Palaeogenomics and interbreeding

DNA is providing intriguing insights into human evolution. Oxford University Professor of Archaeological Science Tom Higham talks about interbreeding, our Neanderthal genes and the likelihood of multiple introgressions.

Jargon alert

In genetics, introgression, also known as introgressive hybridisation, is the movement of a gene (gene flow) from one species into the gene pool of another.

Transcript

PROF TOM HIGHAM

Interbreeding is a very, very key part of our understanding of the process of the replacement of Neanderthals by modern humans.

So this is a site on the banks of the Irtysh River in Siberia, and in 2008, some Russian fossil hunters discovered an interesting bone – a femur of a modern human. And a small piece of it was sent to us in 2010 for dating, and it produced a date – two dates identical – about 4 years apart. We dated these two samples 4 years apart. And the corrected ages for this is between 44 to 46,000 years ago. That’s the oldest directly dated modern human outside of Africa – just a chance find on the banks of this river.

A small piece of this bone was then sent to Leipzig to the geneticist that we work with, Svante Pääbo, and they found exceptionally good preservation of DNA – so good, they were able to get a complete genome.

Now this is a fearsome diagram that I want to share with you, and let me just take the time to explain it because it’s really interesting. So basically, these are parts of the genome of modern people – a French person, someone from Sardinia, China, South America, Papua New Guinea, Australia – and this is a section of the genome from chromosome 12, so one of the chromosomes. And everywhere you see a coloured line, this little yellow or the blue, this is Neanderthal-derived DNA, so alleles that expressed coming from Neanderthals. So you can see across each one of these individuals’ chromosome 12, we’ve got one or two little bits and pieces here of the genome, so adding up to around 1.5–2% of the genome, across all of these sections of the chromosome.

Now if you imagine that you’re a modern human and you have an interbreeding event with a Neanderthal, your offspring will have half the genome from them and half from you, and subsequently that material will be broken up, and it’ll become recombined into smaller fragments. This fragmentation takes place in successive generations. So the closer we go back to the original interbreeding events, we should expect that these DNA sections that come from Neanderthals should be bigger and more chunky. So what did the DNA from the Ust’-Ishim look like? Well this is it at the top.

And you can see here, these are characteristically quite large chunks of DNA coming from Neanderthals into this modern human person dating to 46 to 44,000 years ago. Now it’s possible because we have this data and this information – we have lots of genome data now – that it’s possible to calculate how long since this introgression, this person – since this person lived – how long back was this introgression, this gene flow, this interbreeding event from a Neanderthal. And it calculates out to around 330 generations prior to the life of this person, which means that about 50,000 to 60,000 years ago, which is interesting because it’s about the same date as we think modern humans come out in this last movement out of Africa.

Some really interesting information about this came out in the journal Nature. This is the Peştera cu Oase mandible, which we dated, remember, 39 to 41,000 years ago. This one also produced a genome – this shows 22 chromosomes of genome data from this incredibly preserved piece of bone that was analysed in Leipzig, and you can see here on this particular chromosome, we’ve got individuals from Africa at the bottom, the D is Dinka – that’s a sub-Saharan Africa person – French, and then a Han Chinese, and then our friend U, which is Ust’-Ishim – this one here with the yellow – and then above that is Oase, and where you see green, this is Neanderthal introgression. So that’s Neanderthal DNA in this person. And you can see that it’s present in big chunks here, really big chunks. In fact, around half, maybe, or a third of this entire section of this chromosome is deriving from Neanderthal.

This suggests that this person lived much closer to the introgression, much closer to the gene flow period than the Ust’-Ishim man. This man probably has a Neanderthal great great grandparent. Four to six generations before this person lived, he had a very close relative that was a Neanderthal. So this puts an incredibly tight amount of time on the introgression in this particular part of the world in Romania. So now we know there was not just one introgression, there were probably several, and the other really intriguing thing to point out here as well is that both of these modern humans are evolutionary dead ends. They have no relatives amongst us today. So we’re still looking for those people at the moment, and more DNA data, more dating evidence is needed until we can be sure.

The Science Learning Hub would like to acknowledge: Professor Tom Higham, University of Oxford The Allan Wilson Centre for Molecular Ecology and Evolution Re-enactment footage of Neanderthal family, courtesy Max Planck Institute for Evolutionary Anthropology Photos of Svante Pääbo with femur, courtesy Max Planck Institute for Evolutionary Anthropology/Bence Viola Photo of Ust’Ishim femur bone, courtesy Max Planck Institute for Evolutionary Anthropology Bone fragment drilling image, Frank Vinken, Max Planck Institute for Evolutionary Anthropology Figure of Spatial distribution of alleles matching Neanderthals in modern humans and figure showing 22 chromosomes of genome data, An early modern human from Romania with a recent Neanderthal ancestor. Qiaomei Fu, Mateja Hajdinjak, Oana Teodora Moldovan, Silviu Constantin, Swapan Mallick, Pontus Skoglund, Nick Patterson, Nadin Rohland, Iosif Lazaridis, Birgit Nickel, Bence Viola, Kay Prüfer, Matthias Meyer, Janet Kelso, David Reich and Svante Pääbo. Nature, 524, 216–219 (13 August 2015). doi:10.1038/nature14558 Photo of Peştera cu Oase mandible from An early modern human from the Peştera cu Oase, Romania. Erik Trinkaus, Oana Moldovan, Stefan Milota, Adrian Bîlgăr, Laurenţiu Sarcina, Sheela Athreya, Shara E Bailey, Ricardo Rodrigo, Gherase Mircea, Thomas Higham, Christopher Bronk Ramsey and Johannes van der Plicht. PNAS, 2003 100 (20) 11231-11236; published ahead of print September 22, 2003, doi:10.1073/pnas.2035108100