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Revealing the "mile mark" of the orangutan genome errors may have an impact on orangutan reproductive plans. Image source: Fiona Rogers
Sumatra's female orangutan Susie is the first of her kind to complete genome sequencing. It and other orangutan genome information were published in Nature in 2011, laying the foundation for hundreds of subsequent studies.
But in August this year, researchers found that eight genomic sequences in the paper were misallocated to orangutans. Nature later published a correction from the author of the paper.
However, these mistakes sparked anger on social media. Some scientists warn that these mistakes may have an impact on orangutan breeding plans.
It is not clear how these interchangeable identities information affects orangutan research. But researchers involved in the new analysis believe the finding may highlight some of the scientific community’s problems, namely how these mistakes actually arise in scientific records.
"I think there are such errors in many published papers," said Graham Banes, an evolutionary biologist who worked at the University of Wisconsin-Madison. He led a reanalysis of the 2011 paper. "In a way, we're lucky because it only involves misinformation from orangutans. What if this was a biomedical paper, people developed treatments based on published data?"
"This kind of thing happens easily," added Robert Fulton, a genome scientist at the University of Washington School of Medicine. He is a member of the original essay team and a co-author of the reanalysis. "It is important that the data are now correct." The detailed genome that can be referenced by
is a key tool for biologists to conduct research. In 2017, the Banes team used the genome to study the results of different types of orangutan hybridization. They noticed that some samples had names that did not match the gender reported by the animals.
For example, a 2011 paper reported that an orangutan named Dolly was a male. But in the zoo orangutan record, Dolly is a female. What's even more strange is that Banes found that some genomes marked as males lacked Y chromosome , and there was a series of things that didn't make sense.
Banes team finally found that in the 2011 paper, all other genomes except the genomes of two orangutans, were wrong, and some of the errors seemed to be the result of text input errors. In addition, they found that the ID number given by a male orangutan sample actually corresponds to the sample from African pigs in the tissue library. Other samples appear to have been exchanged identities in the lab.
2011 This research paper helped determine the time when Borneo and Sumatra orangutans differentiate into different species and compared their genomes with those of other primates. These conclusions were largely unaffected by this confusion. But Banes said the errors could have an impact on other studies, including his own.
Banes used genetic data to provide recommendations for captive breeding programs for zoos. He said the zoo tried to avoid captive hybrid orangutan species, partly to mimic wild populations, and hybrid orangutans had high miscarriage rates and birth defects. When reexamining samples from the 2011 paper, the Banes team found that one of the sequences believed to be Sumatra orangutans was actually Borneo orangutan . Unfortunately, the paper mistakenly assigns the genome to other orangutans.
Anthropologist Vincent Nijman of Brooks University in Oxford, UK said zoo administrators must stop breeding the offspring of the orangutan with false genomic information to avoid further hybridization. However, Nijman also believes that these errors have little effect on orangutan protection overall.
Evolutionary geneticist Michael Krützen, a Swiss University of Zurich, also believes that while these errors are "annoying", their impact on downstream research may be minimal. As researchers race to publish papers in high-level journals, he argues that these mistakes may be an example of the “sloppy” work that academia “destroys without publishing” environment has led to “sloppy” work.
Banes agrees that this pressure may cause errors to occur in the paper. But he stressed that scientists cannot be blamed for this, which may weaken future efforts to correct mistakes. "I think any scientist could make these mistakes, but if we all jump out and say, 'Oh my goodness, how could they be so stupid?' Then no one will correct anything. It's harmful to science."
