Genomic research advances orang-utan conservation

Dr. Banes shows a blood sample from this orang-utan pictured in the Pongo database.
Graham L. Banes checks a blood sample, collected during a routine veterinary exam, against records in The Orang-utan Conservation Genetics Project’s Pongo database. Pongo tracks every orang-utan in the project, plus about 3,800 biomaterials curated for analysis at the WNPRC. All are being processed using the method described in BMC Genomics. (Photo of Chinta used with permission from the Woodland Park Zoo in Seattle.)

By Jordana Lenon
Jan. 13, 2020

The Orang-utan Conservation Genetics Project, led by Graham L. Banes, associate scientist at the Wisconsin National Primate Research Center, is ramping up. After more than a decade of sample collection and study, Banes and his team have published their standardized method for analyzing orang-utan genomes. Their work is described in a recent publication in the journal BMC Genomics.

In their paper, Banes and his collaborators describe new genomic targets for building pedigrees, inferring ancestry, and for the study of genes that are thought to be linked to disease in orang-utans. The work is co-authored by scientists at Roche Sequencing Solutions, including long-time collaborators of the WNPRC’s Genetics Services Unit, plus by conservation geneticists at Taipei Zoo and by Banes’s post-doc and student at UW-Madison. Capitalizing on a tri-fold discovery approach, combining data from whole genomes, whole exomes and microarrays, the team presented genomic co-ordinates for approximately 177,000 informative targets, plus identified about 152 genes that warrant comparative study between individuals. As opposed to whole-genome sequencing, which is harder to achieve and more expensive, the team’s method allows high-resolution analysis of only the regions that are known or thought to be useful.

Le Shen, a male orang-utan from the Nanjing Hongshan Forest Zoo in Jiangsu province, China.
Using the method published in BMC Genomics, Banes determined that Le Shen of the Nanjing Hongshan Forest Zoo in Jiangsu province, China, was a hybrid Bornean-Sumatran cross. This meant he could be removed from the breeding program. (Photo by G.L. Banes)

“Surviving wild orang-utans are increasingly intensively managed by humans, whether intended or not,” Banes said. “As a consequence, and for decades, we’ve been introducing and inter-breeding orang-utans from wholly different populations that couldn’t naturally meet in the wild, often without even realizing.” Banes hypothesizes that this human interference could be linked to chronic respiratory and cardiovascular diseases, which are yet to be observed in wholly natural populations, as well as to increased rates of infant mortality. “By applying the same methods to every orang-utan we study, we can consistently sequence the same portions of their genomes. That can show us what’s happening at the molecular level when we interfere with evolution.”

Banes first suspected years ago that zoo breeding programs and reintroductions of orang-utans into the wild had caused distinct genetic pools to mix and that this might not be a good thing. These studies formed the basis of his master’s and doctoral theses at the University of Cambridge in England. As a field researcher, he was primarily based in Tanjung Puting National Park in Central Kalimantan, Indonesian Borneo, where he led an orang-utan population census, disentangled their social and sexual behavior, and determined that historical reintroductions have led to hybridization in the wild between subspecies. His discoveries have been featured in The Washington PostScience magazine, and the PBS documentary Sex in the Wild: Orang-utans.

Over 11 years, Banes has amassed more than 3,700 samples from wild, ex-captive and zoo-housed orang-utans globally. These are thought to comprise the largest biomaterials collection in the United States from a critically endangered species – and the collection is growing. The European Association of Zoos and Aquariums recently agreed to partner with Banes, providing DNA from an additional 300 individuals, and significantly expanding the project. All are being analyzed using the same standardized method. Yet when it comes to getting results, Banes is playing the long game: “It could be 10, 20 or 50 years before we have enough data to answer our research questions: we need samples from multiple generations of orang-utan, and they only reproduce once every 8 to 10 years.”

This reintroduced female, pictured carrying her wild-born offspring on her head, was displaced due to oil palm plantations, rescued, then reintroduced into the wild. The Orang-utan Genetics project can help guide reintroductions such as hers. . (Photo by G.L. Banes)
This reintroduced female, pictured carrying her wild-born offspring on her head, was displaced due to oil palm plantations, rescued, then reintroduced into the wild. The Orang-utan Genetics project can help guide reintroductions such as hers. (Photo by G.L. Banes)

So is he feeling the pressure to publish? “Not at all, because we’re in this for the long haul,” explains Banes, who spends much of his time working on other species, including South China tigers and snub-nosed monkeys, and as a mentor for the Undergraduate Research Scholars program. “Our results will have real implications for the management of captive and displaced orang-utans, so we need to be absolutely certain we get this right. That means any recommendations we make have to be supported by solid, longitudinal data. This isn’t science for the sake of doing science: this is science for doing good.”

The research was funded by grants from the Arcus Foundation, the Association of Zoos and Aquariums’ Conservation Grants Fund (with a subaward from the Disney Conservation Fund), The Ronna Noel Charitable Trust, The Eppley Foundation for Research, Inc., The Orang-utan Conservation Genetics Project, Inc., and the National Institutes of Health under Award Number P51OD011106 to the Wisconsin National Primate Research Center, University of Wisconsin–Madison.