Web address:
http://www.sciencedaily.com/releases/2011/01/
110126131536.htm
Orangutan DNA More Diverse Than Human's, Remarkably Stable Through the Ages
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In the Malay language, orang-utan means "man of the forest." Washington
University scientists led an international project to sequence the orangutan
genome. The work is expected to aid conservation efforts and the study of human
evolution. (Credit: Perry van Duijnhoven/Carel van Schaik)
ScienceDaily (Jan. 26, 2011) 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.
Now, an international team of scientists, led by Washington University School
of Medicine in St. Louis, has decoded, or sequenced, the DNA of a Sumatran
orangutan. With this genome as a reference, the scientists then sequenced the
genomes of five additional Sumatran and five Bornean orangutans.
Their research, published Jan. 27 in Nature, reveals intriguing clues about the
evolution of great apes, including humans, and showcases the immense genetic
diversity across and within Sumatran and Bornean orangutans. Diversity is
important because it enhances the ability of populations to stay healthy and
adapt to changes in the environment.
"The average orangutan is more diverse -- genetically speaking -- than the
average human," says lead author Devin Locke, PhD, an evolutionary geneticist
at Washington University's Genome Center. "We found deep diversity in both
Bornean and Sumatran orangutans, but it's unclear whether this level of
diversity can be maintained in light of continued widespread deforestation."
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 human genome possesses about 5,000 human-specific Alus, while the chimp has
about 2,000 chimp-specific Alus.
"In the orangutan genome, we found only 250 new Alu copies over a 15
million-year time span," Locke says. "This is the closest thing we have to a
smoking gun that may explain the structural stability in the orangutan genome."
The initial Sumatran orangutan genome was sequenced using legacy technology and
cost $20 million to complete. Using more sophisticated technology, the cost of
sequencing the additional orangutans dropped substantially to about $20,000
each. The project was funded by the National Human Genome Research Institute,
the National Science Foundation and other organizations.
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.
But 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."
The research was funded by the National Human Genome Research Institute with
further support from the National Institutes of Health, National Science
Foundation, David and Lucile Packard Foundation, Cornell University Provost's
Fellowship, United Kingdom Medical Research Council, Marie Curie Fellowship,
Ministerio de Ciencia e Innovación-Spain (MCI-Spain) and Fundación M. Botín,
MCI-Spain, Spanish National Institute for Bioinformatics (INAB) and the
Fundação para a Ciência e a Tecnologia, PRIN and CEGBA, and the Commission of
the European Communities.
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Story Source:
The above story is reprinted (with editorial adaptations by ScienceDaily
staff) from materials provided by Washington University School of Medicine. The
original article was written by Caroline Arbanas.
Journal Reference:
1. Devin P. Locke, LaDeana W. Hillier, Wesley C. Warren, Kim C. Worley,
Lynne V. Nazareth, Donna M. Muzny, Shiaw-Pyng Yang, Zhengyuan Wang, Asif T.
Chinwalla, Pat Minx, Makedonka Mitreva, Lisa Cook, Kim D. Delehaunty, Catrina
Fronick, Heather Schmidt, Lucinda A. Fulton, Robert S. Fulton, Joanne O.
Nelson, Vincent Magrini, Craig Pohl, Tina A. Graves, Chris Markovic, Andy Cree,
Huyen H. Dinh, Jennifer Hume, Christie L. Kovar, Gerald R. Fowler, Gerton
Lunter, Stephen Meader, Andreas Heger, Chris P. Ponting, Tomas Marques-Bonet,
Can Alkan, Lin Chen, Ze Cheng, Jeffrey M. Kidd, Evan E. Eichler, Simon White,
Stephen Searle, Albert J. Vilella, Yuan Chen, Paul Flicek, Jian Ma, Brian
Raney, Bernard Suh, Richard Burhans, Javier Herrero, David Haussler, Rui Faria,
Olga Fernando, Fleur Darré, Domènec Farré, Elodie Gazave, Meritxell Oliva,
Arcadi Navarro, Roberta Roberto, Oronzo Capozzi, Nicoletta Archidiacono,
Giuliano Della Valle, Stefania Purgato, Mariano Rocchi, Miriam K. Konkel,
Jerilyn A. Walker, Brygg Ullmer, Mark A. Batzer, Arian F. A. Smit, Robert
Hubley, Claudio Casola, Daniel R. Schrider, Matthew W. Hahn, Victor Quesada,
Xose S. Puente, Gonzalo R. Ordoñez, Carlos López-Otín, Tomas Vinar, Brona
Brejova, Aakrosh Ratan, Robert S. Harris, Webb Miller, Carolin Kosiol, Heather
A. Lawson, Vikas Taliwal, André L. Martins, Adam Siepel, Arindam RoyChoudhury,
Xin Ma, Jeremiah Degenhardt, Carlos D. Bustamante, Ryan N. Gutenkunst, Thomas
Mailund, Julien Y. Dutheil, Asger Hobolth, Mikkel H. Schierup, Oliver A. Ryder,
Yuko Yoshinaga, Pieter J. de Jong, George M. Weinstock, Jeffrey Rogers, Elaine
R. Mardis, Richard A. Gibbs, Richard K. Wilson. Comparative and demographic
analysis of orang-utan genomes. Nature, 2011; 469 (7331): 529 DOI:
10.1038/nature09687
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Washington University School of Medicine (2011, January 26). Orangutan DNA more
diverse than human's, remarkably stable through the ages. ScienceDaily.
Retrieved January 27, 2011, from http://www.sciencedaily.com
/releases/2011/01/110126131536.htm
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