The team found that the Christmas Island rat genome mapped to about 95 percent of the Norway brown rat genome. Further analyses showed that the roughly 5 percent that was missing could not be explained solely by a flaw in the technique or an inadequate reference genome. Rather, because of evolutionary divergence between the two species, most of that genetic information was simply lost. Gilbert said old DNA was like a book that has gone through a shredder, while the genome of a modern species is like an intact "reference book" that can be used to piece together the fragments of its degraded counterpart.

SAMN05425704 (NZ2), SAMN05425705 (SG1) SAMN05425706 (SG2), SAMN05425709 (NZ1), SAMN05425641 (WH1), SAMN05425642 (WH2), and SAMN05425643 (WH3). Gilbert admitted that, while the science was fascinating, he had mixed feelings on de-extinction projects. The team used brown rats, commonly used in lab experiments, as the modern reference species, and found they could reconstruct 95 percent of the Christmas Island rat genome.By doing these kinds of analyses, which is not hard to do, you can at least come up with the what will you get, what will you not get, and you can use that to decide is it worth doing,” Gilbert says. Instead of focusing on iconic species like the woolly mammoth or the Tasmanian tiger, a team of paleogeneticists have studied how, using gene editing, they could resurrect the humble Christmas Island rat, which died out around 120 years ago. This may be a story written for kids, but there is a lot to take away for adults. I found myself thinking about the story and meanings that could be found in the plot. Even if gene-editing were perfected, replica animals created with the technique would thus have certain critical deficiencies.

The reference assembly problem will always be a barrier to de-extinction,” Novak says. “Anyone pursuing de-extinction has to settle on the fact that we want to get as close as we can to something that fools the environment.” The rat is named after Captain John Maclear (1838–1907) of the British survey-ship HMS Flying-Fish, who collected the specimen from Christmas Island in 1886. It was described as a new species by Oldfield Thomas the next year, although it was originally described under the genus Mus. [2] [7] Maclear was earlier commander on HMS Challenger for the Challenger Expedition of 1872–1876 under its commission captain, Sir George Nares. CRX019583 (Mali), CRX019522 (Cambodia5), CRX019633 (China1), CRX019515 (AH1), CRX019516 (AH2), CRX019517 (BJ1) and CRX019639 (SD1) To get the extinct rat’s genome, Gilbert and his colleagues took ancient DNA from two preserved skin samples of the Christmas Island rat. Ancient DNA, extracted from specimens that died anywhere from a few decades to thousands of years ago, is far from perfect ( SN: 5/19/08). Gilbert describes an extinct species’ genome as a book that has been shredded. One way to reconstruct this shredded book is to scan the fragments and compare them with a reference.

I am not doing de-extinction, but I think it's a really interesting idea, and technically it's really exciting," senior author Tom Gilbert, an evolutionary geneticist at the University of Copenhagen, told AFP. This has important implications for de-extinction efforts, such as a project by US bioscience firm Colossal to resurrect the mammoth, which died out around 4,000 years ago. His interest in Christmas Island rats was piqued when a colleague studied their skins to look for evidence of pathogens that caused their extinction around 1900. The two species diverged around 2.6 million years ago: close in evolutionary time, but not close enough to fully reconstruct the lost species' full genome.

With an intact copy of the original book, someone could theoretically reconstruct the book perfectly. When identifying a reference genome, researchers look for a species that diverged evolutionarily from the extinct species fairly recently —in other words, a very similar book. The genomes will match closely, but not perfectly. Wyatt KB, Campos PF, Gilbert MT, Kolokotronis SO, Hynes WH, etal. (2008). "Historical mammal extinction on Christmas Island (Indian Ocean) correlates with introduced infectious disease". PLOS ONE. 3 (11): e3602. Bibcode: 2008PLoSO...3.3602W. doi: 10.1371/journal.pone.0003602. PMC 2572834. PMID 18985148. With the advent of gene-editing technology such as CRISPR, scientists have shifted from cloning to genetic engineering as the most promising method for “de-extinction,” or the resurrection of species that have died out ( SN: 10/7/20). But unlike cloning, genetic engineering wouldn’t create an exact replica of an extinct species. Instead, the technique would edit an existing animal’s genome so that it resembles that of the desired extinct animal. The challenge is making that proxy as similar to the extinct species as possible. Mammoths have roughly the same evolutionary distance from modern elephants as brown rats and Christmas Island rats. a b Thomas, Oldfield (1887). "Report on a Zoological Collection made by the Officers of HMS Flying-Fish at Christmas Island, Indian Ocean. Communicated by Dr. A. Gunther, VPZS, Keeper of the Zoological Department, British Museum". Proceedings of the Zoological Society of London: 513–514.For that reason, the Christmas Island rat ( Rattus macleari) was an obvious choice for analysis for the scientists. It diverged from a close relative, the Norway brown rat ( Rattus norvegicus), only around 2.6 million years ago.

Flannery, Tim & Schouten, Peter (2001). A Gap in Nature: Discovering the World's Extinct Animals. Atlantic Monthly Press, New York. ISBN 978-0-87113-797-5.In other words, a de-extinct mammoth created using gene editing, if such a thing ever comes to be, won’t exactly be a mammoth; it will be closer to a hairy Asian elephant adapted to live in the cold. And the new analysis suggests that the proxy animal version will probably have enough differences that would make it difficult for the creature to refill its previous ecological niche. For some, that might be enough to defeat the purpose of the exercise. As a science, it’s awesome,” Gilbert says. But “is this the best use of the money in a world where we can’t keep our rhinos alive?”