museum, palaeontological and modern specimens. We investigate the potential to reconstruct the plumage of pre-historically extinct avian taxa using subfossil remains, rather than assuming morphological uniformity with closely related extant taxa. To test the notion of colour persistence in subfossil feathers, we perform digital comparisons of feathers of the red-crowned parakeet (Cyanoramphus novaezelandiae novaezelandiae) excavated from the same horizons as the moa feathers, with modern samples. The results suggest that the coloration of the moa feathers is authentic, and computer software is used to perform plumage reconstructions of moa based on subfossil remains.

Nearly 25 years ago, Allan Wilson and colleagues isolated DNA sequences from museum specimens of kangaroo rats (Dipodomys panamintinus) and compared these sequences with those from freshly collected animals (Thomas et al. 1990). The museum specimens had been collected up to 78 years earlier, so the two samples provided a direct temporal comparison of patterns of genetic variation. This was not the first time DNA sequences had been isolated from preserved material, but it was the first time it had been carried out with a population sample. Population geneticists often try to make inferences about the influence of historical processes such as selection, drift, mutation and migration on patterns of genetic variation in the present. The work of Wilson and colleagues was important in part because it suggested a way in which population geneticists could actually study genetic change in natural populations through time, much the same way that experimentalists can do with artificial populations in the laboratory. Indeed, the work of Thomas et al. (1990) spawned dozens of studies in which museum specimens were used to compare historical and present-day genetic diversity (reviewed in Wandeler et al. 2007). All of these studies, however, were limited by the same fundamental problem: old DNA is degraded into short fragments. As a consequence, these studies mostly involved PCR amplification of short templates, usually short stretches of mitochondrial DNA or microsatellites. In this issue, Bi et al. (2013) report a breakthrough that should open the door to studies of genomic variation in museum specimens. They used target enrichment (exon capture) and next-generation (Illumina) sequencing to compare patterns of genetic variation in historic and present-day population samples of alpine chipmunks (Tamias alpinus) (Fig. 1). The historic samples came from specimens collected in 1915, so the temporal span of this comparison is nearly 100 years.

Early nineteenth-century zoology in Britain has been characterized as determined by the ideological concerns of its proponents. Taking the zoologist Robert E. Grant as an exemplary figure in this regard, this article offers a differently nuanced account of the conditions under which natural-philosophical knowledge concerning animal life was established in post-Napoleonic Britain. Whilst acknowledging the ideological import of concepts such as force and law, it points to an additional set of concerns amongst natural philosophers - that of appropriate tool use in investigation. Grant's studies in his native Edinburgh relied heavily on the use of microscopes. On his arrival in London, however, he entered a culture in which a different set of objects - museum specimens - held greater persuasive power. This article relates changes in Grant's ideas and practices to the uneven emphases on microscopic and museological evidence amongst European, Scottish and English natural philosophers at this time. In so doing, it identifies the reliance of London-based natural philosophers on museology as constituting a limiting effect on the kinds of claim that Grant sought to make regarding the nature of life.

Animal specimens in natural history collections are invaluable resources in examining the historical context of pathogen dynamics in wildlife and spillovers to humans. For example, natural history specimens may reveal new associations between bat species and coronaviruses. However, RNA viruses are difficult to study in historical specimens because protocols for extracting RNA from these specimens have not been optimized. Advances have been made in our ability to recover nucleic acids from formalin-fixed paraffin-embedded samples (FFPE) commonly used in human clinical studies, yet other types of formalin preserved samples have received less attention. Here, we optimize the recovery of RNA from formalin-fixed ethanol-preserved museum specimens in order to improve the usability of these specimens in surveys for zoonotic diseases. We provide RNA quality and quantity measures for replicate tissues subsamples of 22 bat specimens from five bat genera (Rhinolophus, Hipposideros, Megareops, Cynopterus, and Nyctalus) collected in China and Myanmar from 1886 to 2003. As tissues from a single bat specimen were preserved in a variety of ways, including formalin-fixed (8 bats), ethanol-preserved and frozen (13 bats), and flash frozen (2 bats), we were able to compare RNA quality and yield across different preservation methods. RNA extracted from historical museum specimens is highly fragmented, but usable for short-read sequencing and targeted amplification. Incubation of formalin-fixed samples with Proteinase-K following thorough homogenization improves RNA yield. This optimized protocol extends the types of data that can be derived from existing museum specimens and facilitates future examinations of host and pathogen RNA from specimens.

Key insights into the evolutionary history of recently extinct or critically endangered species can be obtained through analysis of genomic data collected using high-throughput sequencing and ancient DNA from museum specimens, particularly where specimens are rare. For instance, the evolutionary history of the critically endangered Puebla deer mouse, Peromyscus mekisturus, remains unclear due to discordance between morphological and molecular phylogenetic analyses. However, previous molecular analyses were based on PCR and Sanger sequencing of only a few mitochondrial genes. Here, we used ancient DNA from historical museum specimens followed by target enrichment and high-throughput sequencing of several thousand nuclear ultraconserved elements and whole mitochondrial genomes to test the validity of the previous phylogenetic placement of P. mekisturus. Based on UCEs and mitogenomes, our results revealed that P. mekisturus forms a well-supported distinct lineage outside the clade containing all other members of the Peromyscus melanophrys group. Additionally, the mitogenome phylogeny further supports the placement of P. mekisturus as the sister species of the genus Reithrodontomys. This conflicts with the previous mtDNA phylogenetic reconstruction, in which P. mekisturus was nested within the species P. melanophrys. Our study demonstrates that high-throughput sequencing of ancient DNA, appropriately controlling for contamination and degradation, can provide a robust resolution of the evolutionary history and taxonomic status of species for which few or no modern genetic samples exist. In light of our results and pending further analysis with denser taxon sampling and the addition of morphological data, a re-evaluation of the taxonomy and conservation management plans of P. mekisturus is needed to ensure that the evolutionary distinctiveness of this species is recognized in future conservation efforts.

Although biomass values are critical for diverse ecological and evolutionary analyses, they are unavailable for most insect species. Museum specimens have the potential to address this gap, but the variation introduced by sampling and preservation methods is uncertain. This study quantifies species-level variation in the body mass of Canadian Coleoptera based on the analysis of 3,744 specimens representing 3,161 Barcode Index Number (BIN) clusters. Employing the BIN system as a proxy for species allows the inclusion of groups where the taxonomic impediment prevents the assignment of specimens to a Linnaean species. By validating the reproducibility of measurements and evaluating the error introduced by operational complexities such as curatorial practice and the loss of body parts, this study demonstrates that museum specimens can speed the assembly of a mass registry. The results further indicate that congeneric species of Coleoptera generally have limited variation in mass, so a genus-level identification allows prediction of the body mass of species that have not been weighed or measured. Building on the present results, the construction of a mass registry for all insects is feasible.

Understanding demography of vertebrate populations requires quantifying reproductive success. For taxa that are difficult to distinguish, estimates of reproductive success can be biased if species are misidentified or if breeding concludes before identification is confirmed. We surveyed desert grasslands where three species of cryptic sparrows breed: Peucaea botterii, P. cassinii, and Aimophila ruficeps (Emberizidae). Nests, eggs, and nestlings of these species are similar, making it difficult to differentiate nests without observing adults, which can be challenging. We collected seven types of material from nests for DNA analysis: maternal cells from exterior surfaces of unhatched eggs, epithelial cells from the oropharyngeal cavity of nestlings, eggshells, feathers, feather sheaths, feces, and fecal sacs. From these materials, we amplified and sequenced a fragment of the diagnostic locus, mitochondrial cytochrome b (cyt b), and analyzed the data in a phylogenetic framework to classify nests to species. We validated our classification by sequencing the same locus from feathers of museum specimens. Overall, 72% of samples from nests yielded high-quality sequences. We identified to species 44 of 51 nests and identified museum specimens with archival ages of up to 47 years. Our study extends previous research by demonstrating the efficacy of standard kits, inexpensive reagents, low DNA concentrations, and diverse materials in classifying nests of grassland sparrows. Compared to more invasive methods of acquiring DNA, the approaches we describe are less likely to affect nesting behavior and bias estimates of nesting success of birds, issues especially important for species of conservation concern.

Obtaining DNA sequences, particularly nuclear DNA, from museum specimens is challenging. We sequenced nuclear DNA from small bone fragments of skeletonized and fluid‐fixed museum specimens of squamate reptiles by using a forensic protocol developed for isolating DNA from human bones. The method yielded high quality nuclear DNA sequences from bones taken from 11 of 21 (52.4%) skeletonized or desiccated specimens, the oldest of which dated back to 1938, and 1 of 9 (11.1%) fluid‐preserved specimens, which was collected in 1957.

Colour morph variation is widely observed in owls and several studies have described differences In life history traits among the morphs. Traditionally, Glaucidium owls are described as having two colour morphs, rufous and grey, which are supposedly independent of age or sex. During 2010–2012, nest boxes were set up in order to study the basic life history of Collared Pygmy Owls Glaucidium brodiei. We banded the population and followed some of the fledglings for nearly two years. Our results — in combination with data from museum specimens — clearly show that the colour morph In Collared Pygmy Owls is age-dependent, changing from the original fledgling plumage (2–3 months after hatching) to the rufous morph (4–7 months after hatching), and finally to the definitive grey plumage. Our results reject the long-standing polymorphism hypothesis for the pygmy owl. We conclude that the age of the birds should be considered before a colour polymorphism can be confirmed, especially in secretive nocturnal species. The case of within-species polymorphism might be overstated in Strigiformes.

Tineola bisselliella, the webbing clothes moth, is an economically important, globally distributed synanthropic pest species and member of the basal moth lineage Tineidae.Tineola bisselliellais facultatively keratinophagous. Therefore, their larvae can cause extensive damage, particularly to clothing, textiles, and museum specimens. Despite the economic and phylogenetic importance ofTineola bisselliella, there is a lack of quality genomic resources for this species, or for others within the Tineidae family. TheTineola bisselliellagenome presented here consists of 30 pseudochromosomes (29 autosomes and 1 Z chromosome) produced using synteny alignment to a closely related species,Tinea pellionella. The resulting final pseudochromosome-level assembly is 243.630 Mb and has an N50 length of 8.708 Mb. The assembly is highly contiguous and has similar or improved quality compared to other available Tineidae genomes, with 93.1% of lepidopteran orthologs complete and present. Annotation of the pseudochromosome-level genome assembly with the transcriptome we produced ultimately yielded 11,267 annotated genes. Synteny alignments between theTineola bisselliellagenome assembly and other Tineidae genomes found evidence for numerous small rearrangements with high synteny conservation. In contrast, synteny alignments performed betweenTineola bisselliellaand the more distantly relatedBombyx moriandMelitea cinxiarevealed more frequent small and large rearrangements as predicted by their evolutionary divergence. The reference quality annotated genome forTineola bisselliellapresented here will advance our understanding of the evolution of the lepidopteran karyotype by providing a chromosome-level genome for this basal moth lineage and provide future insights into the mechanisms underlying keratin digestion inTineola bisselliella.Significance StatementTineola bisselliella, the webbing clothes moth, is a globally distributed synanthropic pest species that feeds on both keratin-based materials and detritus. This dietary habit can cause substantial damage to clothing, textiles, rugs, taxidermy, and museum specimens. In fact, keratinophagous organisms cause an estimated $1 billion worth of damage annually in the United States. However, the lack of a high-quality annotated reference genome for this basal moth species has thus far limited our understanding of the mechanisms underlying keratin digestion relevant to pest control efforts and has hampered efforts to investigate the broader phylogenetic relationships the Tineidae family necessary to reveal patterns of lepidopteran chromosome evolution. Here, we present the first reference quality genome forTineola bisselliellaand the first annotated genome for any member of the Tineidae family, providing a critical resource for the lepidopteran genomics and pest management communities.

Museum specimens provide a record of past species distribution and are an increasingly important resource for conservation genetic research. The scientific value of these specimens depends upon the veracity of their associated data and can be compromised by inaccurate details; including taxonomic identity, collection locality, and collector. New Zealand contains many endemic species that have been driven to extinction or reduced to relict distributions following the arrival of humans and mammalian predators, including the Acanthisittid wrens (of which only two of the eight species presently persist). One of these is the New Zealand rock wren (Xenicus gilviventris), currently classified as an endangered species and experiencing ongoing population declines. Here we analyse ancient DNA retrieved from New Zealand rock wren museum skins to establish the veracity of their recorded collection localities – New Zealand rock wrens exhibit strong north-south genetic structuring along the Southern Alps of New Zealand’s South Island. We include the only specimen reportedly collected from New Zealand’s North Island, outside the known range of New Zealand rock wrens, specimens collected by Henry Hamersley Travers, a collector known for poor record keeping and potentially fraudulent specimen data, and type specimens of proposed Xenicus taxa. Multiple instances of inaccurate collection locality were detected, including that of the New Zealand rock wren reportedly collected from the North Island, which matches individuals from the southern South Island. Syntypes of X. haasti, and a syntype of X. gilviventris clustered with individuals belonging to the northern New Zealand rock wren lineage. Our results suggest that New Zealand rock wrens have not been historically extirpated from New Zealand’s North Island, and that caution must be taken when utilising museum specimens to inform conservation management decisions. Additionally, we describe the type locality of both X. gilviventris and X. haasti, with genetic and historical evidence suggesting that the specimens used to describe these taxa were collected from the headwaters of the Rakaia River. This study demonstrates that ancient DNA analysis can add value to museum specimens by revealing incorrect specimen data and inform the conservation management and taxonomy of endangered species.

Barcode analysis using mini-amplicons strategy for museum samples of neotropical primates Callithrix spp.

1. Climate change has been occurring at unprecedented rates and its impacts on biological populations is beginning to be well documented in the literature. For many species, however, long‐term records are not available, and trends have not been documented. 2. Using museum specimens from southern USA, we show that the stream‐dwelling beetle Gyretes sinuatus has shown an 8% increase in body size and change in body shape (fineness ratio) from 1928 to 1988. Any directional morphological change observed over time could be an indicator of a microevolutionary response. 3. During these 60 years, there have also been changes in temperature, precipitation, and location of collection sites. Unlike the global trend, mean annual temperature in the region has decreased, and furthermore, total annual precipitation has increased. By investigating how these various ecological and geographical variables may affect body size and shape, we can examine which pressures may promote larger and/or thinner beetles. 4. Results indicate that mean annual temperature was the most predictive variable for the change in size and shape. We suggest there is an adaptive role for temperature on body size and shape of stream dwelling organisms. 5. We found that museum specimens can be invaluable resources of information when collection date and location information is available. We promote the use of such specimens for future studies of the morphological response to climate change.

The black-faced black spider monkey (Ateles chamek) is endangered because of hunting and habitat loss. There are many gaps in our understanding of its geographic distribution. The Ucayali-Solimões-Amazon fluvial complex is currently recognized as the northern boundary of the species' range, although published reports have indicated that it occurs north of the Rio Solimões. In this study we investigate published records, generate new field records, and assess the current information concerning the northern boundary of this species' range. We conducted the study at the Mamirauá Sustainable Development Reserve in the central Brazilian Amazon, an area of 1,124,000 ha that consists entirely of Amazonian flooded forest (várzea). We collected data on the occurrence of the species from museum specimens and through field surveys, including interviews with local residents, direct observations, and the collection of new museum specimens. We confirmed the presence of A. chamek at 17 locations in the reserve, one of which was an island formed by a river bend cut-off that would have effectively taken any resident spider to the (new) north bank of the Solimões. We therefore conclude that fluvial dynamics were involved in creating the conditions for the dispersal and colonization of the species on the northern bank of the Rio Solimões. The data we present extends the known distribution of the species and increases its representation in protected areas.