Our newest relatives hailed from around this cave in Siberia.

In 2008, scientists found a fossil of a humanoid finger in the Denisova Cave in Siberia. The finger was probably from someone (or something) that had been running around Siberia forty thousand years ago.

Until recently, the scientists would have been stuck until they found additional fossils to build up a more complete skeleton. Once they had the skeleton, they could then compare it to other fossils and figure out how it related to modern humans. Of course this might never happen—it would be totally dependent on finding more fossils.

Rather than waiting around, these scientists decided to bring in a geneticist. Nowadays geneticists can sometimes read every base of a fossilized beast’s DNA. In other words, they can read its whole genome.

When geneticists did this, they found that the finger did not come from a modern human or a Neanderthal. This Denisovan (as scientists named it) probably came from a previously unknown relative that was more closely related to Neanderthals than humans. And surprisingly, their legacy lives on in some modern humans.

By comparing the DNA of the Denisovan and various modern ethnic groups, scientists could see Denisovan DNA in modern Melanesians. Apparently the ancestors of Melanesians and Denisovans had babies before the Denisovans went extinct.

The data suggest that Denisovans might have contributed up to 4-5% of their DNA to modern Melanesians. Add the 1-2% Neanderthal DNA found in non-Africans and you get up to 7% of Melanesian DNA coming from nonhuman sources. And that is just based on the two extinct species whose DNA we’ve been able to read so far.

Who knows how much DNA of other ethnic groups comes from relatives whose DNA we haven’t looked at yet. I bet someone is taking a good hard look at various groups’ DNA to see if they can answer this question without having to figure out more fossil DNA.

This all points to an exciting new twist to paleontology…the ability to look at DNA from fossils and to compare that DNA to modern humans and any other close relatives whose DNA has been sequenced. This new avenue of research should provide extra information that scientists didn’t have before and allow them to figure some things out with just a single finger bone.

BBC story on the find.

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Are they related to me? I still don't know…

In my last blog post, I showed how the two most powerful ancestry tests, mitochondrial DNA (mtDNA) and Y chromosome, were useless to me in my hunt. Now I want look at the rest of my DNA.  So here we go!

The Y chromosome and mtDNA are a small fraction of my DNA—something like 0.8% of the total DNA in one of my cells.  But they are incredibly useful because they change very little from generation to generation.  The mtDNA I got from my mom is probably exactly like hers.  Same with most of the Y I got from my dad.

The other 99.2% of my DNA is a lot trickier to look at from an ancestry perspective because it has changed a lot from generation to generation over time.  For example, the chromosomes I inherited from my parents are not the same as the ones they have.  I got a mix of their chromosomes

For example, my mom had two copies of chromosome 1 (and two copies of her other 22 chromosomes too).   As you know, she passed one chromosome 1 to me (my dad gave me my other one).  But, through a process called recombination, her two copies of chromosome 1 swapped DNA so that I got a hybrid of her two copies.  I inherited a unique chromosome never before seen.

This is all well and good from a survival of the species point of view, but it is a problem for ancestry testing.  Imagine that instead of my mom, we look at my Cherokee great-great grandmother.  She has just had a child who inherited a mix of her chromosome 1’s.  This chromosome will look Native American and the child would appear half Native American.

Actually, the test isn’t perfect yet and so there isn’t yet a “Native American” set per se.  Instead, here is how 23andMe describes Native American DNA in their tests:

“…people who identify themselves as Native American exhibit fairly consistent Ancestry Painting proportions of about 75% Asian and 25% European, plus or minus 10%.”

This means the chromosomes the child got from his or her mom won’t look Native American but instead will look 75% Asian and 25% European.  (See a realted post of mine elsewhere for why it looks like this.) Now imagine that this half Native American child grows up and has my grandfather as his or her son.

My grandpa will inherit a mix of his parents’ DNA too.  In this case the Native American DNA will mix with the European DNA to create a hybrid.  On average, you would now see something along the lines of 37.5% Asian (this is a simplification but it gets us into the ballpark of the number we might expect).

Each generation would see, on average, a continued dilution of this Asian part.  My dad would have 18% Asian, I would have 9%, etc.  Here are my ancestry results (click the image to enlarge):

Not a hint of Asian.  Looks like my great-great grandma wasn't Cherokee.  Or was she?

There are lots of ways she could still be Cherokee.  First off, I don’t know how solid the 75% number is for all Native Americans.  I don’t know how many Native Americans are in their database.  I also don’t know how much variation there will be tribe to tribe.

Secondly, you may have noticed that I was very careful to always say, “on average.”  This is because the recombinations don’t have to be a 50-50 swap.  It is true that if you look at a large number of recombination events, the average will be 50%.  But individual recombination events can be biased towards one or more chromosomes.  Occasionally you’ll get mostly one chromosome and sometimes mostly the other.

Sort of like flipping a coin—do it enough and you’ll get pretty close to half heads and half tails.  But if you flip a coin twice, you might get one head and one tail.  And you might not.  Half the time you’ll get two heads or two tails.

This is less a problem than you might think with our chromosomes since the recombination is spread over 23 pairs with each pair being independent of the others.  But it can still throw a monkey wrench into the works.  23andMe actually has a nice chart that hints at this by giving the most likely range of possibilities.  Unfortunately, this chart didn’t come up with my results and I had to stumble on it while I was playing around.

Using the chart, I can see that the bottom end of my expected results in 0.24% “Native American” (if I am reading the chart correctly).  That is pretty low and it seems like a pretty minor mistaken assumption at the beginning might knock this down to zero.

So where am I after this?  Still in the dark.  This is actually how many genetic tests end up.

The positive result tells you a lot.  Had there been Native American DNA, that would have been a slam dunk.  (This isn’t always the case with genetic tests but it would be here.)  But there wasn’t.  Which means, given that I was on the edge of detection, that she may or may not have been Cherokee.

Now, this isn’t 23andMe’s fault.  The test itself couldn’t be conclusive given how far back we need to go and the DNA tests that 23andMe offers.  In fact, 23andMe does an excellent job of presenting the data.  There are pretty chromosome paintings, graphs superimposed on world maps, etc.  All very nice.

I am still worried that the explanations that go along with these images assume an awful lot of knowledge that most people might not have.  Without that knowledge, it can be hard to assess the significance of a certain result.  Next blog that’ll become even more important as I tackle health conditions.

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This former free living bacterium now supplies our cells
their energy.

The hijacked cell has over time become the mitochondrion. This organelle is responsible for making our energy. But it still has the marks of having once been a free living bacterium.

First off, mitochondria still have remnants of their old DNA. There isn’t much there in human mitochondria but there is enough to still get us into trouble. A big part of aging might be due to damage to this mitochondrial DNA (mtDNA). Some genetic diseases are also caused by mutations in mtDNA.

The DNA in mitochondria is also much more like bacterial DNA compared to the rest of our DNA. In fact, the mitochondrion has its own bacteria-like machinery for reading its DNA. This means that mitochondria can’t read the genes in our nucleus and vice versa. Mitochondria are so similar to bacteria that some antibiotics can damage them too.

Even though it was once free living, the mitochondrion doesn’t have a lot of its original DNA left. Over time, most of our mitochondrion’s original genes have traveled to the nucleus. These genes now work in the nucleus to make most of a mitochondrion’s proteins which are then transported back to the mitochondrion.

After all these years, human mtDNA is now only around 16,000 bases long and has only 37 genes left. This is a far cry from even the simplest of bacteria, Mycoplasma genitalium, with its 582,970 bases and 521 genes.

Humans are not unique in having mitochondria. Every plant, animal, and fungus cell in the world that has been looked at has mitochondria. But the DNA in these mitochondria is all wildly different.

The size of mtDNA can range from just 6000 base pairs all the way up to 2 million base pairs. Sometimes the mtDNA is a circle like ours. Sometimes it is spread out over lots of little circles. Sometimes it is one long, linear piece of DNA. Sometimes it is lots and lots of little pieces of linear DNA. And sometimes it is too weird to describe in a short blog like this.

Mitochondria from different species also have different numbers of genes. Some species have mitochondria with nearly 100 genes. While others have as few as 5.

With up to 2000 mitochondria/cell, evolution has had a free hand in tinkering with mtDNA. If a mutation or change in mtDNA causes a problem, that mitochondrion simply goes away. If there is some advantage to the new DNA structure, it is free to sweep through and take over. It is amazing what evolution has done to this bacterium!

Of course, evolution has made the mitochondrion a shell of what it once was. But we could argue that it is one of the most successful beasts ever.

It has gone from humble bacterium to being part of every eukaryote in the world. If humans die out, mitochondria will still be around somewhere else. Mitochondria will outlive us all.

More information on mitochondrial genomes: http://dx.doi.org/10.1016/j.tig.2003.10.012

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