Ancient DNA | Ice Age Siberia | Europe and the Americas
The ghost population in your DNA
In 2012, geneticists predicted a population that no one had ever sampled: Ice Age people of northern Eurasia who had left their mark on both Europeans and Native Americans. Two years later, a 24,000-year-old child from Mal'ta, near Lake Baikal, gave the ghost a genome. We placed him, the two Yana boys and Afontova Gora 3 in Global25.
Hero image: AI generated illustration of an Ice Age camp in southern Siberia about 24,000 years ago, with a dwelling of mammoth bones, tusks and hides, a hunter returning with a young reindeer, a woman scraping a hide and a child holding an ivory bird figurine, inspired by the finds from Mal'ta. The people are drawn with a more East Asian appearance than the genome suggests: the Mal'ta boy was genetically closer to West Eurasians and Native Americans than to East Asians. Clothing, tools and the dwelling are approximations, and the scene does not portray the Mal'ta boy or any documented moment.
Most people of European descent carry a part of their ancestry from Ice Age hunters who lived in Siberia. So do Native Americans, from Alaska to Patagonia. Yet for years nobody knew who these hunters were. They were a ghost: a population whose existence could be inferred from the DNA of living people, but of which no bone had ever been sequenced.
The ghost now has a name, the Ancient North Eurasians, and several genomes. This is the story of how it was predicted, how it was found, and how much of it survives in people today, with a Global25 analysis of the oldest genomes available.
A population predicted before it was found
In 2012, Nick Patterson, David Reich and colleagues developed statistical tests able to detect ancient mixtures in the genomes of living people. Applied to Europeans, they produced a surprise. Northern Europeans looked like a mixture of a population related to Sardinians and Basques and of another population distantly related to Native Americans.
No one thought that Native Americans had migrated to Europe. The simplest explanation was a third population, now vanished, that had contributed to both: Ice Age hunters of northern Eurasia, some of whose relatives moved east towards America while others, much later, moved west towards Europe. The authors called it the Ancient North Eurasians. Population geneticists call this kind of population a ghost.
In 2014, Iosif Lazaridis and colleagues showed that most Europeans descend from three ancestral populations: western European hunter-gatherers, early farmers from Anatolia, and the Ancient North Eurasians, who contributed up to about 20% of the ancestry of present-day Europeans. By then, the ghost had already been found.
The boy from Mal'ta
Mal'ta is an Upper Palaeolithic site on the Belaya river, a tributary of the Angara, northwest of Irkutsk and Lake Baikal in southern Siberia. Discovered in 1928, it was excavated for three decades, above all by the Soviet archaeologist Mikhail Gerasimov, and became famous for about thirty female figurines, the so-called Venus figurines, and for birds carved from mammoth ivory. Among the finds was the skeleton of a young child, known today as MA-1 and kept at the State Hermitage Museum in Saint Petersburg.
In 2014, Maanasa Raghavan, Eske Willerslev and colleagues sequenced his genome. The remains were dated to about 24,000 years ago, just before the coldest phase of the last Ice Age. The result matched the prediction. The Mal'ta boy was related to present-day West Eurasians and to Native Americans, but not specifically to East Asians. His maternal lineage belonged to haplogroup U, common among European hunter-gatherers, and his paternal lineage sat near the root of haplogroup R, the family of R1a and R1b, today the most frequent Y-chromosome lineages in Europe.
The authors estimated that 14 to 38% of Native American ancestry may come from a population related to the Mal'ta boy. They also sequenced Afontova Gora 2, an individual who lived on the Yenisei river near Krasnoyarsk about 17,000 years ago, after the glacial peak, and found that he resembled the Mal'ta boy. Southern Siberia had kept the same population through the harshest phase of the Ice Age.
A better genome later came from the same area: Afontova Gora 3, directly dated to about 16,000 BC, or 18,000 years ago. In 2018, Iain Mathieson and colleagues noticed that this individual carried the variant of the KITLG gene associated with blond hair in Europeans, making Afontova Gora 3 the earliest known carrier. This suggests that the variant reached Europe with people of partly Ancient North Eurasian descent.
Yana: Arctic ancestors 31,600 years ago
In 2019, Martin Sikora, Eske Willerslev and colleagues went further back. At the Yana Rhinoceros Horn Site, on the Yana river above the Arctic Circle, they sequenced two milk teeth from two boys who lived about 31,600 years ago. They called their population the Ancient North Siberians.
The Yana boys were distantly related to the early hunters of western Eurasia, with a share of East Asian related ancestry estimated at 22 to 50%. They carried Y-chromosome haplogroup P1, the common ancestor of haplogroup R, frequent in Europe, and haplogroup Q, which is carried by most Native American men. The two branches of this paternal family tree would end up on opposite sides of the world.
The Mal'ta and Afontova Gora people are later relatives of this northern Ice Age population. In northeastern Siberia, the Ancient North Siberians were later largely replaced by people of mainly East Asian ancestry, the ancestors of the Ancient Palaeo-Siberians, who are closely related both to peoples of the Russian Far East such as the Koryaks and to Native Americans.
What Global25 shows
We placed these genomes in Global25, using Davidski's published coordinates and the Moriopoulos 2026 collection of averages. The files contain the Mal'ta boy (MA-1, 71% of the markers covered), both Yana boys (more than 99%), Afontova Gora 3 (only 20%, so its position is less precise), and the reference genomes needed to model them. Admixture models were fitted by non-negative least squares. The fit distance, multiplied by 1000, measures how well a model reproduces the target: for a single genome, random noise alone produces about 25 units.
| Target | Global25 model | Fit distance | Reading |
|---|---|---|---|
| Yana 1 (31,600 years) | Kostenki 14 71% + Tianyuan 29% | 51 | Within the published range of 22 to 50% East Asian related ancestry |
| Yana 2 (31,600 years) | Kostenki 14 71% + Tianyuan 29% | 47 | Same recipe: two boys of one population |
| Mal'ta boy (24,000 years) | Best model: Yana 100% | 202 | Cannot be built from older genomes: a separate pole |
| Eastern hunter-gatherers | Loschbour 24% + Mal'ta boy 76% | 92 | About three quarters Ancient North Eurasian |
| Eastern hunter-gatherers | Loschbour 26% + Afontova Gora 3 74% | 62 | Same share, better fit with the later Siberian |
| Yamnaya (Samara) | Eastern hunter-gatherers 60% + Caucasus hunter-gatherer 40% | 65 | The steppe herders who carried the ghost into Europe |
| English | Loschbour 13% + Anatolian farmers 39% + Yamnaya 48% | 47 | 48% x 0.60 x 0.76: about 22% Ancient North Eurasian |
Fit distance multiplied by 1000. For a single genome, random noise alone produces about 25 units. Loschbour: western hunter-gatherer from Luxembourg. Caucasus hunter-gatherer: Kotias, Georgia. Our analysis.
The two Yana boys give the same answer: 71% ancestry related to Kostenki 14, a hunter of the Don river 37,000 years ago, and 29% related to Tianyuan, an early East Asian buried near Beijing 40,000 years ago. The proportion falls within the range published by Sikora and colleagues, and the two boys are as close to each other (29 units) as two members of one population.
The Mal'ta boy, by contrast, cannot be built from older genomes. The best model leaves a distance of more than 200 units. Between Yana and Mal'ta, about 7,000 years of separate history, including the coldest phase of the Ice Age, gave the Ancient North Eurasians their own genetic signature. In Global25, this signature works as a separate pole, and that is why it can be detected in later populations.
The principal component analysis shows this clearly. The first axis separates East Asians and Native Americans, on the left, from West Eurasians, on the right. The second axis lifts upwards everyone who carries Ice Age northern ancestry. The Mal'ta boy and Afontova Gora 3 sit in the middle of the first axis and high on the second. Above them, on the left, come the Native Americans; to their right, the Eastern hunter-gatherers of Russia, then Yamnaya, Finns and the English. The Yana boys remain close to Kostenki 14 and the early West Eurasians.
No one alive is close to the Mal'ta boy
Who is genetically closest to the Mal'ta boy today? In Global25, the nearest present-day populations are the Udmurts of the Volga and Ural region (182 units), the Besermyans (189), the Saami (195) and the Pamiri peoples of the Pamir mountains (197). For Afontova Gora 3, the list is similar: Udmurts, Saami, Besermyans, Khanty, and the Tlingit of Alaska. But all these distances are far greater than the 30 to 50 units that usually separate closely related populations in Global25. No one alive descends mainly from this population: its ancestry survives only in mixtures.
How the ghost reached Europe
The Ancient North Eurasians never walked into Europe as such. Their ancestry arrived in two steps. First, it mixed with western hunters to form the Eastern hunter-gatherers of Karelia and the Volga, between about 11,000 and 7,000 years ago. In our test, they are about three quarters Ancient North Eurasian. Then, around 5,000 years ago, the Yamnaya herders of the Pontic steppe, 60% Eastern hunter-gatherer and 40% Caucasus hunter-gatherer in Global25, spread across Europe.
A Global25 model that uses the Mal'ta boy directly as a source for present-day Europeans fits poorly, because it misses this history. We therefore used a chain: each population was modelled as western hunter-gatherer, Anatolian farmer and Yamnaya, and its Yamnaya share was converted into Ancient North Eurasian ancestry (0.60 times 0.76). For western and central Europe, the direct model gives similar values, within about 3 percentage points.
The result is a clear gradient. Sardinians, who descend mostly from early farmers, carry about 2%. Basques and Andalusians carry 12 to 14%, Tuscans and Greeks 17 to 18%, the English, Irish, Norwegians, Hungarians and Poles 22 to 24%, and Estonians, Lithuanians, Russians, Mordvins and Finns 26 to 28%. Our values for northeastern Europe are slightly higher than the figure of about 20% published in 2014, which was estimated with a different method. For Finns, Russians and Mordvins, the direct model gives even more (35 to 39%), because it also absorbs a later Siberian contribution that the Yamnaya chain does not see.
Your own results. If you model your own Global25 coordinates with the Mal'ta boy as a source, expect a margin of error of about 3 percentage points. In our test, single genomes built from a Sardinian profile with no added Ancient North Eurasian ancestry returned 0 to 6%; with 10% added, they returned 9 to 16%. Differences of a few points between two people are not meaningful.
The Native American half of the story
For Native Americans, Global25 cannot give a reliable percentage. During their long isolation in Beringia and their expansion across the Americas, Native American populations accumulated a strong genetic drift of their own. Every model leaves distances of 400 to 500 units for present-day groups such as the Karitiana of Brazil, and about 190 for the Ancient Beringian from Upward Sun River, Alaska, who lived 11,500 years ago.
Global25 can, however, answer a simpler question. Starting from an East Asian source, which West Eurasian ingredient best improves the model? We tested twelve candidates, from the oldest Upper Palaeolithic genomes to early farmers and present-day English.
The answer is the same for all four Native American targets we tested: the Karitiana, the Mixe of Mexico, the Ancient Beringian and Anzick, a child buried in Montana about 12,700 years ago. The best ingredients are always Afontova Gora 3, the Mal'ta boy, or later populations rich in their ancestry, such as the Tyumen hunter-gatherers and the Botai horse herders of Kazakhstan. Western hunter-gatherers, Anatolian and Iranian farmers, and even present-day English improve the models three to seven times less. The West Eurasian part of Native American ancestry is not European: it is Ancient North Eurasian.
Afontova Gora 3 slightly outperforms the Mal'ta boy for every target. This is consistent with a closer link between Native Americans and the Ancient North Eurasians who lived after the glacial peak, but the difference is small and Afontova Gora 3 has low coverage, so we do not over-interpret it. The published estimates, of 14 to 38%, remain the reference for the size of this contribution.
Siberia today: who kept the ghost ancestry?
In Siberia itself, the Ancient North Eurasian legacy is uneven. We modelled present-day Siberian peoples with three sources: the Mal'ta boy, an East Asian genome from Devil's Gate in the Russian Far East, and present-day Russians, to absorb recent admixture. The fits are approximate, because Siberian peoples also have their own drift, so the order matters more than the exact values.
The Kets of the Yenisei river come first, with 48% beyond any Russian admixture, followed by the Selkups, the Khanty and the Mansi of western Siberia. This matches the 2016 genomic study of the Kets by Pavel Flegontov and colleagues, which found that Kets, Mansi and Selkups, together with Native Americans, carry the highest Ancient North Eurasian ancestry among present-day populations. In the far northeast, the Chukchi, Koryaks, Itelmens and Yupik carry 20 to 30%, inherited through the Ancient Palaeo-Siberians, the close relatives of the ancestors of Native Americans. Further east and south, Evenks, Yakuts, Buryats, Ulchi and Nivkhs carry little: their ancestors arrived later from the Amur and Baikal regions and largely replaced older populations.
The last ghosts. In 2021, Fan Zhang and colleagues sequenced the oldest Bronze Age mummies of the Tarim Basin, in Xinjiang, about 4,000 years old. To the surprise of many researchers, they were not migrants from the steppe: they descended mostly from an ancient population related to Afontova Gora 3, with a minority of ancestry from the Baikal region. Isolated in their oasis, they may have been among the last people whose ancestry was largely Ancient North Eurasian.
A ghost in all of us
The Ancient North Eurasians were not ancestors of one people, but a bridge between continents. Their Ice Age relatives in Siberia joined East Asian groups on the way to America. Their descendants on the Russian plains mixed with western hunters, then with Caucasus hunter-gatherers, and the resulting steppe herders spread their ancestry across Europe and into Central and South Asia. When a Briton and a Mixe from Oaxaca share a small part of their ancestry, they are sharing the legacy of people who lived in Ice Age Siberia more than 20,000 years ago.
Key points
- The Ancient North Eurasians were predicted in 2012 from the DNA of living Europeans, before any of their bones had been sequenced.
- The genome of the Mal'ta boy, about 24,000 years old, published in 2014, confirmed their existence: he was related to both West Eurasians and Native Americans.
- The Yana boys, 31,600 years old, belong to the older Ancient North Siberian population; in Global25 both model as 71% Kostenki-like and 29% Tianyuan-like.
- In Europe, the ghost ancestry arrived through Eastern hunter-gatherers and the Yamnaya: about 2% in Sardinians, about 22% in the English, up to 28% in Finns and Russians in our chain model.
- In Native Americans, the West Eurasian part of their ancestry is specifically Ancient North Eurasian; published estimates range from 14 to 38%.
- In Siberia, Kets, Selkups, Khanty and Mansi have kept the most; Evenks, Yakuts, Buryats and Nivkhs carry little.
Global25 coordinates used in this article
The Ice Age genomes and the main model sources. They can be pasted directly into the Vahaduo tool.
Russia_Yana_UP:Yana1,0.030732,-0.072103,-0.014331,0.091086,0.012925,0.001673,-0.011751,-0.010384,0.037019,-0.003827,0.014290,-0.005545,0.006095,-0.009221,0.008007,-0.003713,0.003129,0.000000,-0.004022,0.012631,0.005241,0.005812,-0.010969,-0.030245,-0.002754
Russia_Yana_UP:Yana2,0.026179,-0.070072,-0.023004,0.094316,0.007694,0.000558,-0.013631,-0.015461,0.035792,0.007107,0.013153,-0.001798,0.008028,-0.019130,0.012351,0.011005,0.002738,0.002407,0.004274,0.021885,0.005865,0.009398,-0.010846,-0.025546,-0.001437
Russia_MA1_UP:MA1_Malta_boy,0.076261,-0.024373,0.036581,0.187018,-0.069859,0.045738,-0.050057,-0.059305,-0.019021,-0.068339,0.030691,-0.012589,0.016353,-0.044039,0.018051,0.021214,-0.008084,0.002280,-0.003771,0.002751,-0.028075,0.005070,0.013188,-0.007471,0.000000
Russia_AfontovaGora3_UP:AG3,0.092197,-0.011171,0.079195,0.221902,-0.087709,0.043228,-0.063923,-0.075689,-0.033746,-0.090936,0.050503,-0.010491,0.020664,-0.070463,0.017236,0.018695,-0.015385,0.006588,0.001383,-0.004502,-0.035687,0.011005,0.020582,0.005904,-0.004670
Russia_Kostenki14_UP:Kostenki14,0.029594,0.013202,-0.009428,0.069768,0.019696,0.000000,-0.008225,-0.009923,0.040905,0.010205,0.005846,-0.007044,0.002081,-0.012661,0.010315,0.025590,0.007953,0.001267,-0.011941,0.016633,0.021961,0.001978,-0.009490,-0.054104,0.001197
China_Tianyuan_UP:Tianyuan,-0.030732,-0.262007,-0.075801,0.071383,0.033545,-0.019522,-0.005640,-0.001615,0.041109,0.019864,-0.003897,-0.001349,-0.005500,-0.000826,0.004072,0.003447,0.007041,0.001647,-0.003268,0.026263,-0.002620,0.010758,-0.013804,-0.011086,0.009580
Luxembourg_Mesolithic:Loschbour,0.130897,0.109677,0.203268,0.198323,0.162800,0.059404,0.014571,0.038537,0.100217,0.016401,-0.015589,-0.017684,0.019772,-0.000826,0.061210,0.070272,0.002738,0.007475,-0.009302,0.065656,0.118042,0.010881,-0.048929,-0.174723,0.019399
Russia_EHG,0.117238,0.029450,0.126335,0.204460,-0.018773,0.058009,-0.017626,-0.029306,-0.004704,-0.083464,0.019324,-0.016036,0.029881,-0.050370,0.022122,0.030496,-0.001956,0.005448,0.001257,0.017008,-0.003494,0.022010,0.015159,-0.014942,-0.012933
Georgia_Kotias_CHG,0.089920,0.103584,-0.088246,-0.004845,-0.089555,0.020359,0.023266,-0.001154,-0.130486,-0.080002,-0.007632,0.024878,-0.052626,0.007707,0.026465,-0.029700,0.027772,-0.010769,-0.023757,0.037518,0.030945,-0.006677,0.005300,-0.020846,0.001557
Russia_Samara_EBA_Yamnaya,0.125838,0.089254,0.042908,0.115456,-0.027868,0.044685,0.004491,-0.002949,-0.054858,-0.072996,0.001858,0.000350,-0.001652,-0.023610,0.037263,0.015734,0.000000,-0.001478,-0.001704,0.012506,-0.003120,0.001374,0.011229,0.018436,-0.004524
Turkey_N,0.117902,0.180087,0.003426,-0.101059,0.051240,-0.047969,-0.003799,-0.006846,0.036167,0.080678,0.008261,0.011309,-0.024164,0.000579,-0.042712,-0.010370,0.022556,0.001388,0.013649,-0.010448,-0.014261,0.005693,-0.004904,-0.003750,-0.004436
Russia_DevilsCave_N,0.020868,-0.448187,0.068762,-0.050173,-0.040931,-0.036534,0.004622,0.008000,0.003613,0.021686,-0.051802,-0.005745,0.000545,0.007982,-0.009093,-0.009105,-0.004477,0.007475,0.017723,0.011631,0.008277,-0.026462,-0.020459,-0.001968,-0.013332
USA_Ancient_Beringian:USR1,0.037562,-0.305674,0.088623,0.087533,-0.086478,-0.018407,-0.129256,-0.158763,-0.012271,-0.025149,0.003085,-0.006744,0.008176,-0.007982,-0.009093,0.001326,0.001173,0.008742,0.006285,0.013632,-0.009358,0.003957,0.002465,0.003133,0.002275
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- Data Global25 coordinates by Davidski (Eurogenes), and the Moriopoulos Collection 2026 of averages. Admixture models, principal component analysis and noise tests: ExploreYourDNA.