Extinct Christmas Island Rat Genome Sequenced; Plans for De-Extinction
The genome diverges just 4.85 percent from modern Norway brown rats.
We have since built museums to celebrate the past, and spent decades studying prehistoric lives. And if all this has taught us anything, it is this: no species lasts forever.
— Kenneth Branagh
Woolly mammoth de-extinction efforts often grab headlines, while less conspicuous animals fly under the radar. A study published today marks an important step towards bringing back the Christmas Island rat, eradicated from the earth about 120 years ago.
Christmas Island is a small, Australian island about 130 square kilometers in size. It lies 2,600 kilometers northwest of Perth, Australia and just 350 kilometers south of Java and Sumatra, in Indonesia.
The first European spotted the island in 1615, but Torres Strait Islanders, indigenous peoples, already lived there. Europeans settled there in the 1800s. They brought black rats. Those rats spread disease. The local rats — Rattus macleari — went extinct around 1900.
The first step to any de-extinction effort, that herculean goal of re-creating what has ceased to exist, is to piece together the extinct animal’s genome, letter by letter.
Woolly mammoths went extinct about 4,000 years ago, but many carcasses (some with oozing blood and “fresh” tissue) have been unearthed from melting permafrost across Siberia in recent years. Collecting and sequencing that tissue has proven pivotal for reconstructing the mammoth genome. The ultimate goal is to reconstruct the genome and then transplant it into an embryo. The embryo would then be implanted into a female elephant, where it could develop, grow, emerge.
For the new study, published in Current Biology, researchers sequenced genomes from the extinct Christmas Island rats, using taxidermic samples stored in the Oxford University Museum of Natural History. The extinct genome is highly similar to that of the Norwegian brown rat. Still, about five percent of the ‘ancient’ genome was entirely unrecoverable.
“It is very, very clear that we are never going to be able to get all the information to create a perfect recovered form of an extinct species,” said lead author Tom Gilbert, professor of evolutionary genomics at the University of Copenhagen, according to a Cell press release. “There will always be some kind of hybrid.”
The researchers already have plans to recreate the genome and fill in missing gaps, using CRISPR. Rebuilding the extinct rat genome could give researchers a more “laboratory-friendly” animal with which to hone their de-extinction methods, prior to moving ahead on mammoths.
DNA was extracted from “two dry preserved skin samples” that were “originally collected between 1900-1902 and held as part of the Oxford University Museum of Natural History collections,” according to the study.
The extinct Christmas Island rat’s genome was sequenced with >60x coverage.
Compared to the Norway brown rat (R. norvegicus), about five percent of the Christmas Island rat genome were completely unrecoverable.
An additional 1,600 genes were “recovered at lower than 90 percent completeness,” according to the study, and 26 genes were missing entirely.
The genes with missing information tend to be overrepresented in olfaction and immune response functions. Should this genome be used to “de-extinct” the Christmas Island rat, then, those missing genes would need to be added-in from the Norwegian rat genome.
“With current technology, it may be completely impossible to ever recover the full sequence,” Gilbert said for the press release, “and therefore it is impossible to ever generate a perfect replica of the Christmas Island rat.”
Next steps: Gilbert said he plans to use CRISPR to edit the black rat genome, and will attempt to change it into a Norway brown rat genome. If that proves successful, the gene-editing tools necessary for de-extinction could be applied to the Christmas Island rat.