The hallmarks of an ancient tryst between our early human ancestors and their now extinct Neanderthal cousins are dotted throughout modern human genomes. Two new studies add to our understanding of our Neanderthal paramours and why traces of their DNA remain within us still.
In the first, an international team led by researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, sequenced the genome from a 52,000-year-old female Neanderthal, whose remains were found in the Vindija Cave in Croatia.
The technical feat, described in the journal Science, is just the second time that a near-complete genome of such high quality has been reconstructed from DNA fragments extracted from millennia-old fossils. It’s also the first from a Neanderthal who lived closer to the centre of their known geographic range, which extended from the tip of southern Spain, across central Europe and the Middle East, and into Siberia.
Previously, Neanderthal genome studies have relied on a single high-quality example – that of the 120,000-year-old ‘Altai’ Neanderthal from southern Siberia – and a smattering of lower quality and incomplete genomes from across Europe.
The additional genome bumps up the estimate of how much Neanderthal DNA remains in the modern-day human genome – for those whose roots are outside of Africa – to between 1.8 and 2.6%.
The genome also provides insights into how Neanderthals lived. “What you learn is that there were not many Neanderthals around, and they were all closely related,” says Kay Prüfer, who led the study.
It’s an exciting finding, says palaeontologist Darren Curnoe from the Australia’s University of New South Wales, who wasn’t involved in the study, and could shed light on why Neanderthals went extinct. “If a population like that is inbred, then it doesn’t take very much to push it to extinction,” he says, “and it certainly doesn’t mean necessarily that humans intervened in any way to push them to extinction.”
The Vindija Neanderthal – perhaps because of its more central location – is more closely related to populations that intermingled with early humans, though there were probably multiple occasions where humans and Neanderthals mixed.
Most Neanderthal DNA sequences have been purged from the human genome in the millennia since those ancient pairings, likely because they were detrimental to our ancestors.
But what of the sequences that have stuck around? Previous studies have linked Neanderthal sequence variants to changes in immune function, metabolism and pigmentation.
The Vindija genome adds a handful variants to this list, including one associated with lower levels of artery-clogging LDL cholesterol, and others linked to schizophrenia, eating disorders, visceral fat accumulation, rheumatoid arthritis and our response to antipsychotic drugs. How these variants might change disease risk remains to be investigated.
While most studies have linked Neanderthal genes to medical conditions, a new study, published in the American Journal of Human Genetics sought to find out if Neanderthal sequences play a role in modern human appearance and behaviour.
For this, Michael Dannemann and Janet Kelso, from the Max Planck Institute for Evolutionary Anthropology, turned to the UK Biobank pilot study, a database containing information on 136 measurable traits – detailing everything from a person’s outward appearance or behaviour, to their blood pressure and fat content – for 112,000 Britons.
Dannemann and Kelso identified 15 Neanderthal variants that were strongly associated with measurable characteristics in modern humans. Over half of these were related to skin and hair colour or ease of tanning.
Surprisingly, given Neanderthals’ reputation for giving redheads their fiery locks, few redheads had Neanderthal hair colour variants. However, in most cases, the way in which Neanderthal DNA influences modern human skin tone or hair colour is far from clear. The team identified Neanderthal variants more common in olive-skinned people, as well as variants more common in fair-skinned people, for instance. And human variants were just as influential as Neanderthal variants in determining skin and hair colour.
This higgledy-piggledy mixture likely points to the Neanderthals themselves being varied in skin tone and hair colour, says Dannemann.
Two Neanderthal variants were identified that influence sleep patterns. Combined with the pigmentation variants, there appears to be an outsized contribution of Neanderthal genes related to sunlight exposure.
Dannemann speculates that this could be because Neanderthals adapted to the lower UV levels and more variable day lengths in Europe some 100,000 years earlier than our own forebears, who readily snapped up the Neanderthal variants and then retained them through to present day. But, says Dannemann, “it’s something that we can only speculate on, since we don’t really know the molecular mechanisms behind it.”
Neanderthal variants linked to complex attributes such as smoking, dietary preference, a lack of enthusiasm and loneliness were also identified.
“We’re a complex beast and some of that complexity isn’t inherent to us,” says Curnoe, who wasn’t involved in the study. “Some of that comes from our archaic cousins, which for me also raises questions about how complex they must have been.”
Related reading: Depressed? Blame it on the Neanderthals