Genomic analyses of recently unearthed human remains from around 40,000 years ago have given researchers insight into a previously unknown migration into Europe and suggest that modern humans were mixing with Neanderthals more often than was assumed.

According to an article published April 7 in Nature, genetically modern human specimens recovered from a cave in Bulgaria offer a unique window into the story of early migration into the European continent, during what one researcher called a "crucial time period," when the last Neanderthals lived alongside Homo sapiens.

In 2015, the remains of three individuals were found in Bacho Kiro Cave and dated to between 42,000 and almost 46,000 years ago; this represents the oldest Late Pleistocene modern humans ever recovered in Europe and reveals at least one early migration wave that wasn't already known from the genetic record.

In part, that's because remains from so long ago are famously — and mysteriously — hard to find, according to corresponding author Mateja Hajdinjak, one of 32 researchers on the paper.

Such specimens "are really, notoriously rare," she told The Academic Times, noting that mortuary practices from the Initial Upper Paleolithic period could be to blame for the relative lack of skeletal remains from around 40,000 years ago or earlier. In later periods, humans developed burial practices that have preserved many more skeletons through the present day.

The researchers extracted DNA fragments from five pieces of human remains from Bacho Kiro Cave, comparing the remains dated from before 40,000 years ago to genomic data from other modern humans, both ancient and from the present day. For example, they also analyzed comparably old individuals found at other sites, a later individual from Bacho Kiro Cave, and contemporary humans.

The results from their comparative analyses were "quite surprising," Hajdinjak said, uncovering genetic traces which later disappeared from western Eurasian populations — but are carried on in ancient and present-day populations in East Asia and the Americas.

Even the later Bacho Kiro Cave individual has a "completely different" genetic profile, she added, indicating the three individuals discovered in 2015 came from a population that had migrated into western Eurasia but was later genetically replaced by other groups.

It isn't clear why the migrant population from which the three individuals likely came didn't leave a lasting lineage in Europe, though Hajdinjak noted that further evidence could potentially clarify whether they were outcompeted or simply didn't mix with other incoming human groups at the time.

The finding "changes our understanding of these early human dispersals because it indicates that there are at least several different human groups, very early after 'out-of-Africa' migration, that kind of coexist in Eurasia," she said.

Analysis of the Bacho Kiro Cave individuals also uncovered evidence that the early human population in Europe may have mixed with Neanderthals more than was assumed. 

Neanderthals, modern humanity's closest genetic relatives, lived in ice age Europe and were spread widely across the continent. Recent research found that the archaic humans likely disappeared from northwestern Europe much earlier than previously thought, marking another milestone for understanding where they lived and what might ultimately have led to their extinction.

The three individuals studied in the April 7 paper had seven, six and nine Neanderthal DNA segments longer than 5 centimorgans, respectively, distributed in their genomes in a way that allowed researchers to estimate their most recent Neanderthal ancestors. 

One individual was estimated to have had a Neanderthal ancestor fewer than six generations back in his family tree, while the two other individuals had Neanderthal ancestors about seven generations prior.

That evidence clarifies a previously blurry picture of the interactions between early humans and Neanderthals, Hajdinjak said, noting that there hadn't been enough physical evidence to know for sure how common it was for modern humans to mate with their now-extinct Eurasian counterparts.

Prior research on a 40,000-year-old individual found in Romania revealed that the man had a Neanderthal ancestor between six and nine generations before he lived, according to Hajdinjak, but scientists couldn't be sure that his genome was indicative of a larger trend.

Having found more individuals from the period, researchers can now be more confident that such mixing "wasn't just a rare occurrence but was much more frequent" than previously anticipated, Hajdinjak said.

Interbreeding between modern humans and Neanderthals may also explain archaeological evidence suggesting that later Neanderthals picked up tools that had earlier been used by the Bacho Kiro Cave individuals, among other modern human groups. 

Such archaeological connections could have been forged as members of the respective species mated and mixed closely together, according to Hajdinjak.

The article "Initial Upper Palaeolithic humans in Europe had recent Neanderthal Ancestry," published April 7 in Nature, was authored by Mateja Hajdinjak, Max Planck Institute for Evolutionary Anthropology and Francis Crick Institute; Fabrizio Mafessoni, Laurits Skov, Benjamin Vernot, Elena Essel, Sarah Nagel, Birgit Nickel, Julia Richter, Benjamin M. Peter, Matthias Meyer, Geoff M. Smith, Virginie Sinet-Mathiot, Helen Fewlass, Shannon P. McPherron, Tsenka Tsanova, Janet Kelso and Svante Pääbo, Max Planck Institute for Evolutionary Anthropology; Alexander Hübner, Max Planck Institute for Evolutionary Anthropology and Max Planck Institute for the Science of Human History; Qiaomei Fu, Institute of Vertebrate Paleontology and Paleoanthropology; Oana Teodora Moldovan, Emil Racovita Institute of Speleology and Romanian Institute of Science and Technology; Silviu Constantin, Emil Racovita Institute of Speleology and CENIEH; Elena Endarova, National History Museum, Bulgaria; Nikolay Zahariev and Rosen Spasov, New Bulgarian University; Frido Welker, Max Planck Institute for Evolutionary Anthropology and University of Copenhagen; Lindsey Paskulin, University of Aberdeen; Sahra Talamo, Max Planck Institute for Evolutionary Anthropology and University of Bologna; Zeljko Rezek, Max Planck Institute for Evolutionary Anthropology and University of Pennsylvania; Svoboda Sirakova and Nikolay Sirakov, Bulgarian Academy of Sciences; Jean-Jacques Hublin, Max Planck Institute for Evolutionary Anthropology and Collège de France; and Pontus Skoglund, Francis Crick Institute.