Ancient RNA: A Whole New World of Possibilities for Paleopathology?

imgres-3I just wrote a piece for BiteSize Bio called Ancient RNA: Does Next Generation Sequencing Offer a New Window into the Past?

In it, I describe an article by Fordyce et al that came out earlier this year in PLoS ONE: Deep Sequencing of RNA from Ancient Maize Kernels. This group of researchers was able to obtain RNA sequences from 700-year-old corn kernels. Neat, right? I was really surprised that this paper didn’t get more attention when it came out. I think it’s basically been taken for granted that studying ancient RNA just isn’t possible, due to RNA’s fragility–so a paper showing that aRNA studies may actually be feasible was pretty exciting in my opinion.

Tom Gilbert, the senior author of the article, told me they have encountered some skepticism regarding the results, because the idea that RNA can’t survive over long periods of time has become so ingrained. Maybe that’s why there hasn’t been more chatter. I thought the paper was pretty thorough, though, in ruling out issues such as contamination. I have to say–I’m a believer so far!

Which leads me to wonder… if you can amplify ancient RNA from ancient corn kernels, is it also possible to do so using other types of samples? Tooth pulp, for example, which should also provide a relatively protected environment? If so, perhaps we could look at infection with RNA viruses (e.g., coronaviruses, influenza, hep C) in times past. Or maybe even gene expression under various conditions. The possibilities seem endless! I’m really curious to see where this line of research goes. Is this just the beginning?

The 2013 take on the hobbits of Flores

tumblr_lkg5geJMhG1qagynuo1_500When the first “hobbit” or Homo floresiensis skeleton was found in 2003 in a cave on the island of Flores, it made headlines around the world. But it didn’t take long for the arguing to begin. Did this small skeleton represent a whole new kind of hominin? A petite species that was still around as recently as 12,000 YBP, long after the Neandertals had disappeared? Or was it just the remains of some poor soul with a severe pathology? Scientists tossed around all sorts of ideas about which disorders could result in a person growing to only about a meter tall, with a tiny skull and a curious resemblance to Homo erectus. An Indonesian paleoanthropologist named Teuku Jacob was one of the first scientists who suggested the skeleton could belong to someone suffering from microcephaly. Soon after the remains were discovered, he “borrowed” them, taking them from the center where they were kept and bringing them to his own laboratory. This caused an uproar. Eventually, he returned the hobbit remains to the researchers who found them, but they had been severely damaged. Among other things, the pelvis was smashed and several important bones were missing. As if that wasn’t bad enough, in 2005, Indonesia forbade researchers access to the cave where the hobbit was found. It wasn’t until Jacob’s death a couple of years later that research there was allowed to resume. And the colorful history of the hobbit finds doesn’t end there. Maciej Henneberg, Robert Eckhardt, and John Schofield self-published a book called The Hobbit Trap, in which they called into question the status of the hobbit as a new species. One of their objections was that the teeth showed signs of modern dental work, a claim Peter Brown (one of the hobbit’s discoverers) understandably called “complete lunacy.” Nevertheless, this claim enjoyed a lot of attention from the media. Some people have even speculated that species like H. floresiensis may still be hidden away in remote corners of the world–apparently, rumors of tiny people abound in Indonesia, and in particular, on Flores. I wish we lived in a world where finding another hominin tucked away somewhere seemed like a real possibility!

When the Flores remains were found, the hypothesis that they could have resulted from microcephaly or cretinism was reasonable. After all, when the first Neandertal remains found, people thought maybe they belonged to a Cossack soldier with rickets. In the case of  the hobbit, as in the case of that first Neandertal, there was just the one skeleton–and it’s hard to be sure about a new species designation from a single set of bones. But in-depth study of the skull recovered from the cave demonstrated that its features resembled those of archaic humans. And comparisons to skulls of people suffering from the proposed disorders showed that there wasn’t a good match. Eventually nine tiny sets of remains spanning 3,000 years were discovered in the cave, providing pretty strong evidence that the original find didn’t belong to an isolated individual suffering from a disease. And, early this year, a team of researchers showed that two different Homo floresiensis specimens had wrist bones distinct enough from ours to warrant a separate species designation.

homo-floresiensis-stegodon-florensis-insularisWhat else do we know about the hobbits? Researchers think their short stature may have resulted from “island dwarfism,” a tendency of species to shrink over many generations once they have arrived on an island. A study published this April in Proceedings of the Royal Society by Yousuke Kaifu and colleagues suggests that this idea is reasonable and that the process could have resulted in the hobbit’s body plan. We don’t know much about what life was like for the hobbits, but it may not have been so different from what Homo sapiens were doing around the same time. Possible evidence of stone tools and cooking has been found in their cave. Some scientists believe that a volcanic eruption on Flores may have wiped out both the hobbits and the island’s Stegodon, a species of dwarf, elephant-like creatures that the hobbits liked to hunt. Although Svante Paabo has worked magic in the past, teasing the Neandertal and Denisova genomes out of ancient remains, no one has been able to coax usable DNA from the hobbit remains yet. I am hopeful that the future will reveal additional Hobbit specimens, though, and that one of them may yield DNA suitable for sequencing. Maybe we will find that, like the Denisovans and the Neandertals, hobbit genes live on in us. Wouldn’t THAT be exciting?