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A new perspective on the genomes of archaic humans

Picture of a skull.

Researchers performed a more detailed comparison of the genomes of modern and archaic humans and found that the way genes turned on and off could have resulted in changes in the brain and vocal tract.

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Apr 27 2021

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Research, Faculty

Researchers examined 14,000 genetic differences between modern humans and our most recent ancestors at a new level of detail. They found that differences in gene activation – not just genetic code – could underlie evolution of the brain and vocal tract.

A genome by itself is like a recipe without a chef – full of important information, but in need of interpretation. So, even though we have sequenced genomes of our nearest extinct relatives – the Neanderthals and the Denisovans – there remain many unknowns regarding how differences in our genomes actually lead to differences in physical traits.

“When we’re looking at archaic genomes, we don’t have all the layers and marks that we usually have in samples from present-day individuals that help us interpret regulation in the genome, like RNA or cell structure,” said David Gokhman, a postdoctoral fellow in biology at Stanford University.

Researchers performed a more detailed comparison of the genomes of modern and archaic humans and found that the way genes turned on and off could have resulted in changes in the brain and vocal tract. Their work, published April 22 in eLife, focused on sequences related to gene expression – the process by which genes are activated or silenced, which determines when, how and where DNA’s instructions are followed. Gene expression tends to be the genetic detail that determines physical differences between closely related groups.

“It just seems so implausible that you could make a call like, ‘I think the voice box evolved,’ from the information we have,” said Dmitri Petrov, the Michelle and Kevin Douglas Professor in the School of Humanities and Sciences, who is co-senior author of the paper with Gokhman and Nadav Ahituv, a professor of bioengineering at UCSF. “The predictions are almost science fiction. If five years ago, somebody told me that this would be possible, I would not have put much money on it.” Petrov is a member of Stanford Bio-X and the Maternal & Child Health Research Institute (MCHRI), and an affiliate of the Stanford Woods Institute for the Environment.

Hunter Fraser, associate professor of biology at Stanford, and Fumitaka Inoue (UCSF) is a co-author of the paper. Fraser is also a member of Stanford Bio-X, the Maternal & Child Health Research Institute (MCHRI) and the Stanford Cancer Institute.