Figure 1: New snail species- Plekocheilus cecepeus. These specimens were collected in 1869, but only recognized as a new species in 2015 after careful observation in the muesum. Image credit: Dr. Abraham Breure and Dr. Rafael Araujo (3).

by Patty Rohs
figures by Anna Maurer

New technology is allowing scientists to investigate natural history museum specimens in ways that we never thought were possible. To the public eye, these museums may seem like an unchanging archive of life on earth. But behind the scenes, the very same institutions are centers for cutting-edge research. Curators, who are highly experienced in research and are often affiliated with universities, constantly add new specimens to museum research collections. These collections are used for studies of biodiversity, environmental science, evolutionary biology, and animal physiology. By comparing specimens collected throughout time, museum researchers can determine how urbanization, climate change, and infectious disease are changing ecosystems (1). Furthermore, technologies such as DNA sequencing, chemical analysis, and 3D scanning are allowing scientists to extract new information from specimens that were collected decades, or in some cases centuries ago.

New species discovery

It may sound strange, but the majority of new plant and animal species are discovered not in the field, but rather in museum collections. In fact, three-quarters of newly named mammal species are already part of a museum collection when they are first identified (2). Among all newly described plant and animal species, the average lag time between collection and identification is

Figure 1: New snail species- Plekocheilus cecepeus. These specimens were collected in 1869, but only recognized as a new species in 2015 after careful observation in the muesum. Image credit: Dr. Abraham Breure and Dr. Rafael Araujo (3).

currently 21 years (2). How can it be that so many species are sitting unidentified or mislabeled on museum shelves? For some specimens, the answer simply has to do with a lack of expert examination. For example, Dr. Abraham Breure and Dr. Rafael Araujo recently discovered a new snail species in the Museo Nacional de Ciencias Naturales in Madrid. After making careful observations and measurements of snail shells in the museum, they realized that a collection of snails thought to be of only one species(3), actually consisted of two distinct species. These specimens were originally collected during a large scientific expedition in Ecuador in 1869, but had not been examined and described in sufficient detail until August 2015. (Figure 1).

In other cases, specimens are misidentified because two species look so outwardly similar that they are nearly impossible to distinguish by appearance alone. This is a case in which DNA analysis can be critical. In April 2013, scientists from Chicago’s Field Museum discovered three new species of yellow-shouldered bats by analyzing DNA from 38 field specimens and 94 museum specimens (4,5). This type of analysis of museum specimens is undertaken with great care because it is necessary to destroy part of the specimen to extract DNA. In the Field Museum’s case, DNA was extracted from 0.05 grams of preserved muscle or liver from each specimen, and used to determine the DNA sequence of five genes (Figure 2). The sequences were not only used to identify new species, but they also help scientists to infer evolutionary relationships between existing species. By identifying these new species and determining their current geographic ranges, scientists will be able to more accurately monitor changes to ecosystems in Central and South America.

Figure 2: DNA sequencing to discover new species. By extracting DNA from museum specimens and comparing sequence differences, scientists are able to determine whether similar-looking bats are actually different species.

Tracking disease using museum specimens

Aside from deciphering the phylogeny of museum specimens, DNA analysis also allows researchers to determine which bacterial, viral, or fungal pathogens may have infected them. By collecting the DNA of infected specimens from different times and locations, it is possible to determine the lineage of the pathogen, as well as its geographical and host range.

Recently, this approach has been particularly fruitful for the study of Batrachochytrium dendrobatidis, a deadly fungus responsible for the extinction of over 200 amphibian species. Analysis of museum frog specimens revealed that certain strains of this fungus have coexisted with their amphibian hosts in Korea and Illinois for over 100 years (6). Scientists hypothesize that these hosts coevolved with the fungus, gaining at least partial resistance to its deleterious effects. Serious problems are thought to arise when the fungus is transported out of its native range and exposed to susceptible amphibian populations. Hopefully, researchers will be able to prevent future extinctions by tracking how this fungus is being spread and determining what factors in the native hosts contribute to fungal resistance.

Resolving phylogenetic debates

New molecular techniques are also allowing scientists to solve long-standing mysteries about museum specimens. Darwin described the Toxodon as “perhaps one of the strangest animals ever discovered.” This fossilized South American ungulate (hooved mammal) has been difficult to classify because it possesses teeth like a rodent, eyes and nose like a hippo, some skeletal features like a rhinoceros and others like an elephant.(Figure 3) Using fossil samples from the Museo Argentino de Ciencias Naturales (Argentina), the Museo de La Plata (Argentina), and the Natural History Museum of Denmark, graduate student Frido Welker and his colleagues recently obtained molecular evidence that Toxodons are most closely related to perissodactyls (horses, tapirs, and rhinos).  They did this by extracting and analyzing Toxodon collagen- a protein that is much more stable and abundant than DNA (7). Thanks to museum artifacts and state-of-the-art technology, Darwin’s hundred-year-old mystery has been solved.

Figure 3: Toxodon illustration (left) and skeleton (right). The phylogeny of this species was determined by performing a molecular analysis of protein extracted from museum specimens.

Seeing within fossils

Beyond all the technologies already discussed above, scientists are currently using cutting-edge techniques like micro CT scanning and neutron tomography to get 3D, high-resolution details of the internal structures of museum fossils (Figure 4). These scans allow scientists to study specimens remotely, identify species of fossilized plants by looking at internal structures, and even determine how well extinct species were able to hear! Dr. Michael Laaß of the University of Duisburg-Essen, Germany, is interested in how terrestrial tetrapods evolved the ability to detect airborne sound. The earliest land vertebrates were only able to “hear” vibrations in the ground using their jaw. During the evolution of mammals, some jaw bones were moved and repurposed, forming the malleus, incus, and stapes bones of the inner ear. To determine when this transition happened, Dr. Laaß needed to examine the normally inaccessible middle ear of fossilized specimens. He was able to use neutron tomography to visualize the internal skeletal structures of specimens from the Museum of Natural History in Berlin. This 3D scanning technology allowed him to determine that the Pristerodon, an early mammal-like reptile, could indeed hear airborne sound using transitional jaw/middle ear structures (8).

Figure 4: 3D imaging techniques. Neutron tomography is one strategy that allows scientists to non-destructively analyze both external and internal structures of museum specimens. In this technique, neutrons, charge-less sub-atomic particles, are fired at the fossil. Scientists them measure the way that the neutrons bounce off of the sample, allowing them to make a 3D image of both the inside and outside of the fossil.

Natural history museums in a global community

Scientists from across the globe are collaborating to make maximal use of museum specimens. Researchers often use online databases to identify museum specimens of interest, complete with photographs and the GPS coordinates of where they were collected. One example is idigbio.org, which currently has digital records of over 45 million specimens. Scientists can request a loan of any specimen in the database and obtain permission to extract DNA or protein for molecular analysis. Some museums are taking digitization to the next level by 3D scanning most of their specimens. This allows investigators to make the precise measurements they need for studying subjects such as biomechanics or the evolution of anatomical structures from a remote location. Some 3D scans are even made publicly available (see the Smithsonian’s collection of 3D scans at http://3d.si.edu). Natural history museums around the world continue to be a vast resource for scientific exploration, and new technologies will continue to revolutionize our analysis of museum specimens.

Patty Rohs is a 3rd year PhD student in the Microbiology and Immunobiology department at Harvard University, and a volunteer at the Harvard Museum of Natural History

References

(1) Hanken J (2015). Natural history collections and evolution. Harvard Museum of Natural History Lecture Series. http://hmnh.harvard.edu/file/376186
(2) Kemp C (2015). Museums: The endangered dead. Nature 518: 292-294. http://www.nature.com/news/museums-the-endangered-dead-1.16942#/b2/
(3) Breure A and Araujo R (2015). A snail in the long tail: a new Plekocheilus species collected by the ‘Comisión Científica del Pacífico’ (Mollusca, Gastropoda, Amphibulimidae). Zookeys 516: 85-93. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4547370/
(4) Field museum (2014). Three new species of yellow-shouldered bats discovered in museum collections. Eureka Alert. http://www.eurekalert.org/pub_releases/2014-04/fm-tns041414.php
(5) Velazco PM and Patterson BD (2013). Diversification of the Yellow-shouldered bats, Genus Sturnira (Chiroptera, Phyllostomidae), in the New World tropics. Molecular Phylogenetics and Evolution 518: 683-698.
(6) Phys.org (2015). Deadly frog fungus dates back to 1880s, studies find. http://phys.org/news/2015-03-deadly-frog-fungus-dates-1880s.html
(7) Yong, E (2015). Darwin’s “strangest” beast finds place on tree. National Geographic. . http://phenomena.nationalgeographic.com/2015/03/18/darwins-strangest-beast-finds-place-on-tree/
(8) Phys.org (2015). Neutron tomography shows that the Pristerodon adapted to hear airborne sound 260 million years ago. http://phys.org/news/2015-07-neutron-tomography-pristerodon-airborne-million.html

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