Slivers of bone in caves hundreds of kilometres apart have helped scientists understand when our ancestors and Neanderthals interbred.
Two studies published today, which together cover the past 50,000 years of human evolution, suggest Neanderthal DNA was already well and truly within our species' gene pool by around 42,000 years ago.
Previously, scientists — using single ancient samples or genomes from people alive today — could only estimate when this interbreeding or "admixture" took place, Manjusha Chintalapati, an Ancestry DNA bioinformaticist and a study co-author, said in a release.
"Nobody had tried to model all of the ancient samples together. This allowed us to build a more complete picture of the past."
Archaeologists had already ascertained that Neanderthals (Homo neanderthalensis) showed up in Europe at least 400,000 years ago, and were joined by modern humans (Homo sapiens) about 50,000 years ago.
The two species overlapped for only a few thousand years before the Neanderthals died out about 40,000 years ago.
Before Neanderthals disappeared, they bred with early modern humans, the signs of which can be seen in present-day DNA.
About 2 per cent of the genetic blueprint, or genome, of non-African people living today came from Neanderthals.
But when did this interbreeding happen? Did the two groups mate throughout their shared history? Or was their rendezvous cut short?
Reconstructing this history is difficult, according to Bastien Llamas, an ancient DNA researcher at the University of Adelaide who was not involved with either study.
"There's debate about how many times these [breeding] events happened," he said.
"It could have been just one time and that's it, or it could have been an extended period … or it could have been several distinct events separated by generations."
To better pinpoint when early members of our species started breeding with Neanderthals, one of the new studies, which was published in Science, took a long view of evolution.
The researchers, from Germany, the UK and the US, analysed more than 300 modern human genomes spanning the past 50,000 years, and calculated when and where Neanderthal DNA started showing up in the timeline.
They found that the period of interbreeding began around 50,000 years ago and lasted around 7,000 years.
"It is super exciting that we can look into the past and reconstruct a timeline of what our ancestors were doing 50,000 years ago with such resolution," one of the researchers, Priya Moorjani from the University of California, Berkeley, said.
"[It] is quite incredible."
Thousands of years later, humans have retained some of these Neanderthal genes — they've not been bred out — which suggests they must be beneficial to us, Dr Llamas said.
The study found Neanderthal genes related to skin pigmentation, metabolism and immunity that were advantageous to Homo sapiens.
A familial connection
A second study, led by German researchers and published in Nature, painted a picture of ancient familial ties using some of the oldest modern human genomes sequenced to date.
The team looked specifically at the remains of a family found in the Ilsenhöhle cave in Ranis, Germany, and the bones of a woman found about two days' walk away in the Konepruské cave in Zlatý kun, Czechia (also known as the Czech Republic).
[map]New DNA analysis on a handful of bone fragments from the German cave found they belonged to six modern humans who lived between 42,000 and 49,500 years ago. They included a mother and daughter, with four other biological relatives.
The researchers then compared the Ranis genomes with that from the skull of the Zlatý kun woman, who lived around 43,000 years ago.
"To our surprise, we discovered a fifth- or sixth-degree genetic relationship between Zlatý kun and two individuals from Ranis," Arev Sümer, lead author of the study and anthropologist at the Max Planck Institute in Germany, said in a press release.
"This means that Zlatý kun was genetically part of the extended family of Ranis."
The Ranis and Zlatý kun individuals are the oldest high-quality Homo sapiens genomes so far sequenced.
They likely had dark skin, dark hair and brown eyes, which the team says suggest the group had only left Africa within the last few generations.
They also had Neanderthal ancestry. The team dated that particular "breeding event" to around 80 generations earlier, approximately 45,000 to 49,000 years ago.
According to Dr Llamas, there's still more to understand about how Neanderthal genes affect us in the 21st century.
"It's been quite a few years since we identified that we have Neanderthal DNA in our genomes, but we're still trying to understand the process and consequences for the modern day," Dr Llamas said.
"It is important to understand why and how it happened, as it has an impact in modern day people, in health and disease."
