Are you descended from Neanderthals?

Earlier this year, three Neanderthal females had their genomes sequenced to produce the first draft of the Neanderthal genome.

This post originally appeared on Sciblogs.co.nz.

They huddled in their fur pelts, wrapped against their dark skin with cords made from hide and gut.

No one had travelled this far north before in the history of their people, and it was late enough for the wolves to come out. In the foothills ahead they could see the distinct light of a fire flickering in a grotto. Cold and weary, the explorers trekked toward the light with spears sharp and ready. Maybe they were not the first people to leave the motherland...

Back in 2008 it was announced that the Neanderthal mitochondrial genome had been sequenced, and subsequently that humans and Neanderthals did not interbreed. I was admittedly disappointed with that outcome - as were many other Jean M Auel fans. But the mitochondrial genome is only part (and a small part at that) of an organism's genome. The mitochondria of a cell is a type of organelle (a mini organ), but it's unique in that it has its own genetic code.

The mitochondria genetic code or mtDNA is maternally inherited so can only be used to track events in the maternal lineage. This is because when a woman produces an egg and it's fertilised, in general, the only contribution the sperm makes to the fertilised egg is half the nuclear DNA. All the organelles and machinery of the cell are provided by the female egg. Siblings all have the same mtDNA genome but only daughters pass it on.

However, the nuclear genome, which essentially codes for everything else that makes up an organism, has come from multiple ancestors and is contributed to equally by males and females (sperm and egg). The mitochondria genome of a Neanderthal was very much outside the range of modern human mitochondrial genome sequences - it didn't look like we were descended from them or interbred with them.

But the mitochondrial genome only provides a small part of the picture. And if you think about it, many, many mitochondrial genome lineages die out over the course of history - every time a female has no daughters her mtDNA line ends if she has no other female maternal relatives.

In May this year a very exciting paper came out in Science with the draft of the Neanderthal nuclear genome. Three Neanderthal females had their genomes sequenced to produce the first draft of the Neanderthal genome. The three bones that the DNA for sequencing was extracted from were dated at 38,000 years or older and came from the same site in Croatia. When these Neanderthal females died, bacteria colonised their bones so that 95-99 per cent of the DNA extracted from the bone came from micro-organisms.

A further complication is the predicted similarity of modern human DNA to Neanderthal DNA. These challenges, and others, were met and overcome by the Neanderthal Genome Analysis Consortium, based in labs around the world - California, Beijing, Cambridge, Croatia etc. Over 20 years of knowledge in retrieving ancient DNA was applied to the produce great results with the latest 'Next Generation Sequencing' technology.

So what does the draft sequence tell us? From what the draft tells us it seems likely that humans and Neanderthals did interbreed!

There are some more specifics, though. The inbreeding occurred after humans left Africa but before humans spread out from the Middle East into Europe, Asia and the rest of the world. This was detected by comparing the genome of Africans, non-Africans and the Neanderthal draft genome.

The comparison found that non-Africans all shared the same amount of the Neanderthal genome but African genomes stood apart. The amount of Neanderthal DNA sequence in non-Africans equates to 1-4 per cent of your nuclear. Humans and Neanderthals cohabited in the Middle East for some 50,000 years so there was plenty of time for mixed Homo species liaisons.

The authors of the paper conclude from this that Neanderthal-human interbreeding was rare due to the low percent of Neanderthal DNA sequence in modern humans and the absence of human DNA sequence in the three Neanderthal females analysed. We all know enough about human history to imagine that humans may not have had open arms for their sibling species, so maybe interbreeding was rare. But what about Europe?

With the expansion of human populations and climate change, Neanderthal populations are thought to have shrunk toward Europe and Spain. Europeans and Neanderthals had potentially longer to interbreed compared to other human populations, but there is no evidence for this - so far. Did waves of human migration from the Middle East replace ancient Neanderthal-human Europeans or did the first human inhabitants of Europe and Neanderthals keep to themselves?

The remains of several ancient Hominids in Europe are said to have a hybrid appearance - wouldn't it be great to sequence their genomes to put their origins to the test? Ancient genome sequencing is a very exciting field - and at the moment it seems we can never have enough genomes. We need more Neanderthals, a look at those so-called hybrid remains, and to sequence the remains of pre-agriculture humans to eke out and refine existing theories and models of modern human evolution.

Mary Gray is a PhD student at the Clinical Genetics Research Group at the University of Otago. View her work and that of 30 other scientists and science writers at Sciblogs, New Zealand's largest science blogging network.