by Matthew Cobb

Back in October, we looked at the discovery of anatomically modern human teeth in China, from 100,000 years ago. This was surprising because although archaeological evidence suggested that Homo sapiens first came out of Africa perhaps 125,000 years ago, it was thought that they hung around the Middle East, maybe venturing into Western Asia, but no further. Those teeth told us that we got further East than was thought.

This initial Out Of Africa event was generally thought to have ‘failed’, in that the genetic data from all modern non-African human populations suggest that our common ancestors walked out of Africa around 65,000 years ago. Everyone around the planet who is not from Africa is a descendant of that second wave of migration, which most certainly did succeed – and how.

There was no evidence that the first, ‘failed’ wave of migration left any genetic traces. Until now.

In a paper that has just appeared in Nature, researchers from around the world have studied the genome of a Neanderthal who lived in Denisova cave in the Altai mountains in Siberia over 50,000 years ago, along with genes from two Neanderthals from Spain and Croatia, and the genome of a member of the mysterious Denisovans, who lived in the same cave in Denisova (hence the name), although probably not at the same time as the Neanderthal. They also looked at modern African genomes, which should not have been affected by contact with Neanderthals or Denisovans, as their ancestors did not leave Africa, and at other modern genomes.

This study reveals quite how complex the interactions between these various forms of human were. Above all, they show that the Altai Neanderthal individual had inherited genes from a human who left Africa in that first wave of ‘failed’ migration, tens of thousands of years before the Altai Neanderthal was alive. Perhaps those first bold humans did not leave any genes in us directly, but they did leave genes in our close cousins, the Neanderthals of Siberia. Interestingly, there were no traces of such genetic mixing with the first wave of humans to be found either in the Spanish or Croatian Neanderthals, or in the Denisovan.

Finally, the Denisovan genome itself revealed that those people had not only swapped genes with the second wave of humans as they moved through Asia (this was already known), but also that, some time deep in the past, the Denisovans gained genes from an unknown source, mating with an individual or individuals who branched off from the rest of our lineage hundreds of thousands of years ago. (This final finding helps explain some mysterious results that suggested that some modern African DNA sequences seemed related to Denisovan sequences – in fact they shared DNA from one of our relatives in deep time.)

Here are two useful figures from the paper that help clarify this blizzard of astonishing facts. Firstly a figure showing the patterns of evolution and of swapping of genes between these groups. Time is from top to bottom, with the present at the bottom. Homo sapiens and their ancestors are in light blue, Neanderthals are in pink and the Denisovans are in red.

You can see that the Neanderthal and Denisovan branches (in pink) fade away, showing that they disappeared (the red dots correspond to the samples the paper studied). The slanted lines at the very top are to show that that part of the figure is not to scale. The blue arrow going into the Denisovan is from the unknown forms that split off from the human lineage long ago, but after the chimpanzees. The red arrow going into the Altai Neanderthals shows the introgression from the first human migration, which on this figure stops at around 50,000 years ago, indicating that, for the moment, we do not think these people left any direct modern descendants. The exact relation of this group to modern Africans is not clear, and that’s why they’ve put the odd circle on the left-hand part of the figure.

Genetics is an amazing thing, and by comparing the frequencies of different forms of a given gene (these forms are called ‘alleles’), population geneticists can work out how many individuals must have been involved in producing that variability, in other words, how big the reproductive population was. This ‘effective population size’, as it is called, is much smaller than the demographic population – the actual numbers of individuals – but it gives you an idea of the general size. Here’s the same family tree, but this time with much a finer timeline, and, for each group, the effective population size as calculated using population genetics:

This figure shows you that the effective population size of the Altai Neanderthals was really small – perhaps no more than 1000 individuals, compared to 27,000 for the Yoruba in Africa. The Altai mountains might have been a tough place to hang out, and the Altai Neanderthals, cohabiting in the region with the Denisovans, who appear to have had a larger effective population size, might have found life tough. The Altai individual’s parents were very closely related, perhaps half-siblings. The differences in the population sizes of modern humans and the Neanderthal/Denisovan group are striking. Maybe leaving Africa when they did was a bad idea – they do not seem to have flourished, compared to the humans who remained in Africa.

Here is a summary of our current knowledge in easy-to-digest bullet points. Cut them out and pin them to your bedside table. There will be a test in class next week.

Modern humans and Neanderthals diverged 550,000-765,000 years ago.

Neanderthals and Denisovans diverged 381,000-473,000 years ago.

Modern humans mated with Neanderthals in Asia around 100,000 years ago, during our first failed wave of migration, leaving our genes in their DNA.

Modern humans mated with Neanderthals in the middle East around 50,000 years ago, during the second successful wave of migration. We got some of their DNA, which has been linked with a number of characteristics.

Modern humans mated with Denisovans in Central and Eastern Asia, and got some cool genes from them, including one that enables Tibetans to live at high altitude.

Denisovans mated with an unknown form (NB we don’t know what the Denisovans looked like, beyond the fact that they had whopping teeth), perhaps a relict Homo erectus, the product of the very first wave of Homo migration from Africa

This is just the latest installment in what I think is the most astonishing part of modern biology. All of this would have been science fiction 20 years ago, simply because the data would have seemed impossible to access. Even once Svante Pääbo’s group began to sequence Neanderthal genes, no one could have imagined the discoveries that were to be made. Linking paleogenetics with archaeology and palentology is opening an amazing chapter in the history of our knowledge of ourselves.

Reference: M, et al. (2016) Ancient gene flow from early modern humans into Eastern Neanderthals. Nature (in press)

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