Monday Article #25: Orangutan killing us with genome full of surprises

Among great apes, orangutans are humans most distant cousins. These tree dwellers sport a coat of fine reddish hair and have long been endangered in their native habitats in the rainforests of Sumatra and Borneo in Southeast Asia. The Sumatran and Bornean orangutans have been subject to intense population pressure from loss of habitat, deforestation, hunting and disease. A study in 2004 estimated that both species have remained in the wild in fragmented subpopulations.



An international team of scientist from Washington University School of Medicine has sequenced the genome of five Sumatran and Bornean orangutans with a reference genome sequenced from Sumatran orangutan to carry out a diversity study. Their research reveals intriguing clues about the evolution of great apes, including humans, and showcase the immense genetic diversity across and within Sumatran and Bornean orangutans.


*Diversity, is the variation of live forms present in different ecosystems. It’s the most important factor in the ecosystem as it enhances the ability of populations to stay healthy and adapt to changes in the environment.



Figure 1: Divergence among great apes, a small ape, and an Old-World monkey with respect to humans


The analysis of diversity study indicated that the human and chimpanzee lineages had the highest rates of gene turnover among great apes more than twice the rate of the orangutan lineages and even the nucleotide substitution rate decreased. These data strongly suggest that structural evolution proceeded much more slowly along the orangutan species, compared to the chimpanzee and human genomes which showed acceleration of structural variation.


The scientists catalogued some 13 million DNA variations in the orangutans. This valuable resource can help conservationists assess the genetic diversity of orangutan populations both in the wild and in captivity and help set priorities for aiding subpopulations based on their genetic health. The orangutan genome adds detail to the evolutionary tree and gives scientists insights into the unique aspects of human DNA that set man apart from the great apes, their closest relatives. Overall, the researchers found that the human and orangutan genomes are 97 percent identical.


However, in a surprising discovery, the researchers found that at least in some ways, the orangutan genome evolved more slowly than the genomes of humans and chimpanzees, which are about 99 percent similar.

"In terms of evolution, the orangutan genome is quite special among great apes in that it has been extraordinarily stable over the past 15 million years," says senior author Richard K. Wilson, PhD, director of Washington University's Genome Center, which led the project. "This compares with chimpanzees and humans, both of which have experienced large-scale structural rearrangements of their genome that may have accelerated their evolution."


A genome reads much like an instruction book for creating and sustaining a particular species. The chromosomes are the chapters and within every chapter are paragraphs, sentences, words and single letters, which are like the individual bases of the DNA sequence.

If you are editing a book on your computer, you can highlight a paragraph and copy and paste it, delete it or invert it," Wilson explains. "Duplications, deletions and inversions of DNA are types of structural variations. When we look at the genomes of humans and chimps, we see an acceleration of structural changes over the course of evolutionary history. But for whatever reason, orangutans did not participate in that acceleration, and that was a surprise."


One possible clue to the lack of structural rearrangement in orangutan DNA is a profound lack of repetitive "Alu" elements. These short stretches of DNA make up about 10 percent of the human genome and can pop up in unexpected places to create new mutations or genetic rearrangements. The new research shows that the Sumatran and Bornean orangutans diverged some 400,000 years ago. Earlier estimates had put the split at about 1 million years ago. Today, only about 50,000 Bornean and 7,000 Sumatran orangutans still live in the wild. However, in a finding that seems counterintuitive, the researchers found the smaller population of Sumatran orangutans is genetically more diverse than their Bornean cousins.


"It's quite a mystery how Sumatran orangutans obtained this genetic diversity or whether there has been cleansing of diversity in the Borneans," Locke explains. "We can begin to search for answers using the catalog of genetic variation we developed." Studies of orangutans are important because these great apes, in particular, are under intense ecological pressure. Their numbers continue to erode as humans encroach further on their habitat.


"Orangutans spend more than 95 percent of their time in the trees," Locke says. "They travel through the trees, nest in trees and forage for food in trees. But all the genetic diversity in the world can't save them in the wild if their habitat is destroyed."


References

  1. Caccone, A., & Powell, J. R. (1989). DNA divergence among hominoids. Evolution, 43(5), 925-942.

  2. Locke, D. P., Hillier, L. W., Warren, W. C., Worley, K. C., Nazareth, L. V., Muzny, D. M., ... & Wilson, R. K. (2011). Comparative and demographic analysis of orang-utan genomes. Nature, 469(7331), 529-533.

  3. Nater, A., Nietlisbach, P., Arora, N., van Schaik, C. P., van Noordwijk, M. A., Willems, E. P., ... & Kruetzen, M. (2011). Sex-biased dispersal and volcanic activities shaped phylogeographic patterns of extant orangutans (genus: Pongo). Molecular Biology and Evolution, 28(8), 2275-2288.


 

This article is prepared by: Tanessri Muni Peragas


 

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