Oldest human DNA reveals missing branch of human family tree

The genomes bear evidence of Neanderthal ancestry. The researchers determined that early human ancestors who lived in Ranis and the surrounding area likely encountered Neanderthals about 80 generations ago, or 1,500 years ago, and produced offspring, although that interaction did not occur in the same place.
Since the first Neanderthal genome was sequenced in 2010, scientists have known that early humans interbred with Neanderthals, a bombshell revelation that a genetic legacy can still be found in humans today.

However, it is difficult to pinpoint exactly when, how often and where this complex and mysterious juncture in human history occurred. Scientists believe that interspecies contact occurred somewhere in the Middle East as a wave of Homo sapiens left Africa and clashed with Neanderthals, who lived across Eurasia for 250,000 years.
A comprehensive study of Neanderthal lineages published Thursday in the journal Science, which analyzed data from 59 ancient human genomes and 275 living human genomes to support a more precise timeline, found that the majority of Neanderthal lineages in modern humans can be attributed to a “single, shared period of extended gene flow.”
“We were much more alike than we were different,” Priya Murjani, a senior author of the Science study and an assistant professor in the Department of Molecular and Cell Biology at the University of California, Berkeley, said in a news briefing.
“The differences that we imagined to be very large between these groups were, in fact, very small, genetically speaking. It seems that they mixed with each other for a long time and lived side by side for a long time.”
The study identified a crucial period that began about 50,500 years ago and ended about 43,500 years ago – not long before the now-extinct Neanderthals began to disappear from the archaeological record. During this 7,000-year period, early humans encountered Neanderthals, had sex and had children on a fairly regular basis. The height of the activity was 47,000 years ago, the study suggests.

The study also showed how some genetic variations inherited from our Neanderthal ancestors, which make up between 1% and 3% of our genome today, have changed over time. Some, such as those related to the immune system, were beneficial to humans because they lived during the last ice age, when temperatures were much cooler, and they continue to provide advantages today.
The two studies provide “sufficient confidence” in the timing of when humans and Neanderthals exchanged genes, which geneticists describe as introgression, said evolutionary geneticist Tony Capra, a professor of epidemiology and biostatistics at the Baker Institute for Computational Health Sciences at the University of California, San Francisco.
“Genetic data from this crucial period in our evolution is very rare,” Capra, who was not involved in the study, said by email.  "These studies underscore how even a few ancient genomes provide powerful insights that enable the authors to refine our understanding of human migration and Neanderthal infiltration."
Scientists working on the two research projects decided to publish their work at the same time after realizing that they had reached the same conclusions separately.
How Neanderthal ancestors shaped human genes
Scientific research has shown that genetic variations inherited from our Neanderthal ancestors are unevenly distributed across the human genome.

Some areas, which scientists call “ancient deserts,” are devoid of Neanderthal genes. These deserts likely developed rapidly after the two groups interbred within 100 generations, perhaps because they carried birth defects or diseases that would have affected the offspring’s chances of survival.
“This suggests that the hybrid individuals with Neanderthal DNA in these areas were considerably less fit, perhaps due to severe disease, lethality, or infertility,” Capra said by email.
The X chromosome in particular was desert. Capra said the impact of the disease-causing Neanderthal variant may have been greater on the X chromosome, perhaps because it is present in two copies in women, but only in one copy in men.
“The X chromosome also contains many genes that are linked to male fertility when mutated, so it has been suggested that some of this effect may come from leading to male hybrid infertility,” he said.
Neanderthal gene variants frequently identified in ancient and modern Homo sapiens genomes are associated with traits and functions that include immunity, skin pigmentation and metabolism, some increasing in frequency over time.
“Neanderthals lived in harsh, ice-age climates outside of Africa and adapted to the climate and pathogens of this environment. When modern humans left Africa and interbred with Neanderthals, some individuals inherited Neanderthal genes that likely allowed them to better adapt to and thrive in their environment,” said Leonardo Yassi, co-lead author of the Science paper and a doctoral student at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

The people living at Ranis had 2.9% Neanderthal ancestry, not dissimilar to most people today, the Nature study found.
The new timeline gives scientists a better understanding of when humans left Africa and moved around the world. It suggests that the main wave of migration out of Africa occurred roughly 43,500 years ago because most people outside of Africa have Neanderthal ancestry since this period, the Science study suggests.
However, there is still much that scientists don’t know. It’s not clear why people in East Asia today have more Neanderthal ancestry than Europeans, or why Neanderthal genomes from this period show little evidence of Homo sapiens DNA.
While the genomes of the Ranis individuals are the oldest Homo sapiens genomes, scientists have previously recovered and analyzed DNA from Neanderthals dating back 400,000 years.
Missing branch of the human family tree
The people who call the cave at Ranis home were among the first Homo sapiens to live in Europe.
These early Europeans numbered in the hundreds and included a female who lived 230 kilometers (143 miles) away in Zlatý kůň, Czech Republic. DNA from her skull had been sequenced in previous studies, and researchers involved in nature studies were able to link her to the queen individuals.

These individuals had dark skin, dark hair and brown eyes, according to the study, likely reflecting their relatively recent arrival from Africa. Scientists are continuing to study remains from the site to piece together their diet and how they lived.
The family group was part of a pioneer population that eventually died out, leaving no trace of the lineage among people alive today. Other lineages of ancient humans also went extinct about 40,000 years ago and eventually disappeared, just like the Neanderthals, said Johannes Kraus, director of the Department of Archaeology at the Max Planck Institute for Evolutionary Anthropology. These extinctions could indicate that Homo sapiens did not play a role in the demise of Homo neanderthalensis.
“It’s kind of interesting to see that the human story is not always a success story,” said Kraus, a senior author of the Nature study.