Museums are a repository of many artifacts collected in times gone by, and the Smithsonian holds one of the United States’ best collections. Its Division of Mammals at the National Museum of Natural History houses a world-class collection of roughly 590,000 preserved specimens, many of which are available to researchers, including Dr. Bill Murphy, a mammalian geneticist in the Department of Veterinary Integrative Biosciences at the College of Veterinary Medicine & Biomedical Sciences (CVM).
Murphy’s background in comparative genomics and mammalian phylogenetics helps him determine the ancestral relationships between different groups of species, when they originated, what factors drove them to diversify, and what processes led to their distribution around the globe. In his journey to discover these connections, Murphy has taken advantage of the hard work already accomplished on species collection trips over a century ago.
Since 2002, Murphy has been collaborating with a mammalogist, Dr. Kris Helgen, on the methodology of using museum specimens to extract mammalian DNA. But the practice really advanced in 2008 when the pair started exploring the mammals collection at the Smithsonian, where Helgen is the curator in charge of mammals. Their goal is to use DNA from museum specimens to understand how rare or unusual groups of mammals fit into the mammalian family tree. Murphy brings the genetic component to the collaboration, whereas Helgen brings the curatorial and mammalogy background to help classify and understand mammals more thoroughly.
The field of museum-based genetics had its origins in the early 1990s, according to Murphy. Although many studies with museum specimens have been conducted in the past, Murphy wondered how well DNA could be recovered from these specimens and in large amounts without contamination. Also, he wanted to determine if the new next-generation sequencing techniques might reveal a more accurate resolution of ancient DNA sequences, as well as larger datasets for phylogenetic analysis. Typically, previous researchers have chosen to extract DNA from the hide or hair of specimens because it is more abundant, but there is an increased risk of contamination from being handled over the years. Using hide samples can also be more problematic because hides are often chemically treated for preservation.
To avoid analyzing DNA from specimens where the possibility of sample contamination is high, Murphy and his team implemented an alternative approach to sampling. “We developed an approach where we extract DNA from the ‘crusties’ as we call them,” said Murphy. “When you examine skulls in museum collections, they are usually pretty clean. But if you look inside the brain case you can actually see tidbits, little remnants of dried tissue that have been sitting there for a 100–150 years. For the most part these tissues have never been exposed to human contact, so we figured there would be less contamination. This approach is also less destructive since museums like to avoid damaging specimens, such as drilling into bones or taking hair and tissue samples, at all costs. No one can tell if you’ve removed a bit of tissue from inside a skull.”
Murphy and his team have found that they can get an extraordinary amount of acceptable and quality DNA from these tissues. And with the new sequencing technologies, Murphy has found that the DNA sequencing is simplified with degraded “crusties” more than if one starts with fresh or frozen tissue.
With this methodology researchers can also reduce or avoid the costs and time associated with trapping animals in the field, applying for permits and permissions, and traveling; they can take advantage of the work done a century before that resides within museums. This method also allows geneticists to access and sequence DNA from extinct species. Murphy is working on such a project with a colleague in South America to extract ancient DNA from extinct ungulate megafauna groups, such as a Toxodon, a rhinoceros-like species that went extinct in the Pleistocene.
Historically, mammals have been classified into small groups and researchers believed that if species share the same morphology, or physical characteristic, they must be related. But with the new sequencing technology, genetics has revealed that parallel evolution, the development of similar physical characteristics in related but distinct species, is happening among the whole mammalian tree. According to Murphy, “Among the 4,500 mammal species identified in 2005, geneticists now believe there are roughly 6,000 species as a result of molecular techniques, but there is speculation that there are probably close to 10,000 species of mammals.”
Murphy has used the technology and museum specimens at the Smithsonian to study colugos, the closest known living relative to primates found throughout the islands of Southeast Asia. “Colugos are one of the most poorly known groups of mammals, and the problem is they are not found in zoos and you can’t sample colugos from across Southeast Asia very easily. So we turned to museum specimens,” said Murphy. He feels that by understanding the genome of colugos, we can understand the genetic transition to primates. In his team’s analysis of 13 specimens in one area alone, it was determined there were probably as many as five or 10 species, whereas it was believed that only two existed.
Murphy and his team’s technique has yielded promising and successful results. “We have not had too many limitations. Most of the samples for which we have attempted DNA extraction have been highly successful. The results have been so promising that we have proposed a much more concerted effort of using only museum specimens to identify the true number of mammal species on Earth,” said Murphy.
However, different museums preserve specimens differently, and their location also affects the quality of the samples. For example, a museum located in a tropical environment has to battle with factors such as mold and bacterial growth, and having temperature-controlled rooms to avoid mold and bacterial growth can help with this. Other elements, such as how specimens are preserved and handled, also have an effect on a sample’s quality.
Since 2008, Murphy has been a research associate at the Smithsonian, and he travels there about once every one to two years. In the company of Helgen, Murphy and his graduate student, Victor Mason, have also visited the American Museum of Natural History in New York and the Raffles Museum of Biodiversity Research in Singapore. Along with studying colugos, the pair has also studied cat species and other endangered species in Southeast Asia. “There are probably many undiscovered, cryptic species in Southeast Asia, and this is an ongoing focus of the collaboration with the Smithsonian,” said Murphy.
“Molecular genetic technologies have rapidly changed the way in which mammals are classified. We can also look at genetic diversity within species 100 years ago and compare them with today to see how human influences have affected their genetic diversity,” said Murphy. The technology and use of museum specimens extends beyond studying mammals and can be utilized to study other species as well.