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Shades of Jurassic Park: Museum Specimens Shown to be “Treasure Troves” of Genomic Data

Elsa Call, Ph.D.

Advances in genetic analysis methods have opened new research opportunities using old source material: museum specimens. The new technique has been dubbed “museomics.” Here, researcher Elsa Call, Ph.D., holds a typical museum drawer of specimens. Using a DNA anaylsis technique called target enrichment, Call and colleagues were able to analyze genomic data from moth specimens dating back to 1892 and determine the phylogeny (relatedness) among the three moth families and the species within them. (Photo courtesy of Elsa Call, Ph.D.)

By Leslie Mertz, Ph.D.

Leslie Mertz, Ph.D.

Leslie Mertz, Ph.D.

Around the world, natural history museums are home to thousands of rarely opened cabinet drawers filled with countless neatly pinned insect specimens, some of them many decades or even centuries old. Using an approach reminiscent of Jurassic Park, researchers have found that those long-dead specimens still harbor accessible genomic data, and they are now using it to determine how closely different species and families of insects are related.

“We have this incredible collection of billions of specimens that are like treasure troves and include extinct species and specimens that are really rare. A lot of people thought they would be too degraded or that we cannot access the genomic information in those specimens, but this work taught me that we actually can get good data from very old specimens in museums,” says Elsa Call, Ph.D., lead author of a new article, published April 21 in Insect Systematics and Diversity, that describes the approach, called “museomics.” She conducted the work as a doctoral student in biology at Lund University in Sweden, and is now seeking a post-doctoral appointment. Her co-authors include her doctoral advisor, Niklas Wahlberg, Ph.D., as well as scientists from the Zoological Research Museum Alexander Koenig in Germany.

Call believes this approach can be used to clarify and possibly tweak accepted insect evolutionary relationships, or phylogenies. In addition, she says, it affords an opportunity to conduct time-series analyses to spot potential genetic differences that a species may have accrued over the decades.

Tales From the Crypt

As described in the article, Call and colleagues sequenced the genomes of 31 museum specimens originally collected between 1892 and 2001, all within three small families of moths: swallowtail moths in the families Sematuridae and Epicopeiidae, which include 42 and 25 species, respectively; and the Pseudobistonidae, a family newly named in 2015 and containing only two species. “Small families are a good thing when you do phylogenetic analyses. You want as many species in the family as you can get,” Call says.

The three families had other features that made them appealing for this study. For one thing, phylogenies have traditionally been based on morphology (the insects’ appearance and physical structures), but the species within these three families look confusingly similar to one another and to other moths and even butterflies, making their phylogeny especially challenging. This provided a good opportunity for a genomic study that could provide some clarification. Another attractive feature for studying the three families is that museum specimens are readily available, but live specimens are not: Most species in these families exist only in hard-to-reach geographic locations, such as remote regions of Kazakhstan and Tibet.

The researchers put each of the 31 specimens through the same step-wise process: They carefully removed the abdomen, placed it (without crushing it) in water for about 5 minutes to rehydrate it, and drained off the water. Then, using an off-the-shelf kit (DNeasy Blood & Tissue), they immersed the abdomen in fluid, and with a little heat and a gentle shake, they extracted as much of the insect’s genome (its complement of DNA) as possible. When the process was complete, Call says, the researchers stored each abdomen in alcohol and conserved it with a unique label linked to the rest of the specimen so that it could be used for future morphological studies.

Once the researchers had the DNA, they employed a “target enrichment” technique that uses probes designed to seek out bits of the DNA associated with genes of interest. In this instance, the genes of interest were 378 nuclear genes that help distinguish one species or family from another. The approach not only worked but also revealed some new insights into the phylogenies of the three families.

target enrichment

Using a target enrichment approach, Elsa Call, Ph.D., and colleagues used probes (shown as circles) designed to zero in on certain fragments of DNA (spirals). These fragments are associated with specific genes that can be used to determine how closely species are related. This illustration shows three stages (left to right): the probes latching onto the DNA fragments; the fragments after they have been amplified (multiplied) and separated for ease of analysis; and the genes associated with the DNA. (Image courtesy of Elsa Call, Ph.D.)

The Secrets Within

The analysis of the genomic data for the 31 specimens almost completely corroborated the phylogeny put forth by earlier morphological studies, something Call found quite amazing. “You can read these scientists’ first papers based on morphology and you cannot believe how very close they are to what we find now with sequencing, which is incredible to me. Those guys were really smart,” she says.

The new genomic data did, however, find discrepancies in the family Epicopeiidae: Two species in the genus Nossa and three in the genus Epicopeia didn’t fit the morphology-based phylogeny. Rather than finding that all of the Nossa specimens fell into one closely related group (descended from the same common ancestor) and all of the Epicopeia specimens fell into a separate closely related group, the genomic data suggested that two Nossa species (N. chinensis and N. palaearctica) were more closely related to the genus Epicopeia, and one specimen of Epicopeia (E. philenora) was more closely related to two other Nossa species (N. moorei and N. nagaensis).

Distinctions like these can be very difficult, if not impossible, to see in morphological studies, particularly when mimicry is occurring among species. “But, when you look in detail at the genetics,” Call says, “you can find differences, including that some species may actually be closer to a genus that morphologically looks nothing like them.” She adds, “You need both morphology and genetics, in my opinion, to be able to be as close as we can to the truth of the phylogeny.”

Phylogeny - Sematuridae, Pseudobistonidae, Epicopeiidae

Using museum specimens for genomic analysis—an emerging technique called “museomics”—researchers at Lund University in Sweden and the Zoological Research Museum Alexander Koenig in Germany developed this phylogeny for the moth families Pseudobistonidae (P), Sematuridae (S) and Epicopeiidae (E). As shown, Pseudobistonidae and Sematuridae diverged from one another, and Epicopeiidae later branched off from Pseudobistonidae. Within Epicopeiidae, the largest of the three families, the analysis suggests that previously held phylogenies of species in the genera Nossa and Epicopeia may require retooling and possibly the addition of a new genus. (Adapted from image originally published in Call et al 2021, Insect Systematics and Diversity)

Possibilities of Museomics

This use of genomic data from museum specimens opens many possibilities, Call says. “For instance, can we see genetic differences between bees today and those before pesticides? What is the difference between a butterfly that we find now farther north because of climate change, compared to decades past? And with the massive extinction under way, I see natural history museums as being a sort of Noah’s Ark that has information on species that have unfortunately already disappeared, so perhaps we learn things from them that can help us to save those species that are currently disappearing.”

She sees museomics as the beginning of an era of discovery. “The questions we can ask are infinite, and this technique can allow us to answer these questions and provide a sort of window to the past. I think it’s a really cool thing.”

Leslie Mertz, Ph.D., writes about science and runs an educational insect-identification website, www.knowyourinsects.org. She resides in northern Michigan.

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