Genetic history of indigenous peoples of the Americas

Genetic history of indigenous peoples of the Americas
A  language map with  color. Branch lengths are scaled according to genetic distance, but for ease of visualization, a different scale is used on the left and right sides of the middle tick mark at the bottom of the figure. The tree was rooted along the branch connecting the Siberian populations and the Native American populations, and for convenience, the forced bootstrap score of 100% for this rooting is indicated twice. In the neighbor-joining tree, a reasonably well-supported cluster (86%) includes all non-Andean South American populations, together with the Andean-speaking Inga population from southern Colombia. Within this South American cluster, strong support exists for separate clustering of Chibchan–Paezan (97%) and Equatorial–Tucanoan (96%) speakers (except for the inclusion of the Equatorial–Tucanoan Wayuu population with its Chibchan–Paezan geographic neighbors, and the inclusion of Kaingang, the single Ge–Pano–Carib population, with its Equatorial–Tucanoan geographic neighbors). Within the Chibchan–Paezan and Equatorial–Tucanoan subclusters several subgroups have strong support, including Embera and Waunana (96%), Arhuaco and Kogi (100%), Cabecar and Guaymi (100%), and the two Ticuna groups (100%). When the tree-based clustering is repeated with alternate genetic distance measures, despite the high Mantel correlation coefficients between distance matrices (0.98, 0.98, and 0.99 for comparisons of the Nei and Reynolds matrices, the Nei and chord matrices, and the Reynolds and chord matrices, respectively), higher-level groupings tend to differ slightly or to have reduced bootstrap support.
A genetic tree showing some neighbour-joining relationships within Amerindian language groups

Genetic history of indigenous peoples of the Americas primarily focus on Human Y-chromosome DNA haplogroups and Human mitochondrial DNA haplogroups.[1] Autosomal "atDNA" markers are also used, but differ from mtDNA or Y-DNA in that they overlap significantly.[2] The genetic pattern indicates Indigenous Amerindians experienced two very distinctive genetic episodes; first with the initial peopling of the Americas, and secondly with European colonization of the Americas.[3][4] The former is the determinant factor for the number of gene lineages, zygosity mutations and founding haplotypes present in today's Indigenous Amerindian populations.[3]

Human settlement of the New World occurred in stages from the Bering sea coast line, with an initial layover on Beringia for the small founding population.[5][6][7] The micro-satellite diversity and distributions of the Y lineage specific to South America indicates that certain Amerindian populations have been isolated since the initial colonization of the region.[8] The Na-Dené, Inuit and Indigenous Alaskan populations exhibit haplogroup Q (Y-DNA); however, they are distinct from other indigenous Amerindians with various mtDNA and atDNA mutations.[9][10][11] This suggests that the peoples who first settled the northern extremes of North America and Greenland derived from later migrant populations than those who penetrated further south in the Americas.[12][13] Linguists and biologists have reached a similar conclusion based on analysis of Amerindian language groups and ABO blood group system distributions.[14][15]



A single-nucleotide polymorphism (SNP) is a change to a single nucleotide in a DNA sequence.

The X and Y human chromosomes are thought to have originated from a pair of identical chromosomes[16] (300 – 166 million years ago[17][18][19]), termed Allosome, when an ancient ancestral mammal developed an allelic variation, a so-called 'sex locus' – simply possessing this allele caused the organism to be male.[20] The chromosome with this allele became the Y chromosome, while the other member of the pair became the X chromosome. Over time, genes which were beneficial for males and harmful to (or had no effect on) females developed specifically on the Y chromosome, or were acquired through the process of translocation.[21]

The Y chromosome is passed down exclusively from father to son, all male humans (Y chromosomes) today trace back to a single prehistoric father termed "Y chromosomal Adam" originating from Africa.[22] The Y chromosome spans about 60 million base pairs (the building blocks of DNA) and represents about 2 percent of the total DNA in all human cells.[23] The original "Y chromosomal Adam" DNA sequencing has mutated rarely over the 20,000 generations, but each time a new mutation occurs there is a new branch in a haplogroup resulting in a new subclade (single-nucleotide polymorphism (SNP)).[24] MtDNA mutations are also passed down relatively unchanged from generation to generation; so all humans share the same mtDNA-types, the logical extension of this is that all humans ultimately trace back to one woman, who is commonly referred to as Mitochondrial Eve.[25][26] Both females and males inherit their Mitochondrial DNA (mtDNA) only from their mother.[27] This line of biological inheritance, therefore, stops with each male.[28] Consequently, Y-DNA is more commonly used by the general public for tracing genetic heritage.[28][29][30]

An autosome (atDNA) is a chromosome that is not a sex chromosome – that is to say there are an equal number of copies of the chromosome in males and females.[2] Autosomal DNA testing is generally used to determine the "genetic percentages" of a person's ancestry from particular continents/regions or to identify the countries and "tribes" of origin on an overall basis. Genetic admixture tests arrive at these percentages by examining (SNP), which are locations on the DNA where one nucleotide has "mutated" or "switched" to a different nucleotide.[2] One way to examine the support for particular colonization routes within the American landmass is to determine if a closer relationship between zygosity and geography is observed when “effective” geographic distances are computed along these routes, rather than along shortest-distance paths.[31]


The Y chromosome consortium has established a system of defining Y-DNA haplogroups by letters A through to T, with further subdivisions using numbers and lower case letters.[32]

Haplogroup Q

Spread of Haplogroup Q in Indigenous populations.

Q-M242 (mutational name) is the defining (SNP) of Haplogroup Q (Y-DNA) (phylogenetic name).[8] Within the Q clade, there are 14 haplogroups marked by 17 SNPs.2009[33][34] In Eurasia haplogroup Q is found among Siberian populations, such as the modern Chukchi and Koryak peoples. In particular two populations exhibit large concentrations of the Q-M242 mutation, the Kets (93.8%) and the Selkups (66.4%).[35] The Kets are thought to be the only survivors of ancient nomads living in Siberia.[5] Their population size is very small; there are fewer than 1,500 Kets in Russia.2002[5] The Selkups have a slightly larger population size than the Kets, with approximately 4,250 individuals. 2002[8] Starting the Paleo-Indians period, a migration to the Americas across the Bering Strait (Beringia), by a small population carrying the Q-M242 mutation took place.[36] A member of this initial population underwent a mutation, which defines its descendant population, known by the Q-M3 (SNP) mutation.[37] These descendants migrated all over the Americas.[33]

Q subclades Q1a3a and Q1a3a1a

Haplogroup Q1a3a (Y-DNA) and/or Q-M3 is defined by the presence of the rs3894 (M3) (SNP).[3][5][38] The Q-M3 mutation is roughly 15,000 years old as the initial migration of Paleo-Indians into the Americas occurred.[7][39] Q-M3 is the predominant haplotype in the Americas at a rate of 83% in South American populations,[40] 50% in the Na-Dené populations, and in North American Eskimo-Aleut populations at about 46%.[35] 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.[6][35][41]

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 (SNP) M19 which defines subclade Q1a3a1a.[40] M19 has been detected in (59%) of Amazonian Ticuna men and in (10%) of Wayuu men.[40] Subclade M19 appears to be unique to South American Indigenous peoples, arising 5,000 to 10,000 years ago.[40] This suggests that population isolation and perhaps even the establishment of tribal groups began soon after migration into the South American areas.[5][42]

Haplogroup R1

Spread of Haplogroup R in Indigenous populations.

Haplogroup R1 (Y-DNA) is the second most predominant Y haplotype found among indigenous Amerindians after Q (Y-DNA).[43] The distribution of R1 is believed to be associated with the re-settlement of Eurasia following the last glacial maximum. One theory put forth is that it entered the Americas with the initial founding population.[40] The second theory is that it was introduce during European colonization.[43] R1 is very common throughout all of Eurasia except East Asia and Southeast Asia. R1 (M137) is found predominantly in North American groups like the Ojibwe (79%), Chipewyan (62%), Seminole (50%), Cherokee (47%), Dogrib (40%) and Papago (38%).[43] The principal-component analysis suggests a close genetic relatedness between some North American Amerindians (the Chipewyan and the Cheyenne) and certain populations of central/southern Siberia (particularly the Kets, Yakuts, Selkups, and Altays), at the resolution of major Y-chromosome haplogroups. This pattern agrees with the distribution of mtDNA haplogroup X, which is found in North America, is absent from eastern Siberia, but is present in the Altais of southern central Siberia.[40][44][45]

Haplogroup C3b

Spread of Haplogroup C3 in Indigenous populations.

Haplogroup C3 (M217, P44) is mainly found in indigenous Siberians, Mongolians and Oceanic populations. Haplogroup C3 is the most widespread and frequently occurring branch of the greater (Y-DNA) haplogroup C. Haplogroup C3 decedent C3b (P39) is commonly found in today's Na-Dené speakers with the highest frequency found among the Athabaskan's at 42%.[36] This distinct and isolated branch C3b (P39) includes almost all the Haplogroup C3 Y-chromosomes found among all indigenous peoples of the Americas.[46] The Na-Dené groups are also unusual among indigenous peoples of the Americas in having a relatively high frequency of Q-M242 (25%).[35] This indicates that the Na-Dené migration occurred from the Russian Far East after the initial Paleo-Indian colonization, but prior to modern Inuit, Inupiat and Yupik expansions.[9][10][13]


Mitochondrial Eve is defined as the woman who was the matrilineal most recent common ancestor for all living humans. Mitochondrial Eve is generally estimated to have lived around 200,000 years ago.[47] Mitochondrial Eve is the most recent common matrilineal ancestor, not the most recent common ancestor.[48][49]

Schematic illustration of maternal geneflow in and out of Beringia. Colours of the arrows correspond to approximate timing of the events and are decoded in the coloured time-bar. The initial peopling of Berinigia (depicted in light yellow) was followed by a standstill after which the ancestors of indigenous Americans spread swiftly all over the New World while some of the Beringian maternal lineages–C1a-spread westwards. More recent (shown in green) genetic exchange is manifested by back-migration of A2a into Siberia and the spread of D2a into north-eastern America that post-dated the initial peopling of the New World.
Schematic illustration of maternal (mtDNA) gene-flow in and out of Beringia, from 25,000 years ago to present.

When studying human mitochondrial DNA (mtDNA) haplogroups, the results indicate that Indigenous Amerindian haplogroups, including haplogroup X, are part of a single founding east Asian population.[50] It also indicates that the distribution of mtDNA haplogroups and the levels of sequence divergence among linguistically similar groups were the result of multiple preceding migrations from Bering Straits populations.[27][51] All Indigenous Amerindian mtDNA can be traced back to five haplogroups, A, B, C, D and X.[52] More specifically, Indigenous Amerindian mtDNA belongs to sub-haplogroups that are unique to the Americas and not found in Asia or Europe: A2, B2, C1, D1, and X2a (with minor groups C4c, D2, D3, and D4h3).[51] This suggests that 95% of Indigenous Amerindian mtDNA is descended from a minimal genetic founding female population, comprising sub-haplogroups A2, B2, C1b, C1c, C1d, and D1.[52] The remaining 5% is composed of the X2a, D2, D3, C4, and D4h3 sub-haplogroups.[51][52]

X is one of the five mtDNA haplogroups found in Indigenous Amerindian peoples. Unlike the four main American mtDNA haplogroups (A, B, C and D), X is not at all strongly associated with east Asia.[5] Haplogroup X genetic sequences diverged about 20,000 to 30,000 years ago to give two sub-groups, X1 and X2. X2's subclade X2a occurs only at a frequency of about 3% for the total current indigenous population of the Americas.[5] However, X2a is a major mtDNA subclade in North America, where among the Algonquian peoples it comprises up to 25% of mtDNA types.[3][53] It is also present in lower percentages to the west and south of this area — among the Sioux (15%), the Nuu-chah-nulth (11%–13%), the Navajo (7%), and the Yakama (5%).[54] Haplogroup X is more strongly present in the Near East, the Caucasus, and Mediterranean Europe.[54] The predominant theory for sub-haplogroup X2a's appearance in North America is migration along with A, B, C, and D mtDNA groups, from a source in the Altai Mountains of central Asia.[44][45][55][56]

Sequencing of the mitochondrial genome from Paleo-Eskimo remains (3,500 years old) are distinct from modern Amerindians, falling within sub-haplogroup D2a1, a group observed among today's Aleutian Islanders, the Aleuts and Siberian Yupik populations.[57] This suggests that the colonizers of the far north and subsequently Greenland originated from later coastal populations.[57] Then a genetic exchange in the northern extremes introduced by the Thule people (proto-Inuit) approximately 800–1,000 years ago began.[11][58] These final Pre-Columbian migrants introduced haplogroups A2a and A2b to the existing Paleo-Eskimo populations of Canada and Greenland, culminating in the modern Inuit.[11][58]


genetic groups according to DNA Tribes
  1. Arctic
  2. Salishan
  3. Athabaskan
  4. North Amerindian
  5. Ojibwa
  6. Mexican
  7. Mayan
  9. Andean
  10. Amazonian
  11. Gran Chaco
  12. Patagonian

Genetic diversity and population structure in the American landmass is also done using autosomal (atDNA) micro-satellite markers genotyped; sampled from North, Central, and South America and analyzed against similar data available from other indigenous populations worldwide.[31][59] The Amerindian populations show a lower genetic diversity than populations from other continental regions.[59] 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 (the genetic entry point).[31][59] Also observed is evidence of a higher level of diversity and lower level of population structure in western South America compared to eastern South America.[31][59] There is a relative lack of differentiation between Mesoamerican and Andean populations, a scenario that implies that coastal routes were easier for migrating peoples (more genetic contributors) to traverse in comparison with inland routes.[31] The over-all pattern that is emerging suggests that the Americas were recently colonized by a small number of individuals (effective size of about 70), which grew by a factor of 10 over 800 – 1000 years.[5][60] The data also shows that there have been genetic exchanges between Asia, the Arctic and Greenland since the initial peopling of the Americas.[60][61]

Overlaps between DNA types

Populations that have a specific combination of autosome, Y and MT-haplogroup mutations can generally be found with regional variations. Autosomes, Y mutations and mt mutations do not necessarily occur at a similar time and there are differential rates of sexual selection between the two sex chromosomes.[62] This combined with population bottlenecks, the founder effect, mitochondrial mutations and genetic drift will alter the genetic composition of isolated populations, resulting in very distinguishable mutation patterns.[63] (i.e. Taínos,[64] Fuegians,[65] Inuit,[66] Yupik[67] and Algonquian[5])

The rough overlaps between Y-DNA and mtDNA between the Americas, Circumpolar north, and Siberian indigenous populations are:

Y-DNA haplogroup(s) - mtDNA haplogroup(s) - Geographical area(s)
Q, R1, C3 A, X, Y, C, D
(M types), (N types
Russian far east, Americas, Arctic

Old world genetic admixture

Interracial marriage and interracial sex and, more generally, the process of racial admixture, has its origins in prehistory. Racial mixing became widespread during European colonialism in the Age of Discovery.[68] Genetic exchange between two populations reduces the genetic distance between the populations and is measurable in DNA patterns.[62] During the Age of Discovery, beginning in the late 1400s CE, European explorers sailed the oceans, eventually reaching all the major continents.[69] During this time Europeans contacted many populations, some of which had been relatively isolated for millennia.[70] The genetic demographic composition of the Eastern Hemisphere has not changed significantly since the age of discovery. However, genetic demographics in the Western Hemisphere were radically altered by events following the voyages of Christopher Columbus.[70] The European colonization of the Americas brought contact between peoples of Europe, Africa and Asia and the Amerindian populations. As a result, the Americas today have significant and complex multiracial populations.[70] Many individuals who self-identify as one race exhibit genetic evidence of a multiracial ancestry.[71]

The European invasion of Latin America was initially executed by male soldiers and sailors from Iberia, Spain and Portugal.[72] The new soldier-settlers fathered children with Amerindian women and later with African slaves.[73] These mixed-race children were generally identified by the Iberian colonists as Castas.[74] In the 1600s CE, the North American fur trade brought more European men, from France and Great Britain, who took North Amerindian women as wives.[75] Their children became known as Métis or Bois-Brûlés by the ethnic French and mixed-bloods, half-breeds or country-born by the English and Scots.[76] From the second half of the 19th century to the beginning of the 20th century, new waves of immigrants from northern, eastern and southern Europe went to the Americas and consequently altered the demographics.[77] Following World War II and subsequent worldwide migrations, the current American populations' genetic admixture can be traced to all corners of the world.[5][78]

Blood groups

Frequency of O group in indigenous populations. Note the predominance of this group in Indigenous Americans.

Prior to the 1952 confirmation of DNA as the hereditary material by Alfred Hershey and Martha Chase, scientists used blood proteins to study human genetic variation.[79][80] The ABO blood group system is widely credited to have been discovered by the Austrian Karl Landsteiner, who found three different blood types in 1900.[81] Blood groups are inherited from both parents. The ABO blood type is controlled by a single gene (the ABO gene) with three alleles: i, IA, and IB.[82]

Research by Ludwik and Hanka Herschfeld during World War I found that the frequencies of blood groups A,B and O differed greatly from region to region.[80] The "O" blood type (usually resulting from the absence of both A and B alleles) is very common around the world, with a rate of 63% in all human populations.[83] Type "O" is the primary blood type among the indigenous populations of the Americas, in-particular within Central and South America populations, with a frequency of nearly 100%.[83] In indigenous North American populations the frequency of type "A" ranges from 16% to 82%.[83] This suggests again that the initial Amerindians evolved from an isolated population with a minimal number of individuals.[84][85]

Distribution of ABO blood types
in various modern Indigenous Amerindian populations
Test results as of 2008[86]
PEOPLE GROUP O (%) A (%) B (%) AB (%)
Blackfoot (N. Am. Indian) 17 82 0 1
Bororo (Brazil) 100 0 0 0
Eskimos (Alaska) 38 44 13 5
Inuit (Eastern Canada & Greenland) 54 36 23 8
Hawaiians 37 61 2 1
Indigenous North Americans (as a whole Native Nations/First Nations) 79 16 4 1
Mayas (modern) 98 1 1 1
Navajo 73 27 0 0
Peru 100 0 0 0

Genealogical testing

A genealogical DNA test examines the nucleotides at specific locations on a person's DNA for genetic genealogy purposes.[87] The test results are not meant to have any medical value; they are intended only to give genealogical information. Genealogical DNA tests generally involve comparing the results of living individuals to historic populations.[87] The general procedure for taking a genealogical DNA test involves taking a painless cheek-scraping (also known as a buccal swab) at home and mailing the sample to a genetic genealogy laboratory for testing. The most popular ancestry tests are Y chromosome (Y-DNA) testing and mitochondrial DNA (mtDNA) testing which test direct-line paternal and maternal ancestry, respectively. DNA tests (autosomal DNA) for other purposes attempt, for example, to determine a person's comprehensive genetic make-up and/or ethnic origins. A man's patrilineal ancestry, or male-line ancestry, can be traced using the DNA on his Y chromosome (Y-DNA) through Y-STR testing. This is useful because the Y chromosome passes down almost unchanged from father to son. Results showing specific sub-Haplogroups of Q, R1 and C3b implies that he is, in whole or in-part, indigenous to the Americas.[88] A person's matrilineal or mother-line ancestry can be traced using the DNA in his or her mitochondria, the mtDNA. This mtDNA is passed down by the mother unchanged, to all children. If one's mtDNA belonged to specific sub-Haplogroups of, A, B, C, D or X2a, the implication would be that he or she is, in whole or part, indigenous to the Americas.[89]

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