Genetic history of the Indigenous peoples of the Americas
The genetic history of the Indigenous peoples of the Americas is divided into two distinct periods: the initial peopling of the Americas from about 20,000 to 14,000 years ago, and European contact, after about 500 years ago. The first period of the genetic history of Indigenous Americans is the determinant factor for the number of genetic lineages, zygosity mutations, and founding haplotypes present in today's Indigenous American populations.
Indigenous American populations descend from and share ancestry with an Ancient East Asian lineage which diverged from other East Asian peoples prior to the Last Glacial Maximum. They also received geneflow from Ancient North Eurasians, a distinct Paleolithic Siberian population with deep affinities to both "European hunter-gatherers" and "Basal East Asians". They later dispersed throughout the Americas after about 16,000 years ago.
Analyses of genetics among Indigenous American and Siberian populations have been used to argue for early isolation of founding populations on Beringia and for later, more rapid migration from Siberia through Beringia into the New World. The microsatellite diversity and distributions of the Y lineage specific to South America indicates that certain Indigenous American populations have been isolated since the initial peopling of the region. The Na-Dene, Inuit and Native Alaskan populations exhibit Haplogroup Q-M242; however, they are distinct from other Indigenous Americans with various mtDNA and atDNA mutations. This suggests that the peoples who first settled in the northern extremes of North America and Greenland derived from later migrant populations than those who penetrated farther south in the Americas. Linguists and biologists have reached a similar conclusion based on analysis of Indigenous American language groups and ABO blood group system distributions.
Autosomal DNA
Genetic diversity and population structure in the American landmass is also measured using autosomal micro-satellite markers genotyped; sampled from North, Central, and South America and analyzed against similar data available from other Indigenous populations worldwide. The Indigenous American populations show a lesser genetic diversity than populations from other continental regions, while their overall strongest affinity for other populations is observed for Paleosiberian peoples. Observed is a decreasing genetic diversity as geographic distance from the Bering Strait occurs, as well as a decreasing genetic similarity to Siberian populations from Alaska. Also observed is evidence of a greater level of diversity and lesser level of population structure in western South America compared to eastern South America. There is a relative lack of differentiation between Mesoamerican and Andean populations, a scenario that implies that coastal routes were easier for migrating peoples to traverse in comparison with inland routes.The overall pattern suggests that the Americas were colonized by a small number of individuals, which grew by many orders of magnitude over 800 – 1000 years. The data also shows that there have been genetic exchanges between Asia, the Arctic, and Greenland since the initial peopling of the Americas.
According to an autosomal genetic study from 2012, Indigenous Americans descend from at least three main migrant waves from Northern Asia. Most of it is traced back to a single ancestral population, called 'First Americans'. However, those who speak Inuit languages from the Arctic inherited almost half of their ancestry from a second East Asian migrant wave, and those who speak Na-Dene inherited a tenth of their ancestry from a third migrant wave. The initial settling of the Americas was followed by a rapid expansion southwards along the west coast, with little gene flow later, especially in South America. One exception to this are the Chibcha speakers of Colombia, whose ancestry comes from both North and South America.
In 2014, the autosomal DNA of a 12,500+ year old infant from Montana was sequenced. The DNA was taken from a skeleton referred to as Anzick-1, found in close association with several Clovis artifacts. Comparisons showed strong affinities with DNA from Siberian sites, and virtually ruled out that particular individual had any close affinity with European sources. The DNA also showed strong affinities with all existing Indigenous American populations, which indicated that all of them derive from an ancient population that lived in or near Siberia.
Two 2015 autosomal DNA genetic studies confirmed the Siberian origins of the Indigenous peoples of the Americas. However, an ancient signal of shared ancestry with Australasians was detected among the Indigenous peoples of the Amazon region. This signal, also dubbed as 'population Y' has been more recently linked to a deep East Asian population, which can be associated with the Tianyuan man, and which is ancestral to modern East Asians. The deep Tianyuan and East Asian lineages form a sister branch to Andamanese and Australasian populations, with all of them being branches of Ancient East Eurasians. The main migration coming out of Siberia into the Americas would have happened 23,000 years ago.
A 2018 study analysed ancient Indigenous samples. The genetic evidence suggests that all Indigenous Americans ultimately descended from a founding population that diverged from East Asians and subsequently admixed with Ancient North Eurasians. The authors also provided evidence that the basal northern and southern Indigenous American branches, to which all other Indigenous peoples belong, diverged around 16,000 years ago.
A study published in the Nature journal in 2018 concluded that Indigenous Americans descended from a single founding population which initially divided from East Asians about ~36,000 years BP, with gene flow between this divided group of Ancestral Indigenous Americans and Siberians persisting until about ~25,000 years BP, before merging with Ancient North Eurasians and subsequently becoming isolated in the Americas or Beringia at ~22,000 years BP. Northern and Southern American Indigenous sub-populations split from each other at roughly ~17,500 to 14,600 years BP. There is also some evidence for a back-migration from the Americas into Siberia after ~11,500 years BP.
A study published in the Cell journal in 2019, analysed 49 ancient Indigenous American samples from all over North and South America, and concluded that all Indigenous American populations descended from a single ancestral source population which divided from Ancient East Asians, and admixed with Ancient North Eurasians, and gave rise to the "Ancestral Indigenous Americans", which later diverged into the various Indigenous groups. The authors further dismissed previous claims for the possibility of two distinct population groups among the peopling of the Americas. Both Northern and Southern Indigenous Americans are closest to each other and do not show evidence of admixture with hypothetical previous populations.
A review article published in the Nature journal in 2021, which summarized the results of previous genomic studies, similarly concluded that all Indigenous Americans descended from the movement of people from Northeast Asia into the Americas. These Ancestral Americans, once south of the continental ice sheets, spread and expanded rapidly, and branched into multiple groups, which later gave rise to the major subgroups of Indigenous American populations. The study also dismissed the existence, inferred from craniometric data, of a hypothetical distinct non-Indigenous American population, sometimes called "Paleoamerican". However, the possibility of other sources contributing to the genetic makeup of Indigenous Americans is not dismissed and are speculated to exist as 'genetic ghosts'.
According to a 2021 study, indigenous Pacific Coast and Amazonian populations share an ancestral component known as 'Y ancestry', which is believed to be related to ancestral East Asians or Australasians. This ancestry existed prior to the separation of the Pacific and Amazonian branches and likely arrived through the Pacific coastal route.
Genetic studies also show Amerindian-like backflow into present Siberian groups, especially those from the Kamchatka Peninsula.
Overall, the 'Ancestral Native Americans' descended from the admixture of an Ancient East Asian lineage, and a Paleolithic Siberian population known as Ancient North Eurasians. Ancestral Native Americans are most closely related to 'Ancient Paleo-Siberians' and 'Ancient Beringians'. Native Americans have also been described as being of "primarily East Asian ancestry, with a smaller contribution from palaeolithic West Eurasian populations", via their Ancient North Eurasian component, which has been described as the "result of a palaeolithic admixture" between ancient West Eurasians and ancient East Eurasians. A 2023 study describes the East Asian ancestry as arising from northern coastal China, which also contributed to other groups such as East Asians, Jōmon people and East Siberians.
Y-chromosome DNA
A "Central Siberian" origin has been postulated for the paternal lineage of the source populations of the original migration into the Americas.Membership in haplogroups Q and C3b implies Indigenous American patrilineal descent.
The micro-satellite diversity and distribution of a Y lineage specific to South America suggest that certain Indigenous American populations became isolated after the initial colonization of their regions. The Na-Dene, Inuit, and Native Alaskan populations exhibit haplogroup Q mutations, but are distinct from other Indigenous Americans with various mtDNA and autosomal DNA mutations. This suggests that the earliest migrants into the northern extremes of North America and Greenland derived from later migrant populations.
Haplogroup Q
is the defining of Haplogroup Q . In Eurasia, haplogroup Q is found among the ancient Afontova Gora specimens, and Indigenous Siberian populations, such as the modern Chukchi and Koryak peoples, as well as some Southeast Asians, such as the Dayak people. In particular, two groups exhibit large concentrations of the Q-M242 mutation, the Ket and the Selkup peoples. The Ket are thought to be the only survivors of ancient wanderers living in Siberia. Their population size is very small; there are fewer than 1,500 Ket in Russia.2002 The Selkup have a slightly larger population size than the Ket, with approximately 4,250 individuals.Starting the Paleo-Indigenous American period, a migration to the Americas across the Bering Strait by a small population carrying the Q-M242 mutation occurred. A member of this initial population underwent a mutation, which defines its descendant population, known by the Q-M3 mutation. These descendants migrated all over the Americas.
Haplogroup Q-M3 is defined by the presence of the rs3894 . The Q-M3 mutation is roughly 15,000 years old as that is when the initial migration of Paleo-Indigenous Americans into the Americas occurred. Q-M3 is the predominant haplotype in the Americas, at a rate of 83% in South American populations, 50% in the Na-Dene populations, and in North American Eskimo-Aleut populations at about 46%. With minimal back-migration of Q-M3 in Eurasia, the mutation likely evolved in east-Beringia, or more specifically the Seward Peninsula or western Alaskan interior. The Beringia land mass began submerging, cutting off land routes.
Since the discovery of Q-M3, several subclades of M3-bearing populations have been discovered. An example is in South America, where some populations have a high prevalence of M19, which defines subclade Q-M19. M19 has been detected in of Amazonian Ticuna men and in of Wayuu men. Subclade M19 appears to be unique to South American Indigenous peoples, arising 5,000 to 10,000 years ago. This suggests that population isolation, and perhaps even the establishment of tribal groups, began soon after migration into the South American areas. Other American subclades include Q-L54, Q-Z780, Q-SA01, and Q-M346 lineages. In Canada, two other lineages have been found. These are Q-P89.1 and Q-NWT01.