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The Native Americans Before the Native Americans

'The Negroid Indigenous population predates the Ice Bridge descendants' RAZIB KHAN FEBRUARY 2, 2024 ARTICLES

In 2021, scientists radiocarbon-dated pollen found in human footprints at the White Sands National Park in New Mexico and came back with dates of greater than 20,000 years. Critics demanded more evidence, and in 2023, using new data and more advanced methods seems to have confirmed the date. Though there are still skeptics, the White Sands discovery is not the only site that dates to the Last Glacial Maximum between 20-26,000 years ago.

For decades, paleoanthropologists believed the ancestors of American natives were a Siberian tribe that came over from Asia to North America just 13,500 years ago, crossing over Beringia, a landmass exposed by sharply reduced sea levels during the last Ice Age. They called these people the Clovis Culture based on distinct spear points first discovered next to the remains of mammoths at a site in New Mexico. The paradigm posited that over 300 years these big game hunters spread across the New World, driving megafauna into extinction and eventually diversifying into the people we know today as Native Americans.

Yet, already 25 years ago, the evidence contradicting this paradigm became quite strong. There were too many sites that predated Clovis by centuries. Monte Verde in Chile, where archaeologists have been excavating since 1977, is extensively documented and is over 1000 years older than Clovis. In Mexico, Chiquihuite Cave has yielded 1900 stone artifacts, and dates were returned as early as 31-33,000 years ago, long before the Last Glacial Maximum. Being more conservative, the researchers at this site are convinced that humans were claiming it 20,000 years ago at the latest. These dates imply that this population, presumably part of the same group that was leaving footprints at White Sands National Park, arrived much earlier because the expansion of the ice sheets beginning 26,000 years ago definitively blocked the interior migration path and would have made a sea-borne route along the western periphery very difficult as glaciers pushed to the edge of the Pacific.

In 2014, geneticists discovered and sequenced the 24,000-year-old remains of a boy who died on the shores of Lake Baikal and concluded that people related to him contributed 10-15% of the ancestry of modern Europeans and 40% of the ancestry of Native Americans. In one fell swoop, earlier anthropological and genetic suspicions of connections between the two populations were explained. Then, in 2015, the same group of geneticists found that some tribes in the Amazon had ancestry which tied them more closely to Australian Aboriginals and Papuans than to Siberians! This seemed to be a crazy result, but follow-up work not only confirms its correctness, but shows that this exotic ancestry is found across the central band of South America, from the coast into the Amazon. The latest controversial but methodologically cutting-edge models imply that humans arrived in the New World more than 30,000 years ago, long before the proto-Beringian population was even hypothesized to exist. The world we thought we knew in the 1990s turns out not to be anything close to the world that might have been. Over the last 25 years, there has been a revolution in our understanding of how the first humans arrived in the Americas and who they were. But these revelations have not illuminated the totality of the past; there still are dragons in the blank spots in our map of this surprisingly ancient New World.  Native Americans And Europeans Share Paleo-Siberian Ancestors

Some of the more sensational arguments on the ancestry of Native Americans turn out to have fallen flat. The Solutrean hypothesis, which argued that Native Americans descended at least in part from an Ice Age European culture that flourished 20,000 years ago based on similarities between that culture’s tools and that of the Clovis people, is clearly wrong. The similarities in tool types, separated by 4000 years between the extinction of the former and the emergence of the latter, are likely just convergence, the product of the constraints in functionality and physics.

You don’t need fancy genetics to reach this conclusion. Not only do many native peoples of the New World look like they have anthropological affinities with the people of eastern Eurasia, but 20th-century physical anthropological metrics like the shape of teeth or the dimensions of the skull tended to cluster Native Americans with East Asians. Additionally, before the Norse, all the evidence points to contacts with Asia rather than the continent to North America’s east. The native peoples of the Arctic clearly have cultural connections to the indigenous tribes of far east Siberia, in particular the Chukchi. 

This contact was profoundly impactful in the first millennium AD when the recurved Asian war bow arrived in Alaska in the 7th century AD over the Bering Strait, to be followed several centuries later by laminar armor familiar from medieval Japan. The New World is characterized by stark isolation, with North American civilizations at the late Neolithic and early Bronze Age stages of complexity when Eurasia was on the precipice of early modernity, but it was also permeable across the sieve of the circumpolar world. A physical anthropologist once told me that even after more than 10,000 years, the indigenous people of the Amazon retain “Siberian proportions”—shorter legs and arms and a longer torso. In many ways, it is easier for cold-adapted people to flourish in the tropics; after all, our lineage was originally tropical, and the cultural toolkit for the cooler latitudes can simply be discarded—literally, in the case of clothes. The world of the early Amerindians was not the lush and verdant Amazon basin; it was the vast expanse of land exposed during the last Ice Age between Alaska and Siberia, Beringia. Here they arrived 20,000 years ago, likely following herds of mammoth on its north slope, on the tundra facing the Arctic, while they exploited marine resources in the south, along the seas characterized by fog and peat-bogs. 

Genetic and anthropological work with blood groups and skeletal features established that the closest population to New World natives were the people of East Asia, supporting the theory promoted by geologist David Hopkins in the 1960s of a migration over a Bering land bridge. Nevertheless, simple physical inspection yielded the inference that these were not quite the same people as those of China, Korea, and Japan. Geography pointed to Siberia, but even here, the modern-day Yakut looks somewhat different from Native Americans, who often have prominent aquiline noses. Of course, aquiline noses are common in western Eurasia, suggesting possible connections with Europeans. The answer was prefigured by paternal lineage as traced through the genealogy transmitted from father to son. By the first decade of the 21st century, it was clear that the overwhelming majority of Native American Y chromosome lineages belong to the Q haplogroup—the class of related men bracketed together as a distinct cluster with a common ancestor defined by informative mutations. 

The nomenclature of Y chromosomes is alphabetic, and the closest “sibling” to Q is R, which, in the forms of R1a and R1b, is the dominant haplogroup in Europe. The Y chromosomal data points to a genetic relationship between the forefathers of Europeans and Native Americans, which remained inexplicable. More suggestively, in 2012, a new method of constructing genetic relationships that use graphs or networks instead of trees, with the gene flow represented by “edges” connecting different branches, yielded a hypothetical migration on the schematic connecting Europeans and Native Americans. Though this jumped out of the data, there was no historical paradigm to integrate the result.  Two years later, the Ma’lta boy, dating to 24,000 years ago, was the first of many finds from Siberia where ancient DNA provided the “missing link” between these two populations, one in the New World and the other at the western antipode of Eurasia. The perplexities of the past could finally find an elegant explanation.

After the expansion of modern humans into Eurasia more than 45,000 years ago, one branch of Homo sapiens related to the foragers of Pleistocene Europe continued to move eastward until their furthest outliers reached northeastern Siberia. Called “Ancient North Eurasians” (ANE) by scholars, no human population is a direct singular descendent of this group. Modern Siberians descend predominantly from later waves of migrants from East Asia, who absorbed the first modern human populations.

The ancestors of Native Americans are often called, originally, “Paleo-Siberians,” a fusion of ANE and East Asians moving up from the south. Though the overall ancestry, around 65%, tilts toward East Asians, the paternal lineage is biased toward the remainder, the ANE heritage. The ANE and East Asian ancestors of Native Americans seem to have diverged from the ancestors of the populations that later contributed to modern Siberians and Europeans between 20-25,000 years ago.

Walking From Siberia to Alaska, Sailing to America

As sea levels dropped 400 feet lower than today during the Last Glacial Maximum, a vast tundra opened up between the eastern tip of Siberia and northern Alaska. This now sunken land was a prime megafauna habitat. Despite its northern location, this dry ecosystem was not glaciated and likely supported large human populations that followed the migration of mammoths. In contrast, the area to the south—the exposed land that is today the northern Bering Strait—was dominated by peat bogs, and any forager populations would likely have had to rely on marine resources. Rather than a single tribe with a single culture, the early Beringians were likely adapted to numerous local ecologies. And yet, these people did not move east and into North America; the Last Glacial Maximum resulted in the expansion of the Cordilleran and Laurentide ice sheets in western and eastern North America, closing a potential path through the interior of North America. The ice age closed as many paths as it opened. The best data indicates that these two ice sheets did not open a corridor until 14,000 years ago, post-dating evidence of human occupation in Monte Verde in Chile by 500 years. Rather than indefatigable mammoth hunters killing their way through the interior, the Beringians likely arrived in the New World along the western fringe of North America, hugging the coast and hopping across islands as marine foragers. Island hopping was feasible beginning 17,000 years ago, resulting in pockets of human occupation along the southern Alaskan coast while the sea levels began to rise as the Ice Age abated.

While genetic evidence strongly points to a bottleneck that began around 20,000 years ago, the archaeological evidence strongly points to the opening of a viable path southward into the Americas after 17,000 years ago. This 3000 years or so is sometimes termed the “Beringian standstill,” when the ancestors of the Native Americans occupied ecologically favored territory east of Siberia but were blocked by ice sheets from moving further east into North America.  Over these more than one hundred generations, a homogeneous genetic population emerged in Beringia, isolated from populations to the east. The genetic influences evidenced in eastern Siberians and the Inuit, who arrived to the Arctic long after the Ice Age, are not present in Native Americans because their Beringian ancestors were sealed off from Eurasia, first by the extreme conditions of the Last Glacial Maximum and then rising sea levels, which broke the connection between the Americas and Eurasia. 

Looking at the genetic network of haplogroup Q, more than 90% of full-blooded Native American males, a massive demographic expansion seems to have occurred around 14,000 years ago, just before the rise of the Clovis people, along with a later expansion in South America 12,000 years ago. This, seemingly, was most of the story.  The Na-Dene people of western North America, most prominent of whom are the Navajo tribe, have more East Asian ancestry, and observers have long-observed their more East Asian features, while the Paleo-Eskimos and the Thule Culture of the modern Inuit date to the period after 3000 BC. Though the source and timing of the Na-Dene migration has not been entirely established, ancient DNA makes it seem likely that they arrived after the end of the Ice Age, but before the Paleo-Eskimos. 

A fusion between two Siberian groups more than 20,000 years ago gave Native Americans ties to populations of western and southern Eurasia. A later migration eastward was halted by glaciers, until a final radiation began to occur 15,000 years ago, likely through the Pacific route, and then a switch to big game mammoth-hunting again with the Clovis people. Finally, secondary supplementary migrations from Siberia during the Holocene point to the long-term periodic exchanges across the Bering Strait that continued after the sea levels rose. But this was not to be the end of what genetics told us.  Cousins on Opposite Ends of the Pacific Ocean

For many decades, geneticists had access to the samples from two tribes in the Amazon, the Karitiana and the Surui. Earlier methodologies showed they were similar to other native peoples of the New World, except they were more isolated and genetically homogeneous, indicating a bottleneck due to small population sizes. But by the middle of the 2010s, geneticists were applying more robust and rigorous methods to pry out any aberrations or novelties in the broadly-sketched earlier genetic relationships. 

Looking at hundreds of thousands of genetic markers across hundreds of individuals, the researchers noticed a subtle but clear signal of affinity between the Amazonian tribes and their Australasian samples, which included Onge from the Andaman Islands in the Bay of Bengal, Papuans, and indigenous Australians. The results were so surprising that the researchers repeated the analysis over and over, and in the last decade, others have also found the same result, even more broadly in modern South America. Calling it “Population Y,” the signature appeared in only one ancient individual from Brazil dated to 8400 BC and is lacking in all other early Amerindian samples. To this day, this genetic signature is mysterious in terms of its provenance and what it tells us about the peopling of the New World. There are three major explanations for how this signal came to be present across contemporary South America. One hypothesis, crazy as it might seem, is that a group of Melanesians crossed the Pacific and mixed with the descendants of Beringians. Since the oldest Brazilian individual who carries this signature lived only 1000 years after the Ice Age, this would open up the strange possibility of Pleistocene mariners. Another less strange possibility is the Beringians had an internal population structure. This is just a fancy way of saying that, in fact, the early Beringians were not homogeneous and well-admixed, but some tribes had different ancestry from others. When there was a massive push southward between 15,000 and 16,000 years ago, some populations that moved into South America carried Population Y ancestry, and they persisted as an independent structured population down to the present. 

At this point you might be wondering how Melanesians got to Siberia, but the reality here is that it may not be that Population Y is Melanesian at all, just that that’s the closest modern population in the databases. When you look at the genetics of the people of the world east beyond India, there is a clear divide between the north and the south that seems to date back to more than 40,000 years ago. The southern populations include Melanesians, Australians, Andaman Islanders, and the Negritos of Malaysia and the Philippines. The northern populations include Siberians, Han Chinese, and Japanese, as well as most Southeast Asians. However, the current distribution of these populations was not always the same At the end of the last Ice Age, the southern branch was dominant as far north as China, with Neolithic Age farmer migrations southward slowly erasing its signal until there were only relict populations remaining. And, interestingly, it seems that Ice Age Tibetans were also more genetically related to the southern population than the northern one. This is still clear in the Y chromosomal haplogroup they share with Andamanese, D, as well as many Japanese, indicating more complexity in ancient East Asia than we are used to imagining. It is entirely possible that during the Ice Age, some “southern” populations were present in Siberia, considering that Tibet was a reservoir of one of these peoples. A People in America Before the Beringians

Though there is nothing impossible about the persistence of ancient structure in Beringia for thousands of years—after all, the Hindu caste system has maintained genetic structure for at least 1500 years—it is less parsimonious than one more explanation for population Y—that it was an earlier group than Beringians that was later absorbed in South America. 

This would explain why the signal is not present in any ancient samples from Alaska or North America; population Y simply did not leave an imprint on the northerners. It would obviate the need to maintain genetic substructure in Beringia, as population Y was presumably south and east of the glaciers when the Beringians were coalescing on the Arctic tundra. Population Y being an earlier arrival to the New World before the Beringians is attractive as a hypothesis as it explains the now substantial archeological evidence that there were earlier Americans before the Last Glacial Maximum. A speculative model then beckons that an early branch of humanity distantly related to Melanesians crossed from Asia to North America just as Ancient North Eurasians were pushing east into Siberia. In all likelihood, these people were coastal foragers and may have had some primitive vessels. If they arrived before the Last Glacial Maximum, they would have had the New World for tens of thousands of years to themselves. But this presents a conundrum: where are their human remains? 

Archaeologists have been able to find primitive tools that date to this early period, though there are still disputes about dating and the human-created nature of the stone flakes. No ancient DNA or fossil has been found at these Last Glacial Maximum and earlier sites. But to be fair, much the same could be said for the pre-Clovis Beringians, who are now understood to have existed. With the exception of coprolites from Paisley Caves in Oregon, they too left no human remains. More curiously, the massive explosion of sites, human remains, and megafaunal extinctions that date to the Clovis period, starting 13,500 years ago, suggests a huge ramp-up of the anthropogenic impact of our species qualitatively different from what came before. The genetic and archaeological data now point to the tentative but plausible possibility that humans were present before the Last Glacial Maximum, though very sparse on the ground and highly mobile. These people were likely very distantly related to the people of Australasia rather than the main line of East Asians or the western-related ANE. The presence of Y chromosomal haplogroup D among the Japanese, derived from the indigenous Jomon who were resident in the islands for more than 10,000 years, shared with Andamanese and Tibetans, presents a scenario where beach-combing foragers drift upward from Southeast Asia and eventually across the north Pacific littoral. 

In the thousands of years they occupied the New World, their impact on the local ecosystems was marginal; there was no massive megafaunal die-off as occurred in Australia or the New World after the Last Glacial Maximum. The absence of human remains indicates a very low-density mobile population, perhaps tied predominantly to the sunken shorelines of the Pleistocene. Today, environmentalists idealize the native people of the New World, but as Charles C. Mann has written in 1492 and 1493, the Amerindians were much more complicated than that, resculpting the landscape with fire and driving charismatic creatures like mammoths to extinction.  Early reports of scientists discovering large settlements in the Amazon have now been confirmed with 21st-century surveying technology. The greatest rainforest in the world might have been subject to extensive terraforming, and tribes like the Kariatania and Surui aren’t so much untouched hunter-gatherers but the descendants of fallen civilizations wandering a post-apocalyptic world.

There may also have been those who came before, leaving telltale marks in the genomes of modern Amazonians and their neighbors to the west along the Pacific coast. Their genetics and date of arrival indicate they were modern humans, but like Neanderthals and Denisovans, they did not reshape the ecology and biodiversity of their locales with a blitzkrieg of human exploitation or demographic excess. In this way, the Beringians resembled the Europeans that would conquer them thousands of years later, rather than the earliest of all Americans. The Enduring Mystery of the New World

Perhaps the New World, in the end, is the greatest anthropological experiment of all, recording a society of modern Homo sapiens that doesn’t drive megafauna to extinction—Mother Nature’s mostly independent and newer trial run of the human species, distinct from the earlier and separate creation of the Old World of Afro-Eurasia and Near Oceania. Far Oceania is, however, known to have experienced a genetic imprint of Amerindians, perhaps through captives brought back from the South American mainland and the transmission of the South American sweet potato to the Pacific peoples. 

When Hernán Cortés arrived in Mexico, the pre-metal age civilization of the Aztecs was reminiscent of 1492 BC rather than 1492 AD to the Spaniards. Not only were the Aztecs heathens, but they were still sacrificing humans in blood rituals, a practice stamped out in Europe by the pagan Romans in their conquest of the Celts 2000 years ago. Upon realizing they had not stumbled upon the Indies, Europeans began calling it Mundus Novus, or the New World. Though pre-modern geography and anthropology were filled with blank spaces on the map, by 1492, the centuries-earlier Pax Mongolica had removed the veil of mystery from China for most Westerners. Leading up to the arrival of Europeans in Hispaniola, the Portuguese were pushing their way inexorably around Africa, tracing the outline of what was to remain the Dark Continent until the 1800s.

But with Christopher Columbus’ navigation across the Atlantic, entire continents of races and civilizations were discovered, with immediate cultural consequences like Thomas More setting his Utopia in the New World and Shakespeare’s play The Tempest clearly influenced by English contact with North America. The Western understanding of what they had discovered, or perhaps more accurately made contact with, unfolded over centuries. When it comes to Western understanding of the ancient history of this New World, it unfolds still.  

The world that the Greeks and Romans had known was not the entire world; there were deep mysteries in the universe hidden even from the ancients. Early Americans in the decades after U.S. independence still hadn’t come to terms with the native peoples of the continent, whether it be their political and social role in the young republic as citizens or not or their origins as a race. The religion founded by Joseph Smith, Mormonism, was bathed with cutting-edge scientific and historical theories from the 1820s, like that Native Americans descended from ancient Hebrew tribes. Today, we might laugh at Mormons. Yet do we really know the truth either? There are mysteries in the world still, even in 2024. Perhaps in some strange way, More’s Utopia captured the possibilities of the New World, though in a way he would never have anticipated. And yet the archaeological and genetic record is also clear that if these earlier people existed, they are but shadows, overwhelmed and absorbed by the Beringians, forged into the bitter coldness of the Arctic 20,000 years ago. Though the Beringians clung to the cold edge of the New World for thousands of years, it seems clear that, 13,500 years ago, the material and social technology of the Clovis Culture unlocked their human rapacity, with the extinction of mammoths, sloths, and all their predators, followed by the demographic radiation all across South America replacing any earlier arrivals. The New World became just as the Old was to be, both worlds born in blood and conquest.

Razib Khan is a co-founder and CXO of GenRAIT, a deep tech company that deploys a platform for the life sciences. He also writes at Razib Khan’s Unsupervised Learning. You can follow him at @razibkhan.

Genetic differentiation of Andaman Islanders and their relatedness to Nicobar Islanders


The Andaman Islanders, living in isolation for centuries, have been subject to recent molecular scrutiny with their Asian origins being established. Although marked linguistic and physical variations are known to exist among the different extant population groups, the underlying genetic structure with reference to indigenous populations of adjacent Nicobar Islands has been poorly understood. To decipher the genetic structure of three indigenous Andaman Islanders; the Great Andamanese, Jarawa and the Onge, molecular analyses with autosomal, mitochondrial and Y-chromosomal markers were carried out and compared with indigenous Nicobar Islanders; the Nicobarese and Shompen. Biparental analyses revealed the Great Andamanese exhibiting considerable population substructuring owing to their present-day conglomeration of several erstwhile segregate tribes, in addition to discernable admixture from mainland Indian populations and other Andaman and Nicobar Islanders especially the Nicobarese. Distant separation between the Great Andamanese and Nicobarese was also discerned by the shared R22 mitochondrial lineage. The R22 lineage was previously reported in the Shompen of Nicobar Islands and Southeast Asian populations. The Nicobarese also exhibited mitochondrial haplogroup M74b, which has a Southeast Asian and East Asian distribution.

The Onge-Jarawa group demonstrated a close genetic relatedness, consistent with their linguistic proximity. However, recent differentiation of the Jarawa from the Onge was also inferred from their separation on both mitochondrial M31 and M32 lineages as well as from autosomal and Y-chromosomal divergences. Our analyses indicate considerable genetic drift among the Andaman Islanders, a result of long-term isolation and inbreeding.

Autosomal and mitochondrial data suggest considerable admixture between the ‘Negrito’ Great Andamanese and ‘non-Negrito’ Nicobarese. Discussion

The ‘Negrito’ populations found scattered among parts of southern India, Andaman and Nicobar Islands, Malaysia and Philippines were considered to be remnants of descendants of early modern humans. However, their grouping based on short stature as an archaic retention is questioned (Bulbeck, 2013), and short stature is suggested to have a convergent evolution among different pygmy groups (Migliano et al., 2013). Our molecular analyses of the Andaman Islanders support a terminal Pleistocene

Reconstructing the Origin

of Andaman Islanders

" The Andaman and Nicobar Islands are inhab-

ited by six indigenous tribal populations. Our

previous work (1) suggested that Andamanese

Negritos have closer affinities with Asian

than with African populations and that the Nic-

obarese have close genetic affinities to South-

east Asians "


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