UW researchers discover orangutan genome mix-ups that could affect zoo animals – Madison.com

UW-Madison scientists studying the genetics of orangutans in zoos were stumped. The lineages they found didnt match those made public when the orangutan genome was sequenced in 2011.

When they pulled a photo for one animal from the 2011 research, supposedly a female, it had cheek pads, a distinctly male trait. In further digging, they learned a label for one orangutan was really for a pig. Another orangutan, marked as Doris from Dallas Zoo, was actually Sibu from Zoo Atlanta.

Things just didnt add up, said Graham Banes, who now directs the Madison-based Orangutan Conservation Genetics Project. Our data just could not reconcile with what had already been published.

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At the same time, the related journal Nature Scientific Data included a paper by Banes and his colleagues detailing their finding that nine of 10 samples in the 2011 research were inadvertently switched.

I was aghast, said Michael Sweet, who researches coral genomes at the University of Derby in England and worries that recent examples of scientific fraud have already increased public skepticism about topics such as climate change. The general public is going to start mistrusting science.

Marc Tollis, whose research at Northern Arizona University involves bioinformatics and genomics, called the orangutan genome mishap a nightmare scenario for almost all scientists.

The revelation about the orangutan research doesnt only raise questions about scientific error, public trust and the validity of subsequent studies based on the genome work. Banes said it has implications for the management of orangutans in zoos, as there is now proof that at least several orangutans in American zoos are from a new third species announced only in 2017. Should they be prevented from breeding with other species, which he argues can increase the risk of disease and birth defects?

This is a really massive problem for zoos, Banes said. If zoos allow different species of the animals to mate freely, at that point, its not a conservation breeding program, he said. Its an experiment.

Rob Vernon, spokesperson for the American Association of Zoos and Aquariums, said the group would review the research and consult with experts for advice. Ronda Schwetz, leader of the associations Orangutan Saving Animals from Extinction program and director of Vilas Zoo in Madison where orangutan Chelsea had a baby in June did not respond to requests for comment.

Devin Locke, lead author of the 2011 genome paper and of the recent correction, could not be reached for comment. Formerly with Washington University Genome Center in St. Louis, which headed up the genome-sequencing project, Locke is now with the Massachusetts-based cancer research company Foundation Medicine, according to his LinkedIn profile.

Sweet, one of numerous scientists who have raised concerns about the new report on social media, is part of a group that published standards on sequencing coral genomes to help prevent such mistakes. He said misconduct recently identified in investigations of a University of Delaware coral scientist and a spider behavior ecologist at McMaster University in Canada have already damaged scientific credibility.

The whole mess (about the orangutan genome) underlines the need for careful curation of genomic data, including checking apparently solid identification in the genomic databases, said Michael Cobb, a zoologist at the University of Manchester in England.

Different species

It wasnt until the 1980s, decades after orangutans were first captured from the islands of Borneo and Sumatra in Southeast Asia for placement in zoos, that two distinct species were identified: Bornean orangutans and Sumatran orangutans.

Interbreeding was discouraged and zoos separated the populations, Banes said.

Graham Banes heads up theOrangutan Conservation Genetics Project, based in Madison, and was part of a research team that discovered orangutan genome mix-ups.

The genome published in 2011 was based on a Sumatran female. Ten other orangutans five identified as Sumatran and five as Bornean were also sequenced in less detail, serving as reference samples of the diversity of orangutan genetics.

The orangutan was the third nonhuman primate genome to be sequenced, after the chimp and the rhesus macaque. The analysis showed humans and orangutans share about 97% of their DNA, compared with 99% between humans and chimps.

Banes, who left UW-Madisons Wisconsin National Primate Research Center in May but still conducts primatology research in Madison, focuses on the effects of inbreeding, or mating between closely related groups, and outbreeding, or mating between divergent groups.

In 2016, his research showed a non-native subspecies of Bornean orangutan, released into Tanjung Puting National Park on Borneo in Indonesia, bred with apes in the park, creating a cocktail hybrid species. One of two non-native females rescued from the pet trade, Siswoyo, had fewer surviving offspring than any other female in the park.

Banes said preliminary data suggest outbreeding may be connected to birth defects he saw among intermixed orangutans at zoos in China and chronic respiratory disease found in some captive orangutans.

It appears theyre ill-adapted to each others novel pathogens, he said.

Science sleuths

In 2018, Banes UW-Madison research team was testing orangutans in U.S. zoos to determine the extent of interbreeding. Graduate student Alyssa Karklus, now a veterinarian with the Wisconsin Humane Society, noticed that the genetics of some animals didnt line up with the reference genomes from 2011.

A female orangutan reintroduced to the wild is pictured carrying her wild-born offspring. UW-Madison researchers found a mix-up in a genome-sequencing research project that could have implications for orangutan-breeding programs at zoos.

Banes and Karklus, along with post-graduate researcher Emily Fountain, became sleuths, sifting through volumes of data and eventually finding that even the sex reported for five animals in the 2011 paper was wrong. Three researchers from Washington University, who participated in the initial genome work, assisted the UW-Madison group and are co-authors of the paper about the mix-ups.

Its not clear who made the mistakes or how, Banes said. The errors likely occurred at several stages, from when samples were collected from animals and labeled in vials to when sequencing data was linked to individuals, he said.

It was probably multiple people, he said. It was a series of unfortunate events.

Banes said hes not out to vilify the genome researchers and is glad they agreed to do the correction. He said his goal is to improve the integrity of science.

Theres no shame in making mistakes. What is critically important is that we correct them, he said. I personally mixed up three samples on Wednesday last week, but I caught it.

Tapanuli orangutans

Banes said one of the switches in the genome samples has implications for managing Tapanuli orangutans the newly discovered third species, from part of Sumatra.

One of the five animals identified as Sumatran in the 2011 paper turned out to be Tapanuli, which scientists wouldnt have been expected to know at the time. But it wasnt Baldy, a long-deceased male animal from the Sacramento Zoo that had only two offspring and no second-generation offspring, as identified by the genome researchers, Banes said. The Tapanuli was Bubbles, from the San Diego Zoo, a female that had eight descendants, some of which are still alive and in zoos, he said.

That led Banes and his colleagues to discover additional Tapanulis in zoos in the U.S. and elsewhere, with studies underway in Europe. He plans to publish a report soon on the extent of Tapanulis found, which he said raises questions for the future of orangutans in zoos.

What are the zoos going to do if 50% of their population now has to be taken out of the breeding program? he asked.

Visitors enter Henry Vilas Zoo on the first day of the reopening since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Deynah Thao, 7, gets a close look at a grizzly bear during a trip to Henry Vilas Zoo on the first day of the reopening of the zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Visitors to Henry Vilas Zoo follow one way walking paths on the first day of the reopening of the zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Visitors stop to see the grizzly bears on the first day of the reopening of Henry Vilas Zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Visitors follow the paw prints as they check out animal exhibits on the first day of the reopening of Henry Vilas Zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Visitors enter Henry Vilas Zoo on the first day of the reopening since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

The first day of the reopening of Henry Vilas Zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Employee Ryan Brockner, right, shows off an umbrella cockatoo named Reggie to visitors Samia Sanders, 4, front, Nazilah Lites, 4, and Miyauna Sanders, 10, on the first day of the reopening of Henry Vilas Zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Nicole Josi Lema, with her daughters Arianna, 7, and Akemi, 5, right, are greeted by Courtney Cordova, educational specialist, as she explains the rules before entering Henry Vilas Zoo on the first day of the reopening since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Employee Debbie Scheffel cleans picnic tables after they are used by guests on the first day of the reopening of Henry Vilas Zoo since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Dan Tortorice, center, sits with his grandchildren, Aria Oettiker, 9, left, and her brother, Anthony, 6, as they eat ice cream during a visit to Henry Vilas Zoo on the first day of the reopening since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

Signs reminding visitors to social distance are seen at Henry Vilas Zoo on the first day of the reopening since it closed due to COVID-19 in Madison, Wis., Thursday, June 18, 2020. AMBER ARNOLD, STATE JOURNAL

The whole (genome) mess underlines the need for careful curation of genomic data, including checking apparently solid identification in the genomic databases.

Michael Cobb, University of Manchester zoologist

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UW researchers discover orangutan genome mix-ups that could affect zoo animals - Madison.com