How our DNA differs from that of Denisovans, our extinct cousins

Scientists recently reported they had pieced together a high-quality sequence of an archaic human relative, the Denisovans.

Among other things, the researchers took a close look at the ways in which we differ from these people, who were named after the place where their traces were discovered: Denisova Cave in the Altai Mountains of Siberia.

Here’s a little more about the things the scientists found that didn’t make it into the article about the Denisovan genome we published Thursday.

It’s “fascinating” to see the DNA changes that spread to most or all modern humans since our line split off from that of the Denisovans and the Neanderthals, said senior author Svante Paabo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. It’s like taking a look at the last steps in human evolutionary history.

“The amazing thing to me is that [it is] not an astronomically long list,” he said at a press conference on Wednesday.

The tally:

About 100,000 places where single nucleotides -- the individual building blocks of DNA -- have changed, so that one type of nucleotide has been swapped out for another.

About 10,000 places where a piece of DNA has been lost, or a new bit added.

Most of the changes will make no difference to the structure of proteins our genomes carry codes for. But the scientists identified 260 changes that would alter a protein’s form by changing one of the amino acids it contains.

Boring down even further, the researchers found 23 amino-acid changes that we have but Denisovans and monkeys and apes don’t have. These might be especially likely to be important in making us who we are, Paabo said.

“It’s quite interesting to me that eight have to do with brain function and brain development ... and some of them have to do with genes which, for example, can cause autism when the genes are mutated,” he said.

That these genes affect the way nerves wire up is interesting because enlargement of the brain happened quite early -- Neanderthals already had large heads -- so alterations in connectivity could have a big part to play in the modern human ability to create large, complicated societies and rich culture, Paabo said.

And the autism-linked genes are interesting because a lot of what it takes to get by in human society, with all its politics and manipulation, has to do with being able to “read” the likely feelings of others, to get inside the head of another person.

Not that it will be easy to track down the crucial alterations. “Unfortunately,” Paabo said, “at the moment we know too little about the genome to really say what these things mean.”

Adding to the complexity, some key changes may have nothing to do with altered protein structure. They will affect how different genes turn on and off -- in what cells, and at what moments in time. Scientists know that such changes in so-called gene expression can have large effects on the development and function of a creature and have had important parts to play in evolution.

But they are harder to identify based on scientists’ current state of knowledge, says John Hawks of the University of Wisconsin in Madison, who wasn’t an author of the paper.

“The first strategy is to look at what you can see,” Hawks says.

The Denisovan sequence was reported this week in the journal Science.

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