Homo sapiens and Neanderthals didn’t just share space and time. They interbred, exchanged ideas

While new studies have reinforced the idea of Neanderthal and Homo sapiens admixture in Europe, the picture in South Asia regarding Homo sapiens’ relationship with Denisovans remains unclear.

In December 2024, two groundbreaking studies published in Nature and Science journals sparked a conversation about our evolutionary cousins, the Neanderthals. These papers shed new light on the complex relationship between Neanderthals and modern humans, revealing that their coexistence wasn’t just a matter of sharing space and timelines but involved a closer, more intimate connection, resulting in significant Neanderthal genetic ancestry getting archived in Homo sapiens population.

The papers deepen the discussion by refining the timeline of interbreeding to approximately 50,000 years ago. By analysing samples from multiple sites, the research reveals that this was not a single event but a process that unfolded over 7,000 years. The research also highlights that earlier Homo sapiens population in Europe (and beyond) was highly structured, where most of these sapiens population interacted with the Neanderthals with varying frequency, but some of these population, like Ranis and Zlatý kůň, went extinct and some prevailed, like the ones from the Bacho Kiro Cave in Bulgaria.

After this period, traces of Neanderthal DNA gradually diminished as evolution progressed. Additionally, the studies suggest that non-African modern human populations older than 50,000 years were not part of this genetic exchange. In essence, pre-50 ka (ka=thousand years) fossils and archaeological data likely represent populations that never established themselves and eventually disappeared.

While these discoveries have sparked intense debates among global human origins researchers, they add a layer of complexity to the story of South Asia. With limited fossil evidence, the wealth of archaeological data from this region remains unlinked to any specific hominid species. In light of recent research, we are compelled to confront some crucial questions: Who were the makers of the stone tools? Could there have been multiple groups living in South Asia, some of whom, like the populations of Ranis and Zlatý kůň, vanished without contributing to the genetic makeup of contemporary populations? This brings us back to the timeless quest of understanding: ‘Who are we, and how did we come to be?’

The evolutionary cousins

Around 1.8 million years ago in Africa, a new chapter in human evolution began. Homo erectus, not content with being confined to their African homeland, ventured into the vast landscapes of Europe and Asia. They were the first hominid species to leave Africa, setting the stage for a transformative chapter in evolutionary history. But the story takes an intriguing turn: the branch of Homo erectus that remained in Africa eventually gave rise to Homo sapiens—our own species. Meanwhile, those who travelled to Europe and Asia evolved into Homo neanderthalensis and the Denisovans—our distinct evolutionary cousins. 

It is crucial to note that evolution was not a linear process, nor was it a straightforward progression where one species disappeared to make way for the next. Instead, multiple species—often referred to as “ghost species”—coexisted and thrived simultaneously, until modern humans emerged as the dominant species.

In this complex story of one big family with multiple branches, there was a time when Neanderthals, Denisovans, and Homo Sapiens lived together. They communicated, cooperated, exchanged ideas, and innovated—leaving behind a cocktail of genetic data for future palaeontologists and archaeologists to piece together. Today, almost every non-African modern human population carries one to three per cent Neanderthal and Denisovan DNA. However, little is known about the genetics of the modern humans who interacted with their distinct cousins and the precise timing of this admixture.

The paper published in Nature on 12 December, led by Arev P Sumer (Sumer, A.P. et al. 2024), presents findings based on the analysis of seven individuals who lived around 45,000 years ago at Ilsenhöhle in Ranis, Germany. The study further compared it with genetic data from Zlatý Kûň in the Czech Republic that is dated back 47,000 years ago.

The results reveal a distinct familial connection between the Ranis and Zlatý Kûň individuals, showing that they were part of a small, isolated group representing the earliest known divergence from the ‘Out of Africa’ lineage. The genome of the Ranis individuals contains Neanderthal DNA from a single admixture event shared by all non-Africans, which occurred approximately 49,000 to 43,000 years ago. The findings also suggest that modern human remains older than 50,000 years found outside Africa likely belong to some of the oldest high-quality modern human genomes sequenced to date.  

The second paper, published in Science and led by Leonardo NM Iasi (Iasi et al 2024), analyses genomic data from 59 ancient individuals, sampled between 45,000 and 2,200 years before present, and 275 diverse present-day individuals from the global population. This study strongly supports a single extended period of Neanderthal gene flow into the common ancestors of all non-Africans, occurring between 50,500 and 43,500 years ago. The research highlights that this admixture lasted for approximately 7,000 years, and crucially, no evidence of interbreeding events after 40,000 years ago has been observed.

Both research papers establish a minimum time frame for the ‘Out of Africa’ migration and the interbreeding event that left a clear genetic imprint on non-African modern human populations. 

The ‘South Asian story’

While the new studies have reinforced the idea of Neanderthal and Homo sapiens admixture in Europe, the picture in South Asia regarding interbreeding and Homo Sapiens’ relationship with Denisovans remains unclear. The primary reason for this uncertainty is the lack of robust fossil evidence. 

South Asia, a region comprising culturally diverse countries like India, Pakistan, Sri Lanka, and Bangladesh, is rich in archaeological heritage, especially from prehistoric times. At Attirampakkam in Tamil Nadu, one of its most important sites, archaeologist Shanti Pappu and Akhilesh Kumar, along with others from the Sharma Centre for Heritage Education, have re-evaluated South Asia’s role in the ‘Out of Africa’ migration and early hominid dispersals. The Lower Palaeolithic, or early Acheulian level at this site, often associated with Homo erectus dispersals, is dated to approximately 1.5 million years ago. In contrast, the Middle Palaeolithic—which in Europe is linked with Neanderthals—has been dated to 385,000-172,000 years ago, revising the timeline for ‘Out of Africa’ migration into South Asia. 

Moreover, recent evidence from Hanumanthunipadu, excavated by archaeologist Anil Devara and others (Devara, Anil et al 2022), has yielded Middle Palaeolithic artefacts dated to 2,47,000 years ago. This points to a regional and indigenous development of toolkits by archaic hominin. Recent evidence such as late persistence of older stone tool technology (i.e., Acheulean), early emergence of highly advanced Middle Palaeolithic tech, and evidence of interbreeding with Archaics or ‘ghost lineages’ “makes Indian subcontinent an exciting place, [it] has all the potential to become a center of Human origins research which is often bound or focused to African continent or Europe,” remarked archaeologist Gopesh Jha, a doctoral researcher at the Max Planck Institute of Geoanthropology.

The identity of the archaic hominid species associated with early archaeological records in South Asia is still unknown, as there is no fossil evidence directly linked to these sites. However, in the early 1980s, at Hathnora, archaeologist Arun Sonakia found a fossilised cranium of an archaic hominin, which anthropologist Kenneth AR Kennedy later identified as remains of Homo sapiens (undated). The earliest reliably dated evidence of Homo sapiens in South Asia, however, comes from Sri Lanka, dated 38,000 years ago, with sites like Batadomba-lena—a rockshelter in the rainforests of southwestern Sri Lanka—yielding remains of Homo sapiens foragers dating to approximately 36,000 calibrated years before present (cal BP).

South Asia is surrounded by significant sites that have contributed to understanding human evolution. These include Al Nufud Al Kabir in Saudi Arabia, where Homo sapiens footprints were discovered; Iraq’s Shanidar Cave and the Zagros Mountains in Iran, home to Neanderthals; Teshik Tash in Uzbekistan, where a young Neanderthal burial was found; and the Baishiya Karst Cave on the Tibetan Plateau, where evidence of Denisovans—our distant cousins—was unearthed.

Amidst this diverse landscape of archaic hominins, South Asia occupies a unique yet often overlooked role in the grand evolutionary narrative. Often sidelined due to lack of fossil evidence, the region’s rich archaeological data, however, is a testament to the complex and nuanced lives of not just Homo sapiens but also archaic hominins. It reminds us that although fossils may be few, the echoes of ancient lives resonate through the land, telling a story that is far from finished.

Disha Ahluwalia is an archaeologist and research fellow at the Indian Council Of Historical Research. Views are personal. She tweets @ahluwaliadisha.

(Edited by Aamaan Alam Khan)