Amerindians Are Even More Genetically Diverse and Older Than You Thought

Amerindians Are Even More Genetically Diverse and Older Than You Thought

Science DOI: 10.1126/science.aab3884

Genomic evidence for the Pleistocene and recent population history of Native Americans

Raghavan, Maanasa, Matthias Steinrücken, Kelley Harris, Stephan Schiffels, Simon Rasmussen, Michael DeGiorgio, Anders Albrechtsen, …Eske Willerslev.

How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Following their arrival to the Americas, ancestral Native Americans diversified into two basal genetic branches around 13 KYA, one that is now dispersed across North and South America and the other is restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians (including Siberians) and, more distantly, Australo-Melanesians. Putative ‘Paleoamerican’ relict populations, including the historical Mexican Pericúes and South American Fuego-Patagonians, are not directly related to modern Australo-Melanesians as suggested by the Paleoamerican Model.


Nature doi:10.1038/nature14895

Genetic evidence for two founding populations of the Americas

Skoglund, Pontus, Swapan Mallick, Maria C. Bortolini, Niru Channagiri, Tabita Hunemeier, Maria L. Petzl-Erler, Francisco M. Salzano, Nick Patterson, and David Reich.

Genetic studies have consistently indicated a single common origin of Native American groups from Central and South America. However, some morphological studies have suggested a more complex picture, whereby the northeast Asian affinities of present-day Native Americans contrast with a distinctive morphology seen in some of the earliest American skeletons, which share traits with present-day Australasians (indigenous groups in Australia, Melanesia, and island Southeast Asia). Here we analyse genome-wide data to show that some Amazonian Native Americans descend partly from a Native American founding population that carried ancestry more closely related to indigenous Australians, New Guineans and Andaman Islanders than to any present-day Eurasians or Native Americans. This signature is not present to the same extent, or at all, in present-day Northern and Central Americans or in a ~12,600-year-old Clovis-associated genome, suggesting a more diverse set of founding populations of the Americas than previously accepted.


Whole-genome and ancient DNA studies continue to topple conventional paradigms, befuddle academic researchers and fulfill out-of-America predictions. The two brand new studies by teams from the Reich lab at Harvard and the Willerslev lab at the University of Copenhagen postulate no fewer than three ancestry components in Amerindians related to three major population clusters in the Old World. Just 10 years ago the opinion was split between those scholars who imagined genetic and cultural continuity between Amerindians and East Asians and the peopling of the Americas at 15,000 years ago and those who postulated discontinuity from the ancestors of modern East Asians and the isolation of proto-Amerindians for some 15,000 years in Beringia. The latter model known as the “Beringian Standstill Hypothesis” (Tamm et al. 2007) sought to explain the presence of unique genetic signatures in modern Amerindians which required time and geographic isolation from the ancestral East Asian pool to accrue and stabilize. The Yana Rhinoceros Horn site located in close proximity to the East Siberian Sea shore and dated at 30,000 YBP provided the material evidence and the lowest chronological horizon for a proto-Amerindian source population presumably locked in a northern refugium during the LGM times and waiting for the ice shield to melt before spreading into the New World. While the two mental models differed in the extent to which they allowed for discontinuity between East Asians and Amerindians, they both imagined a homogeneous East Asian gene pool yielding an even more homogeneous Amerindian population.

With the sequencing of the DNA from the Mal’ta boy located in South Siberia and dated at 24,000 YBP, this thinking proved to be false. The Mal’ta site itself was located thousands of miles south of the mouth of the Yana River. More importantly, its DNA showed affinity to modern Amerindians and West Eurasians to the exclusion of modern East Asians (Raghavan et al. 2014). So, during the LGM times distinct Amerindian ancestry was already detectable in a geographically northeast Asian sample, while East Asian ancestry was not. Contrary to the prediction of both the East Asian Continuity and the Beringian Standstill models, a distinctive Amerindian genetic signature predated a distinctive East Asian genetic signature in the heart of Siberia and its closest affinities were with modern Europeans and not East Asians. Amerindians turned out to be older, more heterogeneous and less East Asian than everybody thought. The academic community responded to this puzzling finding by postulating an extinct “Ancient Northern European” (ANE) population that admixed with an East Asian population to generate ancestors of modern Amerindians. The ANE signature was later also found west of the Urals in ancient Kostenki DNA at 36,000 YBP (Seguin-Orlando et al. 2014; also covered here) as well as across a wide range of modern European, Middle Eastern and Caucasus populations including the putative Yamnaya ancestors of Indo-European speakers (Haak et al. 2015). But the best living example of that ancient Eurasian population continue to be Amerindians. The genetic impact of ANE on West Eurasians is so significant that all of the ancient samples discovered in Europe, from La Brana foragers to Stuttgart farmers, as well as all of the modern European populations score closer to modern Amerindians than to modern East Asians or Australo-Melanesians.

Up until now, Australo-Melanesians have never been a factor in the population genetic theories of the peopling of the Americas. Whether imagined as the earliest and sovereign wave of modern humans emanating from Africa along a “southern” migratory route or an early offshoot of an East Asian population, Australo-Melanesians have always been considered too old in terms of their divergence time and too southern in their geographic distribution to play a role in the peopling of the Americas via the Bering Strait bridge. Linguists, ethnologists, folklorists and ethnomusicologists, on the other hand, have long pointed out suggestive parallels between grammatical traits, mythological motifs, rituals and musical styles and instruments between some New World regions (especially, Amazonia but also North America) and the Sahul (see more here).

Physical anthropologists, too, advanced an argument that the earliest craniological material from the Americas is closer to Australo-Melanesians than to modern Amerindians or East Asians. This observation was so consistent across their Paleoindian sample that it warranted a formalization into a theory of two large-scale migrations to the Americas: the first one followed a coastal route and brought populations related to Australo-Melanesians from the deep south of the Circumpacific region, while the second one was derived from an inland source in northeast Asia (Neves & Hubbe 2005). Historic Fuegians and Pericues from Baha California were presented as the only surviving examples of the ancient Australo-Melanesian craniological pattern in the Americas (Gonzalez-Jose et al. 2003). However, ancient mtDNA extracted from Paleoindian skulls has invariably showed close affinities to all of modern Amerindians, thus undermining claims for a two-migration scenario (see, e.g., Chatters et al. 2014). Raghavan et al. (2015) re-examined the Paleoindian, Fuegian and Pericue craniological dataset and rejected the original conclusion:

“The results of analyses based on craniometric data are, thus, highly sensitive to sample structure and the statistical approach and data filtering used. Our morphometric analyses suggest that these ancient samples are not true relicts of a distinct migration, as claimed, and hence do not support the Paleoamerican model.”

But while the Australo-Melanesian hypothesis cannot be defended using craniological material, Skoglund et al. (2015) and Raghavan et al. (2015) have now furnished whole-genome evidence for a distinct Australo-Melanesian, or Oceanic ancestry in modern Amerindians. (Note that, ironically, the craniologists failed to see the Australo-Melanesian signature in modern Amerindian skulls.) Raghavan et al. (2015) report results from their in-depth D statistic analysis of shared drift between various populations:

“We found that some American populations, including the Aleutian Islanders, Surui, and Athabascans are closer to Australo-Melanesians compared to other Native Americans, such as North American Ojibwa, Cree and Algonquin, and the South American Purepecha, Arhuaco and Wayuu (fig. S10). The Surui are, in fact, one of closest Native American populations to East Asians and Australo-Melanesians, the latter including Papuans, non-Papuan Melanesians, Solomon Islanders, and South East Asian hunter-gatherers such as Aeta.”

Two examples from their Fig. S10 can be seen below.

Anthropogenesis-AustraloMelanesianAdmixture-2 copy

Anthropogenesis-AustraloMelanesianAdmxiture-1 copy








What it shows is that some Amerindian populations markedly shift in the direction of Papuans or Aeta compared to the majority of Amerindians. Importantly, this shift affects some of the same populations (e.g., Aleutians and Saqqaq) that also shift toward Han and Koryaks but, remarkably, the Australo-Melanesian pull is stronger than the East Asian pull! (see below from Fig. S10 in Raghavan et al. 2015, where negative D values are lower when Han and Koryaks are compared to Amerindians than when Papuans and Aeta are compared to them).

Anthropogenesis-AustraloMelanesianAdmixture-4 copy

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Importantly, the Australo-Melanesian shift is displayed by populations from both South America and North America, so it’s a low-frequency but pan-American phenomenon. Raghavan et al. (2013) showed that some North American populations are more East Asian shifted and less ANE-shifted than Central and South American populations. Now, they present evidence that those populations are more Australo-Melanesian-shifted than East Asian-shifted.

Working with a different sample, Skoglund et al. (2015) echo Raghavan et al. (2015) findings. They write:

“Andamanese Onge, Papuans, New Guineans, indigenous Australians and Mamanwa Negritos from the Philippines all share significantly more derived alleles with the Amazonians (4.6 . Z . 3.0 standard errors (s.e.) from zero). No population shares significantly more derived alleles with the Mesoamericans than with the Amazonians.”

Extended Data Table 2 in Skoglund et al. (2015) (see below) shows this excess of Australo-Melanesian alleles (Z values positive) in Amazonians (Surui, Karitiana and Xavante) compared to Central American Indians (as proxies for other Amerindians including the 12,000-year-old Anzick sample from Montana).

Anthropogenesis-AustraloMelanesianAdmixture-5 copy

Interestingly, the “Australo-Melanesian” footprint in the Old World is geographically broad spanning South Asia, Southeast Asia as well as the Sahul. It’s clearly the pre-Mongoloid and pre-Austronesian “substrate” in the eastern provinces of the Old World.

Predictably, Skoglund et al. (2015) and Raghavan et al. (2015) struggled to interpret these results. Raghavan et al. (2015) concluded:

“The data presented here are consistent with a single initial migration of all Native Americans and with later gene flow from sources related to East Asians and, more distantly [this statement is contradicted by their own data, as I showed above. – G.D.], Australo-Melanesians.”

But the conclusion from Skoglund et al (2015) is radically different:

“[O]ur results suggest that the genetic ancestry of Native Americans from Central and South America cannot be due to a single pulse of migration south of the Late Pleistocene ice sheets from a homogenous source population, and instead must reflect at least two streams of migration or alternatively a long drawn out period of gene flow from a structured Beringian or Northeast Asian source. The arrival of Population Y ancestry in the Americas must in any scenario have been ancient: while Population Y shows a distant genetic affinity to Andamanese, Australian and New Guinean populations, it is not particularly closely related to any of them, suggesting that the source of population Y in Eurasia no longer exists…”

Skoglund et al. (2015) seem to be more reasonable in their judgment. Their phylogenetic tree with admixture arrows (see on the left) captures well the ever-more-complex prehistory of the New World.

Anthropogenesis-AustraloMelanesianAdmixture-6 copy

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It used to be that Amerindians were depicted as a simple offshoot of a Han-like population (see the tree on the right, from McEvoy et al. 2010, Fig. 1). The branch connecting them to East Asians has always been long but it was interpreted as the effect of a bottleneck induced by the Beringian Standstill and subsequent further isolation in a newly-colonized continent. Now, Amerindian ancestry, whether northern or southern, spans the whole gamut of extra-African genetic diversity. In addition, the Australo-Melanesian link in the New World is clearly connected to the discovery of a stronger Denisovan signal in Amerindians vs. East Asians (Qin & Stoneking 2015), which suggests that Amerindians must be older than the LGM time frame entertained by Raghavan et al. (2015).

While Raghavan et al. (2015) dismiss the Australo-Melanesian hypothesis advanced by craniologists, Skoglund et al. hope that direct DNA analysis of the Paleoindian material from Amazonia will yield support to their finding. Importantly, just like the mythical “Ancient Northern Eurasian” (ANE) population to which the Mal’ta boy belonged is claimed to no longer exist in the Old World, the ancient Population Y ceased to exist, too. But apparently their descendants are well and alive in the New World.

Out-of-America can end the torturous guesswork that the population genetic community is engaged in trying to explain the high allelic diversity and the diverse set of continental connections to the Old World exhibited by Amerindian genomes. Phenomenal linguistic and cultural diversity in the Americas (with its well-documented connections to West Eurasia, East Asia and the Sahul) now receives full corroboration from population genetics. One pulse from a single, structured ancient Amerindian population followed by long-range migrations to the Sahul, Middle East/Caucasus, Europe and East Asia around 60-40,000 YBP provides an elegant explanation to the observed cross-disciplinary pattern.