In a “Jurassic Park”-esque development in the field of phylogenetics, a joint research venture between faculty from Rutgers University-Newark and LSU developed a method for recovering and sequencing DNA from museum specimens, some over 100 years old.
As tissue samples of animals age, their DNA is degraded over time as it is broken down by light and temperature. These processes shred previously long chains of DNA into small fragments, leaving the genetic code unreadable. Old genetic sequencing techniques required longer “high molecular weight” genetic code in order to be useful, meaning samples pre-dating the advent of genetics which weren’t preserved with DNA in mind were essentially useless for genetic classification.
Current animal samples are now stored in large liquid nitrogen vaults at a temperature that prevents deterioration, a technique previously unthought of or too expensive for tissue samples of animals collected in the 1950s or before.
Professor Christopher Austin, a curator at the LSU Museum of Natural Science, had another issue with old sequencing techniques. Samples of amphibians, reptiles and fish are kept “wet.” This process involves preserving the animals using a chemical called formalin, and then submerging the samples in jars of ethanol. This process is exceptional for the preservation of the tissue, meaning samples can last for hundreds of years, but the formalin used to preserve the animals wreaks havoc on DNA, breaking it down into small fragments, just like time.
The advent of Next-Generation Sequencing techniques has turned the previous concept of old DNA being unusable on its head.
NGS employs using these small DNA fragments, some in the region of only 150 to 200 base pairs, in a computational rebuilding of the genome. These small stretches of genes are compared to each other, thousands or millions of times, quickly building back the original genome.
A process like this would have been completely inconceivable before high speed computers and has only recently become the method of choice for its speed and cost efficiency, putting genetics in the hands of universities and museums the world over.
This has opened the doors for phylogeneticists to use older samples and properly classify animal samples previously deemed too deteriorated.
Austin realized this technique could be employed for samples of amphibians and reptiles preserved in formalin, meaning animal samples over a hundred years old — some extremely rare or even extinct — could have their genetic codes unlocked and properly classified on the tree of life for the first time in history.
“My former post-doc, Sara Ruane, and I thought we would try some relatively novel methods for extracting DNA using longer protocols,” Austin said. “But then using these Next-Generation Sequencing techniques, we were able to actually sequence the DNA, thousands of different chunks of DNA from a variety of snake specimens — some of which were over a hundred years old.”
Austin and Ruane extracted and sequenced the DNA of 13 historic or rare snake specimens from all over the world, many of which had never been analyzed using modern genetic methods.
The LSU Museum of Natural Science possesses one of the largest collections of animal samples anywhere in the United States, many in this formalin-based wet sample form.
“LSU is really lucky, we’re one of a handful of university-based natural history museums,” Austin said.
The idea came from Austin’s research in Papua New Guinea related to green-blooded reptiles, a genetic anomaly that Austin has received a National Science Foundation grant to study.