Genomic Data Reveal a Complex Making of Humans

The 24,000-year-old remains of a young boy from the Siberian village of Mal’ta have added a new root to the family tree of indigenous Americans. While some of the New World's native ancestry clearly traces back to east Asia, the Mal’ta boy’s genome — the oldest known of any modern human — shows that up to one-third of that ancestry can be traced back to Europe.

The results show that people related to western Eurasians had spread further east than anyone had suspected, and lived in Siberia during the coldest parts of the last Ice Age. “At some point in the past, a branch of east Asians and a branch of western Eurasians met each other and had sex a lot,” says palaeogeneticist Eske Willerslev at the University of Copenhagen, who led the sequencing of the boy’s genome. This mixing, he says, created Native Americans — in the sense of the populations of both North and South America that predated — as we know them. His team's results are published today in Nature1.


Two Khanty women in Man uskve nomad camp, Berezovsky, Khanty-Mansia, Russia

The team found that DNA from the boy's mitochondria — the energy-processing organelles of living cells — belonged to a lineage called haplogroup U, which is found in Europe and west Asia but not in east Asia, where his body was unearthed. The result was so bizarre that Willerslev assumed that his sample had been contaminated with other genetic material, and put the project on hold for a year.

But the boy’s nuclear DNA — the bulk of his genome — told the same story. “Genetically, this individual had no east Asian resemblance but looked like Europeans and people from west Asia,” says Willerslev. “But the thing that was really mind-blowing was that there were signatures you only see in today’s Native Americans.” This signal is consistent among peoples from across the Americas, implying that it could not have come from European settlers who arrived after Christopher Columbus. Instead, it must reflect an ancient ancestry. The Mal’ta boy’s genome showed that Native Americans can trace 14% to 38% of their ancestry back to western Eurasia, the authors conclude. Willerslev’s team suggests that after the ancestors of Native Americans split off from those of east Asians, they moved north. Somewhere in Siberia, they met another group of people coming east from western Eurasia — the people to whom the Mal’ta boy belonged. The two groups mingled, and their descendants eventually travelled east into North America.

This new origin story helps to resolve several peculiarities in New World archaeology. For example, ancient skulls found in both North and South America have features that do not resemble those of East Asians. They also carry the mitochondrial haplogroup X, which is related to western Eurasian lineages but not to east Asian ones. On the basis of these features, some scientists have suggested that Native Americans descended from Europeans who sailed west across the Atlantic. However, says Willerslev, “you don’t need a hypothesis that extreme”. These features make sense when you consider that Native Americans have some western Eurasian roots.


Figure 2: Admixture graph for MA-1 and 16 complete genomes.

We reconstructed admixture graphs using TreeMix21 to relate the population history of MA-1 to 11 modern genomes from worldwide populations22, 4 new genomes from Eurasia (Mari, Avar, Indian and Tajik ancestry) and the Denisova genome22 (Supplementary Information, section 11). The maximum-likelihood population tree inferred without admixture events places MA-1 on a branch that is basal to western Eurasians (Supplementary Fig. 12). However, a significant residual was observed between the empirical covariance for MA-1 and Karitiana, a Native American population, and the covariance predicted by the tree model (Supplementary Fig. 12). Consequently, gene flow between these lineages was inferred in all graphs incorporating two or more migration events (Fig. 2 and Supplementary Fig. 13). Bootstrap support for the migration edge from MA-1 to Karitiana, rather than from Karitiana to MA-1, was 99% in this analysis.

We investigated further the population history of MA-1 by conducting sequence read-based D-statistic tests23 on proposed tree-like histories comprising MA-1 and combinations of 11 modern genomes (Supplementary Information, section 13). In agreement with the TreeMix results, these tests reject the tree ((X, Han), MA-1) where X represents Avar, French, Indian, Mari, Sardinian and Tajik, consistent with the MA-1 lineage sharing more recent ancestry with the western Eurasian branch after the split of Europeans and east Asians (Supplementary Table 13). This result also holds true when the Han Chinese is replaced with Dai, another east Asian population (Supplementary Table 13). Notably, we can also reject the tree ((Han,Karitiana),MA-1) (Z510.8), suggesting gene flow between MA-1 and ancestral Native Americans, in accordance with the admixture graphs (Supplementary Table 13). This result is consistent with allele frequency-based D-statistic tests20 on SNP arrays for 48 Native American populations of entirely First American ancestry19, indicating that all tested populations are equally related to MA-1 and that the admixture event occurred before the population diversification of the First American gene pool/

The genetic affinity between Native Americans and MA-1 could be explained by gene flow after the split between east Asians and Native Americans, either from theMA-1 lineage into Native American ancestors or from Native American ancestors to the ancestors of MA-1. However, MA-1, at approximately 24,000 cal. BP, pre-dates time estimates of the Native American–east Asian population divergence event24,25. This presents little time for the formation of a diverged Native American gene pool that could have contributed ancestry to MA-1, suggesting gene flow from the MA-1 lineage into Native American ancestors. Such gene flows hould also be detectable using modern-day western Eurasian populations in place of MA-1. Consistent with this, D-statistic tests western Eurasian ancestry and 62–86% east Asian ancestry, but we caution that these estimates assume unadmixed ancestral populations.

Our study has four important implications. First, we find evidence that contemporary Native Americans and western Eurasians share ancestry through gene flow from a Siberian Upper Palaeolithic population into First Americans. Second, our findings may provide an explanation for the presence of mtDNA haplogroup X in Native Americans, which is related to western Eurasians but not found in east Asian populations29. Third, such an easterly presence in Asia of a population related to contemporary western Eurasians provides a possibility that non-east Asian cranial characteristics of the First Americans13 derived from the Old World via migration through Beringia, rather than by a trans-Atlantic voyage from Iberia as proposed by the Solutrean hypothesis30. Fourth, the presence of an ancient western Eurasian genomic signature in the Baikal area before and after the LGM suggests that parts of south-central Siberia were occupied by humans throughout the coldest stages of the last ice age.


Raghavan, M. et al. Nature dx.doi.org/10.1038/nature12736 (2013).

The study (Canfield et al. 2013) shows that Europeans and East Asians share common ancestry and they split around 50,000 years ago with a lighter skin mutation. It's known that both Europeans (5.9±0.08%) and East Asians (6.2±0.06%) inherited some portions of Neanderthal DNA because human-Neanderthal admixture occurred somewhere in the Middle East prior to Europeans' genetic split from proto-Asians, while Africans had not interbred with Neanderthals. Environmental factors may have contributed to the further differentiation of the two ethnic groups after the A111T mutation, which gave rise to modern Caucasians with lighter skin tones. Europeans who lived in colder climates in Scandinavia were positively selected to accumulate fat more effectively than East Asians to cope better with the cold weather, while East Asians went through another genetic mutation to adapt to the humid environment in Asia. This process of positive selection may explain the physical differences between Europeans and East Asians and Europeans are prone to gain more weight than their Asian counterparts, who are rarely overweight without making conscious efforts to lose weight. In other words, the metabolite concentration associated with Neanderthal ancestry among contemporary Europeans is directly linked to obesity, hypertriglyceridemia and coronary heart disease and Europeans are three times more likely to have a body mass index (BMI) of more than 40 (class III obesity) than Asians.



Although Neanderthals are extinct, fragments of their genomes persist in contemporary humans. Here we show that while the genome-wide frequency of Neanderthal-like sites is approximately constant across all contemporary out-of-Africa populations, genes involved in lipid catabolism contain more than threefold excess of such sites in contemporary humans of European descent. Evolutionally, these genes show significant association with signatures of recent positive selection in the contemporary European, but not Asian or African populations. Functionally, the excess of Neanderthal-like sites in lipid catabolism genes can be linked with a greater divergence of lipid concentrations and enzyme expression levels within this pathway, seen in contemporary Europeans, but not in the other populations. We conclude that sequence variants that evolved in Neanderthals may have given a selective advantage to anatomically modern humans that settled in the same geographical areas.

The ancestors of Neanderthals and modern humans diverged from a common ancestral population ~800–400 thousand years ago (KYA)1, 2, 3, 4, 5. Subsequently, Neanderthals evolved in Europe and Central Asia and possibly spread further east into the Asian continent6. The first successful migration of modern humans out of Africa can be traced back in the archaeological and genetic records to ~70–60 KYA7. After that, modern humans spread quickly across all continents and could have coexisted with Neanderthals in Europe and Central Asia for thousands of years before the Neanderthal extinction 45–30 KYA7, 8. Studies comparing the complete nuclear genome sequences of Neanderthals and contemporary modern humans indicate that out-of-Africa human populations, but not sub-Saharan African populations, contain genomic regions with unusually high similarity to the Neanderthal genome9, 10. In each individual, these regions were reported to occupy 1–4% of the total genome sequence10. This phenomenon implies the occurrence of gene flow from Neanderthals into those human populations that migrated from the African continent11, 12.


Figure 1: Proportions of NLS in contemporary human populations.

In this study, we asked whether genomic regions with high sequence similarity to the Neanderthal genome are distributed randomly across the genomes of contemporary modern humans. If certain regions in the modern human genome show a decreased Neanderthal gene flow, these regions may contain genetic changes essential to the modern human phenotype that are undergoing purifying selection against the Neanderthal alleles. By contrast, the presence of genomic regions experiencing excessive gene flow from Neanderthal may indicate that genetic changes that evolved in Neanderthals gave modern humans carrying the Neanderthal genotype a selective advantage.

In agreement with previous observations10, the genomes of contemporary humans of European and Asian descent showed greater similarities to the Neanderthal genome than did the genomes of the three populations of purely African descent. On average, the NLS frequency was 6.1±0.2% for contemporary humans of European and Asian descent, thus indicating a substantial excess of NLS in contemporary out-of-Africa populations (Fig. 1b,c, blue bars; Supplementary Tables 1–3). This D-statistic estimate is similar to the ones reported by other studies (4.8±0.2%)10, with the higher values obtained in our study potentially arising from the additional filtering of genomic sites polymorphic in Neanderthals. Further, in agreement with other studies10, there was no substantial difference in the genome-wide frequencies of NLS between European and Asian populations, with a slight tendency for higher frequencies in Asians: 5.9±0.08 and 6.2±0.06%, respectively18, 19.


Figure 2: Outstanding genetic features of lipid catabolism genes.

The excess of NLS observed in LCP genes for populations of European descent was based on a large number of sites (n=498), and was robust to bootstrapping across sites (P<0.01, 1,000 bootstraps, Supplementary Table 5; Supplementary Fig. 2). Notably, NLS were located in 23 independent genomic regions. Among the remaining 15 LCP genes that did not contain NLS, 8 did not contain sites showing divergence between Neanderthals and chimpanzees and the remaining 7 contained only a few such divergent sites (Supplementary Table 6). It is furthermore robust to the potential effects of DNA damage characteristic of ancient DNA samples, as excluding the C/T and A/G substitutions that may stem from deamination of cytosine residues in ancient DNA22, 23 did not affect the results (Supplementary Table 4). Repeating the analysis using the genome sequences of African (ASW, LWK, YRI), European (CEU, FIN, GBR, IBS) and East Asian (CHB, JPT) individuals, which were sequenced to deeper coverage at the pilot stage of the 1,000 genomes project, as well as the high-coverage genome sequences of African (ASW, LWK, YRI, MKK—Maasai in Kinyawa, Kenya), European (CEU, TSI) and East Asian (CHB, JPT) individuals provided by the Complete Genomics human diversity set24, confirmed our observations (Supplementary Tables 7 and 8). Finally, repeating the analysis using the high-coverage (Altai) and the low-coverage (Vindjia) Neanderthal genomes, separately, resulted in similar findings (Supplementary Table 9).

The excess of NLS in LCP genes in the genomes of contemporary Europeans may be due to a rapid spread of Neanderthal alleles in European ancestors because of their adaptive significance. Specifically, one may hypothesize that, over time, Neanderthals acquired changes to lipid catabolism, which were beneficial for survival in the environmental conditions of prehistoric Europe and Central Asia. These adaptive variants may then have been acquired by the modern humans through introgression and rapidly brought to high frequency by positive selection. To test this hypothesis, we searched for signatures of positive selection in the genomes of contemporary humans of European, Asian and African decent using composite of multiple signals (CMS) scores25. High CMS values indicate genomic regions under recent positive selection based on three distinct signatures of selection: long-range haplotypes, differentiated alleles and high-frequency-derived alleles. We indeed found a significant excess of high CMS scores in the LCP gene regions of contemporary Europeans but not Asians or Africans (Fig. 2b). This effect was robust at different CMS score cutoffs and was specific to LCP: no significant excess of high CMS scores in individuals of European descent was observed in comparable genomic regions containing other metabolic genes (Supplementary Fig. 3). Furthermore, within the LCP term, high CMS scores found in contemporary Europeans were associated with genes containing the excess of NLS, but were not associated with other LCP genes (two-sample Wilcoxon test, P=0.0003; n=45 and 20;

It is appealing to speculate that genetic variants affecting lipid catabolism in modern Europeans were acquired by modern human ancestors through genetic flow from Neanderthals, and then spread rapidly though the ancestral population by means of positive selection. Action of positive selection could be further explained by the adaptive significance of these variants in the geographic environment where Neanderthals had evolved and where Neanderthals and archaic Europeans later coexisted. It is noteworthy, however, that our observations are compatible with both introgression and incomplete lineage sorting hypotheses explaining the excess of genetic variants shared between contemporary humans and Neanderthals in out-of-Africa populations. Furthermore, while the excess of NLS in lipid catabolism genes is not observed in East Asian populations, we cannot assume that it is specific to Europeans. Complete genome sequences from a larger spectrum of human populations, especially from geographical regions coinciding with the Neanderthal living range, are needed to determine the full geographical spectrum of this effect. This is particularly true, given the fact that the Neanderthal area included Asian regions, such as the Altai Mountains. Still, the absence of NLS frequency increase in lipid catabolism genes in East Asian populations accompanied by no increase in the lipid concentration and enzyme expression divergence in the corresponding pathways indicates the geographical specificity of this phenomenon.

One further argument indirectly supporting geographical specificity and local adaptive significance of the lipid catabolism changes potentially induced by Neanderthal variants comes from a comparison with the genome of another archaic human species—Denisovans36. Analysis of lipid catabolism gene sequences with the Denisova genome revealed a higher frequency of sites shared between Neanderthals and moderns humans, derived respective to both the chimpanzees and Denisovans, in contemporary Europeans than in East Asians (Supplementary Table 14). Notably, no such difference was observed in the genome-wide analysis. This result shows that changes in lipid catabolism genes shared between Neanderthals and contemporary Europeans were not fully present in Denisovans. Given that the presumed geographical area of Denisovans includes most of Asia36, this result indirectly supports specificity of observed lipid catabolism change to the European part of the Eurasian continent.

We further note that a high frequency of NLS in lipid catabolism genes of contemporary Europeans does not require introgression, but is compatible with alternative scenarios. For instance, an alternative explanation of the general increase in NLS frequency in humans outside Africa, postulating the existence of a complex population structure within the African continent at the time of human and Neanderthal lineage divergence, has been hypothesized4. This hypothesis explains the presence of Neanderthal variants in non-African human populations by shared ancestry specific to ancestral human populations that left the African continent. If the lipid catabolism gene variants we find in Neanderthals and contemporary Europeans were already present in the ancestors of Neanderthals and out-of-Africa human populations, they may have independently increased in frequency in Neanderthals and humans situated in the European region. This scenario is probable if these genetic variants provided an adaptive advantage to both Neanderthal and human populations in the conditions of prehistoric Europe. While the presence of a recent positive selection signal in lipid catabolism gene variants containing NLS in modern Europeans supports such an adaptive scenario, the environmental pressures or functional mechanisms of this possible adaptive change remain elusive. Further studies of LCP conducted across multiple tissues and multiple contemporary human populations are needed to more fully assess the potential functional effects of this event.


Khrameeva, Ekaterina E., et al. "Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans." Nature communications 5 (2014).