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Gorilla Genome Analysis Reveals New Details of Great Ape Evolution

By Andrea Anderson

NEW YORK (GenomeWeb News) – An international research team led by investigators at the Wellcome Trust Sanger Institute has sequenced and started analyzing the gorilla genome, using it to better understand gorilla biology and the evolutionary history of great apes.

As they reported online today in Nature, the researchers sequenced the genome of a female western lowland gorilla — Gorilla gorilla gorilla — and compared it with the genomes of great apes sequenced previously: humans, chimpanzees, and orangutans. Along with the reference genome, the team also looked at sequence data for three other gorillas, two more from the western gorilla species and one from a lowland population of the eastern gorilla species.

Genetic patterns in those additional gorilla representatives "allow us to see more recent evolutionary events that have taken place within gorillas, understand some of the pressures on modern gorillas, and also get a better insight on great ape evolution overall," corresponding author Richard Durbin, joint head of human genetics at the Wellcome Trust Sanger Institute, said during a telephone briefing with reporters.

The gorilla, the last of the living great apes to have its genome sequenced, is generally considered a more distant relative to humans than chimpanzees, with available genetic and fossil evidence pointing to a split between gorilla ancestors and the lineage leading to chimpanzees and humans prior to chimp and human speciation.

But without the genome sequence for the gorilla, details of these evolutionary events have been difficult to discern, researchers explained.

"The gorilla genome is particularly important for our understanding of human evolution because it tells us about this crucial time when we were diverging from our closest living relatives, the chimpanzees," first author Aylwyn Scally, a post-doctoral researcher in Durbin's Sanger Institute lab, said during the press briefing.

Using a combination of Sanger and Illumina sequencing, the researchers sequenced genomic DNA from a female western lowland gorilla known as Kamilah to an average of 30 to 40 times coverage.

Based on comparisons between the gorilla, humans, chimpanzee, orangutan, and macaque genomes, combined with available fossil evidence, the researchers estimated that the human-chimpanzee group diverged from the lineage leading to gorillas an estimated 10 million years ago — around four million years before human and chimpanzees split from one another.

Study authors cautioned that the exact timing of these speciation events is still difficult to determine, since it relies on estimates of past mutation rates.

Overall though, researchers saw that the relatively short time between gorilla-chimpanzee-human and chimpanzee-human divergence events has produced somewhat variable ancestry patterns across the gorilla, chimpanzee, and human genomes.

For instance, they reported, some 15 percent of human genome sequences are more similar to those found in gorilla than chimpanzee, while 15 percent of the chimpanzee genome is more similar to the gorilla than the human genome.

Though the analysis confirmed that humans and chimpanzees are more genetically similar to one another over most of the genome than both are to the more distantly related gorilla, all three share very similar sequences and genes.

"Most of our genes are very similar or even identical to the gorilla version of the same gene," Sanger Institute human evolution researcher Chris Tyler-Smith, a co-author on the study, told reporters. "It's the few that differ that are of particular interest here."

Among the differences detected, the team tracked down examples of gorilla genes that contain variants linked to genetic disease in humans, including a substitution in the growth factor gene PGRN that has been implicated in dementia and a variant in the muscle protein-coding gene TCAP that's been tied to heart failure.

Whereas the variants signal disease in humans, though, in gorilla they appeared to be part of the standard form of the genes, Tyler-Smith noted, adding, "If we could understand more about why those variants are so harmful in humans but not in gorillas, that would have important medical implications."

Other genetic features seem to fit with what's known about gorilla social groups, in which individual males live with groups of females, he said. Consistent with the reduced emphasis on sperm competition in such a setting, the team found inactivations and copy number changes in genes with roles in sperm formation and function.

A gene called EVPL, which contributes to keratin formation on the skin, showed signs of rapid evolution in the gorilla, perhaps related to animal's keratin-rich knuckle pads, the team noted, while other groups of genes showed signs of rapid evolution in the human, chimpanzee, and gorilla.

For instance, gorillas, like humans, seem to have experienced especially rapid evolution in genes related to hearing, researchers reported, a finding that conflicts with the notion that human hearing improved to coincide with the birth of human language.

"It's been known for some time that hearing genes in humans have shown accelerated evolution," Tyler-Smith said. "But what we could see by sequencing the gorilla genome was that this acceleration goes back millions of years and affects hearing genes not only in humans but also in gorillas."

Within gorillas, sequence data from both eastern and western gorilla species indicate that these two species split as recently as within the past one million years, apparently continuing to exchange genetic information for some time after that.

"This fits a broader pattern within the great apes, perhaps even including humans, of populations splitting up, fragmenting, but maintaining some genetic contact," Scally noted.

Researchers will continue using the gorilla genome as a resource for studying great ape evolution and speciation.

They are also interested in sequencing additional gorillas, including representatives from the eastern mountain gorilla population, to get a better sense of the genetic diversity present in gorillas, now found in just a few remaining wild populations in central Africa.