Scientists Use DNA to Find Our Newest Relatives, the Denisovans

Gone but not Forgotten, Their DNA Lives on in Melanesians

January 6, 2011

Scientists found humankind's newest relative, the Denisovan, by looking at the DNA of a thirty thousand year old fossilized finger from the Denisova Cave in Siberia. This is the first time DNA has been used to discover a new hominid. As scientists get better and better at looking at ancient DNA, they may find additional relatives this way too.

Our newest relative was
identified from the DNA of
a fossilized pinky found
in this cave.

Finding new hominids by looking at DNA has another advantage--scientists can learn whether any of that DNA lives on in modern humans. Scientists had already shown that 1-2% of non-African DNA might have come from Neanderthals. Now it looks like 4-5% of Melanesian DNA may have come from Denisovans.

Apparently before humans wiped out all of their competition, they had children with some of them first. This legacy lives on in modern human DNA.

Looking at the DNA of related hominids is also changing how scientists look at and think about human prehistory. Before scientists could sequence DNA, there were two main theories to explain the fossil evidence.

The Out of Africa theory held that all humans evolved in Africa and then spread out and destroyed any hominid species they found. The multiregional hypothesis proposed that each ethnic group of humans evolved separately.

Looking at the DNA of modern humans pretty much eliminated the multiregional hypothesis. Everyone's DNA is way too similar to have evolved separately.

But it does look like the hominids from different regions of the world may have contributed their DNA to specific human groups. This isn't quite multiregional hypothesis but it does have some of the same consequences. Different groups of humans have small amounts of DNA that evolved in a completely different context.

It will be interesting to see if this "other" DNA contributes to any special traits of certain populations. Or if they are really just markers from human's distant past that no longer do much of anything.

Being able to look at DNA promises to shake up this field like it has nearly every other field in biology. New results with human and, hopefully, hominid DNA are going to be coming in fast and furious as sequencing gets cheaper and cheaper. This won't only help everyone live longer and healthier lives, but it will also help scientists learn about humankind's past and how all humans are related in ways they never would have thought possible.

Out of Africa explained.

Traveling Man

The Out of Africa theory proposes that modern humans broke out of Africa around fifty thousand years ago. Scientists have been able to piece together the path they took by looking at the DNA of various modern human groups.

Humans first went from Africa to the Arabian Peninsula. A group split off and traveled along the southern edge of Asia where there was another split. Some traveled south to Australia and beyond while others went north into China and Russia. Some of this northern group finally got around to traveling to North and eventually South America.

Meanwhile, some of the humans on the Arabian Peninsula headed north and west. These folks went on to populate Europe and central Asia.

The route humans took in their
conquest of the world.

These humans weren't settling empty areas. Instead, they were invading areas already populated by closely related hominids. Humans wiped them all out and took their lands.

But as noted previously, these humans also apparently bred with the hominids they found before killing them all. This mixing of DNA can add a new wrinkle into human prehistory.

Scientists have mostly used modern human DNA to chart out the course of early human migrations. Now they need to contend with the fact that the humans who traveled the southern route to Australia apparently had children with the Denisovans of Siberia.

Either the Melanesian migration was not as simple as believed or the Denisovans were spread out over a wide range of Asia. Right now scientists don't know which is true. More DNA sequencing will help figure this out particularly if fossils can be found closer to the southern route that match the Denisovan DNA.

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Too Little DNA, Too Big a Conclusion

The Out of Africa theory also proposes that Neanderthals' ancestors left Africa around 300-500 thousand years ago. When scientists first got a hold of Denisovan DNA, they concluded in the first study that the ancestors of the Denisovans must have left Africa before those of the Neanderthals. Later sequencing in the second study showed that this was probably incorrect and that most likely, Neanderthals and Denisovans split from the same group after their ancestors left Africa.

The reason for the different interpretations has to do with the DNA the scientists looked at in each case. And frankly with trying to rewrite human prehistory with DNA from a single individual.

When the scientists first extracted some Denisovan DNA, they did what any good scientist would. They sequenced the mitochondrial DNA (mtDNA). This DNA is much easier to look at than other kinds mostly because there is so much more of it in each cell.

Using just the DNA from
mitochodria like these,
scientists came to the
wrong conclusions.

When they compared human, Neanderthal and Denisovan mtDNA, the researchers found that Denisovan mtDNA was very different. So different that Denisovans must have split before humans and Neanderthals did. This is why they concluded that Denisovans must have left Africa even before the Neanderthals.

A few years ago scientists would have had to stop there. The field would go on thinking that the ancestors to these hominids left Africa before those of Neanderthals. The field would be going forward with faulty data.

Luckily scientists can now look at more than mtDNA. When they looked at the rest of the Denisovan DNA, the researchers got a different result.

Now it looked like Denisovans were more closely related to Neanderthals than humans. Which means that there was no need to invoke another group leaving Africa at a different time. The most likely explanation is that the ancestors to Neanderthals and Denisovans left Africa and then split into the two separate groups.

The second study is definitely the one to believe. Nuclear DNA (as all the other DNA is called) is much less likely to be misinterpreted than is mtDNA for many different scientific reasons. These scientists knew this and so probably should not have rushed to the conclusion that another group of hominids had left Africa before Neanderthals. This was premature especially since they made their conclusions based on DNA from a single individual.

Of course this sort of thing does sometimes happen in science. Because of the need for lots of splashy stories, scientists end up concluding more than they should, sooner than they should. And it doesn't help that the popular press tends to play up the sexiest aspect of scientific stories.

The key result was not when Denisovan ancestors left Africa. What was most important and exciting was that scientists had found a new human relative and that they had used DNA to find it. That should have been story enough. The later story could then focus on when the ancestors left Africa and that Denisovan DNA can still be found in modern human DNA.