The Mal’ta Boy and the Ghost Population That Turned Out to Be Real

In 2009, a team of geneticists visited the State Hermitage Museum in St Petersburg and sampled an upper arm bone. It belonged to a child excavated decades earlier at Mal’ta, a site on the Belaya River near Lake Baikal in south-central Siberia. Radiocarbon dating put the bone at about 24,400–23,900 years old. Its DNA would become the oldest modern human genome reported at the time.

Researchers call him MA-1. Most people know him as the Mal’ta boy. His genome turned out to be one of the most surprising ever read, because a child from the heart of Asia carried no close genetic link to East Asians.

The site: Venus figurines in Siberia

Mal’ta was excavated between 1928 and 1958. It yielded a wealth of finds, including about 30 carved human figurines. Such “Venus” figurines are rare in Siberia but well known from Upper Palaeolithic sites across Europe, a hint of connections long before genetics confirmed them. Our article on Venus figurines follows that tradition from France to Siberia.

The people of Mal’ta lived through the coldest stretch of the last Ice Age. Their survival this far north at that time is itself remarkable.

Three surprises in one genome

Maanasa Raghavan, Eske Willerslev and colleagues sequenced MA-1 to an average depth of about 1-fold. That is thin coverage, enough for population comparisons but too little to read every gene reliably. Even so, three results stood out when the paper appeared in Nature.

1. A European-linked mother’s line

MA-1’s mitochondrial DNA, passed down the maternal line, belongs to haplogroup U. That lineage is found at high frequency in Upper Palaeolithic and Mesolithic hunter-gatherers of Europe, thousands of kilometres to the west.

2. A Y chromosome near two roots

His Y chromosome sits at the base of haplogroup R, the group that today includes the most common lineages in western Eurasia and South Asia. Its sister lineage, haplogroup Q, is the most common Y lineage among Native Americans. MA-1 sits close to the branching point of both.

3. No close tie to East Asia

Across the rest of his genome, MA-1 is basal (an early offshoot) to modern western Eurasians and genetically close to modern Native Americans, but shows no close affinity to East Asians. Populations related to today’s western Eurasians, the authors concluded, lived much further north-east 24,000 years ago than anyone had assumed.

A ghost becomes a person

Before MA-1, population geneticists had noticed that present-day Europeans carry some ancestry from a population related to Native Americans. With no ancient sample to represent it, that source was a “ghost”: inferred from patterns in living people, with Native Americans standing in as the closest available proxy.

The Mal’ta boy gave that ghost a body. In 2014, Iosif Lazaridis and colleagues modelled most present-day Europeans as a mix of three ancestral groups. One they named the Ancient North Eurasians, related to Upper Palaeolithic Siberians like MA-1. They also showed that MA-1-related ancestry in Europe has increased since the time of the early farmers.

How did it get there? A 2015 study by Wolfgang Haak and colleagues found that hunter-gatherers from Russia share more alleles with MA-1 than other ancient or modern groups do. Those eastern European hunter-gatherers are a plausible source of the Ancient North Eurasian ancestry in Europeans today. Their descendants include the Yamnaya herders, who carried a diluted share of it west about 5,000 years ago.

Can the Mal’ta boy’s 1-fold genome be trusted?

A genome read only once on average invites suspicion, especially when its result is unexpected. Contamination from modern handlers, most of them of European ancestry, could in principle make an ancient Siberian look “western”.

The authors addressed this directly. They reported low contamination rates, and MA-1’s maternal and paternal lineages are rare or extinct today, which is hard to explain by modern contamination. Later work also supported the result: Lazaridis’s team found that MA-1 was a better stand-in for this hidden ancestry in Europe than the Native Americans first used to detect it.

The link to the first Americans

The most quoted result concerns the Americas. Raghavan’s team estimated that 14 to 38% of Native American ancestry may come from gene flow from the population MA-1 belonged to. That mixing likely happened after the ancestors of Native Americans split from East Asian ancestors, but before Native American populations diversified in the New World.

Two cautions matter here. First, the range is wide, and the authors warn that it assumes the ancestral populations were themselves unmixed. Second, the paper raises the possibility that this ancestry explains why some early American skulls look unlike East Asian ones. That idea links genes to skull shape, and skull shape is a weak guide to ancestry. The famous dispute over Kennewick Man shows how misleading skull shape can be.

The bigger point is secure. Some western Eurasian signals in Native Americans do not come from European colonists after 1492. They are far older, part of the mixed ancestry of the first Americans themselves. For the archaeology of how and when people crossed into the continent, see when did humans reach the Americas.

A population that lasted through the Ice Age

The same study sequenced a second Siberian, Afontova Gora-2, who lived about 17,000 years ago further west near Krasnoyarsk. Its genome showed similar signatures to MA-1, suggesting that people related to MA-1 occupied south-central Siberia throughout the Last Glacial Maximum, the peak of the last Ice Age.

The data behind our AADR Genome Atlas includes both individuals. MA-1 carries a mean date of about 24,320 years before present and a Y chromosome recorded as haplogroup R. Afontova Gora-2, at about 16,770 years, is recorded as R1b, and a third Afontova Gora individual dates to about 18,040 years. Ice Age genomes from Siberia remain rare, which is why each one carries so much weight.

Together, MA-1 and Afontova Gora-2 anchor the Ancient North Eurasians in time and place. When later studies describe a population as carrying “ANE” ancestry, from Bronze Age steppe herders to Native Americans, they are measuring how much it resembles these two Siberians. A 2015 study called MA-1 the type specimen for the group, in the way a named fossil anchors a species.

What one child can and cannot tell us

MA-1 is a single individual, sequenced at low coverage. He tells us that a population with this ancestry existed near Lake Baikal 24,000 years ago. He cannot tell us how large it was, how far it ranged, or exactly when it mixed with the ancestors of Native Americans. Later ancient genomes have refined the picture, and the exact proportions remain open.

Still, few fossils have done more with less. One small arm bone connected the hunters of Ice Age Siberia to Bronze Age Europe and to the first people of the Americas. To see where these branches fit on the full human story, open the interactive family tree.