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Newly Sequenced Bonobo Genome Offers Evolutionary Clues

NEW YORK (GenomeWeb News) – An international team reported online today in Nature that it has sequenced the genome of the bonobo, the last great ape to have its genome sequence deciphered.

Using this reference sequence, along with additional sequence data for 19 more bonobos or chimpanzees, the researchers went on to not only characterize the bonobo genome itself, but to do comparative analyses on the bonobo, chimpanzee, and human genomes.

Along with new clues about the evolutionary history of humans and African apes, the work is laying the groundwork for more detailed studies on the genetic features that underlie specific behaviors and traits of interest. Such analyses should be possible, in part, using information on sequences that are especially similar between humans and one of the two apes, researchers explained.

For instance, while the current study confirmed that chimps and bonobos are more closely related to one another than they are to humans, it also revealed stretches of sequence in the human genome where humans are more closely related to one of the two ape species than they are to one another.

Such sequences, found in over 3 percent or more of the human genome, "can be used to illuminate the population history and selective events that affected the ancestor of bonobos and chimpanzees," senior author Svante Pääbo, director of the evolutionary genetics department at the Max Planck Institute for Evolutionary Anthropology, and colleagues explained.

Bonobos are African apes found in the Democratic Republic of Congo, south of the Congo River that divides north the country's north and south. The bonobo species, Pan paniscus, is most closely related to the chimpanzee, P. troglodytes, the study's authors explained, and together the two species represent humans' closest living relatives.

But, researchers explained, the shared evolutionary history of chimpanzees and bonobos belies important differences in the animals' range, social organization, and behavior. For instance, whereas bonobos are known for their playfulness and pronounced sexual behavior, chimpanzees are generally more aggressive and competitive.

"[C]himpanzees and bonobos each possess certain characteristics that are more similar to human traits than they are to one another's," the researchers wrote. "No parsimonious reconstruction of the social structure and behavioral patterns of the common ancestor of humans, chimpanzees, and bonobos is therefore possible."

Moreover, they speculated that this ancestor "may in fact have possessed a mosaic of features, including those now seen in bonobo, chimpanzee, and human."

In an effort to explore ape evolution and improve their view of this shared ancestor, the researchers started by generating a bonobo reference genome using DNA from a female bonobo named Ulindi from a zoo in Leipzig.

The team's subsequent analyses suggest that this 2.7 billion base sequence, generated with Roche 454 technology, contains two errors per 10,000 bases. The overall bonobo assembly appears to be on par with the quality of the chimpanzee reference genome.

To aid in their subsequent analyses, researchers also used the Illumina GAIIx to do low coverage genome sequencing on another 19 animals, including three more bonobos and 16 chimpanzees from different populations in Africa. The latter included two western chimpanzees, 14 eastern chimpanzees, and 14 central chimpanzees.

Overall, the results support the notion that the ancestors of bonobos and chimpanzees split from one another in central Africa around 1 million years ago, a few million years after the divergence of human ancestors from the lineage.

Unlike some other primates, which carry genetic evidence of historical intermixing with related species, patterns in the bonobo genome do not point to hybridization between bonobos and chimpanzees after the species split from one another.

Indeed researchers suspect that the same division in territory that led to the speciation event — the formation of the Congo River between 1.5 and 2 million years ago — also kept the species separated from one another, preventing such interbreeding.

Consistent with a relatively recent split between bonobos and chimps, the researchers found that bonobo reference genome was 99.6 percent identical to that of chimpanzee, showing slightly less identity with human genome sequences — around 98.7 percent.

Even so, their analyses uncovered examples of human and bonobo sequences that are more similar to one another than to the corresponding sequences in the chimpanzee genome. Likewise, in other parts of the genome, humans and chimpanzees share more sequence similarities than do chimpanzees and bonobos.

All told, more than 3 percent of the human genome appears to be more closely related to one of the two great ape genomes than they are to one another, a pattern that the study's authors attribute to so-called incomplete lineage sorting.

In particular, 1.6 percent of the human genome appears especially similar to the bonobo sequence and 1.7 percent of the human genome shows greater-than-usual resemblance to the chimp genome.

Researchers have yet to tease apart how these genetic similarities and differences relate to the behavioral patterns found in bonobos, chimpanzees, and humans, though they were able to make inferences about the shared Pan ancestor, including effective population size and regions of the genome that were subject to selection pressure.

Down the road, the study authors are optimistic that sequences associated with incomplete lineage sorting in humans, bonobos, and chimps will make it possible to tease apart the genetic features underlying specific features and behaviors, particularly since roughly a quarter of human genes seem to contain sequences stemming from these events.