Ancestry, Neanderthals and Mitochondrial DNA

What the Genographic Project is teaching us about our DNA
The Genographic Project is this cool way to figure out your ancestry. And by ancestry, I don't mean if your great grandmother came from Ireland. I mean it can tell you if your ancestors were one of the original folks to leave Africa 80,000 or more years ago. Or if your great-great (etc.) grandpa was the founder of Europeans. So I'm talking way back. The way the project works is that people send in samples of their DNA and the scientists at the Genographic Project analyze it. Not all of it, just the mitochondrial and/or Y chromosomal DNA. By looking at this DNA, the scientists can figure out which great migration some of your ancestors were in. And possibly localize these ancestors to a general area of the globe. One important byproduct of all of this is that the scientists have amassed a giant database of DNA they can study. As of June 2007, they've collected around 78,590 different samples. This means they can answer some questions better than other groups. For example, they can compare the mitochondrial DNA (mtDNA) in their database to the Neanderthal ones scientists have recovered. And conclude that they see no evidence that any of the ancestors of the people tested had a Neanderthal for a mom. The scientists can also look at the database and try to figure out if the DNAs they are looking at can really be used to study ancestry. And when they look hard at the mtDNA, what they find is that this DNA doesn't undergo big changes between generations. Which means it is the right DNA to look at.
No mixing and matching
Most of our DNA is useless for distant ancestry analysis because it changes too much from generation to generation. These changes ensure that humans have a lot of genetic diversity. But it can be a real pain when you want to study your distant past. The Y chromosome and mtDNA are thought to be different though. Scientists have shown that these weird outliers of our DNA don't change much between generations. And the work the Genographic Project has done confirms this. Before getting to the specifics of their results though, we need to understand more about what makes mtDNA and the Y chromosome so special. And to understand this, we need to dig a bit deeper into why the rest of our DNA does change so much. The Y chromosome is the chromosome that determines the sex of a person. A person with an X and a Y chromosome is usually male. And a person with two X chromosomes is usually female. Mitochondrial DNA is a cool relic from our evolutionary past (click here to learn more). Unlike the rest of our DNA, mtDNA is found outside of the nucleus in little compartments in our cells called mitochondria. Both mtDNA and the Y chromosome are loners—they don't have a partner they are paired with. This is different than the rest of our DNA. And this is the reason why mtDNA and the Y chromosome don't change much between generations. The rest of our DNA recombines. That's a fancy genetic term for shuffling between partners. See, at birth you get half your DNA from your mother and half from your father. In fact, with the exception of the Y chromosome and mtDNA, you get one of each chromosome from each parent. But you don't get the exact same chromosomes from your mother. Her own two copies of chromosome 1 mix and match with each other first. Then you end up with a mix of both of her chromosome 1's. You also get a mix of her chromosomes 2-22 and her X chromosome as well. Because the mtDNA and the Y chromosome don't have a partner, they don't swap DNA with anyone. They pass virtually unchanged from generation to generation. Why recombination causes problems Recombination really messes up any attempts to look into our distant past with DNA. To understand why recombination can make things difficult, we need to go into a bit more detail about what these tests are looking at. Humans are genetically almost identical to one another. In order to tell different groups apart, we have to look at small sections of the DNA that tend to have a lot of differences. We call these regions "genetic markers". Genetic markers are really just mutations or random DNA changes that happened in our past. There is no one mutation that makes one ethnic group stand apart from the rest. Instead, we have to look at many of these markers and try to find a pattern that fits each ethnic group. Let's think of these markers as stamps on a passport, and the DNA as the traveler. Imagine there is a group of travelers that all begin traveling together. Their passports will start out looking exactly the same. Then, let's say they start to split up and travel on their own or in small groups to different countries. With time, each traveler will acquire new stamps of where they have been. At the end you can look at all the passports. All the travelers should have the same stamps, up until they split from the group. You can then estimate how long it has been since each person was last in the group. This is basically how we believe ethnic groups came about. All humans originally started out in one place, but then started splitting up. With time, each group can be considered a different ethnicity with a different set of hereditary markers. This is all fine and good until the DNA starts recombining. This quickly messes up everything and hides our ancestor's tracks. Let's imagine our DNA as world travelers again. Imagine that before each traveler splits from the group, they exchange half of their passport pages with another person. And then, they split them again. And again. It would then be really hard, after a few months, to tell when each person split! This is why we can't trace our ancestry back very far using most of our DNA. Now a number of studies have shown that mtDNA doesn't recombine between generations. The folks at the Genographic Project decided to look for evidence of recombination in their 78,500 samples. And they saw no evidence that it happens. The way they did this was to compare their samples to some known reference samples. If any DNA got shuffled, then some of the mtDNA the scientists looked at should look like a combination of two of the reference sequences. And none of them do. Actually, 538 of them looked different than the reference DNA. But when they looked closer, they could all be explained by a mutation event. What I mean is that a mutation happened that changed one base into the base of another reference sequence. This isn't surprising given the high mutation rate of mtDNA (click here for more details). So they confirmed that mtDNA is very useful for studying our past. These data are important because some people think that the evidence that mtDNA does not recombine is weak. Well, it looks like they aren't right. Which means that our ancestors did probably start out in Africa and spread across the globe over the last 80,000 or so years.

More Information

Recombination helps
ensure genetic diversity.
My mother was not a Neanderthal
Another finding of the Genographic Project was that they saw no evidence that Neanderthals were our "recent" ancestors. This is important because we don't know what happened to these guys. For hundreds of thousands of years, Neanderthals ruled Europe. Then our ancestors moved in and pretty quickly, the Neanderthals were gone. Some scientists think we killed them off. Some think we were just better and so they died out. And some others think that they had babies together and we all have a little Neanderthal in us. To figure out which idea is correct, scientists have compared our mtDNA to that of the Neanderthal's. Why did they want to look at mtDNA? Because they could. There is a whole lot of it in a cell making it relatively easy to get. Instead of just two copies per cell like our chromosomes, our cells have thousands of copies of mtDNA. Because there is so much of this DNA, we are able to get some from unlikely sources. Like hair or mammoths. Or Neanderthals. The Genographic Project provides a great resource for answering the question of whether there was any monkey business between humans and Neanderthals. The scientists found no evidence of any. As you can imagine, getting DNA from a 30,000 or 40,000 year old fossil is not a simple thing. But scientists have managed in six cases to get a chunk of 300 bases of mtDNA from Neanderthals that looks very good. Studying these six samples showed five DNA differences that Neanderthals had that we do not. Previously scientists looked at all of the human mtDNA so far collected and did not find any that had all 5 changes. But the number of human samples was relatively small. The folks at the Genographic Project could look at many more samples. And none of the 78,500 or so samples had more than one of these DNA differences. This suggests that there isn't any Neanderthal DNA in modern human mtDNA. They also just looked at the whole 300 bases and compared them to the human samples. None of the human samples was as different as the Neanderthal ones. So they found no evidence that our "recent" ancestors were Neanderthals. This is more evidence that Neanderthals simply died out and that we did not interbreed. Recently scientists have begun to look at more than mtDNA. This will either confirm these findings or tell us that we may have Neanderthals in our family tree. We'll just have to wait and see.
There is no evidence
for monkey business
between this Neanderthal
and our ancestors.