Modern technology can help solve an ancient puzzle, the Dead Sea Scrolls, parchments that have disintegrated into a confusion of fragments. Ever since the Dead Sea Scrolls were discovered, scholars have tried to piece together the fragments as though they were jigsaw puzzle pieces. This approach, however, failed to clarify many fragment relationships. Consequently, in a recent study, scientists decided to follow a paleogenomic approach. That is, they used DNA sequencing to establish the genetic signatures for the scroll materials made of animal skins.

In this study, scientists representing Tel Aviv University, Uppsala University, Weill Cornell Medicine, and other institutions extracted the DNA left by the animals that were used to make the parchments. Then, using a forensic-like analysis, the scientists worked to establish the relationship between the pieces based on that DNA evidence and on scrutiny of the language within the texts under investigation.

“The discovery of the 2000-year-old Dead Sea Scrolls is one of the most important archaeological discoveries ever made,” said Oded Rechavi, PhD, associate professor at Tel Aviv University. “However, it poses two major challenges: first, most of them were not found intact but rather disintegrated into thousands of fragments, which had to be sorted and pieced together, with no prior knowledge on how many pieces have been lost forever, or—in the case of nonbiblical compositions—how the original text should read. Depending on the classification of each fragment, the interpretation of any given text could change dramatically.”

The second challenge is that most of the scrolls were acquired not directly from eleven Qumran caves near the Dead Sea but through antiquity dealers. As a result, it’s not clear where many of the fragments came from in the first place, making it that much more difficult to put them together and into their proper historical context.

The new study, however, indicates that “genetic sorting” has been used to illuminate the textual relationships and historical implications of the Dead Sea Scrolls. Details appeared in the journal Cell, in an article titled, “Illuminating Genetic Mysteries of the Dead Sea Scrolls.”

“Here we show that a paleogenomic approach can shed new light on a range of issues pertaining to Dead Sea Scroll history, including the compositional history of the biblical book of Jeremiah, the dissemination of the Songs, and the provenience of the scrolls at large,” the article’s authors wrote. “Because most of the scrolls were written on processed animal skin, we used DNA sequencing to ‘fingerprint’ (or ‘genotype’) fragments based on their genetic signature. The genetic evidence suggests that the manuscripts found in the Qumran caves reflect the scribal and textual diversity that prevailed in this period with regard to transmission of scriptural and nonscriptural literature.”

Despite the antiquity and degraded state of most scrolls, the study’s authors were hopeful that their approach would succeed. They were aware that 20 years ago, other researchers had shown that it is possible to amplify animal DNA from the Dead Sea Scrolls using PCR. Following this study and more recent studies, the authors used deep sequencing and found that the samples of scroll material they obtained contained workable levels of DNA.

The DNA sequences revealed that the parchments were mostly made from sheep, which wasn’t known. The researchers then reasoned that pieces made from the skin of the same sheep must be related, and that scrolls from closely related sheep were more likely to fit together than those from more different sheep or other species.

The researchers stumbled onto an interesting case in which two pieces thought to belong together were in fact made from different animals—sheep and cow. It suggested they don’t belong together at all. The most notable example came from scrolls that comprise different copies of the biblical, prophetic book of Jeremiah, which are also some of the oldest known scrolls.

“Analysis of the text found on these Jeremiah pieces suggests that they not only belong to different scrolls, they also represent different versions of the prophetic book,” said Noam Mizrahi, PhD, a scholar at Tel Aviv University and one of the corresponding authors of the current study. “The fact that the scrolls that are most divergent textually are also made of a different animal species is indicative that they originate at a different provenance.”

Most likely, he explained, the cow fragments were written elsewhere because it wasn’t possible to raise cows in the Judean desert. The discovery also has larger implications. The researchers write that the fact that different versions of the book circulated in parallel suggests that “the holiness of the biblical book did not extend to its precise wording.” That’s in contrast to the mutually exclusive texts that were adopted later by Judaism and Christianity, they noted.

“This teaches us about the way this prophetic text was read at the time and also holds clues to the process of the text’s evolution,” Rechavi said.

Other highlights include insight into the relationship among different copies of a nonbiblical, liturgical work known as the Songs of the Sabbath Sacrifice, found in both Qumran and Masada. The analysis shows that the various copies found in different Qumran Caves are closely related genetically, but the Masada copy is distinct. The finding suggests that the work had a wider currency in the period.

“What we learn from the scrolls is probably relevant also to what happened in the country at the time,” Mizrahi said. “As the Songs of the Sabbath Sacrifice foreshadows revolutionary developments in poetic design and religious thinking, this conclusion has implications for the history of Western mysticism and Jewish liturgy.”

The evidence also confirmed that some other fragments of uncertain origin likely came from other places and not the Qumran caves. In one case, the DNA evidence suggests a fragment from a copy of the biblical book of Isaiah—one of the most popular books in ancient Judea—likely came from another site, which suggests to the researchers the potential existence of an additional place of discovery that still awaits identification.

Although the DNA evidence adds to understanding, it can only “reveal part of the picture and not solve all the mysteries,” Rechavi noted. The researchers had to extract DNA from tiny amounts of materials—what they refer to as scroll “dust” in certain cases—and say there are also many scrolls that have yet to be sampled and others that can’t be, for fear it might ruin them.

Nevertheless, the researchers hope that more samples will be tested and added to the database to work toward a more complete Dead Sea Scroll “genome.” They now think they can apply the same methods to any ancient artifact that contains enough intact DNA or perhaps other biological molecules.

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